title: S12.G12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.G11

status: Public on Feb 07 2019

type: SRA

city: Santa Cruz

first: Christopher

last: Villarreal

state: CA

address: 1156 Hight Street, Engineering-2 Rm. 501, MS: GENOMICS INSTITUTE

department: Genomics Institute

country: USA

description: PrimaryOrganoidAndPublishedCPM.txt

library_source: transcriptomic

data_processing:
Trim Galore 3.7
HISAT2
subread-1.5.0 function featureCounts
Human GRCh38.79.gtf
The listed genes in the processed data file are human genes mapped to each respective species using the comparative annotation toolkit (PMID: 29884752). Reads are mapped to each species' native genome and quantified based transcript models from comparative annotation toolkit.
The file GSE124299-metadata on processed samples.xlsx  includes the metadata for all samples in this study-- both the new samples listed in this Series and the re-analyzed samples, including accession IDs, when available.
Genome_build: Human: GRCh38.p2; NCBI:GCA_000001405.17
Genome_build: Chimpanzee: Clint_PTRv2 / UCSC: panTro6
Genome_build: Macaque: RheMac8
Supplementary_files_format_and_content: log(CPM+1)

molecule: polyA RNA

organism: Pan troglodytes

source_name: iPS-derived cerebral organoid

growth_protocol: Cerebral organoids using Kadoshima et al., 2013 from Sasai lab

extract_protocol:
Fluidigm C1 small IFC (100-5759; 100-6201);  SMARTer® Ultra™ Low RNA Kit (634832)
Nextera XT tagmentation kit (FC-131-096)

tag: tissue

value: iPS-derived cerebral organoid

tag: donorid

tag: cloneid

tag: age (weeks)

tag: datecaptured

tag: Sex

value: Male

tag: organoidid

tag: protocol

value: Kadoshima

tag: captureplate

tag: capturechamber


title: HEK_CHX_HS_RPB1_ChIP_Rep2

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the human genome build hg38 using Bowtie2. Duplicate and discordant reads were removed. Peak calling was done with MACS2 using "--keep-dup all", "--nomodel", "--extsize" and "--broad". Gene annotations and transcript start site (TSS) information for human genes were from taken from Gencode annotation release 26.
Cutadapt was used to cut adapter from sequenced reads. Filtered reads were first mapped to a single copy of ribosomal DNA to remove the contribution of nascent RNAs from ribosomal genes. The remaining reads were mapped to human genome build hg38 using Bowtie2 using default parameters. PRO-seq libraries were normalized using 3’-end of long genes as described by Mahat et al., 2016
DESeq2 was used to identify differentially express.ed genes upon heat shock. Differential gene expression was done using DESeq2
Genome_build: hg38

molecule: genomic DNA

organism: Homo sapiens

source_name: Flp-In T-REx 293 Cell Line

growth_protocol: Flp-In T-REx 293 were cultured in DMEM High Glucose supplemented with 10% FBS. K562 cells were cultured in IMDM supplemented with 10% FBS.

extract_protocol: Cells were fixed using 1% methanol-free formaldehyde (CAT no) in DMEM (HEK293) or IMDM (K562) at room temperature for 10 minutes, followed by 5 minutes blocking in 0.125M glycine. Cells were washed twice with ice-cold PBS. Cell pellet was resuspended in Farnham Buffer (5 mM PIPES pH 8; 85 mM KCl; 0.5% Igepal). Cell suspensions were sonicated in 1ml Covaris tubes using Covaris S220 with the following settings: Peak Power=75; Duty Factor=2; Cycles/Burst=200. Sonication time varied from cell type to cell type; K562=~2.5minutes and HEK293=~3minutes. Isolated nuclei were washed with Farnham Buffer and suspended in shearing buffer (10 mM Tris-HCl pH 8; 0.1% SDS; 1 mM EDTA). Chromatin was sheared by sonication in 1ml Covaris tubes using the following settings: Peak Power=140; Duty Factor=5; Cycles/Burst=200, Time=25-30 minutes. Debris was removed by centrifugation. A DNA fragment-size distribution of 200-600bp was considered as ideal chromatin for ChIP. Chromatin was diluted 1:1 with IP buffer to achieve a final 0.05% SDS concentration. 200 μg of good quality chromatin was used for immunoprecipitation. Protein A or G magnetic beads (CAT) were incubated (rotated) with 5-10μg of antibody for 6h at 4ºC. This bead-antibody complex was then incubated overnight at 4ºC with chromatin.

treatment_protocol: Cycloheximide and NSC624206 (Ub-E1 inhibitor) were used as pretreatments prior to Heat shock, always using an appropriate solvent control. To inhibit translation, 30ug/ml Cycloheximide were used for 1.5h. To inhibit ubiquitin-activating enzyme E1 (Ub-E1 inhibitor), 2uM NSC624206 was used for 0.5h.

tag: chip antibody

value: RNA PolII (RPB1) Cell Signaling 14958

tag: treatment

value: Cycloheximide

tag: condition

value: Heat-Shock


title: S12.G10

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-100

type: RNA

city: Hong Kong

first: Tongtong

last: Kan

address: 83 Tat Chee Avenue

country: China

institute: City University of Hong Kong

data_processing:
Raw Crt, “relative threshold”, values were generated by OpenArray system, the undetected Crt values were replaced by 40 (Matrix non-normalized); the Crt values were normalized to 18S using the -△Crt method (Matrix normalized); fold change was calculated by 2^-△Crt.
Fold Change worksheet reports relative single cell gene expression level.

label: TaqMan

molecule: total RNA

label_protocol: The single-cell reverse transcription and pre-amplification procedures were provided by the same kit. Single-cell RT-PCR was performed in OpenArray chips, using QuantStudio 12K Flex Real-Time PCR System (Applied Biosystems).

extract_protocol: The single cells were lysed directly using Single cell-to-CT qRT-PCR Kit (Ambion).

treatment_protocol: The cell clusters were picked up then dissociated into single cells. Both the cell clusters and single cells were picked up manually under a microscope using Kuiqpick through a glass capillary.

tag: subgroup

value: DTCC-R

tag: cell type

value: Epithelial ovarian cancer ascites


title: Random DTCC-103


title: Random DTCC-99


title: HEK_HS_Proseq_Rep2

data_processing:
Library strategy: Pro-Seq
ChIP-seq reads were aligned to the human genome build hg38 using Bowtie2. Duplicate and discordant reads were removed. Peak calling was done with MACS2 using "--keep-dup all", "--nomodel", "--extsize" and "--broad". Gene annotations and transcript start site (TSS) information for human genes were from taken from Gencode annotation release 26.
Cutadapt was used to cut adapter from sequenced reads. Filtered reads were first mapped to a single copy of ribosomal DNA to remove the contribution of nascent RNAs from ribosomal genes. The remaining reads were mapped to human genome build hg38 using Bowtie2 using default parameters. PRO-seq libraries were normalized using 3’-end of long genes as described by Mahat et al., 2016
DESeq2 was used to identify differentially express.ed genes upon heat shock. Differential gene expression was done using DESeq2
Genome_build: hg38

extract_protocol: 10X106 HEK293 cells were used for each PROseq experiment. Cells were harvested and permeabilized. A 2-biotin label run on reaction was done to label nascently transcribed RNA. 2X nuclear run-on mix was mixed with biotin labeled CTP and UTP. Nuclear run-on reaction was carried out for 3 minutes at 37ºC. Reaction was stopped by adding Trizol LS (CAT no) followed by vigorous vortexing. RNA was isolated by standard procedure. Nascently transcribed RNA was fragmented by base hydrolysis (NaoH) resulting in 100bp long RNA suitable for sequencing. Streptavidin coated magnetic beads were used to enrich for biotin labeled RNA using affinity purification. RNA was mixed with pre-washed streptavidin beads and incubated at room temperature. Beads were washed and resuspended in Trizol and RNA was isolated. A 3’ RNA adaptor (VRA3-5uM) was ligated at the 3’-end of biotin labeled nascent RNA using ligation mix (T4 RNA ligase buffer, 1mM ATP, 10% PEG, RNase Inhibitor, T4 RNA ligase I). A second biotin-RNA enrichment was done to enrich for labeled nascent RNA and remove unligated adaptors. The 5’ OH generated by base hydrolysis was then converted to 5’ phosphate by treatment with T4 polynucleotide kinase. A 5’ RNA adaptor (VRA5) was ligated at the 5’ end of RNA using the ligation mix described previously. A 3rd round of enrichment was done to enrich for labeled RNA and remove any unligated adaptors. Nascent RNA is then reverse transcribed using RP1 and RTP reverse transcription primers (2.5μM each). A test PCR amplification was then done to determine number of PCR cycles for amplification. A PCR cycle that gave sufficient amount of product, no over amplification and 50-75 % of unused primers was considered optimal and used for final amplification. Full scale PCR amplification was done using the following PCR mix (1x HF buffer, 1M Betaine, 250μM dNTP mix, 250 nM RP1 primer, 250 nM RP1-n primer, 0.04 units/μl Phusion DNA polymerase). PCR amplified DNA was then size selected (150-350 bp) by PAGE purification with some modifications from the original protocol (Mahat 2016 Nat Prot). DNA was then extracted using phenol-chloroform extraction. DNA pellet was re-dissolved in nuclease free water and DNA library size distribution was monitored by capillary electrophoresis.


title: S12.F5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.F3

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-97


title: Random DTCC-102


title: Random DTCC-96


title: HEK_NHS_Proseq_Rep3

value: Non Heat-Shock


title: S12.F8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.F2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.F10

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-98


title: S12.E9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.E8

description: PrimaryOrganoidAndPublishedCPM.txt


title: HEK_NHS_Proseq_Rep2


title: Random DTCC-95


title: S12.E6

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-94


title: S12.G1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.E5

description: PrimaryOrganoidAndPublishedCPM.txt


title: HEK_NHS_Proseq_Rep1


title: HEK_HS_Proseq_Rep3


title: S12.E12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.E11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.F9

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-93


title: HEK_HS_Proseq_Rep1


title: smallRNAseq_DMS3-ZF_line1_x_NRPD1-ZF_T1_Figure7

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

description: small RNAseq of DMS3-ZF line1 x NRPD1-ZF T1 Figure7

data_processing:
For sRNA-seq data analysis, raw reads were trimmed for Illumina adaptors using Cutadapt (v 1.9.1) and mapped to the TAIR10 reference genome using Bowtie (v1.1.0) (Langmead et al., 2009) allowing only one unique hit (-m 1) and zero mismatch. In order to define off-target sites with 24-nt siRNAs production, flanking 1kb of off-target region with NRPE1 recruitment were first divided into 100bp bins. Then 24-nt siRNAs count were calculated over those 100bp bins and DEseq2 (Love et al., 2014) was applied using 4 fold change and FDR less than 0.05 as cut off for DMS3-ZF vs ZF, NRPD1-ZF vs ZF and DMS3-ZF X NRPD1-ZF vs ZF.
Genome_build: tair10
Supplementary_files_format_and_content: bigwig

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: All plants in this study were grown under long-day conditions (16h light/8h dark). Transgenic plants were obtained by agrobacterium-mediated floral dipping. T1 transgenic plants were selected on 1/2 MS medium + Glufosinate 50 μg/ml (Goldbio) or 1/2 MS medium + Hygromycin B 25 μg/ml (Invitrogen) in growth chambers under long day conditions and subsequently transferred to soil. Successive transgenic generations were germinated directly on soil.

extract_protocol:
RNA from inflorescences was extracted using the Zymo Direct-zol Kit (ZYMO research).
For sRNA-seq libraries, 2ug total RNA was run in 15% UREA gels and small RNAs from 15 to 30bp were cut and precipitated. This RNA was used to prepare libraries using the Truseq small RNA kit (Illumina) following manufacturer’s instructions.

