title: WT_H3K4me3_2nd

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were cleaned with trim-galore and aligned to the human genome, hg19, using bowtie2. PCR duplicated reads were removed by SAMtools
ChIP-seq peaks were identified by MACS2 with the parameter of narrow peak for H3K36M peaks, and broad peak calling for H3K36 and H3K27 methylations. For -in ChIP-seq results, the sequencing reads were aligned and normalized according to previous published procedures (Orlando et al., 2014). In brief, human (hg19) and drosophila (dm6) genome sequences were combined to produce a reference genome. Cleaned sequencing reads were aligned to the reference genome by bowtie2 with default parameters. The mapped reads were then separated into human and drosophila reads, where the reads mapped to the drosophila genome were used to determine the normalization factor. The number of reads in each sequencing results was counted and normalized by the normalization factor.
For RNA sequencing. Sequence reads were cleaned with trim-galore and then aligned to the human genome hg19 using STAR. The mapped reads were annotated to Refseq genes using TopHat and the FPKM of genes was calculated by Cufflinks. Cuffdiff was used to identify and analyze the differential gene expression using false discovery rate (FDR) < 0.05 as the cutoff.
Genome_build: hg19

source_name: Astrocyte

growth_protocol: T/C28a2 cell, which was the immortalized human juvenile costal chondrocyte, was cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Cells were crosslinked by 1% formaldehyde for 10 mins, and then quenched in 125 mM glycine for 5mins. After washing with cold TBS twice, cells were incubated in lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) for 10 mins on ice. Nuclei were washed and resuspended in MNase digestion buffer (20 mM Tris-HCl, pH 7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2) supplemented with 1,000 units of MNase (NEB) and incubated at 37 °C with continuous mixing for 20 mins. The reaction was stopped by adding of 2XSTOP buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), followed by sonication for 10 mins (30 secs on / 30 secs off). For -in ChIP-seq, the MNase digested chromatin from drosophila S2 cells was added to 1% to 5% of total chromatin. The chromatin was incubated with antibodies at 4 °C overnight and then subjected to 30 μl of protein G-magnetic beads for additional 2 hours. The beads were extensively washed and bound DNA was eluted with elution buffer (10 mM Tris-HCl, pH8.0, 10 mM EDTA, 150 mM NaCl, 5 mM DTT, 1% SDS) and reverse-crosslinked at 65 °C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen) after treatment of proteinase K and RNase A.
Sequencing libraries were prepared using TruPrep DNA library prep kit (Vazyme) following the manufacturer’s instructions.
The library was sequenced on an Illumina HiSeq Xten platform with pair-end read of 150bp

value: immortalized juvenile costal chondrocyte cell line T/C 28a2

tag: mutation

value: WT


title: WT_H3K4me1_2nd

status: Public on Oct 31 2020

type: SRA

country: China

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: chip antibody


title: WT_H3K36me3__2nd


title: WT_H3K36me2__2nd


title: WT_H3K27me3_2nd


title: UOK269 (SDHB)

type: genomic

city: Bethesda

first: Christopher

middle: James

last: Ricketts

state: Maryland

address: Building 10

department: Urologic Oncology Branch

country: USA

institute: National Cancer Institute

description: SDHB-RCC-derived RCC cell line

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human methylation450k Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing: GenomeStudio

label: Cy5 and Cy3

source_name: Primary renal tumor derived cell line

label_protocol: Standard Illumina Protocol

growth_protocol: All cell lines were maintained in DMEM with High Glucose (4500 mg/L), L-glutamine (4.0mM), and Phenol Red (Thermo Fisher, 11965167) and 10% Fetal Bovine Serum

extract_protocol: DNA for the tumors and normal kidney was obtained from FFPE blocks.  Characteristic tumor or normal histomorphology samples were needle microdissected and microdissected FFPE tissue was lysed in a cocktail containing mineral oil (for deparaffinization), proteinase K, and ATL lysis buffer (Qiagen), and resultant lysates were filter-purified by Qiagen DNA enrichment columns. Purified DNAs were treated with FFPE DNA restoration solution (Illumina).  Cell line genomic DNA was extracted from ~1 million cells using the Maxwell 16 System with a Maxwell 16 Cell DNA Purification Kit (Promega, Madison, WI). DNA quantification was performed using a ThermoScientific NanoDrop 1000 (Wilmington, DE)

tag: disease state

value: Succinate dehydrogenase deficient renal cell carcinoma (SDHB-RCC)

tag: sample type

value: Patient-derived RCC cell line


title: H3.1K36M#2_H3K36me3__2nd

value: hetero K36M mutation at HIST1H3D


title: WT1_H3K27ac_2nd


title: UOK271 (HLRCC)

description: HLRCC-derived RCC cell line

value: Hereditary leiomyomatosis and renal cell carcinoma (HLRCC)


title: H3.1K36M#2_H3K4me1_2nd


title: H3.1K36M#2_H3K4me3_2nd


title: UOK150 (VHL)

description: VHL-derived RCC cell line

value: von Hippel-Lindau disease (VHL)


title: H3.1K36M#2_H3K36me2__2nd


title: UOK269WT

description: SDHB-RCC-derived RCC cell line with wild-type SDHB re-expression


title: UOK262 (HLRCC)

description: HLRCC-derived RCC cell line


title: SDHB-RCC7

description: Primary SDHB-RCC renal tumor

source_name: Primary renal tumor

value: Primary renal tumor


title: H3.1K36M#2_H3K27me3_2nd


title: UOK140 (VHL)

description: VHL-derived RCC cell line


title: SDHB-RCC1 N

description: SDHB-RCC associated normal kidney

source_name: Normal Kidney

value: Associated normal kidney


title: UOK130 (VHL)

description: VHL-derived RCC cell line


title: UOK262WT

description: HLRCC-derived RCC cell line with wild-type FH re-expression


title: RPTEC (Normal)

description: Normal kidney cell line

source_name: Renal Proximal Tubule Epithelial Cells

value: Normal

value: Renal Proximal Tubule Epithelial Cells


title: SDHB-RCC2 N

description: SDHB-RCC associated normal kidney


title: H3.1K36M#1_H3K36me3__2nd


title: SDHB-RCC2

description: Primary SDHB-RCC renal tumor


title: SDHB-RCC7 N

description: SDHB-RCC associated normal kidney


title: H3.1K36M#1_H3K4me3_2nd


title: UOK220 (VHL)

description: VHL-derived RCC cell line


title: H3.1K36M#1_H3K4me1_2nd


title: H3.1K36M#1_H3K36M_2nd


title: SDHB-RCC1

description: Primary SDHB-RCC renal tumor


title: H3.1K36M#1_H3K27me3_2nd


title: H3.1K36M#2_H3K27ac_2nd


title: 1_2892UV, H3K27ac_ChIPSeq

city: Charlottesville

first: Maria

middle: Florencia

last: Martinez

address: 409 Lane Rd. Rm 2006

institute: University of Virginia

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
The two peak callers used at Active Motif are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009)
Genome_build: mm10
Supplementary_files_format_and_content: wig

organism: Mus musculus

source_name: renin cells

growth_protocol: The renin-expressing As4.1 cell line, harboring a Ren-2 5′-flanking sequence/SV40 T antigen hybrid transgene, was cultured in high glucose DMEM (Gibco #11965-092), 10% FBS at 37C in a humidified incubator containing 5% of CO2

extract_protocol:
Native Renin cells were isolated from the kidney cortex of adult animals using FACS sorting, utilizing our Ren1c-YFP reporter mice. Ren1c-YFP and Ren1c-/-; Ren1c-YFP mice were anesthetized with tribromoethanol and the kidneys were excised, decapsulated, demedullated. The kidney cortices from each animal were dissected and minced to a smooth consistency, and transferred into a 15 ml Falcon tube with 5 ml of enzymatic solution [0.3% collagenase A (Roche, Indianapolis, IN), 0.25% trypsin (Sigma- Aldrich, St. Louis, MO), and 0.0021% DNase I (Roche Applied Science)]. The tubes were placed flat inside a shaking incubator (80 RPM) for 15 minutes at 37℃. Then, the solution was pipetted up/down ten times with a sterile transfer pipette and allowed to settle for 2 minutes, and the supernatant was collected with a plastic pipette and transferred to a fresh 15 ml tube on ice. The supernatants collected from the three digestions round were pooled and centrifuged in a Sorvall RT 6000 Refrigerated Centrifuge at 1,200 g for 4 minutes at 4°C. The cell pellet was resuspended with 25 ml of fresh buffer 1 (130 mM NaCl, 5 mM KCl, 2 mM CaCl2, 10 mM glucose, 20 mM sucrose, 10 mM HEPES, pH 7.4), and the suspension was poured through a sterile 100 µm nylon cell strainer (Falcon™ Cell Strainers, Corning, Inc. 352360) and washed with an additional 3–5 ml of buffer 1. The flow-through was poured through a sterile 40 µm nylon cell strainer (Falcon™ Cell Strainers, Corning, Inc. 352340) and washed with 3–5 ml of buffer 1. The flow-through was centrifuged at 1,200 g for 4 min at 4°C. After the centrifugation, the cell pellet was resuspended in 1ml of resuspension buffer [PBS, 1% FBS, 1 mM EDTA, DNAase I (Roche Applied Science)] and analyzed using a fluorescent-activated cell sorter (Influx Cell Sorter).  .Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Active Motif protocol

tag: genotype

value: Ren1c-/-; Ren1c-YFP

tag: strain


title: HLRCC6 Lt

description: Primary HLRCC renal tumor


title: HLRCC5

description: Primary HLRCC renal tumor


title: HLRCC3

description: Primary HLRCC renal tumor


title: VHL1

description: Primary VHL renal tumor


title: H3.3K36M#2_H3K36me2__2nd

value: hetero K36M mutation at H3F3B


title: H3.3K36M#2_H3K4me3_2nd


title: HLRCC4

description: Primary HLRCC renal tumor


title: H3.3K36M#2_H3K36me3__2nd


title: HRCE (Normal)

description: Normal kidney cell line

source_name: Human Renal Cortical Epithelial cells

value: Human Renal Cortical Epithelial cells


title: H3.1K36M#1_H3K27ac_2nd


title: SDHB-RCC6

description: Primary SDHB-RCC renal tumor


title: H3.3K36M#2_H3K27me3_2nd


title: H3.3K36M#2_H3K4me1_2nd


title: H3.1K36M#1_H3K36me2__2nd


title: H3.3K36M#1_H3K36me3__2nd


title: HLRCC1 N

description: HLRCC associated normal kidney


title: H3.3K36M#1_H3K4me3_2nd


title: H3.3K36M#1_H3K36me2__2nd


title: H3.3K36M#1_H3K4me1_2nd


title: HLRCC1

description: Primary HLRCC renal tumor


title: H3.3K36M#1_H3K27ac_2nd


title: H3.3K36M#1_H3K27me3_2nd


title: UOK268 (HLRCC)

description: HLRCC-derived RCC cell line


title: H3.3K36M#2_H3K27ac_2nd


title: Control trophoblasts from  donor1

city: Nanjing

first: Chenrui

last: Cao

address: 321 Zhongshan Road

institute: Drum Tower Hospital

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample ...

