title: EYFP292 [RNA-seq]

description:
TMPRSS2-EYFP292_IGO_05957_G_1_S10_L001
processed data file:
rlog_normalized_counts_RNAseq_02252019_nodup.csv


title: ETV4WT-EWT371 [RNA-seq]

status: Public on Jan 01 2021

type: SRA

city: New York City

first: Dan

last: Li

state: NY

department: HOPP

country: USA

institute: Memorial Sloan-Kettering Cancer Center

description:
EWT371_IGO_05957_F_3_S6
processed data file:
rlog_normalized_counts_RNAseq_02252019_nodup.csv

library_source: transcriptomic

data_processing:
ATAC-seq and primary data processing: ATAC-seq was performed as previously described (Buenrostro et al., 2013). Primary data processing and peak calling was performed using ENCODE ATAC-seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines). Briefly, paired-end reads were trimmed, filtered and aligned against mm9 using Bowtie2 (Langmead et al., 2009). PCR duplicates and reads mapped to mitochondrial chromosome or repeated regions were removed. Mapped reads were shifted +4/-5 to correct for the Tn5 transposase insertion. Peak calling was performed using MACS2(Zhang et al., 2008), with p value < 0.01 as cutoff. Reproducible peaks from two biological replicates were defined as peaks overlapped by more than 50%. On average 25 million uniquely mapped pairs of reads were remained after filtering. The distribution of inserted fragment length shows typical nucleosome banding pattern, and the TSS enrichment score (reads that are enriched around TSS against background) ranges between 28 and 33, suggesting the libraries have high quality and were able to capture the majority of regions of interests.
Differential peak accessibility: Reads aligned to peak regions were counted using R package GenomicAlignments_v1.12.2 (Lawrence et al., 2013). Read count normalization and differential accessible peaks were called with DESeq2_v1.16.1 in R 3.4.1 (Love et al., 2014). Differential peaks were defined as peaks with adjusted p value < 0.01 and |log2(FC)| > 1.  For visualization, coverage bigwig files were generated using bamCoverage command from deepTools2, normalizing using the size factor generated by DESeq2. The differential ATAC-seq peak density plot was generated with deepTools2 (Ramírez et al., 2018), using regions that were significantly more or less accessible in ETV4AAA samples relative to EYFP samples.
Motif analysis: Enriched motif and de novo motif analysis using Homer (findMotifsGenme.pl) (Heinz et al., 2010) with ‘size -given -mask’ was applied to differentially accessible regions in ETV4AAA relative to EYFP, with the non-differentially accessible peaks as background.
RNA-seq analysis: The extracted RNA was processed for RNA-sequencing by the Integrated Genomics Core Facility at MSKCC.  The libraries were sequenced on an Illumina HiSeq-2500 platform with 51 bp paired-end reads to obtain a minimum yield of 40 million reads per sample. The sequenced data were aligned using STAR v2.3 (Dobin et al., 2013) with GRCm38.p6 as annotation. DESeq2_v1.16.1 (Love et al., 2014) was subsequently applied on read counts for normalization and the identification of differentially expressed genes between ETV4AAA and EYFP groups, with adjusted p value < 0.05 as threshold. Genes were ranked by sign(log2(FC)) * (-log(p value)) as input for GSEA analysis using ‘Run GSEA Pre-ranked’ with 1000 permutations (Subramanian et al., 2005).
Genome_build: mm9
Supplementary_files_format_and_content: csv files include log2_normalized_counts of all samples

molecule: total RNA

organism: Mus musculus

source_name: primary prostate cells_ETV4WT

extract_protocol:
Intraperitoneal injection of tamoxifen was administered in 8-week-old mouse. 1 week after tamoxifen treatment, mouse prostate was digested 1 hour with Collagenase/Hyaluronidase (STEMCELL, #07912) and then 30 minutes with TrypLETM Express Enzyme (Thermo Fischer, # 12605028) at 37°C to isolate single prostate cells. The prostate cells were stained with PE/Cy7 conjugated anti-mouse CD326 (EpCAM) antibody (BioLegend, 118216) and then, CD326 and EYFP double positive cells were sorted out by flow cytometry. The mRNA or genomic DNA were extracted from these double positive cells and then were used for ATAC-sequencing and RNA-sequencing analysis.
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: age

value: 2 months old

tag: genotype/variation

tag: tissue/cell type

value: Isolated primary mouse prostate cells

tag: cell population

value: CD326 and EYFP double positive cells


title: ETV4AAA-ETV4298 [RNA-seq]

description:
TMPRSS2-ETV4298_IGO_05957_G_4_S13_L001
processed data file:
rlog_normalized_counts_RNAseq_02252019_nodup.csv

source_name: primary prostate cells_ETV4AAA


title: ETV4WT-EWT357 [RNA-seq]

description:
EWT357_IGO_05957_F_1_S4
processed data file:
rlog_normalized_counts_RNAseq_02252019_nodup.csv


title: ETV4AAA-ETV4299 [RNA-seq]

description:
TMPRSS2-ETV4299_IGO_05957_G_5_S14_L001
processed data file:
rlog_normalized_counts_RNAseq_02252019_nodup.csv


title: 13w_replicate2

city: Epalinges

first: Grégory

last: Verdeil

address: Ch. des Boveresses 155

department: Department of Oncology

country: Switzerland

institute: University of Lausanne

data_processing:
RNAseq quantification was performed with kallisto 0.44.0 with sequence-based bias correction using transcript sequences obtained from ENSEMBLE (GRCm38.p6). All other parameters were set to default when running kallisto.
Kallisto's transcript-level estimates were further summarized at the gene-level using tximport 1.8.0 from Bioconductor.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: CSV table of raw estimated counts as obtained from tximport. Rows represent genes and columns represent samples.

source_name: Bladder tumor cells

growth_protocol: Tumors were induced by the injection of an adenoviral vector that expresses the Cre-recombinase directly in the bladder of P53 Fl/F lPTEN Fl/Fl mice. At 5/9/13 weeks tumors were harvested and tumor cells were isolated using percoll gradient.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (#74034, Qiagen) according to manufacturer’s recommendations
Truseq Stranded RNA, using 500ng of total RNA per sample

tag: tissue

value: Bladder tumor cells

tag: Sex

value: female

tag: batch

tag: cell passage number

tag: time

value: 13 weeks

value: P53 Fl/F lPTEN Fl/Fl mice


title: ETV4AAA-ET620 [RNA-seq]

description:
ET620_IGO_05957_F_5_S8
processed data file:
rlog_normalized_counts_RNAseq_02252019_nodup.csv


title: 25_M1: Control

city: Jerusalem

first: Raz

last: Yirmiya

address: Mount Scopus

country: Israel

institute: Hebrew University of Jerusalem

description: Brain

data_processing:
Reads were trimmed using cutadapt
TopHat (v2.0.10) was used to align the reads to the mouse genome (mm10)
Counting reads on hg19 RefSeq genes was done with HTSeq-count (version 0.6.1p1)
Normalization was performed using DESeq2 (1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 normalized counts

source_name: hippocampus

growth_protocol: Subjects were 4-8 months old male WT C57BL/6 mice. Animals were housed in air-conditioned rooms (23° C), with food and water ad libitum, and were kept in a reversed light/dark cycle, with lights off from 7 a.m. to 7 p.m. All experiments were approved by the Hebrew University of Jerusalem Ethics Committee on Animal Care, and use.

extract_protocol:
5 prime perfect pure RNA kit
Inhouse poly A based RNA seq

treatment_protocol: Subjects were divided into two groups, treated with either a diet containing 1200 mg/g PLX5562 (Plexxicon Inc., U.S.A), a selective CSF1 receptor kinase inhibitor, which when given chronically (i.e., for more than 2-3 weeks) induces near-complete microglial depletion (Elmore et al., 2014; Dagher et al., 2015), or with a control diet (i.e., identical diet not containing PLX5562). Following 3 weeks exposure to the diet (i.e., after attainment of microglial depletion in the PLX5562-treated animals), subjects from the two diet groups were exposed to a Chronic Unpredictable Stress (CUS) schedule, consisting of daily exposure to two stressors in a random order over a 5-week period. The effect of a shorter period of unpredictable stress was examined by exposing mice to various combinations of 2–3 of the same stressors over a period of 2 days. The list of CUS stressors included: cage shaking for 1 h with loud music and lights on, lights on during the entire night (12 h), lights-off for 3 h during the daylight phase, flashing (stroboscopic) light for 6 h, placement in 4ºC cold room for 1 h, mild restraint (in small ventilated cages) for 2 h, 45º cage tilt for 14 h, wet sawdust in the cage for 14 h, exposure to fox, ferret, bobcat, or coyote odor for 2 h, noise in the room for 3 h, and water deprivation for 12 h during the dark period. Another group of subjects administered with the control diet did not undergo the CUS procedure and served as an untreated (non-stressed) control group. At the beginning of the sixth week of the CUS exposure, following verification of CUS-induced depressive-like symptoms, the CUS-exposed mice were further divided into two sub-groups, administered with either ECT (3-times per week for 2.5 weeks) or sham treatment. Before each treatment, mice were lightly anesthetized with isoflurane, and administered a single shock via ear clip electrodes, using a Ugo Basile ECT Unit (Varese, Italy). with the following parameters: frequency of 100 pulses per sec, 18mA current, 0.3 sec shock duration, and 0.5 ms pulse width. Mice in the SHAM group went through the same procedure, but current was not applied through the electrodes. Mice were anestesized, the hippocampus was dissected quickly and flash frozen in liquid nitrogen for further RNA analysis.

