title: S14_1

first: Chengguo

last: Wei

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The RNA-seq data were analyzed by following the procedure described below. Briefly, after sequence quality filtering at a cutoff of a minimum quality score Q20 in at least 90% bases, the good-quality reads aligned to Reads were processed and aligned to the University of California Santa Cruz (UCSC) human reference genome and transcriptome (build hg19) using the Burrows-Wheeler Aligner (BWA) (Li and Durbin 2009).
The reads that are uniquely aligned to the exon and splicing junction sites for each transcript were combined to calculate an expression level for a corresponding transcript and further normalized based on reads per kilobase per million reads in order to compare transcription levels among samples. The transcripts with a low raw read count <100 in all the samples were excluded for downstream analysis. Gene expression value was transformed to the log 2 base scale.
Principle Component Analysis (PCA) was firstly performed to assess the sample correlations using the expression data of all the genes. The differentially expressed genes for mRNA and lncRNA in tumor compared with normal were identified by the R package and we selected the genes based on limma test adjusted P<0.05 and 1.5-fold change. The gene ontology (GO) and pathway analysis for the differentially expressed genes were then performed with fold change cutoff of ≥1.5 using INGENUITY© IPA (www.ingenuity.com/products/ipa) and the online tool Enrichr.
The read coverage of gene functional elements was also visualized by the Integrative Genome Viewer tool (www.broadinstitute.org/igv/) from the genome alignment file. Heatmap was used to visualize the top 50 differentially expressed genes using the limma test after the median center was transformed using Multi-Experiment Viewer software (Saeed, Sharov et al. 2003).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample were generated

source_name: esophageal squamous cell carcinoma

extract_protocol:
Total RNA from tissues was extracted using the Trizol reagent (Ambion, Catalog No.15596026, USA) according to the manufacturer’s protocol. RNA concentrations were quantified using a Nano-drop Spectrophotometer at a wavelength of 260 nm. RNA samples were analyzed by Bioanalyzer at a concentration of 100–200 ng/μl to verify the concentration and the purity of samples. Only the samples with RNA integrity values of >7.0 were used for mRNA and lncRNA sequencing at the Genomic Core Facility at Novogene Co., Ltd (Beijing, China).
PolyA selection strategy of library construction was performed at Novogene Co., Ltd (Beijing, China).

tag: tissue type

value: esophageal squamous cell carcinoma


title: LPS BAL DC2/3 1

status: Public on Feb 23 2019

type: RNA

city: Newcastle

first: Laura

last: Jardine

address: Framlington Place

department: Faculty of Medical Sciences

country: United Kingdom

institute: Newcastle University

hyb_protocol: Transcripts were detected using a NanoString Immunology v2 panel according to the manufacturer's instructions. Experiments using blood and BAL DC2/3 included an additional 30-gene add-on to the Immunology v2 panel, designed to detect DC and monocyte/macrophage genes. Hybridisation occurred under 'High Sensitivity' settings.

scan_protocol: FOV 555

data_processing: Data normalization was performed in nSolver version 3.

molecule: total RNA

organism: Homo sapiens

source_name: LPS BAL, DC2/3

extract_protocol: Lysates from 1-2x10e4 cells per sorted population were prepared using 5μl buffer RLT (Qiagen) with 1% beta-mercaptoethanol (Sigma).

tag: sample type

value: LPS BAL

tag: treatment

value: LPS

tag: cell type

value: BAL, DC2/3


title: LPS BAL DC1 2

source_name: LPS BAL, DC1

value: BAL, DC1


title: LPS BAL DC2 2

source_name: LPS BAL, DC2

value: BAL, DC2


title: S12_1

type: SRA

city: New York

state: NY

country: USA

library_source: transcriptomic


title: T_NPB_1

city: Fuzhou

first: Justice

last: Norvienyeku

state: N/A = Not Applicable

address: shangxia District RD.No#15, Fuzhou

country: China

institute: Fujian Agriculture and Forestry University

description:
Inoculated leaves
PolyA RNA
processed data: Gene_Expression_All_Samples.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house Perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data.
Rice (Oryza sativa Japonica group, IRGSP-1.0) reference genome and gene model annotation files were downloaded from Ensembl Plants genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. Then, RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Oryza_sativa.IRGSP V1.0 (IRGSP-1.0 from Ensembl Plants genome database)
Supplementary_files_format_and_content: GeneExpression.AllSamples.txt: Tab-delimited text file includes RPKM values for each Sample.

organism: Oryza sativa Japonica Group

source_name: NPB rice cultivar

extract_protocol:
Total RNA was extracted using the RNAprep pure Plant Kit (Tiangen, Beijing) by following processes recommended by the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Susceptible (CO39 and NPB) and resistant (Pi_gm) rice cultivars were spray inoculated with P. oryzae spore and incubated for 12-hours.

tag: cultivar

value: NPB

tag: seedlings age

value: 3 weeks

tag: tissue

value: Leaves

value: Inoculated with Pyricularia oryzae

tag: sample group

value: Treatment


title: C_NPB_2

description:
Non-inoculated leaves
PolyA RNA
processed data: Gene_Expression_All_Samples.txt

value: Non-inoculated

value: Control


title: S8_1


title: S10_1


title: C_NPB_1


title: LPS BAL DC2 1


title: LPS BAL CD14++CD16- 3

source_name: LPS BAL, Classical Monocyte

value: BAL, Classical Monocyte


title: LPS BAL CD14++CD16- 2


title: LPS BAL CD14++CD16- 1


title: LPS BAL DC1 1


title: LPS BAL AM 4

source_name: LPS BAL, AM

value: BAL, AM


title: wild type

city: Shanghai

first: weiwei

last: Qi

address: No 99 Shangda Road

institute: Shanghai  University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73 RefGen_v3 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments 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: Ensembl plants release‐19 zea_mays
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: kernel

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: endosperm

tag: age

value: 15 DAP

tag: genotype

value: wild type


title: LPS BAL AM 1

value: LPS BAL


title: S4_1

value: esophageal squamous cell carcinoma


title: S2_1


title: S13_1

source_name: normal tissue

value: normal tissue


title: dek44 mutant


title: C_NPB_3


title: LPS BAL AM 3

value: LPS


title: LPS BAL AM 2


title: S11_1


title: HC Blood non classical mono 2

source_name: Healthy Control, Blood, Non-classical Monocyte

value: Healthy Control

value: Healthy

value: Blood, Non-classical Monocyte


title: HC Blood non classical mono 3


title: S6_1


title: Mv411DAPT rep2

city: Wuhan

first: Dan

last: Li

state: Hubei

address: 1095 Jie-Fang Avenue

institute: Tongji Hospital

data_processing:
online_YX software was used for basecalling
We use internal software SOAPnuke(version:v1.5.2) to filter reads, followed as: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 10%; 3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 50% in a read). After filtering, the remaining reads are called "Clean Reads" and stored in FASTQ format. We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts; HISAT2: Version: v2.0.4) to do the mapping step.
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.   HISAT2:ersion: v2.0.4. Parameters: -p 8 --phred64 --sensitive -I 1 -X 1000. Website: http://www.ccb.jhu.edu/software/hisat
We mapped clean reads to reference using Bowtie2, and then calculate gene expression level with RSEM. Bowtie2 :
Version: v2.2.5
Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200 Website: http://bowtie-bio.sourceforge.net/ Bowtie2 /index.shtml.RSEM : Version: v1.2.12 Parameters: default
Website: http://deweylab.biostat.wisc.edu/ RSEM
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Cells were collected, washed with PBS, and then flash frozen on dry ice. We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value,28S/18S and the fragment length distribution.
1)mRNA enrichment: Oligo dT Selection or rRNA depletion;2)RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer;3)End repair, add A tailing and adaptor ligation:The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments;4)PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer;5)Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase;6) Sequencing on BGISEQ-500 platform.

treatment_protocol: MV4-11 and MOLM-13 cells were treated in duplicate with DMSO, 2.5nM AC220, 25uM DAPT or 2.5nM AC220 plus 25uM DAPT (Combo) for 12h.

tag: cell line

value: Acute Myeloid Leukemia(AML) cell line

value: GSI


title: Mv411DMSO rep2

value: DMSO


title: HC Blood non classical mono 1


title: Mv411DAPT rep1


title: Mv411DMSO rep1


title: S5_1


title: Mv411Combo rep2

value: TKI+GSI


title: S7_1


title: Mv411Combo rep1


title: S3_1


title: Mv411Ac220 rep2

value: TKI


title: S9_1


title: HC Blood int mono 2

source_name: Healthy Control, Blood, int. Monocyte

value: Blood, int. Monocyte


title: Sample 18 miR-205 KO

city: Dallas

first: Igor

middle: M

last: Dozmorov

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

hyb_protocol: Samples were hybridized with GeneChip Mouse clariom S array

scan_protocol: Array scanning was per manufacturer (Affymetrix)

data_processing: Raw data was processed with normalization method  based on the use of “internal standards”, that characterize some aspects of the system’s behavior, such as technical variability. The two-step normalization procedure and the Associative analysis functions are presented in our publications (Dozmorov, I. and I. Lefkovits, Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res, 2009. 37(19): p. 6323-39). These algorithms are also obtainable from an R package diffGeneAnalysis, available as a part of Bioconductor packages (http://www.bioconductor.org/packages/2.5/bioc/html/diffGeneAnalysis.html).

label: biotin

organism: Mus musculus

source_name: pituitary

label_protocol: Single-stranded cDNA was generated from amplified cRNA with the WT plus cDNA synthesis kit (Afffymetrix), fragments and labeled with the WT terminal labeling kit

extract_protocol: A segment of ear was flash frozen in liquid N2, and samples were thawed in 1.4 ml of Qiazol using a mortar and pestle. RNA was extracted using the miRNAEasy kit from Qiagen

tag: strain

tag: gender

value: female

value: 5-6 weeks


title: S1_1


title: Mv411Ac220 rep1


title: HC Blood int mono 1


title: Sample 16 miR-205 KO


title: HC Blood DC3 2

source_name: Healthy Control, Blood, DC3

value: Blood, DC3


title: HC Blood DC3 3


title: Sample 15 lncKO


title: Neu-D3_RNASEQ_rep2

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description:
asc_neurodiff_day3-2
RNA isolation using Qiagen RNeasy kit

data_processing:
ChIP-seq reads were aligned to the hg19 reference genome using bowtie2 version 2.1.0
Hi-C reads were aligned and processed using hiclib
RNA-seq was processed using the tuxedo protocol. 30 bp was trimmed from the read ends
Duplicate reads were removed using picard MarkDuplicates
ChIP and Input experiments were ensured to have equal read depth per chromosome by downsampling the deeper sequenced experiment
Peak calling was done using EDD version 1.1.7
Genome_build: hg19
Supplementary_files_format_and_content: bed files with four columns: chromosome, start position, end position, score; fpkm_tracking files with 13 columns tracking_id, class_code, nearest_ref_id, gene_id, gene_short_name, tss_id, locus, length, coverage, FPKM, FPKM_conf_lo, FPKM_conf_hi, FPKM_status

source_name: Human primary adipose stem cells

growth_protocol: Human normal adipose tissue-derived mesenchymal stem cells were prepared from subcutaneous liposuction material. Cells were cultured under proliferative conditions in DMEM/F12 containing 10% fetal calf serum, 10 ng/ml epidermal growth factor (Sigma-Aldrich E9644) and 20 ng/ml basic fibroblast growth factor (FGF2; Sigma-Aldrich F5392). Cells at passage 5-7 were used in two independent differentiation experiments, each towards adipose or neuronal lineages.

