title: NZM15_I (RRBS)

city: Dunedin

first: Jyoti

last: Motwani

state: Otago

address: PO Box 56

department: Department of Pathology

country: New Zealand

institute: University Of Otago

description: technical replicate

data_processing:
DNA from 12 RRBS libraries were sequenced in Illumina HiSeq machine. Base calling was performed using RTA software. Sequenced libraries were demultiplexed to obtain individual fastq files.
Before alignment, the raw data files were checked run using the FastQC (Babraham Institute, Cambridge, UK) tool to assess the quality of the raw data. Based on the quality reports, adapter trimming and hard trimming was carried out using the cleanadaptors program (from the DMAP package (Stockwell et al., 2014)). The alignment was performed using Bismark v0.14.3 (Krueger & Andrews, 2011) against the GRCh37 (hg19) build of the human genome.
Differential methylation analysis was performed using the differential methylation analysis package (DMAP) (Stockwell et al., 2014).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: A matrix file with methylation % in all analyzed framents across all the samples

source_name: Metastatic melanoma cell line

growth_protocol: The cell lines were cultured in a low oxygen tissue culture incubator (BINDER, Model # CB 60) that was set at 5% O2 at 37°C with a humidified atmosphere of 5% CO2. Cells were subcultured when the confluence reached 80% - 90%. The NZM cell lines were cultured in  MEM   (Gibco, # 12561056) supplemented with 5% Fetal bovine serum (FBS) and 0.1% Insulin-Transferrin-Sodium Selenite Supplement (ITS) (Sigma-aldrich, 11074547001). Skmel28 was cultured in DMEM Gibco, # 11995-065) supplemented with 10% FBS. HemN-LP was cultured in Medium 254 (Gibco, # M254500) and Human Melanocyte Growth supplement (HMGS 0.1%) (Gibco, # S0025).

extract_protocol:
Genomic DNA cell lines was extracted using a QiAamp DNA mini kit (QIAGEN, Catalog # 51104).
The  extracted genomic DNA was digested with MspI. This step was followed by end-repair, A-tailing and adapter ligation. Adapter ligated MspI fragments were size selected, by gel-based size selection method, after 15-20 cycles following which they were bisulfite converted and amplified by PCR. The amplified PCR product was purified and quantified by Qubit dsDNA HS kit (Invitrogen Catalog #Q32854). An Agilent Bioanalyzer assay was used to determine the quality of each library and the size distribution of the DNA fragments within each library. Single-ended RRBS libraries with 100 bp read length were sequenced on an Illumina HiSeq2500 with high output run mode and SBS v4 chemistry.

value: Skin

value: Metastatic melanoma cell line NZM15_I

tag: phenotype

value: Non-invasive - technical replicate


title: NZM42 (RRBS)

status: Public on Apr 06 2021

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

tag: cell line

value: Metastatic melanoma cell line NZM42

value: Non-invasive


title: Skmel28 (RRBS)

value: Metastatic melanoma cell line Skmel28


title: HemNLP (RRBS)

source_name: Melanocyte cell line

value: Melanocyte cell line HemNLP

value: Normal


title: NZM9_II (RRBS)

description: technical replicate

value: Metastatic melanoma cell line NZM9_II

value: Invasive- technical replicate


title: NZM40 (RRBS)

value: Metastatic melanoma cell line NZM40

value: Invasive


title: NZM22 (RRBS)

value: Metastatic melanoma cell line NZM22


title: LC_Serum_Exp6

type: RNA

city: Guangzhou

first: Xiaoxia

last: Zhu

state: Guangdong

address: No. 253 Gongye Street

department: Radiation Oncology Department

country: China

institute: Zhujiang Hospital, Southern Medical University

description: miRNA expression in serum of lung cancer patient

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal.

scan_protocol: Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

molecule: total RNA

source_name: Serum, Lung Cancer Patient, Experimental Group, 06

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRI reagent BD (MRCgene, TB-126) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies).

tag: sample type

value: Serum

tag: pathology

value: AD

tag: tnm

tag: Stage

value: IB

tag: disease state

value: lung cancer


title: HP_Serum_Con1

description: miRNA expression in serum of healthy people

source_name: Serum, Healthy People, Control Group, 01

value: healthy


title: LC_Serum_Exp5

source_name: Serum, Lung Cancer Patient, Experimental Group, 05

value: IA


title: HP_Serum_Con2

source_name: Serum, Healthy People, Control Group, 02


title: LC_Serum_Exp3

source_name: Serum, Lung Cancer Patient, Experimental Group, 03

value: SCC

value: IIB


title: control_line- C3

city: Durham

first: Jiahua

last: Xie

state: NC

address: 302 E. Lawson Street

department: Pharmaceutical Sciences

country: USA

institute: North Carolina Central University

library_source: transcriptomic

data_processing:
Data Pre-processing using the tool FastQC link.
The TopHat application produces aligned reads and FPKM abundance estimates of reference genes and transcripts.
Differential Expression Analysis performed using Cufflinks and Cuffdiff applications, which used the alignment results produced by the TopHat.
The basic annotation performed used gene annotation from NCBI db.
Following comparisons were performed: C vs TA, C vs TB.
Supplementary_files_format_and_content: FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: control line

growth_protocol: Plants were grown in a growth chamber under a light intensity of 75 μmol m−2 s−1, 12/12 h light/dark cycles and temperature at 20°C.

extract_protocol:
RNA samples were prepared using Qiagen RNeasy® Plant Mini kit (Qiagen). All samples were treated with DNase I (Qiagen) to remove any possible DNA contamination which was further confirmed by 36 cycles of PCR. RNA samples were quantified by a spectrophotometer and visualized on a 1.2% agarose gel.
RNA library was prepared using the Kapa Stranded mRNA-Seq library prep kit.

tag: genotype/variation

value: expressing vector contruct udiA

tag: transgene

value: nptII

tag: age

value: 6-8 week old

tag: tissue

value: cluster of unopened flower buds


title: LC_Serum_Exp4

source_name: Serum, Lung Cancer Patient, Experimental Group, 04


title: LC_Serum_Exp2

source_name: Serum, Lung Cancer Patient, Experimental Group, 02


title: NZM12 (RRBS)

value: Skin

value: Metastatic melanoma cell line NZM12

value: Non-invasive


title: NZM15 (RRBS)

value: Metastatic melanoma cell line NZM15


title: NZM9 (RRBS)

value: Metastatic melanoma cell line NZM9

value: Invasive


title: NZM11 (RRBS)

value: Metastatic melanoma cell line NZM11


title: LC_Serum_Exp1

source_name: Serum, Lung Cancer Patient, Experimental Group, 01

value: Serum

value: IB


title: Cast/Test_PC, biological rep4

city: New York

first: Charles

last: Drake

state: New York

address: 650 W. 168th Street

department: Medicine

country: Mexico

institute: Columbia University

description: Gene expression data from luminal prostate epithelial cells from surgically castrated Hoxb13-rtTA|TetO-H2BGFP mice, in which a regeneration cycle was induced with a testosterone pellet

hyb_protocol: Affymetrix Clariom D Array

scan_protocol: Affymetrix Clariom D Array

data_processing: Samples were normalised (Log2) with Affymetrix Expression Console using SST-RMA algorith and annotated on transcript/gene level with the library for Clariom D array (mouse).

label: biotin

organism: Mus musculus

source_name: Luminal prostate epithelial cells from surgically castrated Hoxb13-rtTA|TetO-H2BGFP mice, in which a regeneration cycle was induced with a testosterone pellet

label_protocol: Affymetrix WT Plus Labeling Kit

growth_protocol: Animals were kept in specific pathogen-free conditions under 12hrs light-dark cycles and with temperature and humidity set points at 20-25°C and 30-70%, respectively.

extract_protocol: Samples were directly sorted into Trizol LS, and total RNA extraction was performed followed by on-column clean up with Zymo Research kit according to the manufacturer's instructions. Before Affymetrix ClariomD microarray analysis was performed, the quality and quantity of each RNA sample were checked on a BioAnalyzer (Agilent, inc). High-quality RNA (RNA integrity number ≥9) was used for whole transcript microarray analysis.

treatment_protocol: Mice were randomized to untreated, surgically castrated (orchiectomy, ADT) or ADT + testosterone repletion (TR) treatment groups.  Testosterone was administered for four weeks for prostate regeneration by subcutaneous silastic implants yielding physiological levels of serum testosterone.  All mice received 2mg/ml of doxycycline (Sigma) in the drinking water to induce GFP expression under the control of the luminal epithelial promoter, Hoxb13, one week prior to euthanization.

tag: Sex

value: Male

value: Prostate


title: NZM6 (RRBS)

value: Metastatic melanoma cell line NZM6


title: Intact MCRedAL, biological rep3

description: Gene expression data from prostate tumor cells from untreated MCRedAL tumor allografts

data_processing: Samples were normalised (Log2) with Affymetrix Expression Console using RMA algorith and annotated on transcript/gene level with the library for MTA 1.0 array (mouse).

source_name: Prostate tumor cells from untreated MCRedAL tumor allografts

extract_protocol: Samples were directly sorted into Trizol LS, and total RNA extraction was performed followed by on-column clean up with Zymo Research kit according to the manufacturer's instructions. Before Affymetrix MTA 1.0 microarray analysis was performed, the quality and quantity of each RNA sample were checked on a BioAnalyzer (Agilent, inc). High-quality RNA (RNA integrity number ≥9) was used for whole transcript microarray analysis.

treatment_protocol: Mice were randomized to untreated or degarelix-treated (ADT) treatment groups.  Degarelix was administrated subcutaneously when tumors reached ~500mm2.


title: Intact MCRedAL, biological rep1


title: 7dPC MCRedAL, biological rep2

description: Gene expression data from prostate tumor cells from degarelix-treated MCRedAL tumor allografts

source_name: Prostate tumor cells from degarelix-treated MCRedAL tumor allografts


title: control_line- C2


title: Cast_PC, biological rep1

description: Gene expression data from luminal prostate epithelial cells from surgically castrated Hoxb13-rtTA|TetO-H2BGFP mice

source_name: Luminal prostate epithelial cells from surgically castrated Hoxb13-rtTA|TetO-H2BGFP mice


title: Cast/Test_PC, biological rep1


title: 7dPC MCRedAL, biological rep1


title: MelSt (RNA-seq)

data_processing:
RNASeq libraries for twelve cell lines were multiplexed across two lanes and sequenced in Illumina HiSeq 2500. Base-calling was performed using RTA software. Libraries demultiplexed to obtain individual Fastq files.
Paired end sequencing of 125 bp was carried out in Illumina 2500 V4 sequencer.
Quality of the raw reads was assessed using FastQC tool. Trimmomatic (Bolger et al., 2014) was used to discard low quality reads, trim adapter sequences and eliminate poor-quality bases. Tophat2 (D. Kim et al., 2013) was used for alignment of RNA-Seq data. A pre-built human genome GRCh37 Bowtie2 index from Illumina's iGenomes collection was used as a reference genome. GENCODE19 annotations were used to annotate all the RNAs.
The read counts were generated using the htseq-count script (Anders et al., 2015).  FPKM values were generated using Cufflinks pipeline (Trapnell et al., 2012). DESeq2 R package was used for the differential expression analysis, according to the standard protocol (Love et al., 2014). lncRNAs were annotated using Gencode Version 19 annotation file (Derrien et al., 2012).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Matrix table with FPKM value of all analysed genes across all samples (CSV)

growth_protocol: The cell lines were cultured in a low oxygen tissue culture incubator (BINDER, Model # CB 60) that was set at 5% O2 at 37°C with a humidified atmosphere of 5% CO2. Cells were subcultured when the confluence reached 80% - 90%. The NZM cell lines were cultured in  MEM   (Gibco, # 12561056) supplemented with 5% Fetal bovine serum (FBS) and 0.1% Insulin-Transferrin-Sodium Selenite Supplement (ITS) (Sigma-aldrich, 11074547001). Skmel28 and MelSt were cultured in DMEM Gibco, # 11995-065) supplemented with 10% FBS. HemN-LP was cultured in Medium 254 (Gibco, # M254500) and Human Melanocyte Growth supplement (HMGS 0.1%) (Gibco, # S0025). HemA-LP was cultured in Medium 254 (Gibco, # M254500) and Human Melanocyte Growth supplement 2 (HMGS-2 0.1%) (Gibco, # S0165).

extract_protocol:
The RNA from the cell lines was extracted from the same passage of cells, which were chosen for DNA extraction (for RRBS), using a PureLink RNA mini kit (Invitrogen, Catalog #12183025). The total RNA was extracted according to the manufacturer’s instructions. RNA purity was determined by measuring absorbance using a Nanodrop ND-1000 spectrophotometer (ThermoFisher Scientific, USA). RNA samples with an A260/A280 between 1.8 to 2.0 and A260/A230 close to 2.0 were chosen for downstream analysis. RNA concentration was determined using a Qubit RNA HS kit (Invitrogen, Catalog # Q32852) according to the manufacturer’s instructions. RNA integrity was determined by an Agilent Bioanalyzer 2100 system and associated RNA 6000 Nano kit (Agilent, Catalog # 5067-1511). The RIN values of all the samples used for the RNASeq analysis were >=8.0.
The library preparation was carried out by enrichment of poly-A tailed transcripts from the total RNA and the library type was strand-specific. A TrueSeq mRNA stranded library prep kit (Illumina, Catalog # RS-122-2101) was used for mRNA library preparation. Paired end sequencing of 125 bp was carried out in Illumina 2500 V4 sequencer.

value: Melanocyte cell line MelSt

value: Normal


title: Cast_PC, biological rep3


title: HemALP (RNA-seq)

value: Melanocyte cell line HemALP


title: Intact, biological rep2

description: Gene expression data from luminal prostate epithelial cells from untreated Hoxb13-rtTA|TetO-H2BGFP mice

source_name: Luminal prostate epithelial cells from untreated Hoxb13-rtTA|TetO-H2BGFP mice


title: control_line- C1

value: expressing vector contruct udiA

value: nptII

value: 6-8 week old


title: HemnLP (RNA-seq)

value: Skin

value: Melanocyte cell line HemnLP


title: NZM42 (RNA-seq)

value: Metastatic melanoma cell line NZM42

value: Non-invasive


title: Cast/Test_PC, biological rep3


title: Skmel28 (RNA-seq)

value: Metastatic melanoma cell line Skmel28


title: EaF82_OX_2-TB3

source_name: transgenic lines overexpressing EaF82

value: overexpressing EaF82

value: 6-8 week-old

value: cluster of unopened flower buds


title: 7dPC MCRedAL, biological rep3

value: Male


title: Intact MCRedAL, biological rep2

value: Prostate


title: Cast_PC, biological rep2


title: Intact, biological rep1


title: Cast/Test_PC, biological rep2


title: Intact, biological rep3


title: EaF82_OX_2-TB2


title: EaF82_OX_1-TA1


title: EaF82_OX_1-TA2


title: NZM12 (RNA-seq)

source_name: Metastatic melanoma cell line

value: Metastatic melanoma cell line NZM12


title: NZM22 (RNA-seq)

value: Metastatic melanoma cell line NZM22

value: Invasive


title: NZM11 (RNA-seq)

value: Metastatic melanoma cell line NZM11


title: NZM15 (RNA-seq)

value: Metastatic melanoma cell line NZM15


title: P22_12H

city: Los Angeles

first: Colette

middle: L

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

data_processing:
Reads were trimmed and quality-filtered using Trim Galore v.0.4.1 and aligned using STAR v.2.7.1a. Reads from Col- Cvi crosses were mapped to a Col-Cvi 'metagenome' (TAIR10 sequence appended to a Cvi 'pseudogenome' generated by substituting the Cvi allele at 576,697 Col-Cvi SNPs). Reads from Col-Ler crosses were mapped to a Col-Ler 'metagenome'. Sequences from ThermoFisher ERCC RNA spike-ins were also appended to the metagenome. Reads that mapped uniquely to the ERCC sequences were extracted and omitted from the rest of the analysis. Procedures and scripts for mapping with the metagenome are available in Picard and Gehring (Methods Mol Biol 2020). Reads overlapping a SNP were identified  using a custom script (Picard and Gehring, 2020) and assigned to parent- of-origin. PCR duplicates were removed using MarkDuplicates from the Picard Toolkit (Broad Institute). Total and allele-specific counts over genes were then obtained using htseq-count v.0.9.1 and the Araport11 gene annotations (excluding new Araport11 annotations antisense to existing TAIR10 genes). Single-nuclei samples with a total of at least 1,500 genes detected (≥ 1 overlapping read) and 1,000 genes well-detected (≥ 5 overlapping reads) prior to removing PCR duplicates were considered high quality and kept for subsequent analyses. Raw total expression counts were normalized to CPM (counts per million) while allelic count data for Col,Cvi reciprocal crosses at 4 DAP were normalized using the same procedure used in DESingle (Miao et al. 2018, Bioinformatics).
Genome_build: Araport 11 (excluding new Araport11 annotations antisense to existing TAIR10 genes)
Supplementary_files_format_and_content: Processed files for each library are tab-delimited with four fields: locus_name, all_counts, [parent1]_counts, [parent2]_counts, corresponding to raw counts of total reads, parent1-derived reads, and parent2-derived reads respectively. Additionally, three matrices are provided: CPM_total_expression.txt contains CPM-normalized total expression data for all 1,437 libraries that passed QC checks (and were not controls). norm_maternal_counts.txt and norm_paternal_counts.txt contain maternal and paternal counts for the 4 DAP Col, Cvi dataset (excluding libraries with few allelic counts; N=748 total), respectively; this subset of the data was used for imprinting analyses. Maternal and paternal counts were normalized according to the procedure used in DESingle (Miao et al. 2018, Bioinformatics), separately for the Col x Cvi and the Cvi x Col dataset.

molecule: polyA RNA

source_name: seed nuclei

growth_protocol: All parent plants were grown in a growth chamber under 16h light at 50% relative humidity (16h at 22°C and 120μm light, 8h at 20°C and 0μm light).

extract_protocol:
Seeds were manually removed from siliques (~ 2 siliques per sample) into 50 uL Partec nuclei extraction buffer (Partec CyStain UV Precise P system), ground to release nuclei, DAPI stained by adding 400 uL Partec staining buffer, and filtered through a 30 um mesh. For the last four batches, nuclei were then washed 2x in 1:8 Partec extraction buffer:Partec staining buffer. Other batches did not include this was step. Single nuclei from the 3C or 6C peaks were sorted into a 96 well plate using fluorescence-activated nuclei sorting (FANS); each plate also included at least one negative control (no nucleus sorted into the well).
Libraries were prepared according the Smart-seq v2 protocol with a few minor variations and carried out at reduced volume. Nuclei were sorted into 1 μL lysis buffer (0.19% vol/vol Triton-X 100, 2U SUPERase RNase inhibitor, ERCC RNA spike-ins (ThermoFisher). 1 μL poly-A hybridization mix (final conc. 2.5mM/ea. dNTPs + 2.5 μM oligo-dT primer) was added to each well and the plate was incubated at 72°C 3 min before putting back on ice. 2.85 μL RT reaction mix (final concentration 1μM TSO, 1x Maxima RT buffer (Life Technologies), 1M betaine, 5 mM DTT, 6 mM MgCl2, 0.5 U SUPERase RNase-inhibitor, 2 U Maxima RT) was added and RT reaction was performed either in thermocycler with program 42°C 90', 10 x [50°C 2', 42°C 2'], 70°C 15' or in thermomixer. 7.5 μL pre-amp PCR mix (final conc. 1x KAPA HiFi HotStart Readymix (Kapa Biosystems), 0.1 μM IS PCR primer) was added and plate was incubated in thermocycler: 3' 98°C, [cycle #] x [98°C 20'', 67°C 15'', 72°C 6'], 72°C 5'. Number of pre- amplification cycles used varied between 18-21. cDNA was cleaned up using a 0.8x Ampure XP protocol (Beckman Coulter). Final libraries were built from successful cDNA preps using the Nextera XT kit (Illumina) with reduced volume (1/4 or 1/5 standard volumes). Up to 384 libraries were multiplexed together and sequenced on an Illumina HiSeq 2000 using a 40bp single-end protocol, or on an Illumina NextSeq using a 40x40bp paired-end protocol.

treatment_protocol: Plants were emasculated in the afternoon or evening, and pollinated in the morning two days later. Seeds were harvested either 2, 3, 4 or 5 days after pollination, at approximately the same time in the morning.

tag: female parent

value: Cvi

tag: male parent

value: Col

tag: days after pollination

tag: number of nuclei

tag: fans peak

tag: plate/batch

tag: extra wash steps?

value: yes

tag: control?

value: no


title: P22_12G


title: EaF82_OX_2-TB1

value: nptII


title: NZM9 (RNA-seq)

value: Skin

tag: cell line

value: Metastatic melanoma cell line NZM9

tag: phenotype


title: P22_12F


title: P22_12D


title: Tex14 homozygous mutant shallowly sequenced

city: San Francisco, CA

first: Rebecca

middle: Garrett

last: Jaszczak

address: 35 Medical Center Way, Room 913D

institute: UCSF

data_processing:
cellranger v2.1.0 was run using all default parameters with prebuild mm10 reference genome available from 10X-Genomics
Shallowly sequenced libraries: Seurat v3.1.X was used to select high quality cells and remove cell doublets using the following parameters: genes expressed in at least 3 cells, fewer than 25,000 unique fragments (to exclude cell doublets), greater than 200 genes expressed (to exclude GEMS with no cells), and cells with 7.0% or less mitochondrial gene expression, and cells with less than 0.5% hemogloblin gene expression, to exclude blood cells.
Deeply sequenced libraries: Seurat v3.1.X was used to select high quality cells and remove cell doublets using the following parameters: fewer than 30,000 unique fragments (to exclude cell doublets), greater than 1000 genes expressed (to exclude GEMS with no cells), and cells with 5.0% or less mitochondrial gene expression, cells with less than 0.25% hemoglobin gene expression (to exclude blood cells).
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text file containing a cell by gene raw count expression table

source_name: Embryonic Ovary

extract_protocol:
Tex14+/- and Tex14-/- ovaries were dissociated and the cells submitted for FACS to concentrate Oct4-GFP+ ovary germ cells. Samples were reecombined with Oct4-GFP- somatic cells. These cell populations were used to create two 10X Chromium Single Cell 3' (v2 Chemistry) single cell RNA sequencing libraries (Cat No: PN-120237, PN-1000009, PN-120262).
10X Chromium Single Cell 3' (v2 Chemistry) single cell RNA sequencing libraries (Cat No: PN-120237, PN-1000009, PN-120262) were created following published protocols available at https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v2-chemistry.

tag: strain

value: mixed

value: ovary

value: embryonic day 13.5

tag: genotype


title: P22_12E


title: NZM40 (RNA-seq)

value: Metastatic melanoma cell line NZM40


title: P22_12A


title: Tex14 heterogyous shallowly sequenced

description: Tex14 heterogyous shallowly sequenced


title: P22_12C


title: P22_12B


title: P22_11F


title: P22_11H


title: P22_11G


title: P22_11E


title: P22_11C


title: P22_11D


title: P22_11A


title: P22_10H


title: EaF82_OX_1-TA3

tag: genotype/variation

value: overexpressing EaF82

value: 6-8 week-old

value: cluster of unopened flower buds


title: P22_10F


title: NZM6 (RNA-seq)

value: Metastatic melanoma cell line NZM6

value: Invasive


title: hibHSC_SCF80

city: Cambridge

first: Daniel

last: Bode

email: db704@cam.ac.uk, 1danielbode@gmail.com

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus

department: Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i710_i510

data_processing:
Raw reads were aligned to the Mus musculus genome build (mm10) using GSNAP with parameters -B 5 -t 24 -n 1 -Q -N 1 (version 2015-09-29 for batch1 and batch2; version 2018-03-25 for batch3 and batch4).
Read counts were computed using HTSeq with parameter -s no (version 0.6.0  for batch1 and batch2; version 0.9.1 for batch3 and batch4).
Cells from which low-quality libraries with insufficient sequencing depths were generated were excluded by setting the threshold of number of mapped reads to >2*105, with mapped reads comprising nuclear genes, mitochondrial genes and ERCCs. A minimum threshold of 20% for reads mapping to known genes was set, in order to exclude empty wells and dead cells. In addition, the threshold for reads mapping to mitochondrial genes was >0.2, to ensure a minimum of 20% of reads to map to non-mitochondrial genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing raw counts for each sample (HT-Seq counts)

source_name: Bone marrow

growth_protocol: For hibernation cultures, Haematopoietic Stem Cells (HSCs), isolated from primary mouse bone marrow, were cultured in the presence of 20 ng/mL IL-11 but absence of Stem Cell Factor (SCF) and (TPO) to retain retain HSCs.

extract_protocol:
Haematopoietic Stem Cells (HSCs) were extracted from primary mouse bone marrow, derived from C57BL/6 mice(12-16 weks). For this purpose, lineage depleted bone marrow cells were FACS sorted. HSCs were defined as EPCR-high, CD45+, Sca-1-high, CD48-low/neg, CD150+ (ESLAM). HSCs cultured in hibernated conditions (hibHSCs), hibHSCs stimulted with SCF in culture (hibHSC_SCF), freshly isoalted HSCs (fresh_HSC) and fresh_HSCs stimulated with SCF (fresh_HSC_SCF) were sequenced. Cultured HSCs were FACS sorted to be deposited in 96 well plates (one cell per well), containing lysis buffer and subsequently processed using the previously described Smart-Seq2 protocol (Picelli et al., 2014).
Smart-Seq2 protocol performed as previously described (Picelli et al., 2014). Libraries were prepared using Illumina Nextera libraries, single end reads and 50bp read lengths. The pooled libraries were sequenced on an Illumina HiSeq 4000.

treatment_protocol: Samples including SCF labels were stimulated with Stem Cell Factor (SCF).

value: Bone marrow

value: 12-16 weeks

value: wild type

tag: batch


title: hibHSC_SCF78

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i706_i510

tag: age


title: hibHSC_SCF77

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i705_i510

tag: tissue


title: hibHSC_SCF82

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i712_i510


title: hibHSC_SCF68

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i710_i508


title: hibHSC_SCF79

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i707_i510


title: hibHSC_SCF76

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i704_i510


title: hibHSC_SCF69

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i711_i508


title: P22_10G

value: Cvi

value: Col

value: yes


title: P22_11B

value: no


title: hibHSC_SCF71

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i714_i508


title: P22_10E


title: hibHSC_SCF73

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i701_i510


title: P22_10C


title: P22_10B


title: hibHSC_SCF75

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i703_i510


title: P22_10D


title: P22_10A

value: yes - only water used for Nextera library prep


title: hibHSC_SCF60

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i715_i507


title: P22_9H


title: hibHSC_SCF61

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i701_i508


title: P22_9E


title: hibHSC_SCF81

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i711_i510


title: hibHSC_SCF63

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i703_i508


title: P22_9D


title: hibHSC_SCF64

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i704_i508


title: hibHSC_SCF70

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i712_i508


title: hibHSC_SCF65

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i705_i508


title: hibHSC_SCF62

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i702_i508


title: P22_9F


title: P22_9B


title: hibHSC_SCF66

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i706_i508


title: hibHSC_SCF74

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i702_i510


title: hibHSC_SCF83

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i714_i510


title: hibHSC_SCF51

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i703_i507


title: P22_9A


title: P22_8H


title: hibHSC_SCF67

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i707_i508


title: hibHSC_SCF52

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i704_i507


title: hibHSC_SCF53

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i705_i507


title: hibHSC_SCF59

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i714_i507


title: hibHSC_SCF72

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i715_i508


title: P22_8F


title: P22_8E


title: hibHSC_SCF54

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i706_i507


title: hibHSC_SCF55

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i707_i507


title: P22_9C


title: P22_9G


title: P22_8D


title: hibHSC_SCF56

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i710_i507


title: hibHSC_SCF57

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i711_i507


title: hibHSC_SCF58

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i712_i507


title: P22_8B


title: hibHSC117

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i719_i517


title: P22_8A


title: hibHSC116

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i718_i517


title: hibHSC115

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i716_i517


title: P22_7H


title: P22_7G


title: P22_7F


title: hibHSC114

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i722_i516


title: P22_7D


title: hibHSC113

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i721_i516


title: hibHSC112

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i720_i516


title: hibHSC111

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i719_i516


title: P22_8G


title: P22_7B


title: P22_6H


title: P22_7A

value: yes - no nucleus sorted


title: P22_6G


title: P22_8C


title: hibHSC124

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i720_i518


title: hibHSC123

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i719_i518


title: hibHSC110

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i718_i516


title: hibHSC125

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i721_i518


title: P22_6D


title: P22_7E


title: hibHSC120

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i722_i517


title: hibHSC119

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i721_i517


title: P22_6F


title: P22_6C


title: hibHSC121

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i716_i518


title: P22_6A


title: hibHSC103

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i716_i515


title: P22_5G


title: P22_6B


title: hibHSC102

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i722_i513


title: P22_7C


title: hibHSC101

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i721_i513


title: P22_5H


title: hibHSC108

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i722_i515


title: hibHSC100

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i720_i513


title: P22_5E


title: P22_5D


title: hibHSC122

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i718_i518


title: hibHSC106

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i720_i515


title: P22_5C


title: hibHSC109

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i716_i516


title: P22_6E


title: P22_5A


title: hibHSC107

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i721_i515


title: hibHSC118

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i720_i517


title: hibHSC104

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i718_i515


title: hibHSC_SCF94

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i712_i511


title: P22_4H


title: P22_4G


title: P22_4F


title: P22_5F


title: hibHSC_SCF95

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i714_i511


title: P22_4D


title: hibHSC_SCF92

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i710_i511


title: hibHSC98

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i718_i513


title: P22_4E


title: P22_4A


title: hibHSC99

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i719_i513


title: P22_4C


title: hibHSC_SCF93

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i711_i511


title: P22_3H


title: hibHSC_SCF96

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i715_i511


title: P22_4B


title: hibHSC_SCF86

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i702_i511


title: P22_3G


title: P22_5B


title: hibHSC97

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i716_i513


title: hibHSC_SCF87

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i703_i511


title: hibHSC105

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i719_i515


title: hibHSC_SCF84

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i715_i510


title: P22_3E


title: hibHSC_SCF85

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i701_i511


title: P22_3D


title: P22_3C


title: hibHSC_SCF90

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i706_i511


title: P22_2H


title: hibHSC_SCF88

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i704_i511


title: hibHSC_SCF89

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i705_i511


title: hibHSC_SCF16

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i704_i503


title: P22_2G


title: hibHSC_SCF18

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i706_i503


title: P22_2F


title: hibHSC_SCF15

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i703_i503


title: P22_2E


title: hibHSC_SCF17

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i705_i503


title: P22_2D


title: hibHSC_SCF12

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i715_i502


title: hibHSC_SCF11

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i714_i502


title: P22_2C


title: hibHSC_SCF14

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i702_i503


title: hibHSC_SCF13

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i701_i503


title: P22_1H


title: P22_1G


title: hibHSC_SCF91

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i707_i511


title: hibHSC_SCF8

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i710_i502


title: P22_1E


title: P22_3A


title: P22_3B


title: hibHSC_SCF7

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i707_i502


title: P22_1D


title: hibHSC_SCF3

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i703_i502


title: hibHSC_SCF9

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i711_i502


title: P22_1B


title: P22_1C


title: hibHSC_SCF6

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i706_i502


title: P22_2A


title: P21_12H


title: P21_12G


title: P22_1A


title: P22_1F


title: P21_12E


title: P21_12F


title: hibHSC_SCF50

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i702_i507


title: hibHSC_SCF10

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i712_i502


title: hibHSC_SCF49

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i701_i507


title: P21_12C


title: P21_12A


title: hibHSC_SCF4

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i704_i502


title: hibHSC_SCF45

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i711_i506


title: hibHSC_SCF47

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i714_i506


title: hibHSC_SCF46

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i712_i506


title: hibHSC_SCF48

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i715_i506


title: P21_11H


title: P21_11F


title: hibHSC_SCF1

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i701_i502


title: P21_11G


title: hibHSC_SCF5

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i705_i502


title: hibHSC_SCF43

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i707_i506


title: P21_11E


title: hibHSC_SCF44

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i710_i506


title: P21_11D


title: hibHSC_SCF42

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i706_i506


title: P21_11C


title: hibHSC_SCF41

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i705_i506


title: P21_12D


title: hibHSC_SCF40

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i704_i506


title: P21_11B


title: hibHSC_SCF39

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i703_i506


title: P21_11A


title: hibHSC_SCF37

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i701_i506


title: hibHSC_SCF38

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i702_i506


title: P21_10H


title: P21_10G


title: hibHSC_SCF2

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i702_i502


title: hibHSC_SCF36

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i715_i505


title: P21_12B


title: P21_10F


title: hibHSC_SCF33

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i711_i505


title: P21_10E


title: hibHSC_SCF35

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i714_i505


title: P21_10D


title: P21_10C


title: hibHSC_SCF34

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i712_i505


title: hibHSC_SCF31

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i707_i505


title: P21_10B


title: hibHSC_SCF29

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i705_i505


title: hibHSC_SCF32

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i710_i505


title: P22_2B


title: P21_9G


title: P21_10A


title: P21_9H


title: hibHSC_SCF30

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i706_i505


title: P21_9E


title: P21_9F


title: hibHSC_SCF28

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i704_i505


title: P21_9D


title: hibHSC_SCF27

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i703_i505


title: hibHSC_SCF24

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i715_i503


title: P21_9C


title: P21_9B


title: hibHSC_SCF25

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i701_i505


title: P21_9A


title: P21_8H


title: P21_8G


title: hibHSC_SCF19

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i707_i503


title: hibHSC_SCF22

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i712_i503


title: hibHSC_SCF23

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i714_i503


title: P21_8F


title: hibHSC_SCF21

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i711_i503


title: hibHSC_SCF20

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i710_i503


title: P21_8E


title: P21_8C


title: P21_8D


title: hibHSC_SCF119

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i728_i517


title: hibHSC_SCF26

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i702_i505


title: hibHSC_SCF121

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i723_i518


title: hibHSC_SCF118

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i727_i517


title: P21_8A


title: hibHSC_SCF120

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i729_i517


title: P21_7H


title: hibHSC_SCF123

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i726_i518


title: hibHSC_SCF122

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i724_i518


title: P21_7F


title: P21_7E


title: hibHSC_SCF125

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i728_i518


title: hibHSC_SCF111

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i726_i516


title: P21_7D


title: hibHSC_SCF110

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i724_i516


title: P21_7C


title: P21_7B


title: hibHSC_SCF112

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i727_i516


title: hibHSC_SCF113

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i728_i516


title: P21_6H


title: Oxford Nanopore Long read sequencing of Nuclear RNA from CASMC -Rep2

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

institute: UNIVERSITY OF EDINBURGH

data_processing:
Sequencing was performed using MinKNOWN 127.0.0.1 software using MinKNOW Core 3.6.5, Bream 4.3.16 and Guppy 3.210
Unprocessed reads were recovered using recover_reads command from MinKNOW
Base-calling was performed using Guppy (https://nanoporetech.com/).
Fastq reads were mapped to the human genome (GENCODE GRCh38 primary assembly fasta file) using minimap2 version 2.16 (Li Bioinformatics 2018).
Bam files were converted to bigWig using BEDTools version 2.27.1 (.bam to .bg) and UCSC Genome browser utilities version326 (.bg to .bw)
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig

source_name: CASMC

growth_protocol: Human Coronary Arterial Smooth Muscle Cells (hCASMS), purchased from Lonza (Basel, Switzerland), were cultured in Smooth Muscle Cells Growth Medium 2 (PromoCell) supplemented with 10% foetal bovine serum (Life Technologies, Paisley, UK), Supplement (PromoCell), 50μg/mL penicillin and 50μg/mL streptomycin (Gibco, Paisley, UK) and L-glutamin (Gibco, Paisley, UK). Cells were maintained in culture in humidified atmosphere 37°C (5% CO2) and used between passages 2-6.

extract_protocol:
Nuclear RNA was extracted using the PARIS™ Kit (Thermo Fisher).
Libraries were prepared using cDNA-PCR Sequencing kit from Oxford Nanopoire Technologies (SQK-PCS109) following manufacturer’s instructions. Briefly, ribosomal RNA depletion was performed with Ribominus Eukaryote System V2 (Thermo Fisher) and 296ng of RNA was used for polyadenylation step using Lucigen Poly(A) Polymerase Tailing Kit (Lucigen). Following RNA purification with Agencourt RNA cleanup XP Kit (Beckman Coulter), 5ng of polyadenylated RNA was used for Nanopore library preparation using cDNA-PCR Sequencing kit (SQK-PCS109) and sequenced using Oxford Nanopore Technologies’ (ONT) MinION sequencer using FLO-MIN106 flow cell.
Oxford Nanopore Technology sequencing- MinION

tag: cell type

value: coronary artery smooth muscle cells (CASMCs)

tag: replicate

tag: molecule type

value: nuclear RNA


title: hibHSC_SCF124

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i727_i518


title: hibHSC_SCF115

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i723_i517


title: P21_7A

tag: female parent

tag: male parent

tag: days after pollination


title: P21_8B

tag: number of nuclei

tag: fans peak

tag: plate/batch


title: hibHSC_SCF114

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i729_i516


title: P21_6F

tag: extra wash steps?

tag: control?


title: Oxford Nanopore Long read sequencing of Nuclear RNA from CASMC -Rep1


title: P21_6D


title: P21_6C


title: P21_6E


title: P21_7G


title: P21_6B


title: Min6 C1

type: protein

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing: Normalization and interrun calibration were performed as described elsewhere (http://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf) In brief, correction for systematic effects on the data introduced during the hybridization step, median normalization within an array, and calibration between plates were performed.

molecule: protein

extract_protocol: Primary beta-cells or Min6 cells were culture in serum-free medium and used conditioned media were collected.

value: Min6 cells

tag: treatment

value: Control


title: hibHSC_SCF116

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i724_i517

tag: strain

tag: genotype


title: P21_5G


title: P21_5F


title: P21_5C


title: P21_5H


title: P21_6A


title: hibHSC_SCF136

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i727_i521

tag: batch


title: P21_5D


title: hibHSC_SCF134

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i724_i521

tag: age


title: hibHSC_SCF135

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i726_i521

tag: tissue


title: P21_4G


title: P21_5E


title: P21_4H


title: P21_6G


title: P21_4E


title: P21_4F


title: Bgal-Exp 3

source_name: Bgal-

tag: cell type

value: Primary beta-cells

value: beta cells


title: Min6 C2


title: hibHSC_SCF139

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i723_i522


title: hibHSC_SCF138

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i729_i521


title: hibHSC_SCF137

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i728_i521


title: Min6 B7

value: Bleomycin


title: P21_5B


title: Bgal+Exp 5

source_name: Bgal+


title: Min6 B2


title: Min6 B6


title: Min6 B3


title: hibHSC_SCF117

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i726_i517


title: Min6 B1


title: P21_5A


title: P22_3F


title: P21_4D


title: P21_4B


title: P21_4A


title: P21_4C


title: hibHSC_SCF141

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i726_i522


title: P21_3H


title: hibHSC_SCF140

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i724_i522


title: Bgal-Exp 4


title: Min6 C3


title: P21_3F


title: hibHSC_SCF127

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i723_i520


title: hibHSC_SCF128

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i724_i520


title: P21_3E


title: hibHSC_SCF129

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i726_i520


title: P21_3G


title: P21_3C


title: hibHSC_SCF130

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i727_i520


title: P21_3D


title: Bgal+Exp 1


title: P21_3B


title: P21_2G


title: P21_3A


title: Min6 C7


title: Bgal+


title: hibHSC_SCF131

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i728_i520


title: Bgal+Exp 4


title: P21_2F


title: P21_2E


title: hibHSC_SCF126

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i729_i518


title: P21_2D


title: hibHSC_SCF132

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i729_i520


title: P21_2B


title: hibHSC_SCF133

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i723_i521


title: P21_2A


title: P21_2H


title: hibHSC137

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i721_i521


title: P21_1H

value: yes - two nuclei sorted in same well


title: P21_1G


title: hibHSC136

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i720_i521

value: Bone marrow


title: P21_1F


title: P21_1E


title: hibHSC135

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i719_i521

value: 12-16 weeks


title: P21_1C


title: P21_1B


title: P20_12H


title: P21_2C


title: hibHSC134

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i718_i521

value: wild type


title: P20_12G

value: Cvi


title: P21_1A


title: Bgal-


title: P20_12F

value: Col


title: Bgal+Exp 2


title: Bgal-Exp 1


title: Min6 B5


title: Bgal+Exp 3


title: Bgal-Exp 2


title: Bgal-Exp 5


title: Min6 C5


title: P20_12E

value: yes


title: P20_12D

value: no


title: P21_1D


title: P20_12C


title: hibHSC139

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i716_i522


title: P20_12B


title: hibHSC138

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i722_i521


title: P20_12A


title: Min6 B4


title: Bgal+Exp 6


title: P20_11H


title: hibHSC141

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i719_i522


title: P20_11G


title: Min6 C6


title: hibHSC129

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i719_i520


title: P20_11F


title: hibHSC128

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i718_i520


title: hibHSC140

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i718_i522


title: Bgal-Exp 6


title: P20_11E


title: hibHSC133

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i716_i521


title: hibHSC126

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i722_i518


title: hibHSC127

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i716_i520


title: P20_11D


title: P20_11C


title: P20_10H


title: P20_11B


title: P20_10G


title: P20_11A


title: Min6 C4


title: V615_RNASeq

city: College Station

first: Monique

last: Rijnkels

state: Texas

address: 660 Raymond Stotzer Pkway

department: Department of Veterinary Integrative Biosciences

institute: Texas A&M University

data_processing:
aligned with HISAT2 v 2.0, using options  --rna-strandness RF --dta
converted to sorted bam using samtools
aligned reads were assembled into transcripts using Stringtie (version 1.3.2) including information on strandedness of reads with the reference annotation Ensembl v87 for the genome assembly UMD3.1 (ftp://ftp.ensembl.org/pub/release-87).
the resulting gtf annotation files for all samples were merged into a final gtf annotation file using the Stringtie merge option.
assigned transcripts to existing Ensembl 87 annotations with Gffcompare
counted reads per feature with featureCounts (Liao et al. 2014), v.1.5.2 Subread package, default settings
differential expression analysis on features with at least 10 reads in at least 4 samples (as determined by feature counts) in edgeR. Statistical significance of difference between virgin and lactating stages evaluated with a linear model, likelihood ratio test, and Bonferroni correction.
Genome_build: Bos taurus UMD 3.1
Supplementary_files_format_and_content: tab delimited text file of read counts for every feature with an identified Ensembl87 annotation in all samples
Supplementary_files_format_and_content: tab delimited text file containing sample RPKM, log 2 fold change (virgin / lactating), and corrected p values for every feature with an identified Ensembl87 annotation.

organism: Bos taurus

source_name: Mammary epithelial organoids

extract_protocol:
Tissue was minced to a fine slurry in freshly prepared Collagenase solution (0.2% Collagenase A (Roche), 0.05% Trypsin (1:250 powder, 100U/ ml  Gibco/life sciences), Hyaluronidase (Sigma, St Louis MO), 5% Fetal Calf serum, Pen/Strep/Fung (hyclone) or 5µg/ml Gentamycin (Sigma), in DMEM/F12 (Gibco/Life technologies) 10 ng/ml Insulin). Minced tissue was incubated in Collagenase solution (10 ml solution/g tissue) for 3.5 hours at 37C in 50 ml conical tube with slow shaking (120 rpm). Digested tissue was centrifuged for 10 minutes at 453xg at 4°C, supernatant and fat layer discarded, pellet was gently resuspended by pipetting in 5 ml DMEM/F12 without serum. A further 5 ml DMEM/F12 without serum was added and resuspended sample was centrifuged for 10 minutes at 453xg at 4°C, media was discarded and pellet resuspended gently in 10 ml DMEM/F12 and centrifuged for 10 minutes at 453xg at 4°C . Pellet was resuspend gently in 10 ml followed by brief pulls spins at 453xg (centrifuge set to 1 minute @ 453 x g, hit the brakes 2 seconds after 453 xg is reached). Pulls spins were repeated at least 4 time or until very few single cells and mainly epithelial organoid clusters were observed under a microscope. Organoid pellet for RNA-analysis was resuspended in 1 ml TRIzol and stored at -80C.   To Isolate RNA, Macherey-Nagel NucleoSpin miRNA kit for isolation of small and Large RNA was used according to manufacturers protocol (November 2011/rev.02). RNA was analyzed on Bioanlayzer (Agilent) all  RIN were ≥7.5 and stored at -80C till further use.
Whole-transcriptome RNA sequencing (RNA-seq) was performed using high quality total RNA (RIN>7) extracted from mammary epithelial organoids to prepare strand-specific, poly-A+ RNA-seq libraries for sequencing on the Illumina platform. To monitor sample and process variability, in addition to sequence metrics, RNA developed by the External RNA Controls Consortium (ERCC) which consists of a mix of 92 polyadenylated RNA transcripts was also added to total RNA at the beginning of the library preparation.  Briefly, poly-A+ mRNA was extracted from 1 μg total RNA using Oligo(dT)25 Dynabeads (Life Technologies, Cat. No. 61002) followed by fragmentation of the mRNA by heat at 94oC for 6 minutes. First strand cDNA was synthesized using the Superscript III reverse transcriptase (Life Technologies, Cat. No. 18080-044) and purified using Agencourt RNAClean XP beads (Beckman Coulter, Cat. No. A63987). During second strand cDNA synthesis, dNTP mix containing dUTP was used to introduce strand-specificity.  For Illumina paired-end library construction, the resultant cDNA was processed through end-repair and A-tailing, ligated with Illumina PE adapters, and then digested with 10 units of Uracil-DNA Glycosylase (NEB, Cat. No. M0280L).  Amplification of the libraries was performed for 13-14 PCR cycles using the Phusion High-Fidelity PCR Master Mix (NEB, Cat. No. M0531L); twelve such 6-bp molecular barcodes were also incorporated during this PCR amplification. The cDNA was purified with Agencourt AMPure XP beads after each enzymatic reaction, and after quantification using the Agilent Bioanalyzer 2100 DNA Chip 7500 (Cat. No. 5067-1506), libraries were pooled in equimolar amounts (6-7 libraries/pool).  The library pools were then loaded onto a HiSeq flowcell lane, and following amplification with Illumina’s cBot cluster generation system, sequencing runs were performed in paired-end mode (2 x 100-bp reads) using the Illumina HiSeq2000 platform. On average, 67 million reads were generated per sample.

tag: mammary develpoment stage

value: virgin


title: V595_RNASeq


title: P20_10C


title: P20_10E


title: P20_10D


title: hibHSC132

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i722_i520


title: P20_10B


title: V538_RNASeq


title: V531B_RNASeq


title: P20_10F


title: hibHSC131

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i721_i520


title: P20_10A

value: yes - only water used for Nextera library prep


title: hibHSC_SCF105

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i726_i515


title: P20_9H


title: hibHSC_SCF104

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i724_i515


title: P20_9G


title: P20_9D


title: P20_9C


title: hibHSC130

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i720_i520


title: P20_9F


title: hibHSC_SCF102

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i729_i513


title: P20_9E


title: V581_RNASeq


title: P20_8G


title: P20_8H


title: P20_9A


title: hibHSC_SCF108

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i729_i515


title: P20_8F


title: V479_RNASeq


title: hibHSC_SCF109

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i723_i516


title: hibHSC_SCF103

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i723_i515


title: P20_8D


title: V490_RNASeq


title: hibHSC_SCF106

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i727_i515


title: P20_8C


title: P20_8B


title: P20_8A


title: hibHSC_SCF107

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i728_i515


title: P20_7G


title: P20_7H


title: P20_7F


title: hibHSC144

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i722_i522


title: P20_7E


title: P20_9B


title: P20_7D


title: hibHSC142

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i720_i522


title: P20_7B


title: P20_7C


title: hibHSC143

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i721_i522


title: P20_7A

value: yes - no nucleus sorted


title: hibHSC_SCF97

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i723_i513


title: P20_8E


title: L615_RNASeq

value: lactating


title: P20_6H


title: P20_6G


title: P20_6F


title: hibHSC_SCF101

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i728_i513


title: hibHSC_SCF98

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i724_i513


title: L538_RNASeq


title: L531_RNASeq


title: P20_6C


title: P20_6B


title: P20_6A


title: P20_5H


title: hibHSC_SCF99

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i726_i513


title: P20_5G


title: P20_5F


title: hibHSC_SCF143

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i728_i522


title: hibHSC_SCF100

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i727_i513


title: P20_5E


title: P20_5D


title: P20_5C


title: V478A_RNASeq


title: hibHSC_SCF142

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i727_i522


title: P20_5A


title: P20_6D


title: fresh_HSC237

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i728_i517


title: L581_RNASeq


title: P20_4H


title: P20_6E


title: fresh_HSC238

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i729_i517


title: L495_RNASeq


title: fresh_HSC233

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i723_i517


title: P20_5B


title: P20_4F


title: L490_RNASeq


title: P20_4E


title: hibHSC_SCF144

description:
HTSeq_counts_SLX16046_batch4.txt.gz
SLX_16046.i729_i522


title: L479_RNASeq


title: fresh_HSC234

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i724_i517


title: P20_4D


title: P20_4C


title: P20_4A


title: L595_RNASeq


title: fresh_HSC235

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i726_i517


title: P20_3H


title: fresh_HSC236

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i727_i517


title: P20_3G


title: P20_3F


title: fresh_HSC229

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i719_i517


title: P20_4G


title: PANC-1-siS100A16-3

city: Kunming

first: Hongjin

last: Wu

state: China / Yunnan

address: Xichang Road#295

institute: The NHC Key Laboratory of Drug Addiction Medicine

data_processing:
RNA-seq data were aligned to the human reference genome (GrCH37, Ensembl build 74) using Tophat version 2.0.12.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Gene expression levels, which are represented as fragments per kilo-base per million mapped reads (FPKM), were obtained for 63,783 genes/transcripts annotated using Ensemble GrCH37 database release 74.
Genome_build: human reference genome (GrCH37, Ensembl build 74)
Supplementary_files_format_and_content: All_gene_fpkm.xlsx file includes FPKM values for each Sample

source_name: human cancer cell line

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

tag: cell line

value: S100A16 siRNA transfected

value: S100A16  knockdown


title: fresh_HSC230

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i720_i517


title: PANC-1-siS100A16-2


title: P20_3E

tag: female parent


title: fresh_HSC231

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i721_i517


title: PANC-1-siS100A16-1


title: fresh_HSC232

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i722_i517


title: P20_3A

tag: male parent


title: P20_2H

tag: days after pollination


title: PANC-1-siMYEOV-3

value: MYEOV siRNA transfected

value: MYEOV  knockdown


title: P20_4B

tag: number of nuclei


title: L478_RNASeq


title: PANC-1-siMYEOV-2


title: P20_2G

tag: fans peak


title: fresh_HSC225

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i728_i516


title: P20_2F

tag: plate/batch


title: PANC-1-siMYEOV-1


title: P20_2E

tag: extra wash steps?


title: P20_2D

tag: control?


title: P20_2C


title: PANC-1-siKCNN4-3

tag: treatment

value: KCNN4 siRNA transfected

value: KCNN4  knockdown


title: fresh_HSC226

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i729_i516

tag: strain

value: Bone marrow


title: P20_2B


title: P20_3D


title: PANC-1-siKCNN4-2

tag: genotype


title: P20_2A


title: P20_3B


title: P20_1H

value: yes - two nuclei sorted in same well


title: P20_3C


title: P20_1G


title: fresh_HSC227

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i716_i517

value: 12-16 weeks

value: wild type

tag: batch


title: PANC-1-siKCNN4-1


title: hibHSC1

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i701_i502

tag: age


title: fresh_HSC228

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i718_i517

tag: tissue


title: P20_1F

value: Col

value: Cvi


title: PANC-1-siDDX60L-3

value: DDX60L siRNA transfected

value: DDX60L  knockdown


title: P20_1D

value: yes

value: no


title: P20_1E


title: fresh_HSC198

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i724_i513


title: PANC-1-siDDX60L-2


title: fresh_HSC197

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i723_i513


title: P20_1B


title: PANC-1-siDDX60L-1


title: fresh_HSC200

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i727_i513


title: PANC-1-siControl-3

value: Control siRNA transfected

value: Control


title: P19_12G


title: P19_12H


title: PANC-1-siControl-2


title: P19_12D


title: P19_12F


title: fresh_HSC199

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i726_i513


title: fresh_HSC194

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i720_i513


title: P19_12C


title: PANC-1-siControl-1


title: fresh_HSC196

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i722_i513


title: P19_12A


title: MiaPaCa2-siS100A16-2

value: S100A16 siRNA transfected

value: S100A16  knockdown


title: fresh_HSC195

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i721_i513


title: P19_11G


title: P20_1C


title: P19_11H


title: P19_11F


title: P19_12E


title: P19_11E


title: P20_1A

value: yes - no nucleus sorted


title: fresh_HSC206

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i720_i515


title: MiaPaCa2-siS100A16-1


title: P19_11D


title: fresh_HSC205

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i719_i515


title: P19_11C


title: MiaPaCa2-siMYEOV-3

value: MYEOV siRNA transfected

value: MYEOV  knockdown


title: fresh_HSC208

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i722_i515

value: Bone marrow


title: P19_11B


title: P19_11A


title: P19_10H


title: P19_10G


title: MiaPaCa2-siMYEOV-1


title: MiaPaCa2-siS100A16-3


title: P19_10F


title: fresh_HSC207

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i721_i515


title: P19_12B


title: fresh_HSC202

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i729_i513


title: MiaPaCa2-siKCNN4-2

value: KCNN4 siRNA transfected

value: KCNN4  knockdown


title: fresh_HSC201

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i728_i513

value: 12-16 weeks

value: wild type


title: MiaPaCa2-siKCNN4-3


title: MiaPaCa2-siKCNN4-1


title: fresh_HSC204

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i718_i515


title: P19_10A

value: yes - only water used for Nextera library prep


title: P19_10E

value: Cvi

value: Col


title: fresh_HSC203

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i716_i515


title: P19_10D

value: yes


title: P19_9F

value: no


title: P19_9H


title: MiaPaCa2-siMYEOV-2


title: P19_9E


title: P19_9G


title: P19_9D


title: fresh_HSC214

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i729_i515


title: P19_9C


title: fresh_HSC213

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i728_i515


title: MiaPaCa2-siDDX60L-1

value: DDX60L siRNA transfected

value: DDX60L  knockdown


title: P19_9A


title: fresh_HSC215

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i716_i516


title: P19_8H


title: P19_8G


title: fresh_HSC216

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i718_i516


title: P19_10C


title: P19_9B


title: fresh_HSC209

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i723_i515


title: MiaPaCa2-siDDX60L-3


title: MiaPaCa2-siControl-2

value: Control siRNA transfected

value: Control


title: fresh_HSC210

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i724_i515


title: P19_8E


title: MiaPaCa2-siControl-1


title: P19_8D


title: P19_8C


title: PDAC tissue 3

data_processing:
RNA-seq data were aligned to the human reference genome (GrCH37, Ensembl build 74) using Tophat version 2.0.12.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Gene expression levels, which are represented as fragments per kilo-base per million mapped reads (FPKM), were obtained for 63,783 genes/transcripts annotated using Ensemble GrCH37 database release 74.
Genome_build: human reference genome (GrCH37, Ensembl build 74)
Supplementary_files_format_and_content: PDAC-tissue-ExpressionMatrix.csv  file includes FPKM values for each Sample

source_name: human pancreas

extract_protocol:
Following resection, the tumor tissues were examined by a pathologist and then placed in cryotubes with RNAlater reagent and frozen in liquid nitrogen. Samples were transported on dry ice, and stored at -80 ºC. Total RNA was isolated using RNeasy mini (Qiagen) according to the manufacturer's protocol. The quantity and quality of the samples were assessed using NanoDrop 2000 spectrophotometer and Agilent 2100 Bioanalyzer, respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pancreatic cancer tissues

tag: pathologic types

value: Cancer


title: P19_8F


title: P19_8B


title: MiaPaCa2-siDDX60L-2


title: P19_7H


title: P19_8A


title: PDAC tissue 2


title: fresh_HSC212

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i727_i515


title: fresh_HSC211

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i726_i515


title: P19_10B


title: MiaPaCa2-siControl-3


title: P19_7F


title: P19_7E


title: PDAC tissue 1


title: fresh_HSC221

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i723_i516


title: Normal pancreas tissue 3

value: Pancreatic adjacent tissues

value: Adjacent


title: P19_7D


title: P19_7C


title: fresh_HSC222

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i724_i516

value: Bone marrow


title: Normal pancreas tissue 2


title: P19_6H


title: P19_7A

value: yes - no nucleus sorted


title: Normal pancreas tissue 1


title: fresh_HSC223

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i726_i516

value: 12-16 weeks


title: fresh_HSC224

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i727_i516

value: wild type


title: P19_6D


title: P19_6G


title: P19_6E


title: P19_6C


title: P19_6F


title: fresh_HSC217

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i719_i516


title: P19_6B


title: NP550

city: Hong Kong

first: Hung On Ken

last: Yu

address: Department of Anatomical and Cellular Pathology, Faculty of Medicine

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
The six raw data files in each sample were generated from psirc's identification of BSJs and potential full-length transcript isoforms parts, implemented in psirc_v1.0.pl, which uses (as the only dependency) a forked version of kallisto v0.43.1, taking as input paired-end rRNA depletion RNA-seq data.
The processed data file contains the expression levels of all expressed isoforms in each of the 15 samples. The expression levels were computed from psirc's expression quantification of full-length transcript isoforms part, psirc-quant v1.0, which takes as input a sample's "full_length_isoforms.fa" (one of the included raw data files). After each sample is individually run, the outputs are directly merged using a simple custom script to create the processed data file.
The other (five) raw data files (which are not needed to quantify the expression levels) are still included here as they are required to reproduce various results and supplementary files in the manuscript.
For a given sample, the psirc workflow can go from paired-end RNA-seq fastq to full_length_isoforms.fa (and the other five raw data files) in one step, and from full_length_isoforms.fa to the final quantification result in one additional step.
For more details and a tutorial of running psirc, see https://github.com/Christina-hshi/psirc
Genome_build: hg38
Supplementary_files_format_and_content: Table of the expression levels of all expressed isoforms in each of the 15 samples, where rows are isoform names and columns are sample names

source_name: Normal nasopharynx

extract_protocol:
Total RNA extracted from the NP and NPC samples were subjected to rRNA depletion by Ribo-Zero kit (Illumina)
TruSeq stranded total RNA library construction and sequencing on the Illumina Hi-seq2000 system according to the manufacturer's protocols


title: NP460


title: P19_5G


title: fresh_HSC218

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i720_i516


title: P19_5F


title: P19_6A


title: fresh_HSC219

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i721_i516


title: P19_5H


title: hibHSC75

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i703_i510


title: NPC-M2

description: Tumor specimen

source_name: Nasopharyngeal carcinoma

value: Nasopharyngeal carcinoma


title: NP361


title: fresh_HSC220

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i722_i516


title: NP69


title: P19_5E

value: Cvi


title: NPC-M1

description: Tumor specimen


title: P19_5C

value: Col


title: hibHSC74

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i702_i510


title: P19_5B

value: yes


title: hibHSC73

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i701_i510


title: Xeno-99186

description: Xenograft


title: P19_5A

value: no


title: P19_4H


title: Xeno-2117

description: Xenograft


title: P19_4G


title: P19_4F


title: hibHSC72

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i715_i508


title: P19_5D


title: P19_4D


title: Xeno-666

description: Xenograft


title: P19_4E


title: Xeno-1915

description: Xenograft


title: Xeno-32

description: Xenograft


title: P19_4A

value: yes - only water used for Nextera library prep


title: P19_7G


title: C17

description: Xenograft


title: hibHSC69

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i711_i508


title: P19_3F


title: P19_3E


title: C15

description: Xenograft


title: hibHSC68

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i710_i508


title: P19_3G


title: hibHSC83

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i714_i510


title: P19_3D


title: P19_3B


title: NPC43


title: hibHSC81

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i711_i510


title: hibHSC82

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i712_i510


title: C666-1


title: P19_3C


title: P19_3A


title: P19_4B


title: hibHSC70

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i712_i508


title: P19_2H


title: hibHSC71

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i714_i508


title: P19_4C


title: P19_3H


title: hibHSC80

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i710_i510


title: P19_2G


title: P19_2E


title: THP-1, ETS1, 24 h 1,25(OH)2D3, replicate 2

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description: Chromatin IP against ETS1

data_processing:
Alignment to hg19 using Bowtie v1.0 parameters: -n 1 – k 1 -m 1 -l 32 -t -q –best
Peak discovery using MACS2 parameters: -m 5 50 –bw 150
Genome_build: hg19
Supplementary_files_format_and_content: tdf (merged two replicates)

source_name: human monocytic cell line THP-1

growth_protocol: THP-1 human monocytic leukemia cells were grown in RPMI 1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and the cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
proteins were crosslinked with formaldehyde to DNA, then ETS1-bound fragments were pulled down by chromatin immunoprecipitation
ChIP-seq library was prepared from 5-10 ng ChIP DNA with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) per manufacturer's protocol

treatment_protocol: Treated with EtOH or 100 nM 1,25(OH)2D3 for 24 h

tag: cell type

tag: chip antibody

value: Ets-1 (C-20) (Santa Cruz sc-350 X)

tag: treatment protocol


title: EBV-infected NP-H10 in ALI

city: PITTSBURGH

first: Yulong

last: Bai

state: Pennsