title: OTTA2014_0103_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

value: unknown

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: adnexal

tag: experiment site

tag: site id


title: 7002v2B_run8

status: Public on Jul 22 2020

type: SRA

city: NEW YORK

first: Miriam

last: Merad

state: New York

address: 1470 Madison Ave, Room 5-301

department: Oncological Sciences

country: USA

institute: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI

library_source: transcriptomic

data_processing:
Transcriptomic and TCR library reads were aligned and quantified using Cellranger v3.1.0 (10x Genomics). CITEseq ADT and CITEseq HTO reads were queried for antibody- and cell-specific oligonucleotide sequence barcodes in the designated read positions, including antibody sequences within a Hamming distance of 1 from the reference, using the feature-indexing function of Cellranger. TCR data was aligned using Cellranger vdj function with default parameters.
Genome_build: GRCh38/84
Supplementary_files_format_and_content: Raw feature-barcode matrices, containing UMI counts in Market Exchange Format. Also contains tsv files with feature and barcode sequences to row and column indices, respectively.

molecule: total RNA

organism: Homo sapiens

source_name: lung

extract_protocol: Cell suspensions were split and barcoded using “hashing antibodies” staining beta-2-microglobulin and CD298 and conjugated to “hash-tag” oligonucleotides (HTOs). Hashed samples were pooled and stained with CITEseq antibodies that had been purchased either from the Biolegend TOTALseq catalog or conjugated using the Thunder-Link PLUS Oligo Conjugation kit (Expedeon). Stained cells were then encapsulated for single-cell reverse transcription using the 10X Chromium platform and libraries were prepared as previously described (Stoeckius, Marlon, et al. "Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics." Genome biology 19.1 (2018): 1-12.).

tag: tissue

value: lung

tag: tissue type

value: Normal, Tumor, PBMC, spiked mouse cells

tag: patient id

tag: libraryname

tag: Sex

value: male

tag: library type

value: GEX

tag: 10x chromium encapsulation kit


title: S11P6

city: Beijing

first: Kai

last: Yu

address: Yiheyuan Rd. 5th

country: China

institute: Peking University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
The first 8bp of read2 were used to split the pooled data into single cells according to the barcode sequences. The following 8bp were unique molecular identifier (UMI). The split reads1 were trimmed off ploy(A) tail sequence and template switch oligo (TSO) sequence. Then we did quality control by removing out reads with adaptor contaminants (length < 37bp) and low-quality bases (N > 10%).
Prepared clean data were aligned to hg38 human reference genome with Hisat2 (version 2.0.5). Uniquely mapped reads on each gene were calculated with htseq-count, and PCR redundant reads were eliminated with UMI sequences in each paired-reads, generated a UMI count matrix of each gene in each cell.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include UMI count values for each Sample.

molecule: polyA RNA

source_name: Brain

extract_protocol:
Briefly, we used a mouth pipette to pick single cells into cell lysis buffer. The cell lysis buffer contained barcode-containing reverse transcriptase primers (5′-TCAGACGTGTGCTCTTCCGATCTXXXXXXXXNNNNNNNNT25-3′; X represents the nucleotides of predesigned cell-specific barcodes and N is the unique molecular identifier (UMI).
Single-cell RNA-seq libraries were constructed following STRT-seq protocol with minor modifications. After reverse transcription and cDNA amplification, the PCR products with different cell-specific barcodes were pooled into one tube. The pooled cDNA was purified and tagged with biotin at the 3′ ends using biotin index primers (5′-/biotin/CAAGCAGAAGACGGCATACGAGAT/index/GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3′). After fragmentation, the biotin-tagged 3′ ends were enriched by Dynabeads MyOne streptavidin C1 (Invitrogen, 65002). We used KAPA Hyper Prep Kits (KK8505) to perform library construction. The library amplification primers were an Illumina QP2 primer (5′-CAAGCAGAAGACGGCATACGA-3′) and a short universal primer (5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGAC-3′).

value: Brain

tag: point

tag: pool

tag: gender


title: 7002v2A_run9


title: S11P5


title: LATS1/2 KO Intestinal stromal cell-4

city: Daejeon

first: Hyunsoo

last: Cho

address: Yuseonggu

country: South Korea

institute: IBS/KAIST

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Mus musculus

source_name: PDGFRb+ intestinal stromal cells

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: strain

tag: developmental stage

value: Adult

tag: genotype

tag: cell type

value: PDGFRb+ intestinal stromal cells

tag: sorting method

value: FACS sorted


title: OTTA2014_0102_Clinical

type: RNA

city: Vancouver

first: Michael

middle: S

last: Anglesio

state: BC

department: Obstetrics and Gynecology

country: Canada

institute: University of British Columbia

description: single-sample normalized data

hyb_protocol: NanoString Gene Expression protocol using 500ng of Total RNA as measured by NanoDrop spectrophotmeter. RNA is combined with capture and reporter codesets, and hybridization buffer. Reaction mixtures are hybridized in a thermal cycler at 65C for either short (16H) or long (20H) hybridization. Samples are then washed and fixed to cartridges using the nCounter Prep Station (high-sensitivity mode) for imaging.

scan_protocol: imaging on nCounter Digital Analyzer at maximum FOV

data_processing: Samples data is processed and normalized following protocols described in Talhouk et al (PMID: 27096160) using PrOTYPE. Briefly: Count data is Log2 transformed, the mean of housekeeping genes (ACTB, RPL19, SDHA, POLR1B, and PGK1) subtracted on a per-sample basis, and then normalized relative to reference samples (denoted as Pool1, Pool2, and Pool3). Code available at https://github.com/AlineTalhouk/PrOType

source_name: primary high-grade serous tubo-ovarian carcinoma

label_protocol: NanoString probe-specific unique barcode

extract_protocol: Total RNA extracted with the Qiagen miRNeasy FFPE kit (modified protocol)

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

tag: experiment site

value: AOC


title: 7002v2A_run8

tag: tissue

tag: tissue type

tag: patient id

tag: libraryname

tag: Sex

tag: library type

tag: 10x chromium encapsulation kit


title: S11P4

tag: point

tag: pool

tag: gender


title: LATS1/2 KO LEC-3

source_name: Lacteal LECs

tag: strain

tag: developmental stage

tag: genotype

tag: cell type

value: Lacteal LECs

tag: sorting method


title: S11P3


title: OTTA2014_0101_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: low

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: presumed adnexal

tag: site id


title: LATS1/2 KO Intestinal stromal cell-3

tag: strain

tag: developmental stage

tag: genotype

tag: cell type


title: HS190415I_runbroad6

extract_protocol: 10,000 cells were loaded onto a 10X Chromium single-cell encapsulation chip according to manufacturer instructions. Libraries were prepared according to manufacturer instructions. QC of cDNA and final libraries was performed using CyberGreen qPCR library quantification assay. Sequencing was performed on Illumina sequencers to a depth of at least 80 million reads per library.

tag: tissue

tag: tissue type

value: Tumor

tag: patient id

tag: libraryname

tag: Sex

value: female

tag: library type

tag: 10x chromium encapsulation kit


title: LATS1/2 KO Intestinal stromal cell-2

tag: sorting method


title: S11P2

tag: point

tag: pool

tag: gender


title: LATS1/2 KO LEC-2


title: 7001N5_run3

value: lung

value: Normal


title: 7001v2D-A_run6

data_processing:
Library strategy: CITE-seq
Transcriptomic and TCR library reads were aligned and quantified using Cellranger v3.1.0 (10x Genomics). CITEseq ADT and CITEseq HTO reads were queried for antibody- and cell-specific oligonucleotide sequence barcodes in the designated read positions, including antibody sequences within a Hamming distance of 1 from the reference, using the feature-indexing function of Cellranger. TCR data was aligned using Cellranger vdj function with default parameters.
Genome_build: GRCh38/84
Supplementary_files_format_and_content: Raw feature-barcode matrices, containing UMI counts in Market Exchange Format. Also contains tsv files with feature and barcode sequences to row and column indices, respectively.

value: Normal, Tumor, PBMC, spiked mouse cells

value: ADT


title: OTTA2014_0099_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: omentum

tag: experiment site


title: OTTA2014_0100_Clinical

description: single-sample normalized data

value: any

value: adnexal

tag: site id


title: LATS1/2 KO Intestinal stromal cell-1

tag: strain

tag: developmental stage

value: Adult

tag: genotype

tag: cell type

value: PDGFRb+ intestinal stromal cells

tag: sorting method

value: FACS sorted


title: OTTA2014_0098_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: white

value: dead

value: AOC


title: LATS1/2 KO LEC-1

value: Lacteal LECs


title: 7001v2D_run2

tag: tissue

value: lung

tag: tissue type

tag: patient id

tag: libraryname

tag: Sex

value: female

tag: library type

value: GEX

tag: 10x chromium encapsulation kit


title: 7001v2C_run2

value: Normal, Tumor, PBMC, spiked mouse cells


title: OTTA2014_0096_Clinical

description: single-sample normalized data

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: OTTA2014_0097_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: pathogenic BRCA2 mutation


title: 7001v2C-A_run6

tag: tissue

tag: tissue type

tag: patient id

tag: libraryname

tag: Sex

tag: library type

value: ADT

tag: 10x chromium encapsulation kit


title: OTTA2014_0095_Clinical

description: single-sample normalized data

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: adnexal


title: S9P2

value: Brain

tag: point

tag: pool

tag: gender

value: male


title: WT Intestinal stromal cell-4

tag: strain

tag: developmental stage

value: Adult

tag: genotype

tag: cell type

value: PDGFRb+ intestinal stromal cells

tag: sorting method

value: FACS sorted


title: S9P1

tag: tissue

tag: patient id


title: S8P5


title: S8P4


title: WT Intestinal stromal cell-5


title: WT LEC-4

value: Lacteal LECs


title: OTTA2014_0094_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: unknown

