title: EcoRV_restriction_enzyme

first: Giovanni

last: Marsico

address: Robinson Way

institute: CRUK Cambridge Institute

description: BREAk-seq extracted DNA

data_processing:
Library strategy: Break-Seq
fastq files containing sequencing reads were pre-processed to remove the Illumina adapters and to trim for low quality tails by using trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
reads were aligned to the human reference genome (hg19) using the bwa mem aligner (http://sourceforge.net/projects/bio-bwa/files/) and cleaned for low quality alignments (mapQ < 10) using samtools (http://samtools.sourceforge.net)
Duplicates were identified using picard tools (https://github.com/broadinstitute/picard/) and removed. Only reads from read 1, which are proximal to the break site, are then retained for the downstream analysis and shown in the bedGraph coverage plots.
Specific for the BLESS libraries: during adapter trimming, the BLESS linker sequences are trimmed (TCGAGGTAGTA and TCGAGACGACG for proximal and distal linkers, respectively), and only read pairs showing both linkers are retained. Trimmed fastq files then undergo the same processing pipeline as for BREAk-seq libraries. At the end, only sequencing reads that originally contained the proximal linker (they could be from either read 1 or read 2) are retained for subsequent analysis and shown in the coverage plots
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph, TDF

growth_protocol: HeLa cells were cultured in DMEM (Sigma, D6429) supplemented with 10% FBS (Gibco, U120D). U2OS AID-DIvA cells were cultured in DMEM supplemented with 10% FBS and 800μg/mL G418 (Gibco, 10131). To induce nuclear localisation of AsiSI, AID-DIvA cells were treated with 300 nM 4OHT (Sigma, H7904) for 4 hours. Primary keratinocytes (Gibco, A13401) were cultured in EpiLife Medium (Gibco, M-EPI-500-CA) supplemented with human keratinocyte growth supplement (Gibco, S-001-5) and were detached using accutase (Sigma, A6964).

extract_protocol:
The BLESS extraction protocol was implemented as published in Crosetto et al., 2013 (http://breakome.utmb.edu).
The TruSeq Nano DNA Library Prep Kit (Illumina, FC-121-4001) was used to generate libraries for sequencing (size selection for 550bps). The BREAk-seq protocol was implemented as described in the Methods sectin of the associated paper (Lensing et al., 2016).

value: HeLa


title: input Sync-TRAP WT P12 CB3

status: Public on Jul 18 2016

type: SRA

city: Evanston

first: Yue

last: Yang

state: IL

address: 2200 Campus Dr

department: Neurobiology

country: USA

institute: Northwestern University

library_source: transcriptomic

data_processing:
Reads were aligned to mm9 using bowtie. The number of reads in each sample was normalized by library size and ChIP-Seq datasets were input subtracted. Peak calling was performed using the Sicer program.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated by merging replicate bam files and using bedtools and bedGraphToBigWig. Total reads were normalized to 10 million reads.
Supplementary_files_format_and_content: Bed files were generated by first calling H3K4me3 or H3K27ac peaks using Sicer. H3K4me3 peaks that overlapped with Refseq TSS were considered H3K4me3-bound TSS. H3K27ac peaks that were >1000bp away from Refseq TSS and did not overlap with H3K4me3 peaks were considered H3K27ac-bound enhancers.
Supplementary_files_format_and_content: Txt files are a tabular matrix file generated from RNA-seq datasets. Gene and exon level differential expression was estimated through pair-wise negative binomial tests with EdgeR and DEXSeq, respectively. The Benjamini-Hochberg false discovery rate (FDR) was calculated for all genes. Significantly differentially expressed genes (FDR < 0.05) are indicated.

molecule: total RNA

organism: Mus musculus

source_name: cerebellum

extract_protocol:
For ChIP, lysates were purified from sonicated nuclei and histone-DNA complexes were isolated with the indicated antibodies. Total RNA was harvested with Trizol. For Sync-TRAP, ribosome-bound RNA were purified and amplified with Ovation RNA-Seq System V2 (NuGEN)
ChIP-Seq libraries were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit and RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: WT

tag: developmental stage

value: P12, 6 days post-electroporation

tag: tissue

value: cerebellum


title: IP Sync-TRAP cKO P12 CB1

description: Ribosome-bound RNA

value: Chd4 cKO


title: input Sync-TRAP cKO P12 CB3


title: IP Sync-TRAP WT P12 CB3

description: Ribosome-bound RNA


title: MDA-MB453_PIAS1_R1881_rep1

city: Kuopio

first: Sari

last: Toropainen

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description:
Chromatin IP against PIAS1 in MDA-MB453 cells
processed data file: MDA_PIAS1_R1881_rep1+2_peaks.bed

library_source: genomic

data_processing:
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
Reads were aligned against human genome hg19 with Bowtie software (0.12.7) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19.
Individual background was generated for each AR and PIAS1 ChIP-seq sample. The read ration of IgG/ChIP-seq sample was set to same for all ChIP-seq samples by randomly removing IgG reads.
The peak detection was done by using HOMER software (4.1). Binding sites were determined with findPeaks command (using -factor mode and individual IgG samples as a background).
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed files contain information of the statistically significant peaks (found in both replicates).

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: The cells were grown in DMEM supplemented with 10% (v/v) fetal bovine serum (FBS), 25 U/ml penicillin and 25 mg/ml streptomycin in a 5% CO2 atmosphere at 37 C.

extract_protocol:
Lysates were derived from sonicated nuclei and AR- and PIAS1-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocol, as utilized at the Functional Genomics Unit, Helsinki, Finland.

treatment_protocol: ChIP-seq samples transfected with siNON or siPIAS1 were seeded onto plates in DMEM supplemented with 5% charcoal-stripped FBS. After four days of plating the cells, the cells were exposed to R1881 (10 nM) for 2 h.

tag: origin

value: Metastatic carcinoma of the breast

tag: cell line

value: MDA-MB453 breast cancer cell line

tag: treated with

value: 10 nM R1881 for 2hrs

tag: chip antibody

value: PIAS1 (Abcam 77231)


title: cKO mRNA P27-28 CB3


title: WT_GAF

status: Public on Jul 19 2016

city: Nankang, Taipei

first: Der-Hwa

last: Huang

state: Taiwan

address: 128, Sec2, Academia Rd.

department: Insititute of Molecular Biology

country: Taiwan

institute: Academia Sinica

data_processing:
Raw sequences were aligned to Drosophila Release 5.47 genome sequence by using mapping software CLC Genomics Workbench vision 7
Peaks of ChIP-enriched sequences were identified by using PICS (Probabilistic Inference for ChIP-Seq) with mapping software Avadis-NGS vision 1.2
Reads were adjusted by using RPKM (reads per kilobase per million) for each data sets
Genome_build: Dmel_Release_5.4
Supplementary_files_format_and_content: text file with called peaks.

organism: Drosophila melanogaster

source_name: Or-R

growth_protocol: Fly grew at 25 degree C, harvest at 3rd instar stage

extract_protocol:
Lysates were prepared from sonicated nuclei and GAF-DNA complexes were isolated with antibody.  The GAF antibodies were custom-made by this lab while anti-RNA Pol II antibodies were provided by the lab of Dr. John T. Lis.
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A’ bases were added to the 3’ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments.  This fragment range corresponds to a ChIP fragment range of about 200 -300bp. Size selected fragments were PCR amplified for 12 cycles . Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment.

value: wildtype

value: Imaginal discs and salivary glands

value: 3rd instar stage

tag: antibody

value: anti-GAF


title: WT mRNA P27-28 CB3


title: input Sync-TRAP cKO P12 CB2


title: WT mRNA P27-28 CB4


title: rotarod mRNA P27-28 CB4


title: input Sync-TRAP WT P12 CB1


title: cKO mRNA P27-28 CB2


title: input Sync-TRAP WT P12 CB2


title: rotarod mRNA P27-28 CB1


title: cKO mRNA P27-28 CB4


title: MDA-MB453_IgG

description: Chromatin IP against IgG in MDA-MB453 cells


title: rest mRNA P27-28 CB3


title: WT mRNA P27-28 CB1


title: rest mRNA P27-28 CB2


title: H3K27me3 cKO P22 CB2

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: cKO mRNA P27-28 CB1


title: WT mRNA P27-28 CB2


title: rotarod mRNA P27-28 CB3


title: H3K27me3 WT P22 CB2


title: HEK_GIBCO_4

city: Cambridge

country: United Kingdom

description: RNA-Seq

data_processing:
none proivided by submitter
Supplementary_files_format_and_content: raw counts

molecule: polyA RNA

source_name: HEK

extract_protocol: none proivided by submitter

tag: cell type

value: HEK Gibco


title: HEK_GIBCO_1

description: RNA-Seq


title: rotarod mRNA P27-28 CB2


title: NHEK_bless_seq_rep2

description: BLESS extracted DNA

value: NHEK


title: rest mRNA P27-28 CB1


title: input cKO P22 CB


title: rest mRNA P27-28 CB4


title: input WT P22 CB


title: H3 WT P22 CB2

value: active motif


title: AID-DlvA_AsiSI_restriction_enzyme

description: BREAk-seq extracted DNA

value: U2OS AID-DlvA


title: H3K27me3 cKO P22 CB1


title: H2A.z-ac WT P22 CB

value: WT


title: H2A.z-ac cKO P22 CB


title: U-87_DAC_24-4-15

city: Haifa

first: Arie

last: Admon

state: select a state

address: Kiryat Technion- Emerson building

department: Department of Biology

country: Israel

institute: Technion - Israel Institute of Technology, Haifa, Israel

data_processing:
The experiment was performed by Illumina HiSeq 2500 in 50 base pair single read mode
The RNA-seq reads were mapped to the GRCh38 genome using TopHat version 2.0.13
Only uniquely mapped reads were counted in the analysis, using the HTSeq-count package version 0.6.1 with ‘union’ mode
The counts normalization and the differential expression analysis were done using the DESeq2 package version 1.8.1
Genome_build: GRCh38 genome
Supplementary_files_format_and_content: Excel file includes normalized counts

source_name: Glioblastoma cultured cells

growth_protocol: Three human Glioblastoma cell lines, U-87, T98G and LNT-229 (obtained from the ATCC) were maintained in DMEM supplemented with 10% FBS, 1% L-glutamine, 1% Na-pyruvate, 0.1 mg/ml streptomycin and 100 μ/ml penicillin and 0.1% HEPES. The cells were kept in 5% CO2 humidified incubator at 37°C.

extract_protocol:
Total RNA was prepared from between 1 to 2*106 GBM cells, using the Total RNA Purification Plus kit (Norgen biotec) as per the kit instructions. The isolated total RNA was quantified using Qubit 2.0 machine (Invitrogen) before the sequencing library preparation. The mRNA population in each sample was enriched by removing ribosomal RNA (rRNA) using the Epicenter ScriptSeq Complete kit (human, Illumina) as per the kit instructions.
The experiment was performed by Illumina HiSeq 2500 in 50 base pair single read mode in the Technion Genome Center. The RNA-seq reads were mapped to the GRCh38 genome using TopHat version 2.0.13. Only uniquely mapped reads were counted in the analysis, using the HTSeq-count package version 0.6.1 with ‘union’ mode. The counts normalization and the differential expression analysis were done using the DESeq2 package version 1.8.1.

treatment_protocol: Cells were counted and plated in new 150 mm Petri dishes one day prior to the treatment. The following day, the media was removed and replaced with fresh medium with or without 1 μM of 5'-Aza-2'-deoxycytidine (Decitabine, Enco diagnostics, AdooQ bioscience). After incubation with Decitabine for 72 hours, the cells were harvested, counted and prepared for RNA sequencing.

