title: OVCA429 with shLuciferase rep2

description:
OVCA429shLuc_L002
Control

value: shLuciferase

value: control


title: Gene expression of EFO21 rep1

status: Public on Aug 06 2019

type: RNA

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: Gene expression of EFO21, replicate 1

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Fragmented and biotin labeled cDNA was hybridized to Affymetrix Human Gene 1.0 ST arrays for 18 hours at 45C with rotation at 60 rpm. Arrays were then washed and stained using the FS450_0002 fluidics protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
RMA normalization using R package Affy 1.42.3
HuGene-1_0-st.pgf
HuGene-1_0-st.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Ovarian cancer cell line

label_protocol: Samples were enzymatically fragmented and biotinylated using the NuGEN Applause WT-Amp ST System and Encore Biotin Module.

growth_protocol: Cell lines were grown in media as detailed in samples description.

extract_protocol: Total RNA was extracted by Qiagen miRNEasy Mini kit according to the manufacturer's instructions.

tag: cell line

tag: media condition

value: RPMI 1640, 20% FBS, 1x NEAA


title: Gene expression of DOV13 rep1

description: Gene expression of DOV13, replicate 1

value: DMEM, 10% FBS


title: 72hDM-FK506 rep5

type: SRA

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

description:
umi_counts.txt.gz
sample name in processed data file:
72-FK-8

library_source: transcriptomic

data_processing:
Reads were aligned to the reference genome (GRCm38) using HISAT (v. 2.2.6).
Gene counting was performed with HTSeq (v. 0.6.1) and unique molecular identifier (UMI) duplicates were removed.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file containing UMI counts for each gene and sample

organism: Mus musculus

source_name: C2C12 cells

extract_protocol:
Total RNA from C2C12 cells treated with FK506 or with DMSO was isolated from proliferating and differentiating cultures (time 0, 24h and 72h) with TRIzols.
The libraries were constructed  according to the Illumina and CEL-Seq2 protocols.

tag: treatment

tag: time

value: 72h in differention medium


title: OVCA429shLuc with H3K9me3 ChIP

description: OVCA429shLuc with H3K9me3 ChIP-seq

library_source: genomic

data_processing:
bcl2fastq 2.17.1.14 were used for basecalling.
Sequenced reads were mapped to hg19 using Novoalign v3.02.06 with default parameters settings
Peaks were called using MACS2 v2.1.0.20150731
Genome_build: hg19
Supplementary_files_format_and_content: chip-seq signal in bigwig for each sample

molecule: genomic DNA

growth_protocol: PEO1 and HEYA8 cells were grown in RPMI supplemented with 10% FBS. OVCA429 and SKOV3 cells were grown in DMEM supplemented with 10% FBS. OVCA429 control and shGRHL2 cells were grown in DMEM supplemented with 10% FBS and 2 μg/ml puromycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed from the ChIP-DNA using Illumina TruSeq ChIP Sample Prep kit (IP-202-1012), with 15 to 18 cycles of PCR amplification. DNA size selection was performed using AMPure XP beads.

tag: chip antibody

value: H3K9me3 (ab8898, Abcam)


title: B7-H3 CAR-T mock-2

city: New York

first: Xinyuan

last: Lei

state: New York

address: E5310 Melville library

department: Molecular and Cellular Biology

country: USA

institute: Stony Brook University

description: Gene expression of B7-H3 CAR-T

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through Fold Change filtering.

source_name: T cell

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: agent

value: mock

tag: cell type

value: B7-H3 CAR-T


title: Gene expression of COLO720E rep2

description: Gene expression of COLO720E, replicate 2


title: B7-H3 CAR-T SAHA-2

description: Gene expression of B7-H3 CAR-T after 5 days treatment of 0.5 μM SAHA

value: SAHA


title: OVCA429shLuc with H3K27ac ChIP

description: OVCA429shLuc with H3K27ac ChIP-seq

value: H3K27ac (ab4729, Abcam)


title: Gene expression of CH1 rep1

description: Gene expression of CH1, replicate 1


title: Gene expression of DOV13 rep2

description: Gene expression of DOV13, replicate 2


title: Mnase-seq: scc1-73 rep2

city: Sevilla

first: Eloisa

last: Andujar

state: Sevilla

address: Avda Americo vespucio s/n

department: GENOMICS UNIT

country: Spain

institute: CABIMER-CSIC

description: Mononucleosomes purified from DNA digested with MNaseI

data_processing:
reads mapping by Bowtie2 at galaxy.org
aboundance (occupancy value in wig file) calculated by DANPOS (Dpos funtion)
Dynamic nucleosome were selected with point_diff_log10pval>-15
Genome_build: sacCer3
Supplementary_files_format_and_content: wig files report nucleosome occupancy data (the content is reads density)

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae yeast cells

growth_protocol: The four genetic backgrounds indicated previously were synchronised in G1 with alpha factor (0.5 o 1.0 µg/ml) for 3:00-3:30 hours at 30ºC in the presence of 5µg/ml of doxycicline in minimal complete media (SC). Cells were then washed three times with prewarmed rich media (YPAD, 37ºC) and  released in this media at 37ºC with 50µg/ml of pronase (eliminate remaining alpha factor) and 15 µg/ml of Nocodazole (block cells at the G2/M transition) until all of them reached a G2/M state determined by FACS profile.

extract_protocol:
Extracts for MNase were resuspended in 1M sorbitol and digested 1 hour with 4.5 mg of Zymoliase 20T (AmsBio 120491-1). Samples were then washed with 1 M sorbitol and 1M sorbitol PMSF 0.1mM, suspended gently in solution II (20mM Tris HCl 2mM EDTA 0.15M NaCl 0.1mM PMSF 0.2 % Triton), and treated 30 minutes with different concentrations of MNase (SIGMA N3755). The reaction was then stopped adding SDS (0.4%) and EDTA (8.5mM). Samples were incubated for 90 minutes at 37ºC with proteinase K and overnight at 65ºC for reversal crosslinking. DNA was extracted from samples using a standard phenol-chloroform extraction, treated with RNase A and loaded in a 1% agarose gel to check MNase digestion. MNase digestions enriched in mononucleosomes were loaded in a 1% agarose gel, and the DNA corresponding to mononucleosomes was purified with a DNA purification kit (Qiagen). The DNA size and quality was confirmed by an electropherogram analysis.
Libraries were generated using the Ion Plus Fragment Library Kit (4471252, Thermofisher) with 100ng input DNA. DNA fragments were size-selected around 230 bp after ligation of  adapters. Emulsion PCR allow enrich monocloning libraries

treatment_protocol: Samples for Mnase were fixed with formaldehyde (CF 0.5 %) for 15 minutes. Glycine (CF 125mM) was added after to quench the formaldehyde and end the cross-linking. After crosslinking and quenching cells were sedimented, washed twice with cold TBS and stored at -80ºC until use.

tag: strain

tag: tissue

value: whole organism

tag: genotype

value: MATa leu2-3,112 ura3-1 ade2-1 can1-100 his3-11 RAD5 scc1-73 bar1<delta> natMX4


title: 72hDM-FK506 rep4

description:
umi_counts.txt.gz
sample name in processed data file:
72-FK-5


title: 97DIFF

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

institute: Spanish National Cancer Research Centre (CNIO)

data_processing:
Image analysis and per-cycle basecalling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format and sequence alignment with the ELAND algorithm (v2e) was performed with CASAVA-1.8 (Illumina).
Nextpresso 1.9  was used for RNAseq analysis (http://bioinfo.cnio.es/nextpresso/) (DOI: 10.2174/157489361266617081015385)
Nextpresso use tophat for alignments with these parameters useCuffmergeAssembly="false" nThreads="1" outputFormat="simple-table" libraryNormalizationMethod="geometric"   Seed="123L" normalization="compatibleHits" reportSecondaryAlignments="false" bowtie="1"   ReadEditDist="2" readGapLength="2" referenceIndexing="false"
Nextpresso use cufflinks for measure abundance  with these parameters useGTF="true" nThreads="1" fragBiasCorrect="true" multiReadCorrect="false" libraryNormalizationMethod="classic-fpkm" maxBundleFrags="500000" normalization="compatibleHits" noEffectiveLengthCorrection="true" noLengthCorrection="false"
Nextpresso use cuffquant for measure abundance  with these parameters useCuffmergeAssembly="false" nThreads="1" fragBiasCorrect="true" multiReadCorrect="false" seed="123L" maxBundleFrags="500000" noEffectiveLengthCorrection="true" noLengthCorrection="false" normalization="compatibleHits" noEffectiveLengthCorrection="true" noLengthCorrection="false"
Nextpresso use cuffnorm for measure abundance  normalized for library size  with these parameters useCuffmergeAssembly="false" nThreads="1" fragBiasCorrect="true" multiReadCorrect="false" seed="123L" maxBundleFrags="500000" noEffectiveLengthCorrection="true" noLengthCorrection="false" normalization="compatibleHits" noEffectiveLengthCorrection="true" noLengthCorrection="false"
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample from cuffnorm ; bigwig were generated with nextpresso  1.9

molecule: polyA RNA

source_name: urothelial organoid

growth_protocol: Normal mouse urothelial organoids (NMU-o) were maintained in culture with complete medium (proliferation condition), containing: Advanced DMEM/F12, 1x penicillin/streptomycin, 1x HEPES, 1x GlutaMAX, 50% WNT3A conditioned medium, 5% human RSPO1 conditioned medium, 1x N2 (Gibco, Cat. No. 17502048), 1x B27 (Gibco, Cat. No. 12587010), 50ng/mL human recombinant EGF (Invitrogen, Cat. No. PHG0311L), 1mM N-acetylcysteine (Sigma-Aldrich, Cat. No. 616-91-1), 50μg/mL human Noggin (Peprotech, Cat. No. 120-10C) and 1μM LY-2157299 (AxonChem, Cat. No. 700874-72-2). The ROCK inhibitor Y-27632 (Sigma-Aldrich, Cat. No. 129830-38-2) (10μM) was added during the first 3 days of culture.

extract_protocol:
RNA was isolated from Matrigel drops containing organoid-cultured cells using TRI Reagent® (Sigma-Aldrich, Cat. No. T9424) followed by the PureLinkTM RNA Mini Kit (Life Technologies, Cat. No. 12183020), according to manufacturer’s instructions. For 2D culture, RNA was extracted using ReliaPrepTM RNA Cell Miniprep System Kit (Promega, Cat. No. TM370). Samples were treated with DNase before reverse transcription (Life Technologies, Cat. No. AM1906).
PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in “TruSeq Stranded mRNA Sample Preparation Guide” ( Part #15031047 Rev. E).  Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on a NovaSeq 6000- by following manufacturer's protocols.

treatment_protocol: For differentiation experiments, NMU-o were cultured for the first 7 days in complete medium, reseeded (without disaggregation) in fresh Matrigel, and cultured either with complete medium or with differentiation medium (lacking WNTA3A and RSPO-1 conditioned medium, EGF, LY-2157299 and Noggin) for the following 7 days.