molecule: total RNA

source_name: trophoblasts

growth_protocol: The purified cytotrophoblasts were cultured in DMEM medium with sodium pyruvate and glutamine on 12-well plates coated by Matrigel at 37°C in a 5% CO2 incubator for the indicated time.

extract_protocol:
Pretreated primary CTBs were collected in Trizol and delivered in dry ice to Gene Denovo Biotechnology Co. for transcriptome resequencing analysis with Illumina Hiseq x10.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary CTBs were transfected with JAM-C and CTL plasmids for 24 h.

tag: individual

value: donor 1

tag: cell type

value: villi-derived cytotrophoblasts

tag: treatment

value: CTL


title: JAM-C over-expressed trophoblasts from  donor3

value: donor 3

value: JAM-C


title: Control trophoblasts from  donor2

value: donor 2


title: JAM-C over-expressed trophoblasts from  donor2


title: Control trophoblasts from  donor3


title: JAM-C over-expressed trophoblasts from  donor1


title: SDHB-RCC5

description: Primary SDHB-RCC renal tumor

value: Succinate dehydrogenase deficient renal cell carcinoma (SDHB-RCC)


title: 9hNutlin_rep2

city: Philadelphia

first: Katherine

middle: A

last: Alexander

state: Pennsylvania

address: Smilow Center for Translational Research

institute: University of Pennsylvania

data_processing:
fastq files were aligned using STAR
Htseq2 was used to count the number of reads for each gene
Deseq2 was used to generate normalized counts
Deseq2 was used to identify significant differences
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files of normalized counts for all samples, or for statistics for comparisons of each Nutlin sample with the DMSO control

molecule: polyA RNA

source_name: Primary lung fibroblast

growth_protocol: IMR90 cells were grown under 3% oxygen, 5% carbon dioxide in DMEM with 10% FBS

extract_protocol:
Total RNA was extracted in phenol-chroform, then purified with column purification. PolyA RNAs were selected using NEBNext Poly(A) mRNA Magnetic Isolation Module
RNA-seq libaries were prepared using NEB Next Ultra II Directional RNA library prep kit for Illumina

treatment_protocol: The day after splitting IMR90 cells seeding at 300k cells/mL, cells were treated with DMSO, or Nutlin-3a (3ug/mL) for 6, 9, or 12 hours

tag: passage

tag: agent

tag: time point


title: 6hNutlin_rep2


title: 6hNutlin_rep1


title: H3.1K36M#2_H3K36M_2nd

value: immortalized juvenile costal chondrocyte cell line T/C 28a2

value: hetero K36M mutation at HIST1H3D


title: dmso_rep1

value: DMSO


title: dmso_rep2


title: Hivep3-/- Thymic iNKT17 cells_Mouse2

city: Aurora

first: Laurent

last: Gapin

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical campus

data_processing:
Fastq files were concatened and then  trimmed using Trimmomatic (v 0.39) with MINLEN:36 CROP:50.
Fastq files were then mapped to mouse genome (mm10) using the ENCODE ATAC-seq pipeline, with default parameters, except mapped reads were subsampled to a maximum of 50 million reads for peak calling. NarrowPeak files from individual replicates of all conditions were merged into a global set of peaks, excluding those on the Y chromosome or overlapped the ENCODE blacklist, and condensed to non-overlapping regions with a uniform size of 500 bp using chromVAR (v 1.8.0)
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts for peaks

source_name: iNKT17 cells

extract_protocol:
DNA was purified using the DNA Clean and Concentrator-5 kit (Zymo Research) and barcoding was performed using Illumina compatible index primers designed according to Buenrostro et al
PCR was conducted for 11–12 cycles. Library purification and size selection was carried out using 1.8X AMPureXP beads (Beckman Coulter). Libraries were quantified and size distribution was assessed using the High Sensitivity D1000 ScreenTape System (Agilent)

treatment_protocol:
5,000 to 20,000 cells from each iNKT subset (iNKT1 cells (CD122+, ICOS-), iNKT2 cells (CD122-, ICOS+, Izumo1r+, CD138-) or iNKT17 cells (CD122-, ICOS+, Izumo1r-, CD138+)) from the pooled thymi of C57BL/6 or Hivep3-/- mice were sorted individually and then pooled for a total of 50,000-100,000 cells per transposition.
Cells were then placed in 50 µL of cold lysis buffer (10 mM TrisHCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Molecular biology-grade NP-40, 0.1% (v/v) Tween-20, 0.01% (v/v) Digitonin). Permeabilized cells were pelleted for 10 minutes at 500xg and resuspended in 50 μL of transposition mix (25 μL 2x TD buffer (Illumina), 16.5 μL 1X PBS, 0.5 μL 10% (v/v) Tween-20, 0.5 μL 1% (v/v) Digitonin, 2.5 μL Tn5 transposase (Illumina), 5 μL nuclease-free water).
The volume of lysis buffer/transposition mix was scaled up to 100 μL for 100,000 cells. The transposase reaction was conducted for 30 min at 37 °C with shaking at 1,000 rpm. Cells were then subjected to a second sort to separate the different iNKT cell subsets using the same markers used in the first sort. While the fluorescence corresponding to the CD122 and Izumo1r markers was quenched by the transposition reaction, other markers were unaffected, allowing for the sorting of each of the iNKT cell subsets on the basis of ICOS and CD138 expression (iNKT1 (ICOS- CD138-), iNKT2 (ICOS+, CD138-) and iNKT17 (ICOS+ CD138+))

value: 8-9 week old thymocytes

tag: cell subtype

value: iNKT17 cells

tag: background strain

value: untreated


title: Hivep3-/- Thymic iNKT2 cells_Mouse2

source_name: iNKT2 cells

value: iNKT2 cells


title: Hivep3-/- Thymic iNKT2 cells_Mouse1


title: Hivep3-/- Thymic iNKT1 cells_Mouse2

source_name: iNKT1 cells

value: iNKT1 cells


title: Hivep3-/- Thymic iNKT17 cells_Mouse1


title: C57BL/6 Thymic iNKT17 cells_Mouse2

value: wildtype


title: Hivep3-/- Thymic iNKT1 cells_Mouse1


title: C57BL/6 Thymic iNKT2 cells_Mouse2


title: 4T1 mixed

city: San Diego

first: Stephanie

middle: I

last: Fraley

state: CA

address: 9500 Gilman Drive MC 0412

institute: UCSD

data_processing:
Count matrix for each sample was generated using cellRanger (10x Genomics)
Depth normalization was performed using cellRanger (10x Genomics)
Differential gene expression analysis was performed using Seurat (Stuart et al., 2019)
Genome_build: hg38, mm10
Supplementary_files_format_and_content: RDS files contain Seurat objects with raw and processed counts for each sample

extract_protocol:
Cells were collected using flow cytometry (FACS), and the Chromium Single Cell 3’ v3 kit (10x genomics, Pleasanton, CA) was used to extract the RNA
Chromium Single Cell 3’ v3 kit (10x genomics, Pleasanton, CA) was used for library construction

tag: phenotypic supervision status

value: no

tag: phenotype

value: mixed


title: C57BL/6 Thymic iNKT2 cells_Mouse1


title: C57BL/6 Thymic iNKT1 cells_Mouse2


title: C57BL/6 Thymic iNKT17 cells_Mouse1


title: genetic male - EE2-exposed 18 [MBD-seq]

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description:
CH7EMF1_gDNA
MBDseq_CpG_methylation_profile.txt

data_processing:
[RNA-seq] The color-space raw sequence reads in the CSfasta format were aligned to the galGal3 chicken reference genome sequence using the RNA-seq pipeline of the ABI Lifescope software.
[RNA-seq] Expression of mRNA transcripts from protein-coding genes annotated in the galGal3 reference genome was determined by assigning uniquely aligned reads (bam format) to exons of the galGal3 gene model using Bioconductor (version 3.8) packages Rsubread (version 2.0.1) and edgeR (version 3.28.1). The relative mRNA expression data were normalized using the negative binominal trimmed mean of M-values (TMM) method implemented by the edgeR package.
[RNA-seq] RNA expression from chicken RSs was evaluated using the ERVmap pipeline.
[MBD-seq] The CSfasta raw reads were aligned to the galGal3 chicken reference genome sequence using the MethylMiner-seq pipeline of the ABI Lifescope software.
[MBD-seq] Statistical evaluation of DNA methylome was performed using the Bioconductor package MEDIPS (version 1.38.0).
Genome_build: galGal3
Supplementary_files_format_and_content: RNAseq: Normalized RNA counts for protein-coding genes and repetitive sequences (EXCEL).
Supplementary_files_format_and_content: MBD-seq: Percent averaged methylation of 100-bp windows throughout the genome (text format).

organism: Gallus gallus

source_name: day-19 chicken embryonic gonad

growth_protocol: Fertilized eggs were incubated for 19 days.

extract_protocol:
Both gDNA and RNA were extracted using Qiagen AllPrep Mini kit.
RNA-seq libraries with barcode indexes were synthesized using ABI SOLiD 5500 Fragment Library Core Kit and subjected to 50-nucleotide, single-read multiplex sequencing with ABI SOLiD 5500XL deep sequencers.
Genomic DNA was fragmented to ~200 bp by sonication at 4 °C using the Covaris S2 sonicator and subjected to enrichment of methylated DNA fragments using the MethylMiner kit (Life Technologies). Deep sequencing libraries were synthesized using ABI SOLiD 5500 Fragment Library Core Kit and subjected to 50-nucleotide, single-read sequencing with ABI SOLiD 5500XL deep sequencers.