value: Brain tumor cell line

tag: treatment

value: Cells following treatment with Decitabine


title: H3K27me3 WT P22 CB1

value: cerebellum


title: NHEK_break_seq_lower_input_rep1

description: BREAk-seq extracted DNA

data_processing:
Library strategy: Break-seq
fastq files containing sequencing reads were pre-processed to remove the Illumina adapters and to trim for low quality tails by using trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
reads were aligned to the human reference genome (hg19) using the bwa mem aligner (http://sourceforge.net/projects/bio-bwa/files/) and cleaned for low quality alignments (mapQ < 10) using samtools (http://samtools.sourceforge.net)
Duplicates were identified using picard tools (https://github.com/broadinstitute/picard/) and removed. Only reads from read 1, which are proximal to the break site, are then retained for the downstream analysis and shown in the bedGraph coverage plots.
Specific for the BLESS libraries: during adapter trimming, the BLESS linker sequences are trimmed (TCGAGGTAGTA and TCGAGACGACG for proximal and distal linkers, respectively), and only read pairs showing both linkers are retained. Trimmed fastq files then undergo the same processing pipeline as for BREAk-seq libraries. At the end, only sequencing reads that originally contained the proximal linker (they could be from either read 1 or read 2) are retained for subsequent analysis and shown in the coverage plots
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

value: HeLa


title: H2A.z cKO P22 CB2

value: Chd4 cKO


title: H3 cKO P22 CB1


title: HEK_GIBCO_3

description: RNA-Seq


title: Tumor  core 2

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 East Duarte Road

department: Department of Computational & Quantitative Medicine

institute: Beckman Research Institute of City of Hope, Center for Informatics

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for barcode sequence,  adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat (v1.3.1)  --max-insertion-length 10 --max-deletion-length 10 --segment-length 25
RPKM, Reads Per Kilobase of exon per Megabase of library size (Mortazavi et al. Nat Methods 2008) were estimated using Partek GS v.6.13.1017 based on  RefSeq Transcripts. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values (sample per column)

source_name: melanoma xenograft tumor

extract_protocol:
500ng RNA from each sample were used for polyadenylated RNA enrichment with oligh dT magnetic beads and the poly (A)RNA was fragmented with divalent cations under elevated temperature.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: area

value: core

tag: replicate


title: HEK_GIBCO_2

description: RNA-Seq


title: H3 cKO P22 CB2


title: Primed_WIBR1

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
MethylC-seq data was processed as described in Schultz et al. (Schultz et al., 2015) with some modifications.
Adapter sequence on MethylC-seq reads were trimmed using Cutadapt (version 1.2.1) (Martin, 2011).
Next, cytosines (Cs) in the trimmed reads were then computationally converted to thymines (Ts). The converted reads were mapped twice, to the forward strand of a converted Watson strand reference and the reversed strand of a converted Crick strand reference. A converted reference is created by replacing all cytosines with thymines (Watson strand) or by replacing all guanines with adenines (Crick strand). For mapping single-end reads, Bowtie 2 (version 2.2.5) (Langmead & Salzberg, 2012) was used along with default options. For aligning paired-end reads, bowtie 2 (version 2.2.5) was used with following options: “-k 2 -q --no-mixed --no-discordant --maxins 1000 --score-min L,0,-0.2”. Reads were mapped to hg19 reference genome. Any read that mapped to multiple locations was removed and one read from each starting location on each strand from each library was kept (i.e., clonal reads were removed).
To identify the sites showing evidence of methylation (i.e. methylated sites), we first counted the number of reads that supported methylation and the number of reads covering. Then, binomial test was performed on these counts to test whether the methylation counts are beyond bisulfite non-conversion events. In the test, the probability of success (methylation) in null distribution equal to the non-conversion rate, which was determined by computing the fraction of methylated reads in the lambda genome (spiked in during library construction). For samples (Naïve H9 and Primed H9 ESCs from Takashima et al. (Takashima et al., 2014)) without unmethylated DNA spiked in, the genome-wide non-CG methylation level was used as an estimate of non-conversion rate. The false discovery rate (FDR) was computed using Benjamini-Hochberg method and p-value cutoff was calculated given 1% FDR. Considering that the p-value distributions for each methylation context are different, this procedure was applied to each three nucleotide context independently (e.g., a p-value cutoff was calculated for CAC cytosines). AnnoJ browser (Wang et al., 2013) was used for visualization of MethylC-seq data.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are in tab-separated format. Each file has a header specifying chromosome, position, strand, methylation class, methylation count, total coverage, and methylation call. Each line corresponds the data of one cytosine in the genome. Chromosome, position and strand indicate the location of the cytosine. Methylation class stores its sequence context: cytosine and the followed two bases. Methylation count and total coverage are number of covered reads supporting methylation and the total number of covered reads, respectively. Methylation call is binary value indicating whether methylation level is significantly above noise level.

source_name: Primed human embryonic stem cells

extract_protocol:
Genomic DNA was extracted from human ESCs cells using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA).
2 µg of genomic DNA was spiked with 10 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 150-200 bp, followed by end repair and addition of a 3’ A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16˚C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (≤450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer’s instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 4 cycles of PCR with the following reaction composition: 25 µL of Kapa HiFi Hotstart Uracil+ Readymix (Kapa Biosystems, Woburn, MA) and 5 µl TruSeq PCR Primer Mix (Illumina) (50 µl final). The thermocycling parameters were: 95˚C 2 min, 98˚C 30 sec, then 4 cycles of 98˚C 15 sec, 60˚C 30 sec and 72˚C 4 min, ending with one 72˚C 10 min step. The reaction products were purified using AMPure XP beads. Up to two separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to two independent libraries from the same biological sample.

value: Primed human embryonic stem cells


title: NHEK_break_seq_rep2

description: BREAk-seq extracted DNA


title: Primed_WIBR3_GFP


title: Reprimed_WIBR3_4i


title: NHEK_break_seq_rep1

description: BREAk-seq extracted DNA


title: Chd4 cKO P22 CB2


title: mRNA-associated with polysome in hCINAP overexpressed cells

city: Beijing

first: Dongmei

last: Bai

address: Haidian

country: China

institute: Peking University

description:
Sample 4
Polysome-associated RNA

data_processing:
Raw reads with the sequence of adaptor, high content of unknown bases (more than 10%) and low quality reads were removed before data analysis.
The clean reads were mapped to the UCSC hg19 reference genome using the BWA software. And the clean reads was mapped to the reference genes by the Bowtie software.
Quantifitive analysis of the gene expression was performed with RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM and FPKM

growth_protocol: Cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) at 37°C with 5% CO2.

extract_protocol:
Total RNA extraction was performed with the Qiagen RNeasy KIT. For the polysome RNA-seq, RNA associated with monosome or polysome was precipitated with 2 volumes of 8M guanidine-HCl and 3 volumes of 99% ethanol at -20°C overnight. For extraction of the RNA elutation, using the Qiagen RNeasy KIT.
The RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3′-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification. The integrity and concentration of the library were evaluated by Agilent Technologies 2100 Bioanalyzer and ABI StepOnePlusReal-Time PCR System, respectively.

treatment_protocol: MCF7 cells were transfected with lentivirus expressing GFP-control or GFP-hCINAP.

value: human breast adenocarcinoma cell line

tag: overexpresson

value: Overexpression of GFP-hCINAP


title: transcriptional profile of control cells

description:
Sample 5
Total RNA

value: Overexpression of GFP-control vector


title: Tumor periphery 2

value: periphery


title: mRNA-associated with monosome in  hCINAP overexpressed cells

description:
Sample 3
Monosome-associated RNA


title: H3 WT P22 CB1


title: Primed_WIBR3


title: mRNA-assocatied with polyosme in the control cells

description:
Sample 2
Polysome-associated RNA


title: H2A.z WT P22 CB2

value: Abcam


title: NHEK_bless_seq_rep1

description: BLESS extracted DNA


title: Tumor  core 1


title: H2A.z cKO P22 CB1


title: H2A.z WT P22 CB1


title: transcriptional profile of hCINAP overexpressed cells

description:
Sample 6
Total RNA


title: Tumor periphery 1


title: Primed_WIBR2


title: WIN1_5i

source_name: Naïve human embryonic stem cells

value: Naive human embryonic stem cells


title: Chd4 WT P22 CB1


title: mRNA-assocaited with monosome in the control cells

description:
Sample 1
Monosome-associated RNA


title: WIBR3_DOX_16


title: Chd4 cKO P22 CB1


title: WIBR3_5i


title: Chd4 WT P22 CB2


title: mTXY-deltaA-48hdox

city: Worcester

first: Bryan

last: Lajoie

state: MA

address: 368 Plantation St.

department: Program in Systems Biology

institute: UMMS

data_processing:
Library strategy: Hi-C
Hi-C was performed as previously described (Lieberman-Aiden et al., 2009 Science, Belton JM et al., 2012 Methods). Briefly, Cells were lysed and chromatin was digested with HindIII, then digested ends were filled in with biotinylated dCTP  and ligated.  After reversing the formaldehyde crosslinks by incubation at 65 C  with Proteinase K overnight, unligated biotinylated ends were removed by incubation with T4 DNA polymerase.  To obtain allele-specific Hi-C interaction maps in female ESCs (XacastXa129) and a derived clonal NPC line (XacastXi129) (Methods; Extended Data Figure 1) (20), we first constructed an allelic genome using the reference mm9 genome and all 19,722,473 SNPs. The allelic (Cast and 129) genomes were then combined to create a reference diploid genome (consisting of 44 chromosomes; 1-19 X,Y,M). All reads were aligned to the diploid genome (as described in ref. (31)), thus allowing for a competitive mapping strategy between the two alleles. All reads were trimmed to 50bp and then aligned using the novoCraft novoalign (v 3.02.00) software package. Reads were aligned using the following options (-r all 5 -R 30 -q 2 -n 50, minimumReadDistance=5). The best alignment was selected from the list of the top 5 alignments. The alignment was considered unique (allelic), if it’s alignment score was = 5 from the 2nd best alignment score (alignment score taken from the ZQ tag). Reads that aligned uniquely to an allele were classified as allelic (either Cast or 129) whereas reads that aligned to both alleles equally (= 5 distance) were classified as ambiguous (AMB) (Extended Data Figure 1d). Uniquely aligned Hi-C interactions between loci located on the same chromosome were assigned to a specific parental chromosome in cis when at least one of the two reads contained a diagnostic SNP, and the other either contained a SNP from the same allele, or mapped to both alleles (32). We obtained the following paired-end read counts: For ESC (GUR.2d), a total of 401,684,614 interactions could be aligned, 372,272,389 of which were unique (after PCR duplicate filter), and 95,650,438 of which could be placed to either the Cast or 129 allele (25.69%). For NPC (GEI.72b), a total of 277,440,656 interactions could be aligned, 253,254,798 of which were unique (after PCR duplicate filter), and 82,323,031 of which could be placed to either the Cast or 129 allele (32.51%). For deltaFT NPC (D9B2/B129T3), a total of 229,331,123 interactions could be aligned, 222,941,525 of which were unique (after PCR duplicate filter), and 85,331,870 of which could be placed to either the Cast or 129 allele (38.28%). The difference in percent of reads assignable to either allele is likely due to differences in the percent of cis interactions found in each sample (biological or technical variation). The 82-95 million read depth supported generation of allele-specific chromatin interaction maps at multiple resolutions (10 Mb, 2.5 Mb, 1 Mb, 500 kb, 250 kb, 100 kb, and 40 kb).
Iterative mapping and error filtering/iterative correction (IC) of the chromatin interaction data were performed as previously described (12,31)) . IC was performed on the diploid (44 chromosomes) (replicate pooled) genome-wide matrix for all resolutions
Hi-C for the mTXY (male) samples was performed as previously described 27,28. Reads originating from the mTXY (male) sample was aligned to the mm9 reference genome. Iterative mapping and error filtering/iterative correction (IC) of the chromatin interaction data were performed as previously described. IC was performed genome-wide (22 chromosomes) (replicate pooled) on the genome-wide matrix for all resolutions.  Biological replicates were highly correlated.  We pooled all biological replicates into a single Hi-C data set per sample and subsequently used the pooled data for all analyses.
Hi-C SNP density filter: To remove potential biases in the Hi-C data related to the density of SNPs in each bin, we calculated the number of SNPs residing in each genomic interval (bin) for all Hi-C bins across all bin sizes. We then calculated the median number of SNPs per bin, and produced a minimum required SNP density cutoff defined as the (median - 1.5 * IQR). Any bins with less SNP than the cutoff were removed from all analyses. The SNP density cutoffs used for each bin size were: 40 kb, 43 SNPs; 100 kb, 216 SNPs; 250 kb, 776.5 SNPs; 500kb, 1767.25 SNPs. The non SNP density filtered data was only used for visualization purposes (figure heatmaps). For all intensive purposes, we refer to IC Hi-C as data that has been IC’d and run through the snp-density filter.
Compartment analysis:  The presence and location of the A/B-compartments were calculated as previously described (14) (ref Crane Meyer 2015). Compartments were derived from the 250 kb IC Hi-C data for each chromosome separately using the CIS maps for each sample / allele (Fig 1). The code used to generate the compartments (PC1 from PCA analysis) will be publically available on github following publication (matrix2compartment.pl). Compartments were generated all default options except the (cis alpha) option, set to (-ca 0.005).
Insulation and Boundary calculation:  TAD structure (insulation/boundaries) was defined via the insulation method as previously described with minor modifications (14). The code used to calculate the insulation score will be publically available on github following publication (matrix2insulation.pl). Insulation vectors were detected using the following options: (-is 480000 -ids 320000 -im iqrMean -nt 0 -ss 160000 -yb 1.5 -nt 0 -bmoe 0). The output of the insulation script is a vector of insulation scores, and a list of minima along the insulation vector (inferred as TAD boundaries). The TAD boundaries were not used in this study.
RNA-Seq:  RNA-Seq data for the ESC (GUR.2d) and NPC (GEI.72b) was obtained from previously published work (20). RNA-Seq data for the mutant NPC (D9B2/B129T3) was obtained and processed as previously described (20).
RNA-Seq ‘Expressed/Escapee’ classification:  The allelic RPKM values were derived for each gene by splitting the RPKM value by the 129 ratio. 129 RPKM = (RPKM * 129 ratio); Cast RPKM = (RPKM * (1 - 129 ratio)); Any gene with an allelic RPKM value = 3 RPMK was classified as being expressed. Any gene expressed on the Xi was classified as being an escapee.
Genome_build: mm9