value: bladder

value: urothelial organoid

tag: sampleID


title: 72hDM-FK506 rep3

description:
umi_counts.txt.gz
sample name in processed data file:
72-FK-4


title: OVCA429shLuc input DNA

description: input DNA for OVCA429shLuc histone ChIP-seq


title: Mnase-seq: scc1-73 rep1


title: HEYA8 with H3K9me3 ChIP

description: HEYA8 with H3K9me3 ChIP-seq


title: Gene expression of CAOV3 rep2

description: Gene expression of CAOV3, replicate 2


title: HEYA8 with H3K27me3 ChIP

description: HEYA8 with H3K27me3 ChIP-seq

value: H3K27me3 (07-449, Millipore)


title: HEYA8 with H3K27ac ChIP

description: HEYA8 with H3K27ac ChIP-seq


title: Mnase-seq: tHHF2 rep1

value: t:hhf2 (8d)

value: MATa leu2-3,112 trp1-1 ura3-1 ade2-1 can1-100 his3-11,15 RAD5 hhf1<delta>hphMX4 hhf2<delta>kanMX4 (p413TAR-tet:HHF2) bar1<delta>natMX4


title: 72hDM-FK506 rep1

description:
umi_counts.txt.gz
sample name in processed data file:
72-FK-2


title: Mnase-seq: wt rep2

value: MATa leu2-3,112 trp1-1 ura3-1 ade2-1 can1-100 his3-11 RAD5 bar1<delta>LEU2


title: HEYA8 with H3K4me1 ChIP

description: HEYA8 with H3K4me1 ChIP-seq

value: H3K4me1 (ab8895, Abcam)


title: 72hDM-DMSO rep4

description:
umi_counts.txt.gz
sample name in processed data file:
72-D-4

value: DMSO


title: HEYA8 with H3K4me3 ChIP

description: HEYA8 with H3K4me3 ChIP-seq

value: H3K4me3 (CS-003-100, Diagenode)


title: 72hDM-DMSO rep3

description:
umi_counts.txt.gz
sample name in processed data file:
72-D-3

value: 72h in differention medium


title: 72hDM-DMSO rep2

description:
umi_counts.txt.gz
sample name in processed data file:
72-D-2


title: Gene expression of A2780 rep1

description: Gene expression of A2780, replicate 1


title: Gene expression of CAOV3 rep1

description: Gene expression of CAOV3, replicate 1

value: DMEM, 10% FBS


title: HEYA8 input DNA

description: input DNA for HEYA8 histone ChIP-seq


title: 72hDM-DMSO rep1

description:
umi_counts.txt.gz
sample name in processed data file:
72-D-1


title: Gene expression of A2780 rep2

description: Gene expression of A2780, replicate 2


title: TALL_NMe_WT-1

first: Stuart

middle: Aidan

last: Quinn

state: NY

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
Fastq files from ATAC-Seq experiments were aligned to genome build GRCm38 (mm10) using Bowtie2 v2.3.4.1 and mitochondrial reads were removed using Samtools v.1.7.
Duplicate fragments were removed using PICARD tools v2.18.11.
Bigwig files were generated with bedtools v2.26.0 and UCSC pre-compiled utilities. Bigwig tracks were normalized to total number of mapped reads per sample.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files contain chromatin accessible tags

source_name: Notch-Myc driven T lymphoblastic leukemia

extract_protocol: Library was generated using the protocol described in Buenrostro et al. (Nat Methods, 2013 - PMID: 24097267

treatment_protocol: To generate GS1+2 mutant Myc-rescued tumors, we crossed N-Me GS1+2 homozygous mutant mice, Rosa26TM-Cre mice and Rosa26StopFLMYC (LSL-Myc) mice (44). We infected lineage negative enriched cells from bone marrow of Rosa26CreERT2/LSL-Myc N-MeGS1+2mut/GS1+2mut donors with oncogenic NOTCH1 and transplanted them in NRG mice as described before

value: NMe wild type

value: Notch-driven T cell leukemia blasts


title: TALL_NMe_GSM-1

value: NMe GATA site 1 and 2 homozygous mutant


title: Mnase-seq: tHHF2 rep2

value: t:hhf2 (DMY24)


title: 72hDM-FK506 rep2

description:
umi_counts.txt.gz
sample name in processed data file:
72-FK-3


title: ATACseq_BMDM_KO_IL4

city: Beijing

first: Liangliang

last: Ji

address: Tsinghua University

department: School of Medicine

country: China

institute: Institute for Immunology

data_processing:
Basecalls performed using Real Time Analysis.
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.2.5
Reads were filtered as the unsure bases less than 10% and low quality (I<10) bases less than 50%.
Peaks were called using MACS (version1.4.2) with the following setting: P-value < 10^-5)
Annotation was done by using script annotatePeaks.pl in HOMER
Genome_build: mm10

growth_protocol: Bone marrow isolated from WT and KO mice were cultured with 10% M-CSF for 5 days to differentiate into macrophages.

extract_protocol:
Cells were washed by PBS and 50000 cell  were re-suspended in 50 μL of lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.5% NP-40) and nuclei were digested with Tn5 enzyme.
DNA libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina protocols.

treatment_protocol: Bone marrow-derived macrophages were untreated or treated with IL4 (10 ng/mL) for 6 hours.

tag: strain background

value: Bone marrow-derived macrophages

value: IL4 (10 ng/mL) for 6 hrs


title: SKOV3 with H3K27me3 ChIP

description: SKOV3 with H3K27me3 ChIP-seq


title: TALL_NMe_GSM-2


title: 24hDM-FK506 rep4

description:
umi_counts.txt.gz
sample name in processed data file:
24-FK-7

value: 24h in differention medium


title: ATACseq_BMDM_KO_UT

value: none (untreated control)


title: 24hDM-FK506 rep3

description:
umi_counts.txt.gz
sample name in processed data file:
24-FK-5


title: ATACseq_BMDM_WT_IL4

value: wild-type


title: ICGC_GBM61

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

label: Biotin

source_name: Frozen glioblastoma tumor tissue

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

treatment_protocol: Tumor samples were snap frozen upon resection and stored at -80 oC until RNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).

tag: molecular subgroup

value: WT


title: ICGC_GBM73


title: TALL_NMe_WT-2


title: Mnase-seq: wt rep1

value: whole organism


title: SKOV3 with H3K4me1 ChIP

description: SKOV3 with H3K4me1 ChIP-seq


title: 24hDM-FK506 rep2

description:
umi_counts.txt.gz
sample name in processed data file:
24-FK-4


title: SKOV3 with H3K4me3 ChIP

description: SKOV3 with H3K4me3 ChIP-seq


title: SKOV3 with H3K9me3 ChIP

description: SKOV3 with H3K9me3 ChIP-seq

value: H3K9me3 (ab8898, Abcam)


title: ICGC_GBM66


title: ATACseq_BMDM_WT_UT


title: 24hDM-FK506 rep1

description:
umi_counts.txt.gz
sample name in processed data file:
24-FK-3


title: ICGC_GBM71


title: 24hDM-FK506 rep5

description:
umi_counts.txt.gz
sample name in processed data file:
24-FK-8


title: SKOV3 input DNA

description: input DNA for SKOV3 histone ChIP-seq


title: 24hDM-DMSO rep5

description:
umi_counts.txt.gz
sample name in processed data file:
24-D-8


title: OVCA429 with H3K9me3 ChIP

description: OVCA429 with H3K9me3 ChIP-seq


title: ICGC_GBM67

value: IDH


title: OVCA429 with H3K27me3 ChIP

description: OVCA429 with H3K27me3 ChIP-seq

value: H3K27me3 (07-449, Millipore)


title: SKOV3 with H3K27ac ChIP

description: SKOV3 with H3K27ac ChIP-seq

value: H3K27ac (ab4729, Abcam)


title: ICGC_GBM62


title: 24hDM-DMSO rep3

description:
umi_counts.txt.gz
sample name in processed data file:
24-D-4

value: DMSO


title: OVCA429 with H3K27ac ChIP

description: OVCA429 with H3K27ac ChIP-seq


title: 24hDM-DMSO rep2

description:
umi_counts.txt.gz
sample name in processed data file:
24-D-3


title: OVCA429 with H3K4me1 ChIP

description: OVCA429 with H3K4me1 ChIP-seq

value: H3K4me1 (ab8895, Abcam)


title: ICGC_GBM65


title: 24hDM-DMSO rep1

description:
umi_counts.txt.gz
sample name in processed data file:
24-D-1


title: Eutrema_AtCMT3-L3T2c_H3K9me1 (ChIP-seq)

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
MethylC-seq: analysis was performed by Methylpy 1.3
RNA-seq: analysis was performed by hisat2 v2.1.0 and StringTie v1.3.3b
ChIP-seq: analysis was performed by bowtie1.1.1
Genome_build: Eutrema salsugineum v1.0 reference genome
Supplementary_files_format_and_content: methylome tab delimited text file, see "allc_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: RNA tab delimited text file, see "RNA_seq_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: ChIP bed file, see "ChIP_seq_column_header_descriptions.txt" for column headers

organism: Eutrema salsugineum

growth_protocol: Eutrema salsugineum Shandong ecotype were grown on soil at 21 ºC in long day conditions (16 hours light, 8 hours dark). Plant transgenesis was conducted using the floral dip method (Clough and Bent, 1998). The pEarleyGate 302 vector containing genomic sequence of Arabidopsis thaliana CMT3, including the native promoter, published by (Du et al., 2012) was transformed into Agrobacterium tumefaciens strain C58C1. Bacteria were grown for 2 days at 30 ºC in 200 ml cultures containing gentamicin (25 µg/mL), kanamycin (50 µg/mL), and rifampicin (50 µg/mL) and pelleted by centrifugation at 4 ºC. Bacterial pellets were resuspended in 5% sucrose and 0.03% Silwet L-77 (Phyto Technology Laboratories) and used to dip open E. salsugineum inflorescences. Transgenic plants were selected for using Finale (BASTA, Bayer).

extract_protocol:
MethylC-seq: prepared as previously described in (Urich et al. 2015).
RNA-seq: 1.3 ug of total RNA was prepared for sequencing with the Illumina Truseq mRNA Stranded Library Kit, following the manufacturer's protocol.
ChIP-seq: ChIP-seq was performed following the methods of (Zhang et al. 2007).  Tissues were cross-linked with 1% formaldehyde and chromatin was sonicated, followed by immunoprecipitation.

value: leaf

tag: ecotype

value: Shandong

tag: antibody

tag: genotype/variation

value: heterologous expression of CMT3


title: OVCA429 with H3K4me3 ChIP

description: OVCA429 with H3K4me3 ChIP-seq

value: H3K4me3 (CS-003-100, Diagenode)


title: Eutrema_WT_H3K9me1 (ChIP-seq)

value: wild type


title: 0hDM-FK506 rep5

description:
umi_counts.txt.gz
sample name in processed data file:
0-FK-8

value: 0h in differention medium


title: ICGC_GBM46


title: Eutrema_AtCMT3-L3T2c (WGBS)


title: MCF-7, siKDM4B#1 Replicate 1

city: Hull

first: Mark

last: Wade

state: Humberside

address: Room 121, Hardy Building, University of Hull, Cottingham Road

country: United Kingdom

institute: University of Hull

description: Sample 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed using Illumina GenomeStudio Gene Expression Module. Data was quantile normalizd using the GenomeStudio Gene Expression Module with background subtraction.