value: inflorescence

tag: genotype

tag: ecotype

value: Columbia


title: smallRNAseq_DMS3-ZF_line2_x_NRPD-ZF1_T1_Figure7

description: small RNAseq of DMS3-ZF line2 x NRPD1-ZF T1 Figure7

tag: tissue


title: S12.E1

description: PrimaryOrganoidAndPublishedCPM.txt

tag: donorid


title: S12.E10

description: PrimaryOrganoidAndPublishedCPM.txt

tag: cloneid


title: S12.D7

description: PrimaryOrganoidAndPublishedCPM.txt

tag: age (weeks)


title: Random DTCC-91


title: Random DTCC-92


title: smallRNAseq_NRPD1-ZF_T1-2_Figure7

description: small RNAseq of NRPD1-ZF (T1-2) used for Figure7

value: NRPD1_ZF_in _Col-0


title: S12.D12

description: PrimaryOrganoidAndPublishedCPM.txt

tag: datecaptured


title: S12.D4

description: PrimaryOrganoidAndPublishedCPM.txt

tag: Sex


title: S12.D5

description: PrimaryOrganoidAndPublishedCPM.txt

tag: organoidid


title: Random DTCC-90


title: S12.D1

description: PrimaryOrganoidAndPublishedCPM.txt

tag: protocol


title: Random DTCC-89


title: smallRNAseq_NRPD1-ZF_T1-3_Figure7

description: small RNAseq of NRPD1-ZF (T1-3) used for Figure7


title: smallRNAseq_ZF_line2_rep3_Figure5

description: small RNAseq for ZF in Col-0 line2 replicate 3 used for Figure5


title: S12.C8

description: PrimaryOrganoidAndPublishedCPM.txt

tag: captureplate


title: Random DTCC-88


title: smallRNAseq_ZF_line2_rep2_Figure5

description: small RNAseq for ZF in Col-0 line2 replicate 2 used for Figure5


title: S12.C5

description: PrimaryOrganoidAndPublishedCPM.txt

tag: capturechamber


title: S12.C2

description: PrimaryOrganoidAndPublishedCPM.txt


title: smallRNAseq_ZF_line2_rep1_Figure5

description: small RNAseq for ZF in Col-0 line2 replicate 1 used for Figure5


title: S12.C4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.C6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.C12

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-86


title: Random DTCC-87


title: S12.C11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.C10

description: PrimaryOrganoidAndPublishedCPM.txt


title: smallRNAseq_ZF_line1_rep3_Figure5

description: small RNAseq for ZF in Col-0 line1 replicate 3 used for Figure5


title: smallRNAseq_NRPD1-ZF_T1-1_Figure7

description: small RNAseq of NRPD1-ZF (T1-1) used for Figure7


title: Random DTCC-85


title: S12.D10

description: PrimaryOrganoidAndPublishedCPM.txt


title: smallRNAseq_ZF_line1_rep2_Figure5

description: small RNAseq for ZF in Col-0 line1 replicate 2 used for Figure5


title: S12.C1

description: PrimaryOrganoidAndPublishedCPM.txt


title: smallRNAseq_ZF_line1_rep1_Figure5

description: small RNAseq for ZF in Col-0 line1 replicate 1 used for Figure5


title: S12.B4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.B8

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-84


title: Random DTCC-83


title: Random DTCC-82


title: smallRNAseq_DMS3-ZF_line2_rep3_Figure5

description: small RNAseq for DMS3-ZF in Col-0 line2 replicate 3 used for Figure5


title: S12.B1

description: PrimaryOrganoidAndPublishedCPM.txt


title: smallRNAseq_DMS3-ZF_line2_rep2_Figure5

description: small RNAseq for DMS3-ZF in Col-0 line2 replicate 2 used for Figure5


title: S12.A8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.A5

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-81


title: smallRNAseq_DMS3-ZF_line2_rep1_Figure5

description: small RNAseq for DMS3-ZF in Col-0 line2 replicate 1 used for Figure5


title: S12.A12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.A3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.A10

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-80


title: smallRNAseq_DMS3-ZF_line1_rep3_Figure5

description: small RNAseq for DMS3-ZF in Col-0 line1 replicate 3 used for Figure5


title: smallRNAseq_DMS3-ZF_line1_rep2_Figure5

description: small RNAseq for DMS3-ZF in Col-0 line1 replicate 2 used for Figure5


title: Random DTCC-78


title: Random DTCC-79


title: Random DTCC-77


title: Random DTCC-76


title: S12.B3

description: PrimaryOrganoidAndPublishedCPM.txt


title: PLC-K4me3-1

city: Emeryville

first: Tobias

last: Flecken

address: 5300 Chiron Way

department: Infectious Diseases

institute: Novartis Institutes for Biomedical Research

description:
ChIP for H3K4me3
Aligned to EU594392.1.

data_processing:
base calling: RTA 1.18.54 (from Illumina MCS 2.6.2)
alignment: bowtie2 2.3.0 was used for alignment to 1.1mer viral genomes (with -t -no-unal -no-discordant -no-mixed -I 120 -X 200 option) and all sequences (combined hg38/HBV/phiX; only -t option)
paired read merging: custom script was used to merge paired reads in the output SAM file based on viral genome coordinates. Unsequenced insert was represented as N with low quality score.
BAM conversion: SAM file was converted to BAM, sorted, and indexed using samtools 0.1.19
BEDGRAPH conversion: BAM file was converted to BEDGRAPH using bedtools 2.18.1 (-bg -trackline options)
1mer conversion: custom script was used to wrap around reads that aligned in the overhang of the 1.1mer to the start of the sequence
scaling and wig conversion: custom script was used to convert BEDGRAPH to WIG files while simultaneously scaling it per 106 total reads in the library (hg38+HBV+phiX)
Genome_build: HBV reference genomes are indicated in the sample overview (protocl column). GRCh38.p10 was used for the human genome, NC_001422.1 for phiX
Supplementary_files_format_and_content: WIG files contain the number of HBV reads per million total reads for each position of the respective HBV reference genome. Sequences are shifted by -500 nt compared to EcoRI site.

extract_protocol:
Cells were fixed in freshly prepared 1% formaldehyde in PBS (both ThermoFisher Scientific) for 5 min prior to quenching with 125 mM glycine in PBS. Pelleted cells were either used directly for analysis or snap-frozen and stored at -80°C until use. Next, cells were washed with cold lysis buffer [PBS with 0.1% Triton X-100, 0.1% NP-40, 1 mM dithiothreitol (DTT), 50 ng/ml trichostatin A (TSA) and 1x EDTA-free protease inhibitor (Roche, Basel, Switzerland)] and lysed in the same buffer for 10 min on ice. Nuclei were pelleted, resuspended in digestion buffer [H2O with 50 mM Tris-HCl pH 7.5, 4 mM MgCl2, 1 mM CaCl2, 10% glycerol, 50 ng/ml TSA, and 1x EDTA-free protease inhibitor (Roche)] and digested with 600 IU/ml micrococcal nuclease (MNase; ThermoFisher Scientific) for 12 min at 37°C. Digestion was stopped by addition of 10 mM EDTA. Nuclei were pelleted at 6500 x g and supernatants collected. The pellet was resuspended in digestion buffer with 10 mM EDTA and 300 mM NaCl and mildly sonicated using a W 375 sonicator (Qsonica, Newtown, CT) at 50% duty cycle and power setting 3. Nuclei were again pelleted, supernatants combined and mixed with an equal amount of sucrose buffer [H2O with 50 mM Tris-HCl pH 7.5, 50 mM NaCl, 5 mM EDTA, 0.01% NP-40, 50 ng/ml TSA, and 1x EDTA-free protease inhibitor (Roche)]. Samples were concentrated using Amicon Ultra-4 100 kDa centrifugal filter units (Millipore-Sigma; Merck KGaA, Darmstadt, Germany) and spun on a 5-30% continuous sucrose gradient in sucrose buffer for 4 h at 40,000 x g and 4°C using a SW41Ti rotor (Beckman Coulter Inc., Brea, CA). Chemicals were obtained from Millipore-Sigma unless noted otherwise. Mononucleosome containing fractions were pooled and concentrated to ~500 µl prior to addition of 100 ng/µl bovine serum albumin (ThermoFisher Scientific). Mononucleosomes were either stored at -20°C or used immediately for ChIP. Antibodies were bound to 20 µl/ChIP Dynabeads Protein G (ThermoFisher) in ChIP buffer [H2O with 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 200 µg/ml BSA] at 4°C and added to 2 µg of chromatin in ChIP buffer and allowed to bind overnight. Samples were washed six times in LiCl wash buffer [H2O with 150 mM LiCl, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, and 0.7% sodium deoxycholate] and eluted in 100 µl elution buffer [H2O with 1% SDS and 100 mM NaHCO3]. Crosslinks were reversed by digestion with Proteinase K (ThermoFisher) for 5 h at 65°C and then digested for another 30 min with DNase-free RNase A (ThermoFisher) at 37°C. DNA was purified using the QIAquick PCR purification kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
1 ng of DNA was used for sequencing library construction with the KAPA Hyper Prep Kit (Roche) according to the manufacturer’s instructions. For barcoding, 2 µl of TruSeq RNA adapters stocks were used (Illumina, Inc., San Diego, CA). Up to 6 libraries were pooled per sequencing run and 500 ng pooled library subject to HBV-specific target enrichment using the xGen Lockdown Reagents Hybridization and Wash Kit (Integrated DNA technologies, Skokie, IL) according to the manufacturer’s instructions. A custom set of xGen lockdown probes of 60 bp length tiling the entire HBV genome of genotypes A-D was used for target enrichment (Integrated DNA technologies) together with Dynabeads MyOne T-270 Streptavidin (ThermoFisher). The pull-down was amplified for 12 or 8 PCR cycles (biopsies vs. de novo infected cells/cell lines; KAPA HiFi HotStart ReadyMix, Roche) and the product cleaned up using Agencourt AMPure XP beads (Beckman Coulter, Inc.). The product was used to dilute the original library to 20 nM. Sequencing was performed using an Illumina MiSeq sequencer with a MiSeq v3 reagent kit for 2x76 bp paired-end reads (Illumina, Inc.).

treatment_protocol: Biopsy specimens were thawed in pre-warmed 0.05% Trypsin-EDTA (ThermoFisher Scientific, Waltham, MA) and mixed with 8x106 uninfected HepG2-hNTCP cells.

value: liver

tag: hbv genotype

value: A

tag: agent

value: Hepatitis B virus

tag: cell line

tag: disease stage

tag: antibody

value: ChIP for H3K4me3


title: PLC-H3-2

description:
ChIP for H3
Aligned to EU594392.1.

value: ChIP for H3


title: PLC-H3-1

description:
ChIP for H3
Aligned to EU594392.1.


title: smallRNAseq_DMS3-ZF_fwa_nrpd1_line2_Figure2

description: small RNAseq for DMS3-ZF in fwa x nrpd1 replicate 2 used for Figure 2

tag: genotype


title: PLC-K9me3-1

description:
ChIP for H3K9me3
Aligned to EU594392.1.

value: ChIP for H3K9me3


title: PLC-input-2

description:
input
Aligned to EU594392.1.


title: Random DTCC-75

tag: subgroup

tag: cell type


title: PLC-K4me3-2

description:
ChIP for H3K4me3
Aligned to EU594392.1.

tag: tissue


title: smallRNAseq_DMS3-ZF_fwa_nrpd1_line1_Figure2

description: small RNAseq for DMS3-ZF in fwa x nrpd1 replicate 1 used for Figure 2

tag: ecotype


title: PLC-K9me3-2

description:
ChIP for H3K9me3
Aligned to EU594392.1.


title: S12.B10

description: PrimaryOrganoidAndPublishedCPM.txt

value: iPS-derived cerebral organoid

tag: donorid

tag: cloneid

tag: age (weeks)

value: Male


title: Hep3B-K9me3-2

description:
ChIP for H3K9me3
Aligned to EU594392.1.


title: Random DTCC-74


title: Hep3B-K9me3-1

description:
ChIP for H3K9me3
Aligned to EU594392.1.


title: Random DTCC-73


title: Hep3B-K4me3-2

description:
ChIP for H3K4me3
Aligned to EU594392.1.


title: smallRNAseq_DMS3-ZF_fwa_line1_Figure2

description: small RNAseq for DMS3-ZF in fwa replicate 1 used for Figure 2


title: Hep3B-K4me3-1

description:
ChIP for H3K4me3
Aligned to EU594392.1.


title: smallRNAseq_DMS3-ZF_line1_rep1_Figure5

description: small RNAseq for DMS3-ZF in Col-0 line1 replicate 1 used for Figure5


title: smallRNAseq_fwa_nrpd1_rep2_Figure2

description: small RNAseq for fwa x nrpd1 replicate 2 used for Figure 2


title: Random DTCC-72


title: Hep3B-H3-1

description:
ChIP for H3
Aligned to EU594392.1.


title: PLC-input-1

description:
input
Aligned to EU594392.1.


title: smallRNAseq_fwa_nrpd1_rep1_Figure2

description: small RNAseq for fwa x nrpd1 replicate 1 used for Figure 2


title: smallRNAseq_fwa_rep2_Figure2

description: small RNAseq for fwa replicate 2 used for Figure 2

value: fwa


title: Random DTCC-71


title: Hep3B-input-1

description:
input
Aligned to EU594392.1.


title: HepG2HBV-K9me3-1

description:
ChIP for H3K9me3
Aligned to EU787447.1.

value: D


title: HepG2HBV-K4me3-2

description:
ChIP for H3K4me3
Aligned to EU787447.1.


