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| Status |
Public on Jun 25, 2013 |
| Title |
LIN28B_PARCLIP |
| Sample type |
SRA |
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| Source name |
HEK293 cell culture
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
cell line stably expresses: FLAG-LIN28B
par-clip antibody: FLAG
culture medium: DMEM
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| Extracted molecule |
total RNA |
| Extraction protocol |
PAR-CLIP and small RNA cloning (Hafner et al. 2010 Cell 141, 129–141)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
PARCLIP RNA
binding sites
HEK293 cells stably express FLAG-tagged LIN28B, that may be induced by Tamoxifen.
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| Data processing |
Note: due to special 5p adapter, 2nts need to be removed at 5p of each read in libraries 4SU_1 and 4SU_2 prior to any processing
Adapters were removed by customized script; clipped reads were aligned using BWA (version 0.5.8c) to spliced mature mRNAs (hg18); alignments were processed using samtools (version 0.1.8); clusters were generated based on pileup files and ranked based on G:A transitions and G deletions; overlapping clusters of 6SG and 4SU libraries were fused.
4SU barcodes: TCTCTGCTCGTATGCCGTCTTCTGCTTG for 4SU_1, TCTCGTATCGTATGCCGTCTTCTGCTTG for 4SU_2.
6SG barcode: TCTGGGATCGTATGCCGTCTTCTGCTTG.
4SU_CSD barcode: TCTCCATTCGTATGCCGTCTTCTGCTTG.
4SU_ZND: TCTTTTATCGTATGCCGTCTTCTGCTTG.
Genome_build: hg18
Supplementary_files_format_and_content: The .bed file reports binding sites. Columns: chromosome, start_position, end_position, cluster_id, score, strand, crosslink_start, crosslink_end, nan, nan.
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| Submission date |
May 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Robin Graf |
| E-mail(s) |
robin.graf@mdc-berlin.de
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| Phone |
+493094062396
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| Organization name |
Max Delbrueck Center for Molecular Medicine
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| Department |
Immune Regulation and Cancer
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| Lab |
Klaus Rajewsky
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| Street address |
Robert Rössle Str. 10
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| City |
Berlin |
| ZIP/Postal code |
13092 |
| Country |
Germany |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE46908 |
Identification of LIN28-bound mRNAs reveals features of target recognition and regulation |
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| Relations |
| BioSample |
SAMN02144020 |
| SRA |
SRX277588 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1140829_LIN28B_consensus_sites.bed.gz |
52.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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