extract_protocol:
For RNA-seq, total mRNA was isolated from Neu-D1 and Neu-D3 cells using the Qiagen RNeasy kit and processed for Illumina library preparation and sequencing. For ChIP-seq of lamin B1, cells at each differentiation time point were fixed with 1% formaldehyde for 10 min, lysed for 10 min in ChIP lysis buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS, protease inhibitors and 1 mM PMSF) and sonicated 4 times 10 min in a Bioruptor (Diagenode) to generate 200 base-pair DNA fragments. After sedimentation, the supernatant was collected and diluted 10-fold in RIPA (140 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, protease inhibitors, 1 mM PMSF). Chromatin was incubated overnight at 4oC with the anti-lamin B1 antibody coupled to Dynabeads Protein A/G (Invitrogen). ChIP samples were washed 4 times in ice-cold RIPA, crosslinks reversed and DNA eluted for 6 h at 68oC in 50 mM NaCl, 20 mM Tris-HCl pH 7.5, 5 mM EDTA, 1% SDS and 50 ng/µl Proteinase K. DNA was purified using phenol-chloroform isoamylalcohol and dissolved in H2O prior to processing for Illumina library preparation and sequencing. For Hi-C, 25 million cells per time point and differentiation replicate were cross-linked with fresh 1% formaldehyde (Pierce) for 12 min at room temperature on a rocker. Excess formaldehyde was quenched with 0.125 M glycine for 5 min and cells washed 3 times 5 min in ice-cold PBS. Crosslinked cells were lysed in lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630 and protease inhibitors) on ice for 15 min and homogenised by Douncing with a B-pestle (tight) in lysis buffer until nuclei were released, as assessed by microscopy. The lysate was sedimented, the pellet was resuspended in NEBuffer 2 (10 mM Tris-HCl pH 7.9, 50 mM NaCl, 10 mM MgCl2, 1 mM dithiothreitol) containing 0.1% SDS, and incubated at 65oC for 10 min. SDS was quenched on ice with 1% Triton X-100 and the sample digested with HindIII overnight at 37oC. Digested fragments were labelled with biotin-14-dCTP and blunt-end ligated. Crosslinks were reversed at 65oC overnight, the ligated DNA was purified by phenol-chloroform:isoamylalcohol (Ambion), desalted and RNAse-treated. DNA was sheared to ~100-300 base-pairs by Covaris sonication and size-fractionated on AMpure XP magnetic beads (Beckman Coulter). Biotinylated DNA fragments were pulled-down with Streptavidin beads and processed for Illumina adapter ligation and library preparation.
Illumina sequencing libraries were generated as per Illumina protocols.

treatment_protocol: Two days before induction of differentiation, proliferating cells (hereafter, ‘Pro’ stage) were harvested and processed for Hi-C or ChIP. For adipogenic differentiation, harvested ‘Pro’ cells were reseeded in DMEM/F12/10% serum without growth factors. Adipogenesis was induced 48 h later (D0) by addition of 10 µg/ml insulin, 200 µM indomethacin, 0.5 µM 1-methyl-3 isobutylxanthine and 1 µM dexamethasone. Medium was left with the cells for the 3 days of differentiation. Cells were collected on D1 and D3 (Ad-D1 and Ad-D3) and processed for Hi-C or ChIP. Neuronal differentiation was initiated on D0. In brief, medium was removed on D0 and cells were washed twice 4 min in pre-warmed Gibco serum-free DMEM (Thermo Fisher Scientific). Washing medium was removed and differentiation was induced by adding Gibco Neurobasal medium (Thermo Fisher Scientific) supplemented with 1% fetal calf serum, 1x B27 (Thermo Fisher Scientific), 0.5 mM IBMX, 1 µm dexamethasone, 10 µm forskolin, 200 µm 8CTP-cAMP and 10 mM valproic acid. Medium was left with the cells for the 3 days of differentiation. Cells were collected on D1 and D3 (Neu-D1 and Neu-D3) and processed for Hi-C or RNA isolation for RNA-seq.

tag: time point

value: Day 3

value: ASCs on day 3 after adipogenic induction

tag: chip antibody

tag: replicate


title: Sample 17 miR-205 KO


title: HC Blood int mono 3


title: Molm13DMSO rep2


title: Neu-D3_RNASEQ_rep1

description:
asc_neurodiff_day3-1
RNA isolation using Qiagen RNeasy kit


title: HC Blood DC3 1


title: Neu-D1_RNASEQ_rep2

description:
asc_neurodiff_day1-2
RNA isolation using Qiagen RNeasy kit

value: Day 1

value: ASCs on day 1 after neuronal induction


title: Sample 9 miR-205 KO

source_name: skin


title: Sample 10 wt


title: Sample 14 lncKO


title: Sample 13 lncKO


title: Sample 11 wt


title: HC Blood DC2 3

source_name: Healthy Control, Blood, DC2

value: Blood, DC2


title: Sample 8 miR-205 KO


title: Neu-D1_RNASEQ_rep1

description:
asc_neurodiff_day1-1
RNA isolation using Qiagen RNeasy kit


title: Sample 12 wt


title: Molm13DAPT rep1


title: Molm13Combo rep2


title: HC Blood DC2 2

value: Healthy Control


title: JQ E7 Yellow_2 [E7Y]

city: Los Angeles

first: Masafumi

last: Inaba

state: CA

address: 2011 Zonal Ave.

department: Pathology

institute: University of Southern California

data_processing:
Read alignment was performed using local-installed Galaxy 18.05
Tophat2 (Galaxy Version 2.1.1) was used to perform alignment
Cufflinks package (Galaxy Version 2.2) was used for differential expression analysis.
Gene symbols of the supplied DEG list was added by using QIAGEN Ingenuity Pathway Analysis (IPA) platform.
Genome_build: Coturnix Japonica 2.0 (GCA_001577835.1)
Supplementary_files_format_and_content: One Excel file include a list of defferntially expressed genes with RPKM and p-value compared black strip with yellow strip samples

organism: Coturnix japonica

source_name: Yellow stripe in skin

growth_protocol: fertilized eggs

extract_protocol:
Dissected tissue was extracted in Trizol reagent
Libraries were prepared using Illumina TruSeq RNA Sample Preparation V2

treatment_protocol: untreated

tag: phenotype

value: yellow pigmented embryonic skin

value: fertilized eggs


title: HC Blood DC2 1

value: Healthy


title: JQ E7 Yellow_1 [E7Y]


title: JQ E7 Black_2 [E7B]

source_name: Black stripe in skin

value: black pigmented embryonic skin


title: Sample 7 miR-205 KO


title: HC Blood classical mono 3

source_name: Healthy Control, Blood, Classical Monocyte

value: Blood, Classical Monocyte


title: Sample 5 lncKO


title: Sample 6 lncKO


title: Sample 4 lncKO


title: Molm13Ac220 rep2

value: Acute Myeloid Leukemia(AML) cell line


title: JQ E7 Black_1 [E7B]


title: HC Blood classical mono 2


title: Molm13DMSO rep1

value: DMSO


title: HC Blood classical mono 1


title: Molm13DAPT rep2

value: GSI


title: Molm13Combo rep1

value: TKI+GSI


title: H2228_H1975_A549_H838_HCC827_Mixture_10X

status: Public on Feb 22 2019

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Fastq files were generated using Cellranger. All R1 files were concatenated and all R2 files were concatenated for processing with scPipe.
Sample filtered gene count matrix was generated using scPipe with ENSEMBL GRCh38p10 gene annotation. With scPipe, we processed the 5000 most enriched cell barcodes, with comp=2 used for quality control to remove poor quality cells.
Genome_build: GRCh38 patch 10
Supplementary_files_format_and_content: barcodes.csv: Counts matrix with samples along the columns and genes along the rows
Supplementary_files_format_and_content: gene_count.csv: 5001 most abundant cell barcodes with cell ids, barcode sequence and counts

molecule: polyA RNA

source_name: lung adenocarcinoma

growth_protocol: The human lung adenocarcinoma cell lines H2228, H1975, A549, H838 and HCC827 were retrieved from ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum (FCS) and 1% Penicillin-Streptomycin.  The cells were grown independently at 37C  with 5% carbon dioxide until near 100% confluency.

extract_protocol:
The cells were counted using Chamber Slide and rounghly 2 million cells from each cell line were mixed and processed by 10X. Three CEL-seq2 plates were sorted for the same sample.
following the standard 10X single cell RNA-seq document, using v2 chemistry.

tag: barcode coordinate

value: bases 1 to 16 on R1

tag: umi coordinate

value: bases 17 to 26 on R1


title: Molm13Ac220 rep1

tag: treatment

value: TKI


title: LNCaP-95: DHT_ARE_2

city: Pasadena

first: Peter

last: Dervan

address: 1200 E. California Blvd., MC164-30

institute: California Institute of Technology

library_source: genomic

data_processing:
Aligned to hg19 using Bowtie2-2.2.3 using parameters  -v 2 -k 11 -m 10 -t -p 12 --strata --best
Peak calling was performed using MACS2 using command callpeak -t ar_dht1_csfb.bam -c input1_csfb.bam -f BAM -g hs -n ar_dht1_csfb.bam.macs -B -q 0.001
Reproducible peaks for initial motif discovery were determined by IDR using default parameters
Individual bigWig files were generated from MACS2 bedGraph files. Merged bigWig files (one per condition) were also created and used for visualization
Differentially changed peaks were determined by PePr using peaktype sharp --normalization intra-group
Peak annotation was performed by ChIPseeker using TxDb.Hsapiens.UCSC.hg19.knownGene and 1000 bases around peak centers
Motif finding was performed by MEME-ChIP using default parameters
Motif density was analyzed using the Homer annotatePeaks command using parameters hg19 -size 1000 -hist 5
Genome_build: hg19
Supplementary_files_format_and_content: peaks files were generated using MACS2 and include peak location, length, and enrichment

molecule: genomic DNA

source_name: human prostate cancer cell line

growth_protocol: Cells were plated at 20 million cells per plate in phenol red free RPMI-1640 with 10% CTFBS and allowed to adhere for 24 hours prior to treatment

extract_protocol:
Cell lysates were sonicated and AR antibody used to isolate AR-DNA complexes
Libraries were prepared following Illumina protocol.

treatment_protocol: Cells were treated with vehicle (DMSO), DHT (10 nM), or DHT and Py-Im polyamide (10 uM) for 24 hours

value: human prostate cancer cell line

tag: passages


title: PCDF1_veh_H3K27ac_repl1

city: Nijmegen

first: Suzan

last: Stelloo

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyser (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA9. Reads with a BWA alignment quality score less than 20 were removed.
Peak calling was performed using two algorithms: MACS 1.4 and DFilter. Only the peaks called by both algorithms were used for further analysis.
Peaks present in at least one of two replicates were used to construct the list of peaks present in fibroblasts.
Genome_build: hg19
Supplementary_files_format_and_content: peak lists

growth_protocol: Primary fibroblast cultures were established as previously described (Villegas and McPhaul, 2005). Prostate cancer derived fibroblasts (PCDF) were cultured for a maximum of seven passage.

extract_protocol:
Chromatin immunoprecipitations were performed as described previously with minor changes (Stelloo et al, 2018, Singh et al 2019). Samples were crosslinked with 2 mM DSG (CovaChem) for 25 min at room temperature followed by 1% formaldehyde for 10 minutes at room temperature and subsequently quenched with glycine. Samples were lysed as described (Schmidt et al., 2009) and sonicated for at least 10 cycles of 30s on, 30s off using a Diagenode Bioruptor Pico. For each ChIP, 5ug of antibody was conjugated with 50ul Protein A magnetic beads. Antibodies used were AR (sc-816, Santa Cruz), H3K27ac (39133, Active Motif). Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).

treatment_protocol: Prostate cancer-derived fibroblast cells were hormone‐deprived for 3 days and subsequently treated for 4 hours with 10-7M R1881 (synthetic testosterone) or DMSO control.

