title: ChIP-Seq-WT-L1-SMC1-rep1

data_processing:
ChIP-seq signals were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) to filter low-quality reads and subsequently  aligned to the mouse reference genome (mm10) using Bowtie aligner (Langmead et al., Nature methods, 2012) with the -m 1 parameter to obtain only uniquely mapped reads, except for CTCF samples where the -m 3 and --best parameters were used. HOMER software (Heinz et al., Mol. Cell, 2010) was applied for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of ChIP-seq

source_name: Mammary

growth_protocol: All animals were bred along the guidelines of the NIH and all animal experiments were performed according to the Animal Care and Use Committee (ACUC) of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). The CRISPR/Cas9 system was used to generate mutant mice with CTCF binding site deletions from C57BL/6 mice (Charles River) by the transgenic core of the National Heart, Lung, and Blood Institute (NHLBI). Single-guide RNA (sgRNA) constructs were designed to specifically target the individual CTCF binding sites in the casein (Csn) locus (http://crispr.mit.edu/). Target-specific sgRNA and Cas9 mRNA were in vitro transcribed and microinjected into the cytoplasm of fertilized eggs for founder mouse production. To screen homozygous mice, all mice were genotyped by PCR amplification with genomic DNA from mouse tail and sequencing (Macrogen).

extract_protocol: Libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: Frozen-stored mammary tissues collected at lactation day 1 (L1) were ground into powder. Chromatin was fixed with formaldehyde (1% final concentration) for 15 min at room temperature, and then was quenched with glycine (0.125 M final concentration). Samples were processed as previously described (27). The following antibodies were used for ChIP-seq: CTCF (Millipore, 07-729 and Abcam, ab70303), SMC1 (Bethyl, A300-055A), STAT5A (Santa Cruz Biotechnology, sc-1081), GR (Thermo Scientific, PA1-511A), H3K27ac (Abcam, ab4729) and RNA polymerase II (Abcam, ab5408). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 2500 instrument (Illumina).

value: Mammary gland

tag: state

value: day one of lactation

value: wild-type

tag: chip antibody

value: SMC1 (Bethyl, A300-055A)


title: 4C WT-2

status: Public on Mar 24 2017

type: SRA

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

country: USA

institute: NIH

library_source: genomic

data_processing:
library strategy: 4C-seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then trimmed the first 5'end 25bp
Trimmed reads were mapped to BamHI enzyme based reduced mm10 genome
Mapped reads were processed with 4Cker R package to generate bedgraph files
Supplementary_files_format_and_content: bedGraph files were generated by 4Cker R package

molecule: genomic DNA

organism: Mus musculus

source_name: 4C WT

growth_protocol: Mammary gland is harvested from lactating day1 female mouse

extract_protocol:
Frozen-stored mammary tissues collected at lactation day 1 (L1) were ground into powder. Chromatin was fixed with formaldehyde (final 1%) for 15 min at room temperature, and then was quenched with glycine (final 0.125 M). Pellets were lysed in lysis buffer (10 mM Tris HCI pH 8.0, 10 mM NaCl, 0.5% Nonidet P-40) containing Phenylmethylsulfonyl fluoride (PMSF) and protease inhibitors, incubated on ice for 30 min, and dounced using pre-chilled glass homogenizer, followed by another 10 min incubation on ice. After removal of supernatant, nuclei pellets were re-suspended in restriction endonuclease buffer 2 (NEB; 50 mM NaCl,10 mM Tris-HCl,10 mM MgCl2,1 mM Dithiothreitol; New Englnad Biolabs). SDS was added to a final concentration of 0.2% and samples was incubated for 1 hr at 37°C. 2% Triton X-100 was added, followed incubation for 1 hr at 37°C. Samples were incubated with 400 units each of restriction enzymes BamHI (New Englnad Biolabs) and were incubated overnight at 37°C. To enzyme inactivation SDS was added (final 1%) and incubated for 30 min at 65°C, followed by SDS-sequestration with 1% Triton X-100 at 37°C for 1 hr, T4 ligase (New England Biolabs) was added to each sample and incubated for 1 hr at 16°C. Ligated samples were treated overnight with proteinase K (20 mg/mL, Invitrogen) at 65°C and 1 hr at 37°C with RNase A (10 mg/mL, Thermo Fisher Scientific), and DNA fragments were purified by phenol-chloroform method.
DNA fragments from 3C were digested with NlaIII (New England Biolabs) overnight at 37°C and ligated using T4 ligase overnight at 16°C. DNA was purified by phenol/chloroform method and then amplified with site-specific primers linked to the Illumina DNA adaptors. Libraries for next generation sequencing were prepared and sequenced with HiSeq 2500 (Illumina)

tag: strain

tag: genotype/variation

value: wild type

tag: developmental stage

value: lactating day1(L1)

tag: tissue

value: mammary gland


title: ChIP-Seq-WT-L1-SMC1-rep2

tag: genotype


title: dbl-1_50uM_heme_rep2

first: Michael

last: Krause

state: MD

address: Bld. 5, Rm B104, 5 Memorial Dr.

institute: NIH/NIDDK

library_source: transcriptomic

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequence reads were aligned using Tophat 2, version 2.1.0.
Cufflinks2, version 2.2.1, was used to calculate FPKM values.
Genome_build: ce10
Supplementary_files_format_and_content: Format: gzipped text file format, Content: FPKM value per gene

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole animal

extract_protocol:
RNA extraction protocol not provided.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: ChIP-Seq-delD-L1-CTCF-rep1

value: CTCF-delD

value: CTCF (Abcam ab70303 / Millipore 07-729)


title: WT_for_dbl-1_50uM_heme_rep2

value: wild-type for dbl-1(nk3)


title: ChIP-Seq-delD-L1-CTCF-rep2


title: dbl-1_50uM_heme_rep1


title: WT_for_dbl-1_50uM_heme_rep1


title: ChIP-Seq-delC-L1-STAT5A-rep2

value: CTCF-delC

value: STAT5A (Santa Cruz Biotechnology, sc-1081)


title: dbl-1_0uM_heme_rep2


title: ChIP-Seq-delC-L1-Pol2-rep2

value: RNA polymerase II (Abcam, ab5408)


title: ChIP-Seq-delC-L1-Pol2-rep1


title: ChIP-Seq-delC-L1-STAT5A-rep1


title: ChIP-Seq-delC-L1-SMC1-rep1


title: Kat8 Gdf9 cKO

status: Public on Mar 25 2017

city: Hefei

first: Shi

last: Yin

address: Huangshan Road 443

country: China

institute: The University of Science and Technology of China

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

molecule: total RNA

source_name: Oocyte

extract_protocol:
Oocytes were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: oocyte

tag: age

value: 2 weeks old

value: Kat8 Gdf9 cKO


title: WT_for_dbl-1_0uM_heme_rep1


title: WT_for_hrg-7_50uM_heme_rep3

value: wild-type for hrg-7(tm6801)


title: ChIP-Seq-delC-L1-H3K27ac-rep2

value: Mammary gland

value: H3K27ac (Abcam ab4729)


title: 4C WT-1


title: WT_for_hrg-7_50uM_heme_rep2


title: WT_for_hrg-7_50uM_heme_rep1


title: hrg-7_50uM_heme_rep3


title: 4C CTCF-delA-2

source_name: 4C CTCF-delA

value: CTCF site A mutant


title: ChIP-Seq-delC-L1-GR-rep1

value: day one of lactation

value: GR (Thermo Scientific, PA1-511A)


title: dbl-1_0uM_heme_rep1


title: ChIP-Seq-delC-L1-H3K27ac-rep1


title: ChIP-Seq-delB-L1-CTCF-rep2

value: CTCF-delB


title: WT_for_dbl-1_0uM_heme_rep2


title: hrg-7_50uM_heme_rep1


title: ChIP-Seq-delB-L1-CTCF-rep1


title: ChIP-Seq-delA-L1-SMC1-rep2

value: CTCF-delA

value: SMC1 (Bethyl, A300-055A)


title: WT_for_hrg-7_0uM_heme_rep3


title: hrg-7_50uM_heme_rep2


title: WT_for_hrg-7_0uM_heme_rep1


title: hrg-7_0uM_heme_rep2


title: hrg-7_0uM_heme_rep3


title: ChIP-Seq-delC-L1-CTCF-rep1

data_processing:
ChIP-seq signals were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) to filter low-quality reads and subsequently  aligned to the mouse reference genome (mm10) using Bowtie aligner (Langmead et al., Nature methods, 2012) with the -m 1 parameter to obtain only uniquely mapped reads, except for CTCF samples where the -m 3 and --best parameters were used. HOMER software (Heinz et al., Mol. Cell, 2010) was applied for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

value: CTCF (Abcam ab70303 / Millipore 07-729)


title: ChIP-Seq-delC-L1-CTCF-rep2


title: ChIP-Seq-delA-L1-STAT5A-rep1


title: ChIP-Seq-delA-L1-SMC1-rep1


title: hrg-7_0uM_heme_rep1


title: ChIP-Seq-delC-L1-GR-rep2


title: ChIP-Seq-delA-L1-H3K27ac-rep2


title: ChIP-Seq-delA-L1-Pol2-rep1


title: ChIP-Seq-delA-L1-Pol2-rep2


title: ChIP-Seq-delA-L1-H3K27ac-rep1


title: ChIP-Seq-delA-L1-GR-rep2


title: ChIP-Seq-delA-L1-GR-rep1


title: ChIP-Seq-delA-L1-CTCF-rep1


title: ChIP-Seq-delA-L1-CTCF-rep2


title: 174_FCX_30m_Treatment_input

city: Urbana

first: Lisa

middle: J

last: Stubbs

state: IL

address: 1206 West Gregory Drive | MC-195

department: IGB

institute: University of Illinois Urbana-Champaign

description: supplementary file name: 174_FCX_EX_30min_0.1M_input.ucsc.bigWig

data_processing:
Base calling and demultiplexing into FASTQ files was done using bcl2fastq v1.8.4 software (Illumina, San Diego, CA, USA).
Sequence data were aligned with Bowtie2 (Langmead and Salzberg 2012) to the UCSC Mus musculus mm9 genome, using default settings.
Aligned sequence data were analyzed for peaks using HOMER (Hypergeometric Optimization of Motif EnRichment) v4.7 (Heinz et al. 2010).
After peak calling, peak files were annotated to the mouse mm9 genome using HOMER’s annotation script to assign peaks to genes, and associate peaks with differential expression data.
BigWiggle pileup files were generated using HOMER’s makeBigWig.pl script with default settings.
Genome_build: UCSC Mus musculus mm9 genome
Supplementary_files_format_and_content: BigWig files were generated using HOMER's makeBigWig.pl script with default settings.  Scores represent read depth.  BigWig files for inputs represent single samples.  The remaining BigWig files represent the pooled read depth for the two samples with the same brain region, timepoint, control or treatment, and ChIP antibody.