title: Hep3B-input-2

description:
input
Aligned to EU594392.1.


title: Random DTCC-69


title: HepG2HBV-K9me3-2

description:
ChIP for H3K9me3
Aligned to EU787447.1.


title: BSPCR_DMS3_ZF

description:
PCR amplified DNA
BS-PCR over AP1 in DMS3-ZF_region1to3

data_processing:
Library strategy: BS-PCR-seq
For BS-PCR-seq analysis, raw sequencing reads with designed BS-PCR primers were filtered followed by primer trimming with customized scripts. Trimmed reads were then aligned with BSMAP (v.2.74) (Xi and Li, 2009) to the reference TAIR10 genome by allowing up to 2 mismatches (-v 2), 1 best hit (-w 1) and aligning to both strands (-n 1). The methylation level at each cytosine was then extracted with BSMAP (methratio.py) scripts by allowing only unique mapped reads (-u). Reads with more than 3 consecutive methylated CHH sites were removed. Methylation levels at each cytosine were calculated as #C/(#C+#T). Cytosines with less than 20 reads coverage were discarded. To visualize the BS-PCR- seq data, only cytosines within designated regions were kept and plotted with customized R scripts. For representation of AP1 BS-PCR-seq, the methylation levels present in the three regions analysed were combined.
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text and bigwig

extract_protocol:
Leaf tissue from adult plants of representative T2 lines was collected to analyze FWA methylation. Inflorescences of representative T2 lines were collected to analyze AP1 methylation. DNA was extracted following a CTAB-based method and converted using the EZ DNA methylation-lighting kit (ZYMO research) or the Epitect Bisulfite Conversion kit (Qiagen). For FWA, we analyzed methylation over three different regions: Region 1: chr4: 13038143-13038272; Region 2: chr4: 13038356-13038499; Region3: chr4: 13038568-13038695. For AP1, we analyzed methylation over three different regions: Region 1: chr1: 25986270-25986391; Region 2: chr1: 25985976-25986098; Region 3: chr1:25986235-25986108. To amplify the different regions, Pfu Turbo Cx (Agilent) was used together with primers containing the Illumina adaptors. The primers used are listed in Table S1. Different PCR products for the same sample were pooled and purified by AMPure beads (Beckman Coulter).
Libraries were made from purified PCR products by a TruSeq Nano DNA Library Prep kit for Neoprep automated library preparation machine (Illumina), by Kapa DNA hyper kit (Kapa Biosystems) with Illumina TruSeq DNA adapters or by Ovation Ultralow V2 kit (NuGEN).


title: HepG2HBV-H3-2

description:
ChIP for H3
Aligned to EU787447.1.


title: smallRNAseq_DMS3-ZF_fwa_line2_Figure2

description: small RNAseq for DMS3-ZF in fwa replicate 2 used for Figure 2


title: smallRNAseq_fwa_rep1_Figure2

description: small RNAseq for fwa replicate 1 used for Figure 2


title: Random DTCC-68


title: HepG2HBV-K4me3-1

description:
ChIP for H3K4me3
Aligned to EU787447.1.


title: Random DTCC-70


title: Hep3B-H3-2

description:
ChIP for H3
Aligned to EU594392.1.


title: BSPCR_ZF

description:
PCR amplified DNA
BS-PCR over AP1 in ZF_region1to3


title: HepG2HBV-H3-1

description:
ChIP for H3
Aligned to EU787447.1.


title: HepG2HBV-input-1

description:
input
Aligned to EU787447.1.


title: HepG2NTCP-K9me3-2

description:
ChIP for H3K9me3
Aligned to EU787447.1.


title: HepG2HBV-input-2

description:
input
Aligned to EU787447.1.


title: BSPCR_Hairpin_x_DMS3_ZF_line2

description:
PCR amplified DNA
BS-PCR over AP1 in AP1Hairpin_x_DMS3-ZF_in_Col0_line2_region1to3


title: HepG2NTCP-K9me3-1

description:
ChIP for H3K9me3
Aligned to EU787447.1.


title: HepG2NTCP-K4me3-2

description:
ChIP for H3K4me3
Aligned to EU787447.1.


title: BSPCR_Hairpin_x_DMS3_ZF_line1

description:
PCR amplified DNA
BS-PCR over AP1 in AP1Hairpin_x_DMS3-ZF_in_Col0_line1_region1to3


title: Random DTCC-65


title: Random DTCC-66


title: HepG2NTCP-K4me3-1

description:
ChIP for H3K4me3
Aligned to EU787447.1.


title: BSPCR_Hairpin_x_ZF_line2

description:
PCR amplified DNA
BS-PCR over AP1 in AP1Hairpin_x_ZF_in_Col0_line2_region1to3


title: Random DTCC-64


title: HepG2NTCP-H3-2

description:
ChIP for H3
Aligned to EU787447.1.


title: HepG2NTCP-H3-1

description:
ChIP for H3
Aligned to EU787447.1.


title: BSPCR_Hairpin_x_ZF_line1

description:
PCR amplified DNA
BS-PCR over AP1 in AP1Hairpin_x_ZF_in_Col0_line1_region1to3


title: HepG2NTCP-input-2

description:
input
Aligned to EU787447.1.


title: S12.D9

description: PrimaryOrganoidAndPublishedCPM.txt

tag: datecaptured

tag: Sex

tag: organoidid

value: Kadoshima


title: A549_T100

city: VELLORE

first: Abul

middle: Kalam Azad

last: Mandal

state: Tamil Nadu

address: VELLORE

department: BIOTECHNOLOGY, SCHOOL OF BIOSCIENCES AND TECHNOLOGY

country: India

institute: VELLORE INSTITUTE OF TECHNOLOGY

description:
T100 treatment for 24h.
processed data files:
Rawcounts_known.csv
Rawcounts_novel.csv
Normalized_known.csv
Normalized_novel.csv

data_processing:
Reads were preprocessed to remove adapter and low quality bases. srna-workbenchV3.0_ALPHA1 was used to trim the 3' adapter sequences.
Trimmed reads were filtered based on the length criteria (minimum length 16bp and maximum 40 bp).
The filtered reads were aligned to Homo sapiens GRCh38 using bowtie-1.1.1.
Other non-coding RNAs (rRNA, tRNA, snRNA, snoRNA and piRNA) were filtered.
MiRBase21 was used for known miRNA identification. Further putative novel miRNA sequences were predicted by ncbi-blast-2.2.304 at e-4.
Genome_build: GRCh38 (Genome Reference Consortium Human Build 38)
Supplementary_files_format_and_content: Rawcounts_*.csv: Comma-separate text files include raw counts for each Sample.
Supplementary_files_format_and_content: Normalized_*.csv: Comma-separate text files include RPKM for each Sample.

source_name: Lung cancer cell line

growth_protocol: A549 cancer cells were grown in F-12K medium with 10% FBS and 1% 100X Antibiotic-Antimycotic solution at 37 degrees Celsius with 5% CO2.

extract_protocol:
Trizol method for total RNA isolation was used.
NEBNext® Multiplex Small RNA Library Prep Set for Illumina.

treatment_protocol: A549 cells were treated with 40 micromolar or 100 micromolar EGCG concentration for 24h and was processed for small RNA sequencing.

value: non-small cell lung cancer cell line

tag: passage

tag: treatment

value: 100uM epigallocatechin gallate (EGCG)


title: BSPCR_ZF_DMR2cd_in_drm12_FigureS3

description:
PCR amplified DNA
BS-PCR over FWA in ZF-DRM2cd in fwa x drm1/2_region1to3

source_name: leaf

value: leaf


title: Random DTCC-67

value: DTCC-R

value: Epithelial ovarian cancer ascites


title: HepG2NTCP-input-1

description:
input
Aligned to EU787447.1.

tag: hbv genotype

tag: agent


title: Random DTCC-63


title: Random DTCC-62


title: BSPCR_ZF_DMR2cd_in_nrpe1_FigureS3

description:
PCR amplified DNA
BS-PCR over FWA in ZF-DRM2cd in fwa x nrpe1_region1to3

value: Columbia


title: Random DTCC-61


title: A549_CONTROL

description:
Cancer control.
processed data files:
Rawcounts_known.csv
Rawcounts_novel.csv
Normalized_known.csv
Normalized_novel.csv

tag: cell line

value: control


title: Random DTCC-60


title: BSPCR_ZF_DRM2cd_in_nrpd1_FigureS3

description:
PCR amplified DNA
BS-PCR over FWA in ZF-DRM2cd in fwa x nrpd1_region1to3


title: TCRb_Tumor_rep2-2

city: Noda

first: Hiroyasu

last: Aoki

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo University of Science

data_processing:
Library strategy: TCR-seq
Adapter trimming and quality filtering of sequencing data were performed by using cutadapt-v1.11 and PRINSEQ-0.20.4. Sequencing data were processed by MiXCR-1.8.2.　Filtered reads were aligned to reference mouse TCR V/D/J sequences with the following parameters: -OvParameters.geneFeatureToAlign = VTranscript -OvjAlignmentOrder = JThenV, then identical sequences were assembled and grouped in clones with PCR and sequencing error correlation with the following parameters: -ObadQualityThreshold=10.
List of final clones were analyzed by VDJtools-1.1.1. Non-functional clones containing a stop codon or frameshift in their receptor sequence were eliminated by “FilterNonFunctional” command of VDJtools. Then, the sequencing coverage of sample, which was defined as the ratio of total reads to starting number of T cells, was normalized to ×9 in TCRb and ×5 in TCRa by “DownSample” command of VDJtools.
Genome_build: ImMunoGeneTics (IMGT) reference sequences of mouse TRA and TRB
Supplementary_files_format_and_content: text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