value: white

value: dead

tag: study entry delay

tag: anatomical site

value: peritoneal

tag: experiment site

value: AOC

tag: site id


title: WT Intestinal stromal cell-3

tag: strain


title: 7001v2B_run2

value: lung

tag: tissue type

value: Normal, Tumor, PBMC, spiked mouse cells

tag: libraryname

tag: Sex

value: female

tag: library type

value: GEX

tag: 10x chromium encapsulation kit


title: 7001v2B-A_run6

tag: tissue

tag: patient id

value: ADT


title: OTTA2014_0093_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

value: high

value: any

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: omentum


title: WT Intestinal stromal cell-6

tag: developmental stage

value: Adult

tag: genotype

tag: cell type

value: PDGFRb+ intestinal stromal cells

tag: sorting method

value: FACS sorted


title: 7001v2A_run2

tag: tissue type

tag: libraryname

tag: Sex


title: S11P1

tag: tissue

value: Brain

tag: point

tag: pool

tag: gender

value: male


title: S8P2

tag: patient id


title: OTTA2014_0092_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: hispanic

value: dead

tag: study entry delay

tag: anatomical site

value: adnexal

tag: experiment site

tag: site id


title: OTTA2014_0091_Clinical

description: single-sample normalized data

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: AOC


title: WT LEC-3

tag: strain

tag: developmental stage

tag: genotype

tag: cell type

value: Lacteal LECs

tag: sorting method


title: OTTA2014_0090_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: white


title: S9P3

tag: tissue

tag: patient id

tag: point

tag: pool

tag: gender


title: S8P3


title: OTTA2014_0089_Clinical

description: single-sample normalized data

value: low

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: WT Intestinal stromal cell-2

tag: strain

tag: developmental stage

tag: genotype

tag: cell type

tag: sorting method


title: S7P5

tag: tissue

tag: patient id

tag: point

tag: pool


title: 7001v2A-A_run6

value: lung

tag: tissue type

value: Normal, Tumor, PBMC, spiked mouse cells

tag: libraryname

tag: Sex

value: female

tag: library type

value: ADT

tag: 10x chromium encapsulation kit


title: OTTA2014_0088_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site


title: S7P4

tag: tissue

tag: patient id

tag: point

tag: pool

tag: gender


title: WT Intestinal stromal cell-1

tag: strain

tag: developmental stage

value: Adult

tag: genotype

tag: cell type

value: PDGFRb+ intestinal stromal cells

tag: sorting method

value: FACS sorted


title: OTTA2014_0087_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: experiment site

tag: site id


title: CoVi17_8_S_24_9P_Gex

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

description: Single-cell RNA-seq with 10x Genomics 5' v1 paired-end

data_processing:
mkfastq (Cell Ranger 3.1.0) was used to generate FASTQ files with default parameters
count (Cell Ranger 3.1.0) was used to generate the filtered UMI matrix with default parameters
Seurat (3.1.5) was used to filter (cutoffs as follows: 1. number of genes per cell, at least 800 and 4400 at most; 2. number of UMIs per cell, at least 1500 and 20000 at most; and 3. percentage of mitochondrial counts per cell, 15% at most), normalize (LogNormalize function with default parameters) and scale the UMI matrix (ScaleData function regressing the variables mitochondrial gene percentage and number of UMIs per cell).
Genome_build: GRCh38-alts-ensembl-2.0.0 from Cell Ranger
Genome_build: GRCh37 (hg19-3.0.0 from Cell Ranger)
Supplementary_files_format_and_content: cd8_t24_processed_data_annotations.txt meta data for 84140 cells
Supplementary_files_format_and_content: cd8_t24_processed_data_umi_counts.txt UMI count data matrix for 84140cells
Supplementary_files_format_and_content: cd8_t24_processed_data_normalized_counts.txt log-normalized counts for 84140 cells

source_name: PBMC

extract_protocol:
For combined single-cell RNA-seq and TCR-seq assays (10x Genomics), a maximum of 60,000 virus-reactive memory CD8+ T cells from up to 10 donors were pooled by sorting into low retention 1.5mL collection tubes, containing 500 µL of a1:1 solution of PBS:FBS supplemented with RNAse inhibitor (1:100). Following sorting, ice-cold PBS was added to make up to a volume of 1400 µl. Cells were then centrifuged for 5 minutes (600 g at 4 ˚C) and the supernatant was carefully removed leaving 5 to 10 µl. 25 µl of resuspension buffer (0.22 µm filtered ice-cold PBS supplemented with ultra-pure bovine serum albumin; 0.04 %, Sigma-Aldrich) was added to the tube and the pellet was gently but thoroughly resuspended. Following careful mixing, 33 µl of the cell suspension was transferred to a PCR-tube for processing as per the manufacturer’s instructions (10x Genomics).
Single-cell RNA-seq using 10x genomics platform was performed using Chromium™ Single Cell 5' v1 Reagent Kits following the manufacturer’s protocol
Libraries were constructed using Chromium™ Single Cell 5' v1 Reagent Kits following the manufacturer’s protocol
100 x 100 bp paired-end reads, 3'TAG, Hg19 human reference genome.

treatment_protocol: PBMCs from each donor, were thawed, washed, plated in 24-well culture plates at a concentration of 5 x 106 cells/ml in 1 ml of serum-free TexMACS medium (Miltenyi Biotec) and left overnight (5 % CO2, 37 ˚C). Cells were stimulated by the addition of individual virus-specific peptide polls (1 µg/ml) for 24 h in the presence of a blocking CD40 antibody (1 µg/ml; Miltenyi Biotec). For subsequent MACS-based enrichment of CD137+, cells were sequentially stained with fluorescence-labeled surface antibodies, Cell-hashtag TotalSeq™-C antibody (0.5 µg/condition), and a biotin-conjugated CD137 antibody (clone REA765; Miltenyi Biotec) followed by anti-biotin microbeads (Miltenyi Biotec). Labelled cells were added to MS columns (Miltenyi Biotec) and positively selected cells (CD137+) were eluted and used for FACS sorting of CD137+ memory CD8+ T cells.

tag: tissue

value: Blood

value: Memory CD8 T cells enriched:CD3+ CD8+ CD45RA- CD137+ CD69+


title: CoVi17_8_S_24_9P_CITE

description: Single-cell RNA-seq with 10x Genomics 5' v1


title: CoVi17_8_S_24_9P_TCR

description: Single-cell RNA-seq with 10x Genomics 5' v1 V(D)J


title: WT LEC-2


title: S7P3

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: male


title: CoVi17_8_M_24_9P_TCR

tag: cell type


title: CoVi17_8_M_24_9P_CITE


title: OTTA2014_0086_Clinical

description: single-sample normalized data

value: any

value: all wildtypes

value: hispanic

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: adnexal

value: AOC


title: S7P1


title: MuSC 90 percent library

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Basecalling for the Illumina short-read data was performed using RTA 1.18.66.3 and fastq files were generated using Cell Ranger (1.3). Fastq files for the PromethION data were generated by Guppy (1.8.1).
Illumina short reads were aligned to the mouse genome using Rsubread (1.29.6). Long reads were aligned using minimap2 (2.17) with default parameters.
Short read data were analysed using scPipe (1.4.0) to generate a gene count matrix. Nanopore long-read data were analysed by FLAMES (0.1.0) to generate an isoform count matrix along with isoform annotation.
Genome_build: Gencode Mus musculus GRCm38.p6
Supplementary_files_format_and_content: gene_count_Lib10.csv: Count matrix with samples along the columns and genes along the rows for the Lib10 sample
Supplementary_files_format_and_content: gene_count_Lib90.csv: Count matrix with samples along the columns and genes along the rows for the Lib90 sample
Supplementary_files_format_and_content: isoform_annotated.filtered.gff3: Isoform annotation derived from long-read data (Lib10 sample)
Supplementary_files_format_and_content: transcript_count.csv: Transcript counts from long-read data (Lib10 sample)
Supplementary_files_format_and_content: MuSC_Lib10.csv: 1991 most abundant cell barcodes with cell ids, barcode sequence and counts from the Lib10 sample
Supplementary_files_format_and_content: MuSC_Lib90.csv: 3001 most abundant cell barcodes with cell ids, barcode sequence and counts from the Lib90 sample

source_name: Skeletal muscle stem cell

growth_protocol: Pax7creERT2R26-eYFPfl/fl mice were generated from Pax7creERT2 (Murphy et al., 2011) and R26-eYFPfl/fl (Srinivas et al., 2001) founder mice strains both on a C57BL6 background.

extract_protocol:
Cells were sorted on a FACS Aria III (BD Biosciences) with gating based on YFP.
Cell isolation and library construction was performed using a Chromium 10X v2 protocol that was adapted to accommodate both Illumina and Nanopore sequencing. The 90% sample was sequenced by Illumina short-read sequencing only. The 10% sample was sequenced by both Illumina short-read and Oxford Nanopore Technologies long-read sequencing according to the protocol at dx.doi.org/10.17504/protocols.io.8d9hs96.

treatment_protocol: At 3 months of age, Pax7CreERT2;R26RYFP mice received daily 100uL tamoxifen (20mg/ml in corn oil) for five days to label MuSCs with YFP. Two weeks following the final injection, animals were sacrificed and hindlimb musculature was collected and dissociated as previously characterized (Liu et al., 2015). Mice were anaesthetized with isoflurane. To induce activation of MuSCs muscles were injured with 1.2% barium chloride (Sigma). Lower hindlimbs received 40uL barium chloride via an intramuscular injection. Quiescent MuSCs were isolated from uninjured muscles while activated cells were isolated 72 hrs post injury.