source_name: Embryonic stem cells (male), repA Xist mutant 48h dox induction

growth_protocol: The hybrid mouse ES cell line F121.6 (129Sv-Cast/EiJ), a gift from Prof. Joost Gribnau, was grown on mitomycin C-inactivated MEFs in ES cell media containing 15% FBS (Gibco), 10-4M ß-mercaptoethanol (Sigma), 1000U/ml of leukaemia inhibitory factor (LIF, Chemicon).

extract_protocol:
Hi-C:  Hi-C was performed as previously described (Lieberman-Aiden, E. et al. Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science 326, 289–293 (2009), Naumova, N. et al. Organization of the Mitotic Chromosome. Science 342, 948–953 (2013), Belton JM et al., 2012 Methods). Briefly, Cells were lysed and chromatin was digested with HindIII, then digested ends were filled in with biotinylated dCTP  and ligated.  After reversing the formaldehyde crosslinks by incubation at 65 C  with Proteinase K overnight, unligated biotinylated ends were removed by incubation with T4 DNA polymerase.  RNA-Seq:  RNA-Seq was peformed as previously described (Gendrel, A.-V. et al. Developmental Dynamics and Disease Potential of Random Monoallelic Gene Expression. Dev. Cell 28, 366–380 (2014).).
Hi-C:  Hi-C was performed as previously described (Lieberman-Aiden, E. et al. Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science 326, 289–293 (2009), Naumova, N. et al. Organization of the Mitotic Chromosome. Science 342, 948–953 (2013)).  The ligation products were fragmented by Covaris sonication and then size selected by Ampure fractionation.  The DNA ends were prepared for Illumina sequencing adapter ligation by repairing the DNA ends and adding an ‘A’  to each end.  The biotinylated junctions were then pulled down using MyOne streptavidin beads. Illumina paired end adapters were ligated onto the DNA ends and then the fragments were PCR amplified.   Samples were sequenced on an Illumina HiSeq 2000 using either a PE50 or PE100 bp read (reads were truncated to 50bp during mapping).  RNA-Seq:  RNA-Seq was peformed as previously described (Gendrel, A.-V. et al. Developmental Dynamics and Disease Potential of Random Monoallelic Gene Expression. Dev. Cell 28, 366–380 (2014).).

value: Embryonic stem cells

tag: strain

tag: Sex

value: Male

tag: genotype/variation

value: repA Xist mutant

tag: protocol

value: 48h dox induction


title: WIBR3_DOX_12

tag: genotype


title: mTXY-wt-48hdox

source_name: Embryonic stem cells (male), wt Xist 48h dox induction

value: wt


title: mTXY-deltaA-nodox

source_name: Embryonic stem cells (male), repA Xist mutant (no induction)

value: no induction


title: mTXY-wt-nodox

source_name: Embryonic stem cells (male), wt Xist (no induction)


title: B129T3

data_processing:
Hi-C was performed as previously described (Lieberman-Aiden et al., 2009 Science, Belton JM et al., 2012 Methods). Briefly, Cells were lysed and chromatin was digested with HindIII, then digested ends were filled in with biotinylated dCTP  and ligated.  After reversing the formaldehyde crosslinks by incubation at 65 C  with Proteinase K overnight, unligated biotinylated ends were removed by incubation with T4 DNA polymerase.  To obtain allele-specific Hi-C interaction maps in female ESCs (XacastXa129) and a derived clonal NPC line (XacastXi129) (Methods; Extended Data Figure 1) (20), we first constructed an allelic genome using the reference mm9 genome and all 19,722,473 SNPs. The allelic (Cast and 129) genomes were then combined to create a reference diploid genome (consisting of 44 chromosomes; 1-19 X,Y,M). All reads were aligned to the diploid genome (as described in ref. (31)), thus allowing for a competitive mapping strategy between the two alleles. All reads were trimmed to 50bp and then aligned using the novoCraft novoalign (v 3.02.00) software package. Reads were aligned using the following options (-r all 5 -R 30 -q 2 -n 50, minimumReadDistance=5). The best alignment was selected from the list of the top 5 alignments. The alignment was considered unique (allelic), if it’s alignment score was = 5 from the 2nd best alignment score (alignment score taken from the ZQ tag). Reads that aligned uniquely to an allele were classified as allelic (either Cast or 129) whereas reads that aligned to both alleles equally (= 5 distance) were classified as ambiguous (AMB) (Extended Data Figure 1d). Uniquely aligned Hi-C interactions between loci located on the same chromosome were assigned to a specific parental chromosome in cis when at least one of the two reads contained a diagnostic SNP, and the other either contained a SNP from the same allele, or mapped to both alleles (32). We obtained the following paired-end read counts: For ESC (GUR.2d), a total of 401,684,614 interactions could be aligned, 372,272,389 of which were unique (after PCR duplicate filter), and 95,650,438 of which could be placed to either the Cast or 129 allele (25.69%). For NPC (GEI.72b), a total of 277,440,656 interactions could be aligned, 253,254,798 of which were unique (after PCR duplicate filter), and 82,323,031 of which could be placed to either the Cast or 129 allele (32.51%). For deltaFT NPC (D9B2/B129T3), a total of 229,331,123 interactions could be aligned, 222,941,525 of which were unique (after PCR duplicate filter), and 85,331,870 of which could be placed to either the Cast or 129 allele (38.28%). The difference in percent of reads assignable to either allele is likely due to differences in the percent of cis interactions found in each sample (biological or technical variation). The 82-95 million read depth supported generation of allele-specific chromatin interaction maps at multiple resolutions (10 Mb, 2.5 Mb, 1 Mb, 500 kb, 250 kb, 100 kb, and 40 kb).
Iterative mapping and error filtering/iterative correction (IC) of the chromatin interaction data were performed as previously described (12,31)) . IC was performed on the diploid (44 chromosomes) (replicate pooled) genome-wide matrix for all resolutions
Hi-C SNP density filter: To remove potential biases in the Hi-C data related to the density of SNPs in each bin, we calculated the number of SNPs residing in each genomic interval (bin) for all Hi-C bins across all bin sizes. We then calculated the median number of SNPs per bin, and produced a minimum required SNP density cutoff defined as the (median - 1.5 * IQR). Any bins with less SNP than the cutoff were removed from all analyses. The SNP density cutoffs used for each bin size were: 40 kb, 43 SNPs; 100 kb, 216 SNPs; 250 kb, 776.5 SNPs; 500kb, 1767.25 SNPs. The non SNP density filtered data was only used for visualization purposes (figure heatmaps). For all intensive purposes, we refer to IC Hi-C as data that has been IC’d and run through the snp-density filter.
Compartment analysis:  The presence and location of the A/B-compartments were calculated as previously described (14) (ref Crane Meyer 2015). Compartments were derived from the 250 kb IC Hi-C data for each chromosome separately using the CIS maps for each sample / allele (Fig 1). The code used to generate the compartments (PC1 from PCA analysis) will be publically available on github following publication (matrix2compartment.pl). Compartments were generated all default options except the (cis alpha) option, set to (-ca 0.005).
Insulation and Boundary calculation:  TAD structure (insulation/boundaries) was defined via the insulation method as previously described with minor modifications (14). The code used to calculate the insulation score will be publically available on github following publication (matrix2insulation.pl). Insulation vectors were detected using the following options: (-is 480000 -ids 320000 -im iqrMean -nt 0 -ss 160000 -yb 1.5 -nt 0 -bmoe 0). The output of the insulation script is a vector of insulation scores, and a list of minima along the insulation vector (inferred as TAD boundaries). The TAD boundaries were not used in this study.
RNA-Seq:  RNA-Seq data for the ESC (GUR.2d) and NPC (GEI.72b) was obtained from previously published work (20). RNA-Seq data for the mutant NPC (D9B2/B129T3) was obtained and processed as previously described (20).
RNA-Seq ‘Expressed/Escapee’ classification:  The allelic RPKM values were derived for each gene by splitting the RPKM value by the 129 ratio. 129 RPKM = (RPKM * 129 ratio); Cast RPKM = (RPKM * (1 - 129 ratio)); Any gene with an allelic RPKM value = 3 RPMK was classified as being expressed. Any gene expressed on the Xi was classified as being an escapee.
Genome_build: mm9

source_name: deltaFT Neural progenitor cells

extract_protocol:
Hi-C:  Hi-C was performed as previously described (Lieberman-Aiden, E. et al. Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science 326, 289–293 (2009), Naumova, N. et al. Organization of the Mitotic Chromosome. Science 342, 948–953 (2013)). Briefly, Cells were lysed and chromatin was digested with HindIII, then digested ends were filled in with biotinylated dCTP  and ligated.  After reversing the formaldehyde crosslinks by incubation at 65 C  with Proteinase K overnight, unligated biotinylated ends were removed by incubation with T4 DNA polymerase.  RNA-Seq:  RNA-Seq was peformed as previously described (Gendrel, A.-V. et al. Developmental Dynamics and Disease Potential of Random Monoallelic Gene Expression. Dev. Cell 28, 366–380 (2014).).
Hi-C:   The ligation products were fragmented by Covaris sonication and then size selected by Ampure fractionation.  The DNA ends were prepared for Illumina sequencing adapter ligation by repairing the DNA ends and adding an ‘A’  to each end.  The biotinylated junctions were then pulled down using MyOne streptavidin beads. Illumina paired end adapters were ligated onto the DNA ends and then the fragments were PCR amplified.   Samples were sequenced on an Illumina HiSeq 2000 using either a PE50 or PE100 bp read (reads were truncated to 50bp during mapping).  RNA-Seq:  RNA-Seq was peformed as previously described (Gendrel, A.-V. et al. Developmental Dynamics and Disease Potential of Random Monoallelic Gene Expression. Dev. Cell 28, 366–380 (2014).).