source_name: Frontal Cortex

extract_protocol:
For tissue intended for ChIP-Seq, brain tissue from regions of interest was pooled and kept at 4° C until homogenization in PBS with protease inhibitor cocktail (PIC, Roche, Basel, Switzerland). Fresh brains were homogenized in pools of five on ice by motorized pestle. Homogenized brains were fixed in PBS with 1% formaldehyde for 10 minutes. Fixing reaction was stopped with addition of Glycine to 0.125M. Fixed cells were washed 3x with PBS+PIC to remove formaldehyde. Washed cells were lysed to nuclei with lysis solution – 50 mM Tris-HCl (pH 8.0), 2 mM EDTA, 0.1% v/v NP-40, 10% v/v glycerol, and PIC – for 30 minutes on ice. Cell debris was washed away with PBS with PIC. Nuclei were pelleted and flash-frozen on dry ice.  Frozen nuclei were thawed on ice in lysis solution (1% SDS, 10mM EDTA, 50mM Tris, pH 8.1 with protease inhibitor cocktail). Nuclei were counted using a hemocytometer. Nuclei were sonicated at high power for 7 x 7 minute cycles (30 s on, 30 s off) in a BiorupterTM UCD-200 (Diagenode, Liège, Belgium) sonicator. Remaining cellular debris was pelleted by centrifugation for 10 minutes at 13,000 x g.
Fragmented chromatin was processed for histone H3K27Ac ChIP (Abcam ab4729) with Diagenode iDeal ChIP kits (Diagenode #C01010051, Liège, Belgium), according to manufacturer’s specifications with minor adjustments. One million nuclei were used for each IP. 25 µl of each IP was reserved for input samples. Technical replicate inputs were pooled to 50 µl. 2 ug of h3k27ac antibody was used for each IP. An additional wash in TE buffer was performed after the initial four IP washes. Chromatin was processed for ESRRA ChIP using a customized protocol. Briefly, sonicated samples were pre-incubated with Protein G Dynabeads (Invitrogen 10009D) for three hours. Beads were removed and 10 µg of ESRRA antibody (SC-66882, Santa Cruz Biotechnology, Dallas, TX, USA) was added overnight with rotation at 4° C. Protein G beads were added for 3 hours to bind antibodies. Beads were washed with high salt, low salt, LiCl, and TE buffers for 5 minutes each in succession. Precipitated chromatin was eluted in ChIP elution buffer (1% SDS, 0.1 M NaHCO3) for 15 minutes twice in 25 µl. Samples were reverse cross-linked at 65° C with 1,300 rpm rotation overnight. Samples were phenol-chloroform extracted with standard methods and eluted into 20 µl of nuclease-free water.  After ChIP, immunoprecipitated DNA was quantified using a Qubit 2.0 (Life Technologies, Carlsbad, CA, USA) with a dsDNA HS Assay kit (Life Technologies #Q32854). Libraries were prepared using KAPA LTP library kits (KK8230), with protocol as written, using Bioo Scientific index adapters. Libraries were size selected using AmpureXP beads (Beckman Coulter, Brea, CA, USA), with protocol as written, selecting for DNA between 200-500bp in size. Library quality was checked by Qubit 2.0 and Bioanalyzer (Agilent 2100). Samples were sequenced with an Illumina HiSeq 2500 sequencer using a TruSeq SBS sequencing kit, version 4. All samples were sequenced in single end format with fragment length of 100 bp.

tag: brain region

value: Frontal Cortex

tag: time-point in minutes

tag: control or treatment

value: Treatment


title: 349_FCX_30m_Treatment_input

description: supplementary file name: 349_fcx_ex_30_input.ucsc.bigWig


title: 348_FCX_30m_Treatment_ESRRA

description: supplementary file name: 348_fcx_ex_30_erra.ucsc.bigWig

value: SC-66882, Santa Cruz Biotechnology


title: WT_for_hrg-7_0uM_heme_rep2


title: 168_FCX_30m_Treatment_H3K27AC

description: supplementary file name: 168+169_FCX_EX_30min_1M_H3K27AC.ucsc.bigWig

value: abcam ab4729


title: 167_FCX_30m_Control_input

description: supplementary file name: 167_FCX_CK_30min_0.1M_input.ucsc.bigWig

value: Control


title: 161_FCX_30m_Control_H3K27AC

description: supplementary file name: 160+161_FCX_CK_30min_1M_H3K27AC.ucsc.bigWig


title: 160_FCX_30m_Control_H3K27AC


title: ChIP-Seq-delA-L1-STAT5A-rep2

value: STAT5A (Santa Cruz Biotechnology, sc-1081)


title: 347_FCX_30m_Treatment_ESRRA

description: supplementary file name: 347_fcx_ex_30_erra.ucsc.bigWig


title: 169_FCX_30m_Treatment_H3K27AC


title: 158_Hypo_30m_Treatment_H3k27ac

description: supplementary file name: 157+158_Hypo_EXP_30min_1M_H3k27ac.ucsc.bigWig

source_name: Hypothalamus

value: Hypothalamus


title: 157_Hypo_30m_Treatment_H3k27ac


title: 154_Hypo_30m_Control_H3k27ac

description: supplementary file name: 154+155_Hypo_CK_30min_1M_H3k27ac.ucsc.bigWig


title: 152_Amy_30m_Treatment_H3K27ac

description: supplementary file name: 151+152_Amy_EXP_30min_1M_H3K27ac.ucsc.bigWig

source_name: Amygdala

value: Amygdala


title: 153_Amy_30m_Treatment_input

description: supplementary file name: 153_Amy_EXP_30min_0.1M_input.ucsc.bigWig


title: 155_Hypo_30m_Control_H3k27ac


title: 151_Amy_30m_Treatment_H3K27ac


title: 149_Amy_30m_Control_H3K27ac

description: supplementary file name: 148+149_Amy_CK_30min_1M_H3K27ac.ucsc.bigWig


title: 148_Amy_30m_Control_H3K27ac


title: 150_Amy_30m_Control_input

description: supplementary file name: 150_Amy_CK_30min_0.1M_input.ucsc.bigWig


title: 144_Hypo_120m_Treatment_input

description: supplementary file name: 144_Hypo_EXP_120min_0.1M_input.ucsc.bigWig


title: 140_Hypo_120m_Treatment_H3k27ac

description: supplementary file name: 139+140_Hypo_EXP_120min_1M_H3k27ac.ucsc.bigWig


title: 139_Hypo_120m_Treatment_H3k27ac


title: 138_Hypo_120m_Control_input

description: supplementary file name: 138_Hypo_CK_120min_0.1M_input.ucsc.bigWig


title: 125_Amy_120m_Control_input

description: supplementary file name: 125_Amy_CK_120min_0.1M_input.ucsc.bigWig


title: 159_Hypo_30m_Treatment_input

description: supplementary file name: 159_Hypo_EXP_30min_1M_input.ucsc.bigWig


title: 120_FCX_120m_Treatment_H3K27ac

description: supplementary file name: 119+120_FCX_120min_EX_1M_H3K27ac.ucsc.bigWig


title: 134_Hypo_120m_Control_H3k27ac

description: supplementary file name: 133+134_Hypo_CK_120min_1M_H3k27ac.ucsc.bigWig


title: 156_Hypo_30m_Control_input

description: supplementary file name: 156_Hypo_CK_30min_1M_input.ucsc.bigWig


title: 133_Hypo_120m_Control_H3k27ac


title: 127_Amy_120m_Treatment_H3K27ac

description: supplementary file name: 126+127_Amy_Exp_120min_1M_H3K27ac.ucsc.bigWig


title: 130_Amy_120m_Treatment_input

description: supplementary file name: 130_Amy_Exp_120min_0.1M_input.ucsc.bigWig


title: 118_FCX_120m_Control_H3K27ac

description: supplementary file name: 117+118_FCX_120min_CK_1M_H3K27ac.ucsc.bigWig


title: 126_Amy_120m_Treatment_H3K27ac


title: 121_Amy_120m_Control_H3K27ac

description: supplementary file name: 121+122_Amy_CK_120min_1M_H3K27ac.ucsc.bigWig


title: 122_Amy_120m_Control_H3K27ac


title: 115_FCX_120m_Treatment_input

description: supplementary file name: 115_FCX_120min_EX_input-119+120.ucsc.bigWig


title: 119_FCX_120m_Treatment_H3K27ac


title: FC_120_ex6

data_processing:
Fastq files were generated with the software Casava 1.8.2 (Illumina)
read alignment: Tophat 2.0.8, default parameters
read quantification: Reads inside of exon features were counted in union mode using htseq version 0.6.1.
differential expression: Done in R using the Bioconductor package edgeR.  Pairwise comparisons between control and intruder conditions in each tissue and time after challenge were analyzed using the bin.loess version of trended dispersion in edgeR version 3.2.4 in R version 3.0.0.
Genome_build: mouse NCBI version 37.2
Supplementary_files_format_and_content: mm_mrsb_allcounts_for_GEO_2016-04-12.txt: Tab delimited text file of the matrix of raw read counts mapped to the mouse genome (Ensembl annotation of the NCBIM37 version of the mouse genome) as created by the edgeR function readDGE. TopHat2 version 2.0.8 (Kim et al. 2013) was used to align reads.  Reads inside of exon features were counted in union mode using htseq version 0.6.1 (Anders et al. 2015). Note that the counts include meta tags that are prefixed by "__" that were removed from counts before further processing.

extract_protocol:
Freshly dissected tissue was flash-frozen in liquid nitrogen and frozen at -80° C until RNA could be extracted. Total RNA was disrupted in Trizol (Life Technologies, Carlsbad, CA, USA) with a mechanical pestle according manufacturer’s specifications. The aqueous phase was precipitated in isopropanol, resuspended in nuclease-free water, treated with DNase I (New England Biolabs, Ipswich, MA, USA), and cleaned up using a Zymo RNA Clean & Concentrator™-25 kit (Zymo Research, Irvine, CA, USA) according to manufacturer’s specifications. Prior to library preparation, total RNA was checked for purity using a NanoDrop ND-1000 spectrophotometer, integrity using RNA Nano chips on an Agilent 2100 Bioanalyzer, and concentration using a Qubit fluormeter.
RNA-Seq libraries were prepared from total RNA robotically using TruSeq Stranded mRNA HT (Illumina, San Diego, CA, USA) on an epMotion 5075 robot (Eppendorf, Hamburg, Germany). Single-end reads.

tag: animal id


title: FC_120_ex2


title: FC_120_ex3


title: 117_FCX_120m_Control_H3K27ac


title: FC_120_ex1


title: 114_FCX_120m_Control_input

description: supplementary file name: 114_FCX_120min_CK_input-117+118.ucsc.bigWig


title: FC_120_ex4


title: FC_120_ck6


title: FC_120_ex5


title: FC_60_EX3


title: FC_120_ck4


title: FC_60_EX4


title: FC_120_ck5


title: FC_60_EX5


title: FC_60_EX1


title: FC_60_CK6


title: ChIP-seq from fibroblast of arm (ENCLB486DRD)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR922FLS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR922FLS
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB486DRD
size range: 200-600

data_processing: See GSM*_README.txt supplementary file linked below

organism: Homo sapiens

source_name: Homo sapiens fibroblast of arm primary cell male adult (53 years)

extract_protocol: not provided

tag: antibody

value: fibroblast of arm

value: primary cell

tag: description

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

tag: biosample encode accession

value: 53 year

tag: dev stage

value: adult

tag: Sex

value: male

tag: lab

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS367AAA at ENCODE; https://www.encodeproject.org/ENCBS367AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: FC_60_CK3


title: FC_120_ck1


title: FC_60_CK1


title: FC_60_EX2

value: Treatment


title: FC_60_CK5


title: FC_60_CK2


title: FC_30_Ex3


title: ChIP-seq from OCI-LY1 (ENCLB429FEJ)

description:
https://www.encodeproject.org/experiments/ENCSR189AGR/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR189AGR
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB429FEJ
size range: 200-600

source_name: Homo sapiens OCI-LY1 immortalized cell line

tag: line

value: immortalized cell line

value: established from the bone marrow of a 44-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL; diffuse large cell), stage 4B at relapse in 1983

value: 44 year

tag: health state

value: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS899DSB at ENCODE; https://www.encodeproject.org/ENCBS899DSB/

value: Derived from ENCODE donor ENCDO350AAA; https://www.encodeproject.org/ENCDO350AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1879; http://web.expasy.org/cellosaurus/CVCL_1879


title: FC_120_ck3

value: Control


title: ChIP-seq from OCI-LY3 (ENCLB604HDA)

description:
https://www.encodeproject.org/experiments/ENCSR361GKY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR361GKY
assay title: ChIP-seq
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB604HDA
size range: 200-600

source_name: Homo sapiens OCI-LY3 immortalized cell line

value: Oci-Ly-3- Immortalized diffuse large B cell lymphoma cell line developed at the Ontario Cancer Institute

value: 52 year

value: adult

value: ENCBS018GXW at ENCODE; https://www.encodeproject.org/ENCBS018GXW/

value: Derived from ENCODE donor ENCDO355AAA; https://www.encodeproject.org/ENCDO355AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_8800; http://web.expasy.org/cellosaurus/CVCL_8800


title: ChIP-seq from fibroblast of arm (ENCLB021TGC)

description:
https://www.encodeproject.org/experiments/ENCSR922FLS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR922FLS
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB021TGC
size range: 200-600