tag: condition

value: YFP sorted Quiescent and activated muscle stem cells

tag: barcode coordinate

value: bases 1 to 16 on R1

tag: umi coordinate

value: bases 17 to 26 on R1


title: OTTA2014_0085_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: pathogenic BRCA1 mutation

tag: race/ethnicity

value: white

value: omentum

tag: experiment site


title: S8P1

tag: tissue

tag: patient id

tag: point

tag: pool

tag: gender


title: CoVi15_8_MS_24_6P_TCR

value: Blood

tag: cell type


title: CoVi17_8_M_24_9P_Gex

value: Memory CD8 T cells enriched:CD3+ CD8+ CD45RA- CD137+ CD69+


title: S6P5

value: Brain


title: S6P4

value: male


title: OTTA2014_0084_Clinical

description: single-sample normalized data

value: HGSOC

value: any

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: presumed adnexal

tag: site id


title: CoVi15_8_MS_24_6P_CITE


title: S6P3


title: CoVi15_8_MS_24_6P_Gex


title: WT LEC-1

tag: strain

tag: developmental stage

value: Adult

tag: genotype

value: Lacteal LECs

tag: sorting method

value: FACS sorted


title: OTTA2014_0083_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: unknown

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: dead

value: adnexal

tag: experiment site

value: AOC


title: OTTA2014_0082_Clinical

description: single-sample normalized data

value: high

value: white

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time


title: Aged eWAT SVF Phagocytic rep2

city: Buffalo

first: Brandon

last: Hall

state: NY

address: 640 Ellicott Street, Ste. 444

institute: Everon Biosciences, Inc.

description:
RQ_007851_003
RS-02623857_GCCAAT_L002

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequence reads were trimmed using Trimmomatic v0.36, read quality was estimated using Fastqc. The reads were aligned with TopHat v2.1.0 to mm10 genome in -very-sensitive mode.
Transcript counts were obtained using HTseq-count.
Normalized expression values were measured using DEseq.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with DEseq-normalized raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: SVF of pooled eWAT, pooled from 6 old mice

growth_protocol: Mice were aged naturally, housed under standard conditions and fed a rodent chow diet

extract_protocol:
Cell pellets of isolated and phagocyte-enriched/depleted SVF were flash frozen and RNA was extracted in QIAzol reagent and isolated via miRNeasy Mini Kit (Qiagen)
Sequencing libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina) from 700 ng total RNA, following manufacturer's instructions.

treatment_protocol: Single cell suspension of stromal vascular fraction was obtained from pooled epididymal white adipose tissue using the Adipose Tissue Dissociation Kit (Miltenyi Biotec). Cell pellets were suspended in DMEM containing 10% heat-inactivated FBS and adjusted to 4 million cells per milliliter. One milliliter of washed superparamagnetic nanoparticles (~150-nm) suspension was incubated with five milliliters of cell suspension for 2 hours at 37 degrees Celsius with intermittent agitation. Cells that phagocytized the magnetic particles were then enriched via positive magnetic-activated selection for 5 minutes using EasySep magnets. Cells were washed and selection was repeated three times with non-selected cells pooled at each step to create phagocyte-enriched and phagocyte-depleted stromal vascular fractions, respectively.

tag: strain

tag: age

value: 80 weeks old

tag: tissue

value: epididymal white adipose tissue (eWAT)

tag: cell-enriched fraction

value: Phagocytic stromal vascular fractions (SVF) sub-population


title: Aged eWAT SVF Non-phagocytic rep2

description:
RQ_007851_004
RS-02623858_CTTGTA_L002

value: Non-phagocytic stromal vascular fractions (SVF) sub-population


title: Young eWAT SVF Phagocytic rep2

description:
RQ_007851_001
RS-02623855_ACAGTG_L002

source_name: SVF of pooled eWAT, pooled from 12 young mice

value: 8 weeks old


title: S6P2

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: male


title: MuSC 10 percent library

tag: condition

value: YFP sorted Quiescent and activated muscle stem cells

tag: barcode coordinate

value: bases 1 to 16 on R1

tag: umi coordinate

value: bases 17 to 26 on R1


title: OTTA2014_0081_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: study entry delay

tag: anatomical site

value: presumed adnexal

tag: site id


title: Young eWAT SVF Non-phagocytic rep2

description:
RQ_007851_002
RS-02623856_GTGAAA_L002

tag: strain

tag: age

tag: tissue

tag: cell-enriched fraction


title: S5P4

tag: patient id

tag: point

tag: pool

tag: gender

value: female


title: CoVi13_8_RSV_24_5P_TCR

value: Blood

tag: cell type

value: Memory CD8 T cells enriched:CD3+ CD8+ CD45RA- CD137+ CD69+


title: S6P1


title: Aged eWAT SVF Non-phagocytic rep1

description:
RQ_007851_004
RS-02623858_CTTGTA_L001


title: S5P5


title: OTTA2014_0078_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: high

value: any

value: all wildtypes

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

value: omentum

tag: experiment site

value: AOC


title: CoVi13_8_RSV_24_5P_CITE


title: CoVi13_8_MS_24_4P_TCR


title: Aged eWAT SVF Phagocytic rep1

description:
RQ_007851_003
RS-02623857_GCCAAT_L001

tag: strain

tag: age

value: 80 weeks old

value: epididymal white adipose tissue (eWAT)

value: Phagocytic stromal vascular fractions (SVF) sub-population


title: CoVi13_8_RSV_24_5P_Gex

tag: tissue


title: Young eWAT SVF Non-phagocytic rep1

description:
RQ_007851_002
RS-02623856_GTGAAA_L001

value: 8 weeks old

tag: cell-enriched fraction

value: Non-phagocytic stromal vascular fractions (SVF) sub-population


title: S5P3

value: Brain

tag: patient id

tag: point


title: S5P1

tag: pool

tag: gender


title: OTTA2014_0077_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: Stage

tag: residual disease status

value: unknown

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: white

tag: study entry delay

tag: anatomical site

tag: site id


title: CoVi13_8_MS_24_4P_CITE

value: Blood

tag: cell type


title: OTTA2014_0075_Clinical

description: single-sample normalized data

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: pathogenic BRCA1 mutation

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: experiment site


title: S5P2

tag: tissue

tag: patient id

tag: point

tag: pool

tag: gender

value: female


title: CoVi13_8_Flu_24_5P_TCR

value: Memory CD8 T cells enriched:CD3+ CD8+ CD45RA- CD137+ CD69+


title: CoVi13_8_MS_24_4P_Gex


title: Young eWAT SVF Phagocytic rep1

description:
RQ_007851_001
RS-02623855_ACAGTG_L001

tag: strain

tag: age

tag: cell-enriched fraction


title: S4P5


title: CoVi13_8_Flu_24_5P_CITE

tag: cell type


title: MEF Jmjd3+/+ JMJD3 overexpression P4 (RNA-seq)

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

description:
MEF JMJD3OX P4
genes_ntc_expression.tsv.gz

data_processing:
rsem v1.2.22/bowtie2 v2.2.5 was used to align to the ensembl transcriptome (mm10, v76)
transcripts with more than 63 sequence tags in 2 or more timepoints were kept for further analysis
mapping tag counts were GC normalised using EDASeq v2.0.0
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing ensembl gene accession number, gene name and normalised abundance estimates for each transcript

source_name: Mouse MEFs Passage 4

growth_protocol: MEFs were maintained in DMEM/high glucose (Hyclone) containing 10% fetal bovine serum (FBS, PAA), Glutamax (Invitrogen), nonessential amino acids (Invitrogen), and penicillin/streptomycin (Hyclone). Mouse  iPSCs were cultured on feeder layer (MEF treated with mitomycin-C) in ESC medium ( DMEM/high glucose (Hyclone) supplemented with 15% FBS (GIBCO), Glutamax, nonessential amino acids, sodium pyruvate, penicillin/streptomycin, beta-mercaptoethanol and leukaemia inhibitory factor (LIF))supplemented with 3 μM CHIR99021 and 1 μM PD0325901.

extract_protocol:
Total RNA was extracted from cells using TRIzol following the manufacture’s instruction.
Standard Illumina protocols

treatment_protocol: Plat-E cells were transfected with pMXs vectors for FLAG/JMJD3 to produce virus. Plat-E cells were maintained in DMEM/high glucose containing 10% FBS.  MEFs in P2 or P4 were plated at 20，000 per square centimetre and infected with retrovirus for 24 hours once.

tag: passage

tag: overexpression

tag: knockout

value: Wildtype

tag: presumed cell type

value: mouse embryonic fibroblast


title: OTTA2014_0074_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

tag: study entry delay

tag: anatomical site

value: adnexal

tag: site id


title: TRN11

city: Cambridge

first: Joshua

last: Levin

state: MA

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_A8_S296

data_processing:
RSEM v1.2.87 was run on raw fastq fileswith default parameters on alignments created by Bowtie on UCSC gene annotation
TPM estimates were tranformed to log space by taking log TPM +1
TopHat2 v2.0.10 was used to map fastq files to mm10 reference
RNASeq-QC was run on the TopHat2 bamfiles to get QC metrics
For TRN and patch-seq samples, cells were removed if they had less than 40% genome mapping rate or or less than 1500 detected genes
Clustering and DE analysis of TRN samples was perfomed with biSNE software (https://github.com/yinqingl/nucseq_analysis), including normalizing the log TPM data to a normalized log TPM
For non-TRN samples, nuclei expressing <1500 genes were removed
Seurat v2.2.0 was used for clustering of the non-TRN samples
Genome_build: mm10
Supplementary_files_format_and_content: Formatted expression matrix (tab deliminated text file) with cells as columns, genes as rows, and TPM values as entries

source_name: TRN

extract_protocol:
Sucrose gradient nuclei isolation followed by FACS sorting for Violet+, Violet+ GFP+ or Violet+ NeuN+ nuclei
Modified SMARTseq2 single nuclei RNA-Seq