tag: cell type

value: prostate cancer-derived fibroblasts

tag: group

value: veh

value: H3K27ac (active motif; 39133)


title: PCDF1_veh_AR_repl2

value: AR (Santa Cruz; sc-816,lot:I0215)


title: PCDF2_veh_AR_repl2


title: PCDF1_R1881_AR_repl1


title: PCDF2_veh_H3K27ac_repl1


title: PCDF2_R1881_H3K27ac_repl2


title: PCDF2_R1881_AR_repl1


title: PCDF1_R1881_H3K27ac_repl1


title: LNCaP-95: NT_1

tag: tissue


title: PCDF2_veh_H3K27ac_repl2


title: PCDF2_veh_AR_repl1


title: LNCaP-95: DHT_ARE_1


title: LNCaP-95: DHT_2


title: LNCaP-95: DHT_1


title: PCDF1_R1881_AR_repl2


title: PCDF2_R1881_AR_repl2


title: LNCaP-95: Input_2


title: Sample 2 wt

value: female

value: 5-6 weeks


title: LNCaP-95: Input_1


title: Sample 3 wt


title: Sample 1 wt


title: PCDF2_R1881_H3K27ac_repl1


title: PCDF1_veh_AR_repl1


title: LNCaP-95: NT_2


title: Loxp/loxp, Myh6,Cre+ rep4

city: Philadelphia

first: Jeffrey

last: Field

state: PA

address: 1313 BRB II/III U

department: Pharmacology

institute: University of Pennsylvania

data_processing:
Experiment A was aligned to mm10 by the Ion Torrent Suite and Experiment B was aligned to the reference genome mm10 by STAR v2.6.0c
Experiment A was quantified by ENSEMBL annotations and normalized using Deseq algorithm by the StrandNGS program
Experiment B was qunatified using ENSEMBLv93 annotations and normalized at the gene-level, using a resampling strategy, the code is available at https://github.com/itmat/Normalization (-v0.8.5b-beta)
Genome_build: mm10
Supplementary_files_format_and_content: For experiment A, tab-delimited text file with transcript-level read counts. For experiment B, tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

source_name: heart

extract_protocol:
heart were removed, flash frozen on dry ice, and RNA was harvested using Qiagen Fibrous RNAeasy kit.
Experiment A was constructed with Ion Total RNA-Seq Kit v2 and Experiment B was prepared with Illumina TruSeq RNA Stranded mRNA HT Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: organ

value: heart

value: Loxp/Loxp, Cre+

value: male

tag: experiment

value: B


title: Loxp/loxp rep5

tag: age

tag: genotype

value: Loxp/Loxp,Cre-


title: Loxp/loxp, Myh6,Cre+ rep2

tag: strain


title: Loxp/loxp, Myh6,Cre+ rep1

tag: gender


title: Loxp/loxp rep4


title: Loxp/loxp, Myh6,Cre+ rep3


title: CMP_12928-20_C

city: London

first: M Joaquina

last: Delas

address: 1 Midland Road

department: Briscoe Lab

institute: The Francis Crick Institute

description: fluorescence-activated sorted cells

data_processing:
RNAseq libraries were mapped with STAR aligner (Dobin et al., 2013) against the mm10 mouse genome assembly using default parameters.
Duplicate alignments were removed from the resulting BAM files with Picard (http://broadinstitute.github.io/picard).
HTSeq-count (Anders et al., 2015) was used to calculate gene counts
DESeq2 (Love et al., 2014) was used for quality control analysis, and to extract normalized counts.
Genome_build: mm10
Supplementary_files_format_and_content: Raw read counts and normalized counts.

source_name: Mouse bone marrow

growth_protocol: Animals were transplanted with sorted hematopoietic stem cells transduced with doxycycline-inducible shRNA against lncRNA Spehd or control knockdown. The animals were allow to reconstitute for 10 weeks. The animals were administered doxycycline-containing food for 6 days prior to bone marrow progenitor isolation. Cells were isolated by fluorescence-activated cell sorting based on the appropriate cell type markers and zsGreen (reporting shRNA expression).

extract_protocol:
RNA was extracted using the NucleoSpin RNA XS kit (Machery Nagel), with DNase treatment.
cDNA and libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech), SeqAmp DNA Polymerase (Clontech), and Low Input Library Prep Kit (Clontech).

treatment_protocol: The different samples were expressing different shRNAs against lncRNA Spehd or control.

value: CMP

tag: knockdown

value: C


title: Loxp/loxp rep1


title: Loxp/loxp rep2


title: CMP_Renilla_B

description: fluorescence-activated sorted cells

value: Renilla


title: CMP_Renilla_A

description: fluorescence-activated sorted cells

value: A


title: KLS_12928-10_A

description: fluorescence-activated sorted cells

value: KLS


title: KLS_12928-10_C

description: fluorescence-activated sorted cells


title: CMP_Renilla_C

description: fluorescence-activated sorted cells


title: Loxp/loxp rep3


title: KLS_12928-20_A

description: fluorescence-activated sorted cells


title: KLS_Renilla_A

description: fluorescence-activated sorted cells


title: CMP_12928-10_C

description: fluorescence-activated sorted cells


title: KLS_12928-10_B

description: fluorescence-activated sorted cells


title: KLS_Renilla_B

description: fluorescence-activated sorted cells


title: KLS_Renilla_C

description: fluorescence-activated sorted cells


title: CMP_12928-20_B

description: fluorescence-activated sorted cells


title: CMP_Renilla_D

description: fluorescence-activated sorted cells

value: D


title: CMP_12928-10_B

description: fluorescence-activated sorted cells


title: CMP_12928-10_A

description: fluorescence-activated sorted cells


title: KLS_Renilla_D

description: fluorescence-activated sorted cells


title: KLS_12928-20_C

description: fluorescence-activated sorted cells


title: 0GY IGGseq

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

data_processing:
adaptor-trimming and low quality reads removing by cutadapt (v1.9.1) software
RIP-seq reads were adaptor-trimmed and mapped to human genome (hg19) by bowtie2(v2.2.4)  software with default parameters.
Peak calling was performed with MACS software (v1.4.3). Differentially enriched regions were identified by diffReps software (v1.55.4).
The  enriched peaks were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation
Genome_build: Hg19

source_name: WS1 0GY

growth_protocol: Cell culture

extract_protocol:
RNA extraction protocol
library construction protocol

treatment_protocol: Cell irradiation with 0 or 5 Gy X-rays

tag: cell line


title: KLS_12928-20_B

description: fluorescence-activated sorted cells

tag: replicate


title: 0GY RIPseq


title: 5GY RIPseq

source_name: WS1 5GY


title: 5GY IGGseq


city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description:
scRNA-seq on PBMCs from patient CLL8 after 30 days of ibrutinib treatment
scRNA-seq_CLL8_30d
LiveBulk_CLL8_30d_10xTK118s_S8_L008

data_processing:
Preprocessing was performed using Cell Ranger (version 2.0.0) provided by 10x Genomics. Raw sequencing files were demultiplexed using the Cell Ranger command mkfastq. Each sample was aligned to the human reference genome refdata-cellranger-GRCh38-1.2.0 using Cell Ranger count, and all samples were aggregated using Cell Ranger aggr without depth normalization.
Genome_build: hg38
Supplementary_files_format_and_content: Each csv file contains read counts for each sample for each regulatory element; MTX (Matrix Market file format)

source_name: PBMCs_CLL patient after 30 days of ibrutinib treatment

extract_protocol:
An aliquot of the patient PBMCs was stained with DAPI for LIVE/DEAD discrimination and a maximum of 100.000 LIVE, doublet-excluded cells sorted in 1.5 ml tubes. Cells were pelleted by centrifuging for 5 min at 4 °C at 300 x g and resuspended in PBS with 0.04% BSA.
Single-cell libraries were generated using the GemCode Single-Cell Instrument and Single Cell 3' Library & Gel Bead Kit v2 (10x Genomics) according to the manufacturer’s protocol. In brief, up to 17.000 cells suspended in reverse transcription reagents, along with gel beads, were segregated into aqueous nanoliter-scale gel bead-in-emulsions (GEMs). The GEMs were then reverse transcribed in a T1000 Thermal cycler (Bid-Rad) programed at 53 °C for 45 min, 85 ºC for 5 min, and hold at 4 ºC. After reverse transcription, single-cell droplets were broken and the single-strand cDNA was isolated and cleaned with Cleanup Mix containing DynaBeads (Thermo Fisher Scientific). cDNA was then amplified with a T1000 Thermal cycler programed at 98 ºC for 3 min, 10 cycles of (98 ºC for 15 s, 67 ºC for 20 s, 72 ºC for 1 min), 72 ºC for 1 min, and hold at 4 ºC. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed and index adaptor ligated, with SPRIselect Reagent Kit (Beckman Coulter) with cleanup in between steps. Post-ligation product was amplified with a T1000 Thermal cycler programed at 98 ºC for 45 s, 10 cycles of (98 ºC for 20 s, 54 ºC for 30 s, 72 ºC for 20 s), 72 ºC for 1 min, and hold at 4 ºC. The sequencing-ready library was cleaned up with SPRIselect and sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq4000 platform and the 75-bp paired-end configuration.

treatment_protocol: All patients were diagnosed and treated and diagnosed according to the revised guidelines of the International Workshop Chronic Lymphocytic Leukemia/National Cancer Institute. Patients were recruited through clinical trial NCT01804686, aimed at studying the long-term effect of PCI-32765 (ibrutinib) and reflect the clinical and biological heterogeneity of the disease. The study was approved by the ethics committees of the contributing institutions (Semmelweis University and Medical University of Vienna). Informed consent was obtained from all participants.

value: chronic lymphocytic leukemia patient

value: Peripheral blood mononuclear cells (PBMCs)


description:
scRNA-seq on PBMCs from patient CLL5 after 150 days of ibrutinib treatment
scRNA-seq_CLL5_150d
LiveBulk_10x_CLL57_150d_S2_L006

source_name: PBMCs_CLL patient after 150 days of ibrutinib treatment


description:
scRNA-seq on PBMCs from patient CLL5 after 30 days of ibrutinib treatment
scRNA-seq_CLL5_30d
LiveBulk_CLL5_30d_10xTK118s_S5_L008


description:
scRNA-seq on PBMCs from patient CLL6 after 30 days of ibrutinib treatment
scRNA-seq_CLL6_30d
LiveBulk_CLL6_30d_10xTK118s_S7_L008


description:
scRNA-seq on PBMCs from patient CLL8 after 0 days of ibrutinib treatment
scRNA-seq_CLL8_0d
CLL8_d0_S3_L002

source_name: PBMCs_CLL patient after 0 days of ibrutinib treatment


description:
scRNA-seq on PBMCs from patient CLL8 after 120 days of ibrutinib treatment
scRNA-seq_CLL8_120d
LiveBulk_10x_CLL87_120d_S4_L006

source_name: PBMCs_CLL patient after 120 days of ibrutinib treatment


title: TE10_NEO_rep3

city: Luzhou

first: xu

last: liu

address: 25th Taiping Street

institute: The Affiliated Hospital of Southwest Medical University

data_processing:
Illumina bcl2fastq 2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRch37.p13 whole genome using HISAT2 (version 2.1.0) with default parameters
Read counts are aggregated at the gene level using HTseq(version 0.9.1) and then identified DEGs using R package DESeq2
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: tab-delimited text files include raw counts  for each Sample

extract_protocol:
Total RNA of stably infected cells was isolated with Trizol and the polyadenylated mRNAs were extracted using Dynabeads Oligo (dT) 25 beads
Three replicates were created for RNA-seq library construction using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), following the manufacturer’s instructions.