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS372AAA at ENCODE; https://www.encodeproject.org/ENCBS372AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: ChIP-seq from MCF-7 (ENCLB606MHG)

description:
https://www.encodeproject.org/experiments/ENCSR768LHG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR768LHG
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB606MHG
size range: 200-600

source_name: Homo sapiens MCF-7 immortalized cell line

value: Control

value: immortalized cell line

value: mammary epithelium, doubling time ~ 29hoursATCC HTB-22

value: 69 year

value: female

value: breast cancer (adenocarcinoma)

tag: passage number

value: Bradley Bernstein, Broad

value: ENCBS967MVZ at ENCODE; https://www.encodeproject.org/ENCBS967MVZ/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ATCC sample source; http://www.atcc.org/products/all/HTB-22.aspx


title: FC_30_Ex5

value: Treatment


title: FC_30_Ex1


title: FC_120_ck2


title: FC_30_Ex4


title: FC_30_CK2


title: 1993_H3K27Ac

city: New York

first: Riccardo

last: Dalla-Favera

state: NY

address: 1130 St Nicholas Avenue

institute: Columbia University

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the human genome (UCSC hg19) for human GC B cells using the Bowtie2 aligner v2.1.0, allowing up to two mismatches. Duplicate reads (i.e. reads of identical length mapping to exactly the same genomic locations) were removed with samtools v0.1.19 using the rmdup option.
Reads were normalized to total reads aligned (counts per million). Peak detection was done using ChIPseeqer v2.0, enforcing a minimum fold change of 2 between ChIP and input reads, a minimum peak width of 100 bp, and a minimum distance of 100 bp between peaks.
The threshold for statistical significance of peaks was set at 10-5 for NOTCH1, and 10-15 for H3K4me1, H3K4me3 and H3K27Ac.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain peak locations. Columns 1, 2, and 3 contain the chromosome, start, and end position of the peak respectively. The fourth column is the maximum peak height normalized per million mapped reads in each library.

source_name: Primary CLL cells

growth_protocol: MO1043-ICN1-HA cells were induced to express ICN1-HA with 1 ug/ml of Doxycycline for 36 hours; primary CLL cells were thawed in Iscove's Modified Dulbecco's Medium (Life Technologies) supplemented with 20% fetal bovine serum (FBS) (Sigma-Aldrich), penicillin (100 U/ml) and streptomycin (100 μg/ml) and immediately crosslinked.

extract_protocol:
Crosslinked chromatin was fragmented by sonication with the Bioruptor sonicator (Diagenode) to achieve fragment sizes of ~200–500 base pairs using the following sonication buffer: 10mM Tris-HCl pH 8.0, 100mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine.
ChIP-seq libraries were constructed starting from 4ng of ChIP or Input DNA as reported in Blecher-Gonen et al., 2013, Nature protocol. Libraries were quantified using the KAPA SYBR FAST Universal qPCR Kit (KAPA Biosystems), normalized to 10nM, pooled and sequenced in an Illumina HiSeq 2500 instrument as single-end 101 bp reads.

treatment_protocol: CLL cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature and quenched by the addition of glycine to a final concentration of 0.125M.

value: Histone H3K27ac antibody Active Motif, cat#39133

tag: tissue

value: Peripheral blood Chronic Lymphocytic Leukemia (CLL) cells

tag: conditions


title: FC_30_CK3


title: FC_30_Ex2


title: FC_30_CK1


title: 1958_H3K27Ac


title: 1993_Input

value: none (input)


title: 2062_Input


title: H_120_EX6


title: 2062_H3K27Ac


title: FC_30_CK5


title: 2070_Input


title: FC_30_CK4


title: 2040_H3K27Ac


title: 2040_Input


title: 1958_Input


title: H_120_EX2


title: 1252_H3K27Ac


title: 1239_H3K27Ac


title: H_120_EX4


title: 1239_Input


title: 702_Input


title: H_120_EX3


title: H_120_CK4


title: 2070_H3K27Ac


title: H_120_CK6


title: H_120_EX1


title: 1863_Input


title: H_120_CK3


title: 1863_H3K27Ac


title: MO1043_ICN1_HA_Input

source_name: CLL cell line MO1043

value: Chronic Lymphocytic Leukemia (CLL) cell line

tag: cell line

value: MO1043 CLL cells induced to express ICN1-HA


title: H_60_EX4


title: MO1043_ICN1_HA_H3K27me3_b

value: Histone H3K27me3 antibody Active Motif, cat#39157


title: H_120_CK1

value: Control


title: 702_H3K27Ac


title: MO1043_ICN1_HA_Tc_NOTCH1_b

value: NOTCH1 antisera from Wang et al.,PNAS 108(36):14908-13


title: H_60_EX5


title: H_60_EX2


title: MO1043_ICN1_HA_H3K4me3_b

value: Anti-Histone H3K4me3 antibody Abcam, cat#ab8580


title: H_60_EX1


title: H_60_CK6


title: H_120_CK2


title: 1252_Input


title: MO1043_ICN1_HA_H3K27me3_a


title: MO1043_ICN1_HA_H3K4me1_b

value: Anti-Histone H3K4me1 antibody Abcam, cat#ab8895


title: H_60_EX3


title: MO1043_ICN1_HA_H3K27Ac_a


title: H_60_CK5


title: H_60_CK3


title: MO1043_ICN1_HA_H3K4me3_a


title: H_60_CK2


title: H_60_CK1


title: MO1043_ICN1_HA_H3K4me1_a


title: MO1043_ICN1_HA_Tc_NOTCH1_a


title: RG090

data_processing:
Illumina Casava1.7 software used for basecalling.
RTA (Illumina) was used for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming.
Reads were mapped to the human reference genome NCBI/build37.2 using Tophat (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10) to tackle the mapping issue of reads that are from exon-exon junctions.
Relative abundance of genes and splice isoforms was estimated using cufflinks (version 2.0.2) with default settings.
Genome_build: hg19

growth_protocol: MO1043-ICN1-HA cells were induced to express ICN1-HA or eGFP with 1 ug/ml of Doxycycline for 36 hours; primary CLL cells were thawed in Iscove's Modified Dulbecco's Medium (Life Technologies) supplemented with 20% fetal bovine serum (FBS) (Sigma-Aldrich), penicillin (100 U/ml) and streptomycin (100 μg/ml) and immediately harvested.

extract_protocol:
Total RNA was extracted from primary CLL cases with the RNeasy Mini Kit (QIAGEN) with on column DNAse treatment and poly-A pull-down was performed to enrich mRNAs from total RNA.
RNA-Seq libraries were prepared using the Illumina TruSeq RNA prep kit and sequenced using the Illumina HiSeq2500 instrument.


title: RG089


title: RG088


title: H_30_Ex3


title: H_30_Ex4


title: H_30_Ex1


title: H_30_Ex2


title: RG086


title: MO1043_ICN1_HA_H3K27Ac_b


title: H_30_EX5


title: RG083


title: RG080


title: RG085


title: RG078


title: RG077


title: H_30_CK3


title: RG075


title: RG076


title: A_120_Ex3


title: RG074


title: A_120_Ex2


title: H_30_CK2


title: RG073


title: RG071


title: A_120_Ex4


title: A_120_CK6


title: A_120_Ex1


title: RG068


title: A_120_CK3


title: A_120_CK4


title: A_120_CK1


title: RG061


title: RG063


title: A_120_CK2


title: H_30_CK5


title: RG065


title: A_60_Ex5


title: RG060


title: RG058


title: A_60_Ex4


title: A_60_Ex2


title: RG056


title: A_60_Ex1


title: RG059


title: RG053


title: A_60_CK3


title: A_60_CK5


title: RG051


title: A_60_CK2


title: RG052


title: RG050


title: A_60_CK1


title: A_30_Ex5


title: A_30_Ex2


title: RG041


title: RG042


title: A_30_Ex3


title: RG046


title: A_30_Ex1


title: A_60_Ex3


title: RG040


title: RG039


title: RG055


title: A_30_CK5


title: A_30_CK3


title: A_30_CK4


title: RG038


title: A_30_CK2


title: A_60_CK6


title: RG037


title: RG049


title: A_30_CK1


title: RG048


title: RG036


title: RG035


title: RG029


title: RG030


title: A_30_Ex4


title: RG028


title: RG031


title: RG032


title: A_120_Ex6


title: RG027


title: RG008

value: MO1043 CLL cells induced to express eGFP


title: RG024


title: RG007


title: RG023


title: RG006


title: RG005


title: ChIP-seq from SUDHL6 (ENCLB149NCP)

description:
https://www.encodeproject.org/experiments/ENCSR316KHQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR316KHQ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR179YLS
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB149NCP
size range: 200-600

source_name: Homo sapiens SUDHL6 immortalized cell line

value: immortalized cell line

value: also called SU-DHL-6 (diffuse histiocytic lymphoma) - disease:large cell lymphoma; diffuse mixed histiocytic and lymphocytic lymphoma; follicular B cell lymphoma; ATCC CRL-2959

tag: age

value: 43 year

value: adult

value: male

value: Bradley Bernstein, Broad

value: ENCBS107PVI at ENCODE; https://www.encodeproject.org/ENCBS107PVI/

value: Derived from ENCODE donor ENCDO353AAA; https://www.encodeproject.org/ENCDO353AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2206; http://web.expasy.org/cellosaurus/CVCL_2206


title: RG072

value: Peripheral blood Chronic Lymphocytic Leukemia (CLL) cells


title: RG003

value: Chronic Lymphocytic Leukemia (CLL) cell line

value: MO1043 CLL cells induced to express ICN1-HA


title: RG002


title: huvec-IL8

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to UCSC hg19 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: hg19
Supplementary_files_format_and_content: excel files include RPKM values for each Sample

source_name: primary HUVECs

growth_protocol: HUVEC cells were plated in M200 media with Low Serum Growth Supplement (Gibco) and grown to 80% confluency in a 5% C02 atmosphere at 37 degrees.

extract_protocol:
Cells were harvested after 6 hours of treatment.  Total RNA was extracted using the Qiagen Mini-Plus RNA isolation kit.
Ribosomal RNA was depleted using the Ribo-Zero kit (epicentre) and libraries were prepared using the NEBNext Ultra kit for Illumina

treatment_protocol: Culture media was removed and replaced with M200 without supplementation.  After 12 hours, recombinant human CXCL8/IL-8 (RND Systems) was added at a final concentration of 10 ng/mL.  Water served as a negative control.  Samples were treated in duplicate.

value: primary HUVECs

tag: cell type

value: endothelial cell


title: huvec-neg


title: RG001


title: ASA+CUR replicate 1

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description:
AOM_DSS_Asp_Cur_1
Processed data file: repFpkmMatrix-isoforms.txt

data_processing:
Illumina bcl2fastq2-v2.17.1.14 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to mm10 whole genome using TopHat v2.0.9 (with Bowtie 2.1.0.0) using default settings.
All samples were modeled using cuffdiff with options -p 6 --no-update-check and the UCSC mm10 genes.gtf file from the Illumina iGenomes site.
Raw cuffdiff output files were loaded into the R package cummeRbund.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by cuffdiff and output by cummeRbund.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: repFpkmMatrix-isoforms.txt.gz: Gzipped, tab-delimited text file containing isoform_ID row labels and sample replicate column labels. The values are FPKM.

source_name: tumor samples, AIN-93M+ASA 0.01% + CUR 1%

growth_protocol: Mice were obtained from Jackson Laboratory and maintained at a controlled temperature (20-22C), controlled relative humidity (45-55%), and a 12h light/12h dark cycle at the Rutgers Animal Care Facility.

extract_protocol:
Following sacrifice, colons were removed, cleaned and opened longitudinally followed by careful examination of the tumors. After removing the proximal end and palpable tumors, the remaining right portion of the colon was snap frozen for RNA. Total cellular RNA was isolated using the AllPrep DNA/RNA Mini Kit (Qiagen). RNA quality was determined on an Agilent 2100 Bioanalyzer and concentration determined using a Nanodrop.
RNAs were reverse transcribed and converted to libraries using the Illumina TruSeq RNA Sample Preparation Kit v2.