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: S4P4

tag: tissue

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender


title: MEF Jmjd3+/+ JMJD3 overexpression P2 (RNA-seq)

description:
MEF JMJD3OX P2
genes_ntc_expression.tsv.gz

source_name: Mouse MEFs Passage 2

tag: passage

tag: overexpression

tag: knockout

tag: presumed cell type

tag: strain


title: S4P3


title: MEF Jmjd3+/+ P4 (RNA-seq)

description:
MEF JMJD3WT P4
genes_ntc_expression.tsv.gz


title: CoVi13_8_Flu_24_5P_Gex

tag: cell type


title: S4P2


title: CoVi12_8_S_24_5P_TCR


title: CoVi12_8_S_24_5P_CITE


title: OTTA2014_0079_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

value: pathogenic BRCA2 mutation

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: presumed adnexal

tag: experiment site

value: AOC


title: OTTA2014_0071_Clinical

description: single-sample normalized data

value: low

value: all wildtypes

value: white

tag: site id


title: OTTA2014_0076_Clinical

description: single-sample normalized data


title: CoVi12_8_S_24_5P_Gex

tag: tissue

value: Blood

tag: cell type

value: Memory CD8 T cells enriched:CD3+ CD8+ CD45RA- CD137+ CD69+


title: MEF Jmjd3-/- P2 (RNA-seq)

description:
MEF JMJD3KO P2
genes_ntc_expression.tsv.gz

tag: passage

tag: overexpression

tag: knockout

tag: presumed cell type

value: mouse embryonic fibroblast

tag: strain


title: S4P1

tag: patient id

tag: point

tag: pool

tag: gender

value: female


title: S3P8


title: OTTA2014_0072_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: pathogenic BRCA1 mutation

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time


title: MEF Jmjd3+/+ FLAG overexpression P4 (RNA-seq)

description:
MEF WT P4 FLAG
genes_ntc_expression.tsv.gz

tag: passage

tag: overexpression

value: FLAG

tag: knockout

value: Wildtype

tag: presumed cell type


title: S3P7

tag: tissue

value: Brain

tag: patient id

tag: point

tag: pool


title: OTTA2014_0069_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

value: any

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: adnexal

tag: experiment site

tag: site id


title: MEF Jmjd3+/+ FLAG overexpression P2 (RNA-seq)

description:
MEF WT P2 FLAG
genes_ntc_expression.tsv.gz

tag: strain


title: OTTA2014_0073_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

value: omentum

value: AOC


title: CoVi12_8_M_24_5P_TCR

tag: tissue

tag: cell type


title: OTTA2014_0070_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

value: alive


title: MEF Jmjd3+/+ P2 (RNA-seq)

description:
MEF JMJD3WT P2
genes_ntc_expression.tsv.gz

tag: passage

tag: overexpression

tag: knockout

tag: presumed cell type


title: CoVi12_8_M_24_5P_CITE


title: MEF Jmjd3-/-  P4 (RNA-seq)

description:
MEF JMJD3KO P4
genes_ntc_expression.tsv.gz

tag: strain


title: OTTA2014_0068_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

value: all wildtypes

value: white

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: iPSCs (RNA-seq)

description: iPSCs

source_name: OSK-induced pluripotent stem cells

value: embryonic stem cell


title: CoVi12_8_M_24_5P_Gex

tag: tissue

value: Blood

value: Memory CD8 T cells enriched:CD3+ CD8+ CD45RA- CD137+ CD69+


title: S3P4

tag: patient id

tag: point

tag: pool

tag: gender

value: female


title: CoVi09_8_S_24_7P_CITE

tag: cell type


title: CoVi09_8_S_24_7P_TCR


title: OTTA2014_0066_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time


title: S3P3


title: OTTA2014_0065_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

value: hispanic

value: dead

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: peritoneal

tag: experiment site


title: OTTA2014_0067_Clinical

description: single-sample normalized data

value: presumed adnexal

tag: site id


title: CoVi09_8_S_24_7P_Gex

tag: tissue

tag: cell type


title: OTTA2014_0064_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity


title: OTTA2014_0063_Clinical

description: single-sample normalized data

tag: sample region necrosis

tag: residual disease status

value: any


title: S3P1

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender


title: CoVi09_8_M_24_7P_TCR


title: CoVi09_8_M_24_7P_CITE


title: S2P4

value: male


title: S3P6


title: OTTA2014_0062_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

value: omentum

value: AOC


title: S3P5


title: S2P3


title: CoVi09_8_M_24_7P_Gex


title: S2P2


title: CoVi06_8_S-2_24_8P_TCR


title: OTTA2014_0060_Clinical

description: single-sample normalized data

tag: Stage

value: all wildtypes

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: adnexal

tag: experiment site

tag: site id


title: S1P8

tag: tissue


title: CoVi06_8_S-2_24_8P_Gex

tag: cell type


title: OTTA2014_0059_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: residual disease status

value: white


title: CoVi06_8_S-2_24_8P_CITE

value: Blood


title: OTTA2014_0061_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: brca1 and brca2 germline mutation status

value: pathogenic BRCA1 mutation


title: S2P1

tag: patient id

tag: point

tag: pool

tag: gender


title: S1P7

value: female


title: CoVi06_8_S-1_24_8P_TCR

value: Memory CD8 T cells enriched:CD3+ CD8+ CD45RA- CD137+ CD69+


title: OTTA2014_0057_Clinical

description: single-sample normalized data

tag: Stage

value: high

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: progression-free survival time


title: OTTA2014_0058_Clinical

description: single-sample normalized data

value: hispanic

value: dead

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: OTTA2014_0056_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: residual disease status


title: S3P2

tag: tissue

tag: patient id

tag: point


title: S1P6

tag: pool

tag: gender


title: CoVi06_8_S-1_24_8P_Gex

tag: cell type


title: S1P5


title: OTTA2014_0055_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

value: any

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status


title: CoVi06_8_M_24_8P_TCR


title: S1P4

value: Brain


title: CoVi06_8_M_24_8P_CITE


title: OTTA2014_0054_Clinical

description: single-sample normalized data

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: OTTA2014_0053_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: residual disease status

value: unknown


title: CoVi06_8_M_24_8P_Gex

tag: tissue

tag: cell type


title: OTTA2014_0052_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

value: low

value: presumed adnexal


title: CoVi03_8_S_24_5P_TCR


title: CoVi03_8_S_24_5P_CITE


title: S1P1

tag: patient id

tag: point

tag: pool

tag: gender


title: CoVi06_8_S-1_24_8P_CITE


title: OTTA2014_0051_Clinical

description: single-sample normalized data

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: AOC


title: CoVi03_8_S_24_5P_Gex


title: CoVi03_8_M_24_5P_TCR


title: SHG_24h_3

city: Haikou

first: JunLong

last: Sun

state: Hainan

address: No.58 Renmin Avenue, Haikou City, Hainan Province

institute: Hainan University

description: mRNA derived from liver tissue of severe hypoxia group (SHG) fish

data_processing:
The de novo assembly was performed on cleaned reads using Trinity (Grabherr et al., 2011). Before assembly, raw reads were trimmed by removing adaptor sequences and ambiguous nucleotides. Reads with quality scores less than 20 and length below 30 bp were all trimmed. The resulting high-quality sequences were used in subsequent assembly. Briefly, the raw reads were assembled into the unique sequences of transcripts in Inchworm via greedy K-mer extension (k-mer 25).
After mapping of reads to Inchworm contig bundles, Chrysalis incorporated reads into de Bruijn graphs. Butterfly then processed the individual graphs in parallel, reporting full-length transcripts and paralogous genes. After assembly, the open reading frame (ORF) of each unisequence was predicted by using Trinity software. Unisequences were used for BLAST search and annotation against the NR, NT, STRING (http://string-db.org/) (Franceschini et al., 2013), COG (http://www.ncbi.nlm.nih.gov/COG/), KEGG (http://www.genome.jp/kegg/) databases using an E-value cut-off of 10-5 (Camacho et al., 2009). Functional annotation by gene ontology (GO, http://www.geneontology.org) terms was analyzed by using BLAST2GO software (NCBI) (Conesa et al., 2005).
Supplementary_files_format_and_content: Identified mRNAs in each library with count reads and normalized data

organism: Micropterus salmoides

growth_protocol: 270 fish were selected to use in the trial. Experimental fish were randomly distributed in nine circulation closeness-tanks (30 fish per tank) and kept for two days. The experiment was designed as two hypoxia treatment groups and one control group, i.e. Moderate hypoxia group (MHG) and Severe hypoxia group (SHG) and Control group (CG), each group has three parallel tanks. The tanks were connected to nitrogen (N2) and oxygen (O2) gas cylinders. Dissolved oxygen (DO) concentrations in CG tanks were maintained at 7 mg/L (normoxia). The DO treatments were regulated through the pumping of nitrogen and oxygen in confined tanks. The DO of SHG were maintained at 1.2 ± 0.2 mg/L, MHG were maintained at 3.0 ± 0.2 mg/L in this study. The DO was monitored by measuring the water quality using classic iodine quantity method in each experimental tanks each hour (Beadle 1958) and make appropriate adjustments. Water temperature was kept at 20 ℃ throughout the experiment. Filled with nitrogen (N2) to reduce the DO to the concentration required for the experiment within one hour after the start of the experiment, and it was recorded as 0h. Fish were subjected to the acute hypoxia stress 24 h (moderate hypoxia group and severe hypoxia group) and were fasted during the experiment. Sampled at 0h, 4h, 8h, 12h and 24h after the start of the experiment.

