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Sample GSM1827968

Query DataSets for GSM1827968

Status

Public on Apr 12, 2016

Title

Agg_ATAC_1

Sample type

SRA

Source name

Aggregative stage cells

Organism

Capsaspora owczarzaki

Characteristics

stage/cell type: Aggregative
strain: ATCC 30864
chip antibody: none

Growth protocol

Capsaspora strain ATCC30864 cells were grown axenically in 5 ml flasks with ATCC medium 1034 (modified PYNFH medium) in an incubator at 23¼C

Extracted molecule

genomic DNA

Extraction protocol

For ChIP-seq: Cells were crosslinked in 1% formaldehyde for 10 min at room temperature (RT). Crosslinking was quenched with 0.125 M glycine for 5 min RT. Pelleted cells were lysed in Lysis buffer I (10 mM HEPES.KOH pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.2 % NP40, plus protease inhibitors and 0.5 mM DTT), incubated on ice for 10 minutes and centrifuged at 8000xg 10 min to pellet the nuclei. Nuclei were resuspended in Lysis buffer II (1%SDS, 10 mM EDTA, 50 mM tris ClH pH 8.1 plus protease inhibitors), incubated on ice for 10 min and sonicated for 15 min (15 cycles, each one 30sec “on”, 30 sec “off”) in a Bioruptor (Diagenode, Seraing, Belgium) in order to generate 200bp fragments.
For ChIP-seq: Libraries of immunoprecipitated and input DNA were prepared using the NEBNext DNA sample prep reagent Set 1 kit (New England Biolabs, Ipswich, MA, USA) according to the manufacturer's protocol.
For ATAC-seq: Fresh nuclei were obtained using Lysis Buffer I (10 mM HEPES.KOH pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.2 % NP40)
For ATAC: Fresh nuclei incubated 30min at 37ºC with Tn5 transposases from the Nextera DNA Library Prep Kit (Illumina, San Diego, CA)

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

Illumina HiSeq 2000

Description

processed data file: ATAC _nucleosome_free_peaks_MERGED.bed

Data processing

Library strategy: ATAC-Seq
Genome mapping using Bowtie v1.1.1 with -v 1 -m 1 parameters.
Remove duplicates using samtools v1.1
For ChIP-seq: Peak calling using MACS2 with parameters --nomodel, --shiftsize 100 and a q-value threshold of 0.01; except for H3K36me3 samples, for which additionally used --broad parameter and a q-value threshold of 0.05. Corrected by genome mappability.
For ATAC-seq: Peak calling using MACS2 with parameters -q 0.001 --extsize 40 --call-summits --nomodel
Genome_build: Capsaspora genome v2 (Broad Institute)
Supplementary_files_format_and_content: Peak BED files from MACS2 peak calling

Submission date

Jul 21, 2015

Last update date

May 15, 2019

Contact name

Arnau Sebe-Pedros

E-mail(s)

arnau.sebe@crg.es

Organization name

Centre for Genomic Regulation

Department

Systems Biology