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Sample GSM1827555 Query DataSets for GSM1827555
Status Public on Oct 08, 2015
Title LC3, Replicate 1
Sample type SRA
Source name IMR90 fibroblasts in culture
Organism Homo sapiens
Characteristics cell line: IMR90
antibody: Cell Signaling Technology #3868
Treatment protocol No treatment was performed on these cells.
Growth protocol IMR90 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 μg/ml streptomycin (Invitrogen) under physiological oxygen (3%).
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked with 1% formaldehyde diluted in PBS, without the addition of other co-crosslinkers, for 5 min at room temperature. After glycin quenching, the cell pellets were lysed in buffer containing 50 mM Tris, pH 7.5, 150 mM NaCl, 1% Triton, 0.1% Na-Deoxycholate, 0.1% SDS, supplemented with complete protease inhibitor cocktail (Thermo Scientific), and sonicated with Covaris sonicator, resulting in chromatin fragments of 250 bp average size. The supernatant was diluted 10 times with the above buffer without SDS, and subjected to immunoprecipitations with 2 ug of antibody or control IgG conjugated with Dynabeads Protein A or G (Invitrogen) at 4 °C for overnight. The beads were then washed 5 times with buffer containing 50 mM Tris, pH 7.5, 150 mM NaCl, 1% Triton, and 1 time with final wash buffer (50 mM Tris, pH 8.0, 10 mM EDTA, 50 mM NaCl), followed by elution with incubation of elution buffer (final wash buffer plus 1% SDS) at 65 °C for 30 min with agitation in a thermomixer.
The ChIP and input were purified and used for qPCR analysis or for constructing sequencing libraries with the NEBNext Ultra kit (New England Biolabs).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Data processing Demultiplexing of NextSeq data was performed using bcl2fastq v2.16.0.10 with default parameters.
Data were aligned to the GRCh37 (hg19) assembly of the human genome using bowtie2 with command-line parameters -k1 -N1 --local (allowing and reporting a single alignment per read with one or zero mismatches permitted in the seed region).
ChIP-seq visualization tracks were created in the following way. Aligned sequence tags were subjected to bedtools' genomeCoverageBed tool, making bedGraphs that were multiplied by the RPM coefficient. A similarly normalized input bedGraph was then subtracted from Lamin B1 and LC3, and bedGraphs were made into bigWigs using UCSC Genome Browser's bedGraphToBigWig utility.
Enriched domains for Lamin B1 and LC3 were called using EDD with default bin size estimation and gap penalty estimation and unalignable regions (the hg19 assembly gap track from Genome Reference Consortium) were masked. The FDR was controlled at the default value of 5%.
Genome_build: hg19
Supplementary_files_format_and_content: Tracks (bigWig files) were created by running genomeCoverageBed from the bedtools software package to create bedGraphs and adjusting tag counts by the RPM coefficient for each replicate of lamin B1, LC3, and input. Input bedGraphs were then subtracted from lamin B1 and LC3 bedGraphs and these were converted to bigWigs using bedGraphToBigWig from the UCSC Genome Browser utilities. BED files describing large domains of lamin B1 or LC3 enrichment were obtained by running EDD using default bin size estimation and gap penalty estimation. Unalignable regions (gaps) were masked and the FDR was controlled at 5%.
Submission date Jul 20, 2015
Last update date May 15, 2019
Contact name Gregory Donahue
Organization name The University of Pennsylvania
Department Cell & Developmental Biology
Lab Zaret Lab
Street address 3400 Civic Center Blvd, Bldg 421
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platform ID GPL18573
Series (1)
GSE63440 Autophagy mediates degradation of nuclear lamina
BioSample SAMN03890911
SRA SRX1112995

Supplementary file Size Download File type/resource 718.7 Mb (ftp)(http) BW
GSM1827555_LC3ADs.R1.EDD.bed.gz 3.2 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data provided as supplementary file

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