value: hippocampus

tag: treatment

value: No Treatment

tag: diet

value: Control Diet

tag: stress

value: No Stress


title: 24_S3: Control

description: Brain


title: 22_M2: Control

description: Brain


title: 23_O1: Control

description: Brain


title: 21_L1: PLX Diet, CUS, SHAM

description: Brain

value: SHAM Treatment

value: PLX Diet

value: Chronic Unpredictable Stress


title: 19_J1: PLX Diet, CUS, SHAM

description: Brain


title: 20_J2: PLX Diet, CUS, SHAM

description: Brain


title: 18_I2: PLX Diet, CUS, SHAM

description: Brain


title: 17_I1: PLX Diet, CUS, SHAM

description: Brain


title: 9w_replicate2

value: 9 weeks


title: 9_C2: Control Diet, CUS, SHAM

description: Brain


title: 11_D2: Control Diet, CUS, SHAM

description: Brain


title: 14_H1: PLX Diet, CUS, ECT

description: Brain

value: Electroconvulsive therapy


title: 10_D1: Control Diet, CUS, SHAM

description: Brain


title: 15_H2: PLX Diet, CUS, ECT

description: Brain


title: 7_B1: Control Diet, CUS, SHAM

description: Brain


title: 12_G1: PLX Diet, CUS, ECT

description: Brain


title: WT-ChIP-none-Rep2

city: Los Angeles

first: Quen

last: Cheng

state: CA

address: 611 Charles E Young Dr E

institute: UCLA

description:
WT_H3K4me1-CHIP_counts.txt
None_2

library_source: genomic

data_processing:
Samples were sequenced and base calls performed on Illumina HiSeq 2500
Reads were trimmed of adapter sequences and low-quality reads (q<30), then mapped to mm10 genome with bowtie2 (ChIP, ATAC) or STAR (RNA)
Aligned reads were filtered based on mapping score (MAPQ ≥ 30) by Samtools. For ChIP and ATAC-seq, duplicated reads were removed using Picard MarkDuplicates.
For ChIP-seq, MACS2 version 2.1.0 was used in broad mode to identify peaks for each sample using pooled input samples as control, FDR < 0.01, and extension size of average fragment length. These peaks were merged to generate a single reference peak file, and the number of reads that fell into each peak was counted using deeptools multiBamSummary with extension size of average fragment length
For ATAC-seq, BAM files were analyzed with the R package csaw, using windows 200-nt wide, with 100-nt spacing. Windows with zero or background signal were removed.
Genome_build: mm10
Supplementary_files_format_and_content: Raw count tables are provided (unnormalized). For ChIP and ATAC data, genomic regions of interest were defined by peak-calling (ChIP) or sliding windows in csaw (ATAC). For RNA data, the featureCounts function in the Subread package was used.

molecule: genomic DNA

source_name: bone marrow-derived macrophage

growth_protocol: BMDMs were generated by isolating bone marrow from the femurs and tibias of sex-matched mice between the ages of six and 12 weeks. Bone marrow cells were incubated in L929-conditioned media (RPMI + 30% L929 media, 10% FBS, 100 IU/ml penicillin, 100 ug/ml streptomycin, 2 mM L-glutamine) at 370C for seven days.

extract_protocol:
H3K4me1 ChIP was performed on lysed and sonicated chromatin using rabbit anti-H3K4me1 (Abcam ab8895). ATAC-seq samples were prepared as described in Buenrostro et al, 2013 using Tn5 transposase from Illumina. Total RNA was extracted by Trizol according to manufacturer's instructions.
Libraries were prepared according to manufacturer's instructions: ChIP-seq with NEBNext Ultra II DNA Library Prep Kit (New England Biolabs E7645), ATAC-seq with Nextera DNA Library Preparation Kit (Illumina, FC-121), RNA-seq with KAPA Stranded mRNA-seq Library Preparation kit (KAPA Biosystems)

treatment_protocol: Cells were stimulated with TNFa (10 ng/ml, R&D Systems 410-MT), Pam3CSK4 (100 ng/ml, Invivogen tlrl-pms), CpG (1 uM, Invivogen tlrl-1668), LPS (100 ng/ml, Sigma-Aldrich L2880), or Poly(I:C) (50 ug/ml, Invivogen tlrl-picw).

tag: genotype

value: WT

tag: antibody

tag: agent

tag: time point


title: 2_A3: Control Diet, CUS, ECT

description: Brain


title: 6_F2: Control Diet, CUS, ECT

description: Brain


title: WT-ChIP-CpG-Rep1

description:
WT_H3K4me1-CHIP_counts.txt
CpG_1

tag: strain

value: CpG (10 uM)


title: 13_G2: PLX Diet, CUS, ECT

description: Brain


title: 8_C1: Control Diet, CUS, SHAM

description: Brain


title: 1_A1: Control Diet, CUS, ECT

description: Brain


title: 5_F1: Control Diet, CUS, ECT

description: Brain


title: 3_E1: Control Diet, CUS, ECT

description: Brain


title: ETV4WT-EWT370 [RNA-seq]

description:
EWT370_IGO_05957_F_2_S5
processed data file:
rlog_normalized_counts_RNAseq_02252019_nodup.csv

tag: age

value: 2 months old

value: Isolated primary mouse prostate cells


title: 4_E2: Control Diet, CUS, ECT

description: Brain


title: sdLN_V1_Day5_rep3

type: RNA

city: Salvador

first: Leonardo

middle: Paiva

last: Farias

state: Bahia

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz-Fiocruz

description: Gene expression (mice sdLN) at Day 5 after 1 vaccine dose (500 attenuated cercariae)

hyb_protocol: Sample hybridizations were performed on Agilent slides for 16 h at 65°C. After gentle washing in accordance with Agilent’s protocol, microarrays were scanned on a C scanner (Agilent)

scan_protocol: Slides were scanned immediately after washing on a Agilent G2565CA DNA Microarray Scanner using one color scan setting for SurePrint G3 Mouse GE 8x60K array slides

data_processing: Agilent Feature Extraction software (v10.7) was used to read and process microarray image files. The software determined feature intensities and background, rejected outliers, and generated validated data files for further analyses. Each array was validated via the analysis of additive error, spatial distribution of outliers in the array, a histogram of signal plots, background sub-signal value and linear range spike-in statistics.

source_name: sdLN, V1, Day5, rep3

label_protocol: To produce Cy3-labeled cRNA, total RNA was amplified and labeled using an Agilent Low Input Quick Amplification Labeling Kit in strict accordance with manufacturer instructions. Briefly, 100 ng of template RNA was used for cDNA synthesis, and T7 RNA polymerase was then used for cRNA amplification and Cy3 labeling. After purification, yield and dye incorporation was measured using a Nanodrop spectrophotometer (Thermo Scientific).

extract_protocol: Total RNA was extracted using TRizol® Reagent (Ambion RNA, Life Technologies), with a precipitation step incorporating glycogen (5mg/mL, Ambion, USA) plus 3M sodium acetate (Ambion, USA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: C57BL/6 mice were distributed into five groups: control (C), non-treated animals; vaccinated once (V1) with 500 attenuated cercariae and challenged with 120 normal cercariae; vaccinated three times (V3) with 500 attenuated cercariae (4-week intervals) and challenged with 120 normal cercariae; only challenged with 120 normal cercariae (Chc); and  infected with 500 normal cercariae (Inf) in parallel with the 1V group. Blood was drawn from the same groups of mice in a time-course manner at Days 7 and 17 after imunization/infection, and Day 7 post-challenge and the PBMC was purified.

value: Skin draining lymph nodes

tag: gender

value: Female


title: sdLN_V3_Day5_rep3

description: Gene expression (mice sdLN) at Day 5 after 3 vaccine doses (500 attenuated cercariae)

source_name: sdLN, V3, Day5, rep3


title: sdLN_Cont_Day5_rep3

description: Gene expression (mice sdLN) of control group collected in parallel to Day 5

source_name: sdLN, Cont, Day5, rep3


title: PBMC_Cont_Day7pc_rep4

description: Gene expression (mice PBMC) of control group collected in parallel to Day 7pc

source_name: PBMC, Cont, Day7pc, rep4

value: Peripheral blood mononuclear cells


title: PBMC_Cont_Day7pc_rep1

source_name: PBMC, Cont, Day7pc, rep1


title: PBMC_Cont_Day7_rep5

description: Gene expression (mice PBMC) of control group collected in parallel to Day 7

source_name: PBMC, Cont, Day7, rep5


title: sdLN_VC_Day5_rep2

description: Gene expression (mice sdLN) at Day 5 after infection (500 normal cercariae)

source_name: sdLN, VC, Day5, rep2


title: sdLN_V1_Day5_rep2

source_name: sdLN, V1, Day5, rep2


title: PBMC_Cont_Day7_rep6

source_name: PBMC, Cont, Day7, rep6


title: PBMC_Cont_Day17_rep4

description: Gene expression (mice PBMC) of control group collected in parallel to Day 17

source_name: PBMC, Cont, Day17, rep4


title: sdLN_V1_Day5_rep1

source_name: sdLN, V1, Day5, rep1


title: sdLN_Cont_Day5_rep2

source_name: sdLN, Cont, Day5, rep2


title: PBMC_Cont_Day7_rep3

source_name: PBMC, Cont, Day7, rep3


title: sdLN_Cont_Day5_rep1

source_name: sdLN, Cont, Day5, rep1


title: PBMC_Cont_Day17_rep3

source_name: PBMC, Cont, Day17, rep3


title: PBMC_Cont_Day7pc_rep2

source_name: PBMC, Cont, Day7pc, rep2


title: PBMC_Cont_Day7_rep1

source_name: PBMC, Cont, Day7, rep1


title: sdLN_V3_Day5_rep1

source_name: sdLN, V3, Day5, rep1


title: PBMC_Cont_Day17_rep1

source_name: PBMC, Cont, Day17, rep1


title: PBMC_Cont_Day17_rep2

source_name: PBMC, Cont, Day17, rep2


title: PBMC_Cont_Day7pc_rep3

source_name: PBMC, Cont, Day7pc, rep3


title: sdLN_VC_Day5_rep3

source_name: sdLN, VC, Day5, rep3


title: sdLN_VC_Day5_rep1

source_name: sdLN, VC, Day5, rep1


title: PBMC_Cont_Day7_rep8

source_name: PBMC, Cont, Day7, rep8


title: PBMC_Cont_Day7_rep4

source_name: PBMC, Cont, Day7, rep4


title: PBMC_Cont_Day7_rep7

source_name: PBMC, Cont, Day7, rep7


title: PBMC_CHC_Day7pc_rep4

description: Gene expression (mice PBMC) of challenge control at Day 7 after infection (120 normal cercariae)