organism: Mus musculus

source_name: B16 subcutaneous tumor

extract_protocol:
dLN, peripheral blood and tumor were collected at day 14 post tumor inoculation. For peripheral blood, red blood cells were lysed using Ammonium-Chloride-Potassium lysis buffer. Tumor were cut into small fragments and digested for 45 min at 37 °C with 0.2% collagenase (Wako, Osaka, Japan) and 20 kU/mL DNase I (Sigma-Aldrich, St Louis, MO), and the recovered from tumor were then subjected to 40/70 % Percoll (GE Healthcare, Buckinghamshire, UK) gradient and leukocytes were recovered from the interphase. Resulting cells were pretreated with Fc Block (anti-mouse CD16/CD32 mAb; clone 2.4G2, BioXcell, West Lebanon, NH, USA), then stained with a mixture of fluorophore-conjugated anti-mouse mAbs. CD8+ T cells or CD8+ CD44hi T cells were purified by cell sorting. Then, we performed TCR sequencing analysis on these cells.
TCR sequencing libraries for next generation sequencing were prepared from the mRNA of sorted CD8+ T cell samples. PolyA RNAs were isolated and amplified from sorted T cells according to a previous report (Shichino, et al, GSE110711). To amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed as follows. The first PCR mixture comprised 2.8 μL of distilled water (DW), 0.2 μL of 10 μM primer mix (5′ WTA, Trac_ex and Trbc_ex), 2 μL of cDNA template, and 5 μL of 2x Q5 High-Fidelity DNA Polymerase (New England Biolabs, MA, USA, NEB #M0491). The thermal cycling conditions were programmed as follows: denaturation at 98°C for 30 s, 10 cycles of denaturation for 10 s at 98°C, annealing and extension for 75 s at 65°C, followed by final extension at 65°C for 5 min. Next, 10 μL of the first-PCR products was used for purification with an Agencort AM Pure XP kit (Bexkman-Coulter, CA, USA, #A63881) at a 0.7:1 ratio of beads to sample, and eluted with 10 μL of DW. The second PCR mixture consisted of 7.25 μL of DW, 0.2 μL of 10 μM primer mix (5′ WTA, Trac_in-Bio and Trbc_in-Bio), 4 μL of purified PCR product and 12.5 μL of 2x Q5 High-Fidelity DNA Polymerase (New England Biolabs). The thermal cycling conditions were programmed as follows: denaturation at 98°C for 30 s, 18-23 cycles of denaturation for 10 s at 98°C, annealing and extension for 75 s at 65°C, followed by a final extension at 65°C for 5 min. Next, 25 μL of the second-PCR products were purified using Agencort AM Pure XP kit (Bexkman-Coulter) at a 0.7:1 ratio of beads to sample, and eluted in 16 μL of DW. The purified PCR products were sheared randomly using NEBNext dsDNA fragmentase (New England Biolabs, #M0348). The fragmentation reaction mix consisted of 2.3 μL of DW, 0.2 μL of 10 mg/ml BSA, 1 μL of 100 mM MgCl2, 2 μL of 10x reaction buffer, 10 μL of 8 ng/μL of PCR product, and 2 μL of Fragmentase. The fragmentation reaction was incubated at 37°C for 30 min, and then 5 μL of 0.5 M EDTA was added to stop the reaction. The sheared PCR product was then purified and subjected to size selection using the Agencort AM Pure XP kit (Bexkman-Coulter) at a 0.8:1 ratio of beads to sample to remove large fragments, a 0.8:1 ratio of beads to sample to remove the smaller fragments, and eluted with 20 μL of Tris-HCl (pH 8.0). To capture the TCR cDNA containing the end of Constant region, the purified PCR products were incubated with 30 μL of Dynabeads M-270 Streptavidin (Thermo Fisher Scientific, MA, USA, #DB65305) for 30 min at room temperature (r.t.), washed 3 times with B&W-T buffer [5 mM Tris-HCl (pH 7.5), 1 M NaCl, 0.5 mM EDTA, and 0.1% Tween-20], and once with Tris-HCl (pH 8.0), and DW. The captured TCR cDNA was repaired using NEBNext Ultra II End Repair/ dA-Tailing Module (New England Biolabs, # E7546L). The repair reaction mix contained 1.2 μL of reaction buffer, 8.3 μL of beads re-suspended with DW, and 0.5 μL of enzyme mix. The repair reaction was incubated at 20°C for 30 min, then washed once with lysis buffer [1% LiDS, 100 mM Tris-HCl (pH 7.5), 500 mM LiCl, 10 mM EDTA, and 5 mM DTT], 3 times with B&W-T buffer, and once with Tris-HCl (pH 8.0). The repaired TCR cDNA was attached to the sequencing adaptor using the DNA Ligation Kit ＜Mighty Mix＞ (TaKaRa, Shiga, Japan, #6023). The ligation reaction mix consisted of 1 μL of 10 μM P1 adaptor, 6.5 μL of beads re-suspended in Tris-HCl (pH 8.0), and 15 μL of enzyme mix. The ligation reaction was incubated at 16°C for 60 min using a thermal cycler with the cover open, washed once with lysis buffer, 3 times with B&W-T buffer, and once with Tris-HCl (pH 8.0). The third PCR were carried out using barcoded primers to enrich the TCR cDNA flanked with sequencing adapters. The third PCR mixture consisted of 6 μL of DW, 1.25 μL of 10 μM trP1 primer, 1.25 μL of 10 μM IonA-BC-Trac or IonA-BC-Trbc primer, 4 μL of beads resuspended in DW and 12.5 μL of 2x Q5 High-Fidelity DNA Polymerase (New England Biolabs). The thermal cycling conditions were programmed as follows: denaturation at 98°C for 30 s, 9 cycles of denaturation for 10 s at 98°C, annealing and extension for 75 s at 65°C, followed by final extension at 65°C for 5 min. The PCR product was purified and subjected to size selection using Agencort AM Pure XP kit (Bexkman-Coulter,) at a 0.75:1 ratio of beads to sample to remove large fragments, a 0.65:1 ratio of beads to sample for TCRα or 0.5:1 ratio for TCRβ to remove smaller fragments, and eluted with 20 μL of Tris-HCl (pH 8.0). Amplified TCR libraries were quantified using a KAPA Library Quantification Kit (NIPPON Genetics, Tokyo, Japan, KK4827) and size distribution was analyzed by agarose electrophoresis and SYBR Gold staining (Thermo Fisher Scientific, #S11494).   Final TCR libraries, whose lengths were 200–300 base pairs, were pooled and sequenced using an Ion Hi-Q Chef kit, an Ion PI v3 Chip kit, and an Ion Proton Sequencer (Thermo Fisher Scientific, # A27198, #A26771, # 4476610) according to the manufacturer’s instructions, except the input library concentration (100 pM) and flow number (500).

treatment_protocol: C57BL/6 mice received subcutaneous injections of 5 x 10^5 tumor cells (B16F10) in the right flank.

value: Intravenous staining-negative, lineage-negative (CD11b, CD19, NK1.1 and Ter119) and CD4- CD8+ T cells in dLN

tag: strain

value: subcutaneous tumor


title: TCRb_Tumor_rep2-1


title: TCRb_Tumor_rep1-2


title: TCRb_Tumor_rep1-1


title: BSPCR_ZF_DRM2cd_in_cmt3_FigureS3

description:
PCR amplified DNA
BS-PCR over FWA in ZF-DRM2cd in fwa x cmt3_region1to3

tag: genotype


title: Random DTCC-59

tag: subgroup


title: control_TCRb_Tumor_5

tag: cell type


title: BSPCR_ZF_DRM2cd_in_wt_FigureS3

description:
PCR amplified DNA
BS-PCR over FWA in ZF-DRM2cd in fwa_region1to3

tag: tissue


title: control_TCRb_Tumor_3


title: control_TCRb_Tumor_4


title: BSPCR_NRPD1-ZF_in_T3plus_FigureS1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa T3 minus (with transgene)_region1to3

value: NRPD1-ZF_in_fwa_T3plus (with transgene)

tag: ecotype


title: Random DTCC-57


title: A549_T40

description:
T40 treatment for 24h.
processed data files:
Rawcounts_known.csv
Rawcounts_novel.csv
Normalized_known.csv
Normalized_novel.csv

value: 40uM epigallocatechin gallate (EGCG)


title: Random DTCC-58


title: control_TCRb_Tumor_2


title: aCD4_TCRb_Tumor_5

source_name: B16 subcutaneous tumor following anti-CD4 mAb treatment


title: aCD4_TCRb_Tumor_3


title: aCD4_TCRb_Tumor_4


title: BSPCR_MORC-ZF_in_suvh29_Figure3

description:
PCR amplified DNA
BS-PCR over FWA in MORC-ZF in fwa x suvh2/9_region1to3


title: Random DTCC-56


title: Random DTCC-55


title: aCD4_TCRb_Tumor_2


title: BSPCR_MORC-ZF_in_wt_Figure3

description:
PCR amplified DNA
BS-PCR over FWA in MORC-ZF in fwa_region1to3


title: Random DTCC-54


title: aCD4_TCRb_Tumor_1


title: BSPCR_MORC-ZF_in_nrpd1_Figure3

description:
PCR amplified DNA
BS-PCR over FWA in MORC-ZF in fwa x nrpd1_region1to3


title: control_TCRb_dLN44hi_5

value: tumor draining lymph node


title: Random DTCC-53


title: Random DTCC-52


title: control_TCRb_dLN44hi_4


title: BSPCR_SUVH9-ZF_in_nrpd1_Figure3

description:
PCR amplified DNA
BS-PCR over FWA in SUVH9-ZF in fwa x nrpd1_region1to3


title: control_TCRb_Tumor_1


title: BSPCR_NRPD1-ZF_in_T3minus_FigureS1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa T3 minus (without transgene)_region1to3


title: control_TCRb_dLN44hi_2


title: aCD4_TCRb_dLN44hi_5


title: aCD4_TCRb_dLN44hi_4


title: aCD4_TCRb_dLN44hi_2


title: aCD4_TCRb_dLN44hi_3


title: Random DTCC-50


title: Random DTCC-49


title: BSPCR_DMS3-ZF_in_drd1_Figure2

description:
PCR amplified DNA
BS-PCR over FWA in DMS3-ZF in fwa x drd1_region1to3


title: BSPCR_DMS3-ZF_in_ago69_Figure2

description:
PCR amplified DNA
BS-PCR over FWA in DMS3-ZF in fwa x ago6/9_region1to3


title: control_TCRb_Blood_5

value: lineage-negative (CD11b, CD19, NK1.1 and Ter119) and CD4- CD8+ T cells in PBL

value: peripheral blood


title: Random DTCC-51


title: control_TCRb_dLN44hi_3


title: BSPCR_DMS3-ZF_in_rdr126_Figure2

description:
PCR amplified DNA
BS-PCR over FWA in DMS3-ZF in fwa x rdr1/2/6_region1to3


title: control_TCRb_Blood_4


title: control_TCRb_Blood_3


title: BSPCR_DMS3-ZF_in_nrpe1_Figure2

description:
PCR amplified DNA
BS-PCR over FWA in DMS3-ZF in fwa x nrpe1_region1to3


title: Random DTCC-48


title: control_TCRb_dLN44hi_1


title: Random DTCC-46


title: aCD4_TCRb_dLN44hi_1


title: control_TCRb_Blood_1


title: BSPCR_MORC-ZF_in_morc6_Figure3

description:
PCR amplified DNA
BS-PCR over FWA in MORC-ZF in fwa x morc6_region1to3


title: BSPCR_DMS3-ZF_in_rdr16_Figure2

description:
PCR amplified DNA
BS-PCR over FWA in DMS3-ZF in fwa x rdr1/6_region1to3


title: aCD4_TCRb_Blood_5


title: BSPCR_DMS3-ZF_in_ago469_Figure2

description:
PCR amplified DNA
BS-PCR over FWA in DMS3-ZF in fwa x ago4/6/9_region1to3


title: aCD4_TCRb_Blood_3


title: K562_HS_MAPK14_ChIP_Rep2

description: ChIP-seq

data_processing:
ChIP-seq reads were aligned to the human genome build hg38 using Bowtie2. Duplicate and discordant reads were removed. Peak calling was done with MACS2 using "--keep-dup all", "--nomodel", "--extsize" and "--broad". Gene annotations and transcript start site (TSS) information for human genes were from taken from Gencode annotation release 26.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

growth_protocol: K562 cells were cultured in IMDM supplemented with 10% FBS.

tag: chip antibody

tag: condition

value: Heat-Shock


title: control_TCRa_Tumor_5


title: BSPCR_fwa_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in fwa_region1to3

value: fwa


title: K562_HS_MAPK14_ChIP_Rep1

description: ChIP-seq


title: BSPCR_NRPD1-ZF_in_ago469_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa x ago4/6/9_region1to3


title: Random DTCC-44


title: control_TCRa_Tumor_4


title: control_TCRa_Tumor_3


title: K562_NHS_MAPK14_ChIP_Rep1

description: ChIP-seq

value: Non Heat-Shock


title: Random DTCC-47


title: K562_NHS_MAPK14_ChIP_Rep2

description: ChIP-seq


title: BSPCR_NRPD1-ZF_in_nrpe1_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa x nrpe1_region1to3


title: BSPCR_NRPD1-ZF_in_drm12_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa x drm1/2_region1to3


title: K562_NHS_RPB1_ChIP_Rep1

value: RNA PolII (RPB1) Cell Signaling 14958


title: Random DTCC-40


title: K562_NHS_RPB1_ChIP_Rep2


title: Random DTCC-39


title: BSPCR_NRPD1-ZF_in_rdr2_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa x rdr2_region1to3


title: Random DTCC-43


title: aCD4_TCRb_Blood_4


title: Random DTCC-41


title: BSPCR_Col0_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in Col-0_region1to3


title: aCD4_TCRa_Tumor_5


title: control_TCRa_Tumor_1


title: K562_NHS_NELFE_ChIP_Rep2

value: NELFE Sigma A81919


title: aCD4_TCRa_Tumor_4


title: Random DTCC-45


title: BSPCR_NRPD1-ZF_in_ago69_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa x ago6/9_region1to3

value: leaf


title: at-endosperm-RNAseq_replicate3_Landsberg_wt_x_Columbia_wt

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description:
Arabidopsis thaliana F1-endosperm of Landsberg-0 (female) crossed with Columbia-0 (male)
ler_x_col_rep3

data_processing:
Reads were trimmed by removing the 15 bp from the 5’ end and mapped in a single-end mode to the Arabidopsis (TAIR10) genome previously masked for rRNA genes and for the SNP positions between the TAIR10(Col) and the Landsberg (Ler) genome, using using TopHat v2.1.(Trapnell et al, 2009)  (parameters adjusted as -g 1 -a 10 -i 40 -I 5000 -F 0 -r 130).
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: expression levels (RPKM) are shown for genes  in TAIR10 for each condition and replicate.

source_name: AT F1-Endosperm Landsberg x Columbia

growth_protocol: All seeds were surface sterilized (70%, 30% ethanol 10min), stratified for 2 days at 4°C and germinated on half-strength Murashige and Skoog medium (1% sucrose) in long-day conditions (16 h light/8 h darkness; 21°C). Plants were transferred to soil after 10 to 12 days and grown under long day conditions.

extract_protocol:
For RNA sequencing, endosperm nuclei from seeds derived from indicated crosses were isolated using the INTACT protocol using replicates as indicated. RNA was extracted following a mirVana kit (Ambion). mRNA extraction was performed using NEBNext Poly(A) mRNA Magnetic Isolation kit.
Samples were sequenced at the National Genomic Infrastructure (NGI) from SciLife Laboratory (Uppsala, Sweden) on an Illumina HiSeq2500 in paired-end 125bp read length.