value: esophageal squamous cell carcinoma cell line

tag: genotype/variation

value: control


title: Eca109_NEO_rep2


description:
scRNA-seq on PBMCs from patient CLL6 after 280 days of ibrutinib treatment
scRNA-seq_CLL6_280d
CLL6_d280_S5_L002

source_name: PBMCs_CLL patient after 280 days of ibrutinib treatment


title: TE10_HOXC6_rep2

value: stably transfected with HOXC6


title: Eca109_HOXC6_rep1


description:
scRNA-seq on PBMCs from patient CLL6 after 0 days of ibrutinib treatment
scRNA-seq_CLL6_0d
CLL6_d0_S4_L002


title: Eca109_NEO_rep3


title: TE10_NEO_rep1


title: Eca109_NEO_rep1


title: Eca109_HOXC6_rep2


title: TE10_HOXC6_rep1


title: TE10_HOXC6_rep3


description:
scRNA-seq on PBMCs from patient CLL5 after 0 days of ibrutinib treatment
scRNA-seq_CLL5_0d
LiveBulk_10x_CLL51_0d_S1_L006


title: Leaf_IgG

city: Cambridge

first: Xiao-yu

last: Zheng

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

description: Barcode: ATTCCT

data_processing:
Library strategy: CUT&RUN
Quality filtering and trimming: Paired-end reads were trimmed and quality-filtered using trim_galore with --stringency 3 and quality cutoff -q 20. Both mates in a pair had to be at least 32 bp long after filtering and trimming.
Alignment: Trimmed qualified reads were aligned to TAIR10 genome using bowtie2 allowing zero mismatch in 22 bp seed region. Only reads that are uniquely mapped were retained for further analysis. PCR duplicated reads were removed using Picard “MarkDuplicates.jar”.
Normlization and coverage computing: For each library, bamCoverage from deepTools 2.0 (Ramirez et al. 2016) was used to calculate read coverage per 150-bp bin from the aligned-deduplicated bam file using the reads per genomic content normalization option (--skipNAs --normalizeTo1x 134634692 --binSize 150). This step generated the following processed data: {sample name}_RPGC_150bin.bedgraph.
Peak calling: For each biological replicate, Epic (diffuse domain ChIP-Seq caller based on SICER, https://github.com/endrebak/epic) (Zang et al. 2009) was used to call H3K27me3 peaks using H3K27me3 data and the corresponding H3 data as control with window size 150 bp and gap setting 2 (-w 150 -g 2). This analysis generated the following processed data: {sample name}_epicregions.bed.
All uniquely-mapped unduplicated reads from four CUT&RUN experiments were pooled together by concatenating raw fastq files. The same quality-filtering, trimming and alignment procedures were performed on the pooled data. The deduplicated aligned reads were assigned to a parent-of-origin by single nucleotide polymorphisms (SNPs) between Col and Ler. multiBamSummary from deepTools 2.0 (Ramirez et al. 2016) was utilized to calculate allele-specific coverage of H3K27me3 and H3 in 150 bp windows. This analysis generated the processed data file named Endo_Allele_specific_150bin.txt.
Identification of allele-specific H3K27me3 regions: Windows with less than 20 H3 or H3K27me3 allele-specific reads (sum of Col- and Ler-specific reads) were filtered out. Col fraction of H3K27me3 and H3 respectively in 150 bp bins were calculated (Col-reads / (Col-reads + Ler-reads)). The top and bottom 10% of bins in the H3 Col fraction distribution were further filtered out. We identified allele-biased H3K27me3 regions based on the H3K27me3 Col fraction of each bin. The 90th percentile of H3 Col fraction (0.95) distribution is the cutoff for Col-biased H3K27me3 regions. Bins with H3K27me3 Col fraction higher than 0.95 were considered Col-biased. The 10th percentile of H3 Col fraction (0.68) distribution is the cutoff for Ler-biased H3K27me3 regions. Bins with H3K27me3 Col fraction lower than 0.68 were considered Ler-biased. This analysis generated the processed data files: Endo_H3K27me3_CxL_Colbiasedregions.bedgraph, Endo_H3K27me3_CxL_Lerbiasedregions.bedgraph.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: {sample name}_RPGC_150bin.bedgraph: bedGraph files containing per genomic content (RPGC)-normalized read coverage per 150 bp window, excluding windows with no read coverage. Column titles are Chr, start, end, normalized read coverage.
Supplementary_files_format_and_content: {sample name}_epicregions.bed: bed files containing H3K27me3 peak regions identified through Epic as described above. Column titles are Chr, start, end, FDR score, log2 fold change (H3K27m3/H3), strand. For the value in the fifth column, H3 read counts have been normalized so that total read count of H3 is the same as the total read count of H3K27me3. The sixth contains the strand, although peak regions data is not stranded.
Supplementary_files_format_and_content: Endo_Allele_specific_150bin.txt: tab delimited file containing allele-specific read coverage (unnormalized read coverage) in 150 bp window. Column titles are Chr, start, end, H3K27me3_Col_specific_read_coverage, H3K27me3_Ler_specific_read_coverage, H3_Col_specific_read_coverage, H3_Ler_specific_read_coverage.
Supplementary_files_format_and_content: Endo_H3K27me3_CxL_Colbiasedregions.bedgraph: bedGraph file containing Col-biased H3K27me3 regions with H3K27m3 Col fraction value in the fourth column. Column titles are Chr, start, end, H3K27m3 Col fraction value.
Supplementary_files_format_and_content: Endo_H3K27me3_CxL_Lerbiasedregions.bedgraph: bedGraph file containing Ler-biased H3K27me3 regions with H3K27m3 Col fraction value in the fourth column. Column titles are Chr, start, end, H3K27m3 Col fraction value.

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Col-0 and Ler were grown in a growth chamber at 22℃ and 50% relative humidity under 16 hr light and 8 hr dark cycles.

extract_protocol:
Seeds were removed from siliques four days after pollination and grinded using a blue pestle (Axygen, PES-15-B-SI) in a 1.5 ml microfuge tube with 116.7 µL Nuclei Extraction Buffer (Partec CyStain UV Precise P, Sysmex America # 05-5002) (Protease inhibitor (cOmplete™ mini EDTA-free Protease Inhibitor Cocktail Tablets, Roche # 11836170001) had been added to the Nuclei Extraction Buffer). 800 µL Nuclei Staining Buffer (with protease inhibitor added) was then gently added to the tube and nuclei were collected after filtering twice with Cell Trics 30 µm filter (Partec # 04-0042-2316). For leaf sample, leaves were taken from 3-week-old plants and placed in a petric dish. 100 µL Nuclei Extraction Buffer (with protease inhibitor added) was added to the surface of each leaf. The leaf was then chopped using a razor blade to fine pieces. 800 µL Nuclei Staining Buffer (with protease inhibitor added) was then gently added to the chopped leaves and nuclei were collected after filtering twice with Cell Trics 30 µm filter. The nuclei were then FACS sorted based on DAPI staining and collected in PBS buffer. Bio-Mag Plus Concanavalin A (lectin) coated beads were equilibrated with binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2 and 0.5 mM Spermidine, Roche Complete tablets protease inhibitor). In experiments with fixed nuclei, the sorted nuclei were fixed with 1% formaldehyde for 8 min on ice, and then incubated for 5 min on ice with glycine added to a final concentration of 0.125 mM to stop crosslinking. 10x binding buffer (200 mM HEPES-KOH pH 7.9, 100 mM KCl, 10 mM CaCl2, 10 mM MnCl2 and 5 mM Spermidine) was added to the fixed or unfixed nuclei. The equilibrated Concanavalin A beads (10 µL for each antibody treatment) were added to nuclei, mixed and held at room temperature (RT) for 10 min. The mixtures were then placed on a magnet stand to clear (<1 min), and supernatant was discarded. The nuclei were then incubated for 5 min RT in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine and 0.1% BSA, Roche Complete tablets protease inhibitors) supplemented with 2 mM EDTA pH 8. The mixtures were then placed on a magnet stand to clear (<1 min), and supernatant was discarded. For fixed nuclei, wash buffer needs to be supplemented with 1 % Triton X-100 and 0.05% SDS. The nuclei were incubated 2 hr at 4 ̊C with primary antibodies (1:100), collected using magnet stand, washed twice with wash buffer, and incubated 1 hr at 4 ̊C with protein A-MNase (1:400, batch # 6 pA-MNase from Henikoff lab) in wash buffer. The nuclei were then washed three times with wash buffer, suspended in 100 µL wash buffer and equilibrated to 0 ̊C in ice water. Digestion was activated by adding 2 µL 100 mM CaCl2 to each sample and quickly mixed, incubated in ice water for the designated digestion time (30 min unless specified), and stopped by adding 100 µL 2xStop buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 µg/mL RNase A, 40 µg/mL glycogen and 10 pg/mL heterologous spike-in DNA). The spike-in DNA was yeast DNA from MNase-treated nucleosomes, kindly provided together with the pA-MNase aliquot by Steven Henikoff. The nuclei were incubated at 37 ̊C for 20 min. For unfixed nuclei, the beads were centrifuged at 13,000 rpm at 4 ̊C for 5 min, supernatant was transferred to a new tube and DNA was purified from the supernatant using NucleoSpin® Gel and PCR Clean-up system (MACHEREY-NAGEL #740609.250, #740609.150 and # 740609.100). For fixed nuclei, after the 37 ̊C incubation, 2 µL 10% SDS (to 0.1%), 1.7 µL Proteinase K (20 mg/ml), and 8.3 µL 5M NaCl (to 0.2 M) were added and the nuclei were incubated at 65 oC overnight. Total DNA was extracted at RT once with 200 µL buffered phenol-chloroform-isoamyl alcohol (25:24:1, Sigma P2069) using phase-lock tube (Qiagen, Hilden, Germany, Catalog #129046), re-extracted with 200 µL chloroform, transferred to a new tube containing 2 mL 2 mg/ml glycogen and 100 µL Beckmann Agencourt AMPure XP beads, incubated at room temperature for 10 min. Supernatant was retrieved on a magnet stand and DNA from the supernatant was precipitated by addition of 750 µL ethanol, chilled in ice for 5 to 10 min and centrifuged for 10 min at 13,000 rpm at 4 ̊C. The pellet was rinsed once with 100% ethanol, air-dried and dissolved in dH2O. Antibodies and their concentrations used in this study are: Anti-Histone H3 (Sigma Aldrich # H9289) in 1:100 final concentration (~ 15 µg/mL); Anti-H3K27me3 (EMD Millipore # 07-449) in 1:100 final concentration (10 µg/mL); Normal Rabbit IgG (Cell Signaling Technology # 2729S) in 1:100 final concentration (10 µg/mL).
Libraries were prepared using a protocol modified from the Henikoff protocol (http://blocks.fhcrc.org/steveh/papers/Codomo_Solexa_library_prep_protocol.docx). The purified DNA from CUT&RUN was first end-repaired, phosphorylated and adenylated in one reaction as follows. T4 DNA Polymerase (NEB) was diluted 1:20 in 1x T4 DNA ligase buffer. Taq DNA polymerase (NEB) was diluted 1:20 in 1x Taq buffer. Each DNA sample (36.5 μL) was mixed with 5 μL 10X T4 DNA ligase buffer (NEB), 2.5 μL 10mM dNTPs (KAPA), 1.25 μL 10mM ATP (NEB), 3.13 μL 40% PEG4000, 0.63 μL T4 PNK (NEB), 0.5 μL diluted T4 DNA Polymerase, and 0.5 μL diluted Taq polymerase; and reaction was performed in pre-cooled thermal cycler following the program: 12°C for 15 min, 37°C for 15 min and then 72°C for 20 min. Samples were put on ice immediately and adapter ligation was performed with addition of 5 µL of 1:50 diluted index adapter (Illumina TruSeq DNA PCR-free librariy prep kits FC-121-3001 and FC-121-3002), 55 µL 2x Rapid DNA ligase buffer (Enzymatics #B101L) and 5 µL T4 DNA ligase (Rapid) (Enzymatics #L6030-HC-L) in 20°C for 15 min. Ampure XP beads (Beckmann Agencourt) were immediately added to the sample after ligation reaction in a ratio that excludes DNA fragments smaller than 150 bp and retains fragments larger than 150 bp (around 0.33x, or 38 µL for 115 µL DNA for the batch of Ampure beads we used). The DNA-bead mixture was incubated at room temperature for 15 min, cleared in a magnetic stand and the beads were washed twice with 200 μL 80% ethanol. After residual liquid was removed by pipette after quick spin, beads were air-dried for about 5 min, suspended with 53 μL nuclease-free dH2O and incubated at room temperature for 2 min. The beads were cleared from supernatant on magnetic stand, and 50 μL of supernatant was retained. The DNA in supernatant was purified again with 1.1x (55 μL) Ampure XP beads with the same procedure described above and eluted in 20 μL nuclease-free dH2O. The purified adapter-ligated DNA were mixed with 10 μL 5X KAPA HiFi Fidelity Buffer, 1.5 μL 10mM dNTPs, 1 μL KAPA HiFi HotStart DNA polymerase (KAPA #KK2502), and 0.5 μL each of 20 μM P5 and P7 primers. P5 and P7 primers were ordered from IDT with phosphorothioate bond between the 3' A and G and PAGE purified (P5 Primer: 5’-AATGATACGGCGACCACCGA*G-3’. P7 Primer: 5’-CAAGCAGAAGACGGCATACGA*G-3’. * represents phosphorothioate bond). The mixed sample were PCR amplified to enrich library following the below program: 98°C for 45 seconds, 98°C for 15 seconds, 60°C for 10 seconds, repeat the second and third steps 13 times, and 72°C for 1 minute. The enriched library was purified again with 1.1x (55 μL) Ampure XP beads following the above-mentioned procedure. Purified libraries were examined by BioAnalyzer and if adapter-dimer (about 138 bp peak) or primer-dimer (about 45 bp peak) were detected, the library was purified again with 1x Ampure XP beads following the same procedure described above. The purified libraries were multiplexed and sequenced in Illumina HiSeq 2500s.

