title: WWD_bulk_Dnmt3a2_ChIPSeq

description: H3K4me1_density.txt, H3K4me2_density.txt, H3K4me3_density.txt

data_processing:
ChIP-seq reads were mapped to the mouse genome (mm9) using the Bowtie program. Only tags that mapped uniquely to the genome with no more than 2 mismatches were used for further analysis.
We segmented genomic regions enriched with each H3K4 methylation state (H3K4me3/2/1; based on publically available ENCODE/LICR data), and each state was correlated with ChIP-seq signals of the individual Dnmt3a2 (WT, WWD, and R).
Genome_build: mm9

extract_protocol:
Chromatin from formaldehyde fixed cell (2x107 cells per ChIP) was fragmented to a size range of 160-480 bp using a combination of micrococcal nuclease digestion and sonication with Bioruptor (Diagenode). Solubilized chromatin was immunoprecipitated with antibody.
To generate libraries for Illumina high-throughput sequencing of ChIP and input DNA, end repair, adenylation, ligation with indexed adaptors, and 18 cycles of PCR with Illumina primers were performed following the TruSeq ChIP Sample Preparation guide (Illumina).

value: WWD bulk Dnmt3a2

value: FLAG (Sigma, F1804)


title: R_bulk_Dnmt3a2_ChIPSeq

status: Public on Jun 22 2015

type: SRA

city: Houston

first: Hyunjae

middle: R

last: Kim

state: TX

address: 1102 Bates Ave

department: Pediatric Oncology

country: USA

institute: Baylor College of Medicine

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Dnmt TKO ESCs

growth_protocol: WT/mutant Dnmt3a2 expressing Dnmt TKO mouse ESCs were cultured using standard conditions.

tag: cell type

value: ESC

tag: construct

value: R bulk Dnmt3a2

tag: passages

tag: chip antibody

tag: cell line

value: J1 ES


title: WT_bulk_Dnmt3a2_ChIPSeq

value: WT bulk Dnmt3a2


title: WT_1_set2_RNAseq

library_source: transcriptomic

data_processing:
Reads for mRNA-seq were mapped to the mouse genome mm9 using Bowtie and Tophat  allowing one mismatch and tracking up to 50 best alignments per read and default parameter values.
Expression levels were quantified using Cufflinks (http://cufflinks.cbcb.umd.edu/) that measures transcript abundances in Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Genome_build: mm9

molecule: total RNA

extract_protocol:
Total RNA was extracted from TKO and wild-type/mutant Dnmt3a2 expressing TKO ESCs.
5 μg of RNA was subjected to mRNA selection, fragmentation, and cDNA synthesis following the TruSeq RNA Sample Preparation guide (Illumina). End repair, addition of a single dA, ligation with indexed adaptors, and 15 cycles of PCR with Illumina primers were performed also following the TruSeq RNA Sample Preparation guide.

value: WT Dnmt3a2


title: WT_1_Dnmt3a2_ChIPSeq


title: WT_1_H3K4me3_ChIPSeq

value: WT H3K4me3


title: R_1_Dnmt3a2_ChIPSeq

value: R Dnmt3a2


title: R_2_set1_RNAseq


title: WWD_1_H3K4me3_ChIPSeq

value: WWD H3K4me3


title: WT_1_set1_RNAseq


title: R_1_H3K4me3_ChIPSeq

value: R H3K4me3


title: R_1_RRBS

data_processing:
Reads were aligned to the mouse genome using the Bismark alignment software with a maximum of 2 mismatches and only those reads that mapped to a unique location were retained. Bisulfite converted reads were aligned to in silico bisulfate converted MspI fragments using ELAND aligner.
In order to assign a methylation score for a base position, read bases that aligned to a position were required to have at least 20 phred quality score and 10x coverage. Only CpG dinucleotides that satisfied these coverage and quality criteria were used in the subsequent analysis.
Percent methylation for individual Cs in the genome were calculated as the ratio of the number of alignments with C (methylated), over the number of alignments with either C (methylated) or T (unmethylated).
RRBS data analyses were done with methylKit, a multi-threaded R package.
Genome_build: mm9

extract_protocol:
Genomic DNA was digested with MspI (New England Biolabs, NEB), which cuts DNA at CCGG sequences regardless of the cytosine methylation status, and purified using standard phenol chloroform extraction and ethanol precipitation.
The DNA was end repaired a single dA was added and the DNA was ligated to pre-annealed 5-methylcytosine-containing Illumina adapters according to the manufacturer protocols. Fragments of 150–250 and 250–400 bp were isolated from a 1.5% agarose gel (Biorad, low range ultra agarose) using the Qiaquick Gel Extraction kit, and bisulfite treatment was performed using the EZ DNA Methylation Kit (Zymo Research). PCR amplification was performed for each library with FastStart Hifidelity DNA Polymerase (Roche) and Illumina primers PE1.0 and 2.0, and the PCR products were isolated using AMPure XP beads (Agencort).


title: TKO_input_Dnmt3a2_ChIPSeq

value: TKO input Dnmt3a2


title: WWD_1_Dnmt3a2_ChIPSeq

value: WWD Dnmt3a2


title: Candida albicans Streptococcus gordonii Co culture R3

city: Aberdeen

first: Sophie

last: Shaw

state: Aberdeen City

address: 23 St. Machar Drive

department: Centre for Genome Enabled Biology and Medicine

country: United Kingdom

institute: University of Aberdeen

description: C. albicans in hypha inducing conditions for two hours before co culture with S. gordonii

data_processing:
Base calling was carried out using CASAVA v1.8.2
Reads were filtered for quality and adapters removed using fastq-mcf with the parameters -q 20 -l 35 -p 15 -m 3
ERCC transcripts were removed by alignment to the ERCC reference using Bowtie v 1.0.0
Remaining reads were aligned to the C. albicans and S. gordonii reference genomes using Tophat v 2.0.8 with the following parameters: -G <gff> --library-type fr-secondstrand -l 10000 -r 50 --mate-std-dev 100 -p 8
Bedtools multicov was used to quantify the number of reads aligned at each annotated feature.
Differential expression comparisons were carried out using DESeq v.1.12.1 with default parameters.
Genome_build: Ca21_C_albicans_SC5314 genome
Genome_build: NC_009785 S gordonii CH1 genome
Supplementary_files_format_and_content: Tab delimited matrix containing the number of reads aligned to each feature in each sample.

organism:
Streptococcus gordonii
Candida albicans

source_name: Candida albicans hyphal cells and Streptococcus gordonii cells

growth_protocol: C. albicans wild-type strain SC5314 was grown aerobically for 16 h in YPD medium (2% yeast extract, 1% Bacto peptone, 2% glucose) at 37 degrees, with shaking at 220-rpm. Cells were then harvested by centrifugation (5000 x g for 5 min), washed twice in YPT medium (1 x Difco yeast nitrogen base, 20 mM phosphate buffer pH 7.1, 0.1% Bacto tryptone) by alternate centrifugation (5000 x g for 5 min) and suspension, and finally suspended at optical density 600 nm (OD600) = 1.0 (approximately 1 x 107 cells ml-1) in YPT medium. Aliquots (10 ml; 1 x 107 cells ml-1) were transferred into conical flasks containing YPT medium (90 ml) supplemented with 0.4% glucose (YPT-Glc). The cultures were then incubated at 37 degrees for 2 h with shaking at 50-rpm to induce hypha formation. S. gordonii cells were grown anaerobically for 16 h in 10 ml BHY medium (per litre: 37g Brain Heart infusion broth, 5 g yeast extract) and then harvested by centrifugation (5000 x g for 7 min). The bacterial cells were washed twice with YPT (no glucose) and finally suspended at OD600 = 0.5 (2 x 108 cells ml-1) in YPT-Glc medium.

extract_protocol:
Cells were harvested by centrifugation, flash frozen and stored at -70 °C. RNA was extracted using a Qiagen RNeasy Mini Kit following the manufacturer's instructions for yeast using mechanical disruption. An on-column DNase digest using RNase-free DNase (Qiagen) was performed.
ERCC RNA Spike-In Control Mix (Ambion) was mixed with 2.5 µg RNA. Riobsomal RNA was depleted with RiboZero Magnetic Gold Kit (Epicentre) and Illumina sequencing libraries were prepared using ScriptSeq v2 (Epicentre).

tag: strain

value: SC5314 and Challis Substr. CH3

tag: sample type


title: Candida albicans Streptococcus gordonii Co culture R1

value: SC5314 and Challis Substr. CH1

value: C. albicans in hypha inducing conditions for two hours before co culture with S. gordonii


title: X24_61_1

city: Austin

first: Rebecca

last: Knight

address: 1 University St. A6700

department: Plant Biology

institute: University of Texas

data_processing:
Sequenced reads were trimmed for adaptor sequence using cutadapt
Trimmed reads were mapped and annotated to the BP-1 reference genome on Rockhopper, version 2.0.3, http://cs.wellesley.edu/~btjaden/Rockhopper/index.html
Non-protein coding RNA was computationally removed and sample count data for each gene probe was exported to individual .txt files
Genome_build: GCF_000011345.1
Supplementary_files_format_and_content: File contains probe list in first column and count data for each sample, saved in .txt format

organism: Thermosynechococcus vestitus BP-1

source_name: BP-1_Heat stress 61°C_24hr

extract_protocol:
Frozen cell pellets were mixed in Trizol preheated to 65 °C then incubated 15 minutes for RNA extraction. The sample was solvent separated with chloroform, purified on an miRNEasy kit, processed with TurboDNAse, and cleaned up with an miRNEasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq, analyzed as single-end 100 bp, ≥ 12 million reads on an Illumina HiSeq 2500.

treatment_protocol: Samples were collected over time (starting at time zero). For RNA analysis, 50-100 ml was poured into a manifold and fast-filtered through MF Membrane Filters (0.45 um HAWP, Millipore). The cells were washed off the filter with 1 ml of 1:1 TE buffer-Bacteria Protect, spun, and then stored at -80 ° C until RNA Extraction.

tag: temperature ©

value: Heat stress 61°C

tag: time (hr)

tag: replicate


title: X24_61_2


title: X24_61_3


title: X24_53_2

source_name: BP-1_control 53°C_24hr

value: control 53°C


title: X24_45_3

source_name: BP-1_cold stress 45°C_24hr

value: cold stress 45°C


title: WT_1_RRBS

value: ESC


title: TKO_set1_RNAseq


title: X24_45_2


title: S2A

city: Salamanca

first: Luis

last: Quintales

address: Calle Zacarías González, 2

department: Universidad de Salamanca / CSIC

country: Spain

institute: Instituto de Biología Funcional y Genómica (IBFG)

description: Mononucleosomal DNA

data_processing:
Alignment: bowtie 0.12.7
The smoothed signal generated by using the multilevel 1-D biorthogonal wavelet decomposition/reconstruction tool implemented in the Matlab “Wavelet Toolbox”, is used to calculate the average spacing between boundary peaks for individual nucleosomes.
The resulting combined profile was wavelet-smoothed to generate the final nucleosome positioning profile.
S2A.bw is the mean of the  S2A replicates.
Genome_build: Schizosaccharomyces_pombe.ASM294v2.22.dna.genome.fa from Pombase
Supplementary_files_format_and_content: bigWig files

organism: Schizosaccharomyces pombe

source_name: Mononucleosomal DNA

growth_protocol: Cells were grown in rich medium (YES) at 32ºC until OD595=0.8.