treatment_protocol: Material was generated by manually crossing of pistillata (Ler) mutants with pollen of INT line (Col) and the INT line in dde2 background pollinated with Ler.

value: endosperm

value: Ler x Col


title: at-endosperm-RNAseq_replicate2_Landsberg_wt_x_Columbia_wt

description:
Arabidopsis thaliana F1-endosperm of Landsberg-0 (female) crossed with Columbia-0 (male)
ler_x_col_rep2


title: Random DTCC-38

value: DTCC-R

value: Epithelial ovarian cancer ascites


title: K562_NHS_NELFA_ChIP_Rep2

value: NELFA Santa Cruz sc-23599


title: K562_NHS_Input


title: Random DTCC-37


title: Random DTCC-36


title: aCD4_TCRa_Tumor_3

value: Intravenous staining-negative, lineage-negative (CD11b, CD19, NK1.1 and Ter119) and CD4- CD8+ T cells in dLN

value: subcutaneous tumor


title: aCD4_TCRa_Tumor_2


title: K562_NELFA_HS_ChIP_Rep1


title: at-endosperm-RNAseq_replicate1_Landsberg_wt_x_Columbia_wt

description:
Arabidopsis thaliana F1-endosperm of Landsberg-0 (female) crossed with Columbia-0 (male)
ler_x_col_rep1


title: K562_HS_RPB1_ChIP_Rep2


title: Random DTCC-35


title: control_TCRa_dLN44hi_5


title: at-endosperm-RNAseq_replicate2_Columbia_wt_x_Landsberg_wt

description:
Arabidopsis thaliana F1-endosperm of Columbia-0 (female) crossed with Landsberg-0 (male)
col_x_ler_rep3

source_name: AT F1-Endosperm Columbia x Landsberg

value: Col x Ler


title: aCD4_TCRa_Tumor_1


title: Random DTCC-42


title: at-endosperm-RNAseq_replicate1_Columbia_wt_x_Landsberg_wt

description:
Arabidopsis thaliana F1-endosperm of Columbia-0 (female) crossed with Landsberg-0 (male)
col_x_ler_rep2


title: Random DTCC-34


title: control_TCRa_dLN44hi_4

value: tumor draining lymph node


title: K562_HS_NELFE_ChIP_Rep2


title: K562_HS_RPB1_ChIP_Rep1


title: Transplant BcorWT RNA-seq (2)

city: New York

first: Madison

last: Kelly

state: NY

address: 413 E69th Street

institute: Weill Cornell Medicine

data_processing:
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the mouse reference genome (GRCm38/mm10)
Read counting was performed with featureCounts from the subread package
Genes with read counts under 10 were filtered before the Voom-LIMMA workflow was used to normalise data and compute statistical significance of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: count file

source_name: Myeloid Progenitor Cells

extract_protocol:
Donor-derived myeloid progenitor cells (CD45.2+Lin-cKIT+Sca-1- )were isolated from the BM of experimental mice by FACS and total RNA was extracted using the Direct-zol™  RNA  kit (Zymo Research) as per the manufacturer's instructions.
cDNA libraries were prepared using the QuantSeq 3' mRNA seq kit, Lexogen.

value: Bcorfl/y

value: Bone Marrow

value: Myeloid Progenitor Cells


title: Random DTCC-33


title: control_TCRa_dLN44hi_3


title: Random DTCC-32


title: control_TCRa_dLN44hi_2


title: control_TCRa_dLN44hi_1


title: Transplant BcorWT RNA-seq (1)


title: Random DTCC-31


title: aCD4_TCRa_dLN44hi_5


title: Transplant BcorΔE9-10 RNA-seq (1)

value: scl-Cre-ERT +; Bcorfl/y


title: HEK_Vehicle_NHS_RPB1_ChIP_Rep1

value: Vehicle

value: Non Heat-Shock


title: aCD4_TCRa_dLN44hi_4


title: HEK_Vehicle_HS_RPB1_ChIP_Rep1

value: RNA PolII (RPB1) Cell Signaling 14958

value: Heat-Shock


title: Random DTCC-29


title: Transplant BcorΔE9-10 RNA-seq (2)


title: Random DTCC-30


title: HEK_Ub-E1_NHS_RPB1_ChIP_Rep1

value: NSC624206 (Ub-E1 inhibitor)


title: Random DTCC-28


title: CRISPRscreenT24

data_processing:
The sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
The resulting reads were aligned and statistical significance calculated with Mageck (v0.5.7)
Supplementary_files_format_and_content: normalized count file representing number of reads per guide scored in T0, T24 and T42 samples

source_name: BcorΔE9-10KrasG12D cell line

growth_protocol: Cas9+ BcorΔE9-10KrasG12D  tumor cells were cultured in Anne Kelso media supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, 20% foetal calf serum, 0.1mM L-asparagine, 2 ng/mL IL-3, 2 ng/mL IL-6, 10 ng/mL SCF at 37°C and 10% CO2.

extract_protocol:
Genomic DNA was extracted from cells using DNeasy Blood & Tissue Kit (Qiagen)
Sequencing libraries were prepared by nested PCR method to amplify integrated CRISPR guides.

value: Cas9+ cell line derived from Bcor{delta}E9-10KrasG12D mice

tag: timepoint

value: Day 24


title: aCD4_TCRa_dLN44hi_3


title: KrasG12D RNA-seq (3)

data_processing:
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the mouse reference genome (GRCm38/mm10)
Read counting was performed with featureCounts from the subread package(v1.5.0-p3).
Genes with read counts under 10 were filtered before the Voom-LIMMA workflow was used to normalise data and compute statistical significance of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: count file generated by featureCounts

extract_protocol:
Donor-derived myeloid progenitor cells were isolated from the BM of experimental mice by fluorescence activated cell sorting and total RNA was extracted using the Direct-zol™  RNA  kit (Zymo Research) as per the manufacturer's instructions.
cDNA libraries were prepared using the QuantSeq 3' mRNA seq kit, Lexogen.

value: scl-Cre-ERT +; BcorWT/y;KrasG12D/WT


title: HEK_Ub-E1_HS_RPB1_ChIP_Rep1


title: CRISPRscreenT0

value: Day 0


title: aCD4_TCRa_dLN44hi_1

value: Intravenous staining-negative, lineage-negative (CD11b, CD19, NK1.1 and Ter119) and CD4- CD8+ T cells in dLN


title: aCD4_TCRa_dLN44hi_2


title: Random DTCC-26

value: DTCC-R

value: Epithelial ovarian cancer ascites


title: Random DTCC-25


title: K562_HS_NELFA_ChIP_Rep2

value: NELFA Santa Cruz sc-23599


title: control_TCRa_dLN_4

value: tumor draining lymph node


title: K562_HS_Input


title: HEK_siNELFE_NHS_RPB1_ChIP_Rep1

value: siRNA NELFE


title: HEK_siNELFE_HS_RPB1_ChIP_Rep1


title: Random DTCC-24


title: control_TCRa_dLN_3


title: HEK_Scramble_NHS_RPB1_ChIP_Rep3

value: siRNA Scramble


title: control_TCRa_dLN_2


title: BcorΔE9-10KrasG12D RNA-seq (2)

value: scl-Cre-ERT +; Bcorfl/y;KrasG12D/WT

value: Bone Marrow

value: Myeloid Progenitor Cells


title: Random DTCC-27


title: Random DTCC-23


title: control_TCRa_dLN_1


title: KrasG12D RNA-seq (1)


title: HEK_Scramble_HS_RPB1_ChIP_Rep3

value: RNA PolII (RPB1) Cell Signaling 14958


title: KrasG12D RNA-seq (2)


title: control_TCRa_Tumor_2

value: subcutaneous tumor


title: aCD4_TCRa_dLN_5


title: BcorΔE9-10KrasG12D ChIP-seq Input

description: Input

data_processing:
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The Chip sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using bowtie2(v2.3.3) to the mouse reference genome (GRCm38/mm10)
Read counting over genomic regions, filtering, normalisation and computation of statistical significance  was performed with R package Csaw (v1.10.0). TDF files were generated with IGVTools (v2.3.95)
Genome_build: mm10
Supplementary_files_format_and_content: Browser viewable TDF files

extract_protocol:
Donor-derived myeloid progenitor cells were isolated from the BM of experimental mice by FACS. Nuclei were isolated from cross-linked cells and sonicated to shear chromatin, then histone-DNA complexes were immunoprecipitated using relevant antibodies.
DNA libraries were prepared using the KAPA Hyper Prep Kit for Illuminaplatforms (Kapa Biosystems) and the SeqCap Adapter Kit (Roche) following vendor’s instructions.


title: aCD4_TCRa_dLN_4


title: Random DTCC-21


title: HEK_CHX_NHS_RPB1_ChIP_Rep1

value: Cycloheximide

value: Non Heat-Shock


title: KrasG12D ubChIP-seq (3)

value: H2AK119ub (Cell Signalling Technology, 8240S, lot 2)


title: KrasG12D ubChIP-seq (2)

value: scl-Cre-ERT +; BcorWT/y;KrasG12D/WT


title: aCD4_TCRa_dLN_3


title: HEK_CHX_HS_RPB1_ChIP_Rep1

value: Heat-Shock


title: BcorΔE9-10KrasG12D RNA-seq (3)


title: Random DTCC-18


title: KrasG12D ubChIP-seq (1)


title: HEK_Scramble_NHS_RPB1_ChIP_Rep1


title: aCD4_TCRa_dLN_2

value: Intravenous staining-negative, lineage-negative (CD11b, CD19, NK1.1 and Ter119) and CD4- CD8+ T cells in dLN


title: Random DTCC-22

value: DTCC-R


title: BcorΔE9-10KrasG12D ubChIP-seq (3)


title: HEK_HS_Proseq_Rep4


title: control_TCRa_Blood_5

value: lineage-negative (CD11b, CD19, NK1.1 and Ter119) and CD4- CD8+ T cells in PBL

value: peripheral blood


title: Random DTCC-17

value: Epithelial ovarian cancer ascites


title: Random DTCC-15


title: aCD4_TCRa_dLN_1

value: tumor draining lymph node


title: Random DTCC-20


title: control_TCRa_Blood_4


title: Random DTCC-19


title: 20w BcorWT ATAC-seq

data_processing:
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Bowtie2 to the mouse reference genome (GRCm38/mm10)
Bigwigs were generated and data was visualised with deeptools(v2.5.3)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
Lin-cKIT+Sca-1- myeloid progenitor cells were isolated  from the BM of experimental mice by fluorescence activated cell sorting and ATAC-seq was performed as previously published (Buenrostro, 2015)
Chromatin was tagmented, then adapters ligated and library amplified with KAPA polymerase (KAPA biosystems)

treatment_protocol: Mice aged 3-6 months were administered 1mg tamoxifen via intraperitoneal injection for 5 consecutive days

value: scl-Cre-ERT +; BcorWT/y

value: Tamoxifen IP


title: control_TCRa_Blood_3


title: Random DTCC-16


title: 20w BcorWT RNA-seq (2)

data_processing:
bcl2fastq (v2.17.1.14) was used for de-multiplexing. Sample QC was  performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the mouse reference genome (GRCm38/mm10)
Read counting was performed with featureCounts from the subread package (v1.5.0-p3)
Genes with read counts under 10 were filtered before the Voom-LIMMA workflow was used to normalise data and compute statistical significance of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: count file generated by featureCounts

extract_protocol:
Lin-cKIT+Sca-1- myeloid progenitor cells were isolated  from the BM of experimental mice by fluorescence activated cell sorting and total RNA was extracted using the Direct-zol™  RNA  kit (Zymo Research) as per the manufacturer's instructions.
cDNA libraries were prepared using the QuantSeq 3' mRNA seq kit (Lexogen).

value: scl-Cre-ERT +; Bcorwt/y

value: Bone Marrow


title: Random DTCC-14


title: control_TCRa_Blood_2


title: 20w BcorWT RNA-seq (1)

value: Myeloid Progenitor Cells


title: Random DTCC-12


title: control_TCRa_Blood_1


title: BcorΔE9-10KrasG12D ubChIP-seq (2)

value: scl-Cre-ERT +; Bcorfl/y;KrasG12D/WT


title: Random DTCC-11


title: 20w BcorΔE9-10 RNA-seq (3)

value: scl-Cre-ERT +; Bcorfl/y


title: HEK_Scramble_HS_RPB1_ChIP_Rep1

value: RNA PolII (RPB1) Cell Signaling 14958

value: siRNA Scramble


title: BcorΔE9-10KrasG12D ubChIP-seq (1)

value: H2AK119ub (Cell Signalling Technology, 8240S, lot 2)


title: 20w BcorΔE9-10 RNA-seq (2)


title: Random DTCC-13


title: aCD4_TCRa_Blood_4


title: A549-GFP-1

city: Yilan

first: Chen-Hung

last: Ting

state: Taiwan

address: 23-10 Dawen Rd., Jiaoxi

department: Marine research station, Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

description:
23560_253949442634_1_3
Gene expression at 40hr post-GFP transfection in A549 cells