treatment_protocol: Ethynylestradiol (20 microgram per egg) was injected to day-6 eggs in 50 microLiter oil emulsion.

tag: breed

value: domestics

tag: genetic sex

value: male (ZZ)

tag: tissue

value: Day 19 Embryonic gonad

tag: exposure

value: ethynylestradiol

tag: feminization score


title: genetic male - EE2-exposed 15 [MBD-seq]

description:
CH34EMF1_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic male - EE2-exposed 14 [MBD-seq]

description:
CH18EMF1_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic male - EE2-exposed 17 [MBD-seq]

description:
CH39EMF2_gDNA
MBDseq_CpG_methylation_profile.txt


title: 12hNutlin_rep2

tag: cell line


title: genetic male - EE2-exposed 13 [MBD-seq]

description:
CH17EMF1_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic male - EE2-exposed 12 [MBD-seq]

description:
CH12EMF1_gDNA
MBDseq_CpG_methylation_profile.txt


title: 12hNutlin_rep1


title: genetic male - EE2-exposed 11 [MBD-seq]

description:
CH10EMF2_gDNA
MBDseq_CpG_methylation_profile.txt


title: 9hNutlin_rep1


title: genetic male - EE2-exposed 10 [MBD-seq]

description:
39EMF2_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic male - EE2-exposed 7 [MBD-seq]

description:
34EMF1_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic male - EE2-exposed 8 [MBD-seq]

description:
35EMF2_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic male - EE2-exposed 6 [MBD-seq]

description:
32EMF1_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic male - EE2-exposed 3 [MBD-seq]

description:
26EMF2_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic male - EE2-exposed 4 [MBD-seq]

description:
28EMF2_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic male - EE2-exposed 1 [MBD-seq]

description:
23EMF1_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic male - EE2-exposed 16 [MBD-seq]

description:
CH35EMF1_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic male - EE2-exposed 2 [MBD-seq]

description:
24EMF2_gDNA
MBDseq_CpG_methylation_profile.txt


title: C57BL/6 Thymic iNKT1 cells_Mouse1

tag: genotype


title: genetic female - EE2-exposed 2 [MBD-seq]

description:
CH21EFF3_gDNA
MBDseq_CpG_methylation_profile.txt

value: female (WZ)


title: genetic female - EE2-exposed 1 [MBD-seq]

description:
CH1EFF3_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic female - vehicle 5 [MBD-seq]

description:
7VF_gDNA
MBDseq_CpG_methylation_profile.txt

value: vehicle


title: genetic male - vehicle 2 [MBD-seq]

description:
15VM_gDNA
MBDseq_CpG_methylation_profile.txt


title: CH7EMF1_RNA [RNA-seq]

description:
CH7EMF1_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: genetic male - vehicle 4 [MBD-seq]

description:
6VM_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic male - vehicle 3 [MBD-seq]

description:
18VM_gDNA
MBDseq_CpG_methylation_profile.txt


title: CH17EMF1_RNA [RNA-seq]

description:
CH17EMF1_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: CH12EMF1_RNA [RNA-seq]

description:
CH12EMF1_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: 39EMF2_RNA [RNA-seq]

description:
39EMF2_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: 35EMF2_RNA [RNA-seq]

description:
35EMF2_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: 37EMF1_RNA [RNA-seq]

description:
37EMF1_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: genetic male - vehicle 1 [MBD-seq]

description:
12VM_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic female - vehicle 3 [MBD-seq]

description:
2VF_gDNA
MBDseq_CpG_methylation_profile.txt


title: 34EMF1_RNA [RNA-seq]

description:
34EMF1_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: genetic female - vehicle 4 [MBD-seq]

description:
3VF_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic female - vehicle 1 [MBD-seq]

description:
11VF_gDNA
MBDseq_CpG_methylation_profile.txt


title: genetic female - vehicle 2 [MBD-seq]

description:
16VF_gDNA
MBDseq_CpG_methylation_profile.txt


title: 32EMF1_RNA [RNA-seq]

description:
32EMF1_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: 24EMF2_RNA [RNA-seq]

description:
24EMF2_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: 23EMF1_RNA [RNA-seq]

description:
23EMF1_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: CH39EMF2_RNA [RNA-seq]

description:
CH39EMF2_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: 26EMF2_RNA [RNA-seq]

description:
26EMF2_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: 28EMF2_RNA [RNA-seq]

description:
28EMF2_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: CH21EFF3_RNA [RNA-seq]

description:
CH21EFF3_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: 19VM_RNA [RNA-seq]

description:
19VM_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: 18VM_RNA [RNA-seq]

description:
18VM_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: CH35EMF1_RNA [RNA-seq]

description:
CH35EMF1_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: CH18EMF1_RNA [RNA-seq]

description:
CH18EMF1_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: genetic male - EE2-exposed 5 [MBD-seq]

description:
30EMF2_gDNA
MBDseq_CpG_methylation_profile.txt


title: CH10EMF2_RNA [RNA-seq]

description:
CH10EMF2_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: genetic male - EE2-exposed 9 [MBD-seq]

description:
37EMF1_gDNA
MBDseq_CpG_methylation_profile.txt


title: 30EMF2_RNA [RNA-seq]

description:
30EMF2_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: 2VF_RNA [RNA-seq]

description:
2VF_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: CH1EFF3_RNA [RNA-seq]

description:
CH1EFF3_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: 16VF_RNA [RNA-seq]

description:
16VF_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: 15VM_RNA [RNA-seq]

description:
15VM_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: 6VM_RNA [RNA-seq]

description:
6VM_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: HIS5_hap

city: South San Francisco

first: Rebecca

middle: Y

last: Wang

address: 1170 Veterans Blvd

institute: Calico Life Science LLC

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HIS5] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

data_processing:
Library strategy: Whole Genome Sequencing
RNAseq: Samples were demultiplexed using bcl2fastq, then fastq files were processed using Salmon and aligned using STAR
BARseq: Samples were demultiplexed using Barcas
Whole Genome Sequencing: Samples were demultiplexed using bcl2fastq and then BowTie2 was used to align the samples
Genome_build: SacCer3
Supplementary_files_format_and_content: 20190909_rawTPMtable.csv: csv file with raw TPMs from RNAseq
Supplementary_files_format_and_content: zev_wgs_processeddata.csv: csv file with sequencing information, rDNA coverage, copy number and gc content
Supplementary_files_format_and_content: ZEV_TOF_all_merge.txt: text file with normalized BARseq results (normalized to wild type, time 0, and read depth)

organism: Saccharomyces cerevisiae

growth_protocol: All BARseq, WGS, and RNAseq samples were grown using glutamate as a nitrogen source

extract_protocol:
BARSeq: pooled cultures were propagated at low density (OD < 0.05) and > 2 x 106 cells were collected at each time point. Genomic DNA was extracted using the YeaStar Genomic DNA kit (Zymo Research) and 5 ng of DNA were used to PCR amplify the uptag barcode region with custom primers
Whole Genome Sequencing: Genomic DNA was extracted using the YeaStar Genomic DNA kit (Zymo Research)
RNAseq:  cells were frozen in lysis mastermix, then reverse transcription was done to obtain cDNA, which was then amplified and cleaned up with RNAClean Ampure XP beads
Libraries were constructed using the Nextera DNA Flex kit (Whole Genome Sequencing) and Nextera XT kit (RNAseq)

tag: media

value: SC+ClonNAT

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HIS5] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: 7VF_RNA [RNA-seq]

description:
7VF_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: HIS4_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HIS4] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HIS4] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: 12VM_RNA [RNA-seq]

description:
12VM_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: HIS1_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HIS1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HIS1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: 3VF_RNA [RNA-seq]

description:
3VF_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: HIS2_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HIS2] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HIS2] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: LEU2_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-LEU2] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-LEU2] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: 11VF_RNA [RNA-seq]

description:
11VF_RNA
RNAseq_Normalized_CPM.xlsx
RNAseq_normalized_repetitive_sequences_counts.xlsx


title: HIS6_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HIS6] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HIS6] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: LEU4_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-LEU4] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-LEU4] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: HIS7_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HIS7] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HIS7] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: MET8_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-MET8] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-MET8] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: VMA3_8

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-VMA3] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

data_processing:
RNAseq: Samples were demultiplexed using bcl2fastq, then fastq files were processed using Salmon and aligned using STAR
BARseq: Samples were demultiplexed using Barcas
Whole Genome Sequencing: Samples were demultiplexed using bcl2fastq and then BowTie2 was used to align the samples
Genome_build: SacCer3
Supplementary_files_format_and_content: 20190909_rawTPMtable.csv: csv file with raw TPMs from RNAseq
Supplementary_files_format_and_content: zev_wgs_processeddata.csv: csv file with sequencing information, rDNA coverage, copy number and gc content
Supplementary_files_format_and_content: ZEV_TOF_all_merge.txt: text file with normalized BARseq results (normalized to wild type, time 0, and read depth)

value: SC+ClonNAT+estradiol

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-VMA3] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: VMA3_7


title: MET6_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-MET6] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-MET6] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: VMA3_9


title: VMA3_5


title: VMA3_6


title: VMA3_4


title: VMA3_3


title: HO_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HO] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HO] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: VMA3_2


title: TRP4_9

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-TRP4] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-TRP4] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: VMA3_10


title: VMA3_1


title: TRP4_7


title: TRP4_8


title: Untreated_minibulk_2

city: Hong Kong

first: Danson

middle: Shek Chun

last: Loi

address: HKUST, Clear Water Bay

department: Division of Life Science

institute: Hong Kong University of Science and Technology

data_processing:
Basecalling was performed by Illumina BaseSpace Sequence Hub.
Raw reads at transcript level were aligned and quantified using kallisto 0.46.2.
Gene-level read count was obtained using R package tximport.
Genome_build: Gencode v.29 human reference transcriptome and KY962518.1 (GenBank Accession) rRNA sequence
Supplementary_files_format_and_content: csv containing raw counts

source_name: HCT116 cell line

extract_protocol:
Single cells were sorted using FACS. Lysis and total RNA extraction were performed in accordance with MATQ-seq protocol.
Both single-cell and mini-bulk libraries were constructed following MATQ-seq protocol.