source_name: PBMC, CHC, Day7pc, rep4


title: PBMC_Cont_Day7_rep2

source_name: PBMC, Cont, Day7, rep2


title: PBMC_CHC_Day7pc_rep3

source_name: PBMC, CHC, Day7pc, rep3


title: PBMC_V3_Day7pc_rep2

description: Gene expression (mice PBMC) of V3 group at Day 7 post-challenge with 120 normal cercariae

source_name: PBMC, V3, Day7pc, rep2


title: PBMC_V3_Day7pc_rep5

source_name: PBMC, V3, Day7pc, rep5


title: PBMC_CHC_Day7pc_rep2

source_name: PBMC, CHC, Day7pc, rep2


title: PBMC_V3_Day7pc_rep3

source_name: PBMC, V3, Day7pc, rep3


title: PBMC_V3_Day17_rep4

description: Gene expression (mice PBMC) at Day 17 after 3 vaccine doses (500 attenuated cercariae)

source_name: PBMC, V3, Day17, rep4


title: PBMC_V1_Day7pc_rep3

description: Gene expression (mice PBMC) of V1 group at Day 7 post-challenge with 120 normal cercariae

source_name: PBMC, V1, Day7pc, rep3


title: PBMC_VC_Day17_rep1

description: Gene expression (mice PBMC) at Day 17 after infection (500 normal cercariae)

source_name: PBMC, VC, Day17, rep1


title: PBMC_CHC_Day7pc_rep1

source_name: PBMC, CHC, Day7pc, rep1


title: PBMC_V3_Day7pc_rep4

source_name: PBMC, V3, Day7pc, rep4


title: PBMC_VC_Day17_rep4

source_name: PBMC, VC, Day17, rep4


title: PBMC_V3_Day17_rep5

source_name: PBMC, V3, Day17, rep5


title: PBMC_VC_Day17_rep3

source_name: PBMC, VC, Day17, rep3


title: PBMC_V3_Day17_rep2

source_name: PBMC, V3, Day17, rep2


title: PBMC_V1_Day7pc_rep1

source_name: PBMC, V1, Day7pc, rep1


title: PBMC_VC_Day7_rep4

description: Gene expression (mice PBMC) at Day 7 after infection (500 normal cercariae)

source_name: PBMC, VC, Day7, rep4


title: PBMC_V3_Day17_rep1

source_name: PBMC, V3, Day17, rep1


title: PBMC_V3_Day7pc_rep1

source_name: PBMC, V3, Day7pc, rep1


title: PBMC_V1_Day7pc_rep2

source_name: PBMC, V1, Day7pc, rep2


title: PBMC_VC_Day17_rep2

source_name: PBMC, VC, Day17, rep2


title: PBMC_V1_Day7pc_rep4

source_name: PBMC, V1, Day7pc, rep4


title: PBMC_V1_Day17_rep2

description: Gene expression (mice PBMC) at Day 17 after 1 vaccine dose (500 attenuated cercariae)

source_name: PBMC, V1, Day17, rep2


title: PBMC_V3_Day17_rep3

source_name: PBMC, V3, Day17, rep3


title: PBMC_V1_Day17_rep4

source_name: PBMC, V1, Day17, rep4


title: PBMC_VC_Day7_rep3

source_name: PBMC, VC, Day7, rep3


title: PBMC_VC_Day7_rep2

source_name: PBMC, VC, Day7, rep2


title: PBMC_VC_Day7_rep1

source_name: PBMC, VC, Day7, rep1


title: PBMC_V1_Day17_rep3

source_name: PBMC, V1, Day17, rep3


title: sdLN_V3_Day5_rep2

source_name: sdLN, V3, Day5, rep2


title: PBMC_V1_Day17_rep1

source_name: PBMC, V1, Day17, rep1


title: PBMC_V1_Day7_rep2

description: Gene expression (mice PBMC) at Day 7 after 1 vaccine dose (500 attenuated cercariae)

source_name: PBMC, V1, Day7, rep2


title: PBMC_V3_Day7_rep2

description: Gene expression (mice PBMC) at Day 7 after 3 vaccine doses (500 attenuated cercariae)

source_name: PBMC, V3, Day7, rep2


title: PBMC_V3_Day7_rep5

source_name: PBMC, V3, Day7, rep5


title: PBMC_V1_Day7_rep4

source_name: PBMC, V1, Day7, rep4


title: PBMC_V1_Day7_rep3

source_name: PBMC, V1, Day7, rep3


title: 25MASTBA_sequence

city: San Francisco

first: Srilaxmi

last: Nerella

address: HSE1355A, 513 Parnassus ave

department: Department of Medicine

institute: UCSF

description:
Independent sample
MASTB_025_V2

data_processing:
Removed redundancy in the reads from s_*_sequence.txt file using custom PERL script
Alignment done on unique sequences (after adaptor trimming) by aligning reads using BowTie.The default parameters allowed for 3 mismatches in the first 17 nucleotides from the 3' end.
Genome_build: Data base: miRBase release 16, mature.fa
Supplementary_files_format_and_content: expression profile

organism: Homo sapiens

source_name: Bronchial cells from human bronchial epithelial brushings

extract_protocol:
As per manufacturer's protocol of the miRNeasy Kit (Qiagen)
As per manufacturer's protocol of the TruSeq Small RNA Library Preparation Kit (Illumina)

treatment_protocol: Healthy controls (no asthma or lung disease) or steroid-naive asthmatics (with asthma not using inhaled corticosteroids (ICS) for 6 weeks before enrollment at baseline ('Steroid-naive asthma - Baseline') or after 8 weeks of treatment with budesonide, 200 μg twice a day, ('Steroid-naive asthma - Post-ICS treatment'))

tag: condition

value: Steroid-naive asthma - Baseline

value: Bronchial cells


title: PBMC_V3_Day7_rep3

source_name: PBMC, V3, Day7, rep3


title: 23MASTBA_sequence

description:
Independent sample
MASTB_023_V2


title: Lung fibroblast, adult mice, replicate 3

city: Clayton

first: Hieu

middle: Tri

last: Nim

state: VIC

address: Monash University Clayton Campus, Wellington Rd

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

hyb_protocol: 600ng of Cy3 labeled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60oC for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturerâ€™s instructions. On completion 25ul of 2x Agilent gene expression hybridisation buffer was added and 40ul of sample hybridised for 17 hours at 65oC in a rotating Agilent hybridisation oven. After hybridisation, microarrays were washed 1 minute at room temperature with GE wash buffer 1(Agilent) and 1 minute with 37oC GE wash buffer 2(Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent C, DNA microarray scanner using one color scan settings for 8x60k array slides; scan area 61x21.6mm, scan resolution 3um, dye channel is set to Green and 20 bit Tiff.

data_processing: The scanned images were analysed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1-1100_Jul11 and Grid: (028005_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities. Agilent.SingleColor.28005 microarray, Software GeneSpring 12.6; Threshold: 1.0, Logbase: 2; Normalization: Quantile; Baseline Transformation: None; Filtered on Expression (20.0-100.0); Filtered on Flags (Detected, Not Detected); T test unpaired , P<=:0.05, FC>=2.0 Benjamini-Hochberg

source_name: Adult mice

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared from 0.1ug total RNA using the One-Color Low input Quick Amp labelling Kit (Agilent) according to the manufacturerâ€™s instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared using the mirVana kit (Invitrogen) folowed by DNAseI digestion following the manufacturer's recommendations. RNA was quantified  and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 8-10week old mouse tissues were finely chopped with surgical scissors and cut into 2-3mm pieces. All tissues were subjected to enzymatic digestion [0.05% trypsin/EDTA (Gibco) or 0.5mg/mL collagenase type II (Worthington)] at 37oC under agitation for 40 minutes, washed in HBSS and plated on 10cm dishes in DMEM high glucose supplemented with 10% FBS, 1x pen/strep and sodium pyruvate for 5 days at 37 ÂºC in a humidified incubator with 5% CO2

value: Lung

tag: developmental stage

value: Adult


title: Kidney fibroblast, adult mice, replicate 1

tag: tissue

value: Kidney


title: Liver fibroblast, adult mice, replicate 3

value: Liver


title: Tail fibroblast, adult mice, replicate 3

value: Tail


title: Heart fibroblast, adult mice, replicate 2

value: Heart


title: Liver fibroblast, adult mice, replicate 1


title: PBMC_V1_Day7_rep1

source_name: PBMC, V1, Day7, rep1


title: Skin fibroblast, adult mice, replicate 2

value: Skin


title: Tail fibroblast, adult mice, replicate 2


title: Heart fibroblast, adult mice, replicate 3


title: PBMC_V3_Day7_rep4

source_name: PBMC, V3, Day7, rep4


title: PBMC_V3_Day7_rep1

source_name: PBMC, V3, Day7, rep1


title: Tail fibroblast, adult mice, replicate 1


title: 20MASTBA_sequence

description:
Independent sample
MASTB_020_V2


title: 21MASTBA_sequence

description:
Independent sample
MASTB_021_V2


title: Liver fibroblast, adult mice, replicate 2


title: 17MASTBA_sequence

description:
Independent sample
MASTB_017_V2


title: Gonad fibroblast, adult mice, replicate 1

value: Gonad


title: Skin fibroblast, adult mice, replicate 1


title: Gonad fibroblast, adult mice, replicate 2


title: Lung fibroblast, adult mice, replicate 2


title: Heart fibroblast, adult mice, replicate 1


title: Kidney fibroblast, adult mice, replicate 2


title: Lung fibroblast, adult mice, replicate 1


title: 15MASTBA_sequence

description:
Independent sample
MASTB_015_V2


title: 16MASTAH_sequence

description:
Independent sample
MASTA_016_V2

value: Healthy control


title: Gonad fibroblast, adult mice, replicate 3


title: 14MASTBA_sequence

description:
Independent sample
MASTB_014_V2


title: 12MASTBA2_sequence

description:
Independent sample
MASTB_012_V5

value: Steroid-naive asthma - Post-ICS treatment


title: 10MASTBA2_sequence

description:
Independent sample
MASTB_010_V5


title: 12MASTBA_sequence

description:
Independent sample
MASTB_012_V2


title: 08MASTAH_sequence

description:
Independent sample
MASTA_008_V2


title: 10MASTBA_sequence

description:
Independent sample
MASTB_010_V2


title: 11MASTAH_sequence

description:
Independent sample
MASTA_011_V2


title: 06MASTAHrep_sequence

description:
Repeated sample
MASTA_006_V2_rep


title: 07MASTAHrep_sequence

description:
Repeated sample
MASTA_007_V2_rep


title: 02MASTAH_sequence

description:
Independent sample
MASTA_002_V2


title: 06MASTAH_sequence

description:
Independent sample
MASTA_006_V2


title: 17MASTAH_sequence

description:
Independent sample
MASTA_017_V2


title: TB4

city: Cambridge

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
Illumina software used for basecalling.
Sequences were aligned to the human genome using bowtie2
Raw counts of each gene for each sample were calculated by Rsem program
Raw counts of each sample normaized with TMM in calcNormFactors() of edgeR, values log2-transformed
Differentially expressed genes between paired samples before and after treatment were performed using the program edgeR
Genome_build: hg19
Supplementary_files_format_and_content: txt file includes count values for each sample

source_name: healthy donor 4 NK treated with Ascites 2

extract_protocol:
Qiagen RNeasy Micro Kit
SMARTer Universal Low Input RNA Kit

treatment_protocol: human PBMC NK cells were treated with either medium or ascites of human ovary cancer for 24 hrs.