extract_protocol:
The total RNA was harvested using Trizol-LS reagent.
Total RNA was extracted from liver using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s directions. RNA samples were digested using DNase I to remove potential genomic DNA and stored at -80℃. RNA was quantified and quality was assessed by NanoDrop Spectrophotometer 2000c (NanoDrop Technologies, Wilmington, DE, USA) and 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and all samples were standardised to 500 ng/μl. Three samples from per group at each time point were used for RNA library construction which OD ratios of 260/280 and 260/230 greater than 1.8 and RNA Integrity Number (RIN) greater than 8. RNA-seq library preparation and sequencing were carried out by Annoroad Gene Technology Co., Ltd (Beijing, China), forty five sequencing libraries were constructed using a TruSeq™ RNA Sample Preparation Kit (Illumina) according to the manufacturer’s directions. The next step was KAPA quantifcation and dilution, after which the library was sequenced on an Illumina HiSeq.2500 with 125-bp paired-end reads. After removing adaptor sequences, ambiguous N nucleotides (those an N ratio <5%) and low quality sequences (reads with <50% bases of quality value), the remaining clean reads were assembled using Trinity sofware

treatment_protocol: Five fish were collected from each tank, the fish were anesthetized with MS-222, after weighting fish were killed by cutting the spine, and immediately dissected for sampling their liver. All the samples were immediately frozen in liquid nitrogen, and stored at -80℃ until use.

value: liver

tag: developmental stage

tag: treatment

value: severe hypoxia

tag: time


title: OTTA2014_0050_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: residual disease status

value: pathogenic BRCA1 mutation

value: white

tag: study entry delay

tag: anatomical site

value: adnexal

tag: experiment site

tag: site id


title: OTTA2014_0049_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

value: high

tag: brca1 and brca2 germline mutation status


title: CoVi03_8_M_24_5P_Gex

tag: tissue

value: Blood

tag: cell type

value: Memory CD8 T cells enriched:CD3+ CD8+ CD45RA- CD137+ CD69+


title: SHG_24h_1


title: OTTA2014_0048_Clinical

description: single-sample normalized data

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time


title: CoVi03_8_M_24_5P_CITE


title: SHG_12h_3

tag: developmental stage

tag: treatment

tag: time


title: S1P2

tag: patient id

tag: point

tag: pool

tag: gender

value: female


title: S1P3


title: OTTA2014_0047_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: residual disease status

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: SHG_12h_2

tag: tissue


title: OTTA2014_0046_Clinical

description: single-sample normalized data

tag: Stage

value: any

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: hispanic

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time


title: SHG_8h_2

tag: developmental stage

tag: treatment

tag: time


title: SHG_12h_1


title: OTTA2014_0044_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis


title: SHG_8h_3


title: OTTA2014_0045_Clinical

description: single-sample normalized data

value: low

tag: residual disease status

value: unknown

tag: study entry delay

tag: anatomical site

tag: experiment site


title: SHG_4h_3

tag: tissue


title: SHG_8h_1


title: OTTA2014_0043_Clinical

description: single-sample normalized data

tag: Stage

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

tag: site id


title: SHG_4h_2


title: SHG_24h_2


title: OTTA2014_0041_Clinical

description: single-sample normalized data

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: omentum

value: AOC


title: OTTA2014_0042_Clinical

description: single-sample normalized data

tag: diagnosis


title: STAT5-ChIP_withIkaros

city: Illkirch

first: Peggy

last: Kirstetter

address: 1, rue Laurent Fries

department: Functional Genomic and Cancer

country: France

institute: Institut de Génétique et de Biologie Cellulaire et Moléculaire

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie v0.12.7 with the following parameters -m 1 --strata --best.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)

molecule: genomic DNA

source_name: BH1 cell line

growth_protocol: BH1 cell line were grown in IMDM 10%  heat inactivated FCS, 100U/ml Pen/Strep, 2mM Glutamine, 50uM beta-mercaptoethanol, 8% Il-7 (supernatant from J558L cell line).

extract_protocol:
The ChIP protocol was adapted from the Millipore ChIP Assay Kit (17-295) with minor modifications. Cells were washed in PBS and 100 000 000 cells were cross-linked at 37° C for 10 min in 5ml PBS/0.5%BSA/1% ultra-pure formaldehyde(Electron Microscopy Sciences). Quenching with 125mM glycine and a cold PBS wash (containig 1 protease inhibitor cocktail (PIC); Roche) was followed by cell lysis in 5ml of 1% Triton X-100, 50mM MgCl2, 100mM Tris-HCl pH 7.1, 11% sucrose, 1 PIC for 10 min on ice. Nuclei were pelleted and were lysed in 500 ml of 1% SDS, 50mM Tris-HCl, 10mM EDTA, 1 PIC. Chromatin was sonicated to 500–300 bp using a Bioruptor 200 (Diagenode), cleared by centrifugation and sonication efficiency was verified.
Libraries were prepared according to standard Illumina protocols and were validated with the Agilent Bioanalyzer

treatment_protocol: BH1 cells were grown 24h without IL7 supernatant in the presence of 100nM of 4OH-Tamoxifen.

tag: cell line

tag: cell type

value: Pre B cell line

tag: strain

tag: chip antibody

value: anti-STAT5 antibody (AF2168, R&D System, lot KVE0315111)


title: STAT5-ChIP_noIkaros


title: OTTA2014_0040_Clinical

description: single-sample normalized data

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: residual disease status

value: white

tag: study entry delay

value: presumed adnexal


title: OTTA2014_0039_Clinical

description: single-sample normalized data

tag: Stage

value: high

tag: brca1 and brca2 germline mutation status

tag: anatomical site

tag: experiment site


title: SHG_0h_3

tag: tissue

value: liver

tag: developmental stage

tag: treatment

value: severe hypoxia

tag: time


title: SHG_4h_1


title: SHG_0h_2


title: iopromide 3

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

institute: University of Queensland

data_processing:
Base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the A.baylyi ADP1 reference genome (NC_005966.1) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM), a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_005966.1
Supplementary_files_format_and_content: Excel file includes FPKM values for each sample

organism: Acinetobacter baylyi

source_name: Acinetobacter bacteria

growth_protocol: liquid LB culture at 30 °C

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mixed wild-type strains A.baylyi ADP1 were cultured in triplicate in 10 mL 0.5 mg/L ibuprofen, 0.5 mg/L naproxen, 0.5 mg/L gemfibrozil, 0.5 mg/L diclofenac, 0.5 mg/L propanolol, and 1.0 mg/L  iopromide , at 25 °C, without shaking

tag: agent

value: iopromide


title: OTTA2014_0037_Clinical

description: single-sample normalized data

tag: diagnosis

value: pathogenic BRCA1 mutation

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: site id


title: OTTA2014_0038_Clinical

description: single-sample normalized data

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: residual disease status

value: any

tag: study entry delay


title: Input_re-used

tag: cell line

tag: cell type

tag: strain

tag: chip antibody


title: OTTA2014_0036_Clinical

description: single-sample normalized data

tag: Stage

tag: brca1 and brca2 germline mutation status

tag: anatomical site

value: adnexal

tag: experiment site


title: iopromide 2

tag: agent


title: iopromide 1


title: MHG_24h_3

description: mRNA derived from liver tissue of moderate hypoxia group (MHG) fish

tag: tissue

tag: developmental stage

tag: treatment

value: moderate hypoxia

tag: time


title: SHG_0h_1


title: MHG_24h_1


title: OTTA2014_0033_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

value: all wildtypes

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: site id


title: OTTA2014_0035_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: unknown

tag: brca1 and brca2 germline mutation status

tag: study entry delay


title: OTTA2014_0034_Clinical

description: single-sample normalized data

value: alive

tag: anatomical site

tag: experiment site

value: AOC


title: MHG_24h_2

tag: tissue

tag: developmental stage

tag: treatment

tag: time


title: propanolol 3

tag: strain

tag: agent

value: propanolol


title: propanolol 2


title: MHG_12h_3


title: propanolol 1


title: OTTA2014_0031_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status


title: OTTA2014_0029_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: overall survival time

tag: progression-free survival time

value: peritoneal

tag: site id


title: OTTA2014_0032_Clinical

description: single-sample normalized data

value: low

tag: brca1 and brca2 germline mutation status

tag: study entry delay

tag: anatomical site

tag: experiment site


title: MHG_12h_2

tag: tissue

value: liver

tag: developmental stage

tag: treatment

tag: time


title: MHG_12h_1


title: OTTA2014_0030_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

value: high

tag: race/ethnicity

value: hispanic

value: upper genital track


title: diclofenac 2

tag: strain

tag: agent

value: diclofenac


title: diclofenac 3


title: MHG_8h_2


title: MHG_8h_3


title: diclofenac 1


title: Ikaros-ChIP_re-used

tag: cell line

tag: cell type

value: Pre B cell line

tag: chip antibody

value: anti-Ikaros Polyclonal rabbit made in house


title: gemfibrozil 3

value: gemfibrozil


title: MHG_8h_1

value: moderate hypoxia


title: gemfibrozil 2


title: PC-3M-1E8-nc886-repeat1

city: Peking

first: wang

middle: li

last: yong

state: Peking

address: No 10 xi tou tiao, you an gate

department: medical school

institute: Capital Medical University

data_processing:
RNA sequencing
RNA sequencing data of  PC-3M-1E8 cells and nc886-overexpressing cells were generated by RNA sequencing,using Illumina Xten
Basic UNIX commands, FastQC, and Trimmomatic is applied to  data control
The sequence reads that passed quality filters were analyzed at the transcript isoform level by using sequence analysis programs, including HISAT, Stringtie and DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: count

growth_protocol: DMEM medium cell culture

extract_protocol: nc886-overexpressing cell lines or scramble cell lines

treatment_protocol: stable expression of nc886 or scramble in PC-3M-1E8


title: OTTA2014_0028_Clinical

description: single-sample normalized data

value: HGSOC

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

value: adnexal

tag: site id


title: OTTA2014_0027_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

value: white

value: alive

tag: study entry delay

tag: anatomical site

tag: experiment site

value: AOC


title: PC-3M-1E8-repeat3

value: scramble


title: OTTA2014_0080_Clinical

description: single-sample normalized data

tag: sample region necrosis

value: high

value: unknown

tag: race/ethnicity


title: MHG_4h_2

tag: tissue

value: liver

tag: developmental stage

tag: treatment

tag: time


title: MHG_4h_3


title: OTTA2014_0026_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status


title: gemfibrozil 1

tag: strain

tag: agent


title: MHG_4h_1


title: PC-3M-1E8-nc886-repeat3

tag: cell type


title: naproxen 3

value: naproxen


title: PC-3M-1E8-repeat2


title: PC-3M-1E8-repeat1


title: naproxen 2


title: MHG_0h_3


title: naproxen 1


title: PC-3M-1E8-nc886-repeat2


title: ibuprofen 3

value: ibuprofen


title: Aiolos_KD-2

city: Yokohama

first: Yuki

last: Yamaguchi

address: Nagatsutacho 4259

department: School of Life Science and Technology

country: Japan

institute: Tokyo Institute of Technology

data_processing:
The resulting reads were adapter-trimmed and mapped on hg38 using CLC Genomics Workbench version 11.0 (Qiagen). TPM was also calculated using CLC Genomics Workbench.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values of coding genes that expressed (TPM >0) in one or more samples.