treatment_protocol: no treatment

value: Col

value: 2N, 4N and 8N leaf nuclei

tag: developmental stage

value: 3 week old plant


title: Leaf_H3K27me3

description:
Barcode: GAGTGG
Leaf_H3K27me3_epicregions.bed


title: TE10_NEO_rep2


description:
scRNA-seq on PBMCs from patient CLL1 after 120 days of ibrutinib treatment
scRNA-seq_CLL1_120d
LiveBulk_10x_CLL1_CLL17_d120_10xTK078_S3_L006


description:
scRNA-seq on PBMCs from patient CLL1 after 0 days of ibrutinib treatment
scRNA-seq_CLL1_0d
LiveBulk_10x_CLL1_CLL11_d0_10xTK078_S1_L006


title: 2N_noab_200k_15min

description: Barcode: CAGATC

source_name: seed coat and embryo

value: Col (mother) x Ler (father) F1

value: 2N, 4N and 8N seed coat and embryo nuclei

value: 7 days after pollination


title: Leaf_H3

description:
Barcode: ACTGAT
Leaf_H3K27me3_epicregions.bed


description:
ATAC-seq on PBMCs from patient CLL8 on day 3 of ibrutinib treatment, NK cells
ATAC-seq_CLL8_3d_NK

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder (https://github.com/wtsi-npg/illumina2bam)
Sequenced reads were trimmed for adaptor sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files in bigWig format contain chromatin accessibility profiles and narrowPeak files contain peak calls for each sample

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_NK cells

extract_protocol:
Patient PBMCs were thawed and washed twice with PBS containing 0.1% BSA and 5 mM EDTA (PBS + BSA + EDTA). Cells were then incubated with anti-CD16/CD32 (clone 93, Biolegend) to prevent nonspecific binding. Single-cell suspensions were stained with combinations of antibodies against CD3 (clone UCHT1), CD4 (clone OKT4), CD5 (clone UCHT2), CD8 (clone SK1), CD14 (clone M5E2), CD19 (clone HIB19), CD20 (clone 2H7), CD24 (clone ML5), CD25 (clone BC96), CD27 (clone O323), CD38 (clone HB-7), CD45RA (clone HI100), CD45RO (clone 304218), CD56 (clone NCAM16.2), CD127 (clone A019D5), CD197 (CCR7, clone G043H7), CD223 (LAG3, clone 11C3C65), CD279 (PD-1, clone EH12.2H7), CD366 (Tim3, clone F38-2E2) and DAPI viability dye (all from Biolegend) for 30 min at 4 °C followed by two washes with PBS + BSA + EDTA. Cells were either acquired with a LSRFortessa (BD) cell analyzer or sort-purified with a MoFlo Astrois (Beckman Coulter). Data analysis was performed with FlowJo (Tree Star) software. We obtained whole blood from three healthy donors with informed consent, and isolated PBMCs through Ficoll-Paque density gradient centrifugation and stored them in liquid nitrogen. Following sample thawing, up to ten million cells were incubated with anti-CD16/CD32 (clone 93, Biolegend) to prevent nonspecific binding. Single-cell suspensions were stained with antibodies against CD3 (clone UCTH1), CD4 (clone OKT4), CD8 (clone SK1), CD19 (clone HIB19), CD20 (clone 2H7), CD24 (clone ML5), CD27 (clone M-T271), CD38 (clone HB-7), IgD (clone 1A6-2) and fixable Zombie Red viability dye (all from BioLegend) for 30 min at 4 °C followed by two washes with PBS + BSA + EDTA. Sorting was conducted using a Sony SH800 cell sorter, pre-gated on live singlet lymphocytes before sorting cell subpopulations as follows: T cell (CD3+), total B cell (CD19+, CD20+), naive B cell (CD27-, IgD+), natural effector B cell (CD27+, IgD+), and memory B cell (CD27+, IgD-).
Chromatin accessibility mapping was performed using the ATAC-seq method as previously described (Corces et al, Nature Genetics, 2016), with minor adaptations. In each experiment, a maximum of 50,000 sorted cells were pelleted by centrifuging for 5 min at 4 °C at 300 x g. After centrifugation, the pellet was carefully resuspended in the transposase reaction mix (12.5 µl 2xTD buffer, 2 µl TDE1 (Illumina) and 10.25 µl nuclease-free water, 0.25 µl 5% Digitonin (Sigma)) for 30 min at 37 °C. Following DNA purification with the MinElute kit eluting in 11 µl, 1 µl of the eluted DNA was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles. Library amplification was followed by SPRI size selection to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers (Buenrostro et al, Nature Methods 2013). The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 4000 platform and the 50-bp single-end configuration.

tag: library

value: ATAC-seq


description:
ATAC-seq on PBMCs from patient CLL8 on day 0 of ibrutinib treatment, NK cells
ATAC-seq_CLL8_0d_NK

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_NK cells


title: 2N_H3K27me3_50k_2min

description: Barcode: GCCAAT

tag: read length


description:
scRNA-seq on PBMCs from patient CLL6 after 120 days of ibrutinib treatment
scRNA-seq_CLL6_120d
CLL6_d120_S2_L002


title: Endo_Unfixed_IgG_1

description: Barcode: CCGTCC

source_name: endosperm

value: 6N endosperm nuclei

value: 4 days after pollination


title: 2N_H3K27me3_200k_15min

description: Barcode: TGACCA


description:
ATAC-seq on PBMCs from patient CLL8 on day 030 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL8_030d_CD8

source_name: PBMCs_CLL patient_day 030 of ibrutinib treatment_CD8 cells


description:
ATAC-seq on PBMCs from patient CLL8 on day 3 of ibrutinib treatment, Mono cells
ATAC-seq_CLL8_3d_Mono

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_Mono cells


description:
ATAC-seq on PBMCs from patient CLL8 on day 0 of ibrutinib treatment, Mono cells
ATAC-seq_CLL8_0d_Mono

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_Mono cells


title: Endo_Unfixed_H3K27me3_2

description:
Barcode: AGTTCC
Endo_Unfixed_H3K27me3_2_epicregions.bed
Endo_Allele_specific_150bin.txt
Endo_H3K27me3_CxL_Colbiasedregions.bedgraph
Endo_H3K27me3_CxL_Lerbiasedregions.bedgraph


description:
ATAC-seq on PBMCs from patient CLL8 on day 0 of ibrutinib treatment, CLL cells
ATAC-seq_CLL8_0d_CLL

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CLL cells


title: Endo_Unfixed_H3_2

description:
Barcode: AGTCAA
Endo_Unfixed_H3K27me3_2_epicregions.bed
Endo_Allele_specific_150bin.txt
Endo_H3K27me3_CxL_Colbiasedregions.bedgraph
Endo_H3K27me3_CxL_Lerbiasedregions.bedgraph


description:
ATAC-seq on PBMCs from patient CLL8 on day 0 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL8_0d_CD8

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CD8 cells


description:
ATAC-seq on PBMCs from patient CLL8 on day 3 of ibrutinib treatment, CLL cells
ATAC-seq_CLL8_3d_CLL

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CLL cells


description:
ATAC-seq on PBMCs from patient CLL8 on day 3 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL8_3d_CD4

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CD4 cells


description:
ATAC-seq on PBMCs from patient CLL8 on day 3 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL8_3d_CD8

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CD8 cells


title: Endo_Fixed_H3K27me3_1

description:
Barcode: GTGAAA
Endo_Fixed_H3K27me3_1_epicregions.bed
Endo_Allele_specific_150bin.txt
Endo_H3K27me3_CxL_Colbiasedregions.bedgraph
Endo_H3K27me3_CxL_Lerbiasedregions.bedgraph


title: Endo_Fixed_H3_2

description:
Barcode: ACTGAT
Endo_Fixed_H3K27me3_2_epicregions.bed
Endo_Allele_specific_150bin.txt
Endo_H3K27me3_CxL_Colbiasedregions.bedgraph
Endo_H3K27me3_CxL_Lerbiasedregions.bedgraph


title: 2N_H3K27me3_200k_2min

description: Barcode: AGTCAA


description:
ATAC-seq on PBMCs from patient CLL8 on day 0 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL8_0d_CD4

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CD4 cells


description:
ATAC-seq on PBMCs from patient CLL7 on day 150 of ibrutinib treatment, NK cells
ATAC-seq_CLL7_150d_NK

source_name: PBMCs_CLL patient_day 150 of ibrutinib treatment_NK cells


title: Endo_Fixed_H3K27me3_2

description:
Barcode: ATTCCT
Endo_Fixed_H3K27me3_2_epicregions.bed
Endo_Allele_specific_150bin.txt
Endo_H3K27me3_CxL_Colbiasedregions.bedgraph
Endo_H3K27me3_CxL_Lerbiasedregions.bedgraph


title: Endo_Fixed_IgG_2

description: Barcode: ATCACG


title: Endo_Unfixed_H3_1

description:
Barcode: TAGCTT
Endo_Unfixed_H3K27me3_1_epicregions.bed
Endo_Allele_specific_150bin.txt
Endo_H3K27me3_CxL_Colbiasedregions.bedgraph
Endo_H3K27me3_CxL_Lerbiasedregions.bedgraph


description:
ATAC-seq on PBMCs from patient CLL7 on day 30 of ibrutinib treatment, NK cells
ATAC-seq_CLL7_30d_NK

source_name: PBMCs_CLL patient_day 30 of ibrutinib treatment_NK cells


description:
ATAC-seq on PBMCs from patient CLL7 on day 0 of ibrutinib treatment, NK cells
ATAC-seq_CLL7_0d_NK


title: Endo_Fixed_H3_1

description:
Barcode: GTCCGC
Endo_Fixed_H3K27me3_1_epicregions.bed
Endo_Allele_specific_150bin.txt
Endo_H3K27me3_CxL_Colbiasedregions.bedgraph
Endo_H3K27me3_CxL_Lerbiasedregions.bedgraph


description:
ATAC-seq on PBMCs from patient CLL7 on day 150 of ibrutinib treatment, CLL cells
ATAC-seq_CLL7_150d_CLL

source_name: PBMCs_CLL patient_day 150 of ibrutinib treatment_CLL cells


title: ref4-1 (dataset 2) rep2

city: West Lafayette

first: Clint

last: Chapple

state: IN

address: 175 S. University St.

department: Department of Biochemistry

institute: Purdue University

data_processing:
Casava1.8.2 software was used for basecalling.
Trimmomatic and/or fastx_clipper were used to remove adapters. Poor quality bases (less than Phred-20) were removed (clipped) from both the 5' and 3' ends of the Unaligned reads. After adapter removal and quality clipping any reads below a minimum (30 bases) length were discarded. Reads were then mapped to TAIR10 assembly of the Arabidopsis genome using Tophat v2.1.0 with default parameters.
Digital gene expression (counts) was determined for each sample using HTSeq-count v0.6.1 (Anders et al., 2015) with the following parameters: -s reverse -r pos -m intersection-nonempty -t exon -i gene_id.
Differential expression analysis was performed using the edgeR package as follows: edgeR analysis began with a count table comprising 33,602 genes. Genes expressed at low levels were then filtered out by removing any genes for which there was not at least 1 count per million in at least four of the samples. This resulted in a list of 18,842 expressed genes. Counts were then normalized using TMM normalization. Next, the “ANOVA-like” procedure in EdgeR was used to identify genes that were differentially expressed between any of the genotypes (FDR < 0.05). This resulted in a list of 14,688 differentially expressed genes. To determine which of these genes were differentially expressed in each of the mutants compared to wild type, the exact test for the negative binomial distribution (Robinson and Smyth, 2008) was used followed by a Bonferroni correction to maintain a gene-wise error rate of 0.05
Genome_build: TAIR10
Supplementary_files_format_and_content: Comma-separated values files include count values or normalized count values for each sample.