tag: individual

value: donor 4

tag: cell type

value: Natural Killer (NK) Cells

value: acites donor 2


title: TB5

source_name: healthy donor 5 NK treated with Ascites 2

value: donor 5


title: TB1

source_name: healthy donor 1 NK treated with Ascites 2

value: donor 1


title: TB3

source_name: healthy donor 3 NK treated with Ascites 2

value: donor 3


title: TB6

source_name: healthy donor 6 NK treated with Ascites 2

value: donor 6


title: TA1

source_name: healthy donor 1 NK treated with Ascites 1

value: acites donor 1


title: TA2

source_name: healthy donor 2 NK treated with Ascites 1

value: donor 2


title: Patient6

source_name: patient 6 ascites NK

value: patient 6

value: no treatment


title: TA3

source_name: healthy donor 3 NK treated with Ascites 1


title: TA4

source_name: healthy donor 4 NK treated with Ascites 1


title: Pol2.TAM.ChIP

city: Hangzhou

first: Ruisheng

last: Song

state: Zhejiang

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

description: Biological replicate 1

data_processing:
Sequencing FASTQ reads were aligned to the hg19 human reference genome with Bowtie2 (Langmead and Salzberg, 2012) with the following restrictions “--very-sensitive --score-min L,-0.6,-0.15” for mapping sensitivity and accuracy. Only uniquely mapped reads, and in the case of paired-end sequenced data, only uniquely mapped sequence pairs that were aligned concordantly, were used for subsequent analyses.
In S100A8 or S100A9 ChIP-seq data, confident peaks were defined as fulfilling all the following restrictions: 1) MACS2 peakcalling q-value ≤ 1e-7 against sample-corresponding chromatin input background, 2) peaks called by MACS2 were identified in at least 2 biological replicates, 3) at least 5 raw reads were aligned at the peak region.
Confident Pol II ChIP-seq peaks were defined as MACS2 paired-end peak-calling p-value ≤ 1e-8 against genomic background of 1 megabase genomic region around.
By "wigToBigWig" (UCSC), BigWig files were converted from wiggle files, which were obtained by "igvtools count" with BAM files and were further noramlized with unique alignment depth
Genome_build: HG19
Supplementary_files_format_and_content: narrowPeak files with MACS2 called peak data for S100A8 and S100A9 ChIP; BigWig files with binding signal (reads per million) for Pol II ChIP

source_name: MCF10A cells expressing ER-Src

growth_protocol: Cell culture was performed at 37°C under 5% CO2. MCF10A cells expressing ER-Src were grown in DMEM/F12 with 5% charcoal-stripped fetal bovine serum (Sigma-Aldrich) and supplements as previously described (Iliopoulos et al., 2009).

extract_protocol:
Chromatin preparations were clarified from sonicated nuclei. Anti-Flag was used in ChIP for S100A8-Flag or S100A9-Flag; anti-Pol II (8WG16) was used in ChIP for Pol II.
Sequencing libraries were constructed following standard protocol (Green et al., 2012).

treatment_protocol: Cells were treated with 1 μM 4-hydroxy-tamoxifen (Sigma-Aldrich) for 24 hours to induce transformation; treatment with ethanol as vehicle control was used for non-transformation.

tag: cell line

tag: flag-tagged protein expression

tag: chip antibody

value: anti-Pol II (8WG16, Cat. No. MMS-126R, Covance)

value: TAM

tag: experiment

value: ChIP


title: TB2

source_name: healthy donor 2 NK treated with Ascites 2

tag: treatment


title: Pol2.EtOH.ChIP

description: Biological replicate 1

value: EtOH


title: Patient4

source_name: patient 4 ascites NK

value: patient 4


title: TA6

source_name: healthy donor 6 NK treated with Ascites 1


title: Patient3

source_name: patient 3 ascites NK

value: patient 3


title: 07MASTAH_sequence

description:
Independent sample
MASTA_007_V2

source_name: Bronchial cells from human bronchial epithelial brushings

value: Healthy control

value: Bronchial cells


title: Patient2

source_name: patient 2 ascites NK

value: patient 2

value: Natural Killer (NK) Cells


title: Patient1

source_name: patient 1 ascites NK

value: patient 1


title: Healthy6

source_name: healthy donor 6 NK

value: medium


title: Healthy4

source_name: healthy donor 4 NK

value: donor 4


title: Healthy5

source_name: healthy donor 5 NK

value: donor 5


title: Healthy1

source_name: healthy donor 1 NK

value: donor 1


title: Healthy2

source_name: healthy donor 2 NK

value: donor 2


title: MDA-MB-231_shNSD3_rep2

city: Seoul

first: Gu

last: Kong

address: 17 Haengdang-dong, Seongdong-gu

department: Department of Pathology

country: South Korea

institute: College of Medicine, Hanyang University

data_processing:
Illumina RTA and bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR v2.6.0c
Raw counts were calculated using featureCounts from Subread package v1.6.2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include raw counts for all samples

source_name: breast cancer cell line

extract_protocol:
Total RNA was extracted from shControl and shNSD3 knockdown MDA-MB-231 stable cell lines using TRIzol® RNA Isolation Reagents (Life technologies, Carlsbad, CA). RNA integrity was confirmed by a bioanalyzer using an Agilent RNA 6000 Pico Kit (Agilent, Santa Clara, CA). The isolated total RNA was processed for preparing mRNA sequencing library using TruSeq stranded mRNA sample preparation kit (illumina, San Diego, CA) according to manufacturer’s instruction. Simply, mRNAs were isolated from 400 ng total RNA by RNA purification bead using polyA capture, and followed by enzyme shearing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mammary gland/breast

tag: disease

value: epithelial adenocarcinoma

tag: shRNA


title: MDA-MB-231_shNSD3_rep3


title: Patient5

source_name: patient 5 ascites NK

value: patient 5

value: no treatment


title: Healthy3

source_name: healthy donor 3 NK

value: donor 3


title: MDA-MB-231_shControl_rep2

value: shCon


title: MDA-MB-231_shControl_rep1


title: HBEC 5i rep2

city: New York

first: Edmund

last: Au

address: 630 West 168th Street, room P&S14-401

institute: Columbia University Irving Medical Center

data_processing:
Raw RNA-Seq reads were mapped and processed using the Quantas pipeline (http://zhanglab.c2b2.columbia.edu/index.php/Quantas). Reads were first mapped by OLego v1.1.5 using the default settings. In addition to the reference genome,  a comprehensive database of known exon junctions in human as described above was provided during read mapping (available for download on the Quantas website).Only reads with unambiguous mapping to unique loci (i.e., single hits) were included for further analysis.
After read mapping, transcript structure between the sequenced ends could be ambiguous due to alternative splicing, and if this occurs, the structure was inferred using a bayes method by modeling the size distribution of cDNA fragments
Gene expression was quantified using countit package in the Quantas pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: HBEC 5i rep2

growth_protocol: maintained and passaged in DMEM +10% FBS

extract_protocol:
Trizol RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: switched to serum-free Neurobasal medium for 3 days prior

tag: cell line name

value: HBEC 5i

tag: passage #


title: HBEC 5i rep1

source_name: HBEC 5i rep1


title: HEK 293 rep1

source_name: HEK 293 rep1

value: HEK 293


title: HEK 293 rep2

source_name: HEK 293 rep2


title: MDA-MB-231_shNSD3_rep1


title: MDA-MB-231, Inducible Flag-ZMYND8 Overexpression + Doxorubicin treatment for 6h replicate 2

city: kolkata

first: Chandrima

last: Das

state: West Bengal

address: 1/AF Bidhan nagar, Sector-III, Salt Lake

department: Biophysics & Structural Genomics

country: India

institute: Saha Institute of Nuclear Physics

description:
D8_6hR2
zmynd8_counts.txt

data_processing:
RNA-seq reads were trimmed using TrimGalore and aligned to the human genome (hg38) using the pre-built HISAT2 genome_tran index. FeatureCounts was used to generate gene counts using gencode V31 GTF.
Differential gene expression was determined using DeSeq2. Transcripts with log2 Fold change cutoff of 1 and p value <=0.05 were considered as significantly differential expressed.
Gene ontologies and pathways that harbor significantly expressed transcripts were identified using DAVID Functional Annotation Tool.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited txt files that contains raw counts mapped to genes using featureCounts (reference gencode V31 GTF)

molecule: polyA RNA

growth_protocol: MDA-MB-231 cells were procured from ATCC, and grown in RPMI-1640 +12%FBS+1%Antibiotic-antimycotic and grown in 37oC with 5% CO2

extract_protocol:
RNA-seq libraries were generated from two biological replicates for each condition.  The total RNA was extracted using the RNAeasy kit.  The extracted RNA with an RNA integrity number (RIN) of >7.0 was used for mRNA purification. The mRNA was purified using oligo-dT beads (TruSeq RNA Sample Preparation Kit, Illumina) from 1 ug of intact total RNA. The purified mRNA was fragmented at 90°C in the presence of divalent cations. The fragments were reverse transcribed using random hexamers and Superscript II Reverse Transcriptase (Life Technologies).
The sequencing library was prepared by 5' and 3' adapter ligation, after end-repair and the addition of an ‘A’ base and SPRI cleanup. The prepared cDNA library was amplified using PCR for the enrichment of the adapter-ligated fragments. The individual libraries were quantified using a Qubit fluorometer and validated for quality with a Bioanalyzer (Agilent Technologies). SPRI-based (Beckman Coulter Agencourt Ampure XP)-based purification was used to clean after each enzymatic reaction.