treatment_protocol: To generate the boundary region deletion, 5X106 ESCs were transfected with 5µg each of two plasmids (pX459) each expressing Cas9 and a chimeric guide RNA (gRNA1: CATGTTTGAGCATGGAAACCCGG, chrX:72823838-72823860; gRNA2: GGGTTATGGCGGTCGGTTCCTGG, chrX:73025513-73025535). Subcloning of ESC was made by limiting dilution. Cells were treated for 24 hours with puromycin. As soon as visible, single colonies were picked under a microscope to be screened for deletion by PCR (forward primer: CGTAGACGCGGCAGTAGTTT, reverse primer:ACATAAACTCCTTTTCAGGACCA). To identify the targeted allele, we performed a PCR using primers (F:CTGTCCAAATGGAGGTGCTT R:C CTAGGTCCGCTCTCTATCG) that amplify a 203-bp amplicon specifically on the WT allele, which contains a SNP (rs29035891). After amplification, PCR products were gelpurified and sequenced using the forward or reverse primer used for PCR. Clones positive carrying the deletion were expanded and differentiated into NPC as previously described (20) and subcloned by limiting dilution. NPC lines were maintained in N2B27 medium supplement with EGF and FGF (10ng/ml each), on 0.1% gelatin-coated flasks. Clones carrying the boundary deletion on the inactive X were identified by RNA FISH against Xist with the p510 plasmid probe and DNA FISH with a BAC hybridizing inside the deleted region (RP23-299L1).

value: deltaFT Neural progenitor cells

value: Female


title: WingDisc_PH

city: Montpellier

first: Giacomo

last: Cavalli

address: IGH - CNRS, 141, rue de la Cardonille

country: France

institute: CNRS

description: rep1 and rep2

data_processing:
filtering with CASAVA 1.8.2 from Illumina
Alignment with CASAVA 1.8.2 from Illumina
For PC, PH, K27Ac : Peak calling with MACS 1,3,7, genome at 120Mb, tag size at 36bp, other parameters as standards parameters. Only the peaks wth FDR<=10 % and fold-enrichment>=2 have been kept
For K27me3 : Domain analysis with SICER 1,1 with input as control library, a redundancy threshold of 4, a window size of 500bp, an effective genome fraction of 0.7, a gap size of 2kb and a threshold of 10 %. To define highly confident targets, the 500bp windows with 2 fold enrichment have been considered.
Genome_build: Dm 3

source_name: Wing discs

extract_protocol:
crosslinking was performed for 15 min in the presence of 1.8% formaldehyde during tissue homogenization. Chromatin extracts of embryos were sonicated using a Bioruptor (Diagenode) for 15 min (settings 30 sec on, 30 sec off, high power).
To obtain the recommended quantity of DNA several Ips were prepared, pooled and resuspended in a volume of 20ml (12 to 14 Ips for Pc or Ph, 3 to 4 Ips for H3K27me3 and 3 Ips for H3K27ac). Sample preparation was done with Illumina kit (ref. IP-102-1001) following manufacturer’s instructions.

tag: developmental stage

value: PH


title: WIBR2_4i


title: EyeDisc_PH

description: rep1 and rep2

source_name: Eye discs


title: EyeDisc_PC

description: rep1 and rep2

value: PC


title: WingDisc_PC

description: rep1 and rep2


title: EyeDisc_K27Ac

description: rep1 and rep2


title: WingDisc_Input

description: rep1 and rep2


title: mNPe-deltaRF

description:
Hi-C_mNPe-deltaRF
processed data file: insulation-difference.tar.gz

data_processing:
Library strategy: HiC-seq
Hi-C was performed as previously described (Lieberman-Aiden et al., 2009 Science, Belton JM et al., 2012 Methods). Briefly, Cells were lysed and chromatin was digested with HindIII, then digested ends were filled in with biotinylated dCTP  and ligated.  After reversing the formaldehyde crosslinks by incubation at 65 C  with Proteinase K overnight, unligated biotinylated ends were removed by incubation with T4 DNA polymerase.  To obtain allele-specific Hi-C interaction maps in female ESCs (XacastXa129) and a derived clonal NPC line (XacastXi129) (Methods; Extended Data Figure 1) (20), we first constructed an allelic genome using the reference mm9 genome and all 19,722,473 SNPs. The allelic (Cast and 129) genomes were then combined to create a reference diploid genome (consisting of 44 chromosomes; 1-19 X,Y,M). All reads were aligned to the diploid genome (as described in ref. (31)), thus allowing for a competitive mapping strategy between the two alleles. All reads were trimmed to 50bp and then aligned using the novoCraft novoalign (v 3.02.00) software package. Reads were aligned using the following options (-r all 5 -R 30 -q 2 -n 50, minimumReadDistance=5). The best alignment was selected from the list of the top 5 alignments. The alignment was considered unique (allelic), if it’s alignment score was = 5 from the 2nd best alignment score (alignment score taken from the ZQ tag). Reads that aligned uniquely to an allele were classified as allelic (either Cast or 129) whereas reads that aligned to both alleles equally (= 5 distance) were classified as ambiguous (AMB) (Extended Data Figure 1d). Uniquely aligned Hi-C interactions between loci located on the same chromosome were assigned to a specific parental chromosome in cis when at least one of the two reads contained a diagnostic SNP, and the other either contained a SNP from the same allele, or mapped to both alleles (32). We obtained the following paired-end read counts: For ESC (GUR.2d), a total of 401,684,614 interactions could be aligned, 372,272,389 of which were unique (after PCR duplicate filter), and 95,650,438 of which could be placed to either the Cast or 129 allele (25.69%). For NPC (GEI.72b), a total of 277,440,656 interactions could be aligned, 253,254,798 of which were unique (after PCR duplicate filter), and 82,323,031 of which could be placed to either the Cast or 129 allele (32.51%). For deltaFT NPC (D9B2/B129T3), a total of 229,331,123 interactions could be aligned, 222,941,525 of which were unique (after PCR duplicate filter), and 85,331,870 of which could be placed to either the Cast or 129 allele (38.28%). The difference in percent of reads assignable to either allele is likely due to differences in the percent of cis interactions found in each sample (biological or technical variation). The 82-95 million read depth supported generation of allele-specific chromatin interaction maps at multiple resolutions (10 Mb, 2.5 Mb, 1 Mb, 500 kb, 250 kb, 100 kb, and 40 kb).
Iterative mapping and error filtering/iterative correction (IC) of the chromatin interaction data were performed as previously described (12,31)) . IC was performed on the diploid (44 chromosomes) (replicate pooled) genome-wide matrix for all resolutions
Hi-C SNP density filter: To remove potential biases in the Hi-C data related to the density of SNPs in each bin, we calculated the number of SNPs residing in each genomic interval (bin) for all Hi-C bins across all bin sizes. We then calculated the median number of SNPs per bin, and produced a minimum required SNP density cutoff defined as the (median - 1.5 * IQR). Any bins with less SNP than the cutoff were removed from all analyses. The SNP density cutoffs used for each bin size were: 40 kb, 43 SNPs; 100 kb, 216 SNPs; 250 kb, 776.5 SNPs; 500kb, 1767.25 SNPs. The non SNP density filtered data was only used for visualization purposes (figure heatmaps). For all intensive purposes, we refer to IC Hi-C as data that has been IC’d and run through the snp-density filter.
Compartment analysis:  The presence and location of the A/B-compartments were calculated as previously described (14) (ref Crane Meyer 2015). Compartments were derived from the 250 kb IC Hi-C data for each chromosome separately using the CIS maps for each sample / allele (Fig 1). The code used to generate the compartments (PC1 from PCA analysis) will be publically available on github following publication (matrix2compartment.pl). Compartments were generated all default options except the (cis alpha) option, set to (-ca 0.005).
Insulation and Boundary calculation:  TAD structure (insulation/boundaries) was defined via the insulation method as previously described with minor modifications (14). The code used to calculate the insulation score will be publically available on github following publication (matrix2insulation.pl). Insulation vectors were detected using the following options: (-is 480000 -ids 320000 -im iqrMean -nt 0 -ss 160000 -yb 1.5 -nt 0 -bmoe 0). The output of the insulation script is a vector of insulation scores, and a list of minima along the insulation vector (inferred as TAD boundaries). The TAD boundaries were not used in this study.
RNA-Seq:  RNA-Seq data for the ESC (GUR.2d) and NPC (GEI.72b) was obtained from previously published work (20). RNA-Seq data for the mutant NPC (D9B2/B129T3) was obtained and processed as previously described (20).
RNA-Seq ‘Expressed/Escapee’ classification:  The allelic RPKM values were derived for each gene by splitting the RPKM value by the 129 ratio. 129 RPKM = (RPKM * 129 ratio); Cast RPKM = (RPKM * (1 - 129 ratio)); Any gene with an allelic RPKM value = 3 RPMK was classified as being expressed. Any gene expressed on the Xi was classified as being an escapee.
Genome_build: mm9


title: WIBR3_4i


title: Reprimed_WIBR3_5i

value: Primed human embryonic stem cells


title: Cells infected with pathogen replicate 1

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

description: Infected cells without SL2 treatment

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse GRCm38 reference using the TopHat splice-aware aligner
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: M. musculus (GRCm38)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Bone marrow derived macrophages

growth_protocol: BMDMs were grown into 6-well culture plates at 7×10^6 per well at 37 degree, 5 % CO2

extract_protocol:
Total RNA was isolated from each treatment with the PureLink RNA Mini Kit purchased from Invitrogen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were stimulated with A. phagocytophilum in the presence or absence of 5 µM of SL2. Non-treated and SL2-treated cells were used as controls. Each group was performed in triplicate.

tag: sl2 treatment

value: No treatment

tag: pathogen infection

value: Infected


title: SL2-treated Cells replicate 2

description: Uninfected cells treated with SL2 protein

value: SL2 treatment

value: Not infected


title: WingDisc_K27me3

description: rep1 and rep2


title: SL2-treated Cells infected with pathogen replicate 3

description: Infected cells treated with SL2 protein


title: SL2-treated Cells infected with pathogen replicate 2

description: Infected cells treated with SL2 protein


title: Ctrl_FRT2A

description: rep1 and rep2

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Alignment using TopHat 2.0.8b and Bowtie 2.1.0.0 with standard parameters
Analysis using edgeR 2.6.2
Genome_build: DM3, Transcript annotation BDGP5.74

extract_protocol:
RNA-Seq libraries were constructed with the TruSeq RNA sample preparation (Low throughput protocol) kit from Illumina
One microgram of total RNA was used for the construction of the libraries. The RNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using SuperScript II reverse transcriptase and random hexamer primers. The Second strand cDNA is synthesized. These 20 cDNA fragments then go through an end repair process, the addition of a single 'A' base and the subsequent ligation of the adapter. The products are then purified and enriched with 15 cycles of PCR. The final cDNA libraries are validated with a DNA 1000 Labchip on a Bioanalyzer (Agilent) and quantified with a KAPA qPCR kit. For one sequencing lane of a flowcell V3, three libraries were pooled in equal proportions, denatured with NaOH and diluted to 7 pM in hybridization buffer. Cluster formation, primer hybridisation and single read 50 cycles sequencing were performed

value: WT


title: SL2-treated Cells replicate 1


title: EyeDisc_K27me3

description: rep1 and rep2


title: Cells infected with pathogen replicate 3

description: Infected cells without SL2 treatment


title: Non-treated Cells replicate 1

description: Uninfected cells without SL2 treatment


title: EyeDisc_Input

description: rep1 and rep2


title: Cells infected with pathogen replicate 2

description: Infected cells without SL2 treatment


title: Mutant_PH505_FRT19A

description: rep1 and rep2

value: Mutant PH505


title: SL2-treated Cells replicate 3


title: Ctrl_FRT42D

description: rep1 and rep2


title: Non-treated Cells replicate 3

description: Uninfected cells without SL2 treatment


title: 1P110-IL4

first: Roman

last: Sasik

address: 9500 Gilman Dr.