extract_protocol:
Chromatin was prepared from formaldehyde crosslinked log phase cells and digested with micrococcal nuclease (Fermentas #ENO181) to a final concentration of 180 units/ml (WT) and 300 units/ml (S2A mutant) for 40 minutes at 37 ºC to yield about 90% mononucleosomes. After reverting crosslink DNA of mononucleosomal size was purified from agarose gels
Mononucleosomal DNA libraries were prepared for sequencing using standard Illumina protocols

value: S2A mutant

tag: culture type

value: Asynchronous mitosis


title: X24_53_1


title: WWD_1_set1_RNAseq

value: J1 ES


title: Candida albicans Streptococcus gordonii Co culture R2

value: SC5314 and Challis Substr. CH2


title: X10_61_3

source_name: BP-1_Heat stress 61°C_10hr


title: X10_61_1


title: X10_61_2


title: X24_45_1


title: X10_53_2

source_name: BP-1_control 53°C_10hr


title: X10_45_1

source_name: BP-1_cold stress 45°C_10hr


title: X3_61_3

source_name: BP-1_Heat stress 61°C_3hr


title: X3_61_2


title: X3_61_1


title: X10_53_3


title: X10_45_3


title: X10_45_2


title: X24_53_3


title: X3_53_2

source_name: BP-1_control 53°C_3hr


title: X3_53_3


title: X3_53_1


title: X3_45_1

source_name: BP-1_cold stress 45°C_3hr


title: X3_45_2


title: X0.5_61_2

source_name: BP-1_Heat stress 61°C_0.5hr


title: X3_45_3


title: X0.5_61_1


title: WT

description: Mononucleosomal DNA


title: X0.5_45_3

source_name: BP-1_cold stress 45°C_0.5hr


title: X0.5_45_2


title: X0.5_61_3


title: X0_61_2

source_name: BP-1_Heat stress 61°C_0hr


title: X0_61_3


title: X0.5_45_1


title: X10_53_1


title: X0_45_2

source_name: BP-1_cold stress 45°C_0hr


title: Streptococcus gordonii alone R2

description: S. gordonii cells grown alone for one hour

organism: Streptococcus gordonii

source_name: Streptococcus gordonii cells

value: Challis Substr. CH1


title: X0_45_1


title: X0_61_1


title: Streptococcus gordonii in Candida albicans media R3

description: C. albicans in hypha inducing conditions for two hours, C. albicans cells removed, media added to S. gordonii cells for one hour


title: X0_45_3


title: Streptococcus gordonii in Candida albicans media R1

value: C. albicans in hypha inducing conditions for two hours, C. albicans cells removed, media added to S. gordonii cells for one hour


title: Streptococcus gordonii alone R3

value: S. gordonii cells grown alone for one hour


title: Streptococcus gordonii in Candida albicans media R2


title: TG N6Ecd

city: Barcelona

first: Guillem

last: Ylla

state: Catalonia

address: Passeig Marítim de la Barceloneta, 37

institute: Institute of Evolutionary Biology

data_processing:
Adapters trimming and quality control of reads with  “clean_reads v0.2.3”
Reads mapping to the following genomes were removed since might be contaminations: NC 013454; NC 017924.1;  NC 016621.1; NC 013418.2; NC 016146.1, NC 005041.2, NC 012901.1, GCA 000002985.1, AE014075.1
The PamScan was used in order to search for TF domains.
Supplementary_files_format_and_content: Processed data file contains a qualitative analysis of Tfs.

organism: Blattella germanica

source_name: Tergites 7-8

growth_protocol: Blattella germanica specimens used for the whole transcriptome analysis were obtained from a population reared at the Institut de Biologia Evolutiva (CSIC-UPF). Conditions were 70% humidity at 30 ºC and a commercial dog food diet.

extract_protocol:
Total RNA was extracted with GenElute Mammalian Total RNA kit (Sigma, Madrid, Spain).
Total RNA was send to Genomica service (Universitat Pompeu Fabra) at the PRBB (Barcelona, SPAIN) for the library construction and Sequencing. The technology used was 454,GS Junior system.

tag: treatment

tag: Stage

value: Nymph 6 during Ecdysone peak


title: TG N6D1C

value: Nymph 6 day 1


title: Streptococcus gordonii alone R1


title: TG N5Ecd

value: Nymph 5 during Ecdysone peak


title: TG N6D1T

value: Juvenile Hormone


title: Wildtype H3K27me3 (Upstate) ChIP-seq, replicates 1-2

status: Public on Jun 21 2015

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

description:
This Sample represents 2 replicates.
ChIP-seq single-end 50bp.

data_processing:
Alignment: bowtie2 -sensitive
Merge/sort/index: samtools merge | samtools sort |samtools index
Peak calling: macs2 callpeak (done for each antibody in each cell line using appropriate input control)
bigWig files were generated using a Python script that relies on pybedtools and the bedtools library to generate reads per million mapped reads.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: bigWig files generated from bedtools represent reads per million mapped reads.

source_name: WT ES cells, H3K27me3 ChIP, Upstate antibody

growth_protocol: ES cells were grown without feeders in ES medium, consisting of minimal essential medium-α (Invitrogen, Carlsbad, CA, http://www.invitrogen.com) with 15% fetal calf serum (Invitrogen) supplemented with nonessential amino acids, glutamate, sodium pyruvate, β-mercaptoethanol, penicillin-streptomycin, and leukemia inhibitory factor (LIF). As described in Chamberlain et al. 2008.

extract_protocol:
Lysates from 2e7 cells were sonicated and clarified by centrifugation and used in IP with antibodies specified.
Libraries were prepared using Kapa Hyper ChIP kit for Illumina (catalogue number KK8500).

tag: strain/background

value: mixed

tag: genotype/variation

value: eed fl/fl

value: embryonic stem (ES) cells


title: Wildtype input DNA, replicates 1-3

description:
This Sample represents 3 replicates.
ChIP-seq single-end 50bp.

source_name: WT ES cells, input


title: EED-null input DNA, replicates 1-2

description:
This Sample represents 2 replicates.
ChIP-seq single-end 50bp.
The EED-null animals are maintained on an outbred background.

source_name: EED-null ES cells, input

value: eed fl/fl; cag-cre-ert2; tamoxifen treated


title: CpdA mutant

city: Bedford Park

first: Uwe

middle: Horst

last: Stroeher

state: South Australia

address: Carpark 8

department: School of Biological Sciences

country: Australia

institute: Flinders University

data_processing:
Illumina's software used for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Acineotbacter baumannii (ATCC17978) genome using bowtie
Counts were made using htseq-count tool and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Acinetobacter baumannii ATCC 17978 genome accession # CP000521
Supplementary_files_format_and_content: tab-delimited text files include counts and RPKM values for each Sample.

organism: Acinetobacter baumannii

source_name: bacterial cells

growth_protocol: grown in Mueller-Hinton liquid broth culture to an optical density of OD 0.6

extract_protocol:
RNA was extracted according to manufactures instructions using an Isolate RNA Mini Kit (BioLine, NSW Australia)
Libraries were prepared according to Illumina's instructions. Briefly, RNA was treated with a Epicentre Ribo-Zero kit  RNA library bar-coding was undertaken on RNA for HiSeq. Samples were run on the Illumina HiSeq platform (1X50 base pair single reads )

treatment_protocol: no treatment

tag: source

value: ATCC 17978 Derivative


title: EED-null H3K27me3 (Abcam) ChIP-seq, replicates 1-2

source_name: EED-null ES cells, H3K27me3 ChIP, Abcam antibody


title: EED-null H3K27me3 (Upstate) ChIP-seq, replicates 1-2

source_name: EED-null ES cells, H3K27me3 ChIP, Upstate antibody


title: 17978hm


title: Hela cells  HNRNPA2B1 knockdown_RNA-seq_rep2

status: Public on Jun 20 2015

city: New York

first: Claudio

last: Alarcon

state: New York

address: 1230 York Ave

department: Systems Cancer Biology

institute: The Rockefeller University

data_processing:
Single-end reads were trimmed (cutadapt version 1.8) and alighned to human transcriptome (hg19) using Tophat-2.0.12.
Transcript abundance was quantified using Cuffilnks-2.0.2.
Aligned reads were combined from replicates and MISO (Misopy-0.5.2) was used to compare lternative splicing events (skipped exons, first alternative exon, last alternative exon and intron retention).
Genome_build: hg19

molecule: nuclear RNA

organism: Homo sapiens

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep

extract_protocol:
Cells were lysed using LB1 buffer, the nuclear fraction was then lysed with M-PER (Thermo Scientific) buffer and diluted 10-fold in dilution buffer before the immunoprecipitation. Rabbit α-m6A antibody (Synaptic Systems) and rabbit IgG control bound to protein A Dynabeads were used for the immunoprecipitations. The immunoprecipitated RNA was eluted with N6-methyladenosine (Sigma-Aldrich), ethanol precipitated and resuspended in water.
RNA was barcoded using ScriptSeq V2 kit (Epicentre) and sent for sequencing.

treatment_protocol: stable knockdown of the indicated gene was achieved using lentival particles and puromycin selection

value: Hela


title: Hela cells  HNRNPA2B1 knockdown_RNA-seq_rep1


title: Hela cells  METTL3 knockdown_RNA-seq_rep2


title: Hela cells  METTL3 knockdown_RNA-seq_rep1


title: MDA-MB-231 cells  HNRNPA2B1 knockdown_RNA-seq_rep2


title: Hela cells  control knockdown_RNA-seq_rep2


title: Hela cells  control knockdown_RNA-seq_rep1


title: MDA-MB-231 cells  HNRNPA2B1 knockdown_RNA-seq_rep1


title: MDA-MB-231 cells  METTL3 knockdown_RNA-seq_rep1


title: MDA-MB-231 cells  control knockdown_RNA-seq_rep1


title: MDA-MB-231 cells  control knockdown_RNA-seq_rep2


title: Nuclear HNRNPA2B1 HITS-CLIP rep2

description:
protocol: HITS-CLIP
HNRNPA2B1 co-immunoprecipitated RNA

data_processing:
After linker sequence removal and quality trimming, sequence mapping was performed using Bowtie with default parameters (build hg19).
ChIPseeqer (strand-specific) was then used to identify the HNRNPA2B1 CLIP reads (Giannopoulou et al, BMC Bioinformatics 2011, 12:277). Tags between the replicates were then overlapped between the two biological replicates.
HNRNPA2B1 binding sites were then used to generate shuffled sequences, based on a 1st order Markov model (built-in ChIPseeqer function), for further comparisons.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files containing the chromosomal location and intensities of the peaks obtained from the HITS-CLIP experiments.

extract_protocol:
Cells were UV cross-linked and prepared as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22) and the nuclear fraction was isolated and used for the immunprecipitation of HNRNPA2B1 using an anti-HNRNPA2B1 antibody obtained from PIERCE (cat#PA5-34939).
Samples were prepared for sequencing as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).

treatment_protocol: After cells underwent selection no further treatment was performed


title: MDA-MB-231 cells  METTL3 knockdown_RNA-seq_rep2


title: Nuclear HNRNPA2B1 HITS-CLIP rep1


title: Control_26_4_M

status: Public on Jun 19 2015

first: Yasmin

middle: L

last: Hurd

address: 1470 Madison Avenue, Room 105 (Office)

department: Departments of Psychiatry; Neuroscience; Pharmacology and Systems Therapeutics

institute: Icahn School of Medicine at Mount Sinai

data_processing:
base call files converted to fastq (CASAVA.1.8.2; amp-errbs pipeline)
align reads to genome using Bismark (amp-errbs pipeline)
determine per CpG read coverage, and frequency of C-containing vs. T-containing reads (amp-errbs pipeline)
Genome_build: rn4
Supplementary_files_format_and_content: Processed "methylCall files (e.g., "methylCall_Sample_*_*_*.txt") contain: (1) CpG ID; (2) rn4 genome build chromosome and (3) start bp position; (4) CpG strand; (5) read depth per CpG; (6,7) and the frequencies of C nucleotide- vs. T nucleotide-containing reads per CpG. These files are the final output from the amp-errbs pipeline (https://code.google.com/p/amp-errbs/), and are used as direct input for methylKit (https://code.google.com/p/methylkit/).

organism: Rattus norvegicus

source_name: nucleus accumbens (bulk tissue sample)

extract_protocol:
Bilateral nucleus accumbens tissue was dissected (15-gauge punch), from frozen brains of 32 F1 rats (PND ~62) from adult offspring of parents with repeated exposure to either THC or VEH during adolescence (Szutorisz et al, 2014; PMID: 24385132). Eight females and 8 males from both the THC- and VEH-exposed lines were derived from 5-6 different mothers and fathers in each group. Genomic DNA was extracted (DNeasy Blood & Tissue Kit; Quagen) and ~250ng DNA/sample was processed for ERRBS following established protocols (Akalin et al, 2012; PMID: 22737091).
Enhanced Reduced Representation Bisulfite Sequencing (ERRBS); 250 ng was digested with MspI and Illumina sequencing libraries were prepared following Akalin et al. (2012; PMID: 22737091).

