Result

Search results for the GEO ID: GSE44613

(Click on the check boxes provided under "Select for analysis", to initiate grouping)

(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down)

GSM ID

GPL ID

Select for analysis

Title

Source name

Description

Characteristics

GSM1087801

GPL570

LIN28B_not_induced_rep1 [Affymetrix]

HEK 293 cells inducibly expressing FLAG/HA tagged LIN28B; transgene expression not induced; mock transfected; replicate 1

cell line: HEK293

Gene expression data from HEK293 cells inducibly expressing FLAG/HA tagged LIN28B; FH/LIN28B not induced

Sample_geo_accession	GSM1087801
Sample_status	Public on Feb 26 2013
Sample_submission_date	Feb 25 2013
Sample_last_update_date	Feb 26 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	siRNA transfections of HEK293 T-REx Flp-In cells were performed in 6-well format using Lipofectamine RNAiMAX (Invitrogen) as described by the manufacturer. Detailed experimental procedure can be found in the Methods section of Hafner et al., RNA, in press Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition
Sample_growth_protocol_ch1	HEK293 T-REx Flp-In cells (Invitrogen) were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin, 100 µg/ml zeocin and 15 µg/ml blasticidin. Cell lines stably expressing FLAG/HA-tagged proteins were generated by co-transfection of pFRT/TO/FLAG/HA or pFRT/FLAG/HA constructs with pOG44 (Invitrogen). Cells were selected by exchanging zeocin with 100 µg/ml hygromycin. Expression of FLAG/HA-LIN28B was induced by addition of 250 ng/ml doxycycline 15 to 20 h before crosslinking. Detailed experimental procedure can be found in the Methods section of Hafner et al., RNA, in press, Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	2 µg of purified total RNA was used in the One-Cycle Eukaryotic Target Labeling Assay (Affymetrix) according to manufacturer's protocol. Biotinylated cRNA targets were cleaned up, fragmented, and hybridized to Human Genome U133 Plus 2.0 Array (Affymetrix).
Sample_hyb_protocol	3 µg cRNA hybridized to HGU133 Plus 2.0 Arrays for 16 h at 45ºC
Sample_scan_protocol	Genechips scanned on Affymetrix Genechip 300 7G scanner
Sample_data_processing	We imported the CEL files into the R software (http://www.R-project.org) using the BioConductor affy package (Gentleman et al., 2004). The transcript probe set intensities were background-corrected, adjusted for non-specific binding and quantile normalized with the GCRMA algorithm (Wu, 2006). Probe sets with more than 6 of the 11 probes mapping ambiguously to the genome were discarded, as were probe sets that mapped to multiple genes. We then collected all probe sets matching a given gene, and we selected for further analysis the RefSeq transcript with median 3'UTR length corresponding to that gene. In total 16,063 transcripts were identified. The log-intensity of probe sets mapping to the gene were then averaged to obtain the expression level per RefSeq transcript. The changes of transcript abundances were computed as the logarithm of the ratio of transcript expression in the cocktails of siRNA treated samples and mock-transfected cells. Detailed analysis procedure can be found in the Supplement to Hafner et al. Cell, 2010,141(1),129-141 Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
Sample_platform_id	GPL570
Sample_contact_name	Miguel,,Brown
Sample_contact_email	miguel.a.brown@gmail.com
Sample_contact_institute	The Rockefeller University
Sample_contact_address	1230 York Ave Box 186
Sample_contact_city	New York
Sample_contact_state	New York
Sample_contact_zip/postal_code	10065
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1087nnn/GSM1087801/suppl/GSM1087801_LIN28B_not_induced_rep1.CEL.gz
Sample_series_id	GSE44613
Sample_series_id	GSE44616
Sample_data_row_count	13008

GSM1087802

GPL570

LIN28B_not_induced_rep2 [Affymetrix]

HEK 293 cells inducibly expressing FLAG/HA tagged LIN28B; transgene expression not induced; mock transfected; replicate 2

cell line: HEK293

Gene expression data from HEK293 cells inducibly expressing FLAG/HA tagged LIN28B; FH/LIN28B not induced