source_name: MM.1S, human cell line, peripheral blood

growth_protocol: MM.1S cells were maintained in ATCC-formulated RPMI 1640 with 10% FBS and antibiotics.

extract_protocol:
Total RNA was prepared using Sepasol-RNA I Super G (Nacalai Tesque) and then cleaned up using RNeasy mini kit (Qiagen).
The libraries were prepared using by TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.

treatment_protocol: MM.1S cells were treated with 1 µM pomalidomide for 24, 48, or 72 hours. Alternatively, MM.1S cells were transduced with recombinant lentivirus expressing shRNA against ARID2 or Aiolos for 72 hours.

tag: disease

value: multiple myeloma

tag: genotype/variation

value: Aiolos knockdown

value: Non-treated


title: OTTA2014_0022_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

value: low

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

tag: site id


title: OTTA2014_0024_Clinical

description: single-sample normalized data

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: race/ethnicity

value: hispanic

tag: experiment site


title: Aiolos_KD-1

tag: treatment


title: ibuprofen 2

tag: strain

tag: agent


title: CG_24h_3

description: mRNA derived from liver tissue of control (CG) fish

tag: tissue

tag: developmental stage

value: control

tag: time


title: OTTA2014_0025_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: year of diagnosis

tag: vital status

value: dead

value: adnexal


title: MHG_0h_1

value: moderate hypoxia


title: OTTA2014_0021_Clinical

description: single-sample normalized data

tag: sample region necrosis

value: any

value: white

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: AOC

tag: site id


title: ibuprofen 1

tag: strain


title: OTTA2014_0019_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

value: high

tag: race/ethnicity

tag: experiment site


title: OTTA2014_0020_Clinical

description: single-sample normalized data

tag: diagnosis

value: omentum


title: ARID2_KD-3

tag: disease

tag: genotype/variation

value: ARID2 knockdown

tag: treatment


title: control 2

tag: agent


title: Aiolos_KD-3

value: multiple myeloma


title: control 1


title: Control_KD-3

value: Control knockdown


title: OTTA2014_0017_Clinical

description: single-sample normalized data

tag: sample region cellularity

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: year of diagnosis

tag: vital status

value: presumed adnexal


title: OTTA2014_0016_Clinical

description: single-sample normalized data

value: HGSOC

tag: sample region necrosis

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site


title: ARID2_KD-1

value: Non-treated


title: MHG_0h_2

tag: tissue

value: liver

tag: developmental stage

tag: time


title: CG_24h_2

value: control


title: OTTA2014_0018_Clinical

description: single-sample normalized data

tag: diagnosis

tag: age at diagnosis

tag: Stage

value: all wildtypes

tag: race/ethnicity

tag: experiment site

tag: site id


title: control 3

tag: strain

tag: agent


title: OTTA2014_0023_Clinical

description: single-sample normalized data

tag: sample region cellularity

value: low

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: year of diagnosis

tag: vital status

value: alive


title: CG_12h_3

tag: treatment


title: Control_KD-2

tag: disease

tag: genotype/variation


title: Pom_72h-3

value: Wild type

value: 1 uM pomalidomide for 72 hours


title: CG_12h_1

tag: tissue

tag: developmental stage

tag: time


title: CG_8h_3


title: CG_12h_2


title: OTTA2014_0013_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: unknown

value: white

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site


title: TYR_BR2

city: Pullman

first: Raquel

middle: Cristina

last: Konrad Burin

state: WA

address: 155N Bustad Hall

department: Veterinary Microbiology and Pathology

institute: Washington State University

data_processing:
The paired-end sequence read data generated from each RNA-seq library was trimmed using BBDuk version 38.37 (JGI, Berkley, CA).
The quality trimmed reads were first subsampled and an average of  14M paired-end reads per sample were mapped to the complete genome of S. Enteritidis str. CDC_2010K_0968 (GenBank accession number NZ_CP007528.1) using Geneious pro version 2020.0.5 with sensitivity set to Medium-low/Fast.
The total raw reads/gene obtained for each sample/condition were used to calculate the differential expression (DE) values using DEseq2 and to identify differently expressed (DE) genes between treatment (TYR or DGA) and control (glucose) conditions.
A cut-off of 2-fold difference in the transcript abundance and a P value of < 0.01 were applied to call DE genes
Genome_build: Accession: CP007528
Supplementary_files_format_and_content: Excel file include Differential Expression Log2 Ratio of genes in each condition, being Diff Expression (genes induced in response to Glucose), Diff Expression 2 (genes induced in response to DGA) and Diff Expression 3 (genes induced in response to TYR).

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: bacterial culture

growth_protocol: For routine culture, a frozen stock of WT Salmonella stored in phosphate buffered glycerol at -80°C, was cultured on Luria-Bertani (LB) agar at 37°C for 16 h. A single colony was inoculated in 5 ml of minimal salt media (M9) containing 20 mM of glucose, followed by incubation at 37°C for 16 h with shaking at 180 rpm.

extract_protocol:
Each bacterial culture (5 ml) was centrifuged at 5,000 rpm at 4°C for 10 min. The bacterial pellets were resuspended in RNA later (Invitrogen, USA) and stored at -80°C until further processing. The samples containing RNA later were thawed and resuspended in 750 µl of phosphate buffered saline (PBS) to decrease the viscosity and to facilitate the re-centrifugation of the bacterial cells. The supernatant was discarded, and the bacterial pellets were dissolved in 1.5 ml of TRIzol (Invitrogen, USA) and processed following the total-RNA extraction protocol as recommended by the manufacturer.
The isolated mRNA was purified, fragmented and primed for cDNA library synthesis using TruSeq RNA sample prep kit (Illumina, USA) following manufacturers recommendations.

treatment_protocol: Aliquots of 50 µl from the overnight culture were transferred to 5 ml of M9 media containing either TYR (5 mM) or DGA (20 mM) as test conditions and glucose (20 mM) as a control condition. Each culture was incubated at 37°C with shaking at 180 rpm until the mid-log phase, which corresponded to an incubation period of 36 h (TYR), 8 h (DGA) and 6 h (glucose), respectively.

tag: background strain

tag: genotype

value: wild-type

value: test condition


title: Control_KD-1

value: multiple myeloma


title: TYR_BR3


title: OTTA2014_0015_Clinical

description: single-sample normalized data

tag: sample region cellularity

value: high

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

value: pathogenic BRCA2 mutation

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: adnexal

tag: experiment site

value: AOC

tag: site id


title: OTTA2014_0014_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region necrosis

value: hispanic

value: presumed adnexal


title: ARID2_KD-2

tag: disease

tag: genotype/variation

value: ARID2 knockdown

tag: treatment

value: Non-treated


title: CG_8h_2

tag: tissue

value: liver

tag: developmental stage

value: control

tag: time


title: TYR_BR1

tag: background strain

tag: genotype


title: CG_24h_1


title: OTTA2014_0012_Clinical

description: single-sample normalized data

tag: sample region cellularity

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: all wildtypes

value: white

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site


title: Pom_72h-2

value: Wild type

value: 1 uM pomalidomide for 72 hours


title: DGA_BR3

value: wild-type

value: test condition


title: CG_4h_3


title: DGA_BR1


title: CG_8h_1


title: Pom_72h-1

value: multiple myeloma


title: CG_4h_2


title: CG_4h_1


title: DGA_BR2


title: OTTA2014_0011_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region necrosis

value: high

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

value: omentum

tag: experiment site

tag: site id


title: Pom_48h-3

tag: disease

tag: genotype/variation

tag: treatment

value: 1 uM pomalidomide for 48 hours


title: Glucose_BR3

tag: background strain

tag: genotype

value: control condition


title: Pom_48h-2


title: OTTA2014_0010_Clinical

description: single-sample normalized data

value: HGSOC

tag: sample region cellularity

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: any

tag: overall survival time

value: adnexal

value: AOC


title: Glucose_BR2


title: Pom_24h-3

value: 1 uM pomalidomide for 24 hours


title: Pom_48h-1


title: CG_0h_3

tag: tissue

value: liver

tag: developmental stage

value: control

tag: time


title: C. albicans Bulk RNA

city: Chicago

first: Ryan

middle: Patrick

last: Dohn

state: IL

address: 5841 S. Maryland Ave.

department: Department of Medicine

institute: University of Chicago

description:
Sample 15
Cells not diluted 4 hours prior to experiment

data_processing:
A Snakemake protocol called dropRunner was used to create an expression matrix corresponding to the UMI of each gene in a cell. https://github.com/aselewa/dropseqRunner
STARsolo (STAR 2.7.0a) was used for sequence alignment to the respective yeast genomes
Genome_build: sacCer3_s288c (S. cerevisiae); A21-s02-m09-r10 (C. albicans)
Supplementary_files_format_and_content: Matrix table with raw UMI counts for every gene and every cell, cell barcode file, and gene id file.
Supplementary_files_format_and_content: Tab delimited raw count table with gene and barcode ids (Samples 3 and 4).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene (Samples 14 and 15)

organism: Candida albicans

source_name: C. albicans cells

growth_protocol: Yeast cells were grown in suspension in rich YEPD media over night and diluted 4 hours prior to experiment to obtain log phase growth.