tag: cell loine

tag: method

value: MATQ-seq

tag: type

value: Mini-bulk

tag: rrna depletion

value: No


title: Untreated_singlecell_3

value: Single-cell


title: Untreated_singlecell_2


title: Untreated_singlecell_1


title: Untreated_singlecell_4


title: Untreated_minibulk_1


title: TRP4_4

tag: time point


title: TRP4_5


title: TRP4_3


title: DASHed_minibulk_2

value: Yes


title: DASHed_minibulk_1


title: TRP4_2


title: TRP4_1


title: TRP4_6


title: TRP4_10


title: TIP41_9

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-TIP41] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-TIP41] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: DASHed_singlecell_3


title: TIP41_8


title: DASHed_singlecell_4


title: DASHed_singlecell_2


title: TIP41_6


title: DASHed_singlecell_1


title: TIP41_7


title: TIP41_5


title: TIP41_4


title: TIP41_1


title: TIP41_3


title: TIP41_2


title: THR1_9

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-THR1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-THR1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: TIP41_10


title: THR1_2


title: THR1_5


title: THR1_1


title: THR1_8


title: THR1_6


title: THR1_4


title: THR1_7


title: SNT1_6

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-SNT1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-SNT1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: SNT1_9


title: SNT1_4


title: SNT1_7


title: THR1_10


title: THR1_3


title: SNT1_8


title: SNT1_2


title: SNT1_10


title: SNT1_5


title: SNT1_1


title: SNT1_3


title: SRS2_8

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-SRS2] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-SRS2] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: SRS2_9


title: SRS2_7


title: SRS2_6


title: SRS2_5


title: SRS2_4


title: SRS2_2


title: SRS2_3


title: SRS2_1


title: SRS2_10


title: SRP40_9

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-SRP40] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-SRP40] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: SRP40_8


title: SRP40_6


title: SRP40_5


title: SRP40_3


title: SRP40_1


title: SNF12_9

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-SNF12] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-SNF12] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: HOXC8-FLAG

city: hefei

first: li

last: yong

state: anhui province

address: 安徽省合肥市经开区九龙路111号安大新区

institute: anhui university

data_processing:
Illumina HiSeq 1000 platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT2 software
Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include the expression values of this transcript  for each Sample ...

source_name: NSCLC cells

growth_protocol: A549 cells were grown in RPMI1640 medium supplemented with 10% fetal bovine serum and antibiotics. Cell cultures were maintained at 37  C with 5% CO2.

extract_protocol:
The total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: tumor cell

value: lung

tag: genotype/variation

value: HOXC8-FLAG overexpression


title: SNF12_8

tag: background strain

value: SC+ClonNAT+estradiol


title: SRP40_10


title: SRP40_7


title: SNF12_7


title: SRP40_2


title: SH4

address: 安徽省合肥市经开区九龙路111号安大新区

value: SH4 knockdown


title: PCDH

address: 安徽省合肥市经开区九龙路111号安大新区

value: PCDH empty vector


title: SNF12_5


title: PLV

address: 安徽省合肥市经开区九龙路111号安大新区

value: PLV empty vector


title: SNF12_1


title: SNF12_4


title: SNF12_2


title: SRP40_4


title: SNF12_6


title: SNF12_3


title: SHM2_9

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-SHM2] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-SHM2] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: SNF12_10


title: SHM2_8


title: SHM2_7


title: SHM2_6


title: SHM2_3


title: SHM2_5


title: SHM2_4


title: SHM2_2


title: SHM2_1


title: SHM2_10


title: MET6_8

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-MET6] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-MET6] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: MET6_7


title: MET6_9


title: MET6_6


title: MET6_3


title: MET6_4


title: MET6_5


title: MET6_1


title: MET6_2


title: MET6_10


title: MET2_9

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-MET2] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-MET2] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: 4689_K562_USP15 KD_04

city: Amsterdam

first: Elisabetta

last: Citterio

address: Plesmanlaan 121

department: Molecular Genetics

country: Netherlands

institute: Netherlands Cancer Insitute (NKI-AVL)

description:
4689_8_K562_15_10_CCGTCCC_S30
Chronic myeloid leukemia, blast crisis
diffexp_batch_corrected_GCF4689-K562.txt
s_12

data_processing:
Sequence reads were mapped to Homo sapiens (hg38) using tophat version 2.1.0 with parameters --library-type fr-unstranded, --no-coverage-search -M --transcriptome-index, Ensembl GTF version 77
Readcounts were obtained by counting the number of reads per gene using Itreecount, which gives similar, but faster, results as HTSeq-count.
Differential expression was performed using the R package EdgeR/Limma. Genes that had no expression in all samples were removed upon analysis
Genome_build: Homo sapiens (hg38)
Supplementary_files_format_and_content: The tab-delimited text files contain gene expressions for all samples and the results (including fold change and p-value) of a differential expression analysis for selected samples.

source_name: Hematopoietic tissue

growth_protocol: KBM7 were grown in IMDM (Gibco) medium. K562 were grown in RPMI 1640 (Gibco) medium. Culture medium was supplemented with 2 mM L‐Glutamine (Gibco 25030-164), 10% fetal calf serum (FCS, Thermo Scientific) 100 U ml−1 penicillin, and 100 μg ml−1 streptomycin (Pen/Strep Gibco 15140-163). Cells were incubated at 37C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted, prepared using TruSeq protocol, and standard sample preparation protocols and RNA-seq was performed on a Hiseq2500 machine (Illumina) at the NKI Genomics Core Facility.
RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA Sample Prep protocols.

treatment_protocol: KBM7 or K562 cells were transfected with USP15 (USP15 KD) or control siRNAs (Ctrl) as described above. Total RNA was extracted at 72 h after transfection.

value: K562 cells

value: USP15 knockdown

value: Hematopoietic tissue


title: MET2_8


title: PS+ and PS-

city: Boston

first: Chengyu

last: Zou

address: 240 Longwood Ave

institute: Harvard medical school

description:
The isolated endothelial cells obtained from two male APP/PS1 mice were pooled together for In-Drop sequencing.
The isolated endothelial cells obtained from two male WT mice were pooled together for In-Drop sequencing.
PS+: APP/PS1 mice
PS-: WT mice
mRNA
In-Drop-Seq
library_name: "PS1+", library_index: "CGGAGAGA"
library_name: "PS1-", library_index: "AGGCTTAG"

data_processing:
{library_name: "PS1+", library_index: "CGGAGAGA"} {library_name: "PS1-", library_index: "AGGCTTAG"}
Ignore reads more than 10 alignments.
Ignore counts from UMI that should be split among more than 2 genes.
Maximal distance from transcript end is 400.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.counts.tsv: Tab-delimited matrix tables with raw gene counts for every gene and every cell.

source_name: APP/PS1 and WT mice

extract_protocol:
Endothelial cells were isolated by FACS as CD31+CD45-.
Libraries were constructed by single cell core at Harvard University.

tag: strain

value: mixed sample (non-demultiplexed)

tag: Sex

value: Male

tag: age

value: 6 months

value: Brain

tag: facs-isolated cells

value: Endothelial cells (CD31+CD45-)


title: Sample 5, Mobilized CD34+ progenitor cells, alone

type: RNA

city: Salamanca

first: Silvia

last: Preciado

state: Salamanca

address: Campus Universitario Miguel de Unamuno

country: Spain

institute: Cancer Research Institute of Salamanca

hyb_protocol: Labeled RNA was hybridized to Human Gene 2.0 ST Array

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing:
Expression value for each probe set was calculated using Affymetrix Expression Console that uses RMA (Robust Multi-Array Average) algorithm.
HuGene-2_0-st.pgf
HuGene-2_0-st.mps

label: biotin

source_name: Mobilized CD34+ progenitor cells

label_protocol: Labelling was performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: CD34+ cells from all groups were recovered, washed with PBS and frozen in 500µl of Trizol (Invitrogen, CA) at -80ºC. To isolate RNA, chloroform was added and centrifuged. The aqueous phase was transferred into a new eppendorf and isopropanol was added. The final solution was centrifuged, obtaining the RNA in the pellet. RNA was cleaned with ethanol 70% and resuspended in sterile water. After that, RNA was and purified using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to manufacturer’s instructions.

treatment_protocol:
expansion protocol: In order to isolate MSC, BM mononuclear cells (BM-MNC) were isolated by Ficoll-Paque density-gradient centrifugation (Ficoll-Paque, density: 1.077g/ml, GE Healthcare BioSciences).  Cells were seeded in culture flask at a density of 1x106 cells/cm2 in Dulbecco´s modified Eagle´s medium-low glucose-DMEM- (GIBCO, Life Technologies) supplemented with 10% Fetal Bovine Serum-FBS- (GIBCO, Life Technologies) and 1% penicillin/streptomycin. When cells reached confluence, they were tripsinized and seeded in a bigger surface. After third passage, MSC were assessed in accordance with the minimal definition criteria proposed by the ISCT.
irradiation protocol: To study the effect of EV released by irradiated MSC (IRR-MSC-EV) on HSC, MSC were irradiated on a medical linear accelerator at single dose of 2.5Gy. Two days later, MSC were deprived of FBS in order to recover EV from the supernatant. IRR-MSC-EV were co-cultured with CD34+ cells establishing a third group: (3) 2x105 CD34+ cells with IRR-MSC-EV.

value: Mobilized CD34+ progenitor cells

tag: co-cultured

value: No

tag: irradiated msc

tag: sample


title: Sample 5, Mobilized CD34+ progenitor cells, Co-cultured with non-irradiated MSC-EV

value: Co-cultured with MSC-EV


title: Sample 4, Mobilized CD34+ progenitor cells, alone


title: Sample 5, Mobilized CD34+ progenitor cells, Co-cultured with Irradiated MSC-EV

value: Yes


title: Sample 2, Mobilized CD34+ progenitor cells, alone


title: MET2_7

value: SC+ClonNAT+estradiol

tag: genotype


title: 4651_5_USP15 KO-02

data_processing:
Sequence reads were mapped to mm10 using tophat version 2.1.0 with parameters --library-type fr-unstranded, --no-coverage-search -M --transcriptome-index, Ensembl GTF version 77
Readcounts were obtained by counting the number of reads per gene using Itreecount, which gives similar, but faster, results as HTSeq-count.
Differential expression was performed using the R package EdgeR/Limma. Genes that had no expression in all samples were removed upon analysis
Genome_build: mm10
Supplementary_files_format_and_content: The tab-delimited text files contain gene expressions for all samples and the results (including fold change and p-value) of a differential expression analysis for selected samples.