Sample_geo_accession	GSM1087802
Sample_status	Public on Feb 26 2013
Sample_submission_date	Feb 25 2013
Sample_last_update_date	Feb 26 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	siRNA transfections of HEK293 T-REx Flp-In cells were performed in 6-well format using Lipofectamine RNAiMAX (Invitrogen) as described by the manufacturer. Detailed experimental procedure can be found in the Methods section of Hafner et al., RNA, in press Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition
Sample_growth_protocol_ch1	HEK293 T-REx Flp-In cells (Invitrogen) were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin, 100 µg/ml zeocin and 15 µg/ml blasticidin. Cell lines stably expressing FLAG/HA-tagged proteins were generated by co-transfection of pFRT/TO/FLAG/HA or pFRT/FLAG/HA constructs with pOG44 (Invitrogen). Cells were selected by exchanging zeocin with 100 µg/ml hygromycin. Expression of FLAG/HA-LIN28B was induced by addition of 250 ng/ml doxycycline 15 to 20 h before crosslinking. Detailed experimental procedure can be found in the Methods section of Hafner et al., RNA, in press, Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	2 µg of purified total RNA was used in the One-Cycle Eukaryotic Target Labeling Assay (Affymetrix) according to manufacturer's protocol. Biotinylated cRNA targets were cleaned up, fragmented, and hybridized to Human Genome U133 Plus 2.0 Array (Affymetrix).
Sample_hyb_protocol	3 µg cRNA hybridized to HGU133 Plus 2.0 Arrays for 16 h at 45ºC
Sample_scan_protocol	Genechips scanned on Affymetrix Genechip 300 7G scanner
Sample_data_processing	We imported the CEL files into the R software (http://www.R-project.org) using the BioConductor affy package (Gentleman et al., 2004). The transcript probe set intensities were background-corrected, adjusted for non-specific binding and quantile normalized with the GCRMA algorithm (Wu, 2006). Probe sets with more than 6 of the 11 probes mapping ambiguously to the genome were discarded, as were probe sets that mapped to multiple genes. We then collected all probe sets matching a given gene, and we selected for further analysis the RefSeq transcript with median 3'UTR length corresponding to that gene. In total 16,063 transcripts were identified. The log-intensity of probe sets mapping to the gene were then averaged to obtain the expression level per RefSeq transcript. The changes of transcript abundances were computed as the logarithm of the ratio of transcript expression in the cocktails of siRNA treated samples and mock-transfected cells. Detailed analysis procedure can be found in the Supplement to Hafner et al. Cell, 2010,141(1),129-141 Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
Sample_platform_id	GPL570
Sample_contact_name	Miguel,,Brown
Sample_contact_email	miguel.a.brown@gmail.com
Sample_contact_institute	The Rockefeller University
Sample_contact_address	1230 York Ave Box 186
Sample_contact_city	New York
Sample_contact_state	New York
Sample_contact_zip/postal_code	10065
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1087nnn/GSM1087802/suppl/GSM1087802_LIN28B_not_induced_rep2.CEL.gz
Sample_series_id	GSE44613
Sample_series_id	GSE44616
Sample_data_row_count	13008

GSM1087803

GPL570

LIN28B_induced_rep1 [Affymetrix]

HEK 293 cells expressing FLAG/HA tagged LIN28B; transgene expression induced; mock transfected; replicate 1

cell line: HEK293

Gene expression data from HEK293 cells inducibly expressing FLAG/HA tagged LIN28B; FH/LIN28B induced

Sample_geo_accession	GSM1087803
Sample_status	Public on Feb 26 2013
Sample_submission_date	Feb 25 2013
Sample_last_update_date	Feb 26 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	siRNA transfections of HEK293 T-REx Flp-In cells were performed in 6-well format using Lipofectamine RNAiMAX (Invitrogen) as described by the manufacturer. Detailed experimental procedure can be found in the Methods section of Hafner et al., RNA, in press Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition
Sample_growth_protocol_ch1	HEK293 T-REx Flp-In cells (Invitrogen) were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin, 100 µg/ml zeocin and 15 µg/ml blasticidin. Cell lines stably expressing FLAG/HA-tagged proteins were generated by co-transfection of pFRT/TO/FLAG/HA or pFRT/FLAG/HA constructs with pOG44 (Invitrogen). Cells were selected by exchanging zeocin with 100 µg/ml hygromycin. Expression of FLAG/HA-LIN28B was induced by addition of 250 ng/ml doxycycline 15 to 20 h before crosslinking. Detailed experimental procedure can be found in the Methods section of Hafner et al., RNA, in press, Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	2 µg of purified total RNA was used in the One-Cycle Eukaryotic Target Labeling Assay (Affymetrix) according to manufacturer's protocol. Biotinylated cRNA targets were cleaned up, fragmented, and hybridized to Human Genome U133 Plus 2.0 Array (Affymetrix).
Sample_hyb_protocol	3 µg cRNA hybridized to HGU133 Plus 2.0 Arrays for 16 h at 45ºC
Sample_scan_protocol	Genechips scanned on Affymetrix Genechip 300 7G scanner
Sample_data_processing	We imported the CEL files into the R software (http://www.R-project.org) using the BioConductor affy package (Gentleman et al., 2004). The transcript probe set intensities were background-corrected, adjusted for non-specific binding and quantile normalized with the GCRMA algorithm (Wu, 2006). Probe sets with more than 6 of the 11 probes mapping ambiguously to the genome were discarded, as were probe sets that mapped to multiple genes. We then collected all probe sets matching a given gene, and we selected for further analysis the RefSeq transcript with median 3'UTR length corresponding to that gene. In total 16,063 transcripts were identified. The log-intensity of probe sets mapping to the gene were then averaged to obtain the expression level per RefSeq transcript. The changes of transcript abundances were computed as the logarithm of the ratio of transcript expression in the cocktails of siRNA treated samples and mock-transfected cells. Detailed analysis procedure can be found in the Supplement to Hafner et al. Cell, 2010,141(1),129-141 Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
Sample_platform_id	GPL570
Sample_contact_name	Miguel,,Brown
Sample_contact_email	miguel.a.brown@gmail.com
Sample_contact_institute	The Rockefeller University
Sample_contact_address	1230 York Ave Box 186
Sample_contact_city	New York
Sample_contact_state	New York
Sample_contact_zip/postal_code	10065
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1087nnn/GSM1087803/suppl/GSM1087803_LIN28B_induced_rep1.CEL.gz
Sample_series_id	GSE44613
Sample_series_id	GSE44616
Sample_data_row_count	13008

GSM1087804

GPL570

LIN28B_induced_rep2 [Affymetrix]

HEK 293 cells expressing FLAG/HA tagged LIN28B; transgene expression induced; mock transfected; replicate 2

cell line: HEK293

Gene expression data from HEK293 cells inducibly expressing FLAG/HA tagged LIN28B; FH/LIN28B induced

Sample_geo_accession	GSM1087804
Sample_status	Public on Feb 26 2013
Sample_submission_date	Feb 25 2013
Sample_last_update_date	Feb 26 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	siRNA transfections of HEK293 T-REx Flp-In cells were performed in 6-well format using Lipofectamine RNAiMAX (Invitrogen) as described by the manufacturer. Detailed experimental procedure can be found in the Methods section of Hafner et al., RNA, in press Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition
Sample_growth_protocol_ch1	HEK293 T-REx Flp-In cells (Invitrogen) were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin, 100 µg/ml zeocin and 15 µg/ml blasticidin. Cell lines stably expressing FLAG/HA-tagged proteins were generated by co-transfection of pFRT/TO/FLAG/HA or pFRT/FLAG/HA constructs with pOG44 (Invitrogen). Cells were selected by exchanging zeocin with 100 µg/ml hygromycin. Expression of FLAG/HA-LIN28B was induced by addition of 250 ng/ml doxycycline 15 to 20 h before crosslinking. Detailed experimental procedure can be found in the Methods section of Hafner et al., RNA, in press, Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	2 µg of purified total RNA was used in the One-Cycle Eukaryotic Target Labeling Assay (Affymetrix) according to manufacturer's protocol. Biotinylated cRNA targets were cleaned up, fragmented, and hybridized to Human Genome U133 Plus 2.0 Array (Affymetrix).
Sample_hyb_protocol	3 µg cRNA hybridized to HGU133 Plus 2.0 Arrays for 16 h at 45ºC
Sample_scan_protocol	Genechips scanned on Affymetrix Genechip 300 7G scanner
Sample_data_processing	We imported the CEL files into the R software (http://www.R-project.org) using the BioConductor affy package (Gentleman et al., 2004). The transcript probe set intensities were background-corrected, adjusted for non-specific binding and quantile normalized with the GCRMA algorithm (Wu, 2006). Probe sets with more than 6 of the 11 probes mapping ambiguously to the genome were discarded, as were probe sets that mapped to multiple genes. We then collected all probe sets matching a given gene, and we selected for further analysis the RefSeq transcript with median 3'UTR length corresponding to that gene. In total 16,063 transcripts were identified. The log-intensity of probe sets mapping to the gene were then averaged to obtain the expression level per RefSeq transcript. The changes of transcript abundances were computed as the logarithm of the ratio of transcript expression in the cocktails of siRNA treated samples and mock-transfected cells. Detailed analysis procedure can be found in the Supplement to Hafner et al. Cell, 2010,141(1),129-141 Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
Sample_platform_id	GPL570
Sample_contact_name	Miguel,,Brown
Sample_contact_email	miguel.a.brown@gmail.com
Sample_contact_institute	The Rockefeller University
Sample_contact_address	1230 York Ave Box 186
Sample_contact_city	New York
Sample_contact_state	New York
Sample_contact_zip/postal_code	10065
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1087nnn/GSM1087804/suppl/GSM1087804_LIN28B_induced_rep2.CEL.gz
Sample_series_id	GSE44613
Sample_series_id	GSE44616
Sample_data_row_count	13008

