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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 21, 2017 |
| Title |
DRIP shSMN IgG rep2 |
| Sample type |
SRA |
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| Source name |
SHSY5Y cell line
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| Organism |
Homo sapiens |
| Characteristics |
tissue: SHSY5Y cell line
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| Treatment protocol |
Chromatin was extracted from lentivirally-infected SH-SY5Y cells induced for 7 days with doxycycline
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| Growth protocol |
SH-SY5Y cells were maintained in Ham's F12:DMEM.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DRIP was performed as described in Loomis et al. 2014, with the following changes. Briefly, nucleic acids isolated from ~2x106 cells were digested with a restriction enzyme cocktail (50 units each of BsrGI, XbaI, EcoRI, HindIII, SspI) overnight at 37C in 1x NEB CutSmart buffer. Digests were purified by phenol/chloroform extraction, and 8.8ug of digested DNA per cell culture condition were treated with 3ul RNase H overnight at 37C. For each condition, 4.4ug of RNase H-treated or untreated DNA was immunoprecipitated with 10ug S9.6 antibody (Kerafast, Inc., #ENH001), washed 3x with IP buffer, eluted, treated with Proteinase K and phenol/chloroform extracted. Resulting samples were sonicated using a Bioruptor Pico from Diagenode, with 11 cycles of 15sec ON/ 90sec OFF. Fragments were prepared for sequencing using the NEBNext Ultra II Library Prep Kit for Illumina with barcodes for sample multiplexing. Pooled libraries were sequenced on the Illumina NextSeq platform.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
IgGHminus_shSMN_rep2
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| Data processing |
Library strategy: DRIP-seq
Reads were mapped using Bowtie2 to the hg38 genome annotation.
Enriched DRIPseq regions were determined using MACS2, comparing S9.6 antibody enrichment to IgG enrichment for each respective set of samples.
Genome_build: mRNA-seq: Gencode M4
Genome_build: DRIP-seq: hg38
Supplementary_files_format_and_content: SMArescue_all_RSEM.genes.results.human_names_split.txt: count matrix
Supplementary_files_format_and_content: SMArescue_d20d30_DvsE_all_DESeqOutput.txt: expression matrix
Supplementary_files_format_and_content: SMArescueIJKvsE.DESeq2ContrastTest.txt: expression matrix
Supplementary_files_format_and_content: SHSY5Y_shSMN-1_vs_shCtrl_FDR0.05.sepnames.txt: expression matrix
Supplementary_files_format_and_content: SHSY5Y_shSMN-2_vs_shCtrl_FDR0.05.sepnames.txt: expression matrix
Supplementary_files_format_and_content: SHSY5Y.RSEM.genes.results.human_names.txt: count matrix
Supplementary_files_format_and_content: hiPSC_shSMN-1_vs_shCtrl_FDR0.05.sepnames.txt: expression matrix
Supplementary_files_format_and_content: hiPSC_shSMN-2_vs_shCtrl_FDR0.05.sepnames.txt: expression matrix
Supplementary_files_format_and_content: hiPSC-MN.RSEM.genes.results.human_names.txt: count matrix
Supplementary_files_format_and_content: shCtrlrep1_S96_vs_IgG_summits_win250rep2.bed: peak
Supplementary_files_format_and_content: shSMNrep1_S96_vs_IgG_summits_win250rep2.bed: peak
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| Submission date |
Sep 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
John Carulli |
| Organization name |
Biogen
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| Department |
Computational Biology and Genomics
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| Lab |
Translational Genomics
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| Street address |
115 Broadway
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE87281 |
SMN deficiency in spinal muscular atrophy causes widespread intron retention and DNA damage |
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| Relations |
| BioSample |
SAMN05806560 |
| SRA |
SRX2187022 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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