treatment_protocol: Prior to all treatments and overexpression, the cells were grown for 2 days to 85% confluency in complete growth medium. FLAG ZMYND8 or empty vector  was overexpressed in MDA-MB-231 cells. After 24hrs of transfection, the cells were treated with either 0.6uM of Doxorubicin or vehicle for next 48 hrs. Doxycycline inducble overexpression of ZMYND8: Doxycycline-inducible and lentiviral vectors for the inducible expression of ZMYND8 cDNA, or a GFP-cDNA control, were inserted into pInducer20 and stably introduced into MDA-MB-231 cells under neomycin/G418 selection. And these cells were grown for 2 days to 70% confluency in complete growth medium. GFP or ZMYND8 were induced by 250ng/mL of doxycycline treatment, after 4hrs the cells were treated with 0.6uM of Doxorubicin for next 6 or 48 hours. Doxycycline was present throughout course of doxorubicin treatment.

value: Breast adenocarcinoma epithelial cells


title: MDA-MB-231, Inducible GFP Overexpression + Doxorubicin treatment for 6h replicate 1

description:
GFP_6hR1
zmynd8_counts.txt


title: MDA-MB-231, Inducible GFP Overexpression + Doxorubicin treatment for 48h replicate 1

description:
GFP_48hR1
zmynd8_counts.txt


title: MDA-MB-231, Inducible Flag-ZMYND8 Overexpression + Doxorubicin treatment for 6h replicate 1

description:
D8_6hR1
zmynd8_counts.txt


title: MDA-MB-231, Inducible GFP Overexpression + Doxorubicin treatment for 48h replicate 2

description:
GFP_48hR2
zmynd8_counts.txt


title: MDA-MB-231, Inducible GFP Overexpression replicate 2

description:
GFP_R2
zmynd8_counts.txt

source_name: Inducible GFP Overexpression

value: Inducible GFP Overexpression


title: MDA-MB-231, Inducible Flag-ZMYND8 Overexpression replicate 2

description:
D8_R2
zmynd8_counts.txt

source_name: Inducible Flag-ZMYND8 Overexpression

value: Inducible Flag-ZMYND8 Overexpression


title: MDA-MB-231, Inducible Flag-ZMYND8 Overexpression replicate 1

description:
D8_R1
zmynd8_counts.txt


title: MDA-MB-231, Inducible GFP Overexpression + Doxorubicin treatment for 6h replicate 2

description:
GFP_6hR2
zmynd8_counts.txt


title: MDA-MB-231, Flag-ZMYND8 transient Overexpression + Doxorubicin Treatment replicate 2

description:
D8-DOXII
Zmynd8_CD_counts.txt

value: Transient OverExpression FLAG ZMYND8 + Doxorubicin treated


title: MDA-MB-231, Flag-ZMYND8 transient Overexpression + Doxorubicin Treatment replicate 1

description:
D8-DOXI
Zmynd8_CD_counts.txt


title: MDA-MB-231, Control + Doxorubicin treatment replicate 2

description:
DOXII
Zmynd8_CD_counts.txt

source_name: Control + Doxorubicin treatment

value: Doxorubicin treated


title: MDA-MB-231, Inducible Flag-ZMYND8 Overexpression + Doxorubicin treatment for 48h replicate 1

description:
D8_48hR1
zmynd8_counts.txt


title: MDA-MB-231, Control replicate 2

description:
CONTROLII
Zmynd8_CD_counts.txt

source_name: Control

value: Untreated


title: MDA-MB-231, Control replicate 1

description:
CONTROLI
Zmynd8_CD_counts.txt


title: MDA-MB-231, Control + Doxorubicin treatment replicate 1

description:
DOXI
Zmynd8_CD_counts.txt


title: Gamma3

city: Amsterdam

first: Emile

last: van den Akker

address: Plesman 166

department: Hematopoiesis

country: Netherlands

institute: Sanquin Research

data_processing:
Illumina base caller v1.9
Reads were aligned using STAR
Countdata from STAR was processed using EdgeR package. Lowly expressed genes filter ( 2< cpm in at least 2 out of 6 samples)
Genome_build: ChGR38.v85
Supplementary_files_format_and_content: Tab-delimited txt files include raw count data from STAR and transcript per million from SALMON

source_name: Peripheral blood monocytes

growth_protocol: Erythroid cells expanded in Cellquin culture medium supplemented with SCF, EPO and dexamethasone.

extract_protocol:
Reverse paraformaldehyde crosslinking, Trizol RNA extraction
Library prep on amplified cRNA using HyperPrep Kit with RiboErase (KAPA Biosystems, Pleasanton, CA, USA) according to manufactures protocol

treatment_protocol: After exchanging expansion medium for differentiation medium, cells were fixed permebilized and sorted for beta and gamma globin chain after 48h

value: Erythroid

tag: sorted population

value: Beta/Gamma globin


title: Gamma2


title: MDA-MB-231, Inducible Flag-ZMYND8 Overexpression + Doxorubicin treatment for 48h replicate 2

description:
D8_48hR2
zmynd8_counts.txt


title: Beta2

value: Beta globin


title: Beta1


title: MDA-MB-231, Inducible GFP Overexpression replicate 1

description:
GFP_R1
zmynd8_counts.txt


title: PBMC_HC4

city: Beijing

first: Boyang

last: Xu

address: No.8 Xi Shi Ku Street, Xi Cheng District

institute: Peking University First Hospital

data_processing:
Real time analysis (RTA) 1.18.64 software used for basecalling.
Adaptor sequence, low-quality reads and redundance were removed from raw data, then mapped to hg19 whole genome using bowtie v1.2.1.1 with parameters -p 3 -f -n 1 -e 80 -l 18 -a -m 5 --best --strata  --chunkmbs 512
Tags per million (TPM) were used. The formula of TPM is (miRNA total reads/total reads)*1 million.
Genome_build: hg19
Supplementary_files_format_and_content: An excel file includes TPM values for each Sample.

source_name: PBMC

extract_protocol:
Total RNA, including small RNA fractions, was extracted from PBMC using TRIZOL® Reagent (Invitrogen, Carlsbad, CA, USA), and then eluted with ribonuclease-free water.
Total RNA, containing the small RNA fraction was reverse transcribed into a cDNA library using the Illumina Small RNA library preparation kit. Briefly, after quality assessment using Agilent 2100 Bioanalyzer, 1 µg total RNA per sample were ligated overnight with adapters, reverse transcribed, RNase-treated, and PCR-amplified with unique barcode-labeled amplification primers. Then, size-selection was conducted on 6% native polyacrylamide gels. The cDNA fragments between 145 and 160 bp corresponding to the miRNA populations were excised from the gel, then eluted and precipitated. The final cDNA pellet was air dried and resuspended in 10ul of nuclease-free water. The quantity of cDNA in each final RNA libraries was verified. These libraries were then sequenced on the Illumina platform (50 bp reads).

value: peripheral blood mononuclear lymphocytes

value: female

tag: age

tag: diagnosis

value: healthy control


title: MDA-MB-231_shControl_rep3

value: mammary gland/breast

value: epithelial adenocarcinoma


title: PBMC_HC2

tag: gender


title: PBMC_HC1

value: male


title: PBMC_IgAN2

value: IgAN patient


title: PBMC_IgAN3


title: PBMC_IgAN4


title: PBMC_IgAN5


title: PBMC_IgAN1


title: Gamma1


title: Posi2: CD34+ HSPCs rep2

city: hanghzou

first: xu

middle: yu

last: lin

state: zhejiang province

address: yuhangtang road 388

department: medicine school

institute: zhejiang university

description: mobilized peripheral blood-derived HSPCs with no culture

data_processing:
Illunima Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR virsion 2.5.1b with parameters -q -p 4 -e 100 -y -a -m 10 --best –stratae 100 -y -a -m 10 --best --strata
RHTSeq (version 0.6.0) was applied to calculate the reads mapped to each gene. Based on the length of the genes and read counts, FPKM, the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced was calculated.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values for each Sample.

source_name: mobilized peripheral blood

growth_protocol: The medium consisted with the commercial base culture medium (YankeEr Biosciences Inc., China) for HSPCs plus sets of factors including 100 ng/ml stem cell factor (SCF), 100 ng/ml fms-related tyrosine kinase 3 ligand (FLT3L), 20 ng/ml Thrombopoietin (TPO), 2 ng/ml vascular endothelial growth factor (VEGF), 20 ng/ml interleukin-3 (IL-3), 20 ng/ml IL-6, 1uM StemRegenin-1(SR1), and 20 ug/ml vitamin c (Vc). The culture system was put still for 5 min until three dimension structure formation. The medium was then changed every 1-2 days according to the cell growth.  Cultivation of PBMNCs with conventional two dimension culture system (2DCS) served as controls. The culture media and the procedures are the same with 3DCS except no polypeptide material.

extract_protocol:
The targeted samples were collected and total RNA was harvested using Trizol reagent. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit (NEB, Illumina®, USA) following manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: About 10-15 ml of healthy blood was extracted using single-use containers for human venous blood specimen collection (Becton, Dickinson and Company) with anticoagulation effect. PBMNCs were isolated with Ficoll-Hypaque (Sigma) gradient centrifugation at 400 × g for 25 min. The cell pellets were washed with phosphate-buffered saline (PBS) free of Ca2+ and Mg2+   two times to remove remnant of Ficoll-Hypaque for its poisonous. After washed with PBS followed by all the supernatant removed away, 1 × 106 of PBMNCs were resuspened with 20% (v/w) sterile solution of sucrose, and mixed with 150 ul of 0.5% polypeptide solution at a ratio 1:1 quickly. After seeded in the culture wells, the media were carefully added to the well and changed twice to equilibrate physiological pH in 30 min. Three dimension seeded with PBMNCs were formed.

