title: pGAL-EUC1_Ymr111c/Euc1-ChIP_meanRep1+2

type: genomic

hyb_protocol: standard NimbleGen protocol

scan_protocol: standard NimbleGen protocol

data_processing: Raw signals of all channels in all replicate arrays were normalized and log2 transformed using the 'vsn' package in R/Bioconductor as described ((Prestel et al., 2010) and Tobias Straub Epigenome project PROT43, http://www.epigenesys.eu/).

label: Cy3 (input),Cy5 (ChIP)

source_name: Ymr111c/Euc1-ChIP pGAL-EUC1-OE strain (W303)

label_protocol: standard NimbleGen protocol

growth_protocol: For galactose induction, yeast cell precultures were grown over-night in YP+3% lactic acid medium, main cultures were grown to OD=0.35-0.4 and 2% galactose was added for 3h.

extract_protocol: ChIP was performed based on a protocol (Aparicio et al, 2005), with minor modifications as described (Kalocsay et al, 2009). Briefly, for each IP yeast cells equivalent to 75 OD600-units were crosslinked with formaldehyde (1% final) for 16 minutes and the reaction was quenched by adding glycine (325mM final). Cells were lysed by beat-beating (MM301, Retsch GmbH) with zirconia/silica beads (BioSpec Inc.), chromatin was isolated and sheared to 200-500 bp fragments using a Bioruptor UCD-200 sonication system (Diagenode). Cell debris was pelleted by centrifugation, input samples were collected and chromatin was subjected to immunoprecipitation with Protein A Sepharose CL-4B (GE Healthcare) and specific antibodies as follows: ubiquitin (clone FK2, Merck/Millipore), ubiquitin-K48-specific (Apu2, Merck/Millipore), Myc-tag (9E10, Sigma),  unspecific rabbit IgG (Bethyl Laboratories Inc.) and specific rabbit antibodies raised against Ymr111c/Euc1 (aa 292-462). Enriched DNA was de-crosslinked and subjected to Proteinase K digest (Sigma), purified (Qiagen PCR purification kit) and processed for genome-wide quantification using NimbleGen arrays. ChIP-chip was performed as described before (Kalocsay et al, 2009; Renkawitz et al, 2013). Briefly, input and ChIP DNA samples were treated with RNase (Sigma) and amplified with the GenomePlex Complete Whole Genome Amplification kit (Sigma) in two steps as described (O'Geen et al, 2006). Labeling of input and ChIP DNA (Cy3 or Cy5), hybridization to S. cerevisiae tiling arrays, array scanning and raw data extraction was performed by Source BioScience Berlin (formerly imaGenes, NimbleGen ChIP-chip service). Custom-designed c12plex NimbleGen arrays with 84 bp median genomic probe spacing and only unique probes were used. A dye-swap was included for replicate experiments and genome-wide binding profiles were generated from two independent experiments (except for ub-FK2 rad6∆ and IgG WT profiles in Fig. 1A, performed once).

treatment_protocol: 2% galactose for 3h

tag: chip antibody

tag: raw data

label: Cy5 (input),Cy3 (ChIP)

source_name: Ymr111c/Euc1-ChIP pGAL-EUC1 strain (W303)


title: S20 CD8.12wk.ctrl

status: Public on Mar 29 2019

type: RNA

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

country: USA

institute: Joslin Diabetes Center

hyb_protocol: Illumina whole-genome gene expression direct hybridization assay protocol.

scan_protocol: Illumina BeadArray Reader scanning protocol.

data_processing: The data were background corrected normalised using negative control probes and quantile normalized using negative and positive control probes with neqc in R.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: cDNA was labeled with biotin following the Encore Biotin IL labeling protocol.

extract_protocol: Total RNAs from T-cells were extracted using Trizol.

tag: age

tag: genotype/variation

value: ctrl, NOD-Lox

tag: cell type

value: CD8+ T-cells


title: pGAL-empty_Ymr111c/Euc1-ChIP_meanRep1+2

city: Martinsried/Munich

first: Markus

last: Höpfler

address: Am Klopferspitz 18

department: Molecular Cell Biology

country: Germany

institute: Max-Planck Institute of Biochemistry

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Ymr111c/Euc1-ChIP pGAL-empty control strain (W303)

tag: strain


title: Slx8-9myc/ubc9-1_Myc-ChIP_meanRep1+2

source_name: Slx8-9myc-ChIP in Slx8-9myc ubc9-1 strain

growth_protocol: Yeast cell precultures were grown over-night in YP+2% glucose medium and main cultures were harvested in mid-log-phase (OD600 0.7-1). All cultures were grown under constant shaking at 30°C, except for pre-cultures for temperature sensitive strains (cdc48-6, cdc48-3, ufd1-2) grown at 25°C.

extract_protocol: ChIP was performed based on a protocol (Aparicio et al, 2005), with minor modifications as described (Kalocsay et al, 2009). Briefly, for each IP yeast cells equivalent to 75 OD600-units were crosslinked with formaldehyde (1% final) for 16 minutes and the reaction was quenched by adding glycine (325mM final). Cells were lysed by beat-beating (MM301, Retsch GmbH) with zirconia/silica beads (BioSpec Inc.), chromatin was isolated and sheared to 200-500 bp fragments using a Bioruptor UCD-200 sonication system (Diagenode). Cell debris was pelleted by centrifugation, input samples were collected and chromatin was subjected to immunoprecipitation with Protein A Sepharose CL-4B (GE Healthcare) and specific antibodies as follows: ubiquitin (clone FK2, Merck/Millipore), ubiquitin-K48-specific (Apu2, Merck/Millipore), Myc-tag (9E10, Sigma),  unspecific rabbit IgG (Bethyl Laboratories Inc.) and specific rabbit antibodies raised against Ymr111c/Euc1 (aa 292-462). Enriched DNA was de-crosslinked and subjected to Proteinase K digest (Sigma), purified (Qiagen PCR purification kit) and processed for genome-wide quantification using NimbleGen arrays. ChIP-chip was performed as described before (Kalocsay et al, 2009; Renkawitz et al, 2013). Briefly, input and ChIP DNA samples were treated with RNase (Sigma) and amplified with the GenomePlex Complete Whole Genome Amplification kit (Sigma) in two steps as described (O'Geen et al, 2006). Labeling of input and ChIP DNA (Cy3 or Cy5), hybridization to S. cerevisiae tiling arrays, array scanning and raw data extraction was performed by Source BioScience Berlin (formerly imaGenes, NimbleGen ChIP-chip service). Custom-designed c12plex NimbleGen arrays with 84 bp median genomic probe spacing and only unique probes were used. A dye-swap was included for replicate experiments and genome-wide binding profiles were generated from two independent experiments (except for ub-FK2 rad6-delta-and IgG WT profiles in Fig. 1A, performed once).

value: Myc (9E10-clone)


title: S14 Treg.12wk.ctrl

source_name: Treg

value: Treg


title: WT-untagged_Myc-ChIP_meanRep1+2

source_name: Slx8-9myc-ChIP in WT strain (untagged control)


title: S17 Treg.12wk.MIP

value: MIP, NOD-LIRKO


title: S24 CD8.12wk.MIP


title: S23 CD8.12wk.MIP


title: S22 CD8.12wk.MIP


title: ubx4_ub-K48-ChIP_meanRep1+2

source_name: ub-K48-ChIP in ubx4-delta-strain

value: ubiquitin-K48 (Apu2-clone)


title: WBJPE170996151

type: SRA

city: HangZhou

first: Bingbing

last: Wu

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medcine

country: China

institute: Zhejiang University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
alignment was conducted with Tophat
The final gene expression data was normalized using Cuffnorm and represented as counts
Genome_build: mm9,hg19
Supplementary_files_format_and_content: Excel files include raw counts of each gene from each sample. Columns are sample name, rows are genes.

organism: Homo sapiens

source_name: bmsc HA5-4

extract_protocol:
Trizol for RNAextraction,  reverse transcription for 1st cDNA strand, second strand kit for double strand DNA synthesis.
3' end enrichment with Illumina Nextera XT

treatment_protocol: We collected tissues of heart, liver, spleen, kidney, skeletal muscle, peripheral blood mononuclear cells (PBMC) as well as tissue specific (stem) cells of skeletal muscle derived stem cells (MUSC), Human bone marrow derived stem cells (hBMSC), Human primary umbilical vein endothelial cell lines (HUVEC) for RNA-seq after treated with the two groups (PBS control and HA solution) for 24hours, respectively.

tag: tissue

value: HBMSC

tag: treatment

value: HA


title: cdc48-3/ymr111c_ub-K48-ChIP_meanRep1+2

source_name: ub-K48-ChIP in cdc48-3 ymr111c/euc1-delta-strain


title: DKK1_P

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

data_processing:
Raw paired-end reads generated from the Illumina HiSeq 3000 sequencing platform were cleaned up with the Cutadapt program. The partial adaptors and potential sequencing errors introduced during sequencing or library preparation were trimmed off and reads with a quality and read length <40 bases were excluded.
All processed paired-end reads of each sample were individually mapped to the reference sequences using bowtie2 (v. 2.2.3) with a ‘3 mismatches within a read’ allowance.
The samtools and scripts developed in house at the ICBR were used to detect the potential PCR duplicates and to choose uniquely mapped reads for gene expression analysis.
Gene expression levels were assessed by counting the number of mapped reads for each gene symbol.
Raw counts were processed with the edgeR package for the R software.
Genes with low expression counts (less than 1 count per million) were filtered out before normalization.
The between-samples normalization method applied was TMM (weighted trimmed mean of M-values).
Genome_build: bosTau8
Supplementary_files_format_and_content: tab delimited text file containing raw read counts for each sample.

organism: Bos taurus

source_name: bovine embryo

growth_protocol: Embryos were produced in vitro from oocytes from abattoir and sex-sorted semen, culture for 7 days.

extract_protocol:
RNA was extracted from each embryo using the Qiagen RNeasy Mini kit (Qiagen, Valenciam, CA, USA) following manufacturer instructions, including DNase treatment. 25 ng of total RNA was used for mRNA isolation with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
RNA library construction was performed at the Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression & Genotyping Core, University of Florida. RNA libraries were constructed with NEBNext® Ultra™ Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer's user guide. Briefly, RNA was fragmented followed by first strand cDNA synthesis using reverse transcriptase and oligo-dT primers. Synthesis of double strand cDNA was performed, followed by end-repair and adaptor ligation. At this point, Illumina adaptors were ligated to the sample. The library was enriched (each library had a unique barcode) by 10 cycles of amplification, and purified by Agencourt® AMPure beads (Beckman Coulter Life Sciences, Indianapolis, IN, USA). Finally, equimolar amounts of 20 individual libraries were pooled and sequenced by Illumina HiSeq 3000 2X100 cycles run for total of 3 runs (Illumina Inc., San Diego, CA, USA).

treatment_protocol: Culture medium was supplemented with either 0 or 100 ng/ml human recombinant DKK1 on day 5 of culture. Embryos were transferred to recipient on day 7 and harvested on day 15.