value: Long-Evans

tag: tissue

value: brain

tag: tissue compartment

value: nucleus accumbens

tag: exposure status

value: VEH-exposed

tag: gender

value: Male


title: Control_24_3_M


title: Control_26_1_M


title: Control_22_1_M


title: DGE of GC-1spg

city: Beijing

first: lili

last: hao

address: Beichen west road

country: China

institute: BIG

description: This line shows characteristics of a stage between type B spermatogonia and primary spermatocytes

data_processing:
3' adaptor sequence removal: since Tags are only 21nt long while the sequencing reads are 35nt long, raw sequences are with 3' adaptor sequences
Empty reads removal (reads with only 3' adaptor sequences but no tags)
Low quality tags removal (Tags with unknown sequences 'N')
Removal of tags which are too long or too short, leaving Tags of 21nt long
Removal of Tags with a copy number of 1 (probably be sequencing error)
Genome_build: Mus musculus UniGene Build #18
Supplementary_files_format_and_content: sequence count file contains tag sequence information and the number of tags which are unambiguous clean tags mapped to the sequence

source_name: male germ cells

growth_protocol: GC-1spg is a 10 days’ mouse’s type B spermatogonia transformed with pSV3-neo. GC-2spd(ts) is a spermatocyte cell line obtained from 6 weeks’ mouse and then transformed with SV40 large T antigen.

extract_protocol: Total RNA was extracted from GC-1spg and GC-2spd (ts) cells with TRIZOL® Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. The RNA samples were incubated for 30 min at 37°C with 10 units of DNaseI (Takara, Dalian, China) to remove residual genomic DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Nanodrop® ND-1000 spectrophotometer (LabTech, Holliston, MA, USA). The samples had an average RIN value of 8.9 according to Labon-chip analysis using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: GC-1spg and GC-2spd(ts) were maintained in DMEM medium containing 10% FBS and 1.5 g/L sodium bicarbonate.

tag: developmental stage


title: Wildtype H3K27me3 (Abcam) ChIP-seq, replicates 1-2

source_name: WT ES cells, H3K27me3 ChIP, Abcam antibody

tag: cell type

tag: chip antibody


title: Control_20_5_M

tag: strain


title: Control_20_6_M


title: Control_24_8_F

value: Female


title: Control_24_9_F


title: Control_16_5_M


title: Control_16_8_M


title: Control_26_9_F


title: Control_18_11_F


title: THC_27_4_M

value: THC-exposed


title: THC_27_3_M


title: THC_25_4_M


title: DGE of GC-2spd

description: The cells have lost their differentiation potential, and are currently arrested at a premeiotic stage

tag: cell line

value: premeiotic stage


title: THC_19_5_M


title: THC_19_4_M


title: THC_19_11_F


title: Control_26_11_F


title: THC_25_5_F


title: Control_18_13_F


title: THC_5_10_F


title: THC_3_13_F


title: THC_27_11_F


title: THC_5_15_F


title: THC_3_5_M


title: Control_16_13_F


title: THC_5_6_M


title: THC_3_10_F


title: NeuP-RNAseq-r1

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description:
strand specific polyA+ RNA
RNA-Seq of NeuP
fpkm.txt

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-Seq reads were aligned to the mouse genome (mm9) using bowtie2 (v2.1.0) for ChIP-Seq and DamID and STAR (v2.2.0c) for RNA-Seq, keeping only reads that mapped to a unique genomic location (MAPQ > 10).  DamID reads were further removed if the read was not preceeded by a GATC in the genome (read starting immediately after the GATC).
HOMER (v4.6) was used to process alignment files to generate normalized bedGraphs and bigwigs for the UCSC Genome Browser.  ChIP-Seq peaks were founding using the findPeaks program in HOMER.  Oct4 peaks were found using the "-style factor" option while the Ring1B and Cbx7 peaks were found using "-style histone" due to their more spreadout nature.  Putative DamID peaks were found using the findPeaks program in HOMER with the following options "-style histone -o auto -size 2500 -minDist 2500 -tbp 0 -inputtbp 0 -fragLength 1 -inputFragLength 1 -F 2 -C 0 -ntagThreshold 50" using the GFP DamID experiments as background.  Final DamID peak calls were determined using edgeR to quantify the statistical significance of target and GFP replicates at putative peaks, keeping only peaks with a fold-enrichment of 2 vs. GFP and a FDR < 0.1%.  For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm9
Supplementary_files_format_and_content: BED file Columns: (1) chr (2) start (3) end (4) peakName (5) no used (6) strand.  FPKM Tab delimited text file, Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-12) FPKM

source_name: Neural progenitor cells

growth_protocol: Mouse embryonic stem cells (mESCs) - E14, 16.7 and D3 were cultured on irradiated mouse embryonic fibroblasts (MEFs) in ES-Media: Knockout DMEM (Gibco), 15% Gibco knockout serum replacement (Gibco), MEM non essential amino acids (Gibco), and mLIF (ESGRO, EMD Millipore). Media was changed every day and cells were split every 3-4 days. StemTAG Alkaline phosphatase Staining Kit (Cell Biolabs) was used to identify positive Alkaline Phosphatase (AP) mESC colonies. To induce differentiation, mESCs were grown in low-attachment plates (Corning Life Sciences) with ES-media without mLIF to allow for embryonic bodies (EBs) formation. Differentiation of EBs to neural precursor cells (NeuP) was induced by the addition of mouse Noggin (0.5μg/ml) in N2 media  (DMEM/F12/ glutamax (Invitrogen), 1% B27 supplement (Invitrogen) and 1% N2 supplement (Invitrogen). NeuP cells were grown in N2 media plus 20ng/ml FGF2 and 20ng/ml EGF.

extract_protocol:
RNA-Seq: RNA was extracted from Nup153 knockdown and control mESCs using Trizol (Ambion) and column purified using RNeasy kit (Qiagen).  For ChIP-seq, approximately 107 cells were cross-linked with 1% formaldehyde at room temperature for 10 min and neutralized with 0.125 M glycine. After sonication, 20–30 µg of soluble chromatin was incubated with 5–10 μg of antibody at 4°C overnight. Immunoprecipitated complexes were collected using Dynabeads M280 sheep-anti-rabbit IgG or sheep-anti-mouse IgG (Invitrogen). Subsequently, immuno-complexes were washed, and DNA was extracted and purified by QIAquick Spin columns (Qiagen).  For DamID-Seq,  mECS were harvested and gDNA was isolated using the Qiagen DNeasy Blood & Tissue Kit. 3μg of gDNA was then digested with 0.5μl of DpnI (NEB, 20 U/ μl) and ligated with the adaptor AdR, which was made by mixing and slowly annealing AdR-top (5’ CTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAGGA 3’) and AdR-bottom (5’ TCCTCGGCCG 3’). This ligation was completed using 1uL T4 Ligase (Roche, 5U/μl) for 2 hours at 16°C. The regions flanked by adaptors were amplified by PCR using the Bio-Adr-primer (5’ Bio-GGTCGCGGCCGAGGATC 3’) and purified using the Qiagen MinElute PCR purification kit. 4μg of amplified products were sonicated using a Bioruptor (Diagenode) to obtain DNA fragments of sizes between 100-500bp. Dynabeads MyOne Streptavidin T1 (Invitrogen) beads were used to pull down the biotinylated ends of the sonicated PCR products. The bound DNA was removed off the beads by digestion with DpnII at 370C for 1 hour and cleaned using the MinElute PCR Purification kit.
RNA-Seq strand-specific libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq Stranded RNA LT Kit (Illumina).  ChIP-Seq and DamID-Seq libraries were generated using the TruSeq ChIP sample Prep kit (Illumina) followed by deep sequencing with the Illumina’s HiSeq 2500 system.
ChIP-Seq, DamID-Seq, and strand-specific polyA+ RNA-seq

treatment_protocol: shNup153 #2 (TRCN0000102396), shNup153 #4 (TRCN0000102398) MISSION shRNA plasmid DNAs were obtained from SIGMA. The shCTRL (SHC002) non-target control was also purchased from Sigma. Around 5×106 mESCs per 10cm plate were infected with lentivirus at a multiplicity of infection (MOI) of 50. At 48 hours after transduction, puromycin (2μg/ml) was added to the ES media to select transduced mESCs. Stable knockdown mESCs were harvested for RNA, Western Blot, Immunofluorescence and ChIP-seq after at least 4 days of selection. For DamID-Seq experiments, the heat shock promoter, ecodam tag and RFC.1 region of the pLgw EcoDam-V5-RFC1 vector (a kind gift of Dr. Bas Van Steensel) was cloned into the polylinker of the pMSCV-puro vector yielding pMSCV-ED-puro.  All ORFs (GFP, Oct4 and Nup153) were PCR amplified with gateway compatible sites and cloned into the pDonr207 vector.  The ORFs were transferred to the pMSCV-ED-puro vector by LR reaction. Around 5×106 mESCs per 10cm plate were infected with Dam-fusion proteins lentivirus at a multiplicity of infection (MOI) of 50. At 48 hours after transduction, puromycin (2μg/ml) was added to the ES media to select transduced mESCs.

value: Neural progenitor cells

tag: shRNA

tag: damid tagged factor

tag: antibody


title: NeuP-RNAseq-r2


title: THC_25_6_F


title: ES-RNAseq-shNup153-4

description:
strand specific polyA+ RNA
RNA-Seq of mESC with shNup153 #4
fpkm.txt

source_name: mouse embryonic stem cells E14

value: mouse embryonic stem cells E14

value: shNup153 #4


title: Control_20_14_F


title: Ring1B-ChIPseq-NeuP

description:
ChIP-Seq localization of Ring1B in NeuP
Ring1B.NeuP.bed

value: 39663, Active Motif


title: Input-ChIPseq

description:
ChIP-Seq input control
Oct4.ctrl.bed


title: ES-RNAseq-shCtrl

description:
strand specific polyA+ RNA
RNA-Seq of mESC with shCtrl
fpkm.txt

value: shCtrl (Scramble)


title: ES-RNAseq-shNup153-2

description:
strand specific polyA+ RNA
RNA-Seq of mESC with shNup153 #2
fpkm.txt

value: shNup153 #2


title: shTop2a_RNAseq, replicate 2

city: Cambridge

first: John

middle: Edward

last: Froberg

state: MA

address: 7 Divinity Avenue

department: Stem Cell & Regenerative Biology

institute: Harvard University

data_processing:
ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. The coverage files presented in the paper and in this archive are fpm normalized. Peaks were called using macs2 with default settings. Hi-C: The individual ends of the read-pairs were aligned to the mus and cas reference genomes separately using novoalign with default parameters for single-end alignments, and the quality score of the alignment was used to determine whether each end could be assigned to either the mus or the cas haplotype. The single-end alignments were merged into a HiCsummary file using custom scripts to determine whether a given read-pair could be assigned to the mus or cas haplotype and to pair up the two ends of the read-pair. RNA-seq: To determine the allelic origin of each sequencing read from the hybrid cells, reads were first depleted of adaptors dimers and PCR duplicates, followed by the alignment to custom mus/129 and cas genomes to separate mus and cas reads. Once completed, reads were then mapped back to reference mm9 genome using Tophat v2.0.10 (-g 1 --no-coverage-search --read-edit-dist 3 --read-mismatches 3 --read-gap-length 3 --b2-very-sensitive --mate-inner-dist 50 --mate-std-dev 50 --library-type fr-firststrand). Following alignment, gene expression levels within each library were quantified using Homer v4.7 (rna mm9 -count genes -strand + -noadj -condenseGenes) and the normalized differential expression analyses across samples were performed by using EdgeR.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are fpm-normalized, but not input normalized or smoothed. Hi-C: data is present in a Hi-C summary file, where each line corresponds to the coordinates of the the two end-pairs in the alignment. This format is suitable for generating Hi-C contact matrices using programs such as homer.  As for the ChIP-seq, reads are broken down into comp, cas and mus sets. Supplementary files included in this series consist of an excel file containing .fpkm values and the results of the differential expression analysis using edgeR for all RNA-seq experiments.

source_name: immortalized fibroblast

growth_protocol: Cells were cultured in regular fibroblast medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX) with 10% FBS

extract_protocol:
ChIP-seq: Cells were crosslinked with 1% formaldeyde for 10 min, then nuclei were isolated and lysed. Chromatin was sheared by sonication to a size of ~200-400 bp. Cleared lysates were precleared for 1 hour, then 10% saved as input, and lysates were incubated with Dynabeads Protein G pre-bound with the antibody of choice. After stringent washes, ChIP DNA was eluted from beads, and together with input chromtain was reverse-crosslinked with proteinase K. DNA was purified by phenol/chloroform extraction and ethanol precipitation. Hi-C: Hi-C experiments were conducted using HindIII according to the method described in Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009). RNA-seq: Xi-TgGFP TTFs (68-5-11) with the stable knock down of candidates were treated with 5’-azacytidine and etoposide at 0.3 uM each for 3 days. Strand specific RNA-seq, the library preparation, deep sequencing, and data analysis was followed as described in J. T. Kung et al., Locus-specific targeting to the X chromosome revealed by the RNA interactome of CTCF. Molecular cell 57, 361-375 (2015). All libraries were sequenced with Illumina Hiseq 2000 or 2500 using 50 cycles to obtain paired end reads.
ChIP-seq: Libraries were constructed using the NEBNext ChIP-seq Library Preparation Kit with no modifications to the protocol. We used 16 cycles during the PCR step. Hi-C:  Sequencing libraries were constructed according to the method described in Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009). RNA-seq: Total RNA was harvested using trizol extraction, and ribosomal RNA was removed using RiboMinus. Strand-specific libraries were generated by performing reverse transcription with Superscript III, followed by second-strand synthesis using the NEBNext second-strand synthesis module supplemented with dUTP, and then libraries were generated using the NEBNext ChIP-seq Library Preparation Kit.