department: Center for Computational Biology and Bioinformatics

institute: UCSD

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads aligned to mouse transcriptome using bowtie2
Transcript counts summarized into gene-level summaries
Normalization and differential expression analysis using DESeq
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file of normalized counts

source_name: 1 IL-4 stimulated p110g-/- macrophages

growth_protocol: Freshly isolated mouse bone marrow cells were cultured to differentiate them into macrophages for six days in RPMI + 20% FBS+ 1%Pen/Strep+ 50 ng/ml M-CSF.

extract_protocol:
Macrophages were removed from dishes, and RNA was harvested using Trizol reagent. Qiagen RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and p110g-/- Macrophages were stimulated with RPMI + 10%FBS +1% Pen/Strep +20 ng/ml M-CSF for 24 h, with RPMI + 10%FBS +1% Pen/Strep +20 ng/ml M-CSF + 20gn/ml IFNg + 100 ng/ml LPS for 24 h, RPMI + 10%FBS +1% Pen/Strep +20 ng/ml M-CSF + 20 ng/ml IL-4 for 48 h.

tag: tissue

value: Bone Marrow Derived Macrophages

tag: age

value: 8 weeks post-natal


title: mNPe

description:
Hi-C_mNPe
processed data file: insulation-difference.tar.gz

source_name: Neural progenitor cells

value: Neural progenitor cells


title: 3WT-IL4

source_name: 3 IL-4 stimulated WT macrophages

value: wild type


title: Mutant_Psc_Suz2_1.b8_FRT42D

description: rep1 and rep2

value: Mutant Psc Susz2 1.b8


title: Ctrl_FRT19A

description: rep1 and rep2


title: Mutant_Suz12_FRT2A

description: rep1 and rep2

value: Mutant Suz12


title: 30-35 mm_rep2

city: saint paul

first: Jonathan

last: Schilling

state: minnesota

address: 2004 folwell ave

institute: University of Minnesota

description:
Temporal eparation of brown rot was sptially acomplished by wafer design
FPKM_tracking_0-5 mm, 15-20 mm and 30-35 mm_Cuffidff.txt
Paired_comparison_of_three_sections_Cuffdiff.xlsx

data_processing:
The RNA-seq data analyses were performed in the Galaxy platform (https://galaxy.msi.umn.edu/) according to the routine pipeline of Trapnell et al. (2014). Raw reads were first cleaned up with Trimmomatic (v0.3) by setting the parameters as: java -jar trimmomatic-0.30.jar PE --phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP: TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. The qualities of the trimmed reads were further verified by FastQC (Galaxy Version 0.63). Then, the cleaned reads were mapped against the genome of P. placenta MAD 698-R (v1.0) (Postia_placenta.fasta) with Tophat (v2.0.13): tophat -r 0 -i 20 -I 5000 --min-segment-intron 20 --max-segment-intron 5000 -G Postia_placenta_FilteredModels2.gff -o tophat_out_? $INPUT/Pospl1 trimmomatic/Ppl_?.R1.PE.fastq trimmomatic/Ppl_?.R2.PE.fastq.
By using the reference transcript models Postia_placenta_FilteredModels2.gtf from JGI (http://genome.jgi.doe.gov/Pospl1/Pospl1.download.html), expression levels (FPKM, fragments per kilobase unique exon sequence per megabase of library mapped) were estimate by Cufflinks (Galaxy Version 2.2.1.0) with the classic FPKM normalization method.
By using the reference transcript models Postia_placenta_FilteredModels2.gtf from JGI (http://genome.jgi.doe.gov/Pospl1/Pospl1.download.html), expression levels (FPKM, fragments per kilobase unique exon sequence per megabase of library mapped) and significances of differences were also estimated with Cuffdiff (Galaxy Tool Version 2.2.1.3) using geometric normalization. Difference significances were calculated comparing each pairwise combination of the three section samples. The Cuffdiff output (e.g., all gene expression density distribution, principal component analysis and sample dendrogram for all gene expression) were visualized by cummerbund (Galaxy Version 1.0.1). Comparisons of gene expression from each two sections were presented as scatter plots by using RStudio (Version 0.99.491.).
Genome_build: Postia placenta MAD 698-R v1.0 from JGI (http://genome.jgi.doe.gov/Pospl1/Pospl1.download.html) [Postia placenta V1.0]
Supplementary_files_format_and_content: [.txt] Tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: [.xlsx] file includes pairwise comparison and FPKM levels

organism: Rhodonia placenta

source_name: brown rot decayed wood

growth_protocol: Postia placenta dikaryotic strain MAD 698-R (ATCC 44394) was maintained on 1.5% malt extract agar for routine culturing and to inoculate modified ATSM soil-block microcosms. Vertically-oriented wood wafers were colonized directionally from a pre-developed P. placenta hyphal mat. At harvest, wafers were sectioned to spatially segregate the temporal progression of wood decay, an approach modified from Schilling et al. (2013). In brief, a 1:1:1 mixture of soil, peat and vermiculite hydrated to 40-45% moisture content was packed into pint glass jars to one-third full. Feeder strips on the media surface were inoculated with 1-cm diameter agar plugs from P. placenta cultures and allowed to form a confluent mycelial lawn over 2-3 weeks. Wood wafers were cut 60 × 25 × 2.5 mm, with the largest face being the cross section and with the tangential plane in contact with the mycelium when propped in jars. Cultures were incubated at room temperature for 3-4 weeks until the visible hyphal front had advanced ~50 mm up the wafers. Wafers with flat hyphal fronts (horizontal lines) were then harvested, scraped free of surface hyphae, and sectioned into 5-mm sections using a razor blade sterilized with each cut, with the first cut along the hyphal front. Distance from the hyphal front was used to delineate sections on wafers for analyses per section in triplicate. The sections 0-5 mm, 15-20 mm and 30-35 mm were used for RNA-seq analysis.

extract_protocol:
Total RNA for P. placenta was isolated from each wood section with TRIzol (Life Technologies, Carlsbad, CA) and then cleaned up with a Qiagen RNeasy Mini Kit (Qiagen, Inc., Valencia, CA) to remove organic inhibitors prior to downstream RNA-seq.
For RNA sequencing, TruSeq RNA v2 libraries were prepared and sequenced on a HiSeq 2500 System (Illumina Inc., San Diego, CA) by using the standard protocols from Illumina.

tag: wafer locus

tag: decay stage

value: late decay


title: 2WT-IL4

source_name: 2 IL-4 stimulated WT macrophages


title: 30-35 mm_rep3


title: mF1216

source_name: Embryonic stem cells

tag: cell type

value: Embryonic stem cells

value: Female


title: SL2-treated Cells infected with pathogen replicate 1

description: Infected cells treated with SL2 protein


title: 15-20 mm_rep2

value: middle late decay


title: 15-20 mm_rep3


title: 2WT-MCSF

source_name: 2 MCSF stimulated WTmacropahges


title: Non-treated Cells replicate 2

description: Uninfected cells without SL2 treatment


title: Mutant_Ez731_FRT2A

description: rep1 and rep2

value: Mutant Ez731


title: 3P110-IL4

source_name: 3 IL-4 stimulated p110g-/-macrophages


title: 1WT-LPS

source_name: 1 IFNg/LPS stimulated WT macrophages


title: 3P110-LPS

source_name: 3 IFNg/LPS stimulated p110g-/- macrophages


title: 3P110-MCSF

source_name: 3 MCSF stimulated p110g-/- macropahges


title: 2P110-MCSF

source_name: 2 MCSF stimulated p110g-/-macropahges


title: 33Z

status: Public on Jul 17 2016

first: Jie

last: Guo

state: Beijing

address: No.20 Nanxincun, Xiangshan

institute: Institute of Botany, Chinese Academy of Sciences

description:
Digital gene expression tag profiling
processed data file: gene_raw_counts_all.txt; gene_TPM_all.txt

data_processing:
Basecalls performed using RTA (version1.12.4.2) and BclConverter-1.9.0-11-03-08
For DGE reads, after removing tags containing sequencing adapters and reads of low quality (reads containing Ns), we used BWA (default parameters) to separately map DGE tags to the japonica genome and the cDNA sequences of its annotated gene models (only the longest isoform was retained). For RNA-Seq data, we used BWA (default parameters) for mapping to the annotated cDNA sequences.
For DGE reads, the gene expression level was measured as cumulative counts of all consensus tag mapping on sense strands to a given gene model, and then normalized to TMP (number of transcripts per million tags) by edgeR (version 3.6.8). We defined a gene as an effectively expressed gene if more than two of the 12 samples 10% of the samples had at least 20 mapped reads for each tissue. For RNA-seq reads, we summed the number of reads for each gene model and applied reads per million reads (RPKM) to normalize gene expression levels.
Genome_build: MSU rice build 6.1
Supplementary_files_format_and_content: For DGE data, a tab-delimited text file including read count matrix and a tab-delimited text file including TPM value matrix for all samples were generated. For RNA-seq data,  a tab-delimited text file including RPKM value matrix for six samples is provided.

organism: Oryza nivara

source_name: Oryza nivara  flag leaves at the heading stage

growth_protocol: Seeds were germinated at 30°C in an incubator, and the young seedlings were transplanted to pots at three-leaf stages and grown using standard greenhouse cultivation with the temperature from 25°C to 35°C.

extract_protocol:
Total RNA from each sample was isolated with TRIzol (Invitrogen) following the manufacturer’s instructions and then treated with RNase-free DNase I for 30 min at 37°C (New England BioLabs) to remove residual DNA.
For Illumina’s digital gene expression (DGE) system, the mRNAs were separately isolated with oligo(dT) ligated beads and reverse transcribed into double-stranded cDNA. The cDNAs were digested by the restriction enzymes NlaIII and MmeI. After ligation with sequencing adapters, the molecules were amplified by PCR.  For RNA-seq technology, beads with oligo(dT) were used to isolate poly(A) mRNA. First-strand cDNA was synthesized using random hexamer primers and reverse transcriptase (Invitrogen). The second-strand cDNA was synthesized using RNaseH (Invitrogen) and DNA polymerase I (New England BioLabs). The paired-end cDNA libraries with insert sizes of approximately 200 bp were then prepared according to Illumina’s protocols.

tag: collection year

tag: original place

value: India

value: flag leaves at the heading stage


title: 40Z_RNA-seq

description:
RNA-seq
processed data file: RNA-seq_gene_RPKM_all.txt


title: 26Z

value: Thailand


title: 1P110-LPS

source_name: 1 IFNg/LPS stimulated p110g-/- macrophages


title: 40Z


title: Pitx2-null_H3K4me3

city: Corvallis

first: Chrissa

last: Kioussi

state: Oregon

address: 1601 SW Jefferson Way

department: College of Pharmacy

institute: Oregon State University

data_processing:
Primary Illumina data image analysis, base calling, and filtering was preformed by the Casava pipline (version 1.8.2, Illumina)
Alignment of raw sequence data (fastq files) to mm10 reference genome using Bowtie2 version 2.2.3 with default parameters
Conversion of aligned .sam files into .bam files using  Samtools version 1.0
Peak calling, normalization per ten million mapped reads, and generation of wig files using MACS2 with the following parameters: “-f BAM -B --SPMR --broad --broad-cutoff 0.1 -g 1.87e9  -q 0.01.”
Genome_build: mm10
Supplementary_files_format_and_content: mut_H3K4_peaks.bb: Pitx2-null H3K4me3 peaks
Supplementary_files_format_and_content: mut_H3K27_peaks.bb: Pitx2-null H3K27me3 peaks
Supplementary_files_format_and_content: mut_pol2_peaks.bb: Pitx2-null RNA Pol II peaks
Supplementary_files_format_and_content: mutant_H3K4.bw: Pitx2-null H3K4me3 signal track
Supplementary_files_format_and_content: mutant_H3K27.bw: Pitx2-null H3K4me3 signal track
Supplementary_files_format_and_content: mutant_pol2.bw: Pitx2-null RNA Pol II signal track

source_name: Forelimb

growth_protocol: Mice heterozygous for a null allele of Pitx2 were bred and females checked for the presence of a vaginal plug (E0.5). Multiple litters, each containing 6-15 embryos were isolated at E12.5, and Pitx2-null embryos were visually identified by phenotype. The forelimbs were dissected in ice cold 1x phosphate buffered saline (PBS) and pooled with at least 10 sets per 1.5mL tube; then fixed.