source_name: MCF-7 breast cancer cells

label_protocol: According to manufacturer (Illumina) specifications.

extract_protocol: RNA was extracted with TRIzol reagent (Ambion, Life Technologies) following manufacturers instructions. Quality control was performed with Agilent Bioanalyzer.

value: Human breast adenocarcinoma cell line

tag: transfection

value: KDM4B targetting siRNA transfected cells


title: MCF-7, siSCR Replicate 2

description: Sample 3

tag: cell line

value: Control siRNA (siSCR) transfected cells

value: control


title: 0hDM-FK506 rep4

description:
umi_counts.txt.gz
sample name in processed data file:
0-FK-6


title: 24hDM-DMSO rep4

description:
umi_counts.txt.gz
sample name in processed data file:
24-D-7

value: 24h in differention medium


title: Eutrema_AtCMT3-L1T5xWT_F2_plus_CMT3 (WGBS)


title: 0hDM-FK506 rep3

description:
umi_counts.txt.gz
sample name in processed data file:
0-FK-5


title: ICGC_GBM18


title: ALL_baseline_26

city: Ulm

first: Felix

last: Seyfried

address: Eythstr. 24

department: Department of Pediatrics and Adolescent Medicine

institute: Ulm University Medical Center

hyb_protocol: 15 ug were fragmented; following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA

source_name: ALL cells isolated from spleen

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol starting from 100ng of Total RNA using the Affymetrix 3' IVT Plus Kit

growth_protocol: leukemia cells isolated from spleens of xenografted NOD/SCID mice

extract_protocol: RNA was extracted using the QIAGEN RNeasy Kit.

treatment_protocol: no treatment

value: ALL cells isolated from spleen

value: Pre-B ALL


title: PEO1 with H3K27me3 ChIP

description: PEO1 with H3K27me3 ChIP-seq

value: H3K27me3 (07-449, Millipore)


title: MCF-7, siSCR Replicate 1

description: Sample 1


title: Eutrema_AtCMT3-L1T5xWT_F2_minus_CMT3_2 (WGBS)


title: 0hDM-FK506 rep2

description:
umi_counts.txt.gz
sample name in processed data file:
0-FK-3


title: ALL_baseline_27

value: Common ALL


title: PEO1 with H3K9me3 ChIP

description: PEO1 with H3K9me3 ChIP-seq

value: H3K9me3 (ab8898, Abcam)


title: PEO1 with H3K27ac ChIP

description: PEO1 with H3K27ac ChIP-seq

value: H3K27ac (ab4729, Abcam)


title: Eutrema_AtCMT3-L1T5xWT_F2_minus_CMT3_1 (WGBS)

value: leaf


title: ALL_baseline_25


title: ALL_baseline_24


title: OVCA429 input DNA

description: input DNA for OVCA429 histone ChIP-seq


title: 0hDM-FK506 rep1

description:
umi_counts.txt.gz
sample name in processed data file:
0-FK-1


title: ALL_baseline_23


title: ALL_baseline_22


title: 0hDM-DMSO rep5

description:
umi_counts.txt.gz
sample name in processed data file:
0-D-6

value: DMSO


title: PEO1 with H3K4me3 ChIP

description: PEO1 with H3K4me3 ChIP-seq


title: Eutrema_AtCMT3-L2T5_H3K9me2 (ChIP-seq)

tag: echotype background

value: Shandong

value: heterologous expression of CMT3


title: Eutrema_AtCMT3-L2T3_H3K9me2 (ChIP-seq)


title: ALL_baseline_21

tag: treatment


title: 0hDM-DMSO rep4

description:
umi_counts.txt.gz
sample name in processed data file:
0-D-5

tag: time


title: PEO1 input DNA

description: input DNA for PEO1 histone ChIP-seq

tag: chip antibody


title: Eutrema_AtCMT3-L1T5_H3K9me2 (ChIP-seq)


title: 0hDM-DMSO rep3

description:
umi_counts.txt.gz
sample name in processed data file:
0-D-4


title: ALL_baseline_20


title: Eutrema_AtCMT3-L1T3_H3K9me2 (ChIP-seq)


title: HPV18_10

city: Rio de Janeiro

first: Ayslan

middle: Castro

last: Brant

state: Rio de Janeiro

address: Andre Cavalvanti 37

country: Brazil

institute: National Institute of Cancer

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads with low quality scores (Q < 20 phred score), short reads with lengths < 30 nucleotides, and reads with a high fraction of base ambiguities (> 60% ambiguous bases) were discarded using PRINSEQ.
To analyze likely integration events, a de novo transcriptome construction was carried out with Trinity. Subsequently, to identify chimeric transcripts, assembled transcript sequences were compared to the HPV genomic sequence with Blast tools to obtain high-scoring segment pairs (HSPs) with e-values < 1x10-6 and identity score ≥ 98%. Selected transcripts were additionally compared to the human genome (HG38) using Blast online to identify the Human/HPV chimeric transcripts.
The abundance of different HPV transcripts in cervical cancer samples was estimated by comparing HPV reads from each sample with corresponding HPV16 or HPV18 reference sequences (GenBank K02718.1 and AY262282.1, respectively) with BowTie 2 default settings. To analyze the expression of alternative E6 and E7 transcripts, reference sequences were initially constructed (HPV16_E6E7SJ.fasta and HPV18_E6E7SJ.fasta files) for each likely transcript.
Genome_build: K02718.1 (HPV16), AY262282.1 (HPV18), hg18 (human)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with counts of reads covering each nucleotide from the HPV genome.
Supplementary_files_format_and_content: Fasta files from chimerics contigs obtained from de novo assembly and blast selection. Fasta files constructed to analyse HPV16 and HPV18 E6/E7 alternative transcripts.

organism:
Homo sapiens
human papillomavirus 18

source_name: Uterine cervix tumor

growth_protocol: CaSki was grown in RPMI medium with 10% fetal bovine serum (Gibco) and 5% CO2.

extract_protocol:
DNA and RNA were isolated from each sample and cell line with Qiagen AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. DNA and RNA were quantified and stored at -20°C and -80°C, respectively.
Libraries were prepared with TruSeq RNA Sample Prep Kit (Illumina, USA) according to the manufacturer's recommendations.

treatment_protocol: All biopsies were collected before patient treatment and stored in RNAlater (Qiagen) at -80°C until mRNA isolation.

value: Uterine cervix tumor

tag: hpv-type infection

tag: histological tumor classification

value: Adenocarcinoma


title: Eutrema_WT_input (ChIP-seq)

value: wild type

value: non (input)


title: 0hDM-DMSO rep2

description:
umi_counts.txt.gz
sample name in processed data file:
0-D-3

value: 0h in differention medium


title: HPV18_9

value: Squamous cell carcinoma


title: HPV18_8


title: Eutrema_WT_H3K9me2 (ChIP-seq)


title: 0hDM-DMSO rep1

description:
umi_counts.txt.gz
sample name in processed data file:
0-D-2


title: MCF-7, siKDM4B#1 Replicate 2

description: Sample 4

tag: cell type

value: Human breast adenocarcinoma cell line

value: KDM4B targetting siRNA transfected cells


title: GM-FK506 rep5

description:
umi_counts.txt.gz
sample name in processed data file:
G-FK-7

value: Growth medium


title: HPV18_7

tag: tissue


title: GM-FK506 rep4

description:
umi_counts.txt.gz
sample name in processed data file:
G-FK-4


title: ALL_baseline_18

value: ALL cells isolated from spleen


title: ALL_baseline_19

value: Common ALL


title: ALL_baseline_16


title: ALL_baseline_17

value: Pre-B ALL


title: ALL_baseline_15


title: Eutrema_AtCMT3-L3T2 (RNA-seq)

description: processe data file: expression_profile_eutrema.txt


title: HPV18_6


title: GM-FK506 rep3

description:
umi_counts.txt.gz
sample name in processed data file:
G-FK-3


title: OVCA429shLuc with H3K4me3 ChIP

description: OVCA429shLuc with H3K4me3 ChIP-seq

value: H3K4me3 (CS-003-100, Diagenode)


title: HPV18_4


title: Eutrema_AtCMT3-L2T4 (RNA-seq)

value: leaf


title: Eutrema_AtCMT3-L2T6 (RNA-seq)


title: HPV18_5


title: Eutrema_AtCMT3-L3T2b (RNA-seq)


title: GM-FK506 rep2

description:
umi_counts.txt.gz
sample name in processed data file:
G-FK-2


title: Eutrema_AtCMT3-L2T5 (RNA-seq)


title: GM-DMSO rep5

description:
umi_counts.txt.gz
sample name in processed data file:
G-D-8

value: DMSO


title: Eutrema_AtCMT3-L2T3 (RNA-seq)

value: Shandong


title: HPV18_2


title: GM-DMSO rep4

description:
umi_counts.txt.gz
sample name in processed data file:
G-D-7


title: GM-FK506 rep1

description:
umi_counts.txt.gz
sample name in processed data file:
G-FK-1


title: Eutrema_AtCMT3-L1T5 (RNA-seq)

value: heterologous expression of CMT3


title: CaSki

organism:
Homo sapiens
Human papillomavirus 16

source_name: CaSki cell line

value: CaSki

value: Epidermoid Carcinoma


title: HPV18_3

description: Chimeric transcripts were not identified in this sample.

value: Uterine cervix tumor

value: Adenocarcinoma


title: HPV18_1


title: ALL_baseline_14


title: Eutrema_AtCMT3-L1T4 (RNA-seq)


title: GM-DMSO rep2

description:
umi_counts.txt.gz
sample name in processed data file:
G-D-4


title: ALL_baseline_13


title: ALL_baseline_12

value: Pro-B ALL


title: ALL_baseline_8


title: ALL_baseline_9


title: ALL_baseline_10


title: ALL_baseline_11


title: HPV16_13


title: GM-DMSO rep1

description:
umi_counts.txt.gz
sample name in processed data file:
G-D-1


title: ALL_baseline_7


title: Eutrema_AtCMT3-L1T3 (RNA-seq)


title: ALL_baseline_6


title: E19.5_LG_3

city: Guangzhou

first: Yan

last: Zhang

state: Guangdong

address: No.132, East Outer Ring Road，Guangzhou Higher Education Mega Center

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
Illumina Casava 1.8 software was used for basecalls.
Paired-end clean reads were aligned to the reference genome using Hisat2(v2.0.5)
FeatureCounts  v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, was calculated based on the length of each gene and reads count mapped to this gene (Trapnell, Cole, et al., 2010).
Genome_build: NCBIM37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Embryonic lacrimal gland