treatment_protocol: 6-week-old mice were injected with AOM (Sigma-Aldrich) subcutaneously in the lower flank at a dose of 10 mg/kg body weight. The mice in the control group instead received an injection of saline (Thermo Fisher Scientific, Waltham, MA, USA). One week later, the drinking water for the mice, other than the control group, was replaced with DSS (MP Biomedicals, Solon, OH, USA) at a concentration of 1.2% (w/v) for 7 days.

tag: strain/background

tag: model

value: AOM/DSS

value: tumor samples

tag: treatment


title: ASA+CUR replicate 0

description:
AOM_DSS_Asp_Cur_0
Processed data file: repFpkmMatrix-isoforms.txt


title: RG026


title: CUR replicate 1

description:
AOM_DSS_Cur_1
Processed data file: repFpkmMatrix-isoforms.txt

source_name: tumor samples, AIN-93M+CUR 2%

value: AIN-93M+CUR 2%


title: CUR replicate 0

description:
AOM_DSS_Cur_0
Processed data file: repFpkmMatrix-isoforms.txt


title: ASA replicate 0

description:
AOM_DSS_Asp_0
Processed data file: repFpkmMatrix-isoforms.txt

source_name: tumor samples, AIN-93M+ASA 0.02%


title: RG025


title: IgG_iCLIP_zf_ZGA_rep3

city: New Haven

first: Karla

middle: M

last: Neugebauer

state: CT

address: 333 Cedar St

department: Molecular Biophysics and Biochemistry

institute: Yale University

description:
Each unique and multi mapping file contains significant CLIP tags (FDR<0.01) from the three summed replicates for their respective developental stages (preZGA and ZGA). Data provided for hnRNP A1 and IgG pull-downs.
peaks_id79494_rnd100_flank15_fdr0.01_group_4690_wt-IgG-control-together-1K-data_sum_M_danRer7--ensembl72_from_4342-4344-4345_bedGraph-cDNA.bed.gz_lowFDR.bed
peaks_id79490_rnd100_flank15_fdr0.01_group_4690_wt-IgG-control-together-1K-data_sum_G_danRer7--ensembl72_from_4342-4344-4345_bedGraph-cDNA-hits-in-gen_lowFDR.bed-2

data_processing:
Basecalls performed using CASAVA version 1.4
For detail on data processing see: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959
Genome_build: Zv9 (version 75)
Supplementary_files_format_and_content: .bed files describing significant crosslink sites derived from unique (contain G in the file name) and multi mapped (contain M in the file name) reads for combined replicates for each individual developmental stages and negative controls.

organism: Danio rerio

source_name: zebrafish embryo

growth_protocol: Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.

extract_protocol:
Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1-RNA complexes were immunopurified using mouse anti-hnRNP A1 antibody and protein G-dynabeads (Invitrogen). Anti-IgG antibody (Sigma) was used for negative control immunopurifications.
After RNA dephosphorylation, 3' end linker ligation was performed. Protein-RNA complexes were resolved on SDS-PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently, RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE-Urea gel (Life Technologies) and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959

treatment_protocol: Zebrafish embryos at the desired developmental stages were irradiated with UV light (254 nm) to in vivo crosslink RNA-protein interactions.

tag: developmental stage

value: ZGA (1K cell stage)

tag: antibody

value: anti-IgG

tag: barcode sequence

value: NNNTGGCNN


title: Model replicate 1

description:
AOM_DSS_1
Processed data file: repFpkmMatrix-isoforms.txt

source_name: tumor samples, AIN-93M diet

value: AIN-93M diet


title: IgG_iCLIP_zf_ZGA_rep1

value: NNNGGCGNN


title: IgG_iCLIP_zf_preZGA_rep2

description:
Each unique and multi mapping file contains significant CLIP tags (FDR<0.01) from the three summed replicates for their respective developental stages (preZGA and ZGA). Data provided for hnRNP A1 and IgG pull-downs.
peaks_id79495_rnd100_flank15_fdr0.01_group_4039_IgG-Control-replicates_sum_M_danRer7--ensembl72_from_3714-3717-3718_bedGraph-cDNA.bed.gz_lowFDR.bed
peaks_id79491_rnd100_flank15_fdr0.01_group_4039_IgG-Control-replicates_sum_G_danRer7--ensembl72_from_3714-3717-3718_bedGraph-cDNA-hits-in-genome.bed.g_lowFDR.bed

value: preZGA (32 cell stage)

value: NNNCCGGNN


title: H5N1 infected A549 cells

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

data_processing:
Sequence reads were obtained by Illumina pipeline. Reads of low quality were removed and adaptor sequence were trimed by our Perl scripts.
Supplementary_files_format_and_content: tab-delimited text files including sequences and their counts

source_name: A549 Cells

growth_protocol: A549 cells were maintained at 37℃ in a humidified 5% CO2 incubator with Dulbecco’s modified eagle medium (Gibco, CA, USA) containing 10% fetal bovine serum (FBS, Gibco), 100 units/ml of penicillin, and 100 μg/ml of streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent.
small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549 cells were infected with H5N1 influenza A virusat an MOI of two. After 60 min of virus adsorption, the virus  was removed and the cells were washed with warm culture medium and incubated in  Dulbecco’s modified eagle medium (Gibco, CA, USA) supplemented with 100 U/ml penicillin, 100 μg/ml streptomycin and 2 μg/ml N-p-tosyl-L-phenylalaninechloromethyl ketone-treated trypsin (Sigma, St Louis, MO, USA). The infected cells were maintained at 37℃ in a humidified 5% CO2 incubator for 48h.

tag: treatments

value: H5N1 virus infection


title: High detergent rep 2

city: Waltham

first: Sebastian

last: Kadener

address: 415 South Street

institute: Brandeis University

description: ribosome bound RNA

data_processing:
Illumina adaptors were removed using cutadapt 1.9.1
Removing PCR duplications
Trimming four bases from both ends of the reads (these are UMIs)
Removing ribosoal RNA reads from the files
Alignment aginst circRNA dataset
Genome_build: dm3
Supplementary_files_format_and_content: Table with list of circRNA detected in the footprinting data

organism: Drosophila melanogaster

source_name: Fly heads

extract_protocol:
For head1 and 2 samples we followed the original fly head homogenization protocol (Huang et al 2013 Pbio PMID: 24348200). For the Heads 3 and 4 sample 200 heads were frozen and lysed in 500ul of lysis buffer (30 mM HEPES KOH at pH 7.4, 100 mM KAcetate, 2 mM MgAcetate, 5% glycerol, 0.1% Triton X-100, 1 mM EGTA, 5 mM DTT, 0.4 U/μL murine RNase inhibitor [NEB], protease inhibitors (Complete mini, Roche), and 100ug/ml CHX). ribosome-protected RNA fragments were isolated using previously publish protocol (Calviello L et al 2015 nature methods PMID: 26657557)
RNA libraries were prepared using previously publish protocol (Calviello L et al 2015 nature methods PMID: 26657557)

value: fly heads

value: high detergent


title: Model replicate 0

description:
AOM_DSS_0
Processed data file: repFpkmMatrix-isoforms.txt


title: low detergent rep 2

description: ribosome bound RNA

value: low detergent


title: IgG_iCLIP_zf_preZGA_rep1


title: High detergent rep 1

description: ribosome bound RNA


title: IgG_iCLIP_zf_preZGA_rep3


title: RG004

value: Chronic Lymphocytic Leukemia (CLL) cell line

value: MO1043 CLL cells induced to express ICN1-HA


title: hnRNP A1_iCLIP_zf_ZGA_rep4

description:
Each unique and multi mapping file contains significant CLIP tags (FDR<0.01) from the three summed replicates for their respective developental stages (preZGA and ZGA). Data provided for hnRNP A1 and IgG pull-downs.
peaks_id79492_rnd100_flank15_fdr0.01_group_4359_1K-hnrnpa1-replicates-summed_sum_M_danRer7--ensembl72_from_4341-4343-4346-4347_bedGraph-cDNA.bed.gz_lowFDR.bed
peaks_id79488_rnd100_flank15_fdr0.01_group_4359_1K-hnrnpa1-replicates-summed_sum_G_danRer7--ensembl72_from_4341-4343-4346-4347_bedGraph-cDNA-hits-in-g_lowFDR.bed

value: anti-hnRNP A1

value: NNNGGTCNN


title: Control replicate 1

description:
Control_1
Processed data file: repFpkmMatrix-isoforms.txt

source_name: colonic tissue, AIN-93M diet

value: Control

value: colonic tissue


title: siRNA RNA-seq from K562 (ENCLB276QFQ)

description:
https://www.encodeproject.org/experiments/ENCSR287SHU/
***************
biological replicate number: 1
technical replicate number: 1
description: Control siRNA against no target in K562 cells followed by RNA-seq.
experiment encode accession: ENCSR287SHU
assay title: siRNA RNA-seq
assembly: GRCh38
encode release date: 2017-01-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB276QFQ
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting Non-specific target control

value: immortalized cell line

tag: description

value: K562 cells treated with siRNA knockdown using a human non-targeting control.

tag: biosample encode accession

tag: dev stage

value: adult

tag: Sex

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

tag: lab

value: Sherman Weissman, Yale

value: ENCBS220KXD at ENCODE; https://www.encodeproject.org/ENCBS220KXD/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: wt-clutch2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: GRCz10
Supplementary_files_format_and_content: excel files include RPKM values for each Sample

source_name: endothelial cells

growth_protocol: Zebrafish embryos were grown under standard conditions in a 28 degree incubator.

extract_protocol:
Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation.
Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina (Clontech Laboratories).

value: endothelial cells


title: low detergent rep 1

description: ribosome bound RNA

tag: tissue

value: fly heads

value: low detergent


title: Control replicate 0

description:
Control_0
Processed data file: repFpkmMatrix-isoforms.txt

value: AIN-93M diet


title: hnRNP A1_iCLIP_zf_ZGA_rep2

value: ZGA (1K cell stage)

value: anti-hnRNP A1

value: NNNTTGTNN


title: wt-clutch1


title: ASA replicate 1

description:
AOM_DSS_Asp_1
Processed data file: repFpkmMatrix-isoforms.txt

value: AOM/DSS

value: tumor samples


title: 24 hpi

city: Washington

first: Katherine

middle: Michele

last: Buckley

state: DC

address: 800 22nd St NW

department: Department of Biological Sciences

institute: The George Washington University

description: Larvae exposed to V. diazotrophicus for 24 hr

data_processing:
Low-quality reads were filtered using the Fastx-toolkit and mapped to the S. purpuratus genome, v43.1 using Bowtie (v0.12.7) with the following parameters: -k 50 -m 50 -n 3 -e 900 --snpfrac 0.4.
RPKM values were determined for each gene using the methods outlined in Mortazavi et al., 2008.
Genome_build: Spur3.1

organism: Strongylocentrotus purpuratus

source_name: Larvae (~15,000 from single mating)

growth_protocol: Larvae were grown in artificial sea water (ASW; Instant Ocean) at 15 C.  Beginning at the onset of feeding (4 dpf), larvae were fed Rhodomonas lens (5,000 cells/ml) ever other day.

extract_protocol:
Larvae were collected using 100 uM Nitex mesh, washed three times in ASW, pelleted by centrifugation and stored in Trizol.  Whole RNA was extracted from Trizol preparations using manufacturers instructions. Polyadenylated RNA was purified using the Poly(A)Purist Kit (Ambion).
Libraries were prepared for SOLiD sequencing using standard ABI protocols.