treatment_protocol: Cells were treated with 0.3 uM azacytidine and 0.3 uM etoposide for 3 days

value: CAST/Ei x 129/Sv/Jae

value: Xi GFP tail-tip fibroblast

tag: genetic manipulation

value: Stable shRNA knockdown of Top2a


title: shTop1_RNAseq, replicate 2

value: Stable shRNA knockdown of Top1


title: Ring1B-ChIPseq-shNup153-2

description:
ChIP-Seq localization of Ring1B with shNup153 #2
Ring1B.shNup153-2.bed


title: shSmc1a_RNAseq, replicate 2

value: Stable shRNA knockdown of Smc1a


title: Oct4-ChIPseq-shCtrl

description:
ChIP-Seq localization of Oct4 with shCtrl
Oct4.ctrl.bed

value: sc-5279, Santa Cruz


title: HeLa S3  DNase-seq

first: Yu-Xiang

last: Zhang

address: Fengtai-District,You-An-Men-Wai

department: Biochemistry

institute: Capital Medical University, China

data_processing:
Basecalls performed using RTA version 1.12 to generate bcl files
The bcl file was converted to qseq file with BclConverter version 1.9.0-11-03-08
Reads were aligned using Elend with the reference of HUMAN_refseq_eland
Peaks were called using MACS version 1.4.0
Genome_build: hg18

source_name: Human cell Line

growth_protocol: HeLa S3 cells were purchased from the Cell Culture Center of Peking Union Medical College. They were cultured in F-12 Nutrient Mixture (Ham) (Invitrogen, USA), containing 10% fetal bovine serum (FBS), penicillin/streptomycin at 37 °C and 5% CO2 and used in experiments at a density of 5×106 cells/ml.

extract_protocol: After HeLa S3 nuclear extraction, DNase I digestion and gel-electrophoresis, the target DNA bands were cut from agarose gels and purified with a QIA Quick Gel Extraction Kit (Qiagen). We purified DNA fragments of 100-300bp.The gel-purified DNA products were modified for Illumina Whole-Genome Chromatin IP sequencing using an Illumina Genomic DNA Sample Prep kit as follows: the size-selected DNAs were end-repaired by T4 DNA polymerase and phosphorylated by T4 DNA polymerase and T4 polynucleotide kinase. The products were incubated with Klenow DNA Polymerase (Illumina) to generate 3’ adenine overhangs and then ligated to Illumina adapters, which contain 5’ thymine overhangs. The adapter-ligated products were purified on QIAquick spin columns (Qiagen), PCR-amplified with Phusion DNA Polymerase (Finnzymes) for 10 cycles using Illumina’s genomic DNA primer set. The PCR products were purified on QIAquick and MinElute columns (Qiagen).The quality of the DNA was assessed and quantified using an Agilent DNA 1000 Series II assay and NanoDrop ND-1000 spectrophotometer (Thermo Scientific) and the DNA was diluted to 10nM. Cluster generation and sequencing were performed using a Standard Cluster Generation kit and a Cycle Solexa Sequencing kit on the Illumina Cluster Station and Illumina Genome Analyzer I following the manufacturer’s instructions.

treatment_protocol: To remove the background introduced by actively dividing cells, we used the standard approach for synchronizing cells in G1 by serum deprivation. Cells were arrested in F-12 Nutrient Mixture with 0.2% FBS (24 h) , and then placed on ice prior to harvesting nuclei.

value: cervix

value: adenocarcinoma

value: HeLa S3 cells

tag: morphology

value: epithelial


title: Oct4-ChIPseq-shNup153-2

description:
ChIP-Seq localization of Oct4 with shNup153 #2
Oct4.shNup153.bed


title: GFP-DamID-r2

description:
DamID-Seq localization of GFP (negative control) replicate 2
Nup153.DamID.bed

value: GFP


title: GFP-DamID-r1

description:
DamID-Seq localization of GFP (negative control) replicate 1
Nup153.DamID.bed


title: shSMARCC2_RNAseq, replicate 2

value: Stable shRNA knockdown of SMARCC2


title: shSmarca4_RNAseq, replicate 2

value: Stable shRNA knockdown of Smarca4


title: shRad21_RNAseq, replicate 2

value: Stable shRNA knockdown of Rad21


title: Eu_T24_2

city: Planegg-Martinsried

first: Stephan

last: Hutter

state: Bavaria

address: Grosshaderner Strasse 2

department: Department of Biology II

country: Germany

institute: University of Munich

data_processing:
Standard Illumina pipeline using Bustard for basecalling
Illumina sequence reads were mapped to the reference D. melanogaster transcriptome (FlyBase release 5.57) using NextGenMap (version 0.4.12) and requiring a minimum of 40 mapped residues (option –R 40)
Expression was quantified on a “per gene” basis. For this, if a sequence read mapped to one or more transcripts of the same gene, it was counted as one “hit” for that gene and all subsequent analyses were performed at the gene level.
Genome_build: dmel_r5.57
Supplementary_files_format_and_content: tab-delimited text files include gene specific read counts for each sample; read counts per gene

organism: Drosophila melanogaster

growth_protocol: All flies were maintained on standard cornmeal-molasses medium at 23° with a 14 h light:10 h dark cycle

extract_protocol:
Total RNA extraction and DNase I digestion were performed using the MasterPure RNA Purification Kit (Epicentre)
Poly-A mRNA was purified and fragmented by sonication. First strand single end cDNA was synthesized using random primers. Eight tagged libraries were generated, pooled and run on two lanes of a HiSeq 2000 sequencer (Illumina) to generate single reads of 50 bases

treatment_protocol: Adult males aged 3–5 days were transfered into vials containing Beauveria bassiana spores or control vials for 8 or 24 hours

tag: Sex

value: male

tag: population

value: Europe (The Netherlands)

tag: infection status

value: Infected (24 hours)

tag: age

value: 3-5 days

value: whole flies


title: Ring1B-ChIPseq-shNup153-4

description:
ChIP-Seq localization of Ring1B with shNup153 #4
Ring1B.shNup153-4.bed

value: mouse embryonic stem cells E14

value: shNup153 #4

value: 39663, Active Motif


title: shControl_RNAseq, replicate 2

treatment_protocol: Cells were treated with 0.3 uM azacytidine and 0.3 uM etoposide for 3 days.

value: CAST/Ei x 129/Sv/Jae

value: Xi GFP tail-tip fibroblast

value: Stable expression of scrambled shRNA


title: shCtcf_RNAseq, replicate 2

value: Stable shRNA knockdown of Ctcf


title: Eu_T24_3

tag: tissue


title: Eu_T24_1


title: Cbx7-ChIPseq-shCtrl

description:
ChIP-Seq localization of Cbx7 with shCtrl
Cbx7.shCtrl.bed

value: shCtrl (Scramble)

value: ab21873, Abcam


title: Eu_T08_3

value: Infected (8 hours)


title: Oct4-DamID-r2

description:
DamID-Seq localization of Oct4 (positive control) replicate 2
Oct4.DamID.bed


title: Nup153-DamID-r2

description:
DamID-Seq localization of Nup153 replicate 2
Nup153.DamID.bed


title: Nup153-DamID-r1

description:
DamID-Seq localization of Nup153 replicate 1
Nup153.DamID.bed


title: Eu_T08_2


title: Xist deletion Hi-C, replicate 2

data_processing:
Library strategy: Hi-C
ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. The coverage files presented in the paper and in this archive are fpm normalized. Peaks were called using macs2 with default settings. Hi-C: The individual ends of the read-pairs were aligned to the mus and cas reference genomes separately using novoalign with default parameters for single-end alignments, and the quality score of the alignment was used to determine whether each end could be assigned to either the mus or the cas haplotype. The single-end alignments were merged into a HiCsummary file using custom scripts to determine whether a given read-pair could be assigned to the mus or cas haplotype and to pair up the two ends of the read-pair. RNA-seq: To determine the allelic origin of each sequencing read from the hybrid cells, reads were first depleted of adaptors dimers and PCR duplicates, followed by the alignment to custom mus/129 and cas genomes to separate mus and cas reads. Once completed, reads were then mapped back to reference mm9 genome using Tophat v2.0.10 (-g 1 --no-coverage-search --read-edit-dist 3 --read-mismatches 3 --read-gap-length 3 --b2-very-sensitive --mate-inner-dist 50 --mate-std-dev 50 --library-type fr-firststrand). Following alignment, gene expression levels within each library were quantified using Homer v4.7 (rna mm9 -count genes -strand + -noadj -condenseGenes) and the normalized differential expression analyses across samples were performed by using EdgeR.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are fpm-normalized, but not input normalized or smoothed. Hi-C: data is present in a Hi-C summary file, where each line corresponds to the coordinates of the the two end-pairs in the alignment. This format is suitable for generating Hi-C contact matrices using programs such as homer.  As for the ChIP-seq, reads are broken down into comp, cas and mus sets. Supplementary files included in this series consist of an excel file containing .fpkm values and the results of the differential expression analysis using edgeR for all RNA-seq experiments.

value: dermal fibroblast

value: Post XCI deletion of Xist on inactive X-chromosome


title: shAurkb_RNAseq, replicate 2

value: Stable shRNA knockdown of Aurkb


title: shSmc3_RNAseq, replicate 2

value: Stable shRNA knockdown of Smc3


title: shSun2_RNAseq, replicate 2

value: Stable shRNA knockdown of Sun2


title: Oct4-DamID-r1

description:
DamID-Seq localization of Oct4 (positive control) replicate 1
Oct4.DamID.bed


title: H3K36me3 ChIP 786-O SETD2 ZFN KO Input

city: Rochester

first: Jeff

last: Nie

state: MN

address: 200 First St. SW

institute: Mayo Clinic

description:
786-O SETD2 ZFN KO input (control)
processed data file: 786-38F-K36-3.FCC4J4KACXX_L8_R1_ICCTCGG.PE.U12.dedup.s1-W200-G600-islands-summary-FDR1E-2.bed

data_processing:
bcl2fastq 2.15.0 is used for basecalling
Data was processed with Mayo chip-seq pipeline-- HiChIP (http://www.biomedcentral.com/1471-2105/15/280).
Paired_end reads are aligned to genome with BWA. Duplicated reads are filtered out with picard. Peak calling is performed with Sicer
Genome_build: hg19
Supplementary_files_format_and_content: bed format peak files.  Column headers are: Chr, Peak_start, Peak_end, IP_raw_read_count, CONTROL_raw_read_count, Raw_p_value, Fold_change, FDR

source_name: Renal cell carcinoma cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to ActiveMotif instructions; ChIP and input DNAs were prepared at ActiveMotif  (Carlsbad, CA) by converting overhangs into phosphorylated blunt ends, the addition of an adenine to the 3’ ends, and the addition of Illumina adaptors. The library was size-selected (175-225 base pairs [bp]) and amplified for 18 cycles.