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human V2 GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: Human A549 cell, 14ug GFP vector, 40h, exp3

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: A549 cells were maintained in F-12K medium supplemented with  10% FBS, and antibiotics (100U/mL penicillin G and 100 g/mL streptomycin) at 37°C with 0% CO2 in a humidified incubator.

extract_protocol: RNA was extracted by using the WelPrep cell/tissue RNA lit (WelGene biotech) following the manufacturer's standard protocol.  Total RNA was quantified by a specterophotometer (NanoDrop ND-1000, Thermo Scientific) and  quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies). The RIN values for all RNA samples were between 9.0-10.0.

treatment_protocol: The cells were plated 1 day before transfect with FOSB or GFP vector (14 ug) by using Lipofectamine3000 reagent and harvested after 40hours.

value: lung

tag: gender

value: male


title: aCD4_TCRa_Blood_5


title: 20w BcorΔE9-10 RNA-seq (1)


title: aCD4_TCRa_Blood_3


title: Random DTCC-10

value: DTCC-R


title: WTbl6 ChIP-seq input

description: WTInput

data_processing:
Sample QC was  performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The ChIP-sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using bowtie2 to the mouse reference genome (GRCm38/mm10)
Peak calling was performed with MACS (v2.1.1) and BigWigs were created with deeptools(v2.5.3)
Normalisation,  enrichment over genomic regions,  and computation of statistical significance were performed with R package Csaw (v1.10.0).
Genome_build: mm10
Supplementary_files_format_and_content: Peaks files
Supplementary_files_format_and_content: bigWig Files

extract_protocol:
Lin-cKIT+Sca-1- myeloid progenitor cells were isolated  from the BM of experimental mice by FACS. Nuclei were isolated from cross-linked cells and sonicated to shear chromatin, then histone-DNA complexes were immunoprecipitated using relevant antibodies.
DNA libraries were prepared using the KAPA Hyper Prep Kit for Illuminaplatforms (Kapa Biosystems) and the SeqCap Adapter Kit (Roche) following vendor’s instructions.

treatment_protocol: Mice aged 3-6 months were administered 1mg tamoxifen for 5 consecutive days

value: WT

value: untreated


title: mhcd4_3: 3'SAGE-seq

city: Boston

first: Alex Chang-Yu

last: Chen

state: MA

address: 149 13th Street, 7th floor, Room 7103

department: Krantz Family Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by using Trimommatic-v0.36 and PRINSEQ-0.20.4. Filtered reads were mapped to Refseq mm10 by using Bowtie2-2.2.5. Reads that were not mapped to NlaIII sites were removed, and quantified tag numbers of each gene as the expression level of each gene.
Total tag number was adjusted to 1 million tags, and between-sample normalization was performed by using R-3.1.1 and TCC package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized tag-count values for each sample

source_name: CD8 T cells

extract_protocol:
Transferred lung fibroblasts were isolated from bleomycin-treated lungs of C57BL/6 mice at day 3 post-transfer. Lungs were cut into small pieces with a razor blade and digested enzymatically using 0.2% collagenase (Wako, Osaka, Japan), 0.96 mg/mL Dispase II (Roche, Basel, Switzerland), and 20 kU/mL DNase I (Sigma-Aldrich, St Louis, MO) for 60 min at 37°C. Erythrocytes were removed by 70% Percoll (GE Healthcare, Buckinghamshire, UK) density separation. The single-cell suspensions were then depleted of lineage+ (CD31+, CD45+, EpCAM+, CD146+ and Ter119+) cells by negative selection with an AutoMACS cell separator (Miltenyi Biotech, Bergisch Gladbach, Germany). Lineage− Col1a2GFP+ hLNGFR+ fibroblasts were further purified by cell sorting using a FACS Aria II (BD).
PolyA RNAs were isolated and amplified from CD8+ T cells. 3'SAGE-seq libraries were constructed according to the protocol described in (Matsumura H, Methods Mol Biol, 2012) with some modifications. Sequencing was performed by using Ion Hi-Q Chef Kit, Ion PI v3 Chip Kit and Ion Proton Sequencer (Thermo Fisher Scientific) according to the manufacture’s instructions except the input library concentration (100 pM) and cycle number (200).

treatment_protocol: Colon26 (2 x 10^5 cells / mouse) were subcutaneously inoculated into the right flank of BALB/c mice. HMGN1 protein (at a dose of 0.16 microgram per mouse per injection, unless otherwise noted) was administered intraperitoneally on days 9, 14, 17, and 20 after tumor inoculation. Anti-CD4 depleting antibody (clone GK1.5; BioXcell, USA) was injected intraperitoneally on days 5 and 9 after tumor inoculation (at a dose of 200 microgram per mouse per injection). On day 16, CD8+ T cells were purified from single cell suspensio of each implanted mouse tumor and used as transcriptome analysis sample.

value: lineage (CD45, CD11b, B220, CD49b, Ter119, and CD4) negative, CD8 positive T cell

value: BALB/c

value: tumor

value: wild type


title: Random DTCC-8

data_processing:
Raw Crt, “relative threshold”, values were generated by OpenArray system, the undetected Crt values were replaced by 40 (Matrix non-normalized); the Crt values were normalized to 18S using the -△Crt method (Matrix normalized); fold change was calculated by 2^-△Crt.
Fold Change worksheet reports relative single cell gene expression level.

extract_protocol: The single cells were lysed directly using Single cell-to-CT qRT-PCR Kit (Ambion).

value: Epithelial ovarian cancer ascites


title: A549-FOSB-GFP-1

description:
23556_253949442634_1_1
Gene expression at 40hr post-FOSB transfection in A549 cells

source_name: Human A549 cell, 14ug FOSB-GFP vector, 40h, exp1


title: WTbl6 LSK H2AK119ub ChIP-seq

source_name: Haematopoietic Stem Cells

value: Bone Marrow

value: Haematopoietic Stem Cells


title: Random DTCC-9


title: Random DTCC-7


title: A549-FOSB-GFP-2

description:
23558_253949442634_1_2
Gene expression at 40hr post-FOSB transfection in A549 cells

source_name: Human A549 cell, 14ug FOSB-GFP vector, 40h, exp2


title: mhcd4_2: 3'SAGE-seq


title: Random DTCC-6


title: cd4_3: 3'SAGE-seq


title: Random DTCC-5


title: cd4_2: 3'SAGE-seq


title: HEK_NHS_Proseq_Rep4

data_processing:
Library strategy: Pro-Seq
ChIP-seq reads were aligned to the human genome build hg38 using Bowtie2. Duplicate and discordant reads were removed. Peak calling was done with MACS2 using "--keep-dup all", "--nomodel", "--extsize" and "--broad". Gene annotations and transcript start site (TSS) information for human genes were from taken from Gencode annotation release 26.
Cutadapt was used to cut adapter from sequenced reads. Filtered reads were first mapped to a single copy of ribosomal DNA to remove the contribution of nascent RNAs from ribosomal genes. The remaining reads were mapped to human genome build hg38 using Bowtie2 using default parameters. PRO-seq libraries were normalized using 3’-end of long genes as described by Mahat et al., 2016
DESeq2 was used to identify differentially express.ed genes upon heat shock. Differential gene expression was done using DESeq2
Genome_build: hg38

extract_protocol: 10X106 HEK293 cells were used for each PROseq experiment. Cells were harvested and permeabilized. A 2-biotin label run on reaction was done to label nascently transcribed RNA. 2X nuclear run-on mix was mixed with biotin labeled CTP and UTP. Nuclear run-on reaction was carried out for 3 minutes at 37ºC. Reaction was stopped by adding Trizol LS (CAT no) followed by vigorous vortexing. RNA was isolated by standard procedure. Nascently transcribed RNA was fragmented by base hydrolysis (NaoH) resulting in 100bp long RNA suitable for sequencing. Streptavidin coated magnetic beads were used to enrich for biotin labeled RNA using affinity purification. RNA was mixed with pre-washed streptavidin beads and incubated at room temperature. Beads were washed and resuspended in Trizol and RNA was isolated. A 3’ RNA adaptor (VRA3-5uM) was ligated at the 3’-end of biotin labeled nascent RNA using ligation mix (T4 RNA ligase buffer, 1mM ATP, 10% PEG, RNase Inhibitor, T4 RNA ligase I). A second biotin-RNA enrichment was done to enrich for labeled nascent RNA and remove unligated adaptors. The 5’ OH generated by base hydrolysis was then converted to 5’ phosphate by treatment with T4 polynucleotide kinase. A 5’ RNA adaptor (VRA5) was ligated at the 5’ end of RNA using the ligation mix described previously. A 3rd round of enrichment was done to enrich for labeled RNA and remove any unligated adaptors. Nascent RNA is then reverse transcribed using RP1 and RTP reverse transcription primers (2.5μM each). A test PCR amplification was then done to determine number of PCR cycles for amplification. A PCR cycle that gave sufficient amount of product, no over amplification and 50-75 % of unused primers was considered optimal and used for final amplification. Full scale PCR amplification was done using the following PCR mix (1x HF buffer, 1M Betaine, 250μM dNTP mix, 250 nM RP1 primer, 250 nM RP1-n primer, 0.04 units/μl Phusion DNA polymerase). PCR amplified DNA was then size selected (150-350 bp) by PAGE purification with some modifications from the original protocol (Mahat 2016 Nat Prot). DNA was then extracted using phenol-chloroform extraction. DNA pellet was re-dissolved in nuclease free water and DNA library size distribution was monitored by capillary electrophoresis.

value: Non Heat-Shock


title: 20w BcorWT KL Chip-seq Input

value: scl-Cre-ERT +; Bcorfl/y

value: Myeloid Progenitor Cells

value: Tamoxifen IP


title: Random DTCC-3


title: 20w BcorWT H3K4me3 Chip-seq (2)

value: scl-Cre-ERT +; Bcorwt/y


title: 20w BcorWT H3K4me3 Chip-seq (1)


title: 20w BcorΔE9-10 H3K4me3 Chip-seq (3)


title: A549-GFP-2

description:
23562_253949442634_1_4
Gene expression at 40hr post-GFP transfection in A549 cells

source_name: Human A549 cell, 14ug GFP vector, 40h, exp4

value: lung


title: cd4_1: 3'SAGE-seq


title: ID5_Saliva

type: genomic

city: Penrith

first: Christine

last: Chiu

state: NSW

address: Locked Bag 1797

country: Australia

institute: Western Sydney University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Illumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization). Data was then pre-processed in the R package wateRmelon using the dasen function. processed data: dasen normalized beta

label: Cy3, Cy5

source_name: Saliva

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using a DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.

tag: patient id

value: Patient 5

value: Female

tag: age


title: Random DTCC-2

value: DTCC-R


title: ID4_Saliva

value: Patient 4


title: Random DTCC-1


title: Random DTCC-4


title: SW480-NC-RNA

city: Guangzhou

first: Fengwei

last: Wang

address: No.651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

description: lncRNA expression data from SW480-NC-cell

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (8x60K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505B

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: colorectal carcinoma cell line

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: colorectal cell lines  DLD1 and SW480 were cultured in RPMI 1640 medium with 10% FBS (Invitrogen, Carlsbad, CA, USA)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Colorectal cancer cell line SW480 and DLD-1 cells were transfected with wild-type APC full-length coding sequence or control vector

tag: transfection

value: control vector


title: ID2_Saliva

value: Patient 2


title: 20w BcorΔE9-10 H3K4me3 Chip-seq (2)

tag: treatment


title: SW480-APC-RNA

description: lncRNA expression data from SW480-APC-cell

value: wild-type APC full-length coding sequence


title: DSC-A45-30

treatment_protocol: The single cells were picked up manually under a microscope using Kuiqpick through a glass capillary from purified ascites.