value: day 15 of development

tag: length (mm)

tag: developmental stage

value: embryo

value: 100 ng/ml DKK1


title: DKK1_F


title: WT_Ymr111c/Euc1-ChIP_meanRep1+2

source_name: Ymr111c/Euc1-ChIP in WT strain


title: Slx8-9myc/ymr111c/euc1_Myc-ChIP_meanRep1+2

source_name: Slx8-9myc-ChIP in Slx8-9myc ymr111c/euc1-delta-strain


title: WBJPE170996150

source_name: bmsc HA5-3


title: cdc48-3_ub-K48-ChIP_meanRep1+2

source_name: ub-K48-ChIP in cdc48-3 strain


title: cdc48-6_ub-K48-ChIP_meanRep1+2

source_name: ub-K48-ChIP in cdc48-6 strain


title: S11 CD8.8wk.MIP


title: ymr111c/euc1_Ymr111c/Euc1-ChIP_meanRep1+2


title: S12 CD8.8wk.MIP


title: WBJPE170996148

source_name: bmsc HA5-1


title: DKK1_H


title: ubx5_ub-K48-ChIP_meanRep1+2

source_name: ub-K48-ChIP in ubx5-delta-strain


title: ufd1-2_ub-K48-ChIP_meanRep1+2

source_name: ub-K48-ChIP in ufd1-2 strain


title: WBJPE170996147

source_name: bmsc CTR3

value: control


title: DKK1_G


title: WBJPE170996146

source_name: bmsc CTR2


title: DKK1_C


title: WBJPE170996145

source_name: bmsc CTR1


title: WBJPE170996102

source_name: HUVEC HA-3

value: HUVEC


title: S7 CD8.8wk.ctrl


title: DKK1_R


title: DKK1_W


title: WBJPE170996100

source_name: HUVEC HA-1


title: S10 CD8.8wk.MIP


title: WBJPE170996101

source_name: HUVEC HA-2


title: S8 CD8.8wk.ctrl


title: Slx8-9myc_Myc-ChIP_meanRep1+2

source_name: Slx8-9myc-ChIP in Slx8-9myc strain


title: WT_IgG-control-ChIP1_Rep1

source_name: IgG-control ChIP1 in WT strain

value: IgG (unspecific rabbit IgG)


title: WT_IgG-control-ChIP2_meanRep1+2

source_name: IgG-control ChIP2 in WT strain


title: S6 Treg.8wk.MIP

source_name: Treg


title: cdc48-3_ub-FK2-ChIP_meanRep1+2

source_name: ub-FK2-ChIP in cdc48-3 strain

value: ubiquitin (FK2-clone)

value: ubiquitin FK2


title: S4 Treg.8wk.MIP


title: S2 Treg.8wk.ctrl


title: WT 2

city: dalian

first: liqiu

last: jia

state: liaoning province

address: No.9 West Section Lvshun South Road

institute: Dalian Medical University

description:
monocytic cell line
WT2

data_processing:
Illumina bcl2fastq version 2.19 were used to the basecalling.
Sequenced reads with 10% low quality bases, adapters and artificial sequences (including UP1, UP2, polyA sequences) introduced during the experimental processes were trimmed by in house scripts.
The trimmed clean reads were aligned to the UCSC human hg19 reference using Tophat2 (v2.1.0) with default settings (Trapnell et al., 2009).
Cufflinks (v2.2.1) with defualt settings was used to quantify transcription levels of annotated genes (Trapnell et al., 2010), and FPKM were calculated
FPKM values were log2-transformed with an offset value of 1.0.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes FPKMs (log2-transformed with an offset value of 1.0) for each sample

source_name: THP-1 macrophage cells

growth_protocol: the THP-1 cells were differentiated by PMA  for 24h

extract_protocol:
the RNA was harvested using Trizol reagent
RNA libraries were prepared using TruSeq PE Cluster kit v4-cBot-HS(Illumia, San Diego, USA) according to  the manufacturer's instructions

treatment_protocol: The differentiated  cells were infected with wild type M.smegmatis or MSMEG_5447 gene knockout M.smegmatis strain for 3h and then continue to cultivate for 24h.

value: macrophage cells

tag: cell line


title: Slx8-9myc/cdc48-3_Myc-ChIP_meanRep1+2

source_name: Slx8-9myc-ChIP in slx8-9myc cdc48-3 strain


title: cdc48-6_ub-FK2-ChIP_meanRep1+2

source_name: ub-FK2-ChIP in cdc48-6 strain


title: WT_ub-K48-ChIP_meanRep1+2

source_name: ub-K48-ChIP in WT strain


title: S3 Treg.8wk.ctrl

value: ctrl, NOD-Lox


title: S5 Treg.8wk.MIP


title: S1 Treg.8wk.ctrl


title: KO rep3

city: Turku

first: Akira

last: Takeda

state: South-West Finland

address: Tykistökatu 6A

department: Institute of Biomedicine

country: Finland

institute: University of Turku

data_processing:
Single-end 50 bp reads were aligned to the mm10 mouse genome with STAR version 2.5.2b. Read counting was performed with subreads package.
Read counts were normalized and RPKM was calculated using the TMM normalization method of the edgeR R/Bioconductor package.
The Bioconductor package Limma was used for differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited csv files include RPKM values for each Sample ...

source_name: Spleen endothelial cells

extract_protocol:
Spleens from WT and KO mice were removed, digested with collagenase and CD31+ CD45- endothelial cells were sorted and RNA was extracted. cDNA was synthesized with SMART-Seq v4 ultra low input RNA kit.
Sequencing libraries were generated from the amplified cDNA using Nextera XT (Illumina)

value: Spleen

value: Blood endothelial cells

tag: genotype


title: WBJPE170996099

source_name: HUVEC CTR-3


title: Control_K

source_name: bovine embryo


title: rad6_ub-FK2-ChIP_Rep1

source_name: ub-FK2-ChIP in rad6-delta-strain


title: Control_S


title: WT 1

description:
monocytic cell line
WT1


title: Control_O


title: KO rep2


title: WBJPE170996098

source_name: HUVEC CTR-2


title: KO rep1


title: DM5447 2

description:
monocytic cell line
P5447_K2


title: DM5447 1

description:
monocytic cell line
P5447_K1


title: WBJPE170996097

source_name: HUVEC CTR-1


title: Control_L


title: Control_U


title: WT rep3

value: Wild type


title: Control_Q


title: Control_M


title: WT rep1


title: B1

city: Zhenjiang

first: Qian

last: xin

state: Jiangsu

address: 301 Xuefu Road

institute: Jiangsu University

data_processing:
Raw reads were pre-processed to obtain the clean reads by removing reads containing poly-N, reads containing adapter and low-quality reads from raw data were filtered with FASTQ-Quality-Filter tool.
HISAT2 generate a database of splice junctions based on the gene model annotation ﬁle, which was used to align the paired-end clean reads to the reference genome of Penicillium digitatum(GCF_000315645.1_PdigPd1) .
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. Then, the number of fragments per kilobase of transcript per Million fragments mapped (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GCF_000315645.1_PdigPd1(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/645/GCF_000315645.1_PdigPd1_v1/GCF_000315645.1_PdigPd1_v1_genomic.fna.gz)
Supplementary_files_format_and_content: ctab files and txt files

organism: Penicillium digitatum

source_name: Penicillium digitatum from Citrus wound (44 hours after inoculation of Penicillium digitatum from Potato Dextrose Agar medium)

growth_protocol: Potato Dextrose Agar medium,23-28℃

extract_protocol:
The sample was ground in liquid nitrogen.Extraction of total RNA from Penicillium digitatum by fungal RNA Extraction Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 44 hours


title: B2


title: A2

source_name: Penicillium digitatum grown on Potato Dextrose Agar medium

value: 7 days


title: t2 BrdU_limit (90 min) (Nanopore)

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

description: Raw nanopore sequencing reads and associated processed files

library_source: genomic

data_processing:
Illumina: sequencing reads were demultiplexed and the barcode sequences were trimmed using the FASTX toolkit
Illumina: Sequencing reads were mapped to the sacCer3 genome assembly using bowtie2
Illumina: Read tag counts were determined for the 5’ end of uniquely mapping reads without mismatches in 100 bp nonoverlapping regions
Illumina: The ratio between IP and Input sample was calculated for each bin, excluding bins that had less than 20% of the expected number of reads in the input sample
Illumina: Ratios were median-smoothed over 1 kb windows
Nanopore: Basecalling was perform with Albacore
Nanopore: Aligned reads to sacCer3 reference using minimap2
Nanopore: Detected BrdU in reads using D-NAscent
Nanopore: D-NAscent converts called BrdU sites to psl files
Nanopore: D-NAscent converts regions of called BrdU into bedgraphs
Genome_build: sacCer3
Supplementary_files_format_and_content: bed files show either BrdU-seq data or D-Nascent origin calls
Supplementary_files_format_and_content: bedgraphs show either BrdU calls or fork direction
Supplementary_files_format_and_content: psl files show hard call BrdU detectiondata

source_name: genomic DNA from cells released into media containing 40 ug/ml BrdU for 90 min in the presenc of nocodazole

extract_protocol:
Cells were harvested, spun down, washed in water,  and then resuspended in 500 µL of 1.2 M sorbitol, 200 mM Tris-HCl (pH7.5), 20 mM EDTA, 0.1% b-mercaptoethanol. Cells were spheroplasted with Zymolyase and then treated with SDS, Proteinase K and RNase A. DNA was purified by phenol chloroform extraction.
Library preparation and sequencing was carried out according to Illumina and ONT instructions.

tag: relevant genotype


title: Control_J


title: h2b-K123R_ub-FK2-ChIP_meanRep1+2

source_name: ub-FK2-ChIP in h2b-K123R strain


title: A1


title: Control_V


title: WT_ub-FK2-ChIP_meanRep1+2

source_name: ub-FK2-ChIP in WT strain


title: Control_T


title: t4 HU (130 min) (Nanopore)

description: Raw nanopore sequencing reads and processed files showing individual BrdU calls (psl file) and BrdU-scores in 2 kb windows (bedgraph)

source_name: genomic DNA from cells released synchronously into media containing 0.2 M HU and 40 ug/ml BrdU for 60 min, and then chased with 400 ug/ml thymidine for 70 min


title: NBXOC

city: Nanning

first: Sheng

last: Huang

state: Guangxi

address: 100 Daxue Road

department: College of Life Science and Technology

institute: Guangxi University

description: NBXOC

data_processing:
After removing reads containing the adapter, reads containing poly-N, and low-quality reads, clean reads were obtained. The Q20, Q30 and GC contents of the clean reads were calculated.
Paired-end clean reads from Xoc-rice mixed sample were aligned to the rice reference genome Oryza sativa Japonica Group (Assembly ID=22512) using TopHat v2.0.9.
Clean reads from Xoc-rice mixed sample that cann't aligned on rice genome were subsequently aligned to the Xoc reference genome Xoc BLS256 (Assembly ID=357911) using Bowtie v2.0.6
Paired-end clean from Xoc liquid culture sample that were aligned to the Xoc reference genome Xoc BLS256 (Assembly ID=357911) using Bowtie v2.0.6
Cuffdiff (v2.1.1) was used to calculate the FPKMs of the genes in each sample (Trapnell, C. et al. 2010).
Genome_build: Oryza sativa Japonica Group (Assembly ID=22512), Xanthomonas oryzae pv. oryzicola BLS256 (Assembly ID=357911)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Xanthomonas oryzae pv. oryzicola

source_name: in medium bacteria

growth_protocol: Rice (Oryza sativa L. cv. Nipponbare) seeds were germinated by submersion in water, followed by incubation in the dark for two days at 37°C. Five germinated seeds were planted in a small pot containing autoclaved soil. The plants were grown in the greenhouse under a 14/10-h light/dark cycle with a temperature controlled between 28°C and 30°C till the fourth leaf begins sprouting (about 14 days). Xoc strains were grown in rich medium named nutrient broth (NB) at 28°C (Yang and Bogdanove, 2013).

extract_protocol:
Infiltrated leaf part was collected 24 h after inoculation, snap frozen in liquid nitrogen, and stored at −80°C immediately. Bacteria cultures were collected by centrifugation and the medium discarded. Snap frozen the cell pellets in liquid nitrogen, then stored at −80°C immediately.
Before cDNA library preparation, ribosomal RNA was removed using the Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and the rRNA-free residue was cleaned by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA with the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations. Briefly fragmentation was performed using divalent cations under elevated temperatures in NEB Next First Strand Synthesis Reaction Buffer. First-strand cDNA was synthesized using random hexamer primers and the M-MuLV Reverse Transcriptase (RNaseH-). Second-strand cDNA synthesis was performed subsequently using DNA Polymerase I and RNase H. In the reaction buffer dNTPs, dTTP was replaced with dUTP. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activity. After adenylation of the DNA fragment 3’ ends, the NEBNext Adaptor with a hairpin loop structure was ligated to prepare for hybridization.   To preferentially select cDNA fragments 150-200 bp in length, the library fragments were purified with the AM Pure XP system (Beckman Coulter, Beverly, MA, USA). After that, 3 μL of the USER Enzyme (NEB, USA) was incubated with size-selected, adaptor-ligated cDNA at 37°C for 15 min, followed by incubation for 5 min at 95°C prior to the PCR. The PCR was performed with the Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.   Finally, the products were purified (AM Pure XP system), and the library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Before inoculated, Xoc strains were grown for 24 h at 28°C in NB medium, and the cells were collected by centrifugation and re-suspended in DI water. The concentration of the Xoc suspension was adjusted to O.D.600=0.5 (approximately 5.0 × 107 CFU/mL) prior to infiltration. Two-week-old rice seedlings were inoculated with the Xoc suspension using a syringe infiltration method (Zou et al., 2011). For each plant, the second and third leaves were picked, and 2/3 of the leaf surface was infiltrated. To prepare Xoc bacterial cultures for RNA-seq, Xoc strains were grown for 24 h at 28°C in NB medium, and the cells were collected by centrifugation and re-suspended in DI water. Xoc suspension was adjusted to Optical Density (O.D.)600=1 (approximately 1.0 × 108 CFU/mL), 100 μL of the Xoc suspension was added into 10 mL fresh NB medium and grown for 24 h at 28°C.