value: 786-O SETD2 ZFN KO cell line

value: none (input)


title: Eu_T08_1

value: male

value: Europe (The Netherlands)

value: 3-5 days

value: whole flies


title: H3K36me3 ChIP 786-O input

description:
786-O input (control)
processed data file: 786-K36-1.FCC4J4KACXX_L8_R1_ITTCAGC.PE.U12.dedup.s1-W200-G600-islands-summary-FDR1E-2.bed

value: 786-O RCC cell line


title: H3K36me3 ChIP 786-O SETD2 ZFN KO

description:
786-O SETD2 ZFN KO
processed data file: 786-38F-K36-3.FCC4J4KACXX_L8_R1_ICCTCGG.PE.U12.dedup.s1-W200-G600-islands-summary-FDR1E-2.bed

value: anti-H3K36me3 (ActiveMotif, catalog# 61101, lot# 1)


title: SMC1A ChIP Xist deletion, replicate 2

description: antibody: Bethyl 300-080A

value: CAST/Ei x 129/Sv/Jae


title: wild type Hi-C, replicate 2

value: fibroblast


title: Eu_C_2

value: Control


title: Eu_C_3


title: H3K36me3 ChIP 786-O

description:
786-O
processed data file: 786-K36-1.FCC4J4KACXX_L8_R1_ITTCAGC.PE.U12.dedup.s1-W200-G600-islands-summary-FDR1E-2.bed


title: SMC1A ChIP wild-type, replicate 2

description: antibody: Bethyl 300-080A


title: As_T24_3

value: Asia (Malaysia)

value: Infected (24 hours)


title: shTop2a_RNAseq

description: s11_mus/ reads

data_processing:
ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. The coverage files presented in the paper and in this archive are fpm normalized. Peaks were called using macs2 with default settings. Hi-C: The individual ends of the read-pairs were aligned to the mus and cas reference genomes separately using novoalign with default parameters for single-end alignments, and the quality score of the alignment was used to determine whether each end could be assigned to either the mus or the cas haplotype. The single-end alignments were merged into a HiCsummary file using custom scripts to determine whether a given read-pair could be assigned to the mus or cas haplotype and to pair up the two ends of the read-pair. RNA-seq: To determine the allelic origin of each sequencing read from the hybrid cells, reads were first depleted of adaptors dimers and PCR duplicates, followed by the alignment to custom mus/129 and cas genomes to separate mus and cas reads. Once completed, reads were then mapped back to reference mm9 genome using Tophat v2.0.10 (-g 1 --no-coverage-search --read-edit-dist 3 --read-mismatches 3 --read-gap-length 3 --b2-very-sensitive --mate-inner-dist 50 --mate-std-dev 50 --library-type fr-firststrand). Following alignment, gene expression levels within each library were quantified using Homer v4.7 (rna mm9 -count genes -strand + -noadj -condenseGenes) and the normalized differential expression analyses across samples were performed by using EdgeR.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are fpm-normalized, but not input normalized or smoothed. Hi-C: data is present in a Hi-C summary file, where each line corresponds to the coordinates of the the two end-pairs in the alignment. RNA-seq: aligned reads used for analysis are present in .bed files. Reads aligning to the + strand of the genome are in the "+" files and reads aligning to the - strand are in the - files. As for the ChIP-seq, reads are broken down into comp, cas and mus sets. Supplementary files included in this series consist of an excel file containing .fpkm values and the results of the differential expression analysis using edgeR for all RNA-seq experiments.

extract_protocol:
ChIP-seq:Cells were crosslinked with 1% formaldeyde for 10 min, then nuclei were isolated and lysed. Chromatin was sheared by sonication to a size of ~200-400 bp. Cleared lysates were precleared for 1 hour, then 10% saved as input, and lysates were incubated with Dynabeads Protein G pre-bound with the antibody of choice. After stringent washes, ChIP DNA was eluted from beads, and together with input chromtain was reverse-crosslinked with proteinase K. DNA was purified by phenol/chloroform extraction and ethanol precipitation. Hi-C: Hi-C experiments were conducted using HindIII according to the method described in Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009). RNA-seq: Xi-TgGFP TTFs (68-5-11) with the stable knock down of candidates were treated with 5’-azacytidine and etoposide at 0.3 M each for 3 days. Strand specific RNA-seq, the library preparation, deep sequencing, and data analysis was followed as described in J. T. Kung et al., Locus-specific targeting to the X chromosome revealed by the RNA interactome of CTCF. Molecular cell 57, 361-375 (2015). All libraries were sequenced with Illumina Hiseq 2000 or 2500 using 50 cycles to obtain paired end reads.
ChIP-seq: Libraries were constructed using the NEBNext ChIP-seq Library Preparation Kit with no modifications to the protocol. We used 16 cycles during the PCR step. Hi-C:  Sequencing libraries were constructed according to the method described in Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009). RNA-seq: Total RNA was harvested using trizol extraction, and ribosomal RNA was removed using RiboMinus. Strand-specific libraries were generated by performing reverse transcription with Superscript III, followed by second-strand synthesis using the NEBNext second-strand synthesis module supplemented with dUTP, and then libraries were generated using the NEBNext ChIP-seq Library Preparation Kit.

value: Xi GFP tail-tip fibroblast

value: Stable shRNA knockdown of Top2a


title: WT_Rad21_rep1_extra

description: antibody: Bethyl 300-080A


title: shTop1_RNAseq

description: s6_mus/ reads

value: Stable shRNA knockdown of Top1


title: As_T24_2


title: H3K36me3 ChIP RCC2 Input

description:
RCC2 input (control)
processed data file: 11_T75232_H3K36me3_i78_filtered.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed

source_name: Nephrectomy sample

value: kidney

tag: tissue type

value: tumor


title: H3K36me3 ChIP RCC4 Input

description:
RCC4 input (control)
processed data file: 1_tumor_H3K36me3_s5_r1_iall.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed

value: none (input)


title: H3K36me3 ChIP RCC1 Input

description:
RCC1 input (control)
processed data file: 7_T49834_H3K36me3_1112_filtered.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed


title: shSun2_RNAseq

description: s8_mus/ reads

value: Stable shRNA knockdown of Sun2


title: H3K36me3 ChIP RCC3 Input

description:
RCC3 input (control)
processed data file: 9_T50338_H3K36me3_i34_filtered.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed


title: As_T24_1

value: male


title: As_T08_3

value: Infected (8 hours)

value: 3-5 days


title: H3K36me3 ChIP RCC3

description:
RCC3
processed data file: 9_T50338_H3K36me3_i34_filtered.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed


title: shSmc1a_RNAseq

description: s9_mus/ reads

value: Stable shRNA knockdown of Smc1a


title: As_T08_2

value: whole flies


title: As_T08_1


title: H3K36me3 ChIP RCC2

description:
RCC2
processed data file: 11_T75232_H3K36me3_i78_filtered.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed

value: anti-H3K36me3 (ActiveMotif, catalog# 61101, lot# 1)


title: shSmarca4_RNAseq

description: s13_mus/ reads

value: CAST/Ei x 129/Sv/Jae

value: Stable shRNA knockdown of Smarca4


title: H3K36me3 ChIP RCC1

description:
RCC1
processed data file: 7_T49834_H3K36me3_1112_filtered.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed


title: shSmc3_RNAseq

description: s10_mus/ reads

value: Stable shRNA knockdown of Smc3


title: shSMARCC2_RNAseq

description: s7_mus/ reads

value: Stable shRNA knockdown of SMARCC2


title: H3K36me3 ChIP Uninvolved Kidney 4 Input

description:
Uninvolved kidney 4 input (control)
processed data file: 2_normal_H3K36me3_s6_r1_iall.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed

value: uninvolved kidney


title: Ring1B-ChIPseq-shCtrl

description:
ChIP-Seq localization of Ring1B with shCtrl
Ring1B.shCtrl.bed

value: mouse embryonic stem cells E14

value: shCtrl (Scramble)

value: 39663, Active Motif


title: shRad21_RNAseq

description: s4_mus/ reads

value: Xi GFP tail-tip fibroblast

value: Stable shRNA knockdown of Rad21


title: As_C_2

value: Asia (Malaysia)

value: Control


title: H3K36me3 ChIP Uninvolved Kidney 3 Input

description:
Uninvolved kidney 3 input (control)
processed data file: 10_N50338_H3K36me3_i56_filtered.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed

value: kidney

value: none (input)


title: H3K36me3 ChIP RCC4

description:
RCC4
processed data file: 1_tumor_H3K36me3_s5_r1_iall.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed

value: tumor


title: shControl_RNAseq

description: s3_mus/ reads

value: Stable expression of scrambled shRNA


title: Am_T24_2

value: male

value: America (North Carolina, USA)

value: Infected (24 hours)

value: 3-5 days

value: whole flies


title: As_C_3


title: Eu_C_1

value: Europe (The Netherlands)


title: Am_T24_1


title: Am_T08_3

value: Infected (8 hours)


title: wild type Hi-C

description: Hi-C

value: CAST/Ei x 129/Sv/Jae

value: fibroblast


title: Xist deletion Hi-C

description: Hi-C

value: dermal fibroblast

value: Post XCI deletion of Xist on inactive X-chromosome


title: Am_T08_2


title: H3K36me3 ChIP Uninvolved Kidney 3

description:
Uninvolved kidney 3
processed data file: 10_N50338_H3K36me3_i56_filtered.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed

value: uninvolved kidney

value: anti-H3K36me3 (ActiveMotif, catalog# 61101, lot# 1)


title: SMC1A ChIP Xist deletion, replicate 1

value: Bethyl 300-055A


title: SMC1A ChIP wild-type, replicate 1


title: H3K36me3 ChIP Uninvolved Kidney 2

description:
Uninvolved kidney 2
processed data file: 12_N75232_H3K36me3_i910_filtered.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed

value: kidney


title: As_C_1

value: Asia (Malaysia)

value: Control


title: H3K36me3 ChIP Uninvolved Kidney 1

description:
Uninvolved kidney 1
processed data file: 8_N49834_H3K36me3_i12_filtered.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed


title: H3K36me3 ChIP Uninvolved Kidney 2 Input

description:
Uninvolved kidney 2 input (control)
processed data file: 12_N75232_H3K36me3_i910_filtered.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed

value: none (input)


title: Am_T24_3

value: male

value: America (North Carolina, USA)


title: Am_C_3

value: 3-5 days


title: RAD21 ChIP Xist deletion, replicate 2

value: Bethyl 300-080A


title: Xidel_Rad21_rep1_extra

description: antibody: Bethyl 300-080A


title: Am_C_2

value: whole flies


title: H3K36me3 ChIP Uninvolved Kidney 1 Input

description:
Uninvolved kidney 1 input (control)
processed data file: 8_N49834_H3K36me3_i12_filtered.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed


title: RAD21 ChIP Xist deletion, replicate 1


title: Af_T24_2

value: Africa (Zimbabwe)

value: Infected (24 hours)


title: RAD21 ChIP wild-type, replicate 1

value: CAST/Ei x 129/Sv/Jae

value: fibroblast


title: RAD21 ChIP wild-type, replicate 2


title: H3K36me3 ChIP Uninvolved Kidney 4

description:
Uninvolved kidney 4
processed data file: 2_normal_H3K36me3_s6_r1_iall.SE.U1.dedup.s1.INPUT-W200-G600-islands-summary-FDR1E-2.bed


title: Af_T24_1


title: CTCF ChIP Xist deletion, replicate 2

value: dermal fibroblast

value: Post XCI deletion of Xist on inactive X-chromosome

value: Millipore 07-729


title: Af_T08_3

value: Infected (8 hours)


title: CTCF ChIP Xist deletion, replicate 1


title: Af_T08_2


title: Af_T08_1


title: CTCF ChIP wild-type, replicate 2


title: Am_T08_1


title: CTCF ChIP wild-type, replicate 1


title: Af_C_3


title: Af_C_2


title: Af_T24_3


title: wild-type ChIP input


title: GR ChIP Klf15-/- MEFS 1hr dex 2

status: Public on Jun 18 2015

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

institute: University of Colorado, Denver

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 2 with the default setting.
Mapped reads were compressed, sorted and indexed using Samtools
Peaks were called using MACS version 2 with the default setting
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using MACS version 2

source_name: Cultured Klf15-/- embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts (MEFS) were generated from embryos harvested from dpc 14-17 dams. Cells were maintained in DMEM + 10% FBS and assays were performed on cells between passage 4 and 11

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as described previously described (PMID: 23508109), with the following modifications: cross-linking was performed by adding methanol-free 16% formaldehyde directly to the culture media to a final concentration of 1% and incubating for 5 minutes at room temperature with gentle rocking; samples were subsequently sonicated with a Diagenode Bioruptor at high power in 30-second bursts separated by 30-second incubations in ice water for a total of 23 cycles.
A minimum of 1 ng DNA from ChIP samples were used to prepare libraries using the Nugen Ovation Ultralow System V2 1-16 Part No. 0344 according to the manufacturer’s instructions. Samples were run on an Illumina HiSeq using 1X50 bp end reads

tag: genotype

value: embryonic fibroblast

value: in-house GR antibody


title: GR ChIP Klf15-/- MEFS 1hr vehicle 2


title: GR ChIP WT MEFS 1hr vehicle 1

source_name: Cultured WT embryonic fibroblasts

value: wild type


title: GR ChIP WT MEFS 1hr dex 2


title: GR ChIP WT MEFS 1hr dex 1


title: shRenilla OFF Dox 2

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

data_processing:
All fastq sequencing reads are mapped by STAR 2.3.0e. For data from whole RNA samples, reads are directly mapped to hg19 with standard settings. For data from TRAP protocols, read are mapped to a hybrid genome index containing both hg19 and mm9, and reads that score higher in hg19  are selected for further analysis. This step is designed to avoid potential residual RNA contaminations from mouse stroma tissue in the xenograft tumors during TRAP processing.
HTSeq v0.5.4 is used for feature counting.
DESeq (v1.18.0) is used for the normalization of count table. R3.1.2 is used as the processing platform.
Genome_build: mm9
Supplementary_files_format_and_content: txt files, normalized count tables from each experiment

source_name: Colon Mucosa

growth_protocol: Transgenic mice were born and fed normal chow until 6 weeks of age.  .5mg/ml 4-OHT was injected subQ and then mice were switch to dox supplemented chow.  Tumors were isolated 4-6 weeks later.  Off Dox tumors were isolated 4 days after removing dox food.