value: DSC-L


title: 20w BcorΔE9-10 H3K4me3 Chip-seq (1)


title: SW480-NC-cell


title: DSC-A45-28

value: Epithelial ovarian cancer ascites


title: ID1_Saliva

value: Patient 1


title: 20w BcorWT H3K27me3 Chip-seq (1)

value: Bone Marrow


title: 20w BcorΔE9-10 H3K27me3 Chip-seq (3)


title: 20w BcorWT H3K27me3 Chip-seq (2)


title: control_TCRb_Blood_2

value: lineage-negative (CD11b, CD19, NK1.1 and Ter119) and CD4- CD8+ T cells in PBL

value: peripheral blood


title: DSC-A45-29


title: DLD1-NC-RNA

description: lncRNA expression data from DLD1-NC-cell


title: ID10_Saliva

value: Patient 10


title: SW480-APC-cell


title: DLD1-NC-cell


title: DSC-A45-25


title: DSC-A45-26


title: DLD1-APC-RNA

description: lncRNA expression data from DLD1-APC-cell


title: ID9_Saliva

value: Patient 9


title: 20w BcorΔE9-10 H3K27me3 Chip-seq (1)

value: scl-Cre-ERT +; Bcorfl/y

value: Myeloid Progenitor Cells

value: Tamoxifen IP


title: 20w BcorΔE9-10 H3K27me3 Chip-seq (2)


title: DSC-A45-24


title: ID7_Saliva

value: Patient 7

value: Female


title: ID3_Saliva

value: Patient 3


title: DSC-A45-27


title: ID8_Saliva

value: Patient 8


title: ID10_Intestinal

source_name: Intestinal Mucosa


title: WTbl6 LK H2AK119ub ChIP-seq

value: WT

value: untreated

value: H2AK119ub (Cell Signalling Technology, 8240S, lot 2)


title: DSC-A45-23

value: DSC-L

value: Epithelial ovarian cancer ascites


title: 20w BcorWT H2AK119ub Chip-seq (2)

value: scl-Cre-ERT +; Bcorwt/y

value: Bone Marrow


title: 20w BcorΔE9-10 H2AK119ub Chip-seq (3)


title: 20w BcorWT H2AK119ub Chip-seq (1)


title: DSC-A45-22


title: Wild Type rep2

city: Osaka

first: Shinya

last: Tanaka

state: Osaka

address: 2nd Fl. IFReC Research Building, Osaka University 3-1 Yamadaoka, Suita

department: Immunology Frontier Research Center

institute: Osaka University

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: BeadChips were scanned on an Illumina BeadArray Reader

data_processing: Signal intensities were quantile normalized using the Bioconductor package “lumi”

label: biotin

source_name: Murine marrow

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

extract_protocol: RNA was extracted with QIAGEN RNA/DNA All prep kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: wild type

value: erythroblast


title: ID8_Intestinal


title: ID5_Intestinal

value: Patient 5


title: DSC-A45-20

value: DSC-M


title: ID9_Intestinal

value: Patient 9


title: 20w BcorΔE9-10 H2AK119ub Chip-seq (2)

value: scl-Cre-ERT +; Bcorfl/y

value: Myeloid Progenitor Cells

value: Tamoxifen IP


title: DSC-A45-21


title: c920-K9me3_2

description: Aligned to EU594392.1.

data_processing:
base calling: RTA 1.18.54 (from Illumina MCS 2.6.2)
alignment: bowtie2 2.3.0 was used for alignment to 1.1mer viral genomes (with -t -no-unal -no-discordant -no-mixed -I 120 -X 200 option) and all sequences (combined hg38/HBV/phiX; only -t option)
paired read merging: custom script was used to merge paired reads in the output SAM file based on viral genome coordinates. Unsequenced insert was represented as N with low quality score.
BAM conversion: SAM file was converted to BAM, sorted, and indexed using samtools 0.1.19
BEDGRAPH conversion: BAM file was converted to BEDGRAPH using bedtools 2.18.1 (-bg -trackline options)
1mer conversion: custom script was used to wrap around reads that aligned in the overhang of the 1.1mer to the start of the sequence
scaling and wig conversion: custom script was used to convert BEDGRAPH to WIG files while simultaneously scaling it per 106 total reads in the library (hg38+HBV+phiX)
Genome_build: HBV reference genomes are indicated in the sample overview (protocl column). GRCh38.p10 was used for the human genome, NC_001422.1 for phiX
Supplementary_files_format_and_content: WIG files contain the number of HBV reads per million total reads for each position of the respective HBV reference genome. Sequences are shifted by -500 nt compared to EcoRI site.

organism:
Homo sapiens
Hepatitis B virus

source_name: liver biopsy

extract_protocol:
Cells were fixed in freshly prepared 1% formaldehyde in PBS (both ThermoFisher Scientific) for 5 min prior to quenching with 125 mM glycine in PBS. Pelleted cells were either used directly for analysis or snap-frozen and stored at -80°C until use. Next, cells were washed with cold lysis buffer [PBS with 0.1% Triton X-100, 0.1% NP-40, 1 mM dithiothreitol (DTT), 50 ng/ml trichostatin A (TSA) and 1x EDTA-free protease inhibitor (Roche, Basel, Switzerland)] and lysed in the same buffer for 10 min on ice. Nuclei were pelleted, resuspended in digestion buffer [H2O with 50 mM Tris-HCl pH 7.5, 4 mM MgCl2, 1 mM CaCl2, 10% glycerol, 50 ng/ml TSA, and 1x EDTA-free protease inhibitor (Roche)] and digested with 600 IU/ml micrococcal nuclease (MNase; ThermoFisher Scientific) for 12 min at 37°C. Digestion was stopped by addition of 10 mM EDTA. Nuclei were pelleted at 6500 x g and supernatants collected. The pellet was resuspended in digestion buffer with 10 mM EDTA and 300 mM NaCl and mildly sonicated using a W 375 sonicator (Qsonica, Newtown, CT) at 50% duty cycle and power setting 3. Nuclei were again pelleted, supernatants combined and mixed with an equal amount of sucrose buffer [H2O with 50 mM Tris-HCl pH 7.5, 50 mM NaCl, 5 mM EDTA, 0.01% NP-40, 50 ng/ml TSA, and 1x EDTA-free protease inhibitor (Roche)]. Samples were concentrated using Amicon Ultra-4 100 kDa centrifugal filter units (Millipore-Sigma; Merck KGaA, Darmstadt, Germany) and spun on a 5-30% continuous sucrose gradient in sucrose buffer for 4 h at 40,000 x g and 4°C using a SW41Ti rotor (Beckman Coulter Inc., Brea, CA). Chemicals were obtained from Millipore-Sigma unless noted otherwise. Mononucleosome containing fractions were pooled and concentrated to ~500 µl prior to addition of 100 ng/µl bovine serum albumin (ThermoFisher Scientific). Mononucleosomes were either stored at -20°C or used immediately for ChIP. Antibodies were bound to 20 µl/ChIP Dynabeads Protein G (ThermoFisher) in ChIP buffer [H2O with 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 200 µg/ml BSA] at 4°C and added to 2 µg of chromatin in ChIP buffer and allowed to bind overnight. Samples were washed six times in LiCl wash buffer [H2O with 150 mM LiCl, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, and 0.7% sodium deoxycholate] and eluted in 100 µl elution buffer [H2O with 1% SDS and 100 mM NaHCO3]. Crosslinks were reversed by digestion with Proteinase K (ThermoFisher) for 5 h at 65°C and then digested for another 30 min with DNase-free RNase A (ThermoFisher) at 37°C. DNA was purified using the QIAquick PCR purification kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
1 ng of DNA was used for sequencing library construction with the KAPA Hyper Prep Kit (Roche) according to the manufacturer’s instructions. For barcoding, 2 µl of TruSeq RNA adapters stocks were used (Illumina, Inc., San Diego, CA). Up to 6 libraries were pooled per sequencing run and 500 ng pooled library subject to HBV-specific target enrichment using the xGen Lockdown Reagents Hybridization and Wash Kit (Integrated DNA technologies, Skokie, IL) according to the manufacturer’s instructions. A custom set of xGen lockdown probes of 60 bp length tiling the entire HBV genome of genotypes A-D was used for target enrichment (Integrated DNA technologies) together with Dynabeads MyOne T-270 Streptavidin (ThermoFisher). The pull-down was amplified for 12 or 8 PCR cycles (biopsies vs. de novo infected cells/cell lines; KAPA HiFi HotStart ReadyMix, Roche) and the product cleaned up using Agencourt AMPure XP beads (Beckman Coulter, Inc.). The product was used to dilute the original library to 20 nM. Sequencing was performed using an Illumina MiSeq sequencer with a MiSeq v3 reagent kit for 2x76 bp paired-end reads (Illumina, Inc.).

value: liver

tag: hbv genotype

value: A

tag: disease stage

value: HBeAg- infection

tag: ChIP


title: ID6_Intestinal

value: Patient 6

value: Female


title: c920-K9me3_1

description: Aligned to EU594392.1.


title: Flvcr Deleted rep1

description: replicate 1

tag: strain

value: Flvcr deleted


title: ID7_Intestinal

value: Patient 7


title: c809-K9me3_2

description: Aligned to EU787447.1.

value: D

value: Under therapy (Tenofovir), HBeAg+


title: Wild Type rep1

description: replicate 1

tag: genotype

value: wild type


title: Flvcr Deleted rep2

description: replicate 2

value: erythroblast


title: 20w BcorΔE9-10 H2AK119ub Chip-seq (1)

value: Bone Marrow

value: H2AK119ub (Cell Signalling Technology, 8240S, lot 2)


title: 20w BcorΔE9-10 H3K27Ac Chip-seq (3)


title: DLD1-APC-cell

value: wild-type APC full-length coding sequence

tag: cell line


title: 20w BcorΔE9-10 H3K27Ac Chip-seq (2)

value: scl-Cre-ERT +; Bcorfl/y

tag: cell type


title: DSC-A45-19

tag: subgroup

value: DSC-M

value: Epithelial ovarian cancer ascites


title: c809-K9me3_1

description: Aligned to EU787447.1.

tag: tissue

value: liver


title: Wild Type rep3

description: replicate 3


title: c770-H3_2

description: Aligned to EU787447.1.

value: HBeAg+ infection


title: 20w BcorΔE9-10 H3K27Ac Chip-seq (1)

value: Myeloid Progenitor Cells

value: Tamoxifen IP

tag: chip antibody


title: DSC-A45-17


title: ID3_Intestinal

value: Patient 3

value: Female


title: c770-H3_1

description: Aligned to EU787447.1.


title: DSC-A45-16


title: mRAG-WT1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
mRAG-WT1_S1
Wild type RAG deficient mice

data_processing:
Reads quality control using fastQC and Fastq-scren.
Mapping with STAR_2.4.0a versus mm10 following ENCODE RNA-seq options.
Features quantification using featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -C" options using Ensembl GRCh38.76 release.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix text file with raw read count, rows are genes, columns are samples

source_name: mRAG-WT_Pro-B cells

extract_protocol:
RNA was extracted using miRNeasy kit from QIAGEN, according to the manufacturer instructions
500ng of total RNA were depleted from ribosomal RNA, ligated, reverse transcribed and amplified (12 cycles) with the reagents from the Truseq Stranded Total RNA kit (illumina). Libraries were quantified with the Bioanalyzer 2100 Kit (Agilent) and Qubit (Thermo Fisher) . 4nM of libraries were then diluted and denatured according to the Illumina recommendations. Paired-end 2x150bp reads were sequenced on an Illumina Nextseq 500 sequencer.

tag: genotype/variation

value: deficient for RAG

tag: origin

value: Wild type RAG deficient mice

value: Femoral pro-B cells


title: mRAG-WT2

description:
mRAG-WT2_S2
Wild type RAG deficient mice


title: ID6_Saliva

value: Patient 6

tag: gender


title: ID1_Intestinal

tag: patient id

value: Patient 1


title: c687-K9me3_2

description: Aligned to EU787447.1.

value: D

value: HBeAg- hepatitis


title: ID4_Intestinal

value: Patient 4

tag: age


title: Skmel173 cell line

city: heidelberg

first: Lionel

last: Larribere

address: im neuenheimer Feld

institute: DKFZ

description:
Skmel173
replicate 2
9985134004_J

scan_protocol: Standard Illumina scanning protocol

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

source_name: melanoma patient

extract_protocol: mRNA was isolated with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Clean-up and DNase I treatment was included. Quality control was performed with Agilent Bioanalyser.

value: Skmel173 melanoma cell line

tag: cell source

value: ATCC


title: DSC-A45-15

value: DSC-M

value: Epithelial ovarian cancer ascites


title: c687-K9me3_1

description: Aligned to EU787447.1.

value: liver


title: mRAG-KOKI2

description:
mRAG-KOKI2_S8
Deletion of the 3'RR enhancer (KO) and the RAG protein. Knock in (KI) of a mini 3'RR enhancer devoid of its palindromic structure at the 3'RR locus

source_name: mRAG-KOKI_Pro-B cells

value: deficient for the 3'RR enhancer of the IgH locus and with a mini-3'RR

value: LE NOIR S et al. Functional anatomy of the immunoglobulin heavy chain 3’ super-enhancer needs not only core enhancer elements but also their unique DNA context. Nucleic Acids Res 2017, 45, 5829-5837.