tag: agent

value: GX01 wild type

tag: infiltrated strain

tag: cultivar


title: hemi-labelled gDNA 100 min after release (Nanopore)

description: Nanopore sequencing reads from sample taken after one S phase in the presence of 400 ug/ml BrdU

source_name: genomic DNA from cells released into one round of S phase in media containing 400 ug/ml BrdU


title: constitutive BrdU incorporation

description: Nanopore sequencing reads from cells grown in BrdU-containing media for 24 hours

source_name: genomic DNA from cells grown in YPG media containing different proportions of thymidine and BrdU

value: MATa ADE2 cdc21::kanMX leu2::LEU2-GAL-hENT1 LYS2 RAD5 trp1::TRP1-GAL-dNK ura3-1


title: primer extension

description: Nanopore reads and reference sequences from primer extension experiment

organism: synthetic construct

source_name: synthesized in vitro


title: Control_B

value: day 15 of development


title: flamKG/Df

city: Stockholm

first: Artem

last: Ilin

address: Svante Arrhenius väg 20C

department: MBW

country: Sweden

institute: Stockholm University

data_processing:
Only first pair of paired-end reads was used for further analysis. Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence using cutadapt v1.18 with parameters  -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC -q 30 -m 23 -M 29 -O 10, then mapped to dm3 genome assembly using bowtie2 v2.3.4.3 with standard parameters and then filtered by samtools view with parameter  -q 10
Genome_build: dm3
Supplementary_files_format_and_content: bedgraph files for the 23-29 nt piRNA fraction were generated using htseq-count software and R via Rstudio; counts represent RPM values per 500 nt bin.

organism: Drosophila melanogaster

source_name: Ovaries

growth_protocol: Flies were grown according to standard protocol.

extract_protocol:
Small RNAs 19–29 nt in size from Drosophila ovaries were isolated from 12% polyacrylamide gels of total RNA extracts.
Libraries were barcoded according to IlluminaTrueSeq Small RNA sample prep kit instructions and sequenced using the Illumina NovaSeq-6000 instrument.

value: ovaries

value: flamKG/Df


title: KO_H3K27me3_1

status: Public on Mar 28 2019

city: Shanghai

first: Dan

last: Meng

address: 138 Yixueyuan Rd, P.O.Box: 224

department: Department of Physiology and Pathophysiology

institute: Fudan University

data_processing:
Raw sequencing reads were first processed to remove adaptors and low-quality bases using Trimmomatic (v 0.33). Then clean reads were mapped to human genome GRCh38 (from ENSEMBL) using STAR (020201) with default parameters. Raw counts generated by STAR were concatenated together and fed to DEseq2 (1.16.1) to get normalized expression and screen differentially expressed (DE) genes. Threshold for DE genes are FDR (false discovery rate) less than 0.1 and absolute fold change larger than 1.5. Gene ontology enrichment analysis were performed using GOEAST. All plots were generated using www.ehbio.com/ImageGP.
Raw sequencing reads were first estimated and no preprocessing performed due to high reads quality. Then reads were mapped to human genome GRCH38 using BWA (0.7.15-r1140) with default parameters. Low quality mapped reads and PCR duplicates were removed using samtools (v1.2) and PICARD (1.138) (http://broadinstitute.github.io/picard/index.html). Promoters were defined as upstream 1 kb and downstream 0.5 kb of transcription start sites (TSS). Meta gene profile and TSS profile were generated using deepTools2 (3.0.1). Normalized reads distribution profile were produced using deepTools2 and visualized using UCSC genome browser. MACS2 were used to identify enrichment peaks for Bach1, EZH2 (with default parameters for “sharp” peaks) and H3K27me3 (with default parameters for “broad” peaks).
Genome_build: GRCh38
Supplementary_files_format_and_content: TAB-separated files containing normalzied gene expression values and peak files

source_name: Bach1 knockout_hESC

growth_protocol: Human embryonic stem cells maintained and cultured in serum-free medium mTesR1

extract_protocol:
RNA was harvested using Trizol reagent. TrueLib mRNA Library building kit (ExCell Bio , Cat # NGS00-2012) was used with 1 ug of total RNA for the construction of sequencing libraries. Immunoprecipitated DNA was harvested from Samples which were incubated with 3–5 μg of antibody during CHIP assay. KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series( KAPA biosystems, cat# KK8500) was used with 10-100ng DNA for the construction of sequencing libraries.
RNA-seq and CHIP-seq  libraries were prepared for sequencing using standard protocols In accordance with the instructions.

treatment_protocol: For spontaneous differentiation, ESCs were dissociated into single cells plated aton Ultra Low Cluster Plate for EB formation and were differentiated in defined culture system.

value: embryonic stem cell

value: Bach1 knockout

tag: passages

tag: chip anitbody

value: H3K27me3 (millipore, cat##2699642)


title: KO_EZH2_1

value: EZH2 (Cell signaling, cat##5246)


title: control miR 1

city: Bethesda

first: Luca

last: Gattinoni

state: MD

address: 10 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

hyb_protocol: 10 ng total RNA was used for Nanostring analysis following the NanoString® nCounter®Expression CodeSet Design Manual

data_processing: Background levels were calculated and subtracted from the samples, which were then normalized against the positive control and housekeeping gene probes.

source_name: CD8 T cells

growth_protocol: 3e5 control miR/miR-155 transduced CD8 T cells were tanfered into C57BL/6 mice in conjuction with rvv-gp100 and sorted 5 days later.

extract_protocol: sorted cells were extracted by Qiagen miRNeasy Mini kit

value: CD8 T cells

value: control miR


title: WT rep2

source_name: Spleen endothelial cells


title: WT_EZH2_1

value: wild type


title: miR-155 2

scan_protocol: 10 ng total RNA was used for Nanostring analysis following the NanoString® nCounter®Expression CodeSet Design Manual


title: miR-155 1

label_protocol: 10 ng total RNA was used for Nanostring analysis following the NanoString® nCounter®Expression CodeSet Design Manual


title: DKK1_I

source_name: bovine embryo

value: embryo

value: 100 ng/ml DKK1


title: WTD3_3_1

tag: cell status

value: spontaneously differentiation day3


title: WTD3_2_1


title: control miR 2


title: flamKG/FM7

data_processing:
Only first pair of paired-end reads was used for further analysis. Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence using cutadapt v1.18 with parameters  -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC -q 30 -m 23 -M 29 -O 10, then mapped to dm3 genome assembly using bowtie2 v2.3.4.3 with standard parameters and then filtered by samtools view with parameter  -q 10
Genome_build: dm3
Supplementary_files_format_and_content: bedgraph files for the 23-29 nt piRNA fraction  were generated using htseq-count software and R via Rstudio; counts represent RPM values per 500 nt bin.


title: WTD0_3_1

value: hESC


title: WTD3_1_1


title: WTD0_1_1


title: WTD0_2_1


title: KOD3_1_1

source_name: Bach1 knockout_hESC_D3


title: KOD3_3_1


title: KOD3_2_1


title: KOD0_3_1

source_name: Bach1 knockout_hESC_D0


title: KOD0_1_1


title: WT_H3K27me3_1


title: HiPS-RIKEN-2A, biological rep6

city: Setagaya

first: Takuya

last: Kuroda

state: Tokyo

address: 1-18-1 Kamiyoga

department: Division of cell-based therapeutic products

country: Japan

institute: National Institute of Health and Sciences

hyb_protocol: Labeled RNA were hybridized for 16 hr at 48C on GeneChip miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: miRNA array were scanned using the GeneChip Scanner 3000 7G.

data_processing: Scanned images of microarray chips were analyzed using Affymetrix Expression Console with the default RMA settings. Raw data were processed and Nromalized on basis of organism human using RMA algorithm.

label_protocol: RNA labeling were prepared according to the FlashTagTM Biotin HSR protocol from 1000 ng total RNA.

growth_protocol: Undifferentiated hiPSCs were maintained on Matrigel (Corning)-coated dishes in mTeSR1 medium (StemCell Technologies)

extract_protocol: Extraction of total RNA containing miRNA was performed according to the manufacturer's instructions (miRNeasy  Mini Kit, Qiagen)


title: Tic, biological rep2

source_name: Tic

value: Tic


title: HiPS-RIKEN-12A, biological rep1


title: Tic, biological rep3


title: HiPS-RIKEN-12A, biological rep3


title: hBMSC_0_week

city: Guangzhou

first: Gong

last: Zhang

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

institute: Jinan University

data_processing:
Illumina bcl2fastq2-v2.17 software used for basecalling.
After filtered out less than 50 bp reads with raw reads trimming adapter, the reads of hBMSC and mBMSC sample were mapped to transcript reference libraries Ensemble Homo sapiens GRCh38 and Ensemble Mus musculus GRCm38 with FANSe3 with parameters -L150 -S12 -E8p -U0. The reads of lnc-OB1_ASO and NC samples were mapped to transcript reference libraries refseq Mus musculus GRCm38 with the same parameteres.
Gene expression levels are quantified using RPKM (reads per kilobase per million reads) as unit.
Genome_build: Homo sapiens GRCh38 and Ensemble Mus musculus GRCm38
Supplementary_files_format_and_content: tab-delimited text files include read counts and RPKM values for each Sample.

source_name: BMSCs

growth_protocol: Mouse and human BMSCs were seeded in T25 culture flasks, and osteogenic differentiation was induced when the cells reached approximately 90% confluence. MC3T3 cells seeded in 6-well plates were transient transfected with lnc-ob1 ASO using Lipofectamine 3000 reagent (Life Technologies) and harvested after 48 h.

extract_protocol:
After the cells were harvested, total RNA was isolated from the cells using Trizol reagent (Life Technologies).
Before constructing total RNA libraries, rRNA of the samples were removed via a method Selective Depletion of abundant RNA (SDRNA) which described by Morlan, J.D. (Morlan, J.D. et al. Plos One, 2012). Subsequently, RNA libraries were prepared for next-generation sequencing according to the protocol of VAHTS mRNA-seq v2 Library Prep Kit for Illumina while without isolated poly (A)+ RNA transcripts. The poly (A)+ RNA libraries of lnc-OB1 knockdown KI mice and N.C control KI mice were prepared according to the protocol of VAHTS mRNA-seq v2 Library Prep Kit for Illumina.

treatment_protocol: To induce Mouse and human BMSCs differentiation, the medium was completely replaced with osteogenic differentiation medium containing 10 nM dexamethasone (Sigma-Aldrich, USA), 50 μg/ml ascorbic acid and 5 mM β-glycerophosphate. The differentiation medium was changed every 2 d and cells were harvested after two weeks. KI mice osteoblasts seeded in 6-well plates were transient transfected with lnc-ob1 ASO using Lipofectamine 3000 reagent (Life Technologies) and harvested after 48 h.