extract_protocol:
Tumors were homogenized in Trizol and processed according to instructions with reagent.
RNA samples are used for Hi-Seq library construction with the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions. Samples are barcoded with TruSeq SBS Kit v3 (Illumina).
RNA-Seq on Hi-Seq 2000 platform

tag: dox treatment

value: OFF

value: Colon Mucosa

value: shRenilla


title: shRenilla On Dox 1

value: ON


title: shRenilla On Dox 2


title: shAPC OFF DOX 4

source_name: Colon Polyp

value: Colon Polyp

value: shAPC


title: shRenilla OFF Dox 1


title: shAPC OFF DOX 3


title: shAPC OFF DOX 2


title: shAPC/Kras OFF DOX 2

value: shAPC/Kras


title: shAPC OFF DOX 1


title: shAPC/Kras OFF DOX 4


title: shAPC/Kras OFF DOX 3


title: shAPC/Kras OFF DOX 1


title: shAPC/Kras On Dox 4


title: Xist deletion ChIP input

tag: cell type


title: GR ChIP Klf15-/- MEFS 1hr dex 1


title: shAPC/Kras On Dox 2


title: GR ChIP Klf15-/- MEFS 1hr vehicle 1


title: shAPC/Kras On Dox 1


title: THC_5_7_M

value: Long-Evans

value: brain

tag: tissue compartment

value: nucleus accumbens

tag: exposure status

value: THC-exposed

tag: gender

value: Male


title: shAPC On Dox 4


title: shAPC On Dox 2


title: shAPC On Dox 1


title: shAPC On Dox 3


title: Af_C_1

value: male

value: Africa (Zimbabwe)

value: Control

value: 3-5 days

value: whole flies


title: shAurkb_RNAseq

description: s5_mus/ reads

tag: strain

value: CAST/Ei x 129/Sv/Jae

value: Xi GFP tail-tip fibroblast

value: Stable shRNA knockdown of Aurkb


title: shAPC/Kras On Dox 3

value: ON


title: ΔCT_stage13_input_2

first: Terry

middle: L.

last: Orr-Weaver

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
ΔCT follicle cell stage13 input
deltaCT_13_input_2

data_processing:
Reads were mapped with bowtie setting the seed length to 40, using the option “--best”, and leaving other settings as default.
One kilobase windows were made sliding every 100 nucleotides, and the number of reads overlapping with the windows were counted using “bedtools coverage”
The number of reads in each window was divided by the millions of reads mapped to obtain reads per million (RPM).
The RPM from the ChIP was divided by the RPM of the corresponding i  nput in each window.  To avoid divisions by zero 10-6  was added to each RPM value  before taking the ratio.
The two replicates were summarized by calculating the mean of the log2ratios (ChIP/input).
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: text file with four columns: chr, sliding window start, sliding window start stop, mean of the log2ratios (ChIP/input) of the 2 replicas.

source_name: H2Av[ΔCT]  stage 13 follicle cell nuclei

growth_protocol: Drosophila were grown on standard cornmeal, molasses agar media.

extract_protocol:
Egg chambers were dounced and sonicated using a Bioruptor 300 (Diagenode).
Libraries were constructed using the NEB Next ChIP seq kit (Part # E6200S) according to manufactures recommendations with indexing primers for multiplexing.

treatment_protocol: Ovaries were hand dissected from females fattened for 2 days on wet yeast in Grace’s media. Ovaries were teased apart and fixed in 4% formaldehyde. Ovaries were resuspended in PBS and stage 10B and 13 egg chambers were isolated. Fixed egg chambers were stored at -80ᵒC until 3,000 egg chambers from each genotype were collected. Follicle cell nuclei were isolated from egg chambers prior to ChIP with anti-gammaH2Av (Rockland).

tag: strain background

value: OregonR

tag: genotype/variation

value: w, P{His2Av[deltaCT], w+}; His2Av[810]/TM6B

tag: developmental stage

value: egg chamber


title: ΔCT_stage13_gammaH2Av_ChIP_2

description:
ΔCT follicle cell stage13 gammaH2Av ChIP
processed data file: deltaCTst13_ChIP_SW_log2_Aver.txt
deltaCT_13_gammaH2Av_ChIP_2

tag: chip antibody

value: Anti-Histone H2AvD pS137 (RABBIT) Antibody

tag: chip antibody vendor

value: Rockland Immunochemicals

tag: chip antibody cat.#

tag: chip antibody lot#


title: OrR_stage13_gammaH2Av_ChIP_2

description:
OrR follicle cell stage13 gammaH2Av ChIP
processed data file: WTst13_ChIP_SW_log2_Aver.txt
WT_13_gammaH2Av_ChIP_2

source_name: OrR stage 13 follicle cells nuclei

value: wild type


title: OrR_stage13_input_2

description:
OrR follicle cell stage13 input
WT_13_input_2

source_name: OrR stage 13 follicle cell nuclei


title: ΔCT_stage13_input_1

description:
ΔCT follicle cell stage13 input
deltaCT_13_input_1


title: ΔCT_stage10B_input_1

description:
ΔCT follicle cell stage10B input
deltaCT_10B_input_1

source_name: H2Av[ΔCT] stage 10B follicle cell nuclei


title: ΔCT_stage10B_gammaH2Av_ChIP_1

description:
ΔCT follicle cell stage10B gammaH2Av ChIP
processed data file: deltaCTst10B_ChIP_SW_log2_Aver.txt
deltaCT_10B_gammaH2Av_ChIP_1


title: OrR_stage10B_input_2

description:
OrR follicle cell stage10B input
WT_10B_input_2

source_name: OrR stage 10B follicle cell nuclei


title: OrR_stage13_gammaH2Av_ChIP_1

description:
OrR follicle cell stage13 gammaH2Av ChIP
processed data file: WTst13_ChIP_SW_log2_Aver.txt
WT_13_gammaH2Av_ChIP_1


title: OrR_stage13_input_1

description:
OrR follicle cell stage13 input
WT_13_input_1


title: ΔCT_stage10B_input_2

description:
ΔCT follicle cell stage10B input
deltaCT_10B_input_2


title: OrR_stage10B_input_1

description:
OrR follicle cell stage10B input
WT_10B_input_1


title: ΔCT_stage10B_gammaH2Av_ChIP_2

description:
ΔCT follicle cell stage10B gammaH2Av ChIP
processed data file: deltaCTst10B_ChIP_SW_log2_Aver.txt
deltaCT_10B_gammaH2Av_ChIP_2


title: ChIP-seq_RS_Mnase_Input

city: Cincinnati

first: Satoshi

last: Namekawa

state: Ohio

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Wardrobe#: 334

data_processing:
Data analysis was performed in BioWardrobe Experiment Management System (https://biowardrobe.com/).
Reads were aligned to the mouse genome (mm10) with bowtie (version 1.0.0(8)) and displayed on a local mirror of UCSC genome browser as coverage.
Genome_build: mm10
Supplementary_files_format_and_content: For-ChIP-seq, Islands enrichment were identified using MACS2

source_name: genomic DNA, Mnase

growth_protocol: GS cells were established from P7 testes and maintained on mitotically inactivated mouse embryonic feeder cells as previously described (Hasegawa et al. 2013 Stem Cells). For RNA-seq and ChIP-seq analyses, cells were trypsinized, centrifuged at 200g for 5min, and then resuspended in GS cell culture medium. Cells were further incubated on a gelatin-coated dish for 30min to remove MEFs, and floating cells were collected and used for the experiments.. Pachytene spermatocytes (PS) and round spermatids (RS) were isolated from wild-type adult testes with BSA gravity sedimentation

extract_protocol:
For ChIP-seq of crosslink samples, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies. For ChIP-seq of MNase samples, lysate was digested with Mnase and Histone-DNA complexes were isolated with antibodies.
DNA library for ChIP-seq (both crosslink and MNase samples) was prepared with NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (NEB) and Agencourt AMPure XP (Beckman Coulter).

value: Wild-type

value: Isolated round spermatids


title: ChIP-seq_RS_H4K8ac

description: Wardrobe#: 297

value: Rabbit anti-H4K8ac (Millipore:07-328)


title: ChIP-seq_RS_H3K9me2_1

description: Wardrobe#: 300

value: Mouse anti-H3K9me2 (Abcam:ab1220)


title: ChIP-seq_RS_H3K4me2_Rnf8-KO

description: Wardrobe#: 475

value: Rabbit anti-H3K4me2 (Millipore:07-030)


title: ChIP-seq_RS_H3K9me2_2

description: Wardrobe#: 472


title: ChIP-seq_RS_H4K16ac

description: Wardrobe#: 299

value: Rabbit anti-H4K16ac (Millipore 07-762)


title: ΔCT_stage13_gammaH2Av_ChIP_1

description:
ΔCT follicle cell stage13 gammaH2Av ChIP
processed data file: deltaCTst13_ChIP_SW_log2_Aver.txt
deltaCT_13_gammaH2Av_ChIP_1


title: ChIP-seq_RS_H3K27me3_3

description: Wardrobe#: 658

value: Mouse anti-H3K27me3 (Active Motif:39535)


title: ChIP-seq_RS_H3K4me2_2

description: Wardrobe#: 474


title: ChIP-seq_PS_Kcr_Rnf8-KO

description: Wardrobe#: 554

value: Isolated pachytene spermatocytes

value: Rabbit anti-crotonllysine (PTM Biolabs:#PTM-501)


title: ChIP-seq_PS_H4K16ac

description: Wardrobe#: 301


title: ChIP-seq_RS_H3K4me2_1

description: Wardrobe#: 267


title: ChIP-seq_PS_Kcr

description: Wardrobe#: 303


title: ChIP-seq_PS_H4K8ac

description: Wardrobe#: 336


title: ChIP-seq_GS_H4K16ac_1

description: Wardrobe#: 339

value: CD1 x C57BL/6

value: Cultured germline stem cells


title: ChIP-seq_GS_H4K16ac_2

description: Wardrobe#: 473


title: ChIP-seq_PS_H3K27me3_2

description: Wardrobe#: 647

value: Mouse anti-H3K27me3 (Abcam:ab6002)


title: OrR_stage10B_gammaH2Av_ChIP_2

description:
OrR follicle cell stage10B gammaH2Av ChIP
processed data file: WTst10B_ChIP_SW_log2_Aver.txt
WT_10B_gammaH2Av_ChIP_2

value: OregonR


title: ChIP-seq_PS_H3K9me2_2

description: Wardrobe#: 471


title: OrR_stage10B_gammaH2Av_ChIP_1

description:
OrR follicle cell stage10B gammaH2Av ChIP
processed data file: WTst10B_ChIP_SW_log2_Aver.txt
WT_10B_gammaH2Av_ChIP_1

value: egg chamber


title: ChIP-seq_GS_H4K8ac

description: Wardrobe#: 338


title: ChIP-seq_PS_H3K9me2_1

description: Wardrobe#: 302


title: ChIP-seq_PS_H3K4me2_Rnf8-KO

description: Wardrobe#: 553


title: ChIP-seq_GS_Kcr

description: Wardrobe#: 335


title: ChIP-seq_GS_H3K9me2_2

description: Wardrobe#: 470


title: ChIP-seq_GS_H3K27me3_1

description: Wardrobe#: 212


title: ChIP-seq_GS_H3K27me3_2

description: Wardrobe#: 555


title: ChIP-seq_GS_H3K4me3

description: Wardrobe#: 556

value: Rabbit anti-H3K4me3 (Cell Signaling:#9751)


title: ChIP-seq_PS_H3K4me2

description: Wardrobe#: 341


title: Smolt_Female_17D52

city: Davis

first: Melinda

last: Baerwald

address: 1 Shields Avenue

institute: University of California-Davis

description: Processed data shows differentially methylated cytosines (DMCs) and differentially methylated regions (DMRs) when aligning reads to the O. mykiss reference genomes (Miller and French)

data_processing:
Illumina CASAVA 1.8.0 used for basecalling
Trim Galore! used to remove adapter sequences and low quality bases from reads (-rrbs option)
Bismark used to map reads onto bisulfite converted reference O. mykiss genomes.  Bismark's default parameters were used and only two non-bisulfite mismatches were allowed per read.
methylKit R package used to normalize reads between samples and identify differentially methylated cytosines (DMCs) between migrant and resident groups (default parameters used).
eDMR R package used to identify differentially methylated regions (DMRs) between migrant and resident groups (default parameters used).
Genome_build: Two reference genomes were used since O. mykiss has only been recently sequenced and neither genome is well assembled. Details about one (herein termed the O. mykiss French genome) are available in a publication (Berthelot et al., 2014, Nature Communications) and the genome sequence is in the European Nucleotide Archive under the study PRJEB4421. The other genome draft (herein termed the O. mykiss Miller genome) is available in an online repository (http://www.animalgenome.org/repository/aquaculture/).
Supplementary_files_format_and_content: Processed data files include outputs from: 1) methylKit (differentially methylated cytosines), 2) eDMR (differentially methylated regions); 3) gene annotations for DMRs. Much of the annotation occurred manually [e.g., BLAST searches from Miller genome; searching the Genomicus server (http://www.genomicus.biologie.ens.fr/genomicus-trout-01.01/) for gene names for the French genome].