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen), and mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina®  (NEB) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: strain

value: Lacrimal gland

tag: developmental stage

value: Embryo


title: HPV16_12


title: E19.5_LG_2


title: Eutrema_WT (RNA-seq)

value: wild type


title: Eutrema_AtCMT3-L1T2b (WGBS)

data_processing:
library strategy: MethylC–seq
MethylC-seq: analysis was performed by Methylpy 1.3
RNA-seq: analysis was performed by hisat2 v2.1.0 and StringTie v1.3.3b
ChIP-seq: analysis was performed by bowtie1.1.1
Genome_build: Eutrema salsugineum v1.0 reference genome
Supplementary_files_format_and_content: methylome tab delimited text file, see "allc_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: RNA tab delimited text file, see "RNA_seq_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: ChIP bed file, see "ChIP_seq_column_header_descriptions.txt" for column headers


title: E19.5_LG_1


title: HPV16_11


title: HPV16_10


title: HPV16_14

value: Squamous cell carcinoma


title: Eutrema_AtCMT3-L6T2 (WGBS)


title: E17.5_LG_3


title: HPV16_9


title: E17.5_LG_2


title: Genomic DNA from DU-4475 cell line

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

institute: Josep Carreras Leukaemia Research Institute (IJC)

description: breast cell line from ATCC

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Minfi R package standard protocol
Matrix_signal_intensities.csv file includes Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: breast cell line

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

value: breast

tag: gender

value: Female


title: HPV16_8


title: HPV16_7


title: NM-1-45

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

description: Non-memory line

data_processing:
Illumina for basecalling
The sequences were trimmed using trim_galore 0.4.1 and cutadapt 1.9.1  with cutoff 20
The sequences were aligned using Erne-meth 2.1.1 with default options and set the output as a bismark coverage file
tab-delimited file generated with bismark2bedGraph with options -CX --ample_memory
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited file, 1-based genomic coords with <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated> fields

organism: Arabidopsis thaliana

growth_protocol: Seeds were sown on peat mix in square pots in reach-in chambers at 12hrs daylenght (22 °C, 120-150 μmol/(m^2*s) light)

extract_protocol:
genomic DNA extraction using DNeasy Plant kit (Qiagen, Germany).
Genomic DNA Sonicated to 100-300 bp fragments and purified with MiniElute PCR Purification Kit (Qiagen, Germany), incubated at 20 ℃ after add End Repair Mix. Then purified and added a single ‘A’ nucleotide to the 3’ ends of the blunt fragments, purified again and add Methylated Adapter to the 5’ and 3’ ends of each fragment. Then fragments with 300bp-400bp size-range were purified with QIAquick Gel Extraction kit (Qiagen, Germany) and subjected to bisulfite treatment by using Methylation-Gold kit (ZYMO). Followed with PCR and gel purification (350bp-400bp range fragments were selected). Qualified libraries sequenced pair end on the HiSeq X-ten system.

treatment_protocol: Five memory plants, four non-memory plants, and four Col-0 wild-type plants were sequenced were used. Leaves at bolting were flash freezed in liquid nitrogen.  Tissues were ground by motor and pestle in liquid nitrogen.

tag: replicate type

value: biological rep 2

value: rosette leaves


title: NM-1-70

description: Non-memory line

value: biological rep 3


title: NM-1-86

description: Non-memory line

value: biological rep 4


title: E17.5_LG_1


title: ALL_baseline_3

value: ALL cells isolated from spleen

value: Common ALL


title: ALL_baseline_5


title: Eutrema_AtCMT3-L5T2 (WGBS)

value: Shandong

value: heterologous expression of CMT3

value: leaf


title: Eutrema_AtCMT3-L3T2 (WGBS)


title: Eutrema_AtCMT3-L4T2 (WGBS)


title: HPV16_6

value: Uterine cervix tumor


title: ALL_baseline_2


title: ALL_baseline_4


title: Eutrema_AtCMT3-L2T6 (WGBS)


title: LG_2

source_name: Lacrimal gland

value: Adult


title: ALL_baseline_1

value: Pre-B ALL


title: Eutrema_AtCMT3-L3T2b (WGBS)


title: LG_3

value: Lacrimal gland


title: M-1-179

description: memory line

value: biological rep 5


title: HPV16_4

value: Squamous cell carcinoma


title: HPV16_5


title: LG_1


title: Eutrema_AtCMT3-L2T5 (WGBS)


title: M-1-168

description: memory line


title: LGSCs_L14_3

source_name: Lacrimal gland stem cells

growth_protocol: For LGSCs primary culture, 6-8 week-old mice were sacrificed. Then the LGs were cut into small fragments (about 1 mm3), treated with 25 U/ml Dispase (BD Biosciences) and 0.1% Collagenase Ⅰ (Gibco) for 1 hour at 37℃, and treated with 0.05% trypsin (Sigma) for 10 min at 37℃ to dissociate into single cells by pipetting. 1×104 cells were seeded into 80 μl Matrigel-LGSCM matrix (Matrigel: LGSCM= 1:1) per well of 24-well plate. The well was pre-coated with 20 μl Matrigel-LGSCM matrix. After incubation for 20 min at 37℃, the mix was solidified, then 600 μl LGSCM was added, which contained DMEM/F12 (1:1 mixture of Dulbecco’s Modified Eagle’s Medium and Ham’s F-12) (Sigma), N2 (Gibco), B27 (Gibco), L-glutaMAX (Gibco), NEAA ( Non-Essential Amino Acids, Gibco), murine EGF (PeproTech), FGF10 (PeproTech), Wnt3A (PeproTech) and Y-27632 (Selleck). For LGSCs passage, LGSCs-spheres cultured for 7 days were released by incubating in 10 U/ml Dispase for 1 hour at 37℃, then treated with 0.05% trypsin for 5 min at 37℃ to dissociate single cells, and planted the single cells like the protocol in primary culture.

tag: culture time

value: 14 days

tag: cell passage number


title: HPV16_3


title: Eutrema_AtCMT3-L2T3 (WGBS)

tag: genotype/variation


title: HPV16_2

value: Adenocarcinoma


title: LGSCs_L14_2


title: M-1-105

description: memory line


title: NM-1-12

description: Non-memory line

value: biological rep 1


title: Eutrema_AtCMT3-L2T2 (WGBS)


title: LGSCs_L14_1


title: M-1-3

description: memory line

value: rosette leaves


title: Eutrema_AtCMT3-L2T1 (WGBS)


title: HPV16_1


title: Bif1Bif4_tassel_rep2

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

data_processing:
Illumina software used for base calling
Sequenced reads were trimmed for adaptor sequence using trimmomatic, then mapped to ZmB73v3 whole genome using Tophat v2.1.1
Differentially expressed genes were identified using DESeq2 and ht-seq-count
Genome_build: ZmB73v3.31

organism: Zea mays

source_name: 2-4mm maize B73 field-grown Bif1;Bif4 mutant tassels

growth_protocol: 2-4mm maize B73 field-grown tassels

extract_protocol:
samples were snap frozen in liquid nitrogen and total RNA was extracted using RNeasy kit (Qiagen) with DNAse treatment
Stranded Illumina mRNA sequencing libraries were generated using TruSeq (Illumina)

treatment_protocol: 2-4mm maize B73 field-grown tassels were harvested. ndl1 samples included tassels with a severe phenotype but with a few axillary meristems still formed

tag: background

value: Bif1;Bif4 double heterozygous mutant

value: tassels


title: LGSCs_L10_3

value: 10 days


title: W-1-5

description: Wild-type control

value: biological rep 4


title: Bif1Bif4_tassel_rep1


title: W-1-4

description: Wild-type control

value: biological rep 3


title: PEO1 with H3K4me1 ChIP

description: PEO1 with H3K4me1 ChIP-seq

tag: cell line

value: H3K4me1 (ab8895, Abcam)


title: LGSCs_L10_1


title: Eutrema_AtCMT3-L1T6 (WGBS)

tag: echotype background

value: Shandong

value: heterologous expression of CMT3

value: leaf


title: ndl1_tassel_rep4

source_name: 2-4mm maize B73 field-grown ndl1 mutant tassels

value: ndl1/zmftsh10 mutant


title: LGSCs_L10_2


title: W-1-3

description: Wild-type control

value: biological rep 2


title: Eutrema_AtCMT3-L1T5 (WGBS)


title: Eutrema_AtCMT3-L2T4 (WGBS)


title: ndl1_tassel_rep3


title: LGSCs_L7_2

value: 7 days


title: LGSCs_L7_3


title: W-1-1

description: Wild-type control


title: Eutrema_AtCMT3-L1T3 (WGBS)


title: ndl1_tassel_rep2


title: Eutrema_AtCMT3-L1T2 (WGBS)


title: ndl1_tassel_rep1


title: LGSCs_L7_1


title: Eutrema_AtCMT3-L1T1 (WGBS)


title: LGSCs_L5_3

value: 5 days


title: wildtype_tassel_rep3

source_name: 2-4mm maize B73 field-grown wildtype tassels

value: wildtype


title: Eutrema_WT (WGBS)

value: wild type


title: wildtype_tassel_rep2


title: Eutrema_AtCMT3-L1T4 (WGBS)


title: LGSCs_L5_1


title: Empty_02

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description: The mouse liver cancer cell line BNL-MEA was transfected with empty plasmids and stable clones expressing PD-L1 were selected. An orthotopic HCC model was generated by implanting the cells into the subcapsular space of BALB/c mice.

hyb_protocol: Total RNA was annealed with multiplexed tags to 770 target RNAs through a ligation reaction and purification step. NanoString technology is based on the direct molecular barcoding and digital detection of target molecules through the use of a color-coded probe pair. The probe pair consists of a Reporter Probe, which carries the signal on its 5' end, and a Capture Probe which carries a biotin on its 3' end.

scan_protocol: After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the puried target/probe complexes are eluted o the beads and immobilized on the cartridge for data collection. After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the puri ed target/probe complexes are eluted o the beads and immobilized on the cartridge for data collection.

data_processing: the expression level of each gene is presented by the log2 code count per million (CPM) and then multiplied by a normalization factor computed from TMM.

source_name: BNL-MEA

label_protocol: No label is used in Nanostring

growth_protocol: cultured in Dulbecco’s modiﬁed Eagle’s medium(DMEM) supplemented with 10% fetal bovine serum (FBS), penicillin (100 units/mL), and streptomycin (100 μg/mL). The cells were maintained in a humidiﬁed incubator under 5% CO2 at 37°C.

extract_protocol: Total RNA were isolated from tumor tissues by using the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: PD-L1 or empty plasmids (MR203953 and PS100001; Origene Technologies, Rockville, MD) was transfected into the BNL-MEA cells using PolyJet transfection reagent (Signagen. Laboratories, Rockville, MD) and stable clones were selected by G418 treatment (Life Technologies). Orthotopic liver cancer models were established by injecting about 2 × 105 BNL-1MEA cells into the subcapsular area of the left liver lobe of male BALB/c at the age of 6–7 weeks.

