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| Status |
Public on Aug 19, 2019 |
| Title |
JHdel_GROSeq_rep1 |
| Sample type |
SRA |
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| Source name |
v-Abl transformed pro-B cell line
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| Organism |
Mus musculus |
| Characteristics |
cell type: v-Abl transformed pro-B cell line
genotype: JH-del, Emu-Bcl2, RAG2 deficient
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| Treatment protocol |
3 uM STI-571 treated for 4 days
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| Growth protocol |
RPMI1640+15% FBS
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Briefly, 10 million cells were permeabilized with permeabilization buffer (10 mM Tris-HCl, pH 7.4, 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40 substitute, 0.5 mM DTT, one tablet of protease inhibitors per 50 ml and 4 units Rnase inhibitor per ml) and resuspended in 100 ul storage buffer (10 mM Tris-HCl, pHHH 8.0, 25% (vol/vol) glycerol, 5 mM MgCl2, 0.1 mM EDTA and 5 mM DTT). Permeabilized cells were subjected to nuclear run-on (2xRun-on mix: 5 mM Tris-Cl, PH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.5 mM BrUTP, 10 units of RNase inhibitor, 1% sarkosyl) at 37o for 5 min, followed by Trizol-based RNA extraction.
Illumina adapters were ligated to RNA followed by cDNA generation with reverse transcriptase. Libraries were PCR-amplified with Illumina primers and subjected to sequencing.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
aligned to mm9 genome
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| Data processing |
Library strategy: GRO-Seq
Reads were aligned to mm9 genome using bowtie 2.2.8 with --non-deterministic flag
Aligned reads were separated into positive and negative strand using samtools 1.8
wig files were produced using RSeQC tool 2.6.3 and normalized to a coverage of 10 million 100nt reads for display
Genome_build: mm9
Supplementary_files_format_and_content: wig files contain peak information for samples
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| Submission date |
Apr 23, 2019 |
| Last update date |
Aug 20, 2019 |
| Contact name |
Frederick W Alt |
| E-mail(s) |
jianqiao.hu@childrens.harvard.edu
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| Organization name |
Boston Children's Hospital
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| Department |
PCMM
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| Lab |
Alt
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| Street address |
1 Blackfan Circle
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE130215 |
The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination [GRO-Seq] |
| GSE130224 |
The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination |
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| Relations |
| BioSample |
SAMN11483988 |
| SRA |
SRX5726882 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3733969_JHdel_rep1.neg.bw |
262.9 Mb |
(ftp)(http) |
BW |
| GSM3733969_JHdel_rep1.pos.bw |
274.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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