extract_protocol:
Protein G magnetic beads (NEB S1430S) were prepared by washing 3x in PBS with 0.05% bovine serum albumin (BSA), bound overnight to rabbit anti-H3K4me3 (Abcam, ab1342), rabbit anti-H3K27me3 (Millipore, 07-449), or mouse anti-Pol2 (Millipore, 17-672) at 2 µg/20 µl beads, and washed 3x in PBS-BSA. Material for immunoprecipitation (IP) as diluted 1:10 in dilution buffer (1% Triton X-100, 150mM NaCl, 2mM EDTA pH 8.0, 20mM Tris-HCl pH 8.0, protease inhibitors), and 20 µl of Protein G magnetic beads were added to each ml of sheared chromatin (about 200 µg each) and allowed to rotate overnight at 4° C. The following day, samples were washed 1x in low-salt wash (1% Triton X-100, 0.1% SDS, 150mM NaCl, 2 mM EDTA pH 8.0, 10mM Tris HCl pH 8.0, protease inhibitors), 2x in high-salt wash (1% Triton X-100, 0.1% SDS, 500mM NaCl, 2mM EDTA pH 8.0, 10mM Tris HCl pH 8.0, protease inhibitors), 2x in lithium wash (100 mM Tris HCl pH 9.0, 500mM LiCl, 1% NP40, 1% deoxycholic acid), 3x in TE (10mM Tris-HCl pH 8.0, 1mM EDTA), and eluted in 100 µl of elution buffer containing RNaseA and Proteinase K (1% SDS, 100 mM NaHCO3, 10 mg/ml RNaseA, 5 M NaCl, 0.2 mg/ml Proteinase K). Elutants and respective input controls were de-crosslinked overnight, at 65° C, purified on Qiagen Miniprep columns and eluted in ddH2O. One set from each condition was reserved for qPCR validation and the remaining ChIP DNA were speed-vac dried. DNA was resuspended in 15 µl of ddH2O, quantified with the Qubit fluorometer (Invitrogen) or the NanoDrop spectrophotometer (Thermo Scientific), until at least 10 ng were collected for each sample.
Single-end libraries were generated using the Illumina TruSeq ChIP seq library prep kit using 18 cycles for PCR sample enrichment, with the only protocol modification being size selection after fragment amplification. The library size selected was 200–300 bp in length and, after gel purification, size was confirmed with the Bioanalyzer (Agilent). Libraries were then sequenced on a 51 bp single-end run on the Illumina HiSeq 2000

treatment_protocol: Biopsies from embryos were cross-linked for 20 min in freshly made fixation buffer (1% formaldehyde 100mM NaCl, 0.5mM EGTA, 50mM HEPES, pH 8.0) and quenched by the addition of glycine (125mM). Tissue was washed twice with ice cold PBS and snap-frozen in liquid nitrogen prior to sonication (14 cycles of 10 sec at 20% output with 60 sec on ice between cycles, Branson 450 sonicator) in lysis buffer (1% SDS, 10mM EDTA pH 8.0, 50mM Tris-HCl pH 8.0, protease inhibitors) to achieve an average sheared fragment size of 300bp, with the primary smear between 200–450bp. A portion of sheared chromatin from each preparation was reserved as the input control

tag: antibody

value: H3K4me3 (Abcam, ab1342)


title: 2P110-LPS

source_name: 2 IFNg/LPS stimulated p110g-/-macrophages


title: 3WT-LPS

source_name: 3 IFNg/LPS stimulated WT macrophages


title: 1P110-MCSF

source_name: 1 MCSF stimulated p110g-/- macrophages


title: 133Z

value: Myanmar


title: 3WT-MCSF

source_name: 3 MCSF stimulated WTmacropahges


title: 52Z


title: 30-35 mm_rep1


title: 39H

source_name: Oryza nivara  panicles at the heading stage

value: panicles at the heading stage


title: 2P110-IL4

source_name: 2 IL-4 stimulated p110g-/- macrophages

value: Bone Marrow Derived Macrophages


title: 80H

value: Nepal


title: 1WT-IL4

source_name: 1 IL-4 stimulated WT macrophages

value: 8 weeks post-natal


title: 33H


title: 0-5 mm_rep2

source_name: brown rot decayed wood

value: early decay


title: 52H


title: 0-5 mm_rep1


title: Pitx2-null_Pol_II

value: Pol_II (Millipore, 17-672)


title: Pitx2-null_H3K27me3

value: H3K27me3 (Millipore, 07-449)


title: 40F_RNA-seq

source_name: Oryza nivara  panicles at the flowering stage

value: panicles at the flowering stage


title: 40F


title: 0-5 mm_rep3


title: 197F


title: Pitx2-null_Input

value: none, Input


title: Female Melanogaster CLAMP input Replicate 2

city: Boston

first: Michael

last: Tolstorukov

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
ChIP-seq reads were aligned to the D. melanogaster (dm3) and D. miranda (reference 15, please see the paper) genome assembly using Bowtie with with parameters “-m 1 -I 50 -X 500 --solexa-quals –best”
The positions with anomalously high read counts are potential amplification artifacts and were removed from consideration
Peaks in the ChIP-Seq fragments distribution were identified using the SPP software package with default parameters
Overlapping peaks of two replicates were used in the analysis.
Genome_build: dm3 for D. melanogaster, DroMir_2.2 for D. miranda [PMID 25688566]
Supplementary_files_format_and_content: peak files were generated using spp; scores show the enrichment

source_name: Female Melanogaster CLAMP input

growth_protocol: Melanogaster flies were maintained at 21 degree Celcius, and Miranda flies at 18 degree Celcius

extract_protocol:
Standard ChIP seq protocol - larvae were homogenized in liquid nitrogen followed by lysis and sonication, chromatin was immunoprecipitated with CLAMP antibody.
ChIP-seq libraries were prepared with the illumina TruSeq DNA Prep kit

value: wild type

tag: chip antibody

value: 3rd instar larvae


title: Female Melanogaster CLAMP ChIPseq Replicate 1

source_name: Female Melanogaster CLAMP ChIPseq


title: 80Z


title: 1WT-MCSF

source_name: 1 MCSF stimulated WT macropahges

tag: strain


title: Female Melanogaster CLAMP ChIPseq Replicate 2


title: 133H


title: 39H_RNA-seq


title: 15-20 mm_rep1

value: middle late decay


title: 26H


title: 80F


title: 52F

value: India


title: 47Z_RNA-seq

organism: Oryza rufipogon

source_name: Oryza rufipogon flag leaves at the heading stage

value: flag leaves at the heading stage


title: 47Z


title: 95Z


title: 25F

value: Thailand


title: Female Melanogaster CLAMP input Replicate 1


title: 34F


title: 43Z


title: 230Z


title: 199Z


title: 49H

source_name: Oryza rufipogon panicles at the heading stage


title: 47H


title: 47H_RNA-seq


title: 199F

source_name: Oryza rufipogon panicles at the flowering stage


title: 47F


title: 50F


title: Neuro2a miR-132 mimics

city: Quebec

first: Sebastien

last: Hebert

state: QC

address: 2705 Boul Laurier, Centre de recherche du CHU de Quebec

department: Medecine

country: Canada

institute: Lavay University

data_processing:
Illumina TruSeq RNA Sample Preparation kit version 2 (Low Sample Protocol) was used on 1ug of total RNA. PolyA+ containing RNA molecules were purified using oligo-dT attached magnetic beads. Chemical fragmentation followed after two rounds of enrichment for PolyA+ mRNA.
cDNA was synthesized using reverse transcriptase (Superscript II) and random primers. This was followed by second strand cDNA synthesis, end repair process, adenylation of 3' ends and ligation of the adapters (single index).
The products were then purified with Agencourt Ampure XP SPRI beads (Beckman Courter)  and enriched with 15 cycles of PCR to create the cDNA library. Library PCR product was analyzed for appropriate size distribution with the Agilent Tapestation 2200, and quantitated using Qubit and qPCR  before equimolar pooling of 12 samples. Libraries were subjected to an indexed SR sequencing run of 1x50 cycles on an Illumina HiSeq 2500.
Raw sequencing data was demultiplexed using bcl2fastq 1.8.4.
Quality trimming and size check of the raw reads has been performed using Trimmomatic 0.33.
Trimmed reads have then been mapped to mouse genome (mm10) with TopHat 2.0.14
Genome_build: mm10

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with 50 nM of miR-132 mimics or scrambled mimics.

tag: cell line

value: overexpressing miR-132 mimics


title: 49Z


title: 3xTg-AD; miR-132/212 +/+

tag: strain background

tag: genotype/variation

value: 3xTg-AD wild type

value: 12 Months old

value: Hippocampus


title: 230H

value: panicles at the heading stage


title: 95H

value: Myanmar


title: Untreated Wild-type #3

status: Public on Jul 16 2016

city: San Diego

first: Brian

middle: Patrick

last: James

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

description:
Sample_21794
WT_UTvsX_UT_gene_exp.diff
WT_UTvsX_DTT_gene_exp.diff
WT_UTvsWT_DTT_gene_exp.diff
WT_UTvsWT_DTT_splicing.diff
WT_UTvsKO_UT_gene_exp.diff
WT_UTvsKO_DTT_gene_exp.diff

data_processing:
Bases were called using ELAND
Tophat was used to align splice-specific reads to the genome
RPKM expressions were normalized to the WT untreated samples
The splicing p values are from cuffdiff within cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: [gene_exp.diff] reports RPKMs
Supplementary_files_format_and_content: [splicing.diff] reports sqrt(JS) and FDR corrected p-values for differentially spliced targets

source_name: Untreated Wild-type

growth_protocol: Fibroblasts were grown in 10cm dishes to 70 percent confluency then stressed.

extract_protocol:
Trizol was used for RNA purification followed by DNaseI treatment and concentration normalization to 10ng/ul in 50ul = 50ng total RNA.
magnetic poly-A beads were used to purify mRNAs from 50ng total RNA.

treatment_protocol: 1mM dithiothreitol (Dtt) dissolved in dimethylsulfoxide (DMSO) DMSO alone was incubated with cells for four hours.