value: whole larva

value: 10 dpf

tag: bacterial strain

value: Vibrio diazotrophicus (ATCC strain 33466)


title: IgG_iCLIP_zf_ZGA_rep2

value: anti-IgG

value: NNNCCACNN


title: hnRNP A1_iCLIP_zf_ZGA_rep1

value: NNNGGTTNN


title: kdrl:cxcr1-clutch2


title: 12 hpi

description: Larvae exposed to V. diazotrophicus for 12 hr

value: 9 dpf


title: HIC002

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
AaegL2.mnd.txt.gz
AaegL4.fasta.gz

data_processing:
The paired end reads were processed against the draft genome assemblies using Juicer tool for Hi-C experiments (Durand et al. 2016) to produce merged_nodups.txt files, a duplicate-free list of paired alignments of Hi-C reads to the draft fasta.
The merged_nodups.txt files were used as input into a custom Hi-C assembly pipeline (see Dudchenko et al.) to create chromosome-length assembly fasta files.
The paired end reads were processed against the chromosome-length assemblies using Juicer tool for Hi-C experiments (Durand et al. 2016) to create genome-wide Hi-C contact maps compatible with Juicebox visualization tool for Hi-C contact maps (hic-files). Additional filtration was applied for contact matrices for Samples 2 and 3 (Aedes aegypti) to remove contact pairs from poly-G reads.
Genome_build: Draft genome for Samples 1 and 2 (Aedes aegypti) was downloaded form GenBank (accession number GCA_000004015.2). Draft genome for Sample 3 (Culex quinquefasciatus) was downloaded from VectorBase (INSDC Assembly GCA_000209185.1). Discovar de novo version 52488 was used to create a draft genome for Sample GSM1551550 (GM12878, Homo sapiens, see GSE63525) from reads downloaded from Sequence Read Archive SRX297987.
Supplementary_files_format_and_content: Draft assembly fasta for GSM1551550 (Homo sapiens GM12878 sample).
Supplementary_files_format_and_content: Merged_nodups.txt files for Samples 1/2, 3 and GSM1551550 containing duplicate-free lists of of paired alignment of Hi-C reads to the draft fastas as generated by the Juicer pipeline (Durand et al., 2016). Only the first 100,000,000 read pairs from the data produced for GSM1551550 as part of the SGE63525 study was used.
Supplementary_files_format_and_content: Final assembly fastas for Samples 1/2, 3 and GSM1551550.
Supplementary_files_format_and_content: AaegL2.mnd.txt.gz - duplicate-free list of paired alignments of Hi-C reads
Supplementary_files_format_and_content: CpipJ2.mnd.txt.gz - duplicate-free list of paired alignments of Hi-C reads
Supplementary_files_format_and_content: Hs1.mnd.txt.gz - duplicate-free list of paired alignments of Hi-C reads

organism: Aedes aegypti

source_name: Benzon Research

extract_protocol:
Insect tissue was crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
Standard Illumina library construction protocol. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the NextSeq500 following the manufacturer's protocols.
In situ Hi-C (Rao, Huntley et al., 2014)

tag: strain

value: Orlando strain

value: whole organism


title: kdrl:cxcr1-clutch1

value: endothelial cells


title: HIC001

description:
AaegL2.mnd.txt.gz
AaegL4.fasta.gz


title: hnRNP A1_iCLIP_zf_preZGA_rep3

description:
Each unique and multi mapping file contains significant CLIP tags (FDR<0.01) from the three summed replicates for their respective developental stages (preZGA and ZGA). Data provided for hnRNP A1 and IgG pull-downs.
peaks_id79493_rnd100_flank15_fdr0.01_group_3808_Replicates-together-hnRNPA1_sum_M_danRer7--ensembl72_from_3715-3716-3719_bedGraph-cDNA.bed.gz_lowFDR.bed
peaks_id79489_rnd100_flank15_fdr0.01_group_3808_Replicates-together-hnRNPA1_sum_G_danRer7--ensembl72_from_3715-3716-3719_bedGraph-cDNA-hits-in-genome_lowFDR.bed

value: preZGA (32 cell stage)

value: NNNCAATNN


title: 0 hpi

description: Uninfected larvae

tag: age


title: Liver_male_deep

city: Dunedin

first: Tim

last: Hore

address: 270 Great King Street

department: Department of Anatomy

country: New Zealand

institute: University of Otago

data_processing:
Trimming was performed to remove poor-quality calls, adapter sequences and 10bp from the 5' end of reads using TrimGalore v0.4.0  (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with default parameters.
Trimmed reads were aligned using Bismark v0.14.3 (Krueger and Andrews, 2011) with the --pbat option specified. Only genome scaffolds of at least 277kb were used for alignment.
Data was deduplicated using Bismark v0.14.3 (Krueger and Andrews, 2011) with default parameters.
CG methylation calls were extracted from deduplicated reads using Bismark v0.14.3 (Krueger and Andrews, 2011) with the --comprehensive and --merge_non_CG options specified.
Genome_build: Callorhinchus milii 6.1.3
Supplementary_files_format_and_content: List of mapped CG calls in a tab-delimited text file; + indicates methylated, - indicates unmethylated

organism: Callorhinchus milii

source_name: Liver

extract_protocol:
Elephant shark tissue samples were provided by commercial fishermen from recently deceased animals. DNA was purified using a modified magnetic bead approach (Deangelis et al., 1995). Briefly, cells were first homogenised in “GITC” lysis buffer (4 M Guanidine thiocyanate, Sigma G6639; 50 mM Tris, Thermo 15568-025; 20 mM EDTA; Thermo 15575-020; 2% Sarkosyl, Sigma L9150-50G; 0.1% Antifoam, Sigma A8311-50ML) and this lysate mixture was then combined with TE-diluted Sera-Mag Magnetic SpeedBeads (GE Healthcare, GEHE45152105050250) and isopropanol in a volumetric ratio of 2:3:4 respectively. Following capture with a neodymium magnet, beads were washed once with isopropanol, twice with 70% ethanol and resuspended in filter-sterile milliQ H2O.
WGBS-seq was undertaken using a post-bisulfite adapter tagging (PBAT) method adapted from Peat et al., 2014. Briefly, 50-100 ng of purified DNA was subjected to bisulfite conversion using the Imprint DNA modification kit (Sigma, MOD50).  Converted DNA underwent first strand synthesis with a biotin labelled adapter sequence possessing seven random nucleotides at its 3’ end (BioP5N7, biotin- ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNN). The product of first strand synthesis was captured using streptavidin-coated Dynabeads (Thermo, 11205D) and magnetic immobilisation. Double stranded DNA was created using the immobilized first-strand as a template and an additional adapter also possessing seven random nucleotides at its 3’ end (P7N7, GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNN). Unique molecular barcodes and sequences necessary for binding to Illumina flow-cells were added to libraries by PCR using 1X HiFi HotStart Uracil+ Mix (KAPA, KK2801 and 10 μM indexed Truseq-type oligos, with thermal cycling as follows: 12*(94°C, 80 sec; 65°C, 30 sec; 72°C, 30 sec).

value: Liver

value: Adult

tag: gender

value: Male


title: Liver_female_deep

value: Female


title: 6 hpi

description: Larvae exposed to V. diazotrophicus for 6 hr


title: hnRNP A1_iCLIP_zf_preZGA_rep1

value: anti-hnRNP A1


title: hnRNP A1_iCLIP_zf_ZGA_rep3

value: ZGA (1K cell stage)


title: HIC003

description:
CpipJ2.mnd.txt.gz
CpipJ3.fasta.gz

organism: Culex quinquefasciatus

value: Virginia/Benzon strain


title: Islets_D7_antiIFNa_3

status: Public on Mar 23 2017

city: San Diego

first: Jaroslav

last: Zak

address: 10550 North Torrey Rd

department: Immunology and Microbial Sciences

institute: The Scripps Research Institute

data_processing:
Illumina’s “bcl2fastq” (version 2.17.1.14) Conversion Software was used to demultiplex data and convert BCL files generated by Illumina sequencing systems to FASTQ.
Quality check was performed using fastQC v0.11.3
read mapping: STAR2.5.2a, genome assembly: GRCm38; parameters: --outSAMtype None --readFilesCommand zcat --quantMode GeneCounts --sjdbGTFfile /Ensembl/Mus_musculus.GRCm38.79.gtf --sjdbOverhang 74
read counting: STAR2.5.2a, transcriptome annotations: Ensembl v79
normalization and differential expression: DESeq2 v1.14.1
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts produced by STAR2.5.2a for Ensembl v79 feature set

source_name: pancreatic islets

extract_protocol:
At least 500,000 P14 CD8+ T cells were sorted by FACS from spleens of mice. RNA was extracted using RNAqeous Micro RNA extraction kit. Pancreatic islets were extracted from the pancreata of Rip-LCMV mice at day 3 post-LCMV infection by collagenase digestion. Islets were hand picked and RNA was extracted using RNAqeous Micro RNA kit.
Total RNA was depleted for ribosomal RNA using Ribo-Zero Gold Kit (MRZG12324). Library preparation was carried out using NEBNext UItra Directional RNA Library Prep Kit for Illumina (E7420L) and the libraries sequenced using Illumina NextSeq500.

tag: cell type

value: pancreatic islet

value: pancreas

value: anti-IFN-α + LCMV


title: hnRNP A1_iCLIP_zf_preZGA_rep2

value: NNNTTGTNN


title: Islets_D7_antiIFNa_1


title: Islets_D7_antiIFNa_2


title: Islets_D7_5442_3

value: CYM-5442 + LCMV


title: Islets_D7_Iso_2

value: IgG Isotype + LCMV


title: Islets_D7_Iso_1


title: Islets_D7_5442_1


title: Islets_D7_Iso_3


title: Islets_D3_antiIFNa_3


title: Islets_D3_Iso_3


title: Islets_D3_Iso_1


title: Islets_D3_antiIFNa_1


title: Islets_Naive_2


title: Islets_Naive_1


title: P14_5442_3

description: isolated by FACS gating on Thy1.1+ CD8+ cells

source_name: P14 CD8+ T cell from the spleen

value: P14 CD8+ T cell

value: spleen


title: P14_5442_2


title: Islets_D7_5442_2


title: P14_5442_1


title: P14_Iso_2


title: P14_Naive_3


title: P14_antiIFNa_1


title: P14_antiIFNa_3


title: P14_Iso_3


title: Islets_D3_Iso_2


title: P14_Naive_1

data_processing:
Illumina’s “bcl2fastq” (version 2.17.1.14) Conversion Software was used to demultiplex data and convert BCL files generated by Illumina sequencing systems to FASTQ.
Quality check was performed using fastQC v0.11.3.
read mapping: STAR2.5.2a, genome assembly: GRCm38; parameters: --outSAMtype None --readFilesCommand zcat --quantMode GeneCounts --sjdbGTFfile /Ensembl/Mus_musculus.GRCm38.79.gtf --sjdbOverhang 74
read counting: STAR2.5.2a, transcriptome annotations: Ensembl v79
normalization and differential expression: DESeq2 v1.14.1
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts produced by STAR2.5.2a for Ensembl v79 feature set


title: P14_Iso_1


title: HMLE-TwER_125nM_SMARCE1_ChIP

city: Cambridge

first: Dexter

middle: X

last: Jin

address: 9 Cambridge Center

institute: Whitehead Institute

description: Chromatin IP against SMARCE1

data_processing:
ChIP-Seq reads were aligned to the human genome (hg19) using Bowtie (version 1.1.2).
ChIP-Seq peaks were called using MACS (version 1.0.0) with input DNA from matching cells as a control.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are provided as .BED files

source_name: HMLE-Twist-ER induced to undergo an EMT

growth_protocol: All cells were grown in a 1:1 mixture of DMEM + 10% FBS, insulin (10 μg/ml), hydrocortisone (0.5μg/ml), EGF (10 ng/ml) and MEGM

extract_protocol:
Nuclei were sonicated to retrieve lysates and protein-DNA complexes were isolated with antibody.
To make libraries, TruSeq ChIP protocol was followed.

treatment_protocol: HMLE-Twist-ER_125nM were derived by treating HMLE-Twist-ER_0nM cells with 4-OHT for 14 days.

tag: chip antibody

value: SMARCE1 (Abcam, ab70540)


title: HMLE-TwER_125nM_input_DNA

description: Input DNA


title: HMLE-TwER_125nM_SMARCC1_ChIP

description: Chromatin IP against SMARCC1

value: SMARCC1 (Santa Cruz, sc-9746)


title: HMLE-TwER_0nM_input_DNA

description: Input DNA

source_name: HMLE-Twist-ER Ctrl


title: HMLE-TwER_0nM_SMARCE1_ChIP

description: Chromatin IP against SMARCE1


title: Islets_D3_antiIFNa_2

tag: treatment


title: SKBR3_rep2

city: Durham

first: Charles

middle: A

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

data_processing:
Single-end basecalls were done by using Illumina CASAVA 1.3 software.
First 20 bp of Dnase-seq raw reads were mapped to hg19 with BWA, with 2 mismatches allowed, to generate bam files, then bam files were converted to bed file by bedtools. After removing PCR artifacts bigWig files were created by using fseq (PMID: 18784119).
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were created using MACS2 with parameters --nomodel --shift -100 --ext 200

source_name: Cultured SKBR3 cells

growth_protocol: SKBR3 cells were obtained from the American Tissue Collection Center (ATCC) through the Duke University Cell Culture Facilities and were maintained in McCoy's 5a supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Cells were Lysed and nuclei were digested according to the publication PMID: 20150147.
Libraries were prepared according to the publication PMID: 20150147.