organism: Oncorhynchus mykiss

source_name: caudal fin tissue

growth_protocol: Migratory steelhead (Clearwater) and resident rainbow trout (Oregon State University) double haploid clonal lines, which are each completely homozygous, were crossed to create F1 hybrids.  Gametes from an F1 male then underwent androgenesis, to create F2 progeny, each being homozygous across loci, but genetically different from their siblings due to meiotic recombination.  Doubled haploids were produced in October and reared for ~3 years at the Washington State University research hatchery. Embryos were maintained in recirculating stack egg incubators at a constant 11° until complete yolk absorption. Fish were then transferred to 5-gallon tanks maintained in a recirculating system at similar densities. At 6 months of age, all fish were transferred to a single 200-gallon tank and were fed by automatic feeder, which was replenished once daily. Temperatures in the recirculating systems ranged from 11° to 18° throughout this study.

extract_protocol:
DNA was freshly extracted from caudal fin tissue using the Qiagen DNeasy kit according to the manufacturer's suggested protocol.
RRBS libraries were constructed using a previously published protocol (Boyle et al. 2012, Genome Biology). Briefly, 100 ng genomic DNA was digested using the restriction enzyme MspI. DNA fragments were end-repaired, A-tailed, and ligated to the methylated Illumina TruSeq adapters. Ten samples were multiplexed per library with each sample ligated to unique barcoded Illumina adapters to distinguish samples. Life history types and sex ratios were primarily equalized across libraries. Bisulfite conversion was conducted using Qiagen's EpiTect Bisulfite kit, following the protocol for formalin-fixed paraffin-embedded samples. After two rounds of bisulfite conversion, the DNA was amplified using Illumina TruSeq primers. The optimal number of PCR cycles, in this case 18, was determined empirically by comparing PCR products on a 5% Metaphor agarose gel for 10, 13, 16, 19, and 22 total cycles. Library size selection was gel-free and occurred by using AMPure XP beads as suggested by Boyle et al. 2012. Library DNA quantity was assessed with the Qubit fluorometer and quality was assessed with a 5% MetaPhor agarose gel (Lonza). All sequencing was performed by the Vincent J. Coates Genomics Sequencing Laboratory at the University of California, Berkeley. After a quantitative PCR quality control check, the Illumina HiSeq 2000 platform was used to sequence 50 bp single-end reads for all 20 samples. The mRRBS protocol was repeated for nine samples with fewer than 10 million reads after quality filtering. Read length was increased for these samples up to 100 bp single-end reads. Two of the smolt (migrant) samples had insufficient reads (<10 million reads) and were removed from subsequent analysis. Therefore, 8 smolts were compared to 10 residents.

treatment_protocol: When individuals reached age 1+ or 2+ years old (the temporal period when smoltification is likely to occur), multiple phenotypes strongly associated with smoltification (and thereby migration) were measured after fish were anesthetized with clove oil. These included body morphology, skin reflectance, gill Na+/K+ ATPase activity, body condition factor, and growth rates. Measurements from these phenotypes were compiled together to create a binary phenotype: migrant or resident trout.

value: caudal fin

tag: migration-related phenotype

value: Smolt

tag: Sex

value: Female


title: Smolt_Female_0307

tag: tissue type


title: Smolt_Male_1110

value: Male


title: Smolt_Male_3944


title: Smolt_Female_3C59


title: Smolt_Female_2615


title: Smolt_Female_1478


title: Resident_Female_3F1D


title: Resident_Male_264D

value: Resident


title: Resident_Male_7443


title: Resident_Male_0931


title: Resident_Male_237F


title: Resident_Male_3F40


title: Resident_Female_354C


title: Resident_Female_1B1D


title: Smolt_Male_3B14


title: Resident_Female_0D10


title: ChIP-seq_GS_H3K9me2_1

description: Wardrobe#: 340

tag: genotype

value: Wild-type

value: Mouse anti-H3K9me2 (Abcam:ab1220)


title: Resident_Female_2C11


title: ChIP-seq_GS_H3K4me2

description: Wardrobe#: 337

value: Rabbit anti-H3K4me2 (Millipore:07-030)


title: ChIP-seq_GS_RNAPII

description: Wardrobe#: 277

source_name: genomic DNA, Cross link

value: Mouse anti-RNA Polymerase II, CTD clone 8WG16 (Millipore:05-952)


title: singles-BJ-well-93

status: Public on Jun 17 2015

first: Jason

middle: Daniel

last: Buenrostro

address: 415 Main Street

institute: Broad Institute

description: processed data file: single-BJ.peaks.bed

data_processing:
library strategy: Single-cell ATAC-seq (scATAC-seq)
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 or mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools. Reads were subsequently filtered for alignment quality of >Q30 and were required to be properly paired. Reads mapping to the mitochondria, unmapped contigs and chromosome Y were removed and not considered.
We used MACS2 to call all reported ATAC-seq peaks. MACS2 was used with the following parameters (--nomodel --nolambda --keep-dup all --call-summits). Peaks were filtered using the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and a custom blacklist, designed to remove high-signal causing repeats and mitochondrial homologues. For all subsequent analysis we discarded peaks falling within these regions. Although we saw little effect on calculations of variability, in the case of K562 data, peaks were additionally filtered to exclude copy number amplifications. Using the filtered peak set, peak summits were extended +/-250 bps. The top 50,000 non-overlapping 500 bp summits are available here and were used for all downstream analysis.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Bam files across single-cells representing identical biological conditions have been merged. Reads pertaining to individual cells can be identified by their unique RGID tag corresponding to each assayed well. Bed files represent 500 bp peak summits as described above.

source_name: singles-BJ

growth_protocol: Human BJ fibroblasts (ATCC) were maintained in Eagle’s minimum essential medium (EMEM, ATCC) supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol:
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips. Cells were permeabilized and accessible fragments were captured using 20 µL of Tn5 transposition mix (1.5x TD buffer, 1.5 µL transposease (Nextera DNA Sample Prep Kit, Illumina), 1x C1 Loading Reagent with low salt (Fluidigm), and 0.15% NP40) at 30 minutes at 37°C.
In a 96-well plate, 10 µL of harvested libraries were amplified in 50 µL PCR for an additional 14 cycles (1.25 µM custom Nextera dual-index PCR primers (Supplementary Table 1) in 1x NEBnext High-Fidelity PCR Master Mix) using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. The PCR products were pooled creating a final volume of ~4.8 mL. The pooled library was purified on a single MinElute PCR purification column (Qiagen) yielding libraries at an approximate concentration of ~1 µM. Libraries were quantified using qPCR prior to sequencing.

tag: cell line

value: BJ

value: fibroblasts

tag: treated with

value: none (untreated)


title: singles-BJ-well-96

tag: cell type


title: singles-BJ-well-90


title: singles-BJ-well-92


title: singles-BJ-well-94


title: singles-BJ-well-95


title: singles-BJ-well-91


title: singles-BJ-well-88


title: singles-BJ-well-80


title: singles-BJ-well-86


title: singles-BJ-well-83


title: singles-BJ-well-87


title: singles-BJ-well-82


title: singles-BJ-well-89


title: singles-BJ-well-85


title: singles-BJ-well-81


title: singles-BJ-well-84


title: singles-BJ-well-77


title: singles-BJ-well-75


title: singles-BJ-well-74


title: singles-BJ-well-79


title: singles-BJ-well-71


title: singles-BJ-well-70


title: singles-BJ-well-73


title: singles-BJ-well-72


title: singles-BJ-well-78


title: singles-BJ-well-64


title: singles-BJ-well-62


title: singles-BJ-well-68


title: singles-BJ-well-66


title: singles-BJ-well-63


title: singles-BJ-well-69


title: singles-BJ-well-65


title: shCtcf_RNAseq

description: s12_mus/ reads

source_name: immortalized fibroblast

value: CAST/Ei x 129/Sv/Jae

value: Xi GFP tail-tip fibroblast

tag: antibody

tag: genetic manipulation

value: Stable shRNA knockdown of Ctcf


title: singles-BJ-well-61


title: singles-BJ-well-67


title: singles-BJ-well-60


title: singles-BJ-well-59


title: singles-BJ-well-58


title: singles-BJ-well-56


title: singles-BJ-well-76


title: singles-BJ-well-51


title: singles-BJ-well-53


title: singles-BJ-well-55


title: singles-BJ-well-52


title: singles-BJ-well-54


title: singles-BJ-well-49


title: singles-BJ-well-45


title: singles-BJ-well-50


title: singles-BJ-well-43


title: singles-BJ-well-48


title: singles-BJ-well-44


title: singles-BJ-well-42


title: singles-BJ-well-46


title: singles-BJ-well-47


title: singles-BJ-well-40


title: singles-BJ-well-39


title: singles-BJ-well-36


title: singles-BJ-well-32


title: singles-BJ-well-33


title: singles-BJ-well-38


title: singles-BJ-well-41


title: singles-BJ-well-30


title: singles-BJ-well-31


title: singles-BJ-well-29


title: singles-BJ-well-27


title: singles-BJ-well-28


title: singles-BJ-well-26


title: singles-BJ-well-35


title: singles-BJ-well-25


title: singles-BJ-well-24


title: singles-BJ-well-22


title: singles-BJ-well-21


title: singles-BJ-well-37


title: singles-BJ-well-34


title: singles-BJ-well-17


title: singles-BJ-well-14


title: singles-BJ-well-11


title: singles-BJ-well-20


title: singles-BJ-well-15


title: singles-BJ-well-13


title: singles-BJ-well-18


title: singles-BJ-well-8


title: singles-BJ-well-12


title: singles-BJ-well-10


title: singles-BJ-well-16


title: singles-BJ-well-7


title: singles-BJ-well-6


title: singles-BJ-well-23


title: singles-BJ-well-4


title: singles-BJ-well-5


title: singles-BJ-well-3


title: singles-BJ-well-2


title: singles-BJ-well-19


title: singles-BJ-well-57


title: singles-BJ-well-1


title: singles-TF1-well-95

description: processed data file: single-TF1.peaks.bed

growth_protocol: The erythroleukemia cell line TF-1 (kind gift from the Majeti lab, Stanford) was maintained in RPMI 1640 with 10% FBS, 1% Pen/Strep  and 2 ng/mL rhGM-CSF (Peprotech).