tag: passage

tag: culture

value: no culture


title: Posi3: CD34+ HSPCs rep3

tag: tissue

value: mobilized peripheral blood-derived HSPCs


title: Posi4: CD34+ HSPCs rep4


title: Beta3

tag: cell type


title: Posi1: CD34+ HSPCs rep1


title: Exp3DH2: samples in 3DH rep2

description: peripheral bood monocytes culture in 3DH

source_name: normal peripheral blood

value: normal peripheral blood-derived cells


title: NegaP03: normal primary peripheral blood monocytes  rep1

description: primary peripheral bood monocytes


title: Exp3DH1: samples in 3DH rep1


title: Exp3DH3: samples in 3DH rep3


title: OE_embryonic stem cells - input

city: Shanghai

first: Yixin

last: Huang

address: Siping Road

institute: Tongji University

description: Normalized tag counts

data_processing:
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using bowtie2
ChIP-seq peaks were called with MACS2 (version 2.2.4) with the parameters “--nomodel --keep-dup all –shift = 73” over input files.
Genome_build: mm9
Supplementary_files_format_and_content: Signal tracks for each sample were generated using the bamCompare function of deeptools and were normalized by calculating the reads per kilobase of transcript per million mapped reads.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype

value: Dcaf11 overexpression

value: Embryonic stem cells


title: PBMC_HC3


title: Exp2D2: samples in 2D rep2

description: peripheral bood monocytes culture in 2D


title: Exp2D1: samples in 2D rep1

description: peripheral bood monocytes culture in 2D


title: WT_embryonic stem cells - input

description: Normalized tag counts

value: Wild type

tag: chip antibody


title: OE_embryonic stem cells - H3K9me3_rep2

description: Normalized tag counts

value: H3K9me3 (Active Motif no. 39162)


title: OE_embryonic stem cells - H3K9me3_rep1

description: Normalized tag counts


title: WT_embryonic stem cells - H3K9me3_rep1

description: Normalized tag counts


title: WT_embryonic stem cells - H3K9me3_rep2

description: Normalized tag counts


title: ETV4AAA-1 [ATAC-seq]

description:
Chr3192_ETV4_AAA-1_AT_A12_GTCGTGAT_IGO_08155_5_S36
processed data file:
ATAC_log2_normalized_counts.csv

source_name: primary prostate cells_ETV4AAA

value: 2 months old

tag: genotype/variation

tag: tissue/cell type

value: Isolated primary mouse prostate cells

tag: cell population

value: CD326 and EYFP double positive cells


title: ETV4AAA-2 [ATAC-seq]

description:
Chr3193_ETV4_AAA-2_AT_A12_ACCACTGT_IGO_08155_6_S37
processed data file:
ATAC_log2_normalized_counts.csv


title: EYFP-2 [ATAC-seq]

description:
Chr3165_EYFP-2_AT_A12_GAGGGGTT_IGO_08155_4_S35
processed data file:
ATAC_log2_normalized_counts.csv

source_name: primary prostate cells_EYFP

value: EYFP


title: EYFP-1 [ATAC-seq]

description:
Chr3164_EYFP-1_AT_A12_TGCTGGGT_IGO_08155_3_S34
processed data file:
ATAC_log2_normalized_counts.csv


title: NegaP02: normal primary peripheral blood monocytes  rep1

description: primary peripheral bood monocytes


title: ETV4WT-2 [ATAC-seq]

description:
Chr3163_ETV4WT-2_AT_A12_CCGTTTGT_IGO_08155_2_S33
processed data file:
ATAC_log2_normalized_counts.csv

source_name: primary prostate cells_ETV4WT


title: NegaP01: normal primary peripheral blood monocytes  rep1

description: primary peripheral bood monocytes


title: Exp2D3: samples in 2D rep3

description: peripheral bood monocytes culture in 2D


title: MCF7.rep1 (GRO-seq)

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

institute: Tel Aviv University

description: nascent RNA

data_processing:
Library strategy: GRO-seq
Sequenced reads were aligned to the human genome (hg19) using bowtie2
The wig files were created using in-house scripts.
They summarize read coverage in 10bp bins, scaled to total counts of 10M reads.
Genome_build: hg19
Supplementary_files_format_and_content: wig

growth_protocol: Cells were cultured in DMEM medium (Gibco), supplemented with 10% FCS (Hyclone), and 1% penicillin/streptomycin (Gibco).

extract_protocol:
GRO-Seq was performed as described before with minor modifications. Briefly, 5x106 nuclei were isolated and incubated 5 min at 30°C with equal volume of reaction buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 1mM DTT, 300 mM KCL, 20 units of SUPERase In, 1% sarkosyl, 500 µM ATP, GTP, and Br-UTP, 0.2 µM CTP+32P CTP) for the nuclear run-on. The reaction was stopped and total RNA was extracted with Trizol LS (Invitrogen) according to the manufacturer’s instructions. RNA was fragmented using fragmentation reagents (Ambion) and the reaction was purified through p-30 RNAse-free spin column (BioRad). BrU-labeled RNA was immunoprecipitated with anti-BrU agarose beads (Santa Cruz), washed one time in binding buffer, one time in low salt buffer (0.2X SSPE, 1 mM EDTA, 0.05% Tween-20), one-time high salt buffer (0.25X SSPE, 1 mM EDTA, 0.05% Tween-20, 137.5 mM NaCl) and two times in TET buffer (TE with 0.05% Tween-20). RNA was eluted with elution buffer (20 mM DTT, 300 mM NaCl, 5 mM Tris-Cl pH 7.5, 1 mM EDTA and 0.1% SDS) and isolated with Trizol LS. After the binding step, BrU-labbeled RNA was treated with tobacco acid pyrophosphatase (TAP, Epicenter) to remove 5’-methyl guanosine cap, followed by T4 polynucleotide kinase (PNK; NEB) to remove 3’-phosphate group. BrU-containing RNA was treated with T4 PNK again at high pH in the presence of ATP to add 5’-phosphate group. The reaction was stopped and RNA was extracted with Trizol LS.
Sequencing libraries were prepared using TruSeq Small RNA kit (Illumina) following manufacturer’s instructions. Briefly, end-repaired RNA was ligated to RNA 3’ and 5’ adapters, followed by RT-PCR amplification. cDNA was purified using Agencourt AMPure XP (Beckman Coulter) and amplified by PCR for 12 cycles. Finally, amplicons were cleaned and size-selected using Agencourt AMPure XP (Beckman Coulter), quantified in a Bioanalyzer 2100 (Agilent)

tag: cell line

value: breast cancer cells


title: MDA.MB.231.rep2 (GRO-seq)

description: nascent RNA


title: MCF7.rep2 (GRO-seq)

description: nascent RNA


title: MDA.MB.231.rep1 (GRO-seq)

description: nascent RNA


title: 3 day-old pifq light-grown seedlings rep3

city: Cerdanyola del Vallès

first: Guiomar

last: Martín

state: Barcelona

address: Vall Moronta

country: Spain

institute: Centre for Research in Agricultural Genomics

data_processing:
Gene expression (GE) quantification is performed using vast-tools. vast-tools maps the first 50 nucleotides of the forward read (if longer and paired end) to a library with one reference transcript per gene, the *.1 transcript according to the TAIR 10 nomenclature or else that with the lowest suffix (33,602 genes in total). GE levels are provided using the cRPKM metric (corrected [for mappability] Reads Per Kilobasepair and Million mapped reads), as detailed in Labbé et al., Stem Cells 2012. cRPKM can be converted to TPMs applying the following formula: TPM = 10^6 * cRPKM/sum_all(cRPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include cRPKM values (as defined above), as well as the total read count for each gene's canonical transcript

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Stratified seeds were irradiated with white-light at 21 ºC for 3 h to induce germination and grown in darkness or continuous white light (13 µmol·m-2·s-1) at 21 ºC for 3 days before harvest.

extract_protocol:
Total RNA (1 µg) was extracted from whole Arabidopsis seedlings using the innuPREP Plant RNA kit (Analytik Jena BioSolutions).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole seedlings

tag: developmental stage

value: 3 day-old

tag: growth conditions

value: white light

tag: genetic backgroung

value: Columbia


title: 3 day-old pifq light-grown seedlings rep1


title: 3 day-old hy5 light-grown seedlings rep2


title: ETV4WT-1 [ATAC-seq]

city: New York City

first: Dan

last: Li

institute: Memorial Sloan-Kettering Cancer Center

description:
Chr3162_ETV4WT-1_AT_A12_TGGATCTG_IGO_08155_1_S32
processed data file:
ATAC_log2_normalized_counts.csv

data_processing:
ATAC-seq and primary data processing: ATAC-seq was performed as previously described (Buenrostro et al., 2013). Primary data processing and peak calling was performed using ENCODE ATAC-seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines). Briefly, paired-end reads were trimmed, filtered and aligned against mm9 using Bowtie2 (Langmead et al., 2009). PCR duplicates and reads mapped to mitochondrial chromosome or repeated regions were removed. Mapped reads were shifted +4/-5 to correct for the Tn5 transposase insertion. Peak calling was performed using MACS2(Zhang et al., 2008), with p value < 0.01 as cutoff. Reproducible peaks from two biological replicates were defined as peaks overlapped by more than 50%. On average 25 million uniquely mapped pairs of reads were remained after filtering. The distribution of inserted fragment length shows typical nucleosome banding pattern, and the TSS enrichment score (reads that are enriched around TSS against background) ranges between 28 and 33, suggesting the libraries have high quality and were able to capture the majority of regions of interests.
Differential peak accessibility: Reads aligned to peak regions were counted using R package GenomicAlignments_v1.12.2 (Lawrence et al., 2013). Read count normalization and differential accessible peaks were called with DESeq2_v1.16.1 in R 3.4.1 (Love et al., 2014). Differential peaks were defined as peaks with adjusted p value < 0.01 and |log2(FC)| > 1.  For visualization, coverage bigwig files were generated using bamCoverage command from deepTools2, normalizing using the size factor generated by DESeq2. The differential ATAC-seq peak density plot was generated with deepTools2 (Ramírez et al., 2018), using regions that were significantly more or less accessible in ETV4AAA samples relative to EYFP samples.
Motif analysis: Enriched motif and de novo motif analysis using Homer (findMotifsGenme.pl) (Heinz et al., 2010) with ‘size -given -mask’ was applied to differentially accessible regions in ETV4AAA relative to EYFP, with the non-differentially accessible peaks as background.
RNA-seq analysis: The extracted RNA was processed for RNA-sequencing by the Integrated Genomics Core Facility at MSKCC.  The libraries were sequenced on an Illumina HiSeq-2500 platform with 51 bp paired-end reads to obtain a minimum yield of 40 million reads per sample. The sequenced data were aligned using STAR v2.3 (Dobin et al., 2013) with GRCm38.p6 as annotation. DESeq2_v1.16.1 (Love et al., 2014) was subsequently applied on read counts for normalization and the identification of differentially expressed genes between ETV4AAA and EYFP groups, with adjusted p value < 0.05 as threshold. Genes were ranked by sign(log2(FC)) * (-log(p value)) as input for GSEA analysis using ‘Run GSEA Pre-ranked’ with 1000 permutations (Subramanian et al., 2005).
Genome_build: mm9
Supplementary_files_format_and_content: csv files include log2_normalized_counts of all samples