source_name: Whole rosettes

growth_protocol: Seeds were sown nine per 4" x 4" pot and positions of the pots were randomized. Seeds were held at 4C for two days before transferring to 23C under a 16 hr light, 8 hr dark photoperiod. Material was harvested 6.5 hours after subjective dawn on the 20th day after transferring to the growth chamber.

extract_protocol:
For each sample, five whole rosettes were pooled from different pots and ground under liquid nitrogen. Approximately 100 mg of the ground tissue was used to extract total RNA using the Qiagen RNEasy Plant Mini kit (Cat#74904) with on-column DNAse treatment (Cat#79254). Total rRNA was then enriched for polyA+ RNA.
Illumina TruSeq Stranded mRNA Sample Prep Kit (Cat#RS-122-2103) was used with 2 ug of total RNA for the construction of dual barcoded sequencing libraries.

tag: ecotype

value: 20 days


title: ref4-3 dk8-1 (dataset 2) rep3

value: ref4-3 cdk8-1


title: ref4-1 (dataset 2) rep1


description:
ATAC-seq on PBMCs from patient CLL7 on day 30 of ibrutinib treatment, CLL cells
ATAC-seq_CLL7_30d_CLL

source_name: PBMCs_CLL patient_day 30 of ibrutinib treatment_CLL cells


title: ref4-3 dk8-1 (dataset 2) rep1


description:
ATAC-seq on PBMCs from patient CLL7 on day 150 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL7_150d_CD8

source_name: PBMCs_CLL patient_day 150 of ibrutinib treatment_CD8 cells


description:
ATAC-seq on PBMCs from patient CLL7 on day 8 of ibrutinib treatment, CLL cells
ATAC-seq_CLL7_8d_CLL

source_name: PBMCs_CLL patient_day 8 of ibrutinib treatment_CLL cells


description:
ATAC-seq on PBMCs from patient CLL7 on day 0 of ibrutinib treatment, CLL cells
ATAC-seq_CLL7_0d_CLL


description:
ATAC-seq on PBMCs from patient CLL7 on day 1 of ibrutinib treatment, CLL cells
ATAC-seq_CLL7_1d_CLL

source_name: PBMCs_CLL patient_day 1 of ibrutinib treatment_CLL cells


title: cdk8-1 (dataset 2) rep1


title: ref4-3 (dataset 2) rep2


title: cdk8-1 (dataset 2) rep2


title: ref4-3 (dataset 2) rep1


description:
ATAC-seq on PBMCs from patient CLL7 on day 3 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL7_3d_CD8


description:
ATAC-seq on PBMCs from patient CLL7 on day 3 of ibrutinib treatment, CLL cells
ATAC-seq_CLL7_3d_CLL


description:
ATAC-seq on PBMCs from patient CLL7 on day 30 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL7_30d_CD8

source_name: PBMCs_CLL patient_day 30 of ibrutinib treatment_CD8 cells


title: ref4-3 (dataset 2) rep3


title: cdk8-1 (dataset 2) rep3


title: ref4-1 (dataset 2) rep3


description:
ATAC-seq on PBMCs from patient CLL7 on day 8 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL7_8d_CD8

source_name: PBMCs_CLL patient_day 8 of ibrutinib treatment_CD8 cells


title: ref4-3 dk8-1 (dataset 2) rep2


title: WT (dataset 2) rep3

value: wild type


description:
ATAC-seq on PBMCs from patient CLL7 on day 1 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL7_1d_CD8

source_name: PBMCs_CLL patient_day 1 of ibrutinib treatment_CD8 cells

value: chronic lymphocytic leukemia patient


description:
ATAC-seq on PBMCs from patient CLL7 on day 150 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL7_150d_CD4

source_name: PBMCs_CLL patient_day 150 of ibrutinib treatment_CD4 cells

value: Peripheral blood mononuclear cells (PBMCs)


description:
ATAC-seq on PBMCs from patient CLL7 on day 0 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL7_0d_CD8

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CD8 cells


title: WT (dataset 2) rep2


description:
ATAC-seq on PBMCs from patient CLL7 on day 30 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL7_30d_CD4

source_name: PBMCs_CLL patient_day 30 of ibrutinib treatment_CD4 cells


title: Eca109_HOXC6_rep3

tag: cell type

value: esophageal squamous cell carcinoma cell line


title: WT (dataset 2) rep1


title: H2228_H1975_A549_H838_HCC827_Mixture_CelSeq2

data_processing:
gene counting matrix generated using scPipe 1.4.0
reads were aligned using Rsubread 1.29.6
Genome_build: ENSEMBL Homo_sapiens.GRCh38.88
Supplementary_files_format_and_content: gene counting matrix, rows repsent genes and each column is a well

source_name: lung adenocarcinoma

extract_protocol:
The cells were counted using Chamber Slide and rounghly 2 million cells from each cell line were mixed and processed by 10X. Three CEL-seq2 plates were sorted for the same sample.
For CEL-seq2, Single cells were flow sorted into chilled 384-well PCR plates containing 1.2ul of primer/ERCC mix using a BD FACSAria III flow cytometer. Sorted plates were sealed and immediately frozen upside down at -80C. Then these plates, together with the mRNA mixture plates, were taken from -80C and processed using an adapted Cel-Seq2 protocol with the following variations. We pooled the samples after the first strand synthesis and the second strand synthesis was performed using NEBNext Second Strand Synthesis module. NucleoMag NGS Clean-up and Size select magnetic beads were used for all DNA purification and size selection steps.

tag: umi position

value: Bases 1 to 6 on R1

tag: barcode position

value: Bases 7 to 14 on R1


title: H2228_H1975_A549_H838_HCC827_Mixture_CelSeq3


description:
ATAC-seq on PBMCs from patient CLL8 on day 030 of ibrutinib treatment, CLL cells
ATAC-seq_CLL8_030d_CLL

source_name: PBMCs_CLL patient_day 030 of ibrutinib treatment_CLL cells


title: Endo_Unfixed_H3K27me3_1

description:
Barcode: GGCTAC
Endo_Unfixed_H3K27me3_1_epicregions.bed
Endo_Allele_specific_150bin.txt
Endo_H3K27me3_CxL_Colbiasedregions.bedgraph
Endo_H3K27me3_CxL_Lerbiasedregions.bedgraph

source_name: endosperm

tag: tissue


title: H2228_H1975_A549_H838_HCC827_Mixture_CelSeq1


title: Obese_11

city: Hørsholm

first: Kristoffer

last: Rigbolt

address: Hørsholm Kongevej 11B

country: Denmark

institute: Gubra

data_processing:
bcl2fastq v2.17.1.14 used for basecalling
Sequenced reads were mapped to Ensembl Mus musculus genome using whole genome using STAR v2.5.2a with default parameters
Filtering for protein coding genes
Genome_build: Ensembl GRCh38 89
Supplementary_files_format_and_content: Count table

source_name: Liver needle biopsy

extract_protocol:
TruSeq® Stranded mRNA Library Prep for NeoPrep
RNA was isolated from fine needle biopsies of human livers using NucleoSpin® from MACHEREY-NAGEL according to manufactors protocol

value: Male

value: Liver

tag: disease

value: obese


title: Obese_9


title: Obese_10


title: Obese_8


description:
ATAC-seq on PBMCs from patient CLL7 on day 3 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL7_3d_CD4

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CD4 cells


description:
ATAC-seq on PBMCs from patient CLL7 on day 1 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL7_1d_CD4

source_name: PBMCs_CLL patient_day 1 of ibrutinib treatment_CD4 cells


title: Obese_7


description:
ATAC-seq on PBMCs from patient CLL7 on day 0 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL7_0d_CD4

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CD4 cells


description:
ATAC-seq on PBMCs from patient CLL6 on day 280 of ibrutinib treatment, Mono cells
ATAC-seq_CLL6_280d_Mono

source_name: PBMCs_CLL patient_day 280 of ibrutinib treatment_Mono cells


description:
ATAC-seq on PBMCs from patient CLL6 on day 280 of ibrutinib treatment, NK cells
ATAC-seq_CLL6_280d_NK

source_name: PBMCs_CLL patient_day 280 of ibrutinib treatment_NK cells


description:
ATAC-seq on PBMCs from patient CLL6 on day 030 of ibrutinib treatment, NK cells
ATAC-seq_CLL6_030d_NK

source_name: PBMCs_CLL patient_day 030 of ibrutinib treatment_NK cells


description:
ATAC-seq on PBMCs from patient CLL7 on day 3 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL7_3d_Bcell

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_Bcell cells


description:
ATAC-seq on PBMCs from patient CLL7 on day 0 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL7_0d_Bcell

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_Bcell cells


description:
ATAC-seq on PBMCs from patient CLL6 on day 030 of ibrutinib treatment, Mono cells
ATAC-seq_CLL6_030d_Mono

source_name: PBMCs_CLL patient_day 030 of ibrutinib treatment_Mono cells


description:
ATAC-seq on PBMCs from patient CLL6 on day 120 of ibrutinib treatment, Mono cells
ATAC-seq_CLL6_120d_Mono

source_name: PBMCs_CLL patient_day 120 of ibrutinib treatment_Mono cells


description:
ATAC-seq on PBMCs from patient CLL7 on day 150 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL7_150d_Bcell

source_name: PBMCs_CLL patient_day 150 of ibrutinib treatment_Bcell cells


title: Obese_4


description:
ATAC-seq on PBMCs from patient CLL7 on day 8 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL7_8d_CD4

source_name: PBMCs_CLL patient_day 8 of ibrutinib treatment_CD4 cells


description:
ATAC-seq on PBMCs from patient CLL6 on day 0 of ibrutinib treatment, Mono cells
ATAC-seq_CLL6_0d_Mono

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_Mono cells


title: Obese_12


title: Obese_6


title: Obese_5


title: Obese_1


description:
ATAC-seq on PBMCs from patient CLL6 on day 120 of ibrutinib treatment, CLL cells
ATAC-seq_CLL6_120d_CLL

source_name: PBMCs_CLL patient_day 120 of ibrutinib treatment_CLL cells


title: Normal-weight_13

value: healthy


title: Normal-weight_12


title: Obese_3


description:
ATAC-seq on PBMCs from patient CLL6 on day 280 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL6_280d_CD8

source_name: PBMCs_CLL patient_day 280 of ibrutinib treatment_CD8 cells


description:
ATAC-seq on PBMCs from patient CLL6 on day 280 of ibrutinib treatment, CLL cells
ATAC-seq_CLL6_280d_CLL

source_name: PBMCs_CLL patient_day 280 of ibrutinib treatment_CLL cells


description:
ATAC-seq on PBMCs from patient CLL6 on day 120 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL6_120d_CD8

source_name: PBMCs_CLL patient_day 120 of ibrutinib treatment_CD8 cells


title: Normal-weight_11

source_name: Liver needle biopsy


title: Obese_2


title: RNA from ACC-Meso-4 expressing shRNA targeting CBX8_2

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

description: Gene expression in  ACC-Meso-4 expressing shRNA targeting CBX8_2

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-039494 Whole Mouse Genome Microarray 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1  (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026655_D_20120201). Further analysis were performed by GeneSpring GX 12.1 software (Agilent Technologies). Normalization was performed as follows: (i) intensity-dependent Lowess normalization; (ii) data transformation, with measurements set to ≤0.01; (iii) per-chip 75th-percentile normalization of each array; and, (iv) per-gene: normalized to the median of each gene.

source_name: ACC-Meso-4,CBX8 shRNA, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low RNA Input Fluorescent Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: ACC-Meso-4 cells were cultured with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2

extract_protocol: Total RNA was prepared using TRIZOL reagent (Invitrogen). The quality of RNA samples were assessed by RNA 6000 nano kit (Agilent Bioanalyzer 2100).