source_name: Bone marrow

extract_protocol:
LSKs cells were FACS sorted from freshly isolated bone marrow mononuclear cells, WT n=3, Usp15-/- n=2. Total RNA was extracted, prepared using TruSeq protocol, and standard sample preparation protocols and RNA-seq was performed on a Hiseq2500 machine (Illumina) at the NKI Genomics Core Facility.  Cell sorting was performed by FACSAria (BD Biosciences).
RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA Sample Prep protocols.

value: LSK

tag: tissue

value: Bone marrow

value: 8 weeks


title: 4689_K562_USP15 KD_03

description:
4689_7_K562_5_09_ATGTCAG_S29
Chronic myeloid leukemia, blast crisis
diffexp_batch_corrected_GCF4689-K562.txt
s_11

tag: cell line


title: Sample 4, Mobilized CD34+ progenitor cells, Co-cultured with Irradiated MSC-EV


title: Sample 2, Mobilized CD34+ progenitor cells, Co-cultured with Irradiated MSC-EV


title: Sample 1, Mobilized CD34+ progenitor cells, Co-cultured with Irradiated MSC-EV


title: Sample 4, Mobilized CD34+ progenitor cells, Co-cultured with non-irradiated MSC-EV


title: Sample 1, Mobilized CD34+ progenitor cells, alone


title: 4689_K562_Ctrl_04

description:
4689_6_K562_Ctrl_08_AGTTCCG_S28
Chronic myeloid leukemia, blast crisis
diffexp_batch_corrected_GCF4689-K562.txt
s_10

value: control


title: Sample 2, Mobilized CD34+ progenitor cells, Co-cultured with non-irradiated MSC-EV


title: Sample 3, Mobilized CD34+ progenitor cells, Co-cultured with non-irradiated MSC-EV


title: MET2_6

tag: media

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-MET2] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: 4689_K562_Ctrl_03

description:
4689_5_K562_Ctrl_07_AGTCAAC_S27
Chronic myeloid leukemia, blast crisis
diffexp_batch_corrected_GCF4689-K562.txt
s_9

value: K562 cells


title: Sample 3, Mobilized CD34+ progenitor cells, Co-cultured with Irradiated MSC-EV


title: Sample 3, Mobilized CD34+ progenitor cells, alone


title: 4651_4_USP15 KO-01


title: 4651_3_WT-03

value: wild type


title: 4689_K562_USP15 KD_02

description:
4689_4_K562_15_06_CTTGTAA_S26
Chronic myeloid leukemia, blast crisis
diffexp_batch_corrected_GCF4689-K562.txt
s_8

value: USP15 knockdown

value: Hematopoietic tissue


title: 4651_2_WT-02


title: 4689_K562_USP15 KD_01

description:
4689_3_K562_15_04_CAGATCA_S25
Chronic myeloid leukemia, blast crisis
diffexp_batch_corrected_GCF4689-K562.txt
s_7


title: MET2_3


title: MET2_2


title: MET2_5


title: 4689_K562_Ctrl_01

description:
4689_1_K562_Ctrl_01_ACAGTGA_S23
Chronic myeloid leukemia, blast crisis
diffexp_batch_corrected_GCF4689-K562.txt
s_5


title: MET2_1


title: 4689_K562_Ctrl_02

description:
4689_2_K562_Ctrl_02_GCCAATA_S24
Chronic myeloid leukemia, blast crisis
diffexp_batch_corrected_GCF4689-K562.txt
s_6


title: ATAC_Myod1_KO_MB_rep1

city: New York

last: Zhang

state: New York

address: 522 First Avenue, Smilow Research Building, 1106

department: Pathology

institute: New York University School of Medicine

data_processing:
[Hi-C] All Hi-C datasets were uniformly pre-processed with the HiC-bench platform (Lazaris et al., 2017), outlined briefly as follows. First, all paired-end sequencing reads were aligned against the mouse genome version NCBIM37/mm9 with bowtie2 version 2.2.6 (Langmead and Salzberg, 2012) (specific settings: --very-sensitive-local --local). The aligned reads were further filtered using the GenomicTools (Tsirigos et al., 2012) gtools-hic filter command with the following parameters "--mapq 30 --min-dist 25000 --max-offset 500" (integrated in HiC-bench), which discards multi-mapped reads (“multihit”), read-pairs with only one mappable read (“single sided”), duplicated read-pairs (“ds.duplicate”), read-pairs with a low mapping quality of MAPQ <30, read-pairs resulting from self-ligated fragments and short-range interactions resulting from read-pairs aligning within 25kb (together called “ds.filtered”).
[pCHi-C] Raw sequencing reads from pCHi-C were processed using the HiCUP pipeline (Wingett et al., 2015), which maps the positions of di-tags against the mouse genome (NCBIM37/mm9), filters out experimental artifacts, such as circularized reads and re-ligations, and removes all duplicate reads. High-confidence interactions were identified by CHiCAGO as previously described (Score ≥ 5 in at least one condition) (Cairns et al., 2016).
[ChIP-seq] Raw reads were aligned to the mouse genome version NCBIM37/mm9 with bowtie2 version 2.3.4.1 (Langmead and Salzberg, 2012) (specific settings for paired-end reads: --local --no-mixed --no-discordant; specific settings for single-end reads: --local). Only uniquely mapped reads were selected for downstream analysis. PCR duplicates were removed using Picard-tools version 1.88. Peak-calling was done using MACS2 version 2.1.1 (Zhang et al., 2008) with a default q-value of 0.05.Replicate experiments were merged and the data were normalized per million total reads for visualization.
[ATAC-seq] Raw reads were aligned to the NCBIM37/mm9 reference genome with Bowtie2 version 2.2.6 using the options ‘--local --dovetail --minins 38 --maxins 2000 --no-mixed --no-discordant’. Only uniquely mapped reads were selected for downstream analysis. PCR duplicates were removed using Picard-tools version 1.88. Replicate experiments were merged, and the data were normalized per million total reads for visualization. Transposase-accessible regions were identified using the callpeak command of MACS2 version 2.1.1 with options ‘--nomodel --nolambda --keep-dup all --call-summits’ as described (Zhang et al., 2008).
Genome_build: mm9
Supplementary_files_format_and_content: [Hi-C] Text file with paired contacts from filtered Hi-C data.
Supplementary_files_format_and_content: [pCHi-C] Rds images of chicagoData objects.
Supplementary_files_format_and_content: bigWig and bed (narrowPeak) files for ChIP-seq and ATAC-seq.

source_name: Primary myoblasts

growth_protocol: ESCs containing the inducible Pax7 cassette were maintained in mouse ES medium. iPax7 muscle progenitors were grown on 0.1% gelatin-coated culture plates in GlutaMAX supplemented IMDM (Gibco) with 15% stem cell qualified fetal bovine serum (Gemini), 1% Penicillin/streptomycin (Corning), 200 μg/ml bovine holo-transferrin (Sigma), 50 μg/ml L-ascorbic acid (Sigma), 4.5 mM 1-thioglycerol (Sigma), 5 ng/ml recombinant mouse bFGF (R&D systems), and 0.75 μg/ml doxycycline (Dox; Sigma) for the expression of Pax7. iPax7 progenitor cells lacking Dox were assessed 3 days after removing Dox from the culture media. Mouse wild-type and Myod1 knock-out primary myoblasts were grown in DMEM (cat #15-013-CV Corning) supplemented with 100 IU penicillin, 100 μg/ml streptomycin, 2 mM L-Glutamine and 10% fetal bovine serum.

extract_protocol:
ATAC-seq libraries were prepared as described (Buenrostro et al., 2015).
All libraries were sequenced (2x50 cycles, paired end) on an Illumina HiSeq2500 machine.

value: Primary myoblasts

tag: treatment

value: No Dox treatment

value: MyoD1 KO


title: ATAC_Myod1_KO_MB_rep2

treatment_protocol: iPax7 progenitor cells lacking Dox were assessed 3 days after removing Dox from the culture media.


title: 4625_KBM7_USP15 KD_02

description:
4625_8_KBM7_15_02_GTTTCGG_S35
Chronic myeloid leukemia, blast crisis
diffexp5-8_GCF4625_KBM7.txt
s_4

value: KBM7 cells


title: ATAC_iPax7_ESC-Dox_rep2

description:
mESC_ctrl_ATAC.all.bigWig
mESC_ctrl_ATAC_peaks.narrowPeak

source_name: iPax7 ESC

value: iPax7 ESC

value: mouse ES media


title: 4625_KBM7_USP15 KD_01

description:
4625_7_KBM7_15_01_GTGGCCT_S34
Chronic myeloid leukemia, blast crisis
diffexp5-8_GCF4625_KBM7.txt
s_3


title: HO_7

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HO] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HO] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: MET2_4

value: SC+ClonNAT+estradiol


title: HO_6


title: ATAC_WT_MB_rep2

value: WT


title: 4625_KBM7_Ctrl_01

description:
4625_5_KBM7_Ctrl_01_TAGCTTA_S32
Chronic myeloid leukemia, blast crisis
diffexp5-8_GCF4625_KBM7.txt
s_1


title: ATAC_WT_MB_rep1


title: HO_5


title: siNOX4-2 in hypoxia

city: Mianyang

first: Hao

last: Dang

state: Sichuan

address: No. 190 The East Jiannan Road, Mianyang, 621000, Sichuan, People’s Republic of China

department: Clinical Laboratory

institute: The Third Hospital of Mianyang(Sichuan mental health center)

description:
BCPAP
H_siNOX4_2_1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: PTC Cell line

growth_protocol: BCPAP cells were routinely seeded into 6-well at a density of 1,000,000 cells/well in DMEM (Gibco) supplemented with 10% FBS (Gibco).