value: Wild-type

tag: treatment

value: Untreated

value: Embryonic day 10 primary fibroblasts

tag: passages


title: Dithiothreitol treated Xbp1-Null #1

description:
Sample_21797
WT_UTvsX_DTT_gene_exp.diff

source_name: Dithiothreitol treated Xbp1-Null

value: Dithiothreitol


title: Untreated Ire1α-Null #2

description:
Sample_21792
WT_UTvsKO_UT_gene_exp.diff

source_name: Untreated Ire1α-Null


title: 2WT-LPS

source_name: 2 IFNg/LPS stimulated WTmacrophages

value: Bone Marrow Derived Macrophages

value: 8 weeks post-natal


title: 43H


title: Dithiothreitol treated Wild-type #2

description:
Sample_21791
WT_UTvsWT_DTT_gene_exp.diff
WT_UTvsWT_DTT_splicing.diff

source_name: Dithiothreitol treated Wild-type


title: 47F_RNA-seq

value: panicles at the flowering stage


title: Dithiothreitol treated Ire1α-Null #1

description:
Sample_21789
WT_UTvsKO_DTT_gene_exp.diff

source_name: Dithiothreitol treated Ire1α-Null


title: 199H


title: Female Miranda CLAMP ChIPseq Replicate 2

organism: Drosophila miranda

source_name: Female Miranda CLAMP ChIPseq

tag: genotype

value: wild type

tag: developmental stage

value: 3rd instar larvae


title: Untreated Ire1α-Null #1

description:
Sample_21788
WT_UTvsKO_UT_gene_exp.diff


title: Neuro2a scrambled mimics

value: overexpressing scrambled mimics


title: Dithiothreitol treated Wild-type #1

description:
Sample_21787
WT_UTvsWT_DTT_gene_exp.diff
WT_UTvsWT_DTT_splicing.diff


title: 95F

tag: tissue


title: Female Miranda CLAMP input Replicate 2

source_name: Female Miranda CLAMP input


title: 230F

value: India


title: Untreated Wild-type #2

description:
Sample_21790
WT_UTvsX_UT_gene_exp.diff
WT_UTvsX_DTT_gene_exp.diff
WT_UTvsWT_DTT_gene_exp.diff
WT_UTvsWT_DTT_splicing.diff
WT_UTvsKO_UT_gene_exp.diff
WT_UTvsKO_DTT_gene_exp.diff


title: 43F

value: Thailand


title: Female Miranda CLAMP ChIPseq Replicate 1


title: 3xTg-AD; miR-132/212 -/-

value: 3xTg-AD mice lacking the miR-132/212 cluster

tag: age


title: YY004

city: New Orleans

first: Yao-Zhong

last: Liu

state: LA

address: 1440 Canal Street, Suite 2001

department: Dept. of Biostatistics and Bioinformatics

institute: Tulane University School of Public Health

data_processing:
We use RTA (Illumina) for base calling and CASAVA (version 1.8.2) for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Human: NCBI/build37.2) using Tophat (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks (version 2.0.2) with default settings. We test for differentially expressed genes under various conditions using DEseq
Genome_build: NCBI/build37.2

source_name: Monocytes

extract_protocol:
Monocyte isolation from whole blood was performed with a monocyte-negative isolation kit (Miltenyi Biotec Inc, Auburn, CA) following manufacturer's recommendation. The purity of the isolated monocytes was >85% based on our extensive experience of monocyte isolation using this kit. Total RNA from monocytes was extracted using Qiagen RNeasy Mini kit (Qiagen, Inc., Valencia, CA).
Library construction was performed using TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA), which applied poly-A pull-down for mRNA enrichment and library preparation following the manufacturer’s protocol.

value: Peripheral blood monocytes

tag: disease

value: Chronic periodontitis


title: YY005


title: YY007

value: Health control


title: YY008


title: YY003


title: YY009


title: Female Miranda CLAMP input Replicate 1


title: Untreated Xbp1-Null #1

description:
Sample_21796
WT_UTvsX_UT_gene_exp.diff

source_name: Untreated Xbp1-Null


title: H3K27ac rep2 Chip-Seq KC

status: Public on Jul 15 2016

city: Barcelona

first: Debayan

last: Datta

state: Barcelona

address: C. Baldiri Reixac 10

department: Oncology

country: Spain

institute: IRB Barcelona

data_processing:
The ChIP-seq datasets were aligned to the human genome build hg19 using Bowtie version 1.01. The parameters used were -k 1, -m 1, -n 2.
Peaks of Dnmt3A and Dnmt3B were called using MACS 1.4.1 using the parameters -p 1e-5, -w, -S and -g hs.
For Histone marks, MACS2 was used with parameters -broad, -q 0.01 -g hs.
Genome_build: hg19
Supplementary_files_format_and_content: The BED files were obtained from the output of MACS/MACS2.

source_name: Differentiated Keratinocytes

growth_protocol: Human Epidermal Stem Cells were isolated from neonatal foreskin samples and cultured with a feeder layer of fibroblasts (J2-3T3) as described previously (Gandarillas and Watt, 1997). Undifferentiated epSC were grown in Keratinocyte Serum-Free Medium with supplements (KSFM; GIBCO). For calcium-induced differentiation, after reaching 70% confluence KSFM was exchanged for EMEM (Lonza) supplemented with 8% chelated FBS, EGF (10 ng/ml), 1% penicillin/streptomycin, and 1.2mM CaCl2. After 48 hr differentiated keratinocytes were collected.

extract_protocol: EpiSC and differentiated keratinocytes were trypsinized and crosslinked in 1% formaldehyde (FA) for 10 min at room temperature (RT). For ChIPs from EBs, crosslinking was performed for 30 min at RT in 4% FA. Crosslinking was quenched with 0.125 M glycine. Pelleted cells were lysed in 1 ml ChIP buffer and sonicated for 15 min in a Bioruptor (Diagenode). Soluble material was quantified by Bradford assays. To immunoprecipitate transcription factors, 2000 mg of protein and 100 mg of immunoprecipitated histone/histone modifications were used. Antibodies (10ug for DnmtA/3B and 3ug for histone modifications) were incubated overnight with the chromatin. Immunocomplexes were recovered with 30 ul of protein A bead slurry (Healthcare. Cat # 17-5280-01). Immunoprecipitated material was washed three times with low salt buffer and one time with high salt buffer. DNA complexes were decrosslinked at 65_C overnight, and DNA was then eluted in 50 ul of water using the PCR purification kit (QIAGEN)

treatment_protocol: Epidermal Stem Cells growing in KSM media were infected with precipitated lentiviral particles produced by 293T cells transfected with the mentioned plasmids. Cells were collected for ChIP assay after 5 days of puromycin selection

tag: passage

value: Foreskin

tag: chip-antibody

value: H3K27ac (Merck Millipore. Cat 07-360)


title: H3K4me1 rep2 Chip-Seq KC

value: H3K4me1(Abcam. Cat:ab8895)


title: Dithiothreitol treated Wild-type #3

description:
Sample_21795
WT_UTvsWT_DTT_gene_exp.diff
WT_UTvsWT_DTT_splicing.diff

value: Wild-type

tag: cell type

value: Embryonic day 10 primary fibroblasts


title: JQ1-3hr (RNA-seq)

city: Nashville

first: Scott

middle: W

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

data_processing:
Base-calling, filtering, and demultiplexing were performed using Illumina CASAVA 1.8.2 with default settings.
Raw reads were processed to trim adaptor and low quality sequences using Trimmomatic (version 0.32) with parameters: -phred33 input.txt.gz output.txt.gz ILLUMINACLIP:adaptor.txt:2:30:7 TRAILING:15.
For PRO-seq, reverse complements of the trimmed reads were generated using “fastx_reverse_complement” (version 0.0.13) with default settings, and the reverse complement sequences were aligned to the human genome hg19 using bowtie2 (version 2.2.4) with default settings. For ChIP-exo, pre-processed reads were aligned to hg19 using bowtie2 with default settings. For RNA-seq, pre-processed reads were aligned to hg19 using TopHat (version 2.0.10) with default settings.
H3K27ac peak calling was performed using MACS2 (version 2.0.10) with parameters: MACS2 callpeak -t H3K27ac.bam -c Input.bam --nomodel -f BAM -g hs -n -B.
Genome_build: hg19
Supplementary_files_format_and_content: Genome coverage was normalized and calculated for each strand separately and reported in bedGraph format. The ChIP-exo peak file reports genome coordinates, peak length, read counts, and enrichment significance for each called H3K27ac peak. RNA-seq count files contain gene RefSeq IDs and their normalized read counts in reads per kilobase of transcript per million mapped reads (RPKM).

source_name: t(8;21)-containing acute myeloid leukemia cell line

growth_protocol: RPMI 1640 supplemented with 10% FetalPlex and 2 mM L-Glutamine

extract_protocol:
TRIzol extraction
PolyA enriched RNA was used to build library using TruSeq RNA Library Preparation Kit.

treatment_protocol: 250 nM JQ1, 3 hr

value: Kasumi-1 cells

value: 250 nM JQ1, 3 hr


title: DMSO-3hr (RNA-seq)

treatment_protocol: DMSO, 3 hr

value: DMSO, 3 hr


title: MS417-1hr (RNA-seq)


title: Dithiothreitol treated Ire1α-Null #2

description:
Sample_21793
WT_UTvsKO_DTT_gene_exp.diff

value: Dithiothreitol


title: Pf3D7-TRZGFP-chip

city: Nijmegen

first: Christa

last: Toenhake

state: Netherlands

address: Geert Grooteplein 28

country: Netherlands

institute: Radboud University

description: anti-GFP ChIP

data_processing:
Illumina Casava 1.8.2 software for basecalling.
Data were mapped with BWA samse (Version: 0.7.10-r789) to the P. falciparum 3D7 reference genome from PlasmoDB version 6.1 (http://www.plasmodb.org).
Reads were extended to the average fragment length of the respective library as determined in a Bionanalyzer High Sensitivity run minus adapter length.
Normalized bedGraph files were generated such that a value of 1 would correspond to the situation where all reads would be randomly distributed across the genome using the following formula: ni = ri ×gm/(l×r) where ni is the normalized coverage at site i, ri is the number of fragments covering site i in the sample, gm is the mappable genome size (22248208 bp for single-end 75 bp sequencing), l is the mean fragment size as  and r is the number of mapped reads. These normalized files were used to generate log2 ChIP-over-input ratio tracks. An offset of 0.1 was added to each ChIP and input to prevent +/- infinite values and division by zero.
Peak calling was performed using MACS2 bdgpeakcall (Model-based Analysis of ChIP-seq 2, v 2.0.10.20130306) on log2 ChIP-over-input ratio files with cut-off at 2
Genome_build: PlasmoDB Plasmodium falciparum 3D7 release 6.1
Supplementary_files_format_and_content: .log2ratio.bedGraph.gz: Coverage as log2-ratio of chip-over-input calculated using normalized bedGraph -chip and -input files with offset of +0.1 to prevent +/- infinite values and division by zero. Normalized coverage was calculated for -chip and -input using reads extedend to the mean read length size of respective library and subsequenctly normazing for the number of reads and the mappable genome size such that value of 1 would correspond to the situation where all reads would be randomly distributed across the genome.  _peaks.encodePeak: output from macs2 bdgpeakcall peakcalling on log2ratio.bedGraph.gz files with cut-off at 2.

organism: Plasmodium falciparum

source_name: red blood cell stage, schizont

growth_protocol: Parasite-infected red blood cells were cultured in petri dishes at 5% hematocrit in the presence of  3% O2 and  4% CO2 (rest N2) in RPMI 1640 supplemented with 25mM Hepes, 50mg/l Hypoxanthine, 0.21% NaHCO3, 0.5% Albumax and 50mg/l Neomycin sulphate. The  3D7/TRZGFP parasite line was cultured in presence of 4nM WR99210 (WR).