extract_protocol:
Cells encapsulation into nL droplets using a microfluidic device along with oligo poly-dT beads and zymolyase containing lysis buffer. Cells were then incubated at 37°C for 15-25 minutes for lysis. mRNA was captured by the poly-dT oligo beads.
Reverse tracnription to cDNA was performed using a template switch oligo. Beads then underwent exonuclease treatment and PCR amplification. A Illumina Nextera (cat#FC-131-1096) was used with 500-600 pg cDNA for construction of sequencing libraries.

treatment_protocol: Heat Shock Cells incubated in 42°C thermomixer for 20 minutes prior to microfluidic encapsulation.

tag: strain

value: untreated


title: Pom_24h-2

value: Wild type


title: Glucose_BR1

value: wild-type


title: OTTA2014_0007_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region necrosis

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: progression-free survival time

tag: study entry delay

tag: anatomical site


title: CG_0h_2

tag: treatment


title: OTTA2014_0006_Clinical

description: single-sample normalized data

tag: sample region cellularity

tag: age at diagnosis

tag: Stage

value: white

tag: experiment site

tag: site id


title: CG_0h_1

tag: tissue

tag: developmental stage

tag: time


title: Non-treat-3

tag: disease

value: multiple myeloma

tag: genotype/variation

value: Non-treated


title: OTTA2014_0004_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region necrosis

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: pathogenic BRCA1 mutation

tag: race/ethnicity

value: dead

tag: overall survival time


title: C. albicans cells - 25 minute lysis - rep 1

description:
Sample 9
Cells not diluted 4 hours prior to experiment.

tag: strain

tag: treatment


title: C. albicans Aligned to S. cerevisiae Genome

description:
Sample 13
Cells not diluted 4 hours prior to experiment.
Processed file required for samples 10 and 11 analysis. Contains genes misaligned to the wrong genome for use in species mixing.


title: OTTA2014_0005_Clinical

description: single-sample normalized data

tag: sample region cellularity

tag: age at diagnosis

value: hispanic

tag: year of diagnosis

tag: vital status

tag: progression-free survival time

tag: study entry delay

tag: anatomical site


title: OTTA2014_0008_Clinical

description: single-sample normalized data

value: HGSOC

tag: Stage

value: low

value: alive

tag: experiment site

tag: site id


title: OTTA2014_0009_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region necrosis

value: unknown

value: presumed adnexal

value: AOC


title: C. albicans cells - 20 minute lysis - rep 1

description:
Sample 8
Cells not diluted 4 hours prior to experiment.


title: Non-treat-2

tag: disease

tag: genotype/variation


title: Non-treat-1


title: OTTA2014_0002_Clinical

description: single-sample normalized data

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

tag: overall survival time

value: omentum


title: C. albicans cells - 15 minute lysis

description:
Sample 7
Cells not diluted 4 hours prior to experiment.

tag: strain

tag: treatment

value: untreated


title: OTTA2014_0003_Clinical

description: single-sample normalized data

tag: sample region cellularity

tag: age at diagnosis

value: any

tag: year of diagnosis

tag: vital status

value: adnexal


title: H3

status: Public on Jul 21 2020

city: Tübingen

last: Borg

address: Max Planck Ring 5

department: Algal Development & Evolution

country: Germany

institute: Max Planck Insititue for Biology

description: anti-H3 IP from Input

data_processing:
Raw, unaligned BAM files were first sorted with samtools sort -n and then converted to fastq files with bedtools bamtofastq.
Adapter trimming was performed using TrimGalore version 0.4.1.
Reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie2 version 2.1.0.
Reads were filtered for a MAPQ score > 10 using SAMtools version 1.3 and subsequently filtered for duplicate reads using Picard tools MarkDuplicates version 1.141.
For data visualization, log2 ratio bigwig coverage files relative to input were generated using the deepTools version 2.5.0.1 utility bamCoverage with a bin size of 10 bp.
Genome_build: TAIR10 (Arabidopsis thaliana)
Supplementary_files_format_and_content: *.bw: Normalized log2 ratio coverage of histone marks relative to relevant input sample. Data is generated from merged replicates.

organism: Arabidopsis thaliana

source_name: Seedlings

extract_protocol:
ChIP experiments were performed using formaldehyde-crosslinked 10-day-old seedlings. Chromatin was sheared by sonication and immunoprecipitation of soluble chromatin was carried out with anti-H3 (Abcam, ab1791) or anti-H2B specific antibodies.
TruSeq DNA sample prep kit (Illumina)

tag: ecotype

tag: genotype

value: wild type

tag: chip-antibody

value: anti-H3 (Abcam, ab1791)


title: H2B.4

description: anti-H2B.4 IP from Input


title: H2B.2

description: anti-H2B.2 IP from Input


title: GBM14 crizotinib 2

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from GBM14 glioblastoma cell line treated with crizotinib.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezgcdf R package (version 23.0.0).

label: biotin

source_name: GBM14 glioblastoma cell line

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: DMEM + 10%FBS + primocin

extract_protocol: RNA was isolated according to the manufacturer's instructions. RNA extraction kit was purchased from QIAGEN (miRNeasy Mini Kit: Cat #217004).

treatment_protocol: DMEM + 10%FBS + primocin + 1 µM crizotinib

tag: cell line

tag: cell type

value: glioblastoma

value: crizotinib


title: H2B.3

description: anti-H2B.3 IP from Input


title: Input

description: Formaldehyde-crosslinked sonicated chromatin input DNA


title: GBM14 crizotinib 1


title: KO1: Otic vesicle Meis2 knockout 1

city: Valladolid

first: Thomas

last: Schimmang

address: Sanz y Fores 3

country: Spain

institute: CSIC

data_processing:
Mapping of the reads to the GRCm38 reference genome with Salmon (version 0.9.1)
All data were processed with RaNA-Seq cloud (https://ranaseq.eu)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include TPM values for each Sample

source_name: otic vesicle of mouse embryo

extract_protocol:
RNA was extracted from otic vesicles using the RNeasy Micro kit (QIAGEN, Hilden, Germany), according to manufacturer´s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols and sequenced using the NextSeq 500 system.

tag: tissue

value: otic vesicle

tag: age

value: day 11.5 of embryonic development

value: Meis2 mutant


title: KO2: Otic vesicle Meis2 knockout 2


title: Pom_24h-1

tag: disease

value: multiple myeloma

tag: genotype/variation

value: Wild type

value: 1 uM pomalidomide for 24 hours


title: WT2: Otic vesicle wild-type 2

value: wild-type


title: WT1: Otic vesicle wild-type 1


title: OT-rich bone oim/oim rep3

city: Little Rock

first: Roy

last: Morello

state: AR

address: 4301 W. Markham St #505

department: Physiology and Biophysics

institute: University of Arkansas for Medical Sciences

data_processing:
Initial RNA sequencing data analysis was done using Illumina’s software portfolio including the BaseSpace (Illumina) analysis pipeline and the Tuxedo suite consisting of Bowtie, TopHat and Cufflinks to align sequence reads to the murine reference genome GRCm38, identify splice isoforms, and estimate transcript abundance.
Quantification, quality control, and differential expression analysis of the RNA sequencing data was performed using SeqMonk software (version 0.31.1) which runs R-based statistical analyses and uses Bioconductor packages (DESeq2).
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file with table of FPKM values for all genes and all samples

source_name: osteocyte-enriched cortical bone

growth_protocol: Mice were housed in a pathogen free facility with 12-hour light/dark cycle and unlimited access to water and standard chow diet. All animal work was conducted in accordance to local, state and U.S. federal regulations. Mice were euthanized at 3 months of age and relevant tissues were harvested according to the recommendations of the Guide for Care and Use of Laboratory Animals (8th Edition).

extract_protocol:
Femora and tibiae were harvested from WT, oim/oim, and CrtapKO mice at 3 months of age, N=4/genotype. Osteocyte-enriched bone was obtained by removing the epiphyses, thoroughly flushing the bone marrow, and scraping off the periosteal membrane; all these procedures were performed on ice in less than 10 minutes after the initial harvest. The osteocyte-enriched bone was immediately homogenized in 1 mL of TriPure Isolation Reagent (Roche REF 11667157001) and processed for RNA extraction according to the manufacturer’s instructions until the chloroform separation step. An equal volume of freshly-made, RNase-free 75% ethanol was added to the clear supernatant obtained from the chloroform separation, mixed, and then transferred to an RNeasy Micro column (Qiagen cat# 74004). Digestion with DNase I and elution of RNA was performed according to the manufacturer’s instructions. RNA samples were tested for quality using an Agilent 2100 Bioanalyzer. Only RNA samples with an RNA integrity number (RIN) of ≥7.0 were accepted for sequencing.
Sequencing libraries were prepared from the RNA samples by use of the TruSeq mRNA Sample Prep Kit (Illumina). Briefly, total RNA (1μg) was subjected to polyA selection, then chemically fragmented and converted to single-stranded cDNA using random hexamer-primed reverse transcription. The second strand was then generated to create double-stranded cDNA, followed by fragment end repair and addition of a single A base on each end of the cDNA. Adapters were ligated to each fragment end to enable attachment to the sequencing flow cell. The adapters also contained unique index sequences that allowed the libraries from different samples to be pooled and individually identified during downstream analysis. Library cDNA was PCR amplified and enriched for fragments containing adapters at each end to create the final cDNA sequencing library. Libraries were validated on the Fragment Analyzer for fragment size and quantified by use of a Qubit fluorometer (Life Technologies). Equal amounts of each library were pooled for sequencing on the NextSeq 500 platform using a high output flow cell to generate approximately 25 million 75-base reads per sample.