treatment_protocol: Lentiviruses were produced in 293T cells transfected with packaging plasmids (Sigma-Aldrich) and shRNA constructs by using lipofectamine LTX (Invitrogen). Each shRNA was introduced by lentivuruses into ACC-Meso-4 cells and stable knockdowns in ACC-Meso-4  were selected with 1 µg/ml puromycin in culture medium for 3 weeks.

tag: shRNA

value: Human malignant pleural mesothelioma cell line. Japanese, Male, 59 years


title: RNA from ACC-Meso-4 expressing nontargeting shRNA_2

description: Gene expression in  ACC-Meso-4 expressing nontargeting shRNA_2

source_name: ACC-Meso-4, nontarget shRNA, replicate 2

value: non-sh


title: RNA from ACC-Meso-4 expressing shRNA targeting CBX6_2

description: Gene expression in  ACC-Meso-4 expressing shRNA targeting CBX6_2

source_name: ACC-Meso-4, CBX6 shRNA, replicate 2


title: Normal-weight_10


description:
ATAC-seq on PBMCs from patient CLL6 on day 030 of ibrutinib treatment, CLL cells
ATAC-seq_CLL6_030d_CLL

source_name: PBMCs_CLL patient_day 030 of ibrutinib treatment_CLL cells

value: ATAC-seq


title: RNA from ACC-Meso-4 expressing shRNA targeting CBX6_1

description: Gene expression in  ACC-Meso-4 expressing shRNA targeting CBX6_1

source_name: ACC-Meso-4, CBX6 shRNA, replicate 1


description:
ATAC-seq on PBMCs from patient CLL6 on day 030 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL6_030d_CD8

source_name: PBMCs_CLL patient_day 030 of ibrutinib treatment_CD8 cells


title: Pristine ZnO-MNP - Z5

city: Lexington

first: Olga

last: Tsyusko

state: KY

address: 1100 S. Limestone St

department: Plant and Soil Sciences

institute: University of Kentucky

hyb_protocol: 5.0 µg of the fragmented, labeled ss-cDNA were hybridized to EleGene 1.0 ST arrays for 16 h at 45°C and shaken at 60 RPM.

scan_protocol: Affymetrix GeneChip 7G scanner

data_processing: Raw data files were normalized using the robust multi-array average (RMA) algorithm followed by quantile normalization implemented in Partek Genomics Suite 6.4

organism: Caenorhabditis elegans

source_name: C. elegans exposed to pristine ZnO-MNPs

label_protocol: A total of 100 ng of total RNA was used to generate fragmented, labeled ss-cDNA using Affymetrix WT Plus kit.

growth_protocol: L1 were placed into Simulated soil pore water

extract_protocol: Trizol with Qiagen RNeasy Kit

treatment_protocol: Exposed to ZnO-MNPs in pristine and aged forms as wel ZnSO4  for 72 hr

tag: age

value: started at L15

tag: treatment

value: pristine ZnO-MNPs


title: Pristine ZnO-MNP - Z3

value: started at L13


description:
ATAC-seq on PBMCs from patient CLL6 on day 0 of ibrutinib treatment, CLL cells
ATAC-seq_CLL6_0d_CLL

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CLL cells


title: Sulfidized ZnO-MNP - S3

source_name: C. elegans exposed to sulfidized ZnO-MNPs

value: started at L10

value: sulfidized ZnO-MNPs


title: RNA from ACC-Meso-4 expressing shRNA targeting CBX7_2

description: Gene expression in  ACC-Meso-4 expressing shRNA targeting CBX7_2

source_name: ACC-Meso-4, CBX7 shRNA, replicate 2


title: Pristine ZnO-MNP - Z4

value: started at L14


title: Sulfidized ZnO-MNP - S4

value: started at L11


title: Sulfidized ZnO-MNP - S5

value: started at L12


title: RNA from ACC-Meso-4 expressing shRNA targeting CBX7_1

description: Gene expression in  ACC-Meso-4 expressing shRNA targeting CBX7_1

source_name: ACC-Meso-4, CBX7 shRNA, replicate 1


title: Phosphate ZnO-MNP - P5

source_name: C. elegans exposed to phosphate aged ZnO-MNPs

value: started at L9

value: phosphate aged ZnO-MNPs


title: Normal-weight_14

tag: gender

value: Male


title: Phosphate ZnO-MNP - P4

value: started at L8


title: Phosphate ZnO-MNP - P1

value: started at L7


title: Normal-weight_9

value: Liver

value: healthy


description:
ATAC-seq on PBMCs from patient CLL6 on day 280 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL6_280d_CD4

source_name: PBMCs_CLL patient_day 280 of ibrutinib treatment_CD4 cells

value: chronic lymphocytic leukemia patient

value: Peripheral blood mononuclear cells (PBMCs)


title: Normal-weight_8


description:
ATAC-seq on PBMCs from patient CLL6 on day 0 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL6_0d_CD8

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CD8 cells

value: ATAC-seq


title: Zn ions - I5

source_name: C. elegans exposed to Zn ions

value: started at L6

value: Zn ions


title: Zn ions - I3

value: started at L4


title: Zn ions - I4

value: started at L5


description:
ATAC-seq on PBMCs from patient CLL6 on day 120 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL6_120d_CD4

source_name: PBMCs_CLL patient_day 120 of ibrutinib treatment_CD4 cells


title: Normal-weight_7

source_name: Liver needle biopsy


title: Normal-weight_6


description:
ATAC-seq on PBMCs from patient CLL6 on day 030 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL6_030d_CD4

source_name: PBMCs_CLL patient_day 030 of ibrutinib treatment_CD4 cells


title: RNA from ACC-Meso-4 expressing shRNA targeting CBX8_1

description: Gene expression in  ACC-Meso-4 expressing shRNA targeting CBX8_1

source_name: ACC-Meso-4,CBX8 shRNA, replicate 1

value: Human malignant pleural mesothelioma cell line. Japanese, Male, 59 years


title: Control - C5

source_name: Control replicate

value: started at L3

value: control


title: Normal-weight_4


description:
ATAC-seq on PBMCs from patient CLL6 on day 280 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL6_280d_Bcell

source_name: PBMCs_CLL patient_day 280 of ibrutinib treatment_Bcell cells


description:
ATAC-seq on PBMCs from patient CLL5 on day 30 of ibrutinib treatment, NK cells
ATAC-seq_CLL5_30d_NK

source_name: PBMCs_CLL patient_day 30 of ibrutinib treatment_NK cells


description:
ATAC-seq on PBMCs from patient CLL6 on day 120 of ibrutinib treatment, Bcell cells
ATAC-seq_CLL6_120d_Bcell

source_name: PBMCs_CLL patient_day 120 of ibrutinib treatment_Bcell cells


title: Normal-weight_3


title: Normal-weight_2


description:
ATAC-seq on PBMCs from patient CLL5 on day 030 of ibrutinib treatment, NK cells
ATAC-seq_CLL5_030d_NK

source_name: PBMCs_CLL patient_day 030 of ibrutinib treatment_NK cells


title: Control - C4

value: started at L2


title: UM-SCC46_noTreat_0hr_for_TNF

city: Bethesda

first: Carter

last: Van Waes

state: MD

address: 10 Center Drive

department: Head and Neck Surgery Branch

institute: NIDCD

description:
0 hr
UMSCC_46_NoTx

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

source_name: UM-SCC 46 cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: UM-SCC 46 cells grew in the log phase in the 6 well plates.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: UM-SCC 46 cells were treated with TNF-α (20ng/ml) for 1, 3, 6, 12, and 24 hours.

value: HNSCC HPV(-) cell lines


title: UM-SCC46_TNFa_1hr

description:
1 hr
UMSCC_46_TNF1h


title: UM-SCC46_LTBeta_24hr

description:
24 hr
46_LTb_24h

treatment_protocol: UM-SCC 46 cells were treated with LTB (100ng/ml) for 1, 3, 6, 12, and 24 hours.


title: UM-SCC46_TNFa_3hr

description:
3 hr
UMSCC_46_TNF3h


title: UM-SCC46_TNFa_24hr

description:
24 hr
UMSCC_46_TNF24h


title: UM-SCC46_TNFa_12hr

description:
12 hr
UMSCC_46_TNF12h


description:
ATAC-seq on PBMCs from patient CLL5 on day 8 of ibrutinib treatment, NK cells
ATAC-seq_CLL5_8d_NK

source_name: PBMCs_CLL patient_day 8 of ibrutinib treatment_NK cells


title: NASH_16

value: Male

value: NASH


title: UM-SCC46_LTBeta_6hr

description:
6 hr
46_LTb_6h


description:
ATAC-seq on PBMCs from patient CLL5 on day 3 of ibrutinib treatment, NK cells
ATAC-seq_CLL5_3d_NK

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_NK cells


title: CAP2 -/- rep1

source_name: heart

tag: strain

tag: organ

value: heart

tag: genotype

value: female

tag: experiment

value: A


title: CAP2 -/- rep3


description:
ATAC-seq on PBMCs from patient CLL5 on day 1 of ibrutinib treatment, NK cells
ATAC-seq_CLL5_1d_NK

source_name: PBMCs_CLL patient_day 1 of ibrutinib treatment_NK cells

value: chronic lymphocytic leukemia patient

tag: replicate


title: UM-SCC46_LTBeta_3hr

description:
3 hr
46_LTb_3h

tag: cell line


title: UM-SCC46_LTBeta_12hr

description:
12 hr
46_LTb_12h


title: WT rep2

value: wt


title: RNA from ACC-Meso-4 expressing nontargeting shRNA_1

description: Gene expression in ACC-Meso-4 expressing nontargeting shRNA_1

source_name: ACC-Meso-4, nontarget shRNA, replicate 1

value: non-sh


title: WT rep3


title: NASH_15

value: Liver


title: Normal-weight_5

value: healthy


description:
ATAC-seq on PBMCs from patient CLL5 on day 0 of ibrutinib treatment, NK cells
ATAC-seq_CLL5_0d_NK

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_NK cells

tag: library

value: ATAC-seq

value: Peripheral blood mononuclear cells (PBMCs)


title: WT rep1


title: Normal-weight_1


title: CAP2 -/- rep2


title: NASH_14


title: NASH_12


title: NASH_11

value: Female


description:
ATAC-seq on PBMCs from patient CLL5 on day 3 of ibrutinib treatment, Mono cells
ATAC-seq_CLL5_3d_Mono

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_Mono cells


title: QM6a_DD_2

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

institute: University of Vienna

description: growth on cellulose, 72h, liquid culture

data_processing:
The mapping of reads was performed using bowtie2 with standard parameter setting
The resulting files were further processed using samtools
The comparison to the annotation was performed using bedtools
Values were calculated for each annotated transcript based on the results of the mapping (RSEM)
Genome_build: https://genome.jgi.doe.gov/Trire2/Trire2.home.html
Supplementary_files_format_and_content: The Excel file contains FPKM values of normalized samples (values for all samples in this file).

organism: Trichoderma reesei

source_name: fungal mycelium

extract_protocol:
Mycelia were harvested by filtration and frozen in liquid nitrogen. Total RNA was isolated essentially as described previously (Tisch et al., 2011 PMID  21220037) using the QIAGEN plant RNA kit (QIAGEN, Hilden, Germany) according to manufacturers instructions. Quality control of total RNA was performed using Bioanalyzer 2100 (Agilent) and only high quality RNA was used for further analysis.
Next generation sequencing was performed at the core facility VetCORE (Vienna, Austria) on a HiSeq2000/SR50 machine.