extract_protocol:
Synchronized 3D7/TRZGFP and 3D7/TRZHA schizonts at 5% parasitemia were cross-linked by incubation with a final concentration of 1% formaldehyde for 15 min at 37ºC. The cross-linking reaction was quenched by addition of 0.125M glycine (final concentration). Nuclei were isolated by releasing parasites from iRBCs using 0.05% saponin followed by lysis in CLB (20 mM Hepes, 10mM KCl, 1mM EDTA, 1mM EGTA, 0.65% NP-40, 1mM DTT supplemented with protease inhibitor). Nuclei were washed and snap-frozen in CLB supplemented with 50% glycerol. To obtain fragmented chromatin for ChIP, nuclei were resuspended in sonication buffer (50 mM Tris pH:8.0, 1% SDS, 10mM EDTA, supplemented with protease inhibitor) and sonicated for 20 cycles of 30 sec ON/30 sec OFF (setting high, BioruptorTM Next Gen, Diagenode). Fragment sizes ranged from 200-600 bp as determined by decrosslinking a 50μl aliquot and running the purified DNA on a 1.5% agarose gel.    ChIPs were performed by incubating ~500 ng (DNA-content) sonicated chromatin from 3D7/TRZGFP and 3D7/TRZHA overnight while rotating at 4°C with 1 μg mouse anti-GFP (Roche Diagnostics, #11814460001) or 1 μg rat anti-HA 3F10 (Roche Diagnostics, #12158167001), respectively, in incubation buffer (5% Triton-X-100, 750mM NaCl, 5mM EDTA, 2.5mM EGTA, 100mM Hepes pH 7.6) with 10 μl protA and 10 μl protG Dynabeads (Life Technologies, 10008D and 10009D). Beads were washed for 5 min at 4°C while rotating with 400 μl of the following wash buffers: 2x wash buffer 1 (0.1% SDS, 0.1% DOC, 1.0% Triton-X100, 1mM EDTA, 0.5mM EGTA, 20mM Hepes pH 7.6), 1x wash buffer 2 (0.1% SDS, 0.1% DOC, 1.0% Triton-X100, 500mM NaCl, 1mM EDTA, 0.5mM EGTA, 20 mM Hepes pH 7.6), 1x wash buffer 3 (250mM LiCl, 0.5% DOC, 0.5% NP-40, 1mM EDTA, 0.5mM EGTA, 20mM Hepes pH7.6), 2x wash buffer 4 (1mM EDTA, 0.5mM EGTA, 20 mM Hepes pH7.6). The immunoprecipitated chromatin was eluted in 200 μl elution buffer (1% SDS, 0.1M NaHCO3) while rotating for 20 min at RT and decrosslinked in decrosslinking buffer (1%SDS, 0.1M NaHCO3, 1M NaCl) in a 45°C shaking heat-block overnight. In parallel, 30 μl of sonicated input chromatin was decrosslinked under the same conditions. The DNA was purified over QIAquick PCR columns (Qiagen) and ten separate anti-HA or anti-GFP ChIPs were pooled over one column.
For each line, the purified DNA from ten ChIPs or 5ng of the respective input sample was used for sequencing library preparation. Libraries were end-repaired followed by the addition of 3’ A-overhangs and the ligation of NEXTFlex barcoded adapters (Bio Scientific, #514122). The libraries were then amplified using the KAPA HiFi HotStart ready-mix (KAPA Biosystems) under the following conditions: 98°C for 2 min; 4 cycles of 98°C for 20sec, and 62°C for 3min; 62°C for 5 min. Amplified libraries were gel size-selected for ~230-330 bp fragments on a 2% E-Gel SizeSelection agarose gel (Invitrogen, #G6610-02). The size-selected libraries were amplified for another 8 cycles with the KAPA HiFi HotStart ready-mix and adapter dimers were removed by purification using Agencourt AMPure XP beads (Beckman Coulter, #A63880).     The following NEXTFlex barcode adapters were used:  Pf3D7-TRZGFP-chip       CGATGT NEXTflex ChIP-seq 6 Barcodes 1  Pf3D7-TRZGFP-input      TGACCA NEXTflex ChIP-seq 6 Barcodes 2  Pf3D7-TRZha-chip         ACAGTG NEXTflex ChIP-seq 6 Barcodes 3  Pf3D7-TRZha-input       GCCAAT NEXTflex ChIP-seq 6 Barcodes 4

treatment_protocol: Parasite cultures were synchronized by repeated sorbitol treatments (Lambros and Vanderberg, 1979).

tag: genomic modification

value: endogenous PF3D7_1209300 tagged with C-terminal GFP tag by single cross-over homologous recombination

tag: development stage

value: schizont


title: AML-DMSO (PRO-seq)

data_processing:
Library strategy: PRO-seq
Base-calling, filtering, and demultiplexing were performed using Illumina CASAVA 1.8.2 with default settings.
Raw reads were processed to trim adaptor and low quality sequences using Trimmomatic (version 0.32) with parameters: -phred33 input.txt.gz output.txt.gz ILLUMINACLIP:adaptor.txt:2:30:7 TRAILING:15.
For PRO-seq, reverse complements of the trimmed reads were generated using “fastx_reverse_complement” (version 0.0.13) with default settings, and the reverse complement sequences were aligned to the human genome hg19 using bowtie2 (version 2.2.4) with default settings. For ChIP-exo, pre-processed reads were aligned to hg19 using bowtie2 with default settings. For RNA-seq, pre-processed reads were aligned to hg19 using TopHat (version 2.0.10) with default settings.
H3K27ac peak calling was performed using MACS2 (version 2.0.10) with parameters: MACS2 callpeak -t H3K27ac.bam -c Input.bam --nomodel -f BAM -g hs -n -B.
Genome_build: hg19
Supplementary_files_format_and_content: Genome coverage was normalized and calculated for each strand separately and reported in bedGraph format. The ChIP-exo peak file reports genome coordinates, peak length, read counts, and enrichment significance for each called H3K27ac peak. RNA-seq count files contain gene RefSeq IDs and their normalized read counts in reads per kilobase of transcript per million mapped reads (RPKM).

molecule: nuclear RNA

source_name: primary acute myeloid leukemia patient cells

growth_protocol: IMDM supplemented with 20% BIT 9500 Serum Substitute, 50 ng/ml SCF, 10 ng/ml IL-6, and 10 ng/ml IL-3.

extract_protocol:
Nuclei isolation by douncing in isotonic buffer with 0.1% Triton X-100
Nuclear run-on assays were performed with ATP, UTP, GTP, and biotin-11-CTP or with all 4 biotin-11-NTPs. Nuclei were lyzed with TRIzol, nuclear RNA was extracted and fragmented, and biotinylated RNA was purified with strepavidin magnetic beads, which was followed by 3' adaptor ligation, 5' repair, 5' adaptor ligation, reverse transcription, and PCR full-scale amplification.

treatment_protocol: DMSO, 1hr

value: DMSO, 1hr


title: Input_for_H3K27ac (ChIP-exo)

data_processing:
Library strategy: ChIP-exo
Base-calling, filtering, and demultiplexing were performed using Illumina CASAVA 1.8.2 with default settings.
Raw reads were processed to trim adaptor and low quality sequences using Trimmomatic (version 0.32) with parameters: -phred33 input.txt.gz output.txt.gz ILLUMINACLIP:adaptor.txt:2:30:7 TRAILING:15.
For PRO-seq, reverse complements of the trimmed reads were generated using “fastx_reverse_complement” (version 0.0.13) with default settings, and the reverse complement sequences were aligned to the human genome hg19 using bowtie2 (version 2.2.4) with default settings. For ChIP-exo, pre-processed reads were aligned to hg19 using bowtie2 with default settings. For RNA-seq, pre-processed reads were aligned to hg19 using TopHat (version 2.0.10) with default settings.
H3K27ac peak calling was performed using MACS2 (version 2.0.10) with parameters: MACS2 callpeak -t H3K27ac.bam -c Input.bam --nomodel -f BAM -g hs -n -B.
Genome_build: hg19
Supplementary_files_format_and_content: Genome coverage was normalized and calculated for each strand separately and reported in bedGraph format. The ChIP-exo peak file reports genome coordinates, peak length, read counts, and enrichment significance for each called H3K27ac peak. RNA-seq count files contain gene RefSeq IDs and their normalized read counts in reads per kilobase of transcript per million mapped reads (RPKM).

extract_protocol:
Cells (50 million) were fixed with 1% formaldehyde for 10 minutes at room temperature and reaction was quenched with 125 mM Glycine. Fragmented chromatin before immunoprecipitation was used to extract DNA as input.
ChIP-exo libraries were prepared according to the published method: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/


title: JQ1-1hr (PRO-seq)

treatment_protocol: 250 nM JQ1, 1 hr

value: 250 nM JQ1, 1 hr


title: Mantle cell lymphoma [4772]

city: Bethesda

first: Delong

state: MD

address: 10 Center Drive

institute: NHLBI/NIH

description: RNA-sequencing

data_processing:
Basecalls performed using CASAVA version 1.4
RNAseq reads were aligned to the hg19 genome assembly using MapSplice 2 with default parameters.
Bam files were generated from MapSplice 2.
SNP and INDEL were called from the bam files using VarScan2 package on the NIH Biowulf.
Genome_build: hg 19
Supplementary_files_format_and_content: txt

source_name: peripheral blood

growth_protocol: Mononuclear cells from PB and LN single-cell suspension were isolated by density gradient centrifugation using the lymphocyte separation medium (ICN Biomedicals). Fresh cells were subject to CD19 selection by magnetic beads labeling using the MACS columns (Miltenyi Biotec). CD19 samples with purity of >96% were stored at -80°C for subsequent use.

extract_protocol:
Total RNA was extracted from purified tumor cells of 15 leukemic samples, and one unpurified LN sample. Subsequently, Polyadenylated RNA was enriched by two rounds of oligo(dT) selection (Invitrogen), followed by PA-seq library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flow sorting was used to collect the two fractions, CD19+/CD5+ fraction and the CD19- fraction from viably frozen samples. Cells were stained with CD19-PE and CD5-APC, incubated on ice for 30min, washed with FACS buffer, and resuspended in 1ml of FACS buffer for flow sorting. The collected CD19+/CD5+ cells and CD19- cells were pelleted for DNA extraction

value: CD19+ selected B cells

value: Mantle cell lymphoma

tag: tissue type

value: peripheral blood


title: Mantle cell lymphoma [4931]

description: RNA-sequencing


title: Mantle cell lymphoma [4758]

description: RNA-sequencing


title: Mantle cell lymphoma [4530]

description: RNA-sequencing


title: Mantle cell lymphoma [5435]

description: RNA-sequencing


title: Mantle cell lymphoma [7296]

description: RNA-sequencing

source_name: Unpurified lymph node biopsy

value: mixture of B, T and other cells

value: lymph node mix


title: Untreated Wild-type #1

description:
Sample_21786
WT_UTvsX_UT_gene_exp.diff
WT_UTvsX_DTT_gene_exp.diff
WT_UTvsWT_DTT_gene_exp.diff
WT_UTvsWT_DTT_splicing.diff
WT_UTvsKO_UT_gene_exp.diff
WT_UTvsKO_DTT_gene_exp.diff

tag: strain

value: Untreated


title: Mantle cell lymphoma [3064]

description: RNA-sequencing


title: YY010

value: Peripheral blood monocytes

value: Health control


title: Mantle cell lymphoma [3011]

description: RNA-sequencing


title: YY006


title: Pf3D7-TRZha-input

description: anti-HA input

value: endogenous PF3D7_1209300 tagged with C-terminal 3xHA tag by double cross-over homologous recombination and recycling of selection cassette

tag: chip antibody

value: rat anti-HA 3F10 (Roche Diagnostics, #12158167001)


title: YY001

value: Chronic periodontitis


title: Pf3D7-TRZha-chip

description: anti-HA ChIP


title: H3K4me1 rep 3 Chip-Seq KC

value: Foreskin

value: H3K4me1(Abcam. Cat:ab8895)


title: YY002


title: H3K4me1 rep3 Chip-Seq EpiSC

source_name: Epidermal Stem Cells


title: H3K4me1 rep 2 Chip-Seq EpiSC


title: H3K27ac (ChIP-exo)

extract_protocol:
Cells (50 million) were fixed with 1% formaldehyde for 10 minutes at room temperature and reaction was quenched with 125 mM Glycine. Fragmented chromatin was immunoprecipitated with H3K27ac antibody.
ChIP-exo libraries were prepared according to the published method: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/

tag: cell line

value: Kasumi-1 cells


title: AML-JQ1 (PRO-seq)

treatment_protocol: 250 nM JQ1, 1hr

value: primary acute myeloid leukemia patient cells