extract_protocol:
Intraperitoneal injection of tamoxifen was administered in 8-week-old mouse. 1 week after tamoxifen treatment, mouse prostate was digested 1 hour with Collagenase/Hyaluronidase (STEMCELL, #07912) and then 30 minutes with TrypLETM Express Enzyme (Thermo Fischer, # 12605028) at 37°C to isolate single prostate cells. The prostate cells were stained with PE/Cy7 conjugated anti-mouse CD326 (EpCAM) antibody (BioLegend, 118216) and then, CD326 and EYFP double positive cells were sorted out by flow cytometry. The mRNA or genomic DNA were extracted from these double positive cells and then were used for ATAC-sequencing and RNA-sequencing analysis.
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age


title: 3 day-old hy5 light-grown seedlings rep1


title: 3 day-old phyab light-grown seedlings rep2

value: phyab (phyA211, phyB9)


title: 3 day-old phyab light-grown seedlings rep3


title: 3 day-old phyab light-grown seedlings rep1


title: 3 day-old WT light-grown seedlings rep2

value: WT


title: 3 day-old WT light-grown seedlings rep3


title: 1537 knockout liver

first: Peng

last: Zhang

state: Shanghai

address: 320 Yue-Yang Road

institute: Shanghai Institutes for Biological Sciences

description:
Gene expression data from Cdc42LK mouse liver
1537K_NS

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized according to the protocol of GeneChip® Hybridization, Wash and Stain Kit, Affymetrix, P/N 900720. GeneChips were washed and stained in the Fluidics Station 450: Affymetrix, P/N 00-0079.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000: Affymetrix, P/N 00-00212.

data_processing: The qualified data were analyzed by Gene Spring Software 11.0 (Agilent) for normalization. The algorithm is Microarray Suite version 5.0 (MAS5.0).

label: biotin

source_name: Cdc42 knockout liver form 2-month-old Cdc42LK mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol of 3' IVT Express Kit , Affymetrix, P/N 901229 from 500 ng total RNA

growth_protocol: Mice were housed in a temperature- and light-controlled (12-h light/dark cycle) specific pathogen-free (SPF) animal facility, in individually ventilated cages always with companion mice.

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

treatment_protocol: Livers were perfused with PBS, then placed on ice in the Trizol solution.

value: liver

value: Cdc42 liver-specific knockout

value: 2 month


title: 3 day-old pifq light-grown seedlings rep2


title: 1607 normal liver

description:
Gene expression data from wild type mouse liver
1607N_NS

source_name: normal liver form 2-month-old wild type mice

value: wild type


title: 1555 normal liver

description:
Gene expression data from wild type mouse liver
1555N_NS


title: 3 day-old pifq dark-grown seedlings rep2

value: darkness


title: 1606 normal liver

description:
Gene expression data from wild type mouse liver
1606N_NS


title: 3 day-old hy5 light-grown seedlings rep3


title: 3 day-old pifq dark-grown seedlings rep1


title: 3 day-old phyab dark-grown seedlings rep3


title: 1609 knockout liver

description:
Gene expression data from Cdc42LK mouse liver
1609K_NS


title: 1554 normal liver

description:
Gene expression data from wild type mouse liver
1554N_NS


title: 1536 knockout liver

description:
Gene expression data from Cdc42LK mouse liver
1536K_NS


title: 3 day-old hy5 dark-grown seedlings rep2


title: Day 3 partial hepatectomy active liver regeneration

city: Hong Kong

first: Stephanie

last: Ma

address: Rm 47, 1/F, Lab Block, Faculty of Medicine Bldg, 21 Sassoon Rd, Pok Fu Lam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array (Affymetrix). GeneChips were washed and stained using the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix)

data_processing: GeneChip Operative Software (GCOS) used for data quality control. Data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method

label: Biotin

source_name: Mouse liver at day 3 after partial hepatectomy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (MessageAmp II-Biotin Enhanced Technical Manual Version 0603, Affymetrix)

growth_protocol: BALB/c nude mice

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

treatment_protocol: 70% partial hepatectomy by surgery. Whole liver collected at day 0 and day 3 post partial hepatectomy.

value: Liver


title: 1608 knockout liver

description:
Gene expression data from Cdc42LK mouse liver
1608K_NS


title: 3 day-old hy5 dark-grown seedlings rep1


title: Day 0 control partial hepatectomy liver regeneration

source_name: Mouse liver at day 0 after partial hepatectomy


title: 3 day-old pifq dark-grown seedlings rep3


title: 3 day-old WT light-grown seedlings rep1


title: 3 day-old WT dark-grown seedlings rep3


title: 3 day-old WT dark-grown seedlings rep1


title: 3 day-old phyab dark-grown seedlings rep1


title: 3 day-old phyab dark-grown seedlings rep2


title: 3 day-old WT dark-grown seedlings rep2


title: TA5

source_name: healthy donor 5 NK treated with Ascites 1

tag: individual

value: donor 5

value: Natural Killer (NK) Cells

tag: treatment

value: acites donor 1


title: 16P

city: Salzburg

first: Elvis

last: Ruznic

state: Salzburg

address: Müllner Hauptstraße 48

department: UK f. Radiotherapie & Radio-Onkologie

country: Austria

institute: Gemeinnützige Salzburger Landeskliniken Betriebsges.m.b.H.

description:
breast cancer_FFPE
protein expression data from non-metastasized breast cancer patients

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: R version 4.0.1, oligo version 1.52.0 (RMA), Biobase version 2.48.0, affycoretools version 1.60.1, pd.hta.2.0 version 3.12.2

source_name: breast cancer_relapse

label_protocol: standard Affymetrix protocol

growth_protocol: FFPE fresh frozen paraffin embedded breast cancer tissue from surgical excision

extract_protocol: none provided by the submitter

treatment_protocol: The tissue was retrieved during breast conserving surgery.

value: surgical breast tumor sample

tag: gender

value: female

tag: tumor stage

value: early breast cancer


title: 15P

tag: tissue


title: 13PK

source_name: breast cancer_control


title: 13P


title: 16PK


title: 15PK


title: 11PK


title: 14PK


title: 8P


title: 12PK


title: 4PK


title: 7P


title: 4P


title: 11P


title: 10PK


title: 10P


title: 3PK


title: 8PK


title: 6PK


title: 3P


title: 7PK


title: 6P


title: 14P


title: 5P


title: 2P


title: 2PK


title: sera4, Control group

city: Zhuzhou

first: Long

last: Yunzhu

address: Tian Yuan Qu Chang Jiang Nan Lu

institute: The affiliated Zhuzhou hospital Xiangya medical college, Central South University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: anti-TB patient4 without drug induced liver injury

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: RNA extraction was carried out using the RNeasy Mini Kit from Qiagen AB (Cat. # 217084, German) following the manufacturer’s standard protocol.

treatment_protocol: The serum was collected by centrifugation at 3500 rpm for 5 minutes from the whole blood within 4 hours, and then stored at -80°C in a refrigerator.

value: sera

tag: phenotype

value: patient without anti-TB drug induced liver injury


title: Patient5_untreated_ETP-ALL_rep2_050

city: Boston

first: Birgit

last: Knoechel

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

data_processing:
Adapter trimming was performed using trimmomatic version 0.36
Sequence quality was assessed using fastqc version 0.11.5
Alignment agains human genome was performed using START version 2.5.2b using following parameters -  --twopassMode Basic          --alignIntronMax 100000 --alignMatesGapMax 100000   --alignSJDBoverhangMin 10   --alignSJstitchMismatchNmax 5   -1   5   5 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS
Raw counts were obtained from aligned bam files using htseq version 0.9.1
Genome_build: hg19
Supplementary_files_format_and_content: htseq count file with raw raw counts for all the human genes for individual cells

source_name: Bone marrow

extract_protocol:
PBMCs were isolated using Ficoll-Paque, stained with anti-CD45 FITC, anti-CD3 PerCP-Cy5.5, anti-CD14 APC-Cy7, anti-CD19 PE and DAPI. Live single cells were sorted into 96 well plates containing TCL buffer.
Full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.

tag: who classification

value: ETP-ALL

tag: cell type

value: Peripherial blood mononuclear cells


title: Patient5_untreated_ETP-ALL_rep2_051


title: Patient5_untreated_ETP-ALL_rep2_053


title: Patient5_untreated_ETP-ALL_rep1_050


title: Patient5_untreated_ETP-ALL_rep1_052


title: Patient5_untreated_ETP-ALL_rep1_054


title: Patient5_untreated_ETP-ALL_rep1_051


title: Patient5_untreated_ETP-ALL_rep2_047


title: Patient5_untreated_ETP-ALL_rep2_049


title: sera1, Control group

source_name: anti-TB patient1 without drug induced liver injury


title: Patient5_untreated_ETP-ALL_rep2_048


title: Patient5_untreated_ETP-ALL_rep1_053


title: sera3, Control group

source_name: anti-TB patient3 without drug induced liver injury


title: Patient5_untreated_ETP-ALL_rep1_049


title: Patient5_untreated_ETP-ALL_rep2_052


title: Patient5_untreated_ETP-ALL_048


title: Patient5_untreated_ETP-ALL_rep1_047


title: Patient5_untreated_ETP-ALL_rep2_046


title: sera2, AT-DILI group

source_name: patient2 with anti-TB drug induced liver injury

value: patient with anti-TB drug induced liver injury


title: sera1, AT-DILI group

source_name: patient1 with anti-TB drug induced liver injury


title: Patient5_untreated_ETP-ALL_rep2_045


title: 12P


title: sera3, AT-DILI group

source_name: patient3 with anti-TB drug induced liver injury


title: Patient5_untreated_ETP-ALL_rep1_045


title: sera2, Control group

source_name: anti-TB patient2 without drug induced liver injury


title: Patient5_untreated_ETP-ALL_rep1_048


title: sera4, AT-DILI group

source_name: patient4 with anti-TB drug induced liver injury


title: 5PK


title: Patient5_untreated_ETP-ALL_rep1_043


title: Patient5_untreated_ETP-ALL_rep2_043


title: Patient5_untreated_ETP-ALL_rep2_044


title: Patient5_untreated_ETP-ALL_047


title: Patient5_untreated_ETP-ALL_rep2_039


title: Patient5_untreated_ETP-ALL_rep1_042


title: Patient5_untreated_ETP-ALL_rep2_040


title: Patient5_untreated_ETP-ALL_rep1_040


title: Patient5_untreated_ETP-ALL_044


title: Patient5_untreated_ETP-ALL_rep1_044


title: Patient5_untreated_ETP-ALL_rep1_038


title: Patient5_untreated_ETP-ALL_rep1_036


title: Patient5_untreated_ETP-ALL_rep2_037


title: Patient5_untreated_ETP-ALL_rep1_037


title: Patient5_untreated_ETP-ALL_rep2_035


title: Patient5_untreated_ETP-ALL_rep1_035


title: Patient5_untreated_ETP-ALL_rep2_034


title: Patient5_untreated_ETP-ALL_rep1_041


title: Patient5_untreated_ETP-ALL_rep2_038


title: Patient5_untreated_ETP-ALL_043


title: Patient5_untreated_ETP-ALL_rep2_036


title: Patient5_untreated_ETP-ALL_rep2_042


title: Patient5_untreated_ETP-ALL_rep2_041


title: Patient5_untreated_ETP-ALL_046


title: Patient5_untreated_ETP-ALL_rep1_039


title: Patient5_untreated_ETP-ALL_045


title: Patient5_untreated_ETP-ALL_rep2_032


title: Patient5_untreated_ETP-ALL_rep1_032


title: 3 day-old hy5 dark-grown seedlings rep3

source_name: whole seedlings

value: whole seedlings

value: 3 day-old

tag: genotype

value: Columbia


title: Patient5_untreated_ETP-ALL_rep2_030


title: Patient5_untreated_ETP-ALL_042


title: Patient5_untreated_ETP-ALL_rep2_031


title: Patient5_untreated_ETP-ALL_rep1_029


title: Patient5_untreated_ETP-ALL_rep1_033


title: Patient5_untreated_ETP-ALL_rep1_031


title: Patient5_untreated_ETP-ALL_rep1_034


title: Patient5_untreated_ETP-ALL_rep2_028


title: Patient5_untreated_ETP-ALL_rep1_028


title: Patient5_untreated_ETP-ALL_041


title: Patient5_untreated_ETP-ALL_rep2_029


title: Patient5_untreated_ETP-ALL_rep1_027


title: Patient5_untreated_ETP-ALL_rep2_027


title: Patient5_untreated_ETP-ALL_rep1_030


title: Patient5_untreated_ETP-ALL_rep1_046


title: Patient5_untreated_ETP-ALL_rep2_025


title: Patient5_untreated_ETP-ALL_rep1_025


title: Patient5_untreated_ETP-ALL_040


title: Patient5_untreated_ETP-ALL_rep2_033


title: Patient5_untreated_ETP-ALL_rep1_026


title: Patient5_untreated_ETP-ALL_rep2_026


title: Patient5_untreated_ETP-ALL_036


title: Patient5_untreated_ETP-ALL_039


title: Patient5_untreated_ETP-ALL_035


title: Patient5_untreated_ETP-ALL_038


title: Patient5_untreated_ETP-ALL_rep2_024


title: Patient5_untreated_ETP-ALL_034


title: Patient5_untreated_ETP-ALL_rep1_023


title: Patient5_untreated_ETP-ALL_rep1_024


title: Patient5_untreated_ETP-ALL_032


title: Patient5_untreated_ETP-ALL_rep1_022


title: Patient5_untreated_ETP-ALL_033


title: Patient5_untreated_ETP-ALL_031


title: Patient5_untreated_ETP-ALL_rep2_021


title: Patient5_untreated_ETP-ALL_030


title: Patient5_untreated_ETP-ALL_rep2_023


title: Patient5_untreated_ETP-ALL_rep2_020


title: Patient5_untreated_ETP-ALL_rep1_021


title: Patient5_untreated_ETP-ALL_rep2_019


title: Patient5_untreated_ETP-ALL_rep1_019


title: Patient5_untreated_ETP-ALL_027


title: Patient5_untreated_ETP-ALL_rep1_020


title: Patient5_untreated_ETP-ALL_rep2_018


title: Patient5_untreated_ETP-ALL_rep1_017


title: Patient5_untreated_ETP-ALL_028


title: Patient5_untreated_ETP-ALL_026


title: Patient5_untreated_ETP-ALL_rep2_017


title: Patient5_untreated_ETP-ALL_rep1_016


title: Patient5_untreated_ETP-ALL_rep2_016


title: Patient5_untreated_ETP-ALL_029


title: Patient5_untreated_ETP-ALL_024


title: Patient5_untreated_ETP-ALL_025


title: Patient5_untreated_ETP-ALL_021


title: Patient5_untreated_ETP-ALL_022


title: Patient5_untreated_ETP-ALL_rep2_015


title: Patient5_untreated_ETP-ALL_rep1_015


title: Patient5_untreated_ETP-ALL_020


title: Patient5_untreated_ETP-ALL_rep2_022


title: Patient5_untreated_ETP-ALL_018


title: Patient5_untreated_ETP-ALL_rep1_014


title: Patient5_untreated_ETP-ALL_rep2_013


title: Patient5_untreated_ETP-ALL_019


title: Patient5_untreated_ETP-ALL_017


title: Patient5_untreated_ETP-ALL_rep1_013


title: Patient5_untreated_ETP-ALL_016


title: Patient5_untreated_ETP-ALL_rep2_014


title: Patient5_untreated_ETP-ALL_015


title: Patient5_untreated_ETP-ALL_rep1_011


title: Patient5_untreated_ETP-ALL_rep2_011


title: Patient5_untreated_ETP-ALL_rep2_012


title: Patient5_untreated_ETP-ALL_012


title: Patient5_untreated_ETP-ALL_rep2_010


title: Patient5_untreated_ETP-ALL_013


title: Patient5_untreated_ETP-ALL_023


title: Patient5_untreated_ETP-ALL_014


title: Patient5_untreated_ETP-ALL_037


title: Patient5_untreated_ETP-ALL_rep1_010


title: Patient5_untreated_ETP-ALL_rep1_009


title: Patient5_untreated_ETP-ALL_rep2_009


title: Patient5_untreated_ETP-ALL_rep2_008


title: Patient5_untreated_ETP-ALL_011


title: Patient5_untreated_ETP-ALL_rep1_008


title: Patient5_untreated_ETP-ALL_rep1_007


title: Patient5_untreated_ETP-ALL_010


title: Patient5_untreated_ETP-ALL_008


title: Patient5_untreated_ETP-ALL_rep2_006


title: Patient5_untreated_ETP-ALL_009


title: Patient5_untreated_ETP-ALL_rep1_012


title: Patient5_untreated_ETP-ALL_007


title: Patient5_untreated_ETP-ALL_rep2_005


title: Patient5_untreated_ETP-ALL_rep1_006


title: Patient5_untreated_ETP-ALL_rep1_003


title: Patient5_untreated_ETP-ALL_rep1_004


title: Patient5_untreated_ETP-ALL_rep2_004


title: Patient5_untreated_ETP-ALL_rep2_002


title: Patient5_untreated_ETP-ALL_rep2_003


title: Patient5_untreated_ETP-ALL_006


title: Patient5_untreated_ETP-ALL_002


title: Patient5_untreated_ETP-ALL_001


title: Patient5_untreated_ETP-ALL_005


title: Patient5_untreated_ETP-ALL_rep1_002


title: Patient5_untreated_ETP-ALL_rep1_018


title: Patient5_untreated_ETP-ALL_003


title: Patient5_untreated_ETP-ALL_rep2_007


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title: Patient5_treated_15d_ETP-ALL_303


title: Patient5_treated_15d_ETP-ALL_304


title: Patient5_treated_15d_ETP-ALL_306


title: Patient5_treated_15d_ETP-ALL_301


title: Patient5_treated_15d_ETP-ALL_299


title: Patient5_treated_15d_ETP-ALL_298


title: Patient5_treated_15d_ETP-ALL_297


title: Patient5_treated_15d_ETP-ALL_295


title: Patient5_treated_15d_ETP-ALL_294


title: Patient5_treated_15d_ETP-ALL_291


title: Patient5_treated_15d_ETP-ALL_300


title: Patient5_treated_15d_ETP-ALL_292


title: Patient5_treated_15d_ETP-ALL_290


title: Patient5_treated_15d_ETP-ALL_302


title: Patient5_treated_15d_ETP-ALL_289


title: Patient5_treated_15d_ETP-ALL_283


title: Patient5_treated_15d_ETP-ALL_278


title: Patient5_treated_15d_ETP-ALL_282


title: Patient5_treated_15d_ETP-ALL_281


title: Patient5_treated_15d_ETP-ALL_296


title: Patient5_treated_15d_ETP-ALL_279


title: Patient5_treated_15d_ETP-ALL_280


title: Patient5_treated_15d_ETP-ALL_284


title: Patient5_treated_15d_ETP-ALL_293


title: Patient5_treated_15d_ETP-ALL_272


title: Patient5_treated_15d_ETP-ALL_270


title: Patient5_treated_15d_ETP-ALL_274


title: Patient5_treated_15d_ETP-ALL_273


title: Patient5_treated_15d_ETP-ALL_275