value: bone marrow

value: BMSCs

tag: differentiation stage

value: undifferentiated (0 week)


title: HiPS-RIKEN-12A, biological rep6


title: hBMSC_2_week

value: differentiated (2 week)


title: HiPS-RIKEN-12A, biological rep5


title: Tic, biological rep5


title: Tic, biological rep4


title: HiPS-RIKEN-12A, biological rep4


title: HiPS-RIKEN-2A, biological rep3


title: HiPS-RIKEN-2A, biological rep4


title: HiPS-RIKEN-2A, biological rep1


title: HiPS-RIKEN-2A, biological rep2


title: HiPS-RIKEN-1A, biological rep6


title: WBJPE170996149

source_name: bmsc HA5-2

value: HBMSC

value: HA


title: HiPS-RIKEN-1A, biological rep5


title: HiPS-RIKEN-1A, biological rep3


title: HiPS-RIKEN-1A, biological rep4


title: HiPS-RIKEN-1A, biological rep2


title: HiPS-RIKEN-1A, biological rep1


title: Tic, biological rep6


title: Tic, biological rep1


title: KOD0_2_1

value: embryonic stem cell

tag: genotype/variation

value: Bach1 knockout


title: HiPS-RIKEN-2A, biological rep5


title: mc-iPS, biological rep6

source_name: mc-iPS

value: mc-iPS


title: mc-iPS, biological rep5


title: DKK1_E

tag: age

value: day 15 of development


title: 409B2, biological rep4


title: ATCC-DYR0103hiPSc, biological rep5


title: ATCC-DYR0100hiPSc, biological rep3


title: 409B2, biological rep6


title: 409B2, biological rep2


title: ATCC-DYR0100hiPSc, biological rep4


title: ATCC-DYR0103hiPSc, biological rep1


title: 409B2, biological rep5


title: mc-iPS, biological rep2


title: mc-iPS, biological rep3


title: mc-iPS, biological rep4


title: ATCC-DYR0103hiPSc, biological rep3


title: ATCC-DYR0103hiPSc, biological rep6


title: 253G1, biological rep5


title: ATCC-DYR0100hiPSc, biological rep2


title: 253G1, biological rep6


title: mc-iPS, biological rep1


title: ATCC-DYR0100hiPSc, biological rep1


title: ATCC-DYR0103hiPSc, biological rep4


title: 409B2, biological rep1


title: ATCC-DYR0100hiPSc, biological rep5


title: ATCC-DYR0100hiPSc, biological rep6


title: ATCC-DYR0103hiPSc, biological rep2


title: 409B2, biological rep3


title: 253G1, biological rep3


title: 253G1, biological rep4


title: 253G1, biological rep1


title: 201B7, biological rep5


title: 201B7, biological rep3


title: MMTV-PyVT_Int_1

first: Margaret

middle: C

last: Cam

institute: NIH

description:
Isolated MMTV-PyVT Cells on 30kPa PA gels, biological replicate 1
Gene expression data from proliferating epithilial cancer cells

hyb_protocol: Fragmented samples were hybridized to Affymetrix GeneChip PrimeView Human Gene Expression array or  Affymetrix mouse Gene ST 2.0 GeneChip, for MDA-MB-453 and MMTV-PyVt tumor cells respectively, in an Affymetrix hybridization oven at 45 °C, 60 rpm for 16 hours.  Wash and staining were performed on Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip scanner 3000, and data collected using Affymetrix AGCC software.

data_processing: Affymetrix PrimeView Human Gene Expression and Mouse Gene 2.0 ST Array data were processed using the affy and limma bioconductor packages. For the human MDA-MB-453 cell assays, differentially expressed genes were detected in low and medium stiffness gels compared with glass.  For the mouse data, gene expression changes between cells immediately after isolation from the tumor were compared those same cells plated and cultured on PA gels or glass.

source_name: MMTV-PyVT tumor cells, 5 days on 30 kPa PA gels

label_protocol: For the human MDA-MB-453 cells, 100 ng of RNA was reverse transcribed and labeled with biotin using Affymetrix 3’ IVT Plus kit, following manufacturer’s protocol (Affymetrix, Santa Clara, CA). For mouse tumor cells, 2 ng of RNA was reverse transcribed, amplified and sense strand cDNA was fragmented and labeled using WT Pico expression kit, following the manufacturer’s suggested protocol.

growth_protocol: MDA-MB-453 cells were cultured in a 37°C, 5% CO2 humidified environment in T75 tissue culture treated flasks, and grown in RPMI-1640 cell culture medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 0.1 vol% gentamicin. mouse mammary tumor cells were isolated by aseptically removing the tumors, mincing the tissue into 1 mm cubes, and mammary epithelial cancer cells isolated using collagenase. Cells were suspended in complete EpiCult-B media, transferred to a sterile petri dish and allowed to incubate at 37°C for 1 hour to allow for the adherence of stromal cells. The nonadherent fraction, containing mammary epithelial tumor cells, was collected and used for experimental assays.

extract_protocol: total RNA isolated using the RNeasy micro extraction kit, following the manufacturer’s instructions (Qiagen Sciences, Germantown, MD). RNA quality was checked on an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA), and all samples used in microarray analysis had a high quality score (RIN >7 for mouse, RIN > 9 for human).

treatment_protocol: Human MDA-MB-453 cells, or freshly isolated MMTV-PyVT mouse tumor cells, were seeded onto 96 well arrays containing 5kPa or 30kPa PA gels, as well as the glass control, at 25 x 103 and 50 x 103 cells/well, respectively. After 5 days of culture, the media was removed and cells collected following a 10 min. incubation with trypsin.

value: Adenocarcinoma, mammary fat pad

tag: morphology

value: epithelial

tag: gender

value: female


title: 201B7, biological rep4


title: MMTV-PyVT_Int_4

description:
Isolated MMTV-PyVT Cells on 30kPa PA gels, biological replicate 4
Gene expression data from proliferating epithilial cancer cells

tag: tissue


title: MMTV-PyVT_Isol_1

description:
Freshly Isolated MMTV-PyVT Cells, biological replicate 1
Gene expression data from proliferating epithilial cancer cells

source_name: Fresh isolated MMTV-PyVT tumor cells


title: MMTV-PyVT_Soft_3

description:
Isolated MMTV-PyVT Cells on 5kPa PA gels, biological replicate 3
Gene expression data from proliferating epithilial cancer cells

source_name: MMTV-PyVT tumor cells,  5 days on 5 kPa PA gels


title: MMTV-PyVT_Isol_3

description:
Freshly Isolated MMTV-PyVT Cells, biological replicate 3
Gene expression data from proliferating epithilial cancer cells


title: MMTV-PyVT_Soft_1

description:
Isolated MMTV-PyVT Cells on 5kPa PA gels, biological replicate 1
Gene expression data from proliferating epithilial cancer cells


title: 201B7, biological rep1


title: MMTV-PyVT_Glass_4

description:
Isolated MMTV-PyVT Cells on glass, biological replicate 4
Gene expression data from proliferating epithilial cancer cells

source_name: MMTV-PyVT tumor cells, 5 days on glass


title: MMTV-PyVT_Glass_2

description:
Isolated MMTV-PyVT Cells on glass, biological replicate 2
Gene expression data from proliferating epithilial cancer cells


title: MMTV-PyVT_Glass_3

description:
Isolated MMTV-PyVT Cells on glass, biological replicate 3
Gene expression data from proliferating epithilial cancer cells


title: 201B7, biological rep6


title: MMTV-PyVT_Isol_2

description:
Freshly Isolated MMTV-PyVT Cells, biological replicate 2
Gene expression data from proliferating epithilial cancer cells


title: 201B7, biological rep2


title: MMTV-PyVT_Int_2

description:
Isolated MMTV-PyVT Cells on 30kPa PA gels, biological replicate 2
Gene expression data from proliferating epithilial cancer cells


title: MON26: Endometrial cancer

city: Edinburgh

first: Jeffrey

middle: W

last: Pollard

state: Scotland

address: 47 Little France Cres

department: MRC Centre for Reproductive Health,

institute: Queen's Medical Research Institute, The University of Edinburgh

description: Monocytes Protocol

data_processing:
FastQ files of 2x100bp paired-end reads were quality checked using FastQC. Samples were filtered for low quality reads (Phred score >= 20) and adapters were removed when necessary using Cutadapt. Quality controlled reads were then aligned to the Human reference genome (GRCh37/hg19) using STAR aligner (Dobin et al., 2013) (version 2.3). Quantification of genes was performed using the count function of HTSeq (Anders et al., 2015). Reads were counted at the gene level and the unstranded option was used (-s no).
Genome_build: GENCODE Human reference genome Release 19 (GRCh37.p13)
Supplementary_files_format_and_content: tab-delimited files per sample  include raw counts

source_name: Blood

extract_protocol:
Monocytes Protocol:  Monocytes were isolated from healthy and cancer individuals using Fluorescent- activated cell sorting (FACS) with the following markers (CD45+/CD3-CD19-CD56- /HLA-DR+MHC II+/CD14+CD16+). Immediately after FACS sorting, all samples were centrifuged at 450 RCF for 10 min at 4°C. Cell pellets were re-suspended in 350 ul of RLT lysis buffer and RNA extracted with RNAeasy Microkit (Qiagen) according to manufacturer’s instructions. Macrophages/TAMs Protocol: Isolation and Fluorescence-activated cell sorting (FACS) of human tissue macrophages was performed as described (Cassetta et al. 2016). Briefly, markers for FACS isolation of macrophages included CD45+/CD3-CD19-CD56- /CD11b+/CD14+CD163+. Immediately after sorting, all samples were centrifuged at 450 RCF for 10 min at 4C. Cell pellets were re-suspended in 350 ul of RLT lysis buffer and RNA extracted with RNAeasy Microkit (Qiagen) according to manufacturer’s instructions.
RNA quantity was determined by QUBIT (Invitrogen); total RNA integrity was assessed by Agilent Bioanalyzer and the RNA Integrity Number (RIN) was calculated; samples that had a RIN > 7 were selected for RNA amplification and sequencing. RNA was amplified with Ovation RNAseq Amplification kit v2 (Nugen)
paired-end RNA-seq  illumina Hi-Seq

tag: cell type

value: monocytes

tag: condition

value: Endometrial cancer

tag: sequencing batch

value: Batch 1

tag: pathology

value: UPSC


title: MMTV-PyVT_Soft_4

description:
Isolated MMTV-PyVT Cells on 5kPa PA gels, biological replicate 4
Gene expression data from proliferating epithilial cancer cells


title: MON28: Endometrial cancer

description: Monocytes Protocol


title: MMTV-PyVT_Int_3

description:
Isolated MMTV-PyVT Cells on 30kPa PA gels, biological replicate 3
Gene expression data from proliferating epithilial cancer cells


title: MON24: Endometrial cancer

description: Monocytes Protocol


title: MMTV-PyVT_Glass_1

description:
Isolated MMTV-PyVT Cells on glass, biological replicate 1
Gene expression data from proliferating epithilial cancer cells


title: MON22: Endometrial cancer

description: Monocytes Protocol

value: Carcinoma


title: Wild type autopod at E11.25, biological rep2

city: Nagoya

first: Atsushi

last: Kuroiwa

state: Aichi

address: Furo-cho, Chkusa-ku

department: Graduate School of Science

institute: Nagoya University

description: Gene expresion data from the autopod of E11.25 wild type embryos

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array using GeneChip Hybridization Oven 640 (Applied Biosystems). GeneChips were washed using Fluidics Station 450 (Applied Biosystems) then stained with streptavidin phycoerythrin (Molecular Probes).

scan_protocol: GeneChips were scanned by GeneChip Scanner 3000 (Applied Biosystems) using Genechip Operation Software Ver1.2.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Mouse embryo at E11.25

label_protocol: Biotinylated cRNA were prepared from 1.4-2.6 ug of total RNA using IVT Labeling Kit (Affymetrix) and One-Cycle cDNA Synthesis Kit (Affymetrix) then purified using Sample Cleanup Modules (Affymetrix) according to the manufacture's instruction.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions. Contanimating DNA wad removed using Massage Clean (GenHunter Corporation).

treatment_protocol: Embryos were dissected in the ice cold PBS(-) and stored in the RNA later (Ambion) at 4C for overnight then at -80C. The distal portion of the limb bud corresponding the Hoxd13 expression domain was dissected in the RNA later solution.

value: Distal limb bud (Autopod:Hoxd13 expressing domain)

tag: strain


title: Wild type autopod at E11.25, biological rep1


title: Hox13dKO autopod at E11.25, biological rep2

description: Gene expresion data from the autopod of E11.25 Hox13 dKO embryos


title: Hox13dKO autopod at E11.25, biological rep1


title: MON12: Breast cancer

description: Monocytes Protocol

value: Breast cancer

value: Invasive Breast cancer


title: MON8: Normal

description: Monocytes Protocol

value: Normal


title: MON20: Breast cancer

description: Monocytes Protocol


title: MON4: Normal

description: Monocytes Protocol


title: MON30: Endometrial cancer

description: Monocytes Protocol


title: MON18: Breast cancer

description: Monocytes Protocol


title: MMTV-PyVT_Soft_2

description:
Isolated MMTV-PyVT Cells on 5kPa PA gels, biological replicate 2
Gene expression data from proliferating epithilial cancer cells


title: 253G1, biological rep2

tag: cell line


title: MON14: Breast cancer

description: Monocytes Protocol


title: P5_02_PD1_positive#1

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Liver

extract_protocol:
1,000 cells were double-sorted by Moflo Astrios cel sorter into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X25bp reads.

value: Aire- Foxp3 GFP+ (C57/Bl6)

value: Liver

value: 5 days


title: P10_01_PD1_positive#1

value: 10 days


title: P5_03_PD1_negative#1


title: P5_02_PD1_negative#1


title: P10_01_PD1_negative#1


title: P10_02_PD1_positive#1


title: 171109_5_171115_5: HEK293_TET_WT_+Aza_PRO-Seq_rep_3

city: Oxford

first: Skirmantas

last: Kriaucionis

address: Old Road Campus Research Building

institute: Ludwig Institute for Cancer Research

description: 3' end detection of the RNA-Pol engaged RNA

data_processing:
Library strategy: PRO-Seq
PRO-Seq: Base calls performed using X. Reads were trimmed with trimgalore (v0.4.3) to remove adapters, short reads (<20bp), low quality reads (<20). The 3' 4bp were clipped since those could correspond to UMIs. UMIs were extracted using umitools (v0.5.1), these corresponded to the first 8bp of every read. The reads were aligned to the merged hg19 and galgal5 genome using STAR (v2.4.2), the aligned reads were deduplicated with umitools (v0.5.1) using the previously cleaved UMIs. Only hg19-mapped reads were retained for further analysis and we extracted the first base of each read using bedtools (v2.20.1) and awk (v3.1.7). Using the PRO-Cap-defined initiation and elongation peaks as reference, count the number of (strand-specific) PRO-Seq 5' starts in each region using bedmap from bedops (v2.4.30). Combine the resulting files using awk (v3.1.7) such that we have a single file for each peak group i.e. Initiation, Elongation, Div. Initiation, Div. Elongation. The count tables were converted into GRanges objects (GenomicRanges v1.34.0) in R (v3.5.1) and split according to strand into sense and antisense. We filtered out any regions with less than 10 reads. We used DESeq2 (v1.22.1) with default parameters to calculate differential expression between conditions with "design = ~ Sample + Condition", where Sample is the batch. We used "apeglm" shrinkage when generating the results tables. The tables were combined for each contrast for ease of comparison. Each region-specific set of comparisons is included as a sheet in the resulting Excel files.
genome_build: hg19_full_galGal5_merged.fa
processed_data_files_format_and_content: Each peak type specific set of comparisons is included as a sheet in Supplementary Table 4.xlsx. The DESeq2 result tables for each pairwise comparison (Aza vs Dox, Aza vs Untreated, Dox vs Untreated) are concatenated for each region, i.e. each row corresponds to a single peak and how they compare across conditions.

growth_protocol: all cells were cultured in DMEM (high glucose) containing antibiotics, L-glutamine, 10% FBS at 37°C, 5%CO2

extract_protocol:
TRI reagent followed by the biotin-streptavidin enrichment (Streptavidin M280)
the adaptors were ligated on the purified RNA (-OH 3') followed by the amplification using NEBNext Ultra II Q5 Master Mix (New England Biolabs,M0544S)

tag: treatment

value: 880 nM 5-aza-2'-deoxycytidine for 48 hours

value: TET-CD-GFP

tag: spike-in

value: 10:1 with Chiken DF-1 cells


title: 171109_2_171115_2: HEK293_TET_WT_+Dox_PRO-Seq_rep_1

value: 1 μg/mL Doxycycline for 48 hours


title: 171109_8_171115_8: HEK293_TET_WT_+Dox_PRO-Seq_rep_3


title: P10_02_PD1_negative#1

city: Boston


title: P5_03_PD1_positive#1


title: 171109_4_171115_4: HEK293_TET_WT_+Aza_PRO-Seq_rep_2


title: MON2: Normal

description: Monocytes Protocol

value: monocytes


title: 171109_7_171115_7: HEK293_TET_WT_Untreated_PRO-Seq_rep_2


title: 171109_3_171115_3: HEK293_TET_WT_+Aza_PRO-Seq_rep_1


title: 171109_6_171115_6: HEK293_TET_WT_Untreated_PRO-Seq_rep_3


title: 171109_44_171115_17: HEK293_TET_WT_+Dox_PRO-Cap_rep_3

description: Cappd site detection of the RNA-Pol engaged RNA

data_processing:
Library strategy: PRO-Cap
PRO-Cap: Base calls performed using X. Reads were trimmed with trimgalore (v0.4.3) to remove adapters, short reads (<20bp) and low quality reads (<20) (-q 20 --length 20). UMIs were extracted with umitools (v0.5.1) such that the 5' 4bp and 3' 4bp formed an 8bp UMI (--bc-pattern="^(?P<umi_1>.{4}).*(?P<umi_2>.{4})$"). The reads were aligned to the merged hg19 and galgal5 genome using STAR (v2.4.2) allowing uniquelly mapping reads only (--outFilterMultimapNmax 1). The aligned reads were split based on post-trimming read length into long (var = 63) and short (var = 62), creating 2 files per sample. The 3' UMI (the last 4bp of the 8bp extracted UMI) is removed from the long reads, the short reads retain the 8bp UMI. The long and short reads are deduplicated with umitools (v0.5.1) using the extracted UMIs, and then merged back together. The alignments are then split by species based on the chromosome names (the galgal5 fasta had 'm.' added to each chomosome name pre alignment). Only hg19-mapped reads were retained for further analysis (those without 'm.') and we extracted the first base of each read using bedtools (v2.20.1) and awk (v3.1.7). All PRO-Cap samples were combined and sorted for each strand using bedops (v2.4.30) --everything. We used a HMM to define regions of PRO-Cap enrichment similarly to that proposed by Core et al. (2014) with the exception that global thresholds were used since input wasn't available. The peaks were then trimmed as descibed in the manuscript (XXX). The trimmed peaks were used in combination with GENCODE gene annotation to define multiple region types of interest, e.g. Pr. TSS, Se. TSS. Using each region type as reference separately, we counted the number of (strand-specific) PRO-Cap 5' starts in each region using bedmap from bedops (v2.4.30). The resulting files were combined using awk (v3.1.7) such that we have a single file for each peak group i.e. Initiation, Elongation, Div. Initiation, Div. Elongation. The count tables were converted into GRanges objects (GenomicRanges v1.34.0) in R (v3.5.1) and split according to strand into sense and antisense. We filtered out any regions with less than 10 reads. We used DESeq2 (v1.22.1) with default parameters to calculate differential expression between conditions with "design = ~ Sample + Condition", where Sample is the batch. We used "apeglm" shrinkage when generating the results tables. The tables were combined for each contrast for ease of comparison.
genome_build: hg19_full_galGal5_merged.fa
processed_data_files_format_and_content: Each peak type specific set of comparisons is included as a sheet in Supplementary Table 5.xlsx. The DESeq2 result tables for each pairwise comparison (Aza vs Dox, Aza vs Untreated, Dox vs Untreated) are concatenated for each region, i.e. each row corresponds to a single peak and how they compare across conditions.

extract_protocol:
TRI reagent followed by the biotin-streptavidin enrichment (Streptavidin M280)
the adaptors were ligated on the purified RNA (Capped 5' and -OH 3') followed by the amplification using NEBNext Ultra II Q5 Master Mix (New England Biolabs,M0544S)


title: 171109_9_171115_9: HEK293_TET_WT_Untreated_PRO-Seq_rep_1


title: 171109_38_171115_11: HEK293_TET_WT_+Dox_PRO-Cap_rep_2


title: MON10: Normal

description: Monocytes Protocol


title: 171109_40_171115_13: HEK293_TET_WT_+Aza_PRO-Cap_rep_3


title: 171109_39_171115_12: HEK293_TET_WT_+Dox_PRO-Cap_rep_1


title: 171109_1_171115_1: HEK293_TET_WT_+Dox_PRO-Seq_rep_2


title: 171109_37_171115_10: HEK293_TET_WT_Untreated_PRO-Cap_rep_3


title: 171109_43_171115_16: HEK293_TET_WT_+Aza_PRO-Cap_rep_1


title: 171109_42_171115_15: HEK293_TET_WT_Untreated_PRO-Cap_rep_2


title: 171109_45_171115_18: HEK293_TET_WT_Untreated_PRO-Cap_rep_1


title: 171109_41_171115_14: HEK293_TET_WT_+Aza_PRO-Cap_rep_2


title: F508delCFBE41o- miRseq_6

city: Charlottesville

first: Agnieszka

last: Swiatecka-Urban

state: VA

address: 409 Lane Road

department: Pediatrics

institute: University of Virginia School of Medicine

data_processing:
The raw QIAseq miRNA sequencing files were uploaded to GeneGlobe Data Analysis Center (Qiagen) for quality control, alignment to the human reference genome (GRCh38) and expression quantification.
Briefly, 3’ adapter and low quality bases are trimmed off from reads first using cutadapt. Reads with less than 16bp insert sequences or with less than 10bp UMI sequences are discarded. The remaining reads were collapsed to UMI counts and aligned to miRBase (release v21) mature and hairpin databases sequentially using Bowtie v1.2.
All reads assigned to a particular miRNA or piRNA ID are counted, and the associated UMIs are clustered to count unique molecules. The primary analysis output file is downloaded from GeneGlobe.
EdgeR package is used for the differential analysis based on UMI counts for miRNA. miRNAs were filtered from the analysis if their count per million (as computed by edgeR's cpm function) was not greater than 2 in at least half of the samples.
The trimmed mean of M-values normalization method implemented in edgeR is used for normalization.
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx, reads and UMI counts

source_name: F508delCFBE41o- Cells

growth_protocol: Immortalized human bronchial epithelial cell models: CFBE41o- (bronchial epithelial cells): stably expressing F508del-CFTR and Wild Type (WT)-CFTR were cultured Minimum Essential Media (MEM) containing 10% Fetal bovine serum (FBS), 50µg/mL streptomycin, 50U/mL Penicillin, 2mM L-Glutamine, 0.55 µg/mL Puromycin for WT-CFBE41o- cells and 2.2 µg/mL Puromycin for F508del-CFBE41o- cells. Cells were split at 90% confluency  were seeded (~1 million/24mm insert)  on 24mm inserts (Corning) coated with 10% collagen (PureCol, Type I Bovine Collagen Solution, Advanced BioMatrix) in Opti-MEM (1X Opti-MEM Reduced Serum Medium, gibco, Life Technologies) and cultured in air liquid interface (ALI) for 7-8 days.

extract_protocol:
Total RNA was isolated from cell lysate using the Quick-RNA Miniprep Kit (Zymo Research, R1054) according to the manufacturer’s instructions, with additional on-column DNase treatment with the RNase-free DNase Set (Zymo) to remove contaminating genomic DNA
100ng of total RNA was used with the QIAseqTM miRNA Library Kit ( Qiagen, Maryland, USA) following manufacturer’s instruction.
3’ and 5’ adapters were ligated to total input RNA. Reverse transcription, followed by PCR, was used to create cDNA constructs. PCR was performed with primers that anneal to the ends of the adapters. Quality was examined using Agilent Bioanalyzer Tapestation 2200 and Qubit 2.0 Fluorometer with miRNA library pre sequencing QC protocol mentioned in the QIAseqTM miRNA Library Kit. The cDNA libraries were pooled at a final concentration of 2.5pM. Cluster generation and 75 bp single read single-indexed sequencing was performed on Illumina NextSeq 500’s.

treatment_protocol: Human TGF-b1 (Sigma, St. Louis, MO) was used at concentration (15 ng/mL) for the treatment of cells on 24mm inserts (basolaterally) for 24 hour

value: immortalized  (CFBE) Cells

tag: transfection

value: F508del-CFTR transfected

tag: passages

value: No Treatment


title: F508delCFBE41o- miRseq_1


title: F508delCFBE41o- miRseq_2


title: WT-CFBE41o- miRseq_6

source_name: WT-CFBE41o- Cells

value: WT-CFTR transfected


title: WT-CFBE41o- miRseq_5


title: WT-CFBE41o- miRseq_3


title: F508delCFBE41o- miRseq_5


title: F508delCFBE41o- miRseq_4


title: WT-CFBE41o- miRseq_4


title: FAT1-NNK-2_3pDGE

city: Medford

first: Eric

middle: R

last: Reed

address: 419 Boston Ave.

department: Data Intensive Studies Center

institute: Tufts University

description:
FAT1-NNK-2
Well-H8

data_processing:
All reads containing bases with quality lower than Q10 are filtered out.
Reads that pass filter are assigned to a well and aligned to the transcriptome (UCSC RefSeq hg19) which includes mitochondrial genes using BWA aln version 0.7.10. Reads that only align to multiple isoforms of the same gene are considered uniquely mapped.
Genome_build: UCSC RefSeq hg19
Supplementary_files_format_and_content: Tab-delimited text files contain two columns: (1) HGNC symbols (2)Read Counts.  File names are denoted by the nomencalture {genotypic perturbation}-{chemical perturbation}-{replicateID}.txt. Technical replicates of the same sample have an additional digit.

growth_protocol: Cells were subcultured using Clonetics ReagentPack subculture reagents (Lonza, Portsmouth NH). In preparation for exposure, cells were plated into 24-well plates and allowed to reach confluency for 24 hours.

extract_protocol:
Cells were thawed on ice and each sample was lysed using 1uL of 1mg/mL Proteinase K (ThermoFisher Scientific) followed by incubation at 50oC for 15 min, then 95oC for 10 min uncovered to evaporate all liquid.
Single Cell RNA Barcoding and Sequencing (SCRB-seq) was performed as described in Soumillon M., Cacchiarelli D., Semrau S., van Oudenaarden A. and Mikkelsen T.S. (2014). Characterization of directed differentiation by high-throughput single-cell RNA-Seq. bioRxiv. 10.1101/003236. Sequencing generates two files: read1 and read2.  Read1 contains 17 base reads (6 base barcode + 10 base UMI + an N in the 17th position).  Read2 contains the 46 bp cDNA sequence.

treatment_protocol: Cell culture media was replaced, and compounds added at a concentration of 24 μg/ml CSC, 173μM BaP, 490μM NNK or DMSO. NNK and BaP compounds were obtained from Sigma-Aldrich (St. Louis MO) and CSC obtained from Murty Pharmaceuticals (Lexington, KY). Genotypic perturbations included CRISPR knockouts of FAT1, and CDKN2A, as well as overexpression of NRF2 (NFE2L2), FGFR1, NRG1 and PIK3CA. Cells transfected with a pSpCas9-EGFP (GFP) plasmid (PX458) in the absence of sgRNAs were used as controls for the CRISPR perturbations while overexpression of an empty vector containing the reporter HcRed served as control for the overexpression experiments.

value: AALE

value: immortalized human bronchial epithelial cells (AALE)

tag: genotypic perturbation

tag: genotypic perturbation type

value: knockout

tag: chemical perturbation

value: NNK

tag: well id

tag: barcode

value: GTCGGC


title: FAT1-NNK-3_3pDGE

description:
FAT1-NNK-3
Well-H9

value: TCCCCG


title: FAT1-NNK-1_3pDGE

description:
FAT1-NNK-1
Well-H7

value: GGTGCG


title: WT-CFBE41o- miRseq_2


title: NRG1-NNK-1_3pDGE

description:
NRG1-NNK-1
Well-H4

value: overexpression

value: GGGAGG


title: NRF2-NNK-3_3pDGE

description:
NRF2-NNK-3
Well-H3

value: GGCGGA


title: NRF2-NNK-2_3pDGE

description:
NRF2-NNK-2
Well-H2

value: GGCAGC


title: NRG1-NNK-3_3pDGE

description:
NRG1-NNK-3
Well-H6

value: GGGGTG


title: CDKN2A-NNK-22_3pDGE

description:
CDKN2A-NNK-22
Well-H11

value: TGCGGC


title: CDKN2A-NNK-21_3pDGE

description:
CDKN2A-NNK-21
Well-H10

value: TCGGCG


title: FGFR1-NNK-2_3pDGE

description:
FGFR1-NNK-2
Well-G8

value: GCCGGT


title: NRF2-NNK-1_3pDGE

description:
NRF2-NNK-1
Well-H1

value: GGACGC


title: FGFR1-NNK-1_3pDGE

description:
FGFR1-NNK-1
Well-G7

value: GCCCGA


title: FGFR1-NNK-3_3pDGE

description:
FGFR1-NNK-3
Well-G9

value: AALE

value: GCGACG


title: GFP-NNK-3_3pDGE

description:
GFP-NNK-3
Well-G6

value: immortalized human bronchial epithelial cells (AALE)

value: GFP

value: knockout

value: GCCACC


title: Hoxa13_ChIPSeq_E12.5

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie 2-2.2.2, with the following configurations; -p 4 -t -x .
Peaks were called using MACS2-2.1.0 with setting: effective genome size (2.15e09), band width (300), model fold (5, 50), qvalue cutoff (5.00e-02).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigwig files and bed files were generated using MACS2-2.1.0.

source_name: E12.5 limb bud

extract_protocol:
ChIP was performed according to a standard protocol (Cold Spring Harbor, NY) with the following modifications. Whole limb buds from E11.5 and the autopod from E11.0 wild type ICR mice were dissected in ice-cold PBS. Embryonic tissues were homogenized 13 times with a Dounce homogenizer, then fixed in 1% formaldehyde/PBS for 10minutes at 4C and quenched with 0.1 M glycine. The cross-linked material was sonicated to produce 200-1000 bp fragments with a DNA Shearing System S2 (Covaris). The immunoprecipitations were performed with 11 pairs of autopods from E11.0 embryos, whole limb buds from a litter of E11.5 embryos. PierceTM Protein A/G magnetic beads (Thermo Scientific) were conjugated to each antibody. Sonicated chromatin was incubated with the prepared protein A/G beads overnight at 4C with rotation. 10 ug of anti-Hoxa13 or 8 ug of anti-Hoxa11 were used for each experiment. E12.5 ChIP-Seq was performed as described previously (Beccari et al. 2016. Genes Dev. 30, 1172-1186). Anti-Hoxa13 antibody: Yamamoto et al. Development 125, 1325-1335 and Beccari et al. 2016. Genes Dev. 30, 1172-1186. Anti-Hoxa11 antibody: Yamamoto et al. Development 125, 1325-1335 and manuscript in preparation.
The E11.0 and E11.5 libraries were prepared using NEB Next UltraTM DNA Library Prep kit for Illumina (NEB) according to the manufacturer's protocol. The E12.5 libraries were prepared as described previously (Beccari et al. 2016. Genes Dev. 30, 1172-1186).

tag: strain/background

value: ICR

tag: genotype/variation

value: WT

value: limb bud

tag: developmental stage

tag: chip antibody

value: Hoxa13 (home-made)


title: input DNA for Hoxa13_ChIPSeq_E12.5

tag: tissue


title: input DNA for Hoxa11_ChIPSeq_E11.5_rep2

source_name: E11.5 limb bud


title: CDKN2A-NNK-3_3pDGE

description:
CDKN2A-NNK-3
Well-H12

tag: cell type

value: NNK

value: TGGGGG


title: GFP-NNK-1_3pDGE

description:
GFP-NNK-1
Well-G4

value: GAGCCC


title: GFP-NNK-2_3pDGE

description:
GFP-NNK-2
Well-G5

value: GCACCC


title: Hoxa11_ChIPSeq_E11.5_rep2

value: Hoxa11 (home-made)


title: HCRED-NNK-2_3pDGE

description:
HCRED-NNK-2
Well-G2

value: HCRED

value: overexpression

value: CTCGGG


title: PIK3CA-NNK-3_3pDGE

description:
PIK3CA-NNK-3
Well-G12

value: AALE

value: GCTCCG


title: input DNA for Hoxa13_ChIPSeq_E11.0

source_name: E11.0 autopod

value: autopod


title: Hoxa11_ChIPSeq_E11.5_rep1


title: FAT1-BaP-3_3pDGE

description:
FAT1-BaP-3
Well-F9

value: immortalized human bronchial epithelial cells (AALE)

value: knockout

value: BaP

value: CGCTCG


title: Hoxa13_ChIPSeq_E11.5

value: ICR

value: WT

value: limb bud


title: Hoxa13_ChIPSeq_E11.0

value: Hoxa13 (home-made)


title: FAT1-BaP-2_3pDGE

description:
FAT1-BaP-2
Well-F8

value: CGCGAC


title: WT-CFBE41o- miRseq_1

value: immortalized  (CFBE) Cells

value: WT-CFTR transfected

value: No Treatment


title: F508delCFBE41o- miRseq_3

value: F508del-CFTR transfected


title: HCRED-NNK-1_3pDGE

description:
HCRED-NNK-1
Well-G1

value: HCRED

value: overexpression

value: NNK

value: CGTGCC


title: NRG1-BaP-3_3pDGE

description:
NRG1-BaP-3
Well-F6

value: AALE

value: immortalized human bronchial epithelial cells (AALE)

value: CGAGCG


title: NRG1-BaP-1_3pDGE

description:
NRG1-BaP-1
Well-F4

value: BaP

value: CCGGTG


title: NRG1-BaP-2_3pDGE

description:
NRG1-BaP-2
Well-F5

value: CCTGCG


title: FAT1-BaP-1_3pDGE

description:
FAT1-BaP-1
Well-F7

value: knockout

value: CGCCAG


title: input DNA for Hoxa13_ChIPSeq_E11.5 & Hoxa11_ChIPSeq_E11.5_rep1

value: ICR

value: WT

value: limb bud


title: CDKN2A-BaP-1_3pDGE

description:
CDKN2A-BaP-1
Well-F10

value: CGGCAC


title: NRG1-NNK-2_3pDGE

description:
NRG1-NNK-2
Well-H5

value: GGGCTC


title: NRF2-BaP-3_3pDGE

description:
NRF2-BaP-3
Well-F3

value: CCGCGA


title: Armi-CLIPPARE from Zuc-KD rep1

city: Tokyo

first: Hirotsugu

last: Ishizu

address: 35 Shinanomachi

institute: Keio University

description:
1-2_S8_R1_001
processed data file:
CLIPPARE_RPM.txt

data_processing:
Reads were filtered for quality, and PCR duplicates removed using the random barcode. 3' adaptor sequences were trimmed using Cutadapt, and reads were mapped to the Drosophila genome (dm6) using STAR. 3' adapter sequence is "TGGAATTCTCGGGTGCCAAGG".
RIP-seq: Piwi associated small RNA sequencing data was analyzed as described previously (PMID: 27425411). 3' adapter sequence is "TGGAATTCTCGGGTGCCAAGG".
Armi-CLIPPARE* samples: Reads were filtered for quality, and PCR duplicates removed using the random barcode. 3' adaptor sequences were trimmed using Cutadapt, and reads were mapped to the Drosophila genome (dm6) using STAR. 3' adapter sequence is "TGGAATTCTCGGGTGCCAAGG".
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: Armi-CLIPPARE from Zuc-KD

extract_protocol:
Cells were lysed in CLIPPARE lysis buffer, followed by immunoprecipitation of RNA-protein complexes with an anti-Armi antibody (PMID: 20966047). RNA adapter was ligated to the 5’ end with T4 RNA Ligase1 (NEB). Ligations were performed on-bead. Samples were digested with 0.1 U/μl RNase T1 (Roche), dephosphorylated with T4 PNK (NEB), and then run on NuPAGE gels (Life Technologies) and transferred to nitrocellulose membranes. After cutting out the region of nitrocellulose containing RNA–protein complexes, RNAs were removed from the membrane by Proteinase K (Roche) digestion. A preadenylated DNA adapter was ligated to the 3' end with T4 RNA Ligase2, truncated KQ (NEB).
Samples were processed for reverse transcription with Superscript Ⅲ (Life Technologies), amplification with Q5 DNA polymerase (NEB), and size-selection via polyacrylamide gel electrophoresis. Each sequencing read conatins "HHHAACCHH" (H=A,T, or C) at the 5’ end.

treatment_protocol: OSCs were crosslinked with UV (254 nm, 200 mJ/cm2). Cells were then isolated with cell scrapers and precipitated by centrifugation for 2 min at 10000 rpm.

value: Ovarian Somatic Cells (OSC)

value: Zuc RNAi

tag: ip antibody

value: anti-Armi antibody (PMID:20966047)


title: PIK3CA-NNK-2_3pDGE

description:
PIK3CA-NNK-2
Well-G11

tag: cell line

value: AALE

value: overexpression

value: NNK

value: GCGGGA


title: PIK3CA-NNK-1_3pDGE

description:
PIK3CA-NNK-1
Well-G10

value: immortalized human bronchial epithelial cells (AALE)

value: GCGCGT


title: FGFR1-BaP-32_3pDGE

description:
FGFR1-BaP-32
Well-E9

value: BaP

value: AGGGCG


title: Armi-CLIPPARE from Control-KD rep1

description:
1-1_S7_R1_001
processed data file:
CLIPPARE_RPM.txt

source_name: Armi-CLIPPARE from Control-KD

value: EGFP RNAi


title: Armi-CLIPPARE from Zuc-KD rep2

description:
1-4_S10_R1_001
processed data file:
CLIPPARE_RPM.txt


title: HCRED-NNK-3_3pDGE

description:
HCRED-NNK-3
Well-G3

value: HCRED

value: GACCCG


title: FGFR1-BaP-2_3pDGE

description:
FGFR1-BaP-2
Well-E8

value: AGCGCC


title: MC3T3_lnc-ob1_ASO

molecule: polyA RNA

source_name: osteoblast

tag: strain

value: osteoblast

tag: genotype

value: lnc-ob1 Knockdown


title: HiPS-RIKEN-12A, biological rep2


title: MC3T3_NC

value: control


title: mBMSC_2_week

source_name: BMSCs

value: bone marrow

value: BMSCs

tag: differentiation stage

value: differentiated (2 week)


title: FGFR1-BaP-31_3pDGE

description:
FGFR1-BaP-31
Well-E7

value: AALE

value: overexpression

value: ACGGCC


title: mBMSC_0_week

value: undifferentiated (0 week)


title: NRF2-BaP-1_3pDGE

description:
NRF2-BaP-1
Well-F1

value: immortalized human bronchial epithelial cells (AALE)

value: CCCCCA


title: Armi-CLIPPARE from Control-KD rep2

description:
1-3_S9_R1_001
processed data file:
CLIPPARE_RPM.txt

value: Ovarian Somatic Cells (OSC)

value: anti-Armi antibody (PMID:20966047)


title: P140265_S10: HEK293_TET_WT_+Dox_EpiJet_rep_1

description: 5hmC specifically enzymatically labeled genomic DNA enriched by biotin-streptavidin pull down (EpiJET kit)

data_processing:
Library strategy: EpiJet
EpiJet: Base calls performed using X. Reads were aligned using using bowtie2 (v 2.2.6). Samtools (v0.1.19) was used for merging and sorting bam files. Picard Tools (release 1.139) were used for duplicate removal. Bigwig files were constructed for easy visualisation of the enrichment data in IGV and other genome browsers. The custom script which was run on R (release 3.3.2) using the following packages: chipseq, rtracklayer, BSgenome.Hsapiens. UCSC.hg19. CoverageView version 1.5.2 was used to calculate the read coverage over genic regions.
genome_build: hg19
processed_data_files_format_and_content: N/A

extract_protocol:
GeneJET genomic DNA purification kit
NEBNext DNA Library Prep Master Mix Set for Illumina (E6040S, NEB)

tag: treatment

value: 1 μg/mL Doxycycline for 48 hours

value: TET-CD-GFP


title: CDKN2A-BaP-3_3pDGE

description:
CDKN2A-BaP-3
Well-F12

tag: genotypic perturbation

value: knockout

value: BaP

value: CGGTCC


title: human astrocyte, rep 3 [HA-3]

city: University Park

last: Chen

state: PA

address: Old Main

institute: Penn State University

data_processing:
quality check using FastQC v0.11.3
reads were aligned to hg19 using HISAT2 version 2.0.4
counts summarized using StringTie v1.3.4
Genome_build: hg19
Supplementary_files_format_and_content: for each sample, a tsv file containing FPKM and TPM generated by stringtie

source_name: HA1800, ScienCell

extract_protocol:
total RNA were extracted according to protocols accompanying with Macherey-Nagel NucleoSpin RNA kit, then sent to sequencing center for polyA enrichment
libraries were constructed using KAPA RNA kit at UCLA Technology Center for Genomics & Bioinformatics

value: human fetal cortical astrocytes

tag: passages


title: P140265_S12: HEK293_TET_WT_+Dox_EpiJet_rep_2


title: GFP-BaP-3_3pDGE

description:
GFP-BaP-3
Well-E6

value: GFP

tag: genotypic perturbation type

tag: chemical perturbation

value: ACCGCG


title: human astrocyte, rep 1 [HA-1]


title: GFP-BaP-2_3pDGE

description:
GFP-BaP-2
Well-E5

tag: well id

tag: barcode

value: GGACCA


title: P140265_S13: HEK293_TET_WT_Untreated_EpiJet_rep_2

tag: genotype/variation


title: human astrocyte, rep 2 [HA-2]


title: GFP-BaP-1_3pDGE

description:
GFP-BaP-1
Well-E4

value: AALE

value: TTTGGC


title: P140265_S08: HEK293_TET_WT_+Dox_MeDIP_rep_2

description: genomic DNA enriched by 5mC-DNA specific antibody

data_processing:
MeDIP Base calls performed using X. Reads were aligned using using bowtie2 (v 2.2.6). Samtools (v0.1.19) was used for merging and sorting bam files. Picard Tools (release 1.139) were used for duplicate removal. Bigwig files were constructed for easy visualisation of the enrichment data in IGV and other genome browsers. The custom script which was run on R (release 3.3.2) using the following packages: chipseq, rtracklayer, BSgenome.Hsapiens. UCSC.hg19. DNA methylation probabilities and enrichment correction was performed using MEDIPS (version 1.22.0).
genome_build: hg19
processed_data_files_format_and_content: N/A

tag: antibody


title: P140265_S11: HEK293_TET_WT_Untreated_EpiJet_rep_1


title: P140265_S06: HEK293_TET_WT_+Dox_MeDIP_rep_1


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-105

first: Keji

last: Zhao

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

data_processing:
Raw Sequence reads were aligned to the reference human genome (UCSC, hg18) by Bowtie2 (bowtie2 -D 20 -R 3 -N 1 -L 16 -i S,1,0.5 -X 1000  -p 20 -q -5 0 -3 30). The reads with mapping quality (MAPQ ≤10) or redundant reads that mapped to the same location with the same orientation were removed from further analysis in each single cell library. For scH3K4me3,  To avoid the possibility of doublet (or triplet) outliers, four cells were removed. A cell is defined as a doublet outlier if it satisfies the following two requirements.    1. The log-library size of the cell is larger the averaged the log-library size over all cells.    2. Cells are sorted based on their log-library size. With any of the selected window sizes, the log-library size of the cell is larger than three local scaled median absolute deviation (MAD) from the local median within the sliding window. A number of window sizes are tested. Finally, the remaining 281 cells are used for genome browser visualization and identification of peaks for pooled cells.
Peaks/Enriched regions for the 281 pooled single cell H3K4me3 data were identified using SICER (gap size = 200 bp, window size =200bp and frag size= 150bp). 22293 peaks are identified for the pooled H3K4me3 scChIC-seq data. Peaks/Enriched regions for the 106  pooled single cell H3K4me3 data were identified using SICER (gap size = 600 bp, window size =200bp and frag size= 150bp). 21,465 peaks are identified for the pooled H3K27me3 scChIC-seq data.
For each single cell library (both scH3K4me3 and scH3K27me3), we filtered the reads that are not located in the identified peak regions (22,293 peaks and 21,465 peaks for scH3K4me3 and scH3K27me3 libraries, respectively). Therefore, the *filtered.txt files are obtained for the downstream analysis.
Genome_build: hg18
Supplementary_files_format_and_content: *filtered.txt: bed 6 file. Each line is a peak region. The six columns are chrom, start position, end position, end position-start position, mapq, strand
Supplementary_files_format_and_content: bed: Bed 6 file. Each line is a read. The six columns are chrom, start position, end position, end position-start position, mapq, strand
Supplementary_files_format_and_content: bedgraph: bed 4 file. Each line is a bin, with bin size = 200bp. The four columns are chrom, start position, end position,read density.
Library strategy: scChIC-seq

source_name: white blood cells

extract_protocol:
The DNAs were end-repaired using the End-It™ DNA End-Repair Kit (Lucigen, Radnor, PA, USA). The reaction was done in 10 µL reaction volume according to the manufacturer’s instruction. The reaction was terminated by adding 115 µL 10 mM Tris-Cl buffer (pH7.5) containing 1 mM EDTA, and the DNAs were extracted by the phenol-chloroform extraction, followed by the ethanol precipitation as described above. The precipitate is re-suspended in 5 µL Qiagen Buffer EB (10 mM Tris-Cl buffer (pH 8.5)). The addition of 3’ A overhangs to the end-repaired DNA fragments was done using the Klenow fragment (3’→5’ exo-) (New England BioLabs, Ipswich, MA, USA) and 1 mM deoxyadenosine triphosphate in the reaction buffer. The DNA fragments were incubated at 37°C for 20 min and the enzymes were inactivated at 75°C for 20 min. The Illumina Adaptor Oligo Mix (Illumina, San Diego, CA, USA) was ligated to the 3’ A overhangs of the DNA fragments using the T4 DNA ligase (New England BioLabs) by incubating at room temperature for 3 hr.
The DNA fragment with the adaptors bound was PCR amplified using the Phusion High-Fidelity PCR Master Mix (New England BioLabs) and the 125 nM PE PCR Primer 1.0 (Illumina). The PCR was done under the following condition: 98°C for 10 min, followed by a cycle of 30 sec at 68°C and 30 sec at 72°C (repeat 18 cycles in the case of 3,000 cells or 25 cycles in the case of a single cell). The 2% [w/v] agarose gel electrophoresis was done to isolate the 140-350 bp fragments and purify using the QIAquick Gel Extraction kit (Qiagen). The concentration of the purified DNAs was measured using Qubit dsDNA HS kit (Thermo Fisher Scientific). The paired-end sequencings were run using the Illumina MiSeq and HiSeq2000.

value: white blood cells

tag: antibody-mnase

value: H3K27me3 Ab + PA-MNase


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-101


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-104


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-106


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-103


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-102


title: P140265_S07: HEK293_TET_WT_Untreated_MeDIP_rep_2


title: HCRED-BaP-2_3pDGE

description:
HCRED-BaP-2
Well-E2

value: immortalized human bronchial epithelial cells (AALE)

value: HCRED

value: overexpression

value: GTGACT


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-99


title: PIK3CA-BaP-3_3pDGE

description:
PIK3CA-BaP-3
Well-E12

value: CCAGGG


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-100


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-98


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-97


title: PIK3CA-BaP-1_3pDGE

description:
PIK3CA-BaP-1
Well-E10

value: CACGCG


title: P140265_S08: HEK293_TET_WT_+Dox_hmC-Seal_rep_2

description: 5hmC specifically chemically labeled genomic DNA enriched by biotin-streptavidin pull down

data_processing:
Library strategy: hmSeal
hmSeal: Base calls performed using X. Reads were aligned using using bowtie2 (v 2.2.6). Samtools (v0.1.19) was used for merging and sorting bam files. Picard Tools (release 1.139) were used for duplicate removal. Bigwig files were constructed for easy visualisation of the enrichment data in IGV and other genome browsers. The custom script which was run on R (release 3.3.2) using the following packages: chipseq, rtracklayer, BSgenome.Hsapiens. UCSC.hg19. CoverageView version 1.5.2 was used to calculate the read coverage over genic regions.
genome_build: hg19
processed_data_files_format_and_content: N/A

value: 1 μg/mL Doxycycline for 48 hours

value: TET-CD-GFP


title: HCRED-BaP-31_3pDGE

description:
HCRED-BaP-31
Well-E1

value: BaP

value: GGCAAT


title: P140265_S06: HEK293_TET_WT_+Dox_hmC-Seal_rep_1


title: HCRED-BaP-32_3pDGE

description:
HCRED-BaP-32
Well-E3

value: TCGAAG


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-94


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-93


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-95


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-96


title: FAT1-CSC-3_3pDGE

description:
FAT1-CSC-3
Well-D9

value: knockout

value: CSC

value: CAAGCT


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-92


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-89


title: P140265_S09: HEK293_TET_WT_Untreated_hmC-Seal_rep_2


title: PIK3CA-BaP-2_3pDGE

description:
PIK3CA-BaP-2
Well-E11

value: AALE

value: CAGGCC


title: FAT1-CSC-2_3pDGE

description:
FAT1-CSC-2
Well-D8

value: ACCGTA


title: P140265_S05: HEK293_TET_WT_Untreated_MeDIP_rep_1


title: P140265_S01: HEK293_TET_WT_Untreated_Input

description: HEK293_T-Rex_TET-CD-GFP untreated genomic DNA input


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-90

value: white blood cells

value: H3K27me3 Ab + PA-MNase


title: NRG1-CSC-3_3pDGE

description:
NRG1-CSC-3
Well-D6

value: immortalized human bronchial epithelial cells (AALE)

value: overexpression

value: TTTCAA


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-86


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-87


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-88


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-85


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-91


title: P140265_S07: HEK293_TET_WT_Untreated_hmC-Seal_rep_1


title: FAT1-CSC-1_3pDGE

description:
FAT1-CSC-1
Well-D7

value: TTTTCT


title: MM130820

city: Geneva

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

country: Switzerland

institute: Hopitaux universitaires de Geneve

data_processing:
FASTQ were trimmed with skewer (0.2.2)
Trimmed reads were aligned with STAR (2.5.1a)
Gene counts were obtained from STAR --quantMode TranscriptomeSAM
log normalized counts per million were obtained from edgeR
Genome_build: HG38
Supplementary_files_format_and_content: tab delimited text file with normalized log counts per million for each sample by column and genes by row

source_name: Melanoma cell culture

growth_protocol: Melanoma cells were grown in RPMI 1640 with 10% FCS, 5 mM glutamine, and 1 mM sodium pyruvate.

extract_protocol:
RNA was extracted with the QIAGEN RNeasy Mini kit
RNA-seq-poly-A

tag: group

value: Resistant


title: MM130903


title: NRG1-CSC-12_3pDGE

description:
NRG1-CSC-12
Well-D5

tag: cell type

value: TTTAAC


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-84


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-82


title: MM130604


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-81


title: MM121224


title: NRF2-CSC-3_3pDGE

description:
NRF2-CSC-3
Well-D3

value: TTATGT


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-80


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-78


title: M980513

value: Sensitive


title: NRF2-CSC-2_3pDGE

description:
NRF2-CSC-2
Well-D2

value: TTAGAA


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-77


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-75


title: CDKN2A-CSC-33_3pDGE

description:
CDKN2A-CSC-33
Well-D12

value: knockout

value: GATCGT


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-74


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-83


title: M000921


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-71


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-70


title: CDKN2A-CSC-32_3pDGE

description:
CDKN2A-CSC-32
Well-D11

value: CSC

value: CGATTG


title: CDKN2A-CSC-31_3pDGE

description:
CDKN2A-CSC-31
Well-D10

value: AALE

value: CATGGT


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-69

value: white blood cells


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-76

value: H3K27me3 Ab + PA-MNase


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-68


title: 6h_11

city: Philadelphia

first: Andrei

last: Thomas-Tikhonenko

address: 3501 Civic Center Blvd, CTRB 4056

department: Children's Hospital of Philadelphia

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Alignment with GSNAP (version 2015-12-31)
HTSeq version 0.6.0 (-m intersection-strict)
Differentially expression was calculated using limma (version 3.30.0)
Genome_build: hg19
Supplementary_files_format_and_content: raw gene counts for each sample

source_name: Ramos cells

growth_protocol: Ramos cells were grown in RPMI supplemented with FBS, antibiotics, and glutamine

extract_protocol:
Total RNA was extracted using Qiagen Rneasy spin columns
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ramos cells were untreated or treated with 3 µM CHIR99021 for 3 or 6 hours

tag: tumor stage

value: EBV-negative Burkitt lymphoma

value: Ramos cells

tag: agent

value: GSK-3 inhibitor CHIR99021

tag: time


title: 6h_9

tag: cell line


title: 3h_7


title: 6h_10


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-72


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-73


title: NRF2-CSC-1_3pDGE

description:
NRF2-CSC-1
Well-D1

value: immortalized human bronchial epithelial cells (AALE)

value: overexpression

value: TTAAGA


title: NRG1-CSC-11_3pDGE

description:
NRG1-CSC-11
Well-D4

value: TTCTAA


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-67


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-79


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-66


title: FGFR1-CSC-2_3pDGE

description:
FGFR1-CSC-2
Well-C8

value: TATTCA


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-65


title: FGFR1-CSC-11_3pDGE

description:
FGFR1-CSC-11
Well-C7

value: TATCTA


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-62


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-64


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-63


title: 0h_3

value: control


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-60


title: 0h_2


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-61


title: 0h_1


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-56


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-58


title: GFP-CSC-1_3pDGE

description:
GFP-CSC-1
Well-C4

value: GFP

value: knockout

value: TACATT


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-59


title: GFP-CSC-2_3pDGE

description:
GFP-CSC-2
Well-C5

value: AALE

value: CSC

value: TAGATA


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-57

value: white blood cells

value: H3K27me3 Ab + PA-MNase


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-53


title: HCRED-CSC-3_3pDGE

description:
HCRED-CSC-3
Well-C3

value: HCRED

value: TAATCT


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-55


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-54


title: HCRED-CSC-2_3pDGE

description:
HCRED-CSC-2
Well-C2

value: immortalized human bronchial epithelial cells (AALE)

value: TAACTT


title: FGFR1-CSC-12_3pDGE

description:
FGFR1-CSC-12
Well-C9

value: overexpression

value: TCAATT


title: NRF2-BaP-2_3pDGE

description:
NRF2-BaP-2
Well-F2

value: BaP

value: CCCGGA


title: 3h_6

value: EBV-negative Burkitt lymphoma

value: Ramos cells

value: GSK-3 inhibitor CHIR99021


title: mon159

description: Monocytes Protocol

extract_protocol:
Monocytes Protocol:  Monocytes were isolated from healthy and cancer individuals using Fluorescent- activated cell sorting (FACS) with the following markers (CD45+/CD3-CD19-CD56- /HLA-DR+MHC II+/CD14+CD16+). Immediately after FACS sorting, all samples were centrifuged at 450 RCF for 10 min at 4°C. Cell pellets were re-suspended in 350 ul of RLT lysis buffer and RNA extracted with RNAeasy Microkit (Qiagen) according to manufacturer’s instructions. Macrophages/TAMs Protocol: Isolation and Fluorescence-activated cell sorting (FACS) of human tissue macrophages was performed as described (Cassetta et al. 2016). Briefly, markers for FACS isolation of macrophages included CD45+/CD3-CD19-CD56- /CD11b+/CD14+CD163+. Immediately after sorting, all samples were centrifuged at 450 RCF for 10 min at 4C. Cell pellets were re-suspended in 350 ul of RLT lysis buffer and RNA extracted with RNAeasy Microkit (Qiagen) according to manufacturer’s instructions.
RNA quantity was determined by QUBIT (Invitrogen); total RNA integrity was assessed by Agilent Bioanalyzer and the RNA Integrity Number (RIN) was calculated; samples that had a RIN > 7 were selected for RNA amplification and sequencing. RNA was amplified with Ovation RNAseq Amplification kit v2 (Nugen)

value: monocytes

tag: condition

value: Normal

tag: sequencing batch

tag: pathology


title: mon158

description: Monocytes Protocol


title: 3h_5


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-52


title: mon157

description: Monocytes Protocol


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-51


title: mon156

description: Monocytes Protocol


title: PIK3CA-CSC-2_3pDGE

description:
PIK3CA-CSC-2
Well-C11

value: AALE

tag: genotypic perturbation

value: CSC

value: TGATAA


title: PIK3CA-CSC-3_3pDGE

description:
PIK3CA-CSC-3
Well-C12

tag: genotypic perturbation type

value: TGTTAT


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-49

value: white blood cells

value: H3K27me3 Ab + PA-MNase


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-50


title: mon147

description: Monocytes Protocol


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-47


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-48


title: mon155

description: Monocytes Protocol


title: PIK3CA-CSC-1_3pDGE

description:
PIK3CA-CSC-1
Well-C10

value: immortalized human bronchial epithelial cells (AALE)

tag: chemical perturbation

value: TCTATA


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-45


title: HCRED-CSC-1_3pDGE

description:
HCRED-CSC-1
Well-C1

value: HCRED

value: overexpression

tag: well id

value: TAAACA


title: mon146

description: Monocytes Protocol


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-44


title: FAT1-DMSO-3_3pDGE

description:
FAT1-DMSO-3
Well-B9

value: knockout

value: DMSO

tag: barcode

value: CTTATA


title: mon145

description: Monocytes Protocol


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-43


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-42


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-39


title: mon144

description: Monocytes Protocol


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-40


title: FAT1-DMSO-1_3pDGE

description:
FAT1-DMSO-1
Well-B7

value: CATATT


title: FAT1-DMSO-2_3pDGE

description:
FAT1-DMSO-2
Well-B8

value: CTAATT


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-41


title: mon142

description: Monocytes Protocol

value: monocytes

value: Normal


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-37


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-38


title: GFP-CSC-3_3pDGE

description:
GFP-CSC-3
Well-C6

value: AALE

value: GFP

value: CSC

value: TATACT


title: mon141

description: Monocytes Protocol


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-46

value: white blood cells

value: H3K27me3 Ab + PA-MNase


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-36


title: NRG1-DMSO-2_3pDGE

description:
NRG1-DMSO-2
Well-B5

value: immortalized human bronchial epithelial cells (AALE)

value: ATTTAC


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-34


title: mon140

description: Monocytes Protocol


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-33


title: NRG1-DMSO-1_3pDGE

description:
NRG1-DMSO-1
Well-B4

value: overexpression

value: ATTCAT


title: NRF2-DMSO-3_3pDGE

description:
NRF2-DMSO-3
Well-B3

value: ATTAAG


title: mon139

description: Monocytes Protocol


title: mon138

description: Monocytes Protocol


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-30


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-29


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-31


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-32


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-28


title: mon136

description: Monocytes Protocol


title: mon137

description: Monocytes Protocol


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-26


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-25


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-27


title: CDKN2A-DMSO-2_3pDGE

description:
CDKN2A-DMSO-2
Well-B11

value: knockout

value: DMSO

value: GTAAAT


title: CDKN2A-DMSO-3_3pDGE

description:
CDKN2A-DMSO-3
Well-B12

value: GTTATT


title: NRG1-DMSO-3_3pDGE

description:
NRG1-DMSO-3
Well-B6

value: CAAAAT


title: mon135

description: Monocytes Protocol

value: monocytes

value: Normal


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-23


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-35


title: CDKN2A-DMSO-1_3pDGE

description:
CDKN2A-DMSO-1
Well-B10

value: AALE

value: GAATTA


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-22


title: mon134

description: Monocytes Protocol


title: NRF2-DMSO-1_3pDGE

description:
NRF2-DMSO-1
Well-B1

value: ATATTC


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-21

value: white blood cells


title: mon133

description: Monocytes Protocol


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-20

value: H3K27me3 Ab + PA-MNase


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-19


title: NRF2-DMSO-2_3pDGE

description:
NRF2-DMSO-2
Well-B2

value: immortalized human bronchial epithelial cells (AALE)

value: ATCTTA


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-17


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-24


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-18


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-15


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-13


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-12


title: GFP-DMSO-3_3pDGE

description:
GFP-DMSO-3
Well-A6

value: GFP

value: AATTAG


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-11


title: mon129

description: Monocytes Protocol


title: FGFR1-DMSO-1_3pDGE

description:
FGFR1-DMSO-1
Well-A7

value: overexpression

value: ACAAAT