GSM1087805

GPL570

LIN28B_knockdown_rep1 [Affymetrix]

HEK 293 cells inducibly expressing FLAG/HA tagged LIN28B; transgene not induced; siRNA transfected; replicate 1

cell line: HEK293

Gene expression data from HEK293 cells inducibly expressing FLAG/HA tagged LIN28B after knockdown with siRNA

Sample_geo_accession	GSM1087805
Sample_status	Public on Feb 26 2013
Sample_submission_date	Feb 25 2013
Sample_last_update_date	Feb 26 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	siRNA transfections of HEK293 T-REx Flp-In cells were performed in 6-well format using Lipofectamine RNAiMAX (Invitrogen) as described by the manufacturer. Detailed experimental procedure can be found in the Methods section of Hafner et al., RNA, in press Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition
Sample_growth_protocol_ch1	HEK293 T-REx Flp-In cells (Invitrogen) were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin, 100 µg/ml zeocin and 15 µg/ml blasticidin. Cell lines stably expressing FLAG/HA-tagged proteins were generated by co-transfection of pFRT/TO/FLAG/HA or pFRT/FLAG/HA constructs with pOG44 (Invitrogen). Cells were selected by exchanging zeocin with 100 µg/ml hygromycin. Expression of FLAG/HA-LIN28B was induced by addition of 250 ng/ml doxycycline 15 to 20 h before crosslinking. Detailed experimental procedure can be found in the Methods section of Hafner et al., RNA, in press, Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	2 µg of purified total RNA was used in the One-Cycle Eukaryotic Target Labeling Assay (Affymetrix) according to manufacturer's protocol. Biotinylated cRNA targets were cleaned up, fragmented, and hybridized to Human Genome U133 Plus 2.0 Array (Affymetrix).
Sample_hyb_protocol	3 µg cRNA hybridized to HGU133 Plus 2.0 Arrays for 16 h at 45ºC
Sample_scan_protocol	Genechips scanned on Affymetrix Genechip 300 7G scanner
Sample_data_processing	We imported the CEL files into the R software (http://www.R-project.org) using the BioConductor affy package (Gentleman et al., 2004). The transcript probe set intensities were background-corrected, adjusted for non-specific binding and quantile normalized with the GCRMA algorithm (Wu, 2006). Probe sets with more than 6 of the 11 probes mapping ambiguously to the genome were discarded, as were probe sets that mapped to multiple genes. We then collected all probe sets matching a given gene, and we selected for further analysis the RefSeq transcript with median 3'UTR length corresponding to that gene. In total 16,063 transcripts were identified. The log-intensity of probe sets mapping to the gene were then averaged to obtain the expression level per RefSeq transcript. The changes of transcript abundances were computed as the logarithm of the ratio of transcript expression in the cocktails of siRNA treated samples and mock-transfected cells. Detailed analysis procedure can be found in the Supplement to Hafner et al. Cell, 2010,141(1),129-141 Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
Sample_platform_id	GPL570
Sample_contact_name	Miguel,,Brown
Sample_contact_email	miguel.a.brown@gmail.com
Sample_contact_institute	The Rockefeller University
Sample_contact_address	1230 York Ave Box 186
Sample_contact_city	New York
Sample_contact_state	New York
Sample_contact_zip/postal_code	10065
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1087nnn/GSM1087805/suppl/GSM1087805_LIN28B_knockdown_rep1.CEL.gz
Sample_series_id	GSE44613
Sample_series_id	GSE44616
Sample_data_row_count	13008