value: erythroleukemia cell line


title: singles-TF1-well-90


title: singles-TF1-well-92


title: singles-TF1-well-89


title: singles-TF1-well-91


title: singles-TF1-well-93


title: singles-TF1-well-94


title: singles-TF1-well-96


title: singles-BJ-well-9


title: singles-TF1-well-86


title: singles-TF1-well-87


title: singles-TF1-well-83


title: singles-TF1-well-81


title: singles-TF1-well-82


title: singles-TF1-well-80


title: singles-TF1-well-84


title: singles-TF1-well-78


title: singles-TF1-well-79


title: singles-TF1-well-75


title: singles-TF1-well-77


title: singles-TF1-well-74


title: singles-TF1-well-76


title: singles-TF1-well-73


title: singles-TF1-well-72


title: singles-TF1-well-71


title: singles-TF1-well-70


title: singles-TF1-well-69


title: singles-TF1-well-68


title: singles-TF1-well-85


title: singles-TF1-well-65


title: singles-TF1-well-62


title: singles-TF1-well-67


title: singles-TF1-well-66


title: singles-TF1-well-59


title: singles-TF1-well-60


title: singles-TF1-well-57


title: singles-TF1-well-63


title: singles-TF1-well-64


title: singles-TF1-well-58


title: singles-TF1-well-53


title: singles-TF1-well-50


title: singles-TF1-well-51


title: singles-TF1-well-52


title: singles-TF1-well-55


title: singles-TF1-well-54


title: singles-TF1-well-88


title: singles-TF1-well-46


title: singles-TF1-well-49


title: singles-TF1-well-47


title: singles-TF1-well-48


title: singles-TF1-well-61


title: singles-TF1-well-45


title: singles-TF1-well-44


title: singles-TF1-well-43


title: singles-TF1-well-42


title: singles-TF1-well-41


title: singles-TF1-well-39


title: singles-TF1-well-40


title: singles-TF1-well-38


title: singles-TF1-well-36


title: singles-TF1-well-35


title: singles-TF1-well-32


title: singles-TF1-well-33


title: singles-TF1-well-34


title: singles-TF1-well-56


title: singles-TF1-well-37


title: singles-TF1-well-29


title: singles-TF1-well-30


title: singles-TF1-well-31


title: singles-TF1-well-27


title: singles-TF1-well-22


title: singles-TF1-well-25


title: singles-TF1-well-23


title: singles-TF1-well-24


title: singles-TF1-well-20


title: singles-TF1-well-19


title: singles-TF1-well-15


title: singles-TF1-well-14


title: singles-TF1-well-18


title: singles-TF1-well-17


title: singles-TF1-well-13


title: singles-TF1-well-12


title: singles-TF1-well-11


title: singles-TF1-well-8


title: singles-TF1-well-9


title: singles-TF1-well-7


title: singles-TF1-well-4


title: singles-TF1-well-2


title: singles-TF1-well-6


title: singles-TF1-well-26


title: singles-TF1-well-5


title: singles-TF1-well-3


title: singles-TF1-well-1


title: singles-K562-JNKi-well-95

description: processed data file: single-K562.peaks.bed

growth_protocol: K562 (ATCC) chronic myeloid leukemia cells were maintained in Iscove’s modified Dulbecco’s  medium (IMDM) containing 10% FBS (HyClone, Thermo Scientific) and 1% Penicillin Streptomycin (Pen/Strep). K562 cells were treated with 10 µM JNK inhibitor VIII (CAS 894804-07-0, Calbiochem) for 24 h.

value: chronic myeloid leukemia cells

value: a Jun kinase inhibitor


title: singles-TF1-well-21


title: singles-K562-JNKi-well-96


title: singles-K562-JNKi-well-93


title: singles-K562-JNKi-well-94


title: singles-TF1-well-16


title: singles-K562-JNKi-well-91


title: singles-K562-JNKi-well-89


title: singles-TF1-well-28


title: singles-K562-JNKi-well-86


title: singles-TF1-well-10


title: singles-K562-JNKi-well-83


title: singles-K562-JNKi-well-81


title: singles-K562-JNKi-well-82


title: singles-K562-JNKi-well-80


title: singles-K562-JNKi-well-79


title: singles-K562-JNKi-well-77


title: singles-K562-JNKi-well-78


title: singles-K562-JNKi-well-73


title: singles-K562-JNKi-well-72


title: singles-K562-JNKi-well-75


title: singles-K562-JNKi-well-76


title: singles-K562-JNKi-well-74


title: singles-K562-JNKi-well-70


title: singles-K562-JNKi-well-71


title: singles-K562-JNKi-well-69


title: singles-K562-JNKi-well-68


title: singles-K562-JNKi-well-92


title: singles-K562-JNKi-well-90


title: singles-K562-JNKi-well-65


title: singles-K562-JNKi-well-67


title: singles-K562-JNKi-well-87


title: singles-K562-JNKi-well-66


title: singles-K562-JNKi-well-88


title: singles-K562-JNKi-well-64


title: singles-K562-JNKi-well-85


title: singles-K562-JNKi-well-84


title: singles-K562-JNKi-well-62


title: singles-K562-JNKi-well-63


title: singles-K562-JNKi-well-61


title: singles-K562-JNKi-well-60


title: singles-K562-JNKi-well-59


title: singles-K562-JNKi-well-58


title: singles-K562-JNKi-well-57


title: singles-K562-JNKi-well-55


title: singles-K562-JNKi-well-54


title: singles-K562-JNKi-well-51


title: singles-K562-JNKi-well-53


title: singles-K562-JNKi-well-50


title: singles-K562-JNKi-well-49


title: singles-K562-JNKi-well-48


title: singles-K562-JNKi-well-43


title: singles-K562-JNKi-well-47


title: singles-K562-JNKi-well-46


title: singles-K562-JNKi-well-45


title: singles-K562-JNKi-well-44


title: singles-K562-JNKi-well-40


title: singles-K562-JNKi-well-38


title: singles-K562-JNKi-well-41


title: singles-K562-JNKi-well-36


title: singles-K562-JNKi-well-37


title: singles-K562-JNKi-well-35


title: singles-K562-JNKi-well-33


title: singles-K562-JNKi-well-39


title: singles-K562-JNKi-well-32


title: singles-K562-JNKi-well-31


title: singles-K562-JNKi-well-29


title: singles-K562-JNKi-well-42


title: singles-K562-JNKi-well-34


title: singles-K562-JNKi-well-30


title: singles-K562-JNKi-well-28


title: singles-K562-JNKi-well-56


title: singles-K562-JNKi-well-27


title: singles-K562-JNKi-well-26


title: singles-K562-JNKi-well-52


title: singles-K562-JNKi-well-23


title: singles-K562-JNKi-well-25


title: singles-K562-JNKi-well-24


title: singles-K562-JNKi-well-22


title: singles-K562-JNKi-well-20


title: singles-K562-JNKi-well-19


title: singles-K562-JNKi-well-15


title: singles-K562-JNKi-well-17


title: singles-K562-JNKi-well-13


title: singles-K562-JNKi-well-9


title: singles-K562-JNKi-well-16


title: singles-K562-JNKi-well-12


title: singles-K562-JNKi-well-10


title: singles-K562-JNKi-well-14


title: singles-K562-JNKi-well-6


title: singles-K562-JNKi-well-8


title: singles-K562-JNKi-well-4


title: singles-K562-JNKi-well-7


title: singles-K562-JNKi-well-5


title: singles-K562-JNKi-well-21


title: singles-K562-JNKi-well-3


title: singles-K562-JNKi-well-2


title: singles-K562-Imat1hr-well-96

growth_protocol: K562 (ATCC) chronic myeloid leukemia cells were maintained in Iscove’s modified Dulbecco’s  medium (IMDM) containing 10% FBS (HyClone, Thermo Scientific) and 1% Penicillin Streptomycin (Pen/Strep). K562 cells were treated with 1 µM Imatinib (Gleevec, Novartis) for 1 h.

value: Imatinib for 1 hour


title: singles-K562-Imat1hr-well-95


title: singles-K562-Imat1hr-well-90


title: singles-K562-JNKi-well-1


title: singles-K562-Imat1hr-well-92


title: singles-K562-Imat1hr-well-91


title: singles-K562-Imat1hr-well-89


title: singles-K562-JNKi-well-18


title: singles-K562-JNKi-well-11


title: singles-K562-Imat1hr-well-87


title: singles-K562-Imat1hr-well-86


title: singles-K562-Imat1hr-well-85


title: singles-K562-Imat1hr-well-94


title: singles-K562-Imat1hr-well-78


title: singles-K562-Imat1hr-well-82


title: singles-K562-Imat1hr-well-79


title: singles-K562-Imat1hr-well-76


title: singles-K562-Imat1hr-well-80


title: singles-K562-Imat1hr-well-81


title: singles-K562-Imat1hr-well-93


title: singles-K562-Imat1hr-well-74


title: singles-K562-Imat1hr-well-77


title: singles-K562-Imat1hr-well-73


title: singles-K562-Imat1hr-well-72


title: singles-K562-Imat1hr-well-70


title: singles-K562-Imat1hr-well-69


title: singles-K562-Imat1hr-well-75


title: singles-K562-Imat1hr-well-66


title: singles-K562-Imat1hr-well-68


title: singles-K562-Imat1hr-well-64


title: singles-K562-Imat1hr-well-71


title: singles-K562-Imat1hr-well-65


title: singles-K562-Imat1hr-well-67


title: singles-K562-Imat1hr-well-88


title: singles-K562-Imat1hr-well-63


title: singles-K562-Imat1hr-well-62


title: singles-K562-Imat1hr-well-84


title: singles-K562-Imat1hr-well-61


title: singles-K562-Imat1hr-well-59


title: singles-K562-Imat1hr-well-83


title: singles-K562-Imat1hr-well-60


title: singles-K562-Imat1hr-well-58


title: singles-K562-Imat1hr-well-57


title: singles-K562-Imat1hr-well-56


title: singles-K562-Imat1hr-well-52


title: singles-K562-Imat1hr-well-53


title: singles-K562-Imat1hr-well-55


title: singles-K562-Imat1hr-well-54


title: singles-K562-Imat1hr-well-48


title: singles-K562-Imat1hr-well-51


title: singles-K562-Imat1hr-well-49


title: singles-K562-Imat1hr-well-45


title: singles-K562-Imat1hr-well-46


title: singles-K562-Imat1hr-well-41


title: singles-K562-Imat1hr-well-44


title: singles-K562-Imat1hr-well-39


title: singles-K562-Imat1hr-well-40


title: singles-K562-Imat1hr-well-50


title: singles-K562-Imat1hr-well-43


title: singles-K562-Imat1hr-well-42


title: singles-K562-Imat1hr-well-36


title: singles-K562-Imat1hr-well-37


title: singles-K562-Imat1hr-well-34


title: singles-K562-Imat1hr-well-38


title: singles-K562-Imat1hr-well-35


title: singles-K562-Imat1hr-well-31


title: singles-K562-Imat1hr-well-30


title: singles-K562-Imat1hr-well-32


title: singles-K562-Imat1hr-well-33


title: singles-K562-Imat1hr-well-29


title: singles-K562-Imat1hr-well-28


title: singles-K562-Imat1hr-well-47


title: singles-K562-Imat1hr-well-26


title: singles-K562-Imat1hr-well-25


title: singles-K562-Imat1hr-well-24


title: singles-K562-Imat1hr-well-21


title: singles-K562-Imat1hr-well-22


title: singles-K562-Imat1hr-well-23


title: singles-K562-Imat1hr-well-20


title: singles-K562-Imat1hr-well-27


title: singles-K562-Imat1hr-well-19


title: singles-K562-Imat1hr-well-17


title: singles-K562-Imat1hr-well-14


title: singles-K562-Imat1hr-well-16


title: singles-K562-Imat1hr-well-10


title: singles-K562-Imat1hr-well-9


title: singles-K562-Imat1hr-well-12


title: singles-K562-Imat1hr-well-11


title: singles-K562-Imat1hr-well-15


title: singles-K562-Imat1hr-well-18


title: singles-K562-Imat1hr-well-5


title: singles-K562-Imat1hr-well-4


title: singles-K562-Imat1hr-well-2


title: singles-K562-CDKi-well-96

growth_protocol: K562 (ATCC) chronic myeloid leukemia cells were maintained in Iscove’s modified Dulbecco’s  medium (IMDM) containing 10% FBS (HyClone, Thermo Scientific) and 1% Penicillin Streptomycin (Pen/Strep). K562 cells were treated with 1 µM CDK4/6 inhibitor (PD 0332991, Pfizer) for 24 h.

value: a cell cycle inhibitor


title: singles-K562-Imat1hr-well-1


title: singles-K562-Imat1hr-well-6


title: singles-K562-Imat1hr-well-7


title: singles-K562-Imat1hr-well-8


title: singles-K562-CDKi-well-92


title: singles-K562-CDKi-well-93


title: singles-K562-CDKi-well-91


title: singles-K562-Imat1hr-well-3


title: singles-K562-CDKi-well-89


title: singles-K562-CDKi-well-94


title: singles-K562-CDKi-well-88


title: singles-K562-Imat1hr-well-13