title: HT144 cell line

description:
HT144
replicate 1
8136640001_I

value: HT144 melanoma cell line


title: c537-H3_2

description: Aligned to EU410079.1.

value: C

value: HBeAg+ infection


title: DSC-A45-14


title: DSC-A45-13


title: DSC-A45-18


title: c537-H3_1

description: Aligned to EU410079.1.


title: DSC-A45-12


title: mRAG-KO3'-RR2

description:
mRAG-KO3p-RR2_S4
Deletion of the 3'RR enhancer and the RAG protein

source_name: mRAG-KO3'-RR_Pro-B cells

value: deficient for the 3'RR enhancer of the IgH locus

value: VINCENT-FABERT C et al. Genomic deletion of the whole IgH 3’ regulatory region (hs3a, hs1,2, hs3b, hs4) dramatically affects class switch recombination and Ig secretion to all isotypes. Blood 2010, 116, 1895-1898.


title: neural crest line 2_rep2

description:
VGNC_2
replicate 2
9423641093_E

source_name: healthy donnor

value: neural crest cells (VGNC)

value: generated at DKFZ


title: ID2_Intestinal

value: Patient 2

value: Female


title: DSC-A45-11


title: neural crest line 2_rep1

description:
VGNC_1
replicate 1
9371160014_B


title: neural crest line 2_rep3

description:
VGNC_3
replicate 3
9423641093_F


title: neural crest line 1_rep3

description:
D1NC_3
replicate 3
9347704022_L

value: neural crest cells (D1NC)


title: neural crest line 1_rep2

description:
D1NC_2
replicate 2
9347704022_K


title: mRAG-KO3'-RR1

description:
mRAG-KO3p-RR1_S3
Deletion of the 3'RR enhancer and the RAG protein

value: Femoral pro-B cells


title: c317-K9me3_1

description: Aligned to EU787447.1.

value: D

value: HBeAg- hepatitis


title: c317-K9me3_2

description: Aligned to EU787447.1.


title: mRAG-Emu2

description:
mRAG-Deu2_S6
Deletion of the Emu enhancer and the RAG protein

source_name: mRAG-Emu_Pro-B cells

value: deficient for the Emu enhancer of the IgH locus

value: Marquet M et al. The Eµ enhancer region influences H chain expression and B cell fate without impacting IgVH repertoire and immune response in vivo. J Immunol 2014, 193, 1171-1183.


title: mRAG-Emu1

description:
mRAG-Deu1_S5
Deletion of the Emu enhancer and the RAG protein


title: DSC-A45-10

value: DSC-E

value: Epithelial ovarian cancer ascites


title: c162-K9me3_1

description: Aligned to EU594392.1.

value: liver

value: A


title: neural crest line 1_rep1

description:
D1NC_1
replicate 1
8986302012_J


title: C32 cell line

description:
C32
replicate 3
9985187156_D

value: C32 melanoma cell line

value: ATCC


title: c161-K9me3_2

description: Aligned to EU787447.1.

value: Under therapy (Tenofovir), HBeAg-


title: DSC-A45-8


title: DSC-A45-9


title: c161-K9me3_1

description: Aligned to EU787447.1.


title: DSC-A45-6


title: DSC-A45-5


title: PHH-H3K27me3-ChIP_2

description:
run 2
Primary human hepatocytes were purchased from ThermoFisher Scientific (Waltham, MA) and thawed and cultured per manufacturer's instructions. 5 hours after thawing, cells were infected with cell culture-derived HBV at an MOI of 1:1,000 in the presence of 4% PEG. Cells were washed 1 day post infection (dpi) with 0.05% Trypsin/EDTA (ThermoFisher). Medium was exchanged every other day. Cells were collected at 12 dpi for analysis. Aligned to V01460.1.

source_name: liver

value: primary human hepatocytes

value: rabbit monoclonal C36B11, Cell Signaling Technology 9733S


title: PHH-H3K27me3-ChIP_1

description:
run 1
Primary human hepatocytes were purchased from ThermoFisher Scientific (Waltham, MA) and thawed and cultured per manufacturer's instructions. 5 hours after thawing, cells were infected with cell culture-derived HBV at an MOI of 1:1,000 in the presence of 4% PEG. Cells were washed 1 day post infection (dpi) with 0.05% Trypsin/EDTA (ThermoFisher). Medium was exchanged every other day. Cells were collected at 12 dpi for analysis. Aligned to V01460.1.


title: c162-K9me3_2

description: Aligned to EU594392.1.


title: DSC-A45-7


title: normal human melanocytes_rep2

description:
NHM_2
replicate 2
9347704022_G

value: normal human melanocytes (NHM)

value: isolated at DKFZ


title: PHH-H3K9me3-ChIP_2

value: rabbit polyclonal, abcam ab8898


title: PHH-H3K4me3-ChIP_2

value: rabbit polyclonal, abcam ab8580


title: PHH-H3K9me3-ChIP_1

value: D


title: PHH-H3K4me3-ChIP_1


title: normal human melanocytes_rep3

description:
NHM_3
replicate 3
9347704022_H


title: PHH-input_2

value: input


title: T45

city: Milan

first: Paolo

last: Gandellini

address: Via Amadeo 42

department: Department of Applied Research and Technological Development

country: Italy

institute: Fondazione IRCCS Istituto Nazionale Tumori

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v4. Raw expression data were log2-transformed and normalized using the robust spline normalization method.

label: Biotin

source_name: DMPM frozen tumor specimen

label_protocol: Biotinylated cRNA were prepared with Illumina RNA TotalPrep amplification kit (Ambion)

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

tag: sample type

value: DMPM frozen tumor specimen


title: DSC-A23-29

value: DSC-L


title: DSC-A23-30


title: T44


title: DSC-A45-3

value: DSC-E


title: DSC-A23-28

value: Epithelial ovarian cancer ascites


title: normal human melanocytes_rep1

description:
NHM_1
replicate 1
8986302012_I


title: DSC-A45-1


title: DSC-A45-4


title: T42


title: T43


title: T39


title: T38


title: T36


title: PHH-input_1

value: liver

tag: hbv genotype


title: T37


title: T41


title: DSC-A23-27


title: DSC-A45-2


title: T40


title: c920-H3K27me3-ChIP_1

description:
run 1
Aligned to EU594392.1.

value: liver biopsy

value: A

tag: disease stage

value: HBeAg- infection


title: c920-H3K4me3-ChIP_2

description:
run 2
Aligned to EU594392.1.

tag: ChIP


title: DSC-A23-26


title: c920-H3-ChIP_2

description:
run 2
Aligned to EU594392.1.

value: rabbit monoclonal B0422, abcam ab41969


title: DSC-A23-25


title: DSC-A23-24


title: c920-H3-ChIP_1

description:
run 1
Aligned to EU594392.1.


title: c920-input_1

description:
run 1
Aligned to EU594392.1.


title: T34


title: T35


title: DSC-A23-23


title: c920-H3K4me3-ChIP_1

description:
run 1
Aligned to EU594392.1.


title: c912-H3K9me3-ChIP_2

description:
run 2
Aligned to EU410079.1.

value: C


title: DSC-A23-21


title: DSC-A23-20

value: DSC-M


title: c912-H3K9me3-ChIP_1

description:
run 1
Aligned to EU410079.1.


title: T33


title: c912-H3K4me3-ChIP_2

description:
run 2
Aligned to EU410079.1.


title: T31


title: DSC-A23-19


title: T29


title: T30


title: c912-H3K4me3-ChIP_1

description:
run 1
Aligned to EU410079.1.


title: DSC-A23-22


title: c912-H3-ChIP_2

description:
run 2
Aligned to EU410079.1.


title: c912-H3K27me3-ChIP_1

description:
run 1
Aligned to EU410079.1.

value: rabbit monoclonal C36B11, Cell Signaling Technology 9733S


title: DSC-A23-17


title: DSC-A23-18


title: DSC-A23-15


title: c912-H3-ChIP_1

description:
run 1
Aligned to EU410079.1.


title: DSC-A23-16


title: DSC-A23-14


title: T27


title: T32


title: DSC-A23-13


title: c912-input_2

description:
run 2
Aligned to EU410079.1.


title: T25


title: T28


title: c912-input_1

description:
run 1
Aligned to EU410079.1.


title: T26


title: T24


title: T23


title: T22


title: c812-H3K27me3-ChIP_1

description:
run 1
Aligned to EU594392.1.


title: c812-H3K9me3-ChIP_2

description:
run 2
Aligned to EU594392.1.


title: DSC-A23-12


title: DSC-A23-11


title: T20


title: T21


title: c812-H3K9me3-ChIP_1

description:
run 1
Aligned to EU594392.1.


title: DSC-A23-10


title: c812-H3K4me3-ChIP_1

description:
run 1
Aligned to EU594392.1.


title: DSC-A23-8


title: c812-input_2

description:
run 2
Aligned to EU594392.1.


title: DSC-A23-9


title: DSC-A23-7


title: DSC-A23-6


title: DSC-A23-5


title: T16


title: T19


title: T18


title: c809-H3K27me3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: Under therapy (Tenofovir), HBeAg+


title: c812-input_1

description:
run 1
Aligned to EU594392.1.


title: c809-H3K4me3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: T15


title: DSC-A23-4


title: c809-H3K4me3-ChIP_1

description:
run 1
Aligned to EU787447.1.


title: c812-H3K4me3-ChIP_2

description:
run 2
Aligned to EU594392.1.


title: c809-H3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: DSC-A23-3


title: mRAG-KOKI1

description:
mRAG-KOKI1_S7
Deletion of the 3'RR enhancer (KO) and the RAG protein. Knock in (KI) of a mini 3'RR enhancer devoid of its palindromic structure at the 3'RR locus

value: deficient for the 3'RR enhancer of the IgH locus and with a mini-3'RR

value: LE NOIR S et al. Functional anatomy of the immunoglobulin heavy chain 3’ super-enhancer needs not only core enhancer elements but also their unique DNA context. Nucleic Acids Res 2017, 45, 5829-5837.

value: Femoral pro-B cells


title: DSC-A23-2


title: T17


title: DSC-A23-1


title: T11


title: T14


title: c809-input_1

description:
run 1
Aligned to EU787447.1.

value: D

value: input


title: T13

value: DMPM frozen tumor specimen


title: T12


title: c770-H3K27me3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: HBeAg+ infection


title: DSC-A22-29

value: DSC-L

value: Epithelial ovarian cancer ascites


title: T10


title: c809-H3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: liver biopsy

value: liver


title: T8


title: c770-H3K9me3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: rabbit polyclonal, abcam ab8898


title: DSC-A22-28


title: c770-H3K4me3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: rabbit polyclonal, abcam ab8580


title: DSC-A22-25


title: DSC-A22-24


title: DSC-A22-26


title: DSC-A22-27


title: c770-input_2

description:
run 2
Aligned to EU787447.1.


title: c770-H3K9me3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: DSC-A22-23


title: c770-H3K4me3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: T9


title: c770-input_1

description:
run 1
Aligned to EU787447.1.


title: c765-H3K27me3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: HBeAg- hepatitis


title: DSC-A22-22


title: T7


title: T5


title: DSC-A22-21


title: T4


title: T6


title: T3


title: T2


title: T1


title: DSC-A22-20

value: DSC-M


title: CL2

source_name: DMPM cell line

value: DMPM cell line


title: c765-H3K4me3-ChIP_1

description:
run 1
Aligned to EU787447.1.


title: c765-H3-ChIP_2

description:
run 2
Aligned to EU787447.1.

value: rabbit monoclonal B0422, abcam ab41969


title: DSC-A22-19


title: DSC-A22-18


title: CL1


title: c765-input_1

description:
run 1
Aligned to EU787447.1.


title: DSC-A22-17


title: N3

source_name: normal peritoneum

value: normal peritoneum


title: c765-H3K4me3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: DSC-A22-15


title: DSC-A22-16


title: c706-H3K9me3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: Under therapy (Lamivudin), HBeAg-


title: c706-H3K4me3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: c765-H3-ChIP_1

description:
run 1
Aligned to EU787447.1.


title: c706-H3K4me3-ChIP_1

description:
run 1
Aligned to EU787447.1.


title: DSC-A22-13


title: c706-H3K27me3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: rabbit monoclonal C36B11, Cell Signaling Technology 9733S


title: N2


title: N1


title: DSC-A22-12


title: c687-H3K27me3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: D


title: c687-H3K4me3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: c706-H3K9me3-ChIP_2

description:
run 2
Aligned to EU787447.1.