GSM1087806

GPL570

LIN28B_knockdown_rep2 [Affymetrix]

HEK 293 cells inducibly expressing FLAG/HA tagged LIN28B; transgene not induced; siRNA transfected; replicate 2

cell line: HEK293

Gene expression data from HEK293 cells inducibly expressing FLAG/HA tagged LIN28B after knockdown with siRNA

Sample_geo_accession	GSM1087806
Sample_status	Public on Feb 26 2013
Sample_submission_date	Feb 25 2013
Sample_last_update_date	Feb 26 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	siRNA transfections of HEK293 T-REx Flp-In cells were performed in 6-well format using Lipofectamine RNAiMAX (Invitrogen) as described by the manufacturer. Detailed experimental procedure can be found in the Methods section of Hafner et al., RNA, in press Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition
Sample_growth_protocol_ch1	HEK293 T-REx Flp-In cells (Invitrogen) were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin, 100 µg/ml zeocin and 15 µg/ml blasticidin. Cell lines stably expressing FLAG/HA-tagged proteins were generated by co-transfection of pFRT/TO/FLAG/HA or pFRT/FLAG/HA constructs with pOG44 (Invitrogen). Cells were selected by exchanging zeocin with 100 µg/ml hygromycin. Expression of FLAG/HA-LIN28B was induced by addition of 250 ng/ml doxycycline 15 to 20 h before crosslinking. Detailed experimental procedure can be found in the Methods section of Hafner et al., RNA, in press, Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	2 µg of purified total RNA was used in the One-Cycle Eukaryotic Target Labeling Assay (Affymetrix) according to manufacturer's protocol. Biotinylated cRNA targets were cleaned up, fragmented, and hybridized to Human Genome U133 Plus 2.0 Array (Affymetrix).
Sample_hyb_protocol	3 µg cRNA hybridized to HGU133 Plus 2.0 Arrays for 16 h at 45ºC
Sample_scan_protocol	Genechips scanned on Affymetrix Genechip 300 7G scanner
Sample_data_processing	We imported the CEL files into the R software (http://www.R-project.org) using the BioConductor affy package (Gentleman et al., 2004). The transcript probe set intensities were background-corrected, adjusted for non-specific binding and quantile normalized with the GCRMA algorithm (Wu, 2006). Probe sets with more than 6 of the 11 probes mapping ambiguously to the genome were discarded, as were probe sets that mapped to multiple genes. We then collected all probe sets matching a given gene, and we selected for further analysis the RefSeq transcript with median 3'UTR length corresponding to that gene. In total 16,063 transcripts were identified. The log-intensity of probe sets mapping to the gene were then averaged to obtain the expression level per RefSeq transcript. The changes of transcript abundances were computed as the logarithm of the ratio of transcript expression in the cocktails of siRNA treated samples and mock-transfected cells. Detailed analysis procedure can be found in the Supplement to Hafner et al. Cell, 2010,141(1),129-141 Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
Sample_platform_id	GPL570
Sample_contact_name	Miguel,,Brown
Sample_contact_email	miguel.a.brown@gmail.com
Sample_contact_institute	The Rockefeller University
Sample_contact_address	1230 York Ave Box 186
Sample_contact_city	New York
Sample_contact_state	New York
Sample_contact_zip/postal_code	10065
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1087nnn/GSM1087806/suppl/GSM1087806_LIN28B_knockdown_rep2.CEL.gz
Sample_series_id	GSE44613
Sample_series_id	GSE44616
Sample_data_row_count	13008

Make groups for comparisons

(2 groups will be compared at a time)

Select GSMs and click on "Add groups"

Enter the group name here:

Select expression type

Transcripts profile based on;

A. Differential status (Up/Down regulation)

B. Absolute calls (Transcribed/Not-detected)

Filter results by number of probes