tag: cell line


title: Islets_Naive_3


title: SKBR3_rep1


title: SKBR3_rep3


title: P14_antiIFNa_2


title: NKI_shEZH2_B2_RNASeq

first: Kenneth

middle: N

last: Ross

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for EZH2 (batch 2)

data_processing:
After sequencing, basecalling and demultiplexing were performed using the standard casava pipeline.
Reads trimmed with Trimmomatic version 0.30 in single end mode and trimming steps set to ILLUMINACLIP:illuminaAdapters.fa:  2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35
Reads aligned to human genome with tophat version 2.0.8 using UCSC hg19 gene annotation and default settings.
Aligned reads processed to Fragments Per Kilobase of exon per Million fragments mapped (FPKM) using cuffdiff version 2.1.1 (http://cufflinks.cbcb.umd.edu/index.html).
Split apart the cuffdiff output file genes.read_group_tracking file into sample specific files.
Genome_build: hg19
Supplementary_files_format_and_content: genes.fpkm_tracking files are tab delimited text files output by cufflinks in a generic FPKM tracking format with estimated gene-level expression values in the form of FPKM values

source_name: shEZH2 Batch 2

growth_protocol: MDA-MB-231 LM2 cells (an MDA-MB-231 derivative that specifically metastasizes to the lung, known as LM2, obtained by Minn et al. Nature, 2005) were cultured in Dulbecco's Modified Eagle Medium, supplied with l-glutamine (1%), PenStrep(1%), and FBS (10%) (all Gibco, Life technologies).

extract_protocol:
~5 x 106 cells were harvested and RNA was extracted from exponentially growing cells using TRIzol reagent (Life Technologies).
Libraries were prepared for sequencing using standard Illumina TrueSeq protocols. Libraries were pooled and sequenced 51 bp on a HiSeq2000.

treatment_protocol: Vectors containing a scrambled sequence or a shRNA targeting luficerase gene (Sigma) were used. References of pLKO.1 vectors used in experiments are listed in Supplementary Table 1. Lentiviral particles were produced by transfection of the HEK293T cell line and supernatants were collected 48 h after transfection. Supernatants were used to infect sub-confluent cultures in the presence of 5 ug/ml polybrene overnight. Puromycin (2 ug/ml) was then used to select for stable cell lines.

value: MDA-MB-231 LM2

value: metastatic breast cancer


title: NKI_shp53_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for TP53 (batch 1)

source_name: shTP53 Batch 1


title: NKI_shp53_B2_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for TP53 (batch 2)

source_name: shTP53 Batch 2


title: NKI_shE2F1_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for E2F1 (batch 1)

source_name: shE2F1 Batch 1


title: NKI_shEZH2_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for EZH2 (batch 1)

source_name: shEZH2 Batch 1


title: NKI_shMyc_B2_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for MYC (batch 2)

source_name: shMYC Batch 2

value: shMYC


title: P14_Naive_2


title: NKI_shMyc_I_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for MYC (batch 1)

source_name: shMYC Batch 1


title: NKI_shFra-1_B2_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for FOSL1 (Fra-1) (batch 2)

source_name: shFra1 Batch 2


title: NKI_shSCR-5_B2_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for scrambled (replicate 5, batch 2)

source_name: shScramble Replicate 5 Batch 2

value: shScramble


title: NKI_shSCR-4_B2_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for scrambled (replicate 4, batch 2)

source_name: shScramble Replicate 4 Batch 2


title: HMLE-TwER_0nM_SMARCC1_ChIP

description: Chromatin IP against SMARCC1


title: NKI_shSCR_8_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for scrambled (replicate 8, batch 1)

source_name: shScramble Replicate 8 Batch 1


title: NKI_shSCR_7_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for scrambled (replicate 7, batch 1)

source_name: shScramble Replicate 7 Batch 1


title: NKI_shSCR-3_B2_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for scrambled (replicate 3, batch 2)

source_name: shScramble Replicate 3 Batch 2


title: NKI_shSCR-2_B2_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for scrambled (replicate 2, batch 2)

source_name: shScramble Replicate 2 Batch 2


title: NKI_shSCR_4_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for scrambled (replicate 4, batch 1)

source_name: shScramble Replicate 4 Batch 1


title: NKI_shSCR_1_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for scrambled (replicate 1, batch 1)

source_name: shScramble Replicate 1 Batch 1


title: NKI_shSCR-1_B2_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for scrambled (replicate 1, batch 2)

source_name: shScramble Replicate 1 Batch 2


title: NKI_shSCR_2_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for scrambled (replicate 2, batch 1)

source_name: shScramble Replicate 2 Batch 1


title: LM2_EZH2_ChIPSeq

description: EZH2 ChIP-Seq in MDA-MB-231 derivative LM2 metastatic breast cancer cells

data_processing:
ChIP libraries were indexed, pooled, and sequenced on Illumina HiSeq-2000 sequencers.
Trimming of low quality ChIP-Seq reads and clipping of sequencing adapters was done using the program Trimmomatic (version 0.27) and all reads shorter than 35bp after trimming were dropped using parameters: 'ILLUMINACLIP:repeatadapter.fa:1:40:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35'.
ChIP-seq reads were aligned to the human hg19 genome assembly using bowtie version 0.12.5 with parameters 'bowtie -q -p 12 --phred64-quals -n 0 -l 45 -e 70 -m 1 --sam'.
ChIP-seq duplicate reads were marked with samtools version number 0.1.19.
Peak calling with MACS2 version 2.0.10 and parameters '-g hs -f BAM -B -q 0.01'
Ran the IGVtools version 2.3.18 utility 'count' on aligned bam files to compute the average alignment over 25 base windows across the genome and generate binary tiled data .tdf files.
Genome_build: hg19
Supplementary_files_format_and_content: txt files are ChIP-Seq peak summary files from MACS2 in a tab delimited text file format.
Supplementary_files_format_and_content: bed files are ChIP-Seq peak summary files from MACS2 in a bed file format.
Supplementary_files_format_and_content: tdf files are binary tiled data files of aligned ChIP-Seq data from the IGVtools count utility that conatin average alignment counts across the genome and can viewed in the IGV genome browser.

source_name: EZH2 ChIP-Seq in LM2 Cells

extract_protocol:
Cells were harvested by crosslinking with 1% formaldehyde in cell culture medium for 15 minutes at room temperature. After quenching with the addition of 125 mM glycine for 5 minutes at room temperature, the cells were washed twice with ice cold PBS. After aspiration of all liquid, pellets consisting of ~10E7 cells were flash frozen and stored at -80C. Fixed cells were thawed and sonicated to obtain chromatin fragments of ~200 to 700 bp with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with ~5ug antibody against c-Myc (Santa Cruz; sc-764), Fra-1 (Santa Cruz; sc-183), E2F1 (Millipore; 05-379) and p53 (BD-Pharmingen; 554294). Immunoprecipitation was performed retaining a fraction of input 'whole-cell extract' as a control. Antibody-chromatin complexes were pulled-down using Dynabeads Protein G, washed and then eluted. After crosslink reversal and proteinase K treatment, immunoprecipitated DNA was extracted with phenol, precipitated in ethanol and treated with RNase. ChIP DNA was quantified by fluorometry using the Qubit assay (Invitrogen).
For each ChIP or control sample, ~5ng of DNA was used to generate a standard Illumina sequencing library. Briefly, DNA fragments were end-repaired using the End-It DNA End-Repair Kit (Epicentre), extended with a 3'  'A' base using Klenow (3' 5' exo-, 0.3 U/ul, NEB), ligated to standard Illumina adapters (75 bp with a 'T' overhang) using DNA ligase (0.05 U/ul, NEB), gel-purified on 2% agarose, retaining products between 275 and 700 bp, and subjected to 18 PCR cycles. These libraries were quantified by fluorometry and evaluated by quantitative PCR to confirm representation and specific enrichment of DNA species. Libraries were sequenced in one or two lanes on the HiSeq 2000 using standard procedures for cluster amplification and sequencing by synthesis.

treatment_protocol: ChIP-Seq experiments used untreated MDA-MB-231 LM2 cells.

value: EZH2 (Millipore; 07-689)


title: LM2_ChIPSeq_input

description: ChIP-Seq Input DNA in MDA-MB-231 derivative LM2 metastatic breast cancer cells

source_name: ChIP-Seq Input DNA in LM2 Cells

value: none (input)


title: LM2_TP53_ChIPSeq

description: p53 ChIP-Seq in MDA-MB-231 derivative LM2 metastatic breast cancer cells

source_name: p53 ChIP-Seq in LM2 Cells

value: p53 (BD-Pharmingen; 554294)


title: LM2_E2F1_ChIPSeq

description: E2F1 ChIP-Seq in MDA-MB-231 derivative LM2 metastatic breast cancer cells

source_name: E2F1 ChIP-Seq in LM2 Cells

value: E2F1 (Millipore; 05-379)


title: LM2_MYC_ChIPSeq

description: Myc ChIP-Seq in MDA-MB-231 derivative LM2 metastatic breast cancer cells

source_name: Myc ChIP-Seq in LM2 Cells

value: c-Myc (Santa Cruz; sc-764)


title: Primed_Rep3

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina NextSeq 500 platform.
Reads were trimmed using Trim Galore v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the human GRCh38 genome assembly using HISAT2 2.0.5 guided by the gene models from the Ensembl v70 release. BAM files were imported to Seqmonk v36.0 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Raw read counts per transcript were calculated using the RNA-Seq quantitation pipeline on the Ensembl v70 gene set using non-directional counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: Quantitated RNA-Seq data file is tab delimited and contains the following columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) mRNA ID (Ensembl) (7) Description (Ensembl); (8-31) log2 RPM value

growth_protocol: H9 NK2 human pluripotent stem cells (PSCs) (Takashima et al., 2014) were cultured in 5% O2, 5% CO2 at 37°C. Primed PSCs were maintained in DMEM/F12, 20% Knockout Serum Replacement, 1% nonessential amino acids, 2mM GlutaMAX, 50 U/ml and 50 μg/ml penicillin-streptomycin, 0.1mM β-mercaptoethanol, and 4ng/ml bFGF on irradiated mouse embryonic fibroblasts (MEF). Naïve PSCs were maintained in a 1:1 mixture of DMEM/F12 and Neurobasal, 0.5x N2-supplement, 0.5x B27-supplement, 1x nonessential amino acids, 2mM L-Glutamine, 1x Penicillin/Streptomycin, 0.1mM β-mercaptoethanol, 1μM PD0325901, 1μM CHIR99021, 20ng/ml human LIF  and 2μM Gö6983 (PKCi) on a MEF-layer. For conversion to naïve PSCs, primed H9 NK2 PSCs were dissociated into single cells with Accutase and 2x105 cells per 6-well were plated in primed PSC media with 10μM Y-27632 onto MEF seeded at a density of 2x106 cells per 6-well plate. The following day (day 1), media was changed to primed PSC media with 1μg/ml doxycycline. On Day 2, media was changed for 2i/L+DOX media and replaced daily until day 8 where media was changed to t2i/L+PKCi. Cells were passaged using Accutase on day 3 (1:5 ratio) and day 7 (1:3 ratio).

extract_protocol:
Human PSCs were isolated by flow sorting straight into TRIzol LS (Life Technologies) and total RNA was extracted.
Indexed mRNA-Seq libraries were constructed from 500ng total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina with the Poly(A) mRNA Magnetic Isolation Module

treatment_protocol: Day-10 cell-sorted populations were defined as follow: N4– (CD7–, CD77–, CD130–, CD75–); N3+ (CD7+, CD77+, CD130+, CD75–); N4+ (CD7+, CD77+, CD130+, CD75+); Nmin (CD24–, CD57–, CD130+, CD75+).