tag: treatment

value: Empty

value: BNL-MEA


title: RNAseq_BMDM_KO_IL4

data_processing:
Base-calling made by Zebracall process version 0.5.0.13875
RNA-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.2.5
Reads were filtered as the unsure bases less than 10% and low quality (I<10) bases less than 50%.
FPKM value was quantified by RSEM tools
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

growth_protocol: Mice were intraperitoneally injected with 1 ml of 4%  thioglycollate for 3-4 days and peritoneal macrophages were isolated. Bone marrow isolated from mice were cultured with 10% M-CSF for 5 days to differentiate into macrophages.

extract_protocol:
Cells were washed by PBS and RNA was extracted from whole cell lysates with total RNA purification kit (TR01, GeneMark).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Peritoneal macrophages were untreated or treated with IFNg (10 ng/mL) for 12 hours. Bone marrow-derived macrophages were untreated or treated with IL4 (10 ng/mL) for 6 hours.

tag: strain background

tag: genotype

value: Bone marrow-derived macrophages

value: IL4 (10 ng/mL) for 6 hrs


title: Empty_03


title: wildtype_tassel_rep1

value: tassels


title: Empty_01


title: ovPDL1_02

description: The mouse liver cancer cell line BNL-MEA was transfected with PD-L1 plasmids and stable clones expressing PD-L1 were selected. An orthotopic HCC model was generated by implanting the cells into the subcapsular space of BALB/c mice.

value: PD-L1 plasmids


title: RNAseq_BMDM_KO_UT

value: none (untreated control)


title: ovPDL1_03


title: post2_Blood_CD8_0008

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

institute: Tokyo University of Science

data_processing:
Adapter sequences and low-quality reads were trimmed using cutadapt-v1.11 and PRINSEQ-0.20.4. Filtered reads were processed using “analyze amplicon” command of MiXCR-3.0.2 with following high-level options: -s = hsa, -starting-material = rna, -5-end = no-v-primers, -3-end = c-primers, -adapters = no-adapters, -receptor-type = trb, -region-of-interest = CDR3. In alignment to ImMunoGeneTics (IMGT) reference human TCR V/D/J sequences, we used the following parameters: -OvParameters.geneFeatureToAlign = VTranscript -OvjAlignmentOrder = JThenV. In assembling identical sequences into clones with PCR and sequencing error correlations, we used the following parameters: -ObadQualityThreshold=10, -OseparateByV=true. Only clones with productive CDR3 sequences were analyzed using VDJtools (ver 1.2.1.). Then, the sequencing coverage of samples, which was defined as the ratio of total reads to the starting number of T cells, was normalized to ×5 using the “DownSample” command in VDJtools. After coverage normalization, clones with lead count less than sequencing coverage were excluded as sequencing noise. Finally, for PBMC sample, we identified clones shared between CD4+ and CD8+ T cell repertoire as contamination, and separated these shared clones into CD4+ or CD8+ repertoire by their frequency in CD4+ or CD8+, because these shared clones were very few and their frequencies were biased to either CD4+ or CD8+ (Data not shown)
Genome_build: IMGT reference sequences of human 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

source_name: CD8+ peripheral blood T cells

extract_protocol:
For bulk biopsy samples, total RNA was extracted using a RNA easy mini extraction kit (Qiagen) according to standard protocol, and diluted with Lysis buffer (100 mM Tris-HCl pH7.5, 500 mM LiCl, 10 mM EDTA, 5 mM DTT). For sorted CD4+ and CD8+ T cells, cells were collected directry into the Lysis buffer.
TCR sequencing libraries for next generation sequencing were prepared according to the previous report (Aoki, et al, GSE115425) with some modifications. 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 0.4 μL of 10 μM primer mix (5′ WTA and Trbc_ex), 4.6 μL of template, and 5 μL of KAPA Hifi Hotstart ReadyMix (KAPA Biosystems). The thermal cycling conditions were programmed as follows: denaturation at 95°C for 3 min, 10 cycles of denaturation for 20 sec at 98°C, annealing for 15 sec at 58°C and extension for 30 sec at 72°C, followed by final extension at 72°C for 2 min. Next, 10 μL of the first-PCR products was used for purification with an Agencort AM Pure XP kit (Beckman Coulter) at a 0.7:1 ratio of beads to sample, and eluted with 12 μL of DW. The second PCR mixture consisted of 1.25 μL of 10 μM primer mix (5′ WTA and Trbc_in-Bio), 11.25 μL of template and 12.5 μL of KAPA Hifi Hotstart ReadyMix. The thermal cycling conditions were same as the first PCR except the cycle number; 13 cycles. Next, 25 μL of the second-PCR products were purified using Agencort AM Pure XP kit (Beckman-Coulter) at a 0.8:1 ratio of beads to sample, and eluted in 15 μL of DW. The purified PCR products were sheared randomly using NEBNext dsDNA fragmentase (New England Biolabs). The fragmentation reaction mix consisted of 6 μL of DW, 2 μL of 10X Fragmentase Reaction Buffer v2, 10 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 on ice. The sheared PCR product was then purified and subjected to size selection using the Agencort AM Pure XP kit (Beckman 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 10 μL of Dynabeads M-270 Streptavidin (Thermo Fisher Scientific) 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). 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 Bio). 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 0.35 μL of 10 μM trP1 primer, 1 μL of 3.5 μM IonA-BC-Trbc primer, 3.65 μL of beads resuspended in DW and 5 μL of KAPA Hifi Hotstart ReadyMix. The thermal cycling conditions were same as the first PCR except the cycle number; 12 cycles. The PCR product was purified and subjected to size selection using Agencort AM Pure XP kit (Beckman Coulter,) at a 0.75:1 ratio of beads to sample to remove large fragments, a 0.65:1 ratio of beads to sample 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 ((KAPA Biosystems) and size distribution was analyzed by agarose electrophoresis and SYBR Gold staining (Thermo Fisher Scientific). 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) according to the manufacturer’s instructions, except the input library concentration (100 pM) and flow number (550).

treatment_protocol: Patients with advanced solid tumors for whom no standard therapy was available, were treated with intravenous infusion of IT1208 at dose of 0.1 or 1.0 mg/kg. First patient in each cohort was treated as a single administration and other patients received two administrations of IT1208 on day 1 and 8 followed by safety and efficacy assessment with DLT evaluation period as 4 weeks.

value: CD8+ CD4- T cells

tag: age

tag: Sex

value: male

tag: cancer type

value: gastro-esophageal

tag: dose level

value: 1.0 mg/kg

tag: agent

tag: organ

value: peripheral blood


title: RNAseq_BMDM_WT_IL4

value: wild-type

tag: cell type


title: RNAseq_BMDM_WT_UT


title: post2_Blood_CD8_0007


title: LGSCs_L5_2

tag: strain


title: post2_Blood_CD8_0006

value: female

value: colorectal


title: RNAseq_PM_KO_IFNg

value: IFNg (10 ng/mL) for 12 hrs


title: post2_Blood_CD4_0008

source_name: CD4+ peripheral blood T cells

value: CD4+ CD8- T cells


title: RNAseq_PM_KO_UT


title: ovPDL1_01


title: Periodontal_Tissue_Cells_C_rep3

first: Liping

last: Wu

address: 56 Lingyuanxi Road

description: Gene expression of the third-generation cells

hyb_protocol: The RNA was then hybridized onto an Arraystar Human LncRNA Expression Microarray (version 4.0; Arraystar, Inc., Rockville, MA, USA),

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent)  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: periodontal ligament cells

label_protocol: The total RNA was purified using an RNeasy Mini kit (Qiagen) and labeled by Quick Amp Labeling kit (Agilent). Labeled RNA was purified again using the RNeasy Mini kit.

growth_protocol: Cells  were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 ug/ml streptomycin and cultured at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol reagent. Quantification and quality checks were conducted using a NanoDrop ND-1000 spectrophotometer. RNA integrity and genomic DNA contamination were determined by denaturing agarose gel electrophoresis.

treatment_protocol: When cells reached 80% confluence, they were passaged with a 1:3 ratio using 0.25% trypsin/EDTA. The third-generation cells were used for subsequent experiments.

tag: tissue

value: periodontal ligament


title: post2_Blood_CD4_0007


title: RNAseq_PM_WT_IFNg


title: Periodontal_Tissue_Cells_C_rep1


title: post2_Blood_CD4_0006


title: RNAseq_PM_WT_UT


title: Hek-Lawsone stimulated-24h-rep1

city: Berlin

first: Teresa

last: Domaszewska

state: Berlin

address: Chariteplatz 1

department: Immunology

institute: Max Planck Institute for Infection Biology

hyb_protocol: After precipitation, purification, and quantification, 0.75 μg labeled cRNA was fragmented and hybridized to custom whole genome human 8 × 60k multipack microarrays (Agilent-048908) according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Microarray image data were analyzed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. Scanning of microarrays was performed with 3 μm resolution using a G2565CA high-resolution laser microarray scanner (Agilent Technologies).

data_processing: The microarray results were analyzed with limma (2) R package for differential expression analysis. The data set was background corrected and normalized using loess method.

source_name: primary epidermal keratinocytes, Lawsone, 24h

label_protocol: mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer, T7 RNA Polymerase and Cyanine 3-CTP.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: HEK cells were stimulated with lawsone (10 µM), DMSO or Pam2CSK4 (300 ng/mL) for 4h or 24h.

value: primary epidermal keratinocytes

tag: stimulus

value: Lawsone

tag: time point (h)

source_name: primary epidermal keratinocytes, unstimulated, 24h

value: unstimulated


title: Hek-Lawsone stimulated-24h-rep2


title: Hek-TLR2 stimulated-24h-rep2

source_name: primary epidermal keratinocytes, TLR2, 24h


title: Periodontal_Tissue_Cells_B_rep3

source_name: other periodontal tissue cells

value: other periodontal tissues


title: Periodontal_Tissue_Cells_B_rep2


title: Periodontal_Tissue_Cells_C_rep2


title: Periodontal_Tissue_Cells_B_rep1


title: 3KR2_T

status: Public on Aug 05 2019

city: Smithville

first: Bin

last: Liu

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

description: Primary MEFs at passage 3

data_processing:
read aligment with Tophat
sorting with samtool
read count with HT-seq count
DE Analysis with DESeq
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Raw counts for each gene, text file

source_name: Primary Mouse Embryonic Fibroblasts (MEFs)

growth_protocol: Primary mouse embryonic fibroblasts (MEFs) of wild type and E2f13KR/3KR knock-in mice were isolated from 13.5 days old embryos derived from crossing heterozygous or homozygous mice of each strain following standard procedures and maintained in DMEM supplemented with 10% heat-inactivated FBS, penicillin- streptomycin and 100 μm b-mercaptoethanol at 37°C in 5% CO2 and 5% O2.

extract_protocol:
Total RNA was isolated from wild type and knock-in MEFs, before and 3h after treatment with NCS using GenElute mammalian Total RNA miniprep kit (Sigma) following supplier’s instructions.
DNase I treated RNA samples were fragmented and tagged at both ends for stranded library preparation using TrueSeq Stranded mRNA Kit (Illumina).