extract_protocol:
BCPAP cells was washed by PBS 3 times, and harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Thyproid cancer-derived cell line

value: siRNA against NOX4

value: 1% Oxygen


title: 4651_1_WT-01

value: LSK

value: Bone marrow

value: 8 weeks


title: HO_8


title: Sample 1, Mobilized CD34+ progenitor cells, Co-cultured with non-irradiated MSC-EV

value: Mobilized CD34+ progenitor cells

value: Co-cultured with MSC-EV

value: No


title: Hi-C_iPax7+Dox_rep2

source_name: iPax7 myogenic progenitors

extract_protocol:
Approximately 30,000,000 iPax7 cells (+/-Dox) were cross-linked for 10 min by 2% formaldehyde in fresh media. Cross-linking was quenched by addition of 0.125M glycine. Cells were incubated at room temperature for 5 min and then centrifuged at 4°C for 5 min. Cross-linked cells were washed once in cold PBS, and the cell pellets were flash frozen in liquid nitrogen and stored at −80°C. Hi-C library generation was carried out with in-nucleus ligation as described previously (Nagano et al., 2015), with slight modifications. Briefly, chromatin was digested overnight at 37 °C with HindIII (NEB). Digested ends were filled in using biotinylated d-CTP and ligated in preserved nuclei. Cross-links were reversed by proteinase K treatment at 65 °C overnight and DNA was purified by phenol-chloroform extraction. DNA concentration was measured using Qubit 2.0 Fluorometer (Life Technologies). Biotin was removed from non-ligated restriction fragment ends by incubating the Hi-C library DNA with T4 DNA polymerase (NEB) for 4h at 20 °C in the presence of dATP and dGTP. After DNA purification with phenol:chloroform, 40 μg of DNA was sheared to an average size of 350 bp using Covaris LE220 following the manufacturer’s instructions. Double size selection of DNA was performed using AMPure XP beads (Beckman Coulter) and the sonicated DNA was end-repaired with T4 DNA polymerase, T4 DNA polynucleotide kinase, Klenow (all NEB) and dNTPs in 1× T4 DNA ligase reaction buffer (NEB). Biotin-marked ligation products were isolated using MyOne Streptavidin C1 DynaBeads (Invitrogen), adenine-tailed and ligated to paired-end adaptors (Illumina).
The immobilized Hi-C products were amplified using NEBNext Multiplex Oligos for Illumina (NEB). Paired-end reads for Hi-C libraries were obtained with Illumina Hiseq 2500 (2x50 cycles) and NextSeq 500 (75 cycles).

value: iPax7 myogenic progenitors

value: 0.75ug/ml Dox in iPax7 media


title: HO_4


title: siControl-3 in hypoxia

description:
BCPAP
H_siCon_3_1

value: siRNA scramble


title: HO_3


title: HO_9


title: 4625_KBM7_Ctrl_02

description:
4625_6_KBM7_Ctrl_02_GGCTACA_S33
Chronic myeloid leukemia, blast crisis
diffexp5-8_GCF4625_KBM7.txt
s_2

value: KBM7 cells

value: control

value: Hematopoietic tissue


title: ATAC_iPax7_ESC-Dox_rep1

value: iPax7 ESC

value: mouse ES media


title: Ythdf1-/--VSV

city: beijing

first: fuping

last: you

address: xueyuan street

institute: Peking University Health Science Center

description: VSV

data_processing:
Base calling was performed using  the software bcl2fastq (v2.17.1.14) to obtain pass filter data through preliminary quality analysis.
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Gene expression was quantified as fragments per kilobase of coding sequence per million fragments (FPKM) algorithm.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: bone marrow-derived macrophage

growth_protocol: Cells were cultured in DMEM containing 10% FBS, 1% glutamine and 1% streptomycin-penicillin in a 10 cm dish for further study

extract_protocol:
Supernatant was removed and cells were covered with 350ul Buffer RLT at the end of treatment. Total RNA was extracted following the strandard protocol of RNeasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with VSV for 0 or12 hours

tag: strain background

value: bone marrow-derived macrophage

value: Ythdf1 knockout

value: vesicular stomatitis virus (VSV) for 12 hrs


title: WT-VSV

description: VSV

value: wild type

value: mock control


title: siNOX4-3 in hypoxia

description:
BCPAP
H_siNOX4_3_1

value: Thyproid cancer-derived cell line

value: siRNA against NOX4

value: 1% Oxygen


title: Hi-C_iPax7-Dox_rep2

source_name: Differentiating iPax7 myogenic progenitors

value: -Dox 3 days in iPax7 media


title: WT-CON

description: CON


title: Hi-C_iPax7-Dox_rep1

value: Differentiating iPax7 myogenic progenitors


title: HO_1

tag: time point

value: SC+ClonNAT+estradiol

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-HO] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: HO_12


title: siNOX4-3 in normoxia

description:
BCPAP
N_siNOX4_3_1

tag: cell type

value: 20% Oxygen


title: siControl-1 in hypoxia

description:
BCPAP
H_siCon_1_1

value: siRNA scramble


title: siNOX4-1 in hypoxia

description:
BCPAP
H_siNOX4_1_1


title: siControl-2 in hypoxia

description:
BCPAP
H_siCon_2_1


title: Hi-C_iPax7+Dox_rep1

value: iPax7 myogenic progenitors

value: 0.75ug/ml Dox in iPax7 media


title: Ythdf1-/--CON

description: CON

tag: genotype/variation


title: HO_10

tag: background strain


title: siNOX4-1 in normoxia

description:
BCPAP
N_siNOX4_1_1


title: ChIPseq_6day_dox_EB_rep2

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

description: ChIP-seq

data_processing:
ChIP-seq analysis.The two replicates were merged first and then aligned to the mouse genome (mm9). Peak calling was done using MACS2: macs2 callpeak -t $Treat -c $Contrl -f BAM -g mm -n ${Out} -p 0.01.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: processed files represent list of Pax7 peaks obtained by combining both replicates.

source_name: differentiating mES cells

growth_protocol: Mouse ES cell differentiation was achieved by diluting 40000 cells/ml in EB differentiation medium and incubation in an orbital shaker at 80 RPM. EB differentiation medium: IMDM supplemented with 15% FBS , 1% Penicillin/Streptomycin, 2mM Glutamax, 50 μg/ml Ascorbic acid, 4.5 mM Monothioglycerol. Trangene induction was achieved by adding doxycycline (Sigma-Aldrich) to day 3 EBs cultures (final concentration 1µg/ml), and then maintained throughout the differentiation protocol by replacing the media (including dox) every two days. At day 5, EBs were disgregated and single cells were incubated for 20 minutes with PDGFRα-PE and FLK1-APC conjugated antibodies. PDGFRα+FLK1- cells were sorted using FACSAriaII (BD biosciences) and replated on gelatin coated dishes using EB differentiation media supplemented with 1µg/ml doxycycline and 10ng/ml mouse basic-FGF. Cells were expanded using the same media +doxycycline for 4 addional days before harvesting them for analysis.

extract_protocol:
ChIP-seq: 6-day dox-induced iPax7 mouse cells growing in monolayer were harvested by incubation with trypsin for 1-2 minutes. Cell pellets were incubated in lysis buffer LB1 supplemented with protease inhibitors (50mM HEPES KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 + Complete-mini - Roche) for 10 minutes at +4°C followed by incubation in buffer LB2 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA + Complete-mini - Roche) for 10 minutes at +4°C. Cell pellet was then resuspended in LB3 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-lauroylsarcosine + Complete-mini - Roche) and then sonicated. Cells were sonicated with a Branson sonicator at 18% power for 1 minute with intervals of 10 sec ON-10 sec OFF to achieve an average chromatin size of 300bp. After shearing, samples were centrifuged for 10 minutes at 16000g and snap frozen in liquid nitrogen if not processed immediately. For Pax7 ChIP, 25-40µg of chromatin (diluted to 500µl) were precleared for 4h at 4°C with 20µl of BSA-blocked Protein G-conjugated sepharose beads (GE healthcare). Samples were supplemented with 1/10 volume of 10% Triton X-100 and incubated overnight with anti-Pax7 (Developmental Studies Hybridoma Bank - Pax7) antibody. Immune complexes were recovered by incubation with 20µl of BSA-blocked Protein G-conjugated sepharose beads for 4h at 4°C and then washed 5 times with RIPA wash buffer (50mM HEPES KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP40, 0.25% Triton X-100, 0.7% Sodium Deoxycholate) and one time with TEN buffer (10mM TRIS HCl pH 8, 1mM EDTA, 50mM NaCl). Immunoprecipitated chromatin was recovered by incubating beads with 200µl of Elution buffer (50mM TRIS HCl pH 8, 10mM EDTA, 1% Sodium Dodecyl Sulfate) for 20 minutes at 65°C. Chromatin from IP and Input (equivalent to 1% of starting material) was reverse crosslinked overnight at 65°C, then diluted 1:1 with TE (10mM TRIS HCl pH 8, 1mM EDTA) supplemented with 4µl of RNaseA 20mg/ml and incubated for 2 hours at 37°C followed by Proteinase K treatment (4µl of 20mg/ml stock for each sample) for 30 minutes at 55°C. DNA was purified by Phenol-chloroform-isoamyl alcol extraction (twice) followed by chloroform extraction, then supplemented with 1/10 of volume of 3M Sodium Acetate pH 5 and 1.5µl of Glycogen and precipitated with 2 volumes of 100% Ethanol at -80°C for >1 hour. Followed 30 minutes centrifuge at 16000g, pellet were washed with 75% ethanol, air dried and dissolved in 45µl H2O.
ChIP-seq libraries were generated following a gel-free protocol using AMPure XP beads (Beckman Coulter) for all the purification and size selection steps. 10ng or less of DNA were end repaired using End-it DNA end repair (Epicentre), then A-tailed using Klenow Fragment (3'→5' exo-  NEB) followed by adapter-barcode ligation using T4 DNA ligase (Enzymatics). Illumina compatible adapter-barcodes were purchased from BIOO scientific. After ligation, DNAs were negatively size selected using 0.5x Ampure XP beads and unbound DNAs were positively size selected by adding 0.4x Ampure XP beads (this step allows for retention of DNA fragments ranging 200-500bp). Libraries were amplified using Phusion High Fidelity PCR master mix 2x (NEB) with a 16 cycles program. Libraries from iPax3 NIH3T3 cells were generated using the NEBNext DNA library prep kit (NEB).

tag: differentiation protocol

value: serum

tag: time

value: day9 of differentiation

tag: purification

value: PDGFRα+FLK1- sorted

tag: doxycycline-treatment


title: T16

first: Eric

last: Klann

state: NY

address: 4 Washington Pl

institute: New York University

description: messenger RNA (RNA)

data_processing:
Ribo-Seq and Rna-Seq: Sequencing adapters were removed using CutAdapt 2.0
Ribo-Seq and Rna-Seq: Ribosomal RNA and transfer RNA were excised using BowTie2
Ribo-Seq only: Remaining reads were mapped to mm10 using TopHat2.
Ribo-Seq only: Using the UMI in each read and alignment information, PCR duplicates were excised out.
Ribo-Seq and Rna-Seq: Remaining reads were aligned to the coding sequence of mouse genes using RSEM. Raw counts for all samples were colalted into a tab-delimited text file.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts of sequencing reads aligning to a gene's coding sequence

source_name: Mouse brain cortex

extract_protocol:
Cortices were dissected out from P29-P34 mice and lysed.
Ribo-Seq libraries were prepared as described in
RNA-Seq libaries were prepared using standard Illumina TruSeq (polyA) protocols.