value: H9 embryonic stem cell (ESC)

tag: cell population

value: Primed cells (NK2 line)


title: NKI_shE2F1_B2_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for E2F1 (batch 2)

source_name: shE2F1 Batch 2


title: Primed_Rep2


title: LM2_Fra1_ChIPSeq

description: Fra-1 (FOSL1) ChIP-Seq in MDA-MB-231 derivative LM2 metastatic breast cancer cells

source_name: Fra-1 (FOSL1) ChIP-Seq in LM2 Cells

value: Fra-1 (or FOSL1) (Santa Cruz; sc-183)


title: Primed_Rep1


title: NKI_shFra-1_RNASeq

description: RNA-Seq of MDA-MB-231 derivative LM2 metastatic breast cancer cells treated with shRNA for FOSL1 (Fra-1) (batch 1)

source_name: shFra1 Batch 1


title: Passage10_RNA_Rep3

value: N4+ sorted cells propagated for ten passages in naive conditions


title: Naive_Rep1

value: Naive cells (NK2 line)


title: Passage10_RNA_Rep1


title: Passage5_RNA_Rep3

value: N4+ sorted cells propagated for five passages in naive conditions


title: Naive_Rep3


title: Passage5_RNA_Rep2


title: Passage10_RNA_Rep2


title: Nmin_RNA_Rep2

value: day 10 cells defined as Nmin


title: Nmin_RNA_Rep3


title: Passage5_RNA_Rep1


title: N4_Plus_RNA_Rep2

value: day 10 cells defined as N4+


title: N4_Plus_RNA_Rep3


title: N3_Plus_RNA_Rep3

value: day 10 cells defined as N3+


title: N4_Minus_RNA_Rep2

value: day 10 cells defined as N4–


title: N4_Minus_RNA_Rep1


title: Nmin_RNA_Rep1


title: N4_Plus_RNA_Rep1


title: N4_Minus_RNA_Rep3


title: N3_Plus_RNA_Rep1


title: RNA_Seq_hNEC_Biological_Replicate2

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

description:
processed data file: RNA-seq_rawcounts_hESChNPC.txt.gz
Sample name: RNA_Seq_hNEC_Rep2_Sample1339_Lane1722_GCCAAT_L006_R1.fastq.gz

data_processing:
Standard Illumina base-calling pipeline.
PCHi-C/Hi-C reads were mapped and filtered with HiCUP (v0.4.2) and Bowtie(v1.0.0). Significant interactions were called with CHiCAGO(v0.1.4). RNA-Seq mapping was performed with TopHat (v2.0.8b).
Genome_build: Hg19
Supplementary_files_format_and_content: Hi-C interaction file (Tabix format); RNA-Seq raw counts per gene

source_name: Human ESC-derived Neuroectodermal Cells

growth_protocol: Human ESC (H9/WA09; obtained from WiCell) were cultured at 37°C in 5% CO2 in air in Pluripro media and matrix (Cell Guidance Systems). ESC were routinely verified as mycoplasma-free using a PCR-based assay. ESC were differentiated into NEC using a previously described protocol (Rada-Iglesias, A. Nature 470, 279–283 (2011)) and samples were harvested on day 7.

extract_protocol:
Total RNA was extracted from ESC and NEC using an RNeasy Mini Kit (Qiagen).
Indexed mRNA-seq libraries were constructed from 500ng total RNA using the Tru-Seq RNA Library Prep Kit v2 (Illumina). Library fragment size and concentration was determined using an Agilent Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina HiSeq as single-end libraries.

value: Derived from H9 ESC

value: Human ESC-derived Neuroectodermal Cells


title: RNA_Seq_hNEC_Biological_Replicate1

description:
processed data file: RNA-seq_rawcounts_hESChNPC.txt.gz
Sample name: RNA_Seq_hNEC_Rep1_Sample1339_Lane1722_TGACCA_L006_R1.fastq.gz


title: RNA_Seq_hESC_Biological_Replicate2

description:
processed data file: RNA-seq_rawcounts_hESChNPC.txt.gz
Sample name: RNA_Seq_hESC_Rep2_Sample898_Lane1093_GTGAAA_L001_R1.fastq.gz

source_name: Human Embryonic Stem Cells

value: H9 ESC

value: Human Embryonic Stem Cells


title: RNA_Seq_hESC_Biological_Replicate1

description:
processed data file: RNA-seq_rawcounts_hESChNPC.txt.gz
Sample name: RNA_Seq_hESC_Rep1_Sample898_Lane1093_CTTGTA_L001_R1.fastq.gz


title: PCHiC_hNEC_Biological_Replicate2

description: processed data file: hNPC12_merged_washU.txt.gz

data_processing:
Library strategy: Hi-C-seq
Standard Illumina base-calling pipeline.
PCHi-C/Hi-C reads were mapped and filtered with HiCUP (v0.4.2) and Bowtie(v1.0.0). Significant interactions were called with CHiCAGO(v0.1.4). RNA-Seq mapping was performed with TopHat (v2.0.8b).
Genome_build: Hg19
Supplementary_files_format_and_content: Hi-C interaction file (Tabix format); RNA-Seq raw counts per gene

extract_protocol:
DNA was extracted as described in Wilson, N.K. et al., Blood 127, e12–e23 (2016).
Hi-C and PCHi-C libraries were generated as described  in Wilson, N.K. et al., Blood 127, e12–e23 (2016). For PCHi-C, ligation products containing promoter sequences were captured using a custom-made RNA capture bait system (SureSelect Target Enrichment, Agilent Technologies) designed as previously described in Mifsud, B. et al. Nat. Genet. 47, 598–606 (2015), and containing 37,608 biotinylated RNAs targeting 22,076 HindIII restriction fragment ends. Libraries were paired-end sequenced on an Illumina HiSeq 1000 machine at the Babraham Institute Sequencing Facility.


title: Naive_Rep2


title: PCHiC_hNEC_Biological_Replicate1


title: N3_Plus_RNA_Rep2


title: PCHiC_hESC_Biological_Replicate2

description: processed data file: hESC12_merged_washU.txt.gz


title: PCHiC_hESC_Biological_Replicate1


title: HiC_hESC


title: HiC_hNEC


title: 4-D8-WT-KAP1-KD_S4

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

data_processing:
tophat --library-type fr-firststrand -p 6 -g 1 --no-novel-juncs --no-novel-indels -G $gtf --transcriptome-index $transcriptome --b2-sensitive -o $localdir $index $reads
Counts of reads on genes were computed using HTseq-count v0.6.1 with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: The .pileup files contain read counts on genes

source_name: WT mouse embryonic stem cell clone containing MERVL-GFP reporter

growth_protocol: mESCs were cultured in 2i medium

extract_protocol:
Total RNA from cell lines was isolated using the High Pure RNA Isolation Kit (Roche).
TruSeq stranded RNA sample preparation kit (Illumina).

treatment_protocol: Cells were transduced or transfected 4 days and 2 days before collection respectively.

tag: strain background

tag: source cell type

value: E14 mouse embryonic stem cells

tag: genotype/variation

value: wild type

tag: transduced/transfected with

value: MERVL-GFP / sh Trim28

tag: time point

value: day 4 after LV-sh transduction


title: 22-E7-kap1-2nd_S10

source_name: DUX KO mouse embryonic stem cell clone containing MERVL-GFP reporter

value: DUX knock-out


title: 20-D6-Kap1-KD-2nd_S2


title: 6-F2-WT-KAP1-KD_S6


title: 8-C5-KO-KAP1-KD_S8


title: 5-F2-WT-Ctrl-KD_S5

value: MERVL-GFP / sh control


title: 12-G6-KO-KAP1-KD_S12


title: 3-D8-WT-Ctrl-KD_S3


title: 21-E7-ctrl-2nd_S9


title: 16-E7-4981_S2

value: MERVL-GFP / Gm4981 ORF

value: day 2 after cDNA transfection


title: 19-D6-ctrl-2nd_S1


title: 17-G6-mDux_S3

value: MERVL-GFP / Dux ORF


title: 7-C5-KO-Ctrl-KD_S7


title: 11-G6-KO-Ctrl-KD_S11


title: 14-B2-4981_S14


title: 13-B2-mDux_S13


title: J1IP1

data_processing:
Alignement for ChIP-seqs were done with bowtie2: bowtie2 -p 8 -t --sensitive-local -x $index -U $reads
Peak calling for ChIP-seqs were done using SICER for histone marks (SICER.sh . chip.bed ti.bed . mm9 1 200 150 0.74 400 100) and MACS for Trim28 (macs14 -t $chipbam -c $tibam -g $org -n $name)
Genome_build: mm9
Supplementary_files_format_and_content: A bed file containing the output of the peak called by SICER or MACS is provided

extract_protocol:
Chromatin was prepared from 10 million cells as previously described (Rowe et al., 2013b).
Libraries were ligated with Illumina adaptors

treatment_protocol: Cells were transduced 5 days before fixation

value: mouse embryonic stem cells (mESCs)

tag: transduced with

value: KAP1 (custom rabbit polyclonal)


title: J1TI2


title: J1TI1


title: J1IP2


title: JK2_H3K9

source_name: mESCs_Trim28 shRNA_H3K9_ChIP-seq

value: lentiviral vector encoding for shRNA targeting Trim28

value: H3K9me3 (Diagenode, pAb-056-050)


title: JK1_Ti

source_name: mESCs_Trim28 shRNA_input


title: JE2_Ti

source_name: mESCs_control shRNA_input

value: lentiviral vector encoding for a control shRNA


title: JK2_Ti


title: JE2_H3K9

source_name: mESCs_control shRNA_H3K9_ChIP-seq


title: 18-G6-4981_S4


title: JE1_H3K9


title: JE1_Ti


title: 201_oocyte_SN-Hoechst

city: Basel

first: Ilya

middle: M.

last: Flyamer

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Base calling was performed by VBCF NGS unit
Mapping: iterative mapping (see Imakaev et al, 2012) using bowtie2 with increased stringency parameters: --score-min -L 0.6,0.2--very-  sensitive
Read filtering: if two reads map to the same strands, and each side of the read is within 500 bp of any side of the other read, we retained only one copy of the read.
Additional filtering: we separated the genome into 500 bp bins. If any two bins were interacting more than once, only one interaction was counted. Since each region is only present in the single cell up to 4 times (in oocytes), we eliminated all 500 bp bins that form more than 8 unique interactions with other bins.
Filtered reads were then binned at different resolutions (we provide files at 200Kb resolution) using read start as a read position. No normalization was applied to the data.
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: List of all interactions at single contact, 40Kb or 200 Kb resolution

source_name: oocyte

growth_protocol: Fully grown denuded GV oocytes were isolated from 2-3 month old C57BL/6J mice by puncturing of ovaries with hypodermic needles28. Oocytes were incubated for at least 2 hours before the procedure to ensure viability. Before formaldehyde fixation, the zona pellucida was removed by treatment with Acidic Tyrode's solution (Sigma).

extract_protocol:
Oocytes were fixed in with 2% formaldehyde for 15 minutes at room temperature. Oocytes were washed through drops of complete M2. For SN and NSN distinction oocytes were stained for 15 min with 0.2 µg/ml Hoechst (33342, Invitrogen). Cells were then imaged using a LSM510 (Zeiss) confocal microscope and sorted according to their chromatin structure before proceeding with the Hi-C protocol. After fixation, single oocytes were incubated in 9 μl of lysis buffer for at least 15 minutes on ice. Similarly cells were incubated in 9 μl of 1× NEB3 buffer supplemented with 0.6% SDS for 2 hours at 37° with shaking in humidified atmosphere. Then cells were incubated in 1× DpnII buffer (NEB) with 1× BSA and  5 U DpnII (NEB). After overnight incubation in a humidified incubator at 37° the DNA ends were ligated in 9 μl of 1× T4 DNA ligase buffer containing 5 U T4 DNA ligase (Thermo Scientific) and they were incubated at 16°C for 4.5 hours with 50 rpm rotation, and then were kept for 30 min at room temperature. DNA from each nucleus was amplified using illustra GenomiPhi v2 DNA amplification kit (GE Healthcare) or illustra Single Cell GenomiPhi DNA amplification kit according to manufacturer's recommendations, but both protocols were modified to include a decrosslinking step of an overnight (14-16 hours) incubation at 65°C. After the whole-genome amplification procedure, the DNA was purified. 1 μg (or all available amount, if the yield was lower) of DNA was diluted to 500 μl with sonication buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.1% SDS) and was sonicated using Branson Sonifier 150 for 20 seconds with power setting 3. The sonicated DNA was purified and then submitted for library preparation and sequencing.
The library preparation was done by the VBCF NGS unit (vbcf.ac.at) following the standard DNA sample  preparation protocol for Solexa platforms (NEB reagents).