treatment_protocol: Primary mouse embryonic fibroblasts (MEFs) of wild type and E2f13KR/3KR knock-in mice were seeded at passage 3 for RNA isolation experiment, and either untreated or treated with NCS (250 ng/ml for 3h) before harvesting to induce DNA damage.

value: FVB

value: NCS treatment (250 ng/ml for 3h)


title: 3KR3_T

description: Primary MEFs at passage 3


title: 3KR1_T

description: Primary MEFs at passage 3


title: Hek-Lawsone stimulated-4h-rep2

source_name: primary epidermal keratinocytes, unstimulated, 4h

source_name: primary epidermal keratinocytes, Lawsone, 4h


title: 3KR3_C

description: Primary MEFs at passage 3

value: No Treatment


title: Hek-TLR2 stimulated-24h-rep1


title: Periodontal_Tissue_Cells_A_rep2

source_name: dental follicle cells

value: dental follicle


title: Periodontal_Tissue_Cells_A_rep3


title: Hek-TLR2 stimulated-4h-rep1

source_name: primary epidermal keratinocytes, TLR2, 4h


title: GM-DMSO rep3

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

description:
umi_counts.txt.gz
sample name in processed data file:
G-D-6

data_processing:
Reads were aligned to the reference genome (GRCm38) using HISAT (v. 2.2.6).
Gene counting was performed with HTSeq (v. 0.6.1) and unique molecular identifier (UMI) duplicates were removed.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file containing UMI counts for each gene and sample

source_name: C2C12 cells

extract_protocol:
Total RNA from C2C12 cells treated with FK506 or with DMSO was isolated from proliferating and differentiating cultures (time 0, 24h and 72h) with TRIzols.
The libraries were constructed  according to the Illumina and CEL-Seq2 protocols.

value: DMSO

tag: time

value: Growth medium


title: Periodontal_Tissue_Cells_A_rep1


title: 3KR2_C

description: Primary MEFs at passage 3


title: WT3_T

description: Primary MEFs at passage 3

value: wild type


title: WT2_T

description: Primary MEFs at passage 3


title: Hek-TLR2 stimulated-4h-rep2


title: Hek-Lawsone stimulated-4h-rep1


title: 38DRpos

city: Syracuse

first: Adam

middle: Tully

last: Waickman

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

data_processing:
Raw sequencing data (BCL files) were demultiplexed and coverted to fastq files using the CellRanger v2.1.1 mkfastq pipline (10x Genomics) and bcl2fastq2 v 2.20.0 (Illumina)
Data qualty control, data filtering, cell barcode processing, UMI compression, 5' transcript alignment, and single-cell gene counting was performed using the CellRanger v2.1.1 count pipeline (10x Genomics)
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv, mtx files generated by CellRanger v2.1.1

source_name: PBMC

extract_protocol:
Single-cell RNAseq libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) and the Chromium Single Cell Analyzer (10x Genomics) according to the manufacture's protocol (User guide RevC)
Indexed sequencing libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) according to the manufacture's protocol (User guide RevC). In short, sequencing libraries were generated by  1) transcript fragmentation and end-repair, 2) post-fragmentation size-selection using SPRIselect beads, 3) Adaptor ligation and 4) sample index PCR and SPRIselect cleanup

treatment_protocol: Cryopreserved PBMCs were thawed and washed with RPMI media supplemented with 10% fetal calf serum prior to analysis. Populations of interest (CD3+ CD8+ CD38- HLA-DR- T cells, CD3+ CD8+ CD38+ HLA-DR+ T cells, and CD3+ CD8+ CD71+ HLA-DR+ T cells) were isolated from the unfractionated PBMCs by flow cytometric sorting using a BD FACSAria Fusion instrument. Post-sort population purity was assessed prior to downstream analysis. Sorted cells were washed in PBS supplemented with 2% fetal calf serum prior to scRNAseq library generation

value: CD3+ CD8+ CD38+ HLA-DR+ T cell

tag: day post vaccination


title: 71DRhi

value: CD3+ CD8+ CD71+ HLA-DR+ T cell


title: WT1_T

description: Primary MEFs at passage 3


title: 3KR1_C

description: Primary MEFs at passage 3


title: WT3_C

description: Primary MEFs at passage 3


title: WT2_C

description: Primary MEFs at passage 3


title: MD-12-LSK-Mut-2

city: New York

first: Meelad

middle: M

last: Dawlaty

address: 1301 Morris Park Ave, Price 419, Bronx

institute: Albert Einstein College of Medicine

data_processing:
The reads were trimmed using trim galore (v 0.4.1) to remove adapters.
The trimmed data were mapped to mouse genome (mm10) by tophat software (v 2.0.13) with default parameters
The read pair numbers mapped to each gene in the Refseq gene annotation (downloaded from UCSC genome browser in 03/2017) were calculated with HTseq (v 0.6.1)
The Fragments Per Kilobase of transcript per Million (FPKMs) for each gene were calculated using cufflinks package
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files include raw counts for each gene in each sample

source_name: bone marrow cells

extract_protocol:
LSK and MPP cells were sorted from pooled bone marrow of two 10-week-old Tet2 Mut, Tet2 KO and wild-type mice by FACS. RNA was extracted using QIAGEN RNAeasy Kit.
RNA was amplified and barcoded and used to prepare libraries of two technical replicates, with ERCC spike in controls.

tag: developmental stage

value: bone marrow


title: 38DRneg

value: CD3+ CD8+ CD38- HLA-DR- T cell


title: MD-11-LSK-Mut-1


title: WT1_C

description: Primary MEFs at passage 3

tag: treatment


title: RNAseq_IL1B_2

city: Copenhagen

first: Nils

middle: Billestrup

last: Billestrup

address: Bledamsvej

country: Denmark

institute: University of Copenhagen

description: mouse islet IL1B rep 2

data_processing:
The single-end 50 base pair reads were mapped to the UCSC mouse transcriptome (mm9) by STAR, allowing for up to 10 mismatches.
Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
in homer, function "makeUCSCfile" was used to generate bigWig file
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated

source_name: pancreatic islets

growth_protocol: Isolated pancreatic islets were cultured in RPMI 1640 medium with 11mmol/l D-glucose supplemented with 2% human serum and 1 % penicillin/steptomycin. Medium and IL1B were changed every 5th day

extract_protocol:
RNA was harvest using Rneasy Micro Kit (Qiagen)
RNA libraries were constructed from 35ng of isolated RNA using TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Islets were cultured in the absence or presence of 50pg/ml IL1B

value: IL1B 10 d

tag: gender

value: male

value: 12 weeks

value: pancreatic islets


title: ctrl-MO-24hpf

city: Shanghai

first: Yue

last: Xiao

address: 320 Yue Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument
The pass filter data of FASTQ format were processed by Trimmomatic (v0.30) to remove technical and low-quality sequences.
Hisat2 (v2.0.1) was used to index reference genome sequence (Kim et al., 2015). Clean data were then aligned to reference genome via software Hisat2 (v2.0.1).
Transcripts in the FASTA format were converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) (Anders et al., 2015) was used to estimate gene and isoform expression levels from the pair-end clean data.
Genome_build: Danio_rerio.GRCz10.86
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

organism: Danio rerio

source_name: embryos

growth_protocol: Zebrafish embryos were cultured in Holtfreter’s solution at 28.5°C.

extract_protocol:
Total RNA of each sample was extracted from 50 pooled zebrafish embryos using TRIzol Reagent (Invitrogen).
RNA libraries were prepared for sequencing according to the manufacturer’s protocol (NEBNext® UltraTM RNA Library Prep Kit for Illumina®).  The poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).

treatment_protocol: Morpholinos were dissolved in nuclease-free water and injected at 2 nl (containing 8 ng MO) per embryo at the one-cell stage using a Narishige IM300 micro-injector. 300 pg of GFP mRNA were co-injected as injection marker.

tag: morpholino injected

value: ctrl morpholino 8ng

tag: mrna injected

value: GFP 300pg


title: 14-MO-24hpf

value: rbm14a+rbm14b morpholinos 4+4ng


title: ctrl-MO-10hpf


title: RNAseq_IL1B_1

description: mouse islet IL1B rep 1

tag: age


title: MD-10-LSK-KO-2


title: PC3 siJunD, biological rep1

city: Atlanta

first: Bethtrice

last: Thompson-Elliott

address: 223 James P. Brawley Dr. SW

department: Center for Cancer Research and Therapeutic Development

institute: Clark Atlanta University

description:
PC3 siJunD_1
Gene expression data from PC3 cells following JunD Knockdown by siRNA.

hyb_protocol: Following fragmentation, 30 ug of cRNA were hybridized for 16 hr at 45C on a GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the 7G Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with Affymetrix Expression Console (EC) Software Version 1.4 using the Robust Multi-Array Average (RMA) normalization method.

source_name: prostate

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 500ng total RNA.

growth_protocol: PC3 cells were cultured in the recommended growth media [MEM media supplemented with 5% fetal bovine serum (FBS)] in 100% humidity at 37°C with 5% CO2.

extract_protocol: Seventy-two hours after transfection, total RNA was extracted using Trizol, following manufacturer's instructions.

treatment_protocol: Cells were transfected were plated at a density of 150K cells/well in a 6 well plate (O/N). Next day transfected with 60nM of JunD siRNA, or control siRNA using transfection reagents (Santa Cruz Biotechnology, Dallas, TX) following manufacturer’s recommendations.

tag: cell line

value: prostate cancer cell line

tag: population

value: Caucasian

tag: sirna

value: JunD


title: PC3 Csi, biological rep3

description:
PC3 Csi_3
Gene expression data from PC3 control cells.

value: control


title: PC3 Csi, biological rep1

description:
PC3 Csi_1
Gene expression data from PC3 control cells.


title: PC3 siJunD, biological rep3

description:
PC3 siJunD_3
Gene expression data from PC3 cells following JunD Knockdown by siRNA.


title: PC3 siJunD, biological rep2

description:
PC3 siJunD_2
Gene expression data from PC3 cells following JunD Knockdown by siRNA.


title: PC3 Csi, biological rep2

description:
PC3 Csi_2
Gene expression data from PC3 control cells.


title: MD-9-LSK-KO-1


title: K562 IRF2BP2 rep2

city: Singapore

first: Melissa

middle: Jane

last: Fullwood

address: 14 Medical Drive, #12-01

department: School of Biological Sciences

institute: Nanyang Technological University

data_processing:
Primer sequences at 5' ends of reads were trimmed using Tagdust2.
Extracted reads were then mapped to reference genome (hg19) using Bowtie2 (2.2.6)
Unaligned reads were collected. The first 50 base pairs of the unaligned reads were extracted and realigned to the genome using Bowtie2 (2.2.6). The uniquely aligned reads (MAPQ>= 30) were combined.
R Package r3Cseq was used to call significant interactions.
Genome_build: hg19

source_name: chronic myelogenous leukemia

growth_protocol: Cell cultures were maintained at 37 °C, 5% CO2 humidified incubator.