treatment_protocol: Precultures for cultivation on cellulose were performed on plates with malt extract agar (3 % w/v) in constant darkness for 14 days in order to avoid interference of light pulses or circadian rhythms with transcriptome analysis. An inoculum of 109 conidia/L was applied to 100 ml of Mandels Andreotti minimal medium with 1 % (w/v) microcrystalline cellulose (Alfa Aesar, Karlsruhe, Germany) and 0.1 % (w/v) peptone to induce germination. Strains were grown in constant light (1600 lux) or constant darkness at 28°C for 72 hours at 200 rpm. Harvesting of dark cultures was done under red safety light (darkroom lamp, Philips PF712E, red, 15 W)

tag: genotype/strain

tag: property

value: wildtype

value: constant darkness


title: NASH_10

source_name: Liver needle biopsy


title: YPR2_DD_1

value: recombinant strain


title: QM6a_LL_1

value: constant light


title: YPR2_LL_1


title: YPR2_LL_2


title: QM6a_DD_1


title: NASH_9

value: Male


title: NASH_13

value: NASH


title: NASH_8


description:
ATAC-seq on PBMCs from patient CLL5 on day 150 of ibrutinib treatment, Mono cells
ATAC-seq_CLL5_150d_Mono

source_name: PBMCs_CLL patient_day 150 of ibrutinib treatment_Mono cells


description:
ATAC-seq on PBMCs from patient CLL5 on day 8 of ibrutinib treatment, Mono cells
ATAC-seq_CLL5_8d_Mono

source_name: PBMCs_CLL patient_day 8 of ibrutinib treatment_Mono cells


title: YPR2_DD_2


title: NASH_7


description:
ATAC-seq on PBMCs from patient CLL5 on day 240 of ibrutinib treatment, CLL cells
ATAC-seq_CLL5_240d_CLL

source_name: PBMCs_CLL patient_day 240 of ibrutinib treatment_CLL cells


description:
ATAC-seq on PBMCs from patient CLL5 on day 150 of ibrutinib treatment, CLL cells
ATAC-seq_CLL5_150d_CLL

source_name: PBMCs_CLL patient_day 150 of ibrutinib treatment_CLL cells


title: NASH_6


title: NASH_5


description:
ATAC-seq on PBMCs from patient CLL5 on day 0 of ibrutinib treatment, Mono cells
ATAC-seq_CLL5_0d_Mono

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_Mono cells


description:
ATAC-seq on PBMCs from patient CLL5 on day 1 of ibrutinib treatment, Mono cells
ATAC-seq_CLL5_1d_Mono

source_name: PBMCs_CLL patient_day 1 of ibrutinib treatment_Mono cells


title: UM-SCC46_TNFa_6hr

description:
6 hr
UMSCC_46_TNF6h

tag: cell type

value: HNSCC HPV(-) cell lines


title: UM-SCC46_LTBeta_1hr

description:
1 hr
46_LTb_1h


title: UM-SCC46_noTreat_0hr_for_LTB

description:
0 hr
46_noTx


description:
ATAC-seq on PBMCs from patient CLL5 on day 8 of ibrutinib treatment, CLL cells
ATAC-seq_CLL5_8d_CLL

source_name: PBMCs_CLL patient_day 8 of ibrutinib treatment_CLL cells


title: NASH_4


description:
ATAC-seq on PBMCs from patient CLL5 on day 3 of ibrutinib treatment, CLL cells
ATAC-seq_CLL5_3d_CLL

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CLL cells


title: HiC_Neurons_Rep2

first: Martin

middle: Jin-teng

last: Falk

address: 77 Massachusetts Avenue

department: Physics

institute: MIT

data_processing:
Alignment: Hi-C reads were mapped using bowtie 2.2.4 and the iterative mapping strategy (Imakaev et al, 2011) implemented in the hiclib package.
Binning: the filtered reads pairs were binned into 20kb, 50kb,  and 500kb contact matrices using the cooler library and stored as binary cool HDF5 files.
Filtering: After binning, we remove bins with less than half of the bin sequenced, in addition to bins at the lowest 1% of coverage. We truncate the top 0.05% of trans contacts, likely PCR blowouts.To remove the short-range Hi-C artifacts we also filter contacts mapping to the same or adjacent genomic bins (i.e., first two diagonals).
Normalization: all  filtered contacts matrices were then normalized using the iterative correction procedure (IC), such that the genome-wide sum of contact probability for each row/column equals 1.0.
Genome_build: mm9
Supplementary_files_format_and_content: Cooler HDF5 files (extension .cool) contain contact matrices and were generated using the cooler Python package

source_name: Retina

extract_protocol:
(1) Rods: retinas of 2 mice were dissected, dissociated into single cell suspention using Papain Dissociation System (Worthington Biochemical Corporation) and sorted based on standard forward and sideward scatter settings using FACS Aria II (Becton Dickinson) yielding 1 mln of pure rod perikarya fraction.                                                                               (2) Non-rod neurons: retinas of 3 mice were dissected and dissociated into single cell suspention using Papain Dissociation System (Worthington Biochemical Corporation) yielding ca 10 mln of retinal non-rod neurons        (3) Thymocytes: dissected thymuses were minced, small tissue pieces were disintegrated into a single cell suspension by gentle pipetting and finally pressed through a Cell Strainer Snap Cap with a mesh size of 35 µm yielding 25-30 mln thymoytes                                                                         All single cell suspensions were fixed with 1% formaldehyde (Fisher Scientific, cat # 10532955) for 10 min at RT. Fixation was quenched with 0.1M glycine for 5 min at RT and then for 15 min at 4ºC. Fixed cells were pelleted, snap-frozen and kept at -80ºC until use.
DNA libraries were prepared for sequencing using standard Hi-C protocol. Cross-linked cells were lysed, chromatin was solubilized and digested with HindIII, DNA ends were filled in with biotin and blind ligated. After reversion of crosslinking, DNA was purified and sheared to a size of 100-400 bp by sonication. After end-repair, streptavidin pull-down and paired-end adapter ligation, the libraries were amplified and sequenced on Illumina GAII paired-end sequencing platform.

value: retired breeders


description:
ATAC-seq on PBMCs from patient CLL5 on day 2 of ibrutinib treatment, CLL cells
ATAC-seq_CLL5_2d_CLL

source_name: PBMCs_CLL patient_day 2 of ibrutinib treatment_CLL cells


title: HiC_Neurons_Rep1


title: Control - C1

source_name: Control replicate

value: started at L1

value: control


description:
ATAC-seq on PBMCs from patient CLL5 on day 1 of ibrutinib treatment, CLL cells
ATAC-seq_CLL5_1d_CLL

source_name: PBMCs_CLL patient_day 1 of ibrutinib treatment_CLL cells

value: chronic lymphocytic leukemia patient


title: HiC_Rods_Rep1


title: HiC_LBR_Thym_Rep2

source_name: Thymus

value: C57Bl/6 LBR GT/GT


title: NASH_1

value: Liver


title: HiC_WT_Thym_Rep1


title: HiC_WT_Thym_Rep2


description:
ATAC-seq on PBMCs from patient CLL5 on day 30 of ibrutinib treatment, CLL cells
ATAC-seq_CLL5_30d_CLL

source_name: PBMCs_CLL patient_day 30 of ibrutinib treatment_CLL cells


title: NAFL_15

value: NAFLD


description:
ATAC-seq on PBMCs from patient CLL5 on day 240 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL5_240d_CD8

source_name: PBMCs_CLL patient_day 240 of ibrutinib treatment_CD8 cells

value: ATAC-seq


description:
ATAC-seq on PBMCs from patient CLL5 on day 150 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL5_150d_CD8

source_name: PBMCs_CLL patient_day 150 of ibrutinib treatment_CD8 cells

value: Peripheral blood mononuclear cells (PBMCs)


title: NASH_3

source_name: Liver needle biopsy


title: NASH_2

value: Female


title: NAFL_14


title: HiC_LBR_Thym_Rep1


description:
ATAC-seq on PBMCs from patient CLL5 on day 30 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL5_30d_CD8

source_name: PBMCs_CLL patient_day 30 of ibrutinib treatment_CD8 cells


title: NAFL_13


description:
ATAC-seq on PBMCs from patient CLL5 on day 8 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL5_8d_CD8

source_name: PBMCs_CLL patient_day 8 of ibrutinib treatment_CD8 cells


title: SAMPLE 7: 199559-antiLILRB2-LPS

city: Houston

first: HUIMING

last: CHEN

state: Texas

address: 1613 Wheeler St

institute: Houston Methodist Research institute

description: replicate 2

hyb_protocol: According to the manufacturer's instructions.

scan_protocol: The HumanHT-12 v4 array (Illumina) was scanned on Illumina HiScan according to the manufacturer's instructions.

data_processing: Raw intensity data was processed using Genome Studio (version 2011.1) Gene Expression Module (version 1.9.0) and further processing was done using the lumi R package from Bioconductor. The data was adjusted for background signal before exporting from BeadStudio, and underwent VST transformation and quantile normalization. Probes with no expression were removed. Differential gene expression analysis was performed using the limma R package, and significantly differentially expressed genes were identified based on fold change≥1.5 and p-value<0.05 with Benjamini & Hochberg false-discovery rate correction.

growth_protocol: 2 ^ 106 CD33+ myeloid cells from healthy PBMC donors were grown in the presence of MCSF for 5 days.

extract_protocol: RNA was extracted using QIAzol reagent (Qiagen), following the manufacturer's instructions.

treatment_protocol: M-CSF-treated myeloid cells were subsequently treated with IL4 or LPS for 18 hours. antiLILRB2 or control Ig were added from the beginning of differentiation (5 day of M-CSF treatment plus 18hr IL4 or LPS treatment).

value: human CD33 myeloid cells


title: SAMPLE 1: 199542-IgG-LPS

description: replicate 1

label_protocol: According to the manufacturer's instructions.


title: SAMPLE 11: 341689-antiLILRB2-LPS

description: replicate 3


title: NAFL_11


title: SAMPLE 6: 199559-IgG-IL4

description: replicate 2


title: SAMPLE 8: 199559-antiLILRB2-IL4

description: replicate 2


title: SAMPLE 12: 341689-antiLILRB2-IL4

description: replicate 3


title: SAMPLE 4: 199542-antiLILRB2-IL4

description: replicate 1


description:
ATAC-seq on PBMCs from patient CLL5 on day 2 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL5_2d_CD8

source_name: PBMCs_CLL patient_day 2 of ibrutinib treatment_CD8 cells


description:
ATAC-seq on PBMCs from patient CLL5 on day 3 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL5_3d_CD8

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CD8 cells


title: SAMPLE 2: 199542-IgG-IL4

description: replicate 1


title: NAFL_9


title: NAFL_8


description:
ATAC-seq on PBMCs from patient CLL5 on day 1 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL5_1d_CD8

source_name: PBMCs_CLL patient_day 1 of ibrutinib treatment_CD8 cells


title: NAFL_10


description:
ATAC-seq on PBMCs from patient CLL5 on day 0 of ibrutinib treatment, CD8 cells
ATAC-seq_CLL5_0d_CD8

source_name: PBMCs_CLL patient_day 0 of ibrutinib treatment_CD8 cells


description:
ATAC-seq on PBMCs from patient CLL5 on day 240 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL5_240d_CD4

source_name: PBMCs_CLL patient_day 240 of ibrutinib treatment_CD4 cells


title: SAMPLE 10: 341689-IgG-IL4

description: replicate 3


title: NAFL_7


title: NAFL_6


description:
ATAC-seq on PBMCs from patient CLL5 on day 30 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL5_30d_CD4

source_name: PBMCs_CLL patient_day 30 of ibrutinib treatment_CD4 cells


title: NAFL_4


title: NAFL_5


description:
ATAC-seq on PBMCs from patient CLL5 on day 3 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL5_3d_CD4

source_name: PBMCs_CLL patient_day 3 of ibrutinib treatment_CD4 cells


title: HiC_Rods_Rep2

source_name: Retina


title: NAFL_3


description:
ATAC-seq on PBMCs from patient CLL5 on day 2 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL5_2d_CD4

source_name: PBMCs_CLL patient_day 2 of ibrutinib treatment_CD4 cells


description:
ATAC-seq on PBMCs from patient CLL5 on day 8 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL5_8d_CD4

source_name: PBMCs_CLL patient_day 8 of ibrutinib treatment_CD4 cells


title: NAFL_2


description:
ATAC-seq on PBMCs from patient CLL5 on day 1 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL5_1d_CD4

source_name: PBMCs_CLL patient_day 1 of ibrutinib treatment_CD4 cells


title: NAFL_1


description:
ATAC-seq on PBMCs from patient CLL5 on day 150 of ibrutinib treatment, CD4 cells
ATAC-seq_CLL5_150d_CD4

source_name: PBMCs_CLL patient_day 150 of ibrutinib treatment_CD4 cells