title: 56_oocyte_SN-Hoechst


title: 157_oocyte_SN-Hoechst


title: 164_oocyte_SN-Hoechst


title: 179_oocyte_NSN-Hoechst


title: 188_oocyte_NSN-Hoechst


title: 186_oocyte_NSN-Hoechst


title: 145_oocyte_NSN-Hoechst


title: 176_oocyte_NSN-Hoechst


title: 146_oocyte_NSN-Hoechst


title: 192_oocyte_SN-Hoechst


title: 166_oocyte_SN-Hoechst


title: JK1_H3K9


title: 61_oocyte_SN-Hoechst


title: 193_oocyte_NSN-Hoechst


title: 63_pronucleus_male

source_name: zygote

growth_protocol: 3-4-week-old C57BL/6J females were superovulated by intraperitoneal injection of PMSG (pregnant mare's serum gonadotropin; 5 IU, Folligon, Intervet) followed by hCG (human chorionic gonadotropin; 5 IU, Chorulon, Intervet) injection 48 hours later. Natural matings to C57BL/6J males were set up overnight. Zygotes were released from the ampullae and treated with hyaluronidase (Sigma) to remove surrounding cumulus cells. For isolation of maternal and paternal nuclei, zygotes were pre-incubated in culture medium supplemented with 5 μg/ml cytochalasin B (Sigma) and 1 μM nocodazole (Sigma) for 15 minutes. The zona pellucida of the zygotes was opened and nuclei were extracted one by one. The maternal and paternal origin of the nuclei was determined taking size of the nuclei and position in relation to second polar body into account.

extract_protocol:
Nuclei were fixed in separate drops of M2 (not containing BSA) with 2% formaldehyde for 15 minutes. Nuclei were washed through drops of complete M2. For zygote experiments without pronuclear extraction, zygotes were treated identically to oocytes. Here nuclei were separated into individual wells after SDS treatment and kept separate in the subsequent steps of the protocol. After fixation, zygotes or single isolated pronuclei were incubated in 9 μl of lysis buffer for at least 15 minutes on ice. Similarly zygotes or pronuclei were incubated in 9 μl of 1× NEB3 buffer supplemented with 0.6% SDS for 2 hours at 37° with shaking in humidified atmosphere. Then nuclei were incubated in 1× DpnII buffer (NEB) with 1× BSA and  5 U DpnII (NEB). After overnight incubation in a humidified incubator at 37° the DNA ends were ligated in 9 μl of 1× T4 DNA ligase buffer containing 5 U T4 DNA ligase (Thermo Scientific) and they were incubated at 16°C for 4.5 hours with 50 rpm rotation, and then were kept for 30 min at room temperature. DNA from each nucleus was amplified using illustra GenomiPhi v2 DNA amplification kit (GE Healthcare) or illustra Single Cell GenomiPhi DNA amplification kit according to manufacturer's recommendations, but both protocols were modified to include a decrosslinking step of an overnight (14-16 hours) incubation at 65°C. After the whole-genome amplification procedure, the DNA was purified. 1 μg (or all available amount, if the yield was lower) of DNA was diluted to 500 μl with sonication buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.1% SDS) and was sonicated using Branson Sonifier 150 for 20 seconds with power setting 3. The sonicated DNA was purified and then submitted for library preparation and sequencing.
The library preparation was done by the VBCF NGS unit (vbcf.ac.at) following the standard DNA sample  preparation protocol for Solexa platforms (NEB reagents).


title: 160_oocyte_NSN-Hoechst


title: 138_oocyte_NSN-Hoechst


title: 197_oocyte_SN-Hoechst


title: 131_oocyte_NSN-Hoechst


title: 140_oocyte_NSN-Hoechst


title: 93_oocyte_NSN-Hoechst


title: 158_pronucleus_male


title: 137_pronucleus_male


title: 74_pronucleus_male


title: 120_oocyte_Intermediate-Hoechst


title: 85_pronucleus_male


title: 116_pronucleus_male


title: 171_oocyte_NSN-Hoechst


title: 96_pronucleus_male


title: 97_pronucleus_male


title: 113_pronucleus_male


title: 89_pronucleus_male


title: 126_pronucleus_male


title: 108_pronucleus_male


title: 139_pronucleus_male


title: 128_pronucleus_female


title: 111_pronucleus_female


title: 112_pronucleus_female


title: 213_pronucleus_female


title: 218_oocyte_NSN


title: 216_pronucleus_female


title: 212_pronucleus_w-o-inh-male


title: 214_pronucleus_w-o-inh-female


title: 210_pronucleus_female


title: 211_pronucleus_w-o-inh-undef sex


title: 208_pronucleus_w-o-inh-undef sex


title: 209_pronucleus_male


title: 15-E7-mDux_S1


title: 204_pronucleus_w-o-inh-male


title: 207_pronucleus_w-o-inh-female


title: 206_pronucleus_male


title: 205_pronucleus_female


title: 203_pronucleus_male


title: 195_pronucleus_male


title: 190_pronucleus_female


title: 196_pronucleus_w-o-inh-undef sex


title: 202_pronucleus_w-o-inh-undef sex


title: 191_oocyte_SN


title: 200_pronucleus_w-o-inh-undef sex


title: 194_oocyte_SN


title: 198_pronucleus_female


title: 199_pronucleus_w-o-inh-male


title: 189_oocyte_NSN


title: 219_oocyte_SN


title: 184_pronucleus_w-o-inh-male


title: 187_pronucleus_female


title: 182_oocyte_NSN


title: 173_oocyte_SN


title: 178_pronucleus_w-o-inh-undef sex


title: 167_oocyte_SN


title: 185_oocyte_SN


title: 177_oocyte_SN


title: 172_oocyte_SN


title: 180_oocyte_NSN


title: 174_oocyte_SN


title: 183_pronucleus_w-o-inh-undef sex


title: 165_oocyte_SN


title: 169_pronucleus_female


title: 168_oocyte_NSN


title: 163_oocyte_SN


title: 159_oocyte_NSN


title: 155_oocyte_NSN


title: 152_oocyte_NSN


title: 161_oocyte_SN


title: 153_oocyte_NSN


title: 162_oocyte_SN-Hoechst


title: 154_pronucleus_male


title: 175_oocyte_SN


title: 181_oocyte_SN


title: 150_oocyte_SN


title: 148_pronucleus_female


title: 149_pronucleus_w-o-inh-both


title: 170_oocyte_SN


title: 142_pronucleus_female


title: 144_oocyte_SN


title: 136_pronucleus_w-o-inh-female


title: 133_pronucleus_w-o-inh-male


title: 134_oocyte_NSN


title: 125_oocyte_SN


title: 127_pronucleus_male


title: 115_pronucleus_female


title: 124_oocyte_SN-Hoechst


title: 114_oocyte_SN


title: 118_pronucleus_male


title: 122_oocyte_SN


title: 117_pronucleus_female


title: 119_pronucleus_w-o-inh-female


title: 130_oocyte_SN


title: 99_oocyte_SN


title: 106_oocyte_SN-Hoechst


title: 107_pronucleus_w-o-inh-both


title: 103_pronucleus_w-o-inh-undef sex


title: 105_pronucleus_male


title: 104_pronucleus_female


title: 98_pronucleus_w-o-inh-male


title: 100_pronucleus_male


title: 109_pronucleus_female


title: 135_oocyte_SN-Hoechst


title: 132_oocyte_SN


title: 129_pronucleus_female


title: 95_pronucleus_female


title: 143_oocyte_SN-Hoechst


title: 88_oocyte_SN-Hoechst


title: 90_pronucleus_w-o-inh-male


title: 81_pronucleus_female


title: 84_oocyte_Intermediate-Hoechst


title: 86_oocyte_NSN-Hoechst


title: 82_oocyte_SN


title: 87_pronucleus_w-o-inh-male


title: 76_pronucleus_female


title: 80_pronucleus_w-o-inh-male


title: 78_pronucleus_w-o-inh-female


title: 75_pronucleus_w-o-inh-male


title: 94_pronucleus_female


title: 73_pronucleus_female


title: 92_pronucleus_female


title: 71_pronucleus_female


title: 147_pronucleus_male


title: 68_oocyte_SN


title: 69_pronucleus_w-o-inh-female


title: 77_pronucleus_w-o-inh-male


title: 65_oocyte_NSN


title: 70_pronucleus_w-o-inh-undef sex


title: 91_pronucleus_female


title: 83_oocyte_SN


title: 64_pronucleus_female


title: 67_pronucleus_female


title: 60_pronucleus_female


title: 59_oocyte_NSN


title: 57_oocyte_Intermediate-Hoechst


title: 55_oocyte_NSN


title: 62_oocyte_NSN


title: 46_oocyte_SN


title: 48_oocyte_NSN


title: 121_pronucleus_male


title: 51_oocyte_SN


title: 52_oocyte_SN-Hoechst


title: HER2 Cas9 sat A431 High Rep 4

data_processing:
Library strategy: CRISPR/Cas9 Epigenentic Regulatory Element Screening (CERES)
FASTQ files were aligned to custom indexes (generated from the bowtie2-build function) using Bowtie2 (v2.2.4) with the options -p 32 --end-to-end --very-sensitive -3 1 -I 0 -X 200.
Reads were converted from .sam to .bam using samtools view -bS (v1.3.1).
Sort reads using samtools sort
Index reads using samtools index
Reads were counted using samtools idxstats
Genome_build: hg19
Supplementary_files_format_and_content: Counts of the number of reads aligned to each gRNA sequence (txt format).

source_name: A431 Cells

growth_protocol: A431 cells were obtained from the American Tissue Collection Center (ATCC) through the Duke University Cel Culture Facilities and were maintained in DMEM High Glucose supplemented with 10% FBS and 1% penicillin-streptomycin at 37°C with 5% CO67

extract_protocol:
An aliquot of 1.3x10^6 cells was taken before sorting for a bulk unsorted sample for each screen. The highest and lowest 10% of cells were sorted based on mCherry signal for the dCas9KRAB screen of HBE1 in K562 cells, or Alexa Fluor 488 signal for all HER2 screens. 1.3x10^6 cells were sorted for each group. Cell sorting was performed using a MoFlo Astrios (Beckman Coulter) or SH800 (Sony Biotechnology). After sorting, cells were harvested for genomic DNA using the DNeasy Blood and Tissue Kit (Qiagen).
To amplify the gRNA libraries from each sample, 8.3 µg of gDNA was used as template across 8 100 µL PCR reactions using Q5 hot start polymerase (NEB). Amplification was carried out following the manufacturer’s instructions using 25 cycles at an annealing temperature of 60C. Amplified libraries were purified using Agencourt AMPure XP beads (Beckman Coulter) using double size selection of 0.65X and then to 1X the original volume. Each sample was quantified after purification using the Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher).

treatment_protocol: The A431-Cas9 cell line was derived by transducing A431 cells with a lentivirus containing Cas9-P2A-puromycin and, two days after transduction, selected with puromycin for 7 days.

tag: transduced gene

tag: grna library

value: HER2 Saturation Library

tag: endogenous reporter


title: HER2 Cas9 sat A431 High Rep 3

growth_protocol: A431 cells were obtained from the American Tissue Collection Center (ATCC) through the Duke University Cel Culture Facilities and were maintained in DMEM High Glucose supplemented with 10% FBS and 1% penicillin-streptomycin at 37°C with 5% CO66


title: 40_oocyte_NSN

tag: strain


title: 44_oocyte_NSN