extract_protocol:
Briefly, 4 × 107 cells were cross-linked with 1% formaldehyde. The nuclei pellets were isolated by cell lysis with cold lysis buffer (10mM Tris-HCl, 10mM NaCl, 5mM EDTA, 0.5% NP 40) supplemented with protease inhibitors (Roche). First step digestion was performed overnight at 37°C with HindIII enzyme (NEB). Digestion efficiency was measured by RT-qPCR with HindIII site–specific primers. After confirmation of good digestion efficiency, DNA was ligated overnight at 16°C by T4 DNA ligase (Thermo Scientific) and de-crosslinked. Following de-crosslinking, DNA was extracted by phenol-chloroform. The DNA was then processed for second digestion with DpnII enzyme (NEB) overnight at 37°C. After final ligation, 4C template DNA was obtained and the concentration was determined using Qubit assays (Thermo Scientific).
The 4C template DNA was then amplified using specific primers with illumina Nextera adapters and sent for sequencing on the MiSeq system.
4C-seq


title: MCF-7 SIAH2 naïve rep2

source_name: breast cancer

growth_protocol: Cultured in DMEM/F12 supplemented with 10% FBS and 1% penicillin-streptomycin and maintained at 37◦C, 5% CO2 humidified incubator. MCF-7 cells were grown in hormone-free media: they were washed with PBS and incubated in phenol red-free medium (Invitrogen/Gibco) supplemented with 10% charcoal-dextran stripped FBS (Hyclone) and 1% pencillin-streptomycin for a minimum of 72 hours.

treatment_protocol: Hormone-depleted MCF-7 cells were treated with an equal volume and concentration of vehicle, ethanol (ET, Merck) as the primed cells, for 45 min.

value: vehicle, ethanol


title: MD-8-LSK-WT-2


title: MCF-7 SIAH2 naïve rep1


title: RNAseq_Ctrl_3

description: mouse islets ctrl rep 3

value: Ctrl 10d


title: MCF-7 SIAH2 primed rep1

treatment_protocol: Hormone-depleted MCF-7 cells were treated with oestrogen to a final concentration of 100 nM for 45 mins .

value: oestrogen


title: 14-MO-10hpf


title: RNAseq_Ctrl_2

description: mouse islets ctrl rep 2


title: MCF-7 SIAH2 primed rep2


title: MCF-7 GREB1 naïve rep2


title: MCF-7 GREB1 naïve rep1


title: MD-7-LSK-WT-1


title: RNAseq_Ctrl_1

description: mouse islets ctrl rep 1


title: inputDNA_IL1B_2

description: mouse islets input IL1B rep2

data_processing:
The single-end 50 base pair reads were mapped to the UCSC mouse transcriptome (mm9) by bowtie, allowing for up to 2 mismatches.
Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
in homer, function "makeUCSCfile" was used to generate bigWig file
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using KAPA DNA Library Preparation Kits for Illumina.


title: MD-6-Lin-Mut-2


title: MCF-7 GREB1 primed rep1


title: MCF-7 ELOVL2 naïve rep2


title: MCF-7 GREB1 primed rep2


title: MD-5-Lin-Mut-1


title: MCF-7 ELOVL2 naïve rep1


title: RNAseq_IL1B_3

description: mouse islet IL1B rep 3


title: inputDNA_Ctrl_2

description: mouse islets input ctrl rep2


title: MD-4-Lin-KO-2


title: inputDNA_IL1B_1

description: mouse islets input IL1B rep1


title: MCF-7 ELOVL2 primed rep1


title: inputDNA_Ctrl_1

description: mouse islets input ctrl rep1


title: MCF-7 ELOVL2 primed rep2


title: MD-2-Lin-WT-2


title: H3K27me3_ChIPseq_Ctrl_2

description: mouse islets H3K27me3 ctrl rep2

tag: chip antibody

value: H3K27me3 (Cat#07-449 Milipore)


title: H3K4me3_ChIPseq_IL1B_2

description: mouse islets H3K4me3 IL1B rep2

value: H3K4me3 (Cat#04-745 Milipore)


title: H3K27me3_ChIPseq_IL1B_2

description: mouse islets H3K27me3 IL1B rep2


title: M-1-27

description: memory line

tag: replicate type

value: biological rep 2

value: rosette leaves


title: H3K4me3_ChIPseq_Ctrl_2

description: mouse islets H3K4me3 ctrl rep2

tag: strain

value: male


title: RNA-seq MD12-R-EB (Rinf Knockout Replicate #2 day 6)

data_processing:
ChIP-seq analysis: Raw data files are untrimmed fastq files generated using picard-tools (files ending in fastq.gz files), trimmed fastq files generated using trim-galore (v 0.4.1, https://github.com/FelixKrueger/TrimGalore). Reads were mapped to the mouse genome (mm10) using the software Bowtie2 (VN: 2.2.3) with default parameters (Langmead and Salzberg, 2012). The Rinf binding peaks were called by the software MACS2 using the input as controls (Zhang et al., 2008), with the final peaks from the merged reads of the two biological replicates.
RNA-seq analysis: The reads were trimmed using trim-galore to remove adapters and then mapped to mouse genome (mm10) by tophat software (v 2.0.13) with default parameters (the same to the ChIP-seq data mapping). The reads  mapped to each gene in the Refseq gene annotation (downloaded from UCSC genome browser in 03/2017) were calculated with HTseq (v 0.6.1, (Anders et al., 2015)) using “–s reverse” parameter to obtain read counts for each gene. The Fragments Per Kilobase of transcript per Million (FPKMs) for each gene were calculated using cufflinks package (v 2.2.1, (Trapnell et al., 2010)).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage (deeptools 3.1.0), gene expression FPKM were generated from cuffdiff (cufflinks v2.2.1).

source_name: RNA-seq Rinf Knockout EB day 6 (Replicate #2)

growth_protocol: ESCs were cultured on gelatin in Serum/LIF and then harvested for ChIP-seq or RNA-seq

extract_protocol:
For RNA-seq, RNA extraction was performed using Omega E.Z.N.A Total RNA kit
ChIP-seq libraries were prepared using NEB library kit. RNA-seq libraries were prepared using illumina library prep kit following manufacterer's protocols at Einstein Epigenomcis core.

treatment_protocol: For ChIP-seq, ESCs were crosslinked, lysed, sonicated and subjected to ChIP using an anti-Rinf antibody (84546S, CST).

tag: Stage

value: EB day 6

tag: cell type

value: Embryonic stem cells

tag: passages

value: mixed 129/C57BL/6

tag: genotype

value: Rinf Knockout


title: RNA-seq MD10-R-EB (Rinf Wild type Replicate #2 day 6)

source_name: RNA-seq Rinf Wild type EB day 6 (Replicate #2)

value: Rinf Wild type


title: H3K27ac_ChIPseq_IL1B_2

description: mouse islets H3K27ac IL1B rep2

value: IL1B 10 d

value: 12 weeks

tag: tissue

value: pancreatic islets

value: H3K27ac (Cat#39133 Active Motif)


title: RNA-seq MD9-R-EB (Rinf Wild type Replicate #1 day 6)

source_name: RNA-seq Rinf Wild type EB day 6 (Replicate #1)


title: MD-1-Lin-WT-1

tag: developmental stage

value: bone marrow


title: RNA-seq MD11-R-EB (Rinf Knockout Replicate #1 day 6)

source_name: RNA-seq Rinf Knockout EB day 6 (Replicate #1)


title: RNA-seq MD8-R-EB (Rinf Knockout Replicate #2 day 3)

source_name: RNA-seq Rinf Knockout EB day 3 (Replicate #2)

value: EB day 3


title: K562 IRF2BP2 rep1

tag: treatment


title: RNA-seq MD7-R-EB (Rinf Knockout Replicate #1 day 3)

source_name: RNA-seq Rinf Knockout EB day 3 (Replicate #1)


title: WB_exp2_ActiveCase_Patient13

city: Milan

first: Michaela

last: Fakiola

address: Via Francesco Sforza 35

country: Italy

institute: INGM

description:
Experiment 2
SAMPLE 47

data_processing:
Data were analyzed using lumi, beadarray and limma R packages. Raw data underwent background correction using negative ccontrol probes followed by quantile normalization and log2 transformation. Non-expressed (detection P-value > 0.05 in all arrays) and poor quality probes previously shown to have unreliable annotation were removed. Active Case versus i) Treated or ii) Healthy Controls contrasts were analyzed for differential expression against the fitted linear model using eBayesfunctions in limma.
Matrix non-normalised: software computed raw signal intensity

source_name: Whole Blood

label_protocol: Biotinylated cRNA was generated following manufacturer protocols.

extract_protocol: RNA from whole blood samples was extracted using PAXgene Blood RNA kits (QIAGEN GmbH, Germany) according to manufacturer’s instructions. Globin mRNA was depleted using GLOBINclear™-Human kits (ThermoFischer Scientific, USA). RNA integrity and purity were checked using Tape Station 4200 (Agilent Technologies, USA).

tag: disease state

value: Active Visceral Leishmaniasis Case

tag: gender

value: Female


title: WB_exp2_Treated_Patient13

description:
Experiment 2
SAMPLE 48

value: Active Visceral Leishmaniasis Case, treated with a single dose of liposome-encapsulated Amphotericin B


title: WB_exp2_EHC_Rep10

description:
Experiment 2
SAMPLE 45

value: Endemic Healthy Control (serology and quantiferon negative)

value: Male


title: WB_exp2_HighAb_Rep6

description:
Experiment 2
SAMPLE 46

value: High anti-leishmanial antibody levels by direct agglutination test


title: H3K27me3_ChIPseq_IL1B_1

description: mouse islets H3K27me3 IL1B rep1

value: male

value: H3K27me3 (Cat#07-449 Milipore)


title: WB_exp2_EHC_Rep9

description:
Experiment 2
SAMPLE 41


title: H3K27me3_ChIPseq_Ctrl_1

description: mouse islets H3K27me3 ctrl rep1

value: Ctrl 10d


title: WB_exp2_Quantiferon_Rep9

description:
Experiment 2
SAMPLE 42

value: Quantiferon positive asymptomatic


title: RNA-seq MD6-R-EB (Rinf Wild type Replicate #2 day 3)

source_name: RNA-seq Rinf Wild type EB day 3 (Replicate #2)

value: Embryonic stem cells

value: mixed 129/C57BL/6

value: Rinf Wild type


title: WB_exp2_HighAb_Rep5

description:
Experiment 2
SAMPLE 37


title: WB_exp2_ActiveCase_Patient12

description:
Experiment 2
SAMPLE 43


title: WB_exp2_Treated_Patient12

description:
Experiment 2
SAMPLE 44


title: WB_exp2_Treated_Patient11

description:
Experiment 2
SAMPLE 40


title: WB_exp2_ActiveCase_Patient11

description:
Experiment 2
SAMPLE 39


title: WB_exp2_EHC_Rep8

description:
Experiment 2
SAMPLE 36


title: WB_exp2_Quantiferon_Rep8

description:
Experiment 2
SAMPLE 38


title: H3K4me3_ChIPseq_IL1B_1

description: mouse islets H4me3 IL1B rep1

value: IL1B 10 d

value: 12 weeks

value: pancreatic islets

value: H3K4me3 (Cat#04-745 Milipore)