value: Col1a2 oim/oim

value: femur and tibia

tag: mouse id

value: 3 months

tag: Sex

value: female


title: OT-rich bone oim/oim rep2

tag: strain

value: male


title: OT-rich bone oim/oim rep1


title: OT-rich bone oim/oim rep4


title: OT-rich bone CrtapKO rep2

value: Crtap -/-


title: OT-rich bone CrtapKO rep4


title: OT-rich bone CrtapKO rep1


title: OT-rich bone WT rep3

value: wildtype


title: GBM14 control 1

description: Gene expression data from GBM14 glioblastoma cell line treated with control.

tag: treatment

value: control


title: OT-rich bone WT rep2


title: H2B.1

description: anti-H2B.1 IP from Input

value: wild type


title: OTTA2014_0001_Clinical

city: Vancouver

last: Anglesio

institute: University of British Columbia

description: single-sample normalized data

data_processing: Samples data is processed and normalized following protocols described in Talhouk et al (PMID: 27096160) using PrOTYPE. Briefly: Count data is Log2 transformed, the mean of housekeeping genes (ACTB, RPL19, SDHA, POLR1B, and PGK1) subtracted on a per-sample basis, and then normalized relative to reference samples (denoted as Pool1, Pool2, and Pool3). Code available at https://github.com/AlineTalhouk/PrOType

source_name: primary high-grade serous tubo-ovarian carcinoma

extract_protocol: Total RNA extracted with the Qiagen miRNeasy FFPE kit (modified protocol)

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: Stage

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: hispanic

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: omentum

tag: experiment site

value: AOC

tag: site id


title: 2_01XO_38693Tokyo_ISC-rep1_Input_mm10_i69

city: Tokyo

first: Taku

last: Sato

address: 1-5-45 Yushima Bunkyo-ku

department: Department of Biodefense Research

institute: Medical Research Institute, Tokyo Medical and Dental University (TMDU)

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the mouse genome (mm10) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of pvalue = 1E-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: mm10
Supplementary_files_format_and_content: BAM = standard BAM alignment format
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)
Supplementary_files_format_and_content: BED = standard BED file containing MACS peaks

source_name: Intestinal stem cells

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

tag: tissue

value: small intestine

tag: chip antibody


title: mESC-4sU

city: Philadelphia

first: Peng

last: Hu

state: PA

address: 415 Curie Blvd, 545 CRB

department: Genetics

institute: University of Pennsylvanian

description: Remove the medium from plates and add mESC medium supplemented with 100 μM 4sU for 4 hrs. After 4sU-labeling, cells were harvested and used for Drop-seq analysis.

data_processing:
Library strategy: scNT-seq
Paired-end sequencing reads of scNT-Seq were processed as previously described (Hu et al., Molecular Cell, 2017) with some modifications. Briefly, each mRNA read (read2) was tagged with the cell barcode (bases 1 to 12 of read 1) and unique molecular identifier (UMI, bases 13 to 20 of read 1), trimmed of sequencing adaptors and poly-A sequences, and aligned using STAR v2.5.2a to the mouse (mm10, Gencode release vM13),  human genome (GRCh38, Gencode release v23), or a concatenation of the mouse and human (for the species mixing experiment) reference genome assembly. Both exonic and intronic reads mapped to predicted strands of annotated genes were retained for the downstream analysis. To qualify the labeled and unlabeled transcripts, uniquely mapped reads with mapping score > 10 were grouped by UMI barcodes in every cell and were used to determine the T > C substitution using sam2tsv (https://github.com/lindenb/jvarkit) , T > C substitutions with a base quality of Phred score > 27 were retained. For each experiment, locus with background T > C substitutions (detected in the sample without TFEA/NaIO4 treatment) was determined and was excluded for T > C substitution identification. After background correction of T > C substitution, a UMI was defined as labeled if there is a T > C substitution in any one of the reads belonging to that particular UMI. To this end, every UMI will be assigned to labeled or unlabeled based on the existence of T > C substitution. For each transcript, the total number of uniquely labeled (with T->C mutations) and unlabeled UMI sequences were counted and finally were assembled into 2 matrics using gene name as rows and cell barcode as columns.
Genome_build: Mouse (mm10) and human reference genome (GRCh38)
Supplementary_files_format_and_content: Two gene expression matrics containing labeled and unlabeled UMI count or total UMI count for each gene (rows) in each cell (columns), respectively

source_name: Mouse embryonic stem cell

growth_protocol: Wild-type mESCs were initially cultured in presence of Mitomycin C inactivated mouse embryonic fibroblasts on 0.1% gelatin-coated (Millipore) 6-well-plates in Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco) supplemented with 15% fetal bovine serum (Gibco), 0.1 mM nonessential amino acid (Gibco), 1 mM sodium pyruvate (Gibco), 2 mM L-glutamine (Gibco), 50 μM 2-mercaptoethanol (Gibco), 1 μM MEK inhibitor PD0325901 and 3 μM GSK3 inhibitor CHIR99021 (Axon MedChem), and 1,000 U/mL LIF (Gemini Bio-Products). Human K562 cells (ATCC, CCL-243) were cultured in RPMI media supplemented with 10% FBS (Sigma, F6178).

extract_protocol:
After 4sU-labeling, K562 cells were pelleted and washed once with DPBS. mESCs were rinsed once with DPBS and dissociated with TrypLE-Express (Gibco, 12605010) for 5 min at 37°C. After neutralizing with culture medium, cells were pelleted at 1,000 rpm for 3 min. The cells were resuspended with DPBS-0.01% BSA. After cell counting with Countess II system, the single cell suspension was diluted to 100 cells/uL with DPBS containing 0.01% BSA and mixed at 1:1 ratio (mESCs:K562) for Drop-seq or scNT-seq analysis.
Single cells, polyA-containing barcoded beads (ChemGenes), and droplet generation oil (Bio-Rad) were each flowed into individual input ports on a microfluidic device (uFluidix). Cells were lysed and hybridized to beads in droplets. Beads were isolated and subjected to reverse transcription (Thermo Fisher) and exonuclease I (NEB) treatment, followed by PCR of full length transcripts (Kapa). Final libraries were created by tagmentation of cDNA, amplified by PCR (Illumina, Nextera xT DNA Library Preparation kit) and purified by SPRI beads. For scNT-seq, the beads were treated with either TimeLapse chemistry (TFEA) or SLAM-seq chemistry (IAA) to convert 4sU to cytidine-analog before reverse transcription. For second-strand synthesis, after exonuclease I treatment, the beads were washed once with TE-SDS buffer and twice with TE-TW buffer. After aspiration of TE-TW wash, the beads were resuspended in 500 μL 0.1 M NaOH and incubated for 5 min at room temperature with rotation. Then 500 μL 0.2 M Tris-HCl (pH 7.5) was added to neutralize the solution. The beads were washed once with TE-TW buffer and once with 10 mM Tris-HCl (pH 8.0), then 200 μL 2nd-strand synthesis mix (1x Blue buffer (Enzymatics), 4% Ficoll PM-400, 1 mM dNTPs (Clontech), 2.5 μM Template Switch Oligo-GAATG (TSO-GAATG: /5SpC3/AAGCAGTGGTATCAACGCAGAGTGAATG), 5 μM TSO-N9 (TSO-N9: /5SpC3/AAGCAGTGGTATCAACGCAGAGTGAAT(N1:25252525)(N1) (N1)(N1)(N1)(N1)(N1)(N1)(N1)), and 1.25 U/ μL Klenow exo- (Enzymatics)) were added [N1 stands for mixture of A,T,C,G at 25:25:25:25 ratio]. The reaction was incubated at room temperature for 10 min, followed by incubation at 37°C for 1 hour with end-over-end rotation.  The reaction was stopped by washing the beads once with TE-SDS buffer and twice with TE-TW buffer.

treatment_protocol: Before 4sU labeling experiments, J1 WT mESCs were passaged and cultured in feeder-free conditions for 48 hrs. For 4sU labeling, the mESC or K562 media was replaced with media supplemented with 4sU (100 μM) and cultured for 4 hours.

tag: cell line

value: J1 mESCs (ATCC, SCRC-1010)

tag: cell type

value: Mouse embryonic stem cell

tag: genotype

value: Wild-type

tag: Sex

tag: datatype

value: UMI count matrix of total RNAs


title: mESC-4sU-TFEA-PBS

description: Remove the medium from plates and add mESC medium supplemented with 200 μM 4sU. The fresh medium with 4sU was changed every 4 h to enhance 4sU incorporation and mESCs were labeled for 24 hrs. After 4sU-labeling, the 4sU-containing medium was removed. Cells were harvested and fixed with methanol and stored at -80°C for future use. For sample rehydration, cells were taken out of -80°C freezer and kept on ice throughout the procedure. After cells were spun down at 1,000 g for 5 min at 4°C, methanol-PBS solution was removed, and cells were resuspended in 1 mL of rehydration buffer (PBS).  After cell counting, the single cell suspension was diluted to 100 cells/μL and immediately used for scNT-seq analysis.

tag: treatment

value: Methanol fixation followed by rehydration (PBS); 200 μM 4sU, 24 h; TFEA/NaIO4

value: UMI count matrix of new (C) and old (T) RNAs


title: mESC-4sU-TFEA

description: Remove the medium from plates and add mESC medium supplemented with 100 μM 4sU for 4 hrs. After 4sU-labeling, cells were harvested and used for scNT-seq analysis. For data analysis, down sampling was performed using “samtools view -s 0.63” to subsample the reads from bam files to match the sequencing depth with other conditions

value: male

value: 100 μM 4sU, 4 h; TFEA/NaIO4