value: brain cortex

tag: age

tag: assay

value: mRNA-seq (polyA isolated)

value: DKO

tag: batch


title: T15

description: messenger RNA (RNA)

tag: genotype


title: Input_6day_dox_rep1 (Pax7 control)

description: ChIP-seq


title: HO_2


title: Input_6day_dox_rep2 (Pax7 control)

description: ChIP-seq


title: ChIPseq_6day_dox_EB_rep1

description: ChIP-seq


title: CLN2_8

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-CLN2] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-CLN2] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: T14

description: messenger RNA (RNA)

tag: tissue

value: FXS


title: CLN2_9


title: siControl-1 in normoxia

value: Thyproid cancer-derived cell line


title: T13

description: messenger RNA (RNA)

value: WT


title: CLN2_7


title: MCF-7_+Dox_+all-trans Retinoic acid_+Aldosterone_rep3

city: Westmead

first: Tram

middle: Bich

last: Doan

state: NSW

address: 176 Hawkesbury Rd

country: Australia

institute: Westmead Institute for Medical Research

hyb_protocol: The amplified samples (750ng) were hybridized to human whole genome HT-12 gene expression bead arrays using the recommended Illumina reagents and following the manufacturer’s protocol.

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was background corrected, variance stabilized and quantile normalized using the lumiExpresso function from Bioconductor’s lumi package

label_protocol: Total RNA (500ng) was amplified and biotin labelled using Illumina TotalPrep reagents (Invitrogen).

growth_protocol: MCF-7 Tet-On ER+ breast cancer cells, which stably express the reverse tetracycline-controlled transactivator, were from Clontech Laboratories (Mountain View, CA). Cells were maintained in RPMI-1640 growth medium supplemented with 10% fetal bovine serum and 200 μg/mL G-418. MR inducible MCF-7 cells were generated by stable introduction of the FLAG-MR pTRE-hyg expression construct, expressing Flag-tagged human MR, under the control of a Tet response element-driven minimal CMV promoter, into MCF-7 Tet-On cells with hygromycin selection. MR expression was absent in these cells until induction with 1 ug/ml doxycycline (Dox).

extract_protocol: Total RNA was isolated using RNAqueous purification columns (Invitrogen).

treatment_protocol: MR inducible MCF-7 breast cancer cells were cultured with RPMI+10% charcoal-stripped heat inactivated fetal calf serum with or without Dox (1 ug/ml) for 48 hours with daily media replacement. Cells were then treated for 6 hours with the pure MR agonist, aldosterone (10nM), all-trans retinoic acid (1uM), 17u-estradiol (10nM) or their combination.

tag: cell line

value: Dox inducible MCF-7 cells

tag: replicate


title: HO_11

tag: media

value: SC+ClonNAT+estradiol


title: MCF-7_+Dox_+all-trans Retinoic acid_+Aldosterone_rep1

tag: treatment


title: MCF-7_+Dox_+all-trans Retinoic acid_+Aldosterone_rep2


title: CLN2_6

tag: time point


title: MCF-7_+Dox_+all-trans Retinoic acid_rep2

source_name: MCF-7_+Dox_+all-trans Retinoic acid

value: +Dox_+all-trans Retinoic acid


title: T12

description: messenger RNA (RNA)


title: MCF-7_+Dox_+all-trans Retinoic acid_rep3


title: MCF-7_+Dox_+all-trans Retinoic acid_rep1


title: siNOX4-2 in normoxia

description:
BCPAP
N_siNOX4_2_1

tag: cell type

value: siRNA against NOX4

value: 20% Oxygen


title: siControl-2 in normoxia

description:
BCPAP
N_siCon_2_1

value: siRNA scramble


title: siControl-3 in normoxia

description:
BCPAP
N_siCon_3_1


title: CLN2_5


title: T11

description: messenger RNA (RNA)


title: T9

description: messenger RNA (RNA)


title: CLN2_4


title: 1205-4_d80_hStrS

city: STANFORD

first: Yuki

last: Miura

state: California

address: 318 Campus Drive, W200

department: Department of Psychiatry and Behavioral Sciences

institute: Stanford University

description: Raw data not submitted due to patient privacy concerns

data_processing:
Quality control, UMI counting of Ensemble genes and aggregation of samples were performed by count and aggr functions in the Cell Ranger software (version 3.1.0 with default settings)
Genome_build: Human: GRCh38
Supplementary_files_format_and_content: Count matrices, barcodes, and features

source_name: Human induced pluripotent stem cells

extract_protocol:
Cells were loaded onto a Chromium Single cell 3’ chip (Chromium Chip B Single Cell Kit, 10x Genomics, PN-1000154) with Chromium Single Cell 3’ Library & Gel Bead kit v3 (10x Genomics, PN-1000075) and proceeded according to manufacturer’s instructions.
cDNA library was generated with the Chromium Single Cell 3’ GEM, Library & Gel Bead kit v3 (10x Genomics, PN-1000078) according to manufacturer’s instructions.

value: Human induced pluripotent stem cells

tag: hips cell line

value: 1205-4 hiPS cell line

tag: age (day)


title: CLN2_2

tag: background strain


title: MCF-7_+Dox_+17bEstradiol_+Aldosterone_rep3


title: T10

description: messenger RNA (RNA)


title: 2242-1_d80_hStrS

value: 2242-1 hiPS cell line


title: T8

description: messenger RNA (RNA)


title: MCF-7_+Dox_+17bEstradiol_+Aldosterone_rep2


title: MCF-7_+Dox_+17bEstradiol_+Aldosterone_rep1


title: 8858-4_d83_hStrS

value: 8858-3 hiPS cell line


title: CLN2_1


title: CLN2_10


title: T7

description: messenger RNA (RNA)

value: brain cortex


title: T6

description: messenger RNA (RNA)

value: mRNA-seq (polyA isolated)


title: CLN2_3


title: CAJ1_9

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-CAJ1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-CAJ1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: MCF-7_+Dox_+17bEstradiol_rep3


title: T5

description: messenger RNA (RNA)


title: T4

description: messenger RNA (RNA)

value: DKO


title: CAJ1_8


title: CAJ1_7


title: T3

description: messenger RNA (RNA)


title: T2

description: messenger RNA (RNA)

value: FXS


title: CAJ1_6


title: AEGE_3

city: Nanchang

first: zhifeng

last: li

address: 56 Yangming road

institute: Jiangxi University of Traditional Chinese Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
mRNA was isolated from total RNA using poly-T oligo-attached magnetic beads. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase-H). Second strand cDNA was synthesized using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3'ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated for hybridization. To select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl of USER Enzyme was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR (Polymerase Chain Reaction). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index Primer. At last, PCR products were purified and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Clustering of indexed coded samples was performed on a CBOT Cluster Generation system using HiSeq 4000 PE Cluster Kit (Illumia). After that, RNA-seq (150-bp, pair-ends) were performed using standard Illumina HiSeq 4000 platform protocols. All the downstream analyses were based on the clean data with high quality.
The gene Reads Per Kilobase of exon model (FPKM) was calculated by adding the FPKM of each genome transcript.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: brain

extract_protocol:
Brains were removed, flash frozen on dry ice, total RNA was extracted from about 150 mg of brain tissue by MirVana total RNA extraction kit. RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Fluorometer. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1.5 µg of RNA per sample was used as input material for the RNA sample preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: strain

value: Wistar

value: adult

tag: gender

value: male

tag: group

value: AEGE treatment


title: CAJ1_5

value: SC+ClonNAT+estradiol


title: OPM2_CD24+_cells_rep_3

city: Iowa City

first: Fenghuang

last: Zhan

state: IA

address: Newton rd. CBRB 3269

department: Department of Internal Medicine

institute: University of Iowa

description:
Driven by CD24+ cancer stem cells
Gene expression data from CD24+ or CD24- populations in myeloma cell lines

hyb_protocol: The RNA was then converted to cDNA and they were hybridized to the Human Genome U133Plus 2.0 GeneChip microarrays(Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The microarrays were scanned using the GeneChip® Scanner 3000 7G.

data_processing: All data used in these analyses were derived with the  Affymetrix expression console version1.1 software.

source_name: OPM2 CD24+ myeloma cell lines

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Cells were grown in RPMI-1640 media with 10% FBS and antibiotics in 4% CO2 incubator.

extract_protocol: The total RNA was isolated from these populations using the RNeasy RNA isolation kit (Qiagen).

treatment_protocol: Myeloma cancer stem cell populations (CD24+) from ARP1, OCI-MY5 and OPM2 were isolated by  flow cytometry using CD24 antibodies (Biolegend).