title: RNA-seq MD5-R-EB (Rinf Wild type Replicate #1 day 3)

source_name: RNA-seq Rinf Wild type EB day 3 (Replicate #1)

value: EB day 3


title: H3K4me3_ChIPseq_Ctrl_1

description: mouse islets H3K4me3 ctrl rep1


title: RNA-seq MD4-R-EB Rinf Knockout Replicate #2 day 0)

source_name: RNA-seq Rinf Knockout EB day 0 (Replicate #2)

value: EB day 0

value: Rinf Knockout


title: RNA-seq MD3-R-EB (Rinf Knockout Replicate #1 day 0)

source_name: RNA-seq Rinf Knockout EB day 0 (Replicate #1)


title: H3K27ac_ChIPseq_IL1B_1

description: mouse islets H3K27ac ctrl IL1B rep1

value: H3K27ac (Cat#39133 Active Motif)


title: H3K27ac_ChIPseq_Ctrl_1

description: mouse islets H3K27ac ctrl rep1


title: OLFM4-Active RWPE1 cells

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
Sequencing reads were trimmed for adapter contamination with Cutadapt
then aligned to human genome with HISAT2
read counts were produced by using featureCounts
Genome_build: GENCODE release 26
Supplementary_files_format_and_content: text file with read counts

source_name: Prostate

growth_protocol: ATCC prostate epithelium cell culture protocol

extract_protocol:
Total RNA was extracted  by using RNeasy plus Mini kits (Qiagen)
Illumina’s TruSeq Stranded Total RNA kit with Ribo-Zero following the manufacturer instruction

value: prostate


title: WB_exp2_EHC_Rep7

description:
Experiment 2
SAMPLE 32

value: Endemic Healthy Control (serology and quantiferon negative)

value: Female


title: RNA-seq MD2-R-EB (Rinf Wild type Replicate #2 day 0)

source_name: RNA-seq Rinf Wild type EB day 0 (Replicate #2)


title: OLFM4-Knock out-RWPE1 cells

value: OLFM4-Knock out


title: RNA-seq MD1-R-EB (Rinf Wild type Replicate #1 day 0)

source_name: RNA-seq Rinf Wild type EB day 0 (Replicate #1)


title: WB_exp2_Treated_Patient10

description:
Experiment 2
SAMPLE 34

value: Active Visceral Leishmaniasis Case, treated with a single dose of liposome-encapsulated Amphotericin B


title: WB_exp2_HighAb_Rep4

description:
Experiment 2
SAMPLE 35

value: High anti-leishmanial antibody levels by direct agglutination test


title: WB_exp2_Treated_Patient9

description:
Experiment 2
SAMPLE 30


title: WB_exp2_Quantiferon_Rep7

description:
Experiment 2
SAMPLE 31

value: Quantiferon positive asymptomatic


title: WB_exp2_EHC_Rep6

description:
Experiment 2
SAMPLE 28


title: WB_exp2_ActiveCase_Patient9

description:
Experiment 2
SAMPLE 29

value: Active Visceral Leishmaniasis Case


title: RNA-seq MD6-RKh12 ESC (Rinf Knockout Replicate #2)

source_name: RNA-seq Rinf Knockout mESC (Rinf Knockout Replicate #2)

value: mESC

value: Embryonic stem cells

value: mixed 129/C57BL/6


title: WB_exp2_ActiveCase_Patient10

description:
Experiment 2
SAMPLE 33


title: WB_exp2_Quantiferon_Rep6

description:
Experiment 2
SAMPLE 27

value: Male


title: OLFM4-wild RWPE1 cells

value: OLFM4-wild type


title: WB_exp2_Treated_Patient7

description:
Experiment 2
SAMPLE 24


title: RNA-seq MD4-RKc1 ESC (Rinf Knockout Replicate #1)

source_name: RNA-seq Rinf Knockout mESC (Rinf Knockout Replicate #1)


title: WB_exp2_Quantiferon_Rep4

description:
Experiment 2
SAMPLE 17


title: WB_exp2_HighAb_Rep2

description:
Experiment 2
SAMPLE 18


title: WB_exp2_ActiveCase_Patient7

description:
Experiment 2
SAMPLE 23


title: WB_exp2_Treated_Patient6

description:
Experiment 2
SAMPLE 20


title: RNA-seq MD1-RW1 ESC (Rinf Wild type Replicate #1)

source_name: RNA-seq Rinf Wild type mESC (Rinf Wild type Replicate #1)

value: Rinf Wild type


title: WB_exp2_Treated_Patient8

description:
Experiment 2
SAMPLE 26


title: WB_exp2_HighAb_Rep3

description:
Experiment 2
SAMPLE 25


title: WB_exp2_EHC_Rep5

description:
Experiment 2
SAMPLE 22


title: WB_exp2_ActiveCase_Patient5

description:
Experiment 2
SAMPLE 19


title: Combi-GCR

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

description: 697 cell line - DEXA+KPT treatment - GCR antibody

data_processing:
cleaning .fastq files with fastq-mcf, quality control with fastQC
mapping to genome with HiSat2
count reads with htseq-count
call peaks with MACS2
normlization with deepTools
Genome_build: Homo Sapiens (GRCh38/hg38)
Supplementary_files_format_and_content: tab-delimited text files contain raw mRNA counts
Supplementary_files_format_and_content: narrowpeak / bed files with the called peaks (macs2)
Supplementary_files_format_and_content: bedgraph files with normalized signals

source_name: B-ALL cell line

extract_protocol: all libraries were prepared for sequencing using standard Illumina protocols

tag: protocol

value: ChIPmentation

tag: agent

value: DEXA+KPT

tag: antibody

value: GCR


title: ChIP-seq Rinf –/– (F8) - Input

description: Rinf knockout line input

source_name: ChIP-seq Rinf Knockout Input

value: Rinf Knockout


title: Combi-H3K27ac

description: 697 cell line - DEXA+KPT treatment - H3K27ac

tag: cell line


title: WB_exp2_Quantiferon_Rep5

description:
Experiment 2
SAMPLE 21

tag: age


title: KPT-H3K27ac

description: 697 cell line - KPT treatment - H3K27ac

value: KPT


title: KPT-GCR

description: 697 cell line - KPT treatment - GCR antibody


title: WB_exp2_EHC_Rep4

description:
Experiment 2
SAMPLE 14

value: Endemic Healthy Control (serology and quantiferon negative)

value: Female


title: ChIP-seq Rinf v5/v5 (A9) - Input

description: Rinf tagged line input

source_name: ChIP-seq Rinf tagged Input

tag: chip antibody


title: WB_exp2_Treated_Patient4

description:
Experiment 2
SAMPLE 16

value: Active Visceral Leishmaniasis Case, treated with a single dose of liposome-encapsulated Amphotericin B


title: Dexa-H3K27ac

description: 697 cell line - DEXA treatment - H3K27ac

value: DEXA


title: WB_exp2_ActiveCase_Patient4

description:
Experiment 2
SAMPLE 15


title: ChIP-seq Rinf –/– (F8) CXXC5-AB

description: Rinf Knockout line chipped with anti Rinf antibody

source_name: ChIP-seq Rinf Knockout mESC

value: Anti Rinf Antibody (CST 84546S)


title: Dexa-GCR

description: 697 cell line - DEXA treatment - GCR antibody


title: WB_exp2_EHC_Rep3

description:
Experiment 2
SAMPLE 12


title: WB_exp2_Quantiferon_Rep3

description:
Experiment 2
SAMPLE 13

value: Quantiferon positive asymptomatic


title: WB_exp2_Quantiferon_Rep2

description:
Experiment 2
SAMPLE 11


title: WB_exp2_Treated_Patient3

description:
Experiment 2
SAMPLE 10


title: ChIP-seq Rinf v5/v5 (A9) CXXC5-AB-2 (Replicate #2)

description: ChIP with anti rinf antibody

source_name: ChIP-seq Rinf Wild type mESC (Replicate #2)


title: WB_exp2_ActiveCase_Patient3

description:
Experiment 2
SAMPLE 9

value: Active Visceral Leishmaniasis Case


title: ChIP-seq Rinf v5/v5 (A9) CXXC5-AB-1 (Replicate #1)

description: ChIP with anti rinf antibody

source_name: ChIP-seq Rinf Wild type mESC (Replicate #1)

value: Embryonic stem cells


title: DMSO-GCR

description: 697 cell line - DMSO treatment - GCR antibody

value: DMSO


title: WB_exp2_EHC_Rep2

description:
Experiment 2
SAMPLE 7

source_name: Whole Blood


title: WB_exp2_HighAb_Rep1

description:
Experiment 2
SAMPLE 8

value: High anti-leishmanial antibody levels by direct agglutination test


title: WB_exp2_Treated_Patient2

description:
Experiment 2
SAMPLE 6


title: WB_exp2_EHC_Rep1

description:
Experiment 2
SAMPLE 4


title: SUPT1-Combi-3

description: SUPT-1 cell line - DEXA+KPT treatment

source_name: T-ALL cell line

extract_protocol:
processed with QuantSeq Kit according to manufacturers instructions
all libraries were prepared for sequencing using standard Illumina protocols

value: RNA sequencing


title: SUPT1-Combi-2

description: SUPT-1 cell line - DEXA+KPT treatment


title: DMSO-H3K27ac

description: 697 cell line - DMSO treatment - H3K27ac


title: SUPT1-Combi-1

description: SUPT-1 cell line - DEXA+KPT treatment


title: Artis_B3

city: Cambridge

first: Hattie

last: Chung

state: MA

address: 415 Main St

institute: Broad Institute

description:
Single nucleus polyA RNA transcriptome
snRNAseq data from medial prefrontal cortex of control adult mouse

data_processing:
3' polyA RNA-seq
Cellranger toolkit (v2.2.0)
Genome_build: mm10 mouse transcriptome with pre-mRNA annotations, similar to Bakken et al. 2018.
Supplementary_files_format_and_content: Anndata object of UMI counts and metadata, where rows are cells/barcodes and columns are genes. From cellranger raw gene matrix output.

source_name: medial prefrontal cortex (mPFC)

extract_protocol:
nuclei extraction with EZ prep
3' polyA RNA seq
10X Genomics Chromium Prep V3

value: adult

tag: brain region

value: medial prefrontal cortex

value: Control


title: Artis_B4


title: Artis_A3

description:
Single nucleus polyA RNA transcriptome
snRNAseq data from medial prefrontal cortex of antibiotic treated adult mouse

value: Antibiotic-treated


title: Artis_A4


title: SUPT1-KPT-2

description: SUPT-1 cell line - KPT treatment


title: WB_exp2_Quantiferon_Rep1

description:
Experiment 2
SAMPLE 3

value: Male