value: myeloma

tag: cell markers


title: CAJ1_4

extract_protocol:
BARSeq: pooled cultures were propagated at low density (OD < 0.05) and > 2 x 106 cells were collected at each time point. Genomic DNA was extracted using the YeaStar Genomic DNA kit (Zymo Research) and 5 ng of DNA were used to PCR amplify the uptag barcode region with custom primers
Whole Genome Sequencing: Genomic DNA was extracted using the YeaStar Genomic DNA kit (Zymo Research)
RNAseq:  cells were frozen in lysis mastermix, then reverse transcription was done to obtain cDNA, which was then amplified and cleaned up with RNAClean Ampure XP beads
Libraries were constructed using the Nextera DNA Flex kit (Whole Genome Sequencing) and Nextera XT kit (RNAseq)


title: T1

description: messenger RNA (RNA)

tag: age

tag: assay

value: WT


title: S19

description: ribosome footprint (RNA)

data_processing:
Library strategy: Ribosome profiling
Ribo-Seq and Rna-Seq: Sequencing adapters were removed using CutAdapt 2.0
Ribo-Seq and Rna-Seq: Ribosomal RNA and transfer RNA were excised using BowTie2
Ribo-Seq only: Remaining reads were mapped to mm10 using TopHat2.
Ribo-Seq only: Using the UMI in each read and alignment information, PCR duplicates were excised out.
Ribo-Seq and Rna-Seq: Remaining reads were aligned to the coding sequence of mouse genes using RSEM. Raw counts for all samples were colalted into a tab-delimited text file.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts of sequencing reads aligning to a gene's coding sequence

value: Ribosome profiling

tag: genotype

tag: batch


title: MCF-7_+Dox_+17bEstradiol_rep1

tag: cell line

value: Dox inducible MCF-7 cells


title: AEGE_1

tag: tissue


title: MCF-7_+Dox_+17bEstradiol_rep2

tag: replicate


title: MCF-7_minusDox_+Aldosterone_rep3

tag: treatment


title: MCF-7_minusDox_+Aldosterone_rep2


title: CAJ1_3

data_processing:
RNAseq: Samples were demultiplexed using bcl2fastq, then fastq files were processed using Salmon and aligned using STAR
BARseq: Samples were demultiplexed using Barcas
Whole Genome Sequencing: Samples were demultiplexed using bcl2fastq and then BowTie2 was used to align the samples
Genome_build: SacCer3
Supplementary_files_format_and_content: 20190909_rawTPMtable.csv: csv file with raw TPMs from RNAseq
Supplementary_files_format_and_content: zev_wgs_processeddata.csv: csv file with sequencing information, rDNA coverage, copy number and gc content
Supplementary_files_format_and_content: ZEV_TOF_all_merge.txt: text file with normalized BARseq results (normalized to wild type, time 0, and read depth)

tag: time point

tag: media


title: IR_3

value: cerebral ischemia-reperfusion injury


title: OCI-MY5_CD24+_cells_rep_2

source_name: OCI-MY5 CD24+ myeloma cell lines

tag: cell type


title: ARP1_CD24-_cells_rep_1

source_name: ARP1 CD24- myeloma cell lines


title: OCI-MY5_CD24-_cells_rep_2

source_name: OCI-MY5 CD24- myeloma cell lines


title: MCF-7_minusDox_+Aldosterone_rep1


title: MCF-7_+Dox_+Aldosterone_rep2


title: MCF-7_+Dox_+Aldosterone_rep1


title: S18

description: ribosome footprint (RNA)


title: MCF-7_minusDox_rep2

value: minusDox


title: MCF-7_minusDox_rep3


title: ARP1_CD24+_cells_rep_1

source_name: ARP1 CD24+ myeloma cell lines


title: OPM2_CD24-_cells_rep_3

source_name: OPM2 CD24- myeloma cell lines


title: CAJ1_2


title: IR_2


title: AEGE_2


title: MCF-7_+Dox_+Aldosterone_rep3


title: S16

description: ribosome footprint (RNA)

value: brain cortex


title: CAJ1_1


title: S17

description: ribosome footprint (RNA)


title: sham_3

value: sham


title: IR_1


title: CAJ1_10

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-CAJ1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: sham_2


title: BAT1_9

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-BAT1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-BAT1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: S14

description: ribosome footprint (RNA)

value: DKO


title: MCF-7_minusDox_rep1


title: sham_1

value: brain


title: S15

description: ribosome footprint (RNA)


title: BAT1_8


title: BAT1_7


title: BAT1_6


title: S11

description: ribosome footprint (RNA)

value: FXS


title: S12

description: ribosome footprint (RNA)


title: Intervein_T2_Drought_1 (Recovered)

city: pasco

first: aaron

last: ogden

state: wa

address: 902 battelle boulevard

department: integrative omics

institute: Pacific Northwest National Lab

data_processing:
Quality control, FastQC v0.11.5
Alignment, HISAT2 v2.1.0
Transcript Assembly, StringTie v1.3.3b
Normalization, DESeq2 v1.20.0
Differential Expression, DESeq2 v1.20.0
Genome_build: Solanum lycopersicum (SL3.0)
Supplementary_files_format_and_content: DESeq2 normalized gene count estimate and DESeq2 differential expression matrix for VT1D vs VT1W and IVT1D vs IVT1W, file named Gene_count_matrix.xlsx

organism: Solanum lycopersicum

source_name: Intervein Enriched Tomato Leaf section

growth_protocol: Tomato (Solanum lycopersicum) plants were grown and subjected to drought as described in Ogden et al. 20203. Briefly, plants were grown in 4 inch pots containing 300 g soil within a Percival growth chamber under ~400 PAR light at 16/8 hours light/dark cycle. Plants were selected at random and subjected to drought stress by withholding watering for 6 days, at which point timepoint 1 (T1) samples were collected. Timepoint 2 (T2) leaves were collected 3 days after a return to normal watering. In all cases, the 4th true leaf was excised and dissected to enrich for vasculature and non-vasculature tissue (Figure 1A). Vein and inter-vein tissues were immediately flash frozen in liquid nitrogen and stored at -80° C until protein and RNA extraction.

extract_protocol:
Rneasy Plant Mini Kit, Qiagen Cat#74904, according to manufacturers instructions.
The libraries were made by the Penn State Genomics Core Facility at University Park using the Illumina TruSeq Stranded mRNA kit following the manufacturer's protocol (Illumina Inc.). Library concentration was determined by qPCR using the KAPA Library Quantification Kit Illumina platforms (KAPABiosystems) and used to make an equimolar pool of the libraries. The library pool was sequenced on two NextSeq High Output 75 nt single read sequencing runs."

treatment_protocol: At 25 days post sowing (DPS), timepoint 0 (T0) was collected, and 6 biological replicates of plants selected at random were subjected to drought stress by withholding water for an additional 4 days, while 6 control plants continued to receive 150 mL H2O every other day. After skipping 3 alternate day waterings (totaling 6 days since the last watering), vein and intervein tissue was captured from half of the drought-stressed plants, and half of the control plants at 29 DPS as the initial comparative drought condition, constituting Timepoint 1 (T1, i.e. T1D vs T1W, 3 plants each, 2 tissues). Drought-recovered plants were watered 150 mL H2O on 29 and 30 DPS after which both vein and intervein tissues were collected, and the same was also done for plants that constantly received water throughout the experiment (T2, i.e. T2D vs T2W, 3 plants each, 2 tissues).

value: Intervein

tag: stress

value: drought (recovered)

tag: timepoint


title: MCF-7_+Dox_rep2

value: +Dox


title: Intervein_T2_Drought_2 (Recovered)


title: Intervein_T2_Drought_3 (Recovered)


title: BAT1_5

tag: background strain

value: SC+ClonNAT+estradiol


title: MCF-7_+Dox_rep3


title: MCF-7_+Dox_rep1


title: S10

description: ribosome footprint (RNA)


title: BAT1_4


title: S9

description: ribosome footprint (RNA)


title: MET2_10

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-MET2] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-MET2] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: S13

description: ribosome footprint (RNA)


title: BAT1_3


title: S8

description: ribosome footprint (RNA)


title: BAT1_2


title: S7

description: ribosome footprint (RNA)

value: WT


title: Intervein_T2_Watered_1

value: watered


title: Intervein_T2_Watered_2


title: D9_neg

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were processed and normalised using quantile normalization with BeadStudio software

source_name: Activated Treg isolated from PBMC of healty donor

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

extract_protocol: Total RNA was extracted with Agencourt RNA advance cell V2 system (Beckman Coulte). Quality control was performed with Agilent Bioanalyser.

tag: donor

tag: lag-3 (positive or negative)

value: negative


title: D10_neg


title: D11_neg


title: D10_pos

value: positive


title: S6

description: ribosome footprint (RNA)

value: Ribosome profiling


title: ATG4_9

last: Wang

institute: Calico Life Science LLC

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ATG4] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ATG4] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: Intervein_T2_Watered_3


title: D9_pos


title: Vein_T2_Drought_3 (Recovered)

source_name: Vein Enriched Tomato Leaf section

value: Vein


title: D8_neg


title: ATG4_8


title: S5

description: ribosome footprint (RNA)

value: brain cortex


title: Vein_T2_Drought_2 (Recovered)


title: ATG4_7


title: Vein_T2_Watered_3


title: Vein_T2_Drought_1 (Recovered)


title: D8_pos


title: D7_neg


title: ATG4_6


title: ATG4_5


title: Vein_T2_Watered_2


title: ATG4_4


title: Vein_T2_Watered_1


title: ATG4_3


title: ATG4_1


title: Intervein_T1_Drought_3

value: drought


title: ATG4_2


title: Intervein_T1_Watered_1


title: Intervein_T1_Watered_2


title: ATG4_10


title: ASC1_9

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ASC1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ASC1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: Intervein_T1_Drought_1


title: Young adult Vcan knockout AN-3

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

description: VCAN-AN: 2559__VCAN-4AN

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the mouse genome (mm10)
The resulting BAM files were sorted and input into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison

source_name: Auditory nerve cells

extract_protocol:
Microdissections were performed to isolate the auditory nerve from mouse cochlear structures. Two cochleae from each mouse were pooled for individual samples. Total RNA was purified from each sample using the miRNeasy Mini Kit per the manufacturer’s instructions. Quality of each total RNA isolation was assessed using the Agilent 2100 Bioanalyzer and low-quality samples showing degradation or contamination were excluded.
RNA libraries were prepared for sequencing using standard Illumina protocols using Illumina's TruSeq RNA Library Prep Kit

value: Isolated auditory nerves

value: Young adult

tag: strain

tag: genotype/variation

value: Vcan knockout


title: Intervein_T1_Drought_2

value: Intervein


title: ASC1_8

city: South San Francisco

first: Rebecca

address: 1170 Veterans Blvd


title: Young adult Vcan knockout AN-2

description: VCAN-AN: 2558__VCAN-3AN

tag: age


title: Intervein_T1_Watered_3


title: Young adult Vcan knockout AN-1

description: VCAN-AN: 2557__VCAN-1AN


title: D6_neg


title: Vein_T1_Watered_3


title: D7_pos


title: ASC1_7

tag: genotype


title: D5_neg


title: Vein_T1_Watered_2


title: Young adult C57BL/6 AN-3

description: Control-C57: 2511__C57-3AN

value: wildtype


title: Vein_T1_Watered_1


title: ASC1_6

value: SC+ClonNAT+estradiol


title: D6_pos


title: ASC1_5


title: Young adult C57BL/6 AN-2

description: Control-C57: 2510__C57-2AN


title: D11_pos


title: Young adult C57BL/6 AN-1

description: Control-C57: 2509__C57-1AN


title: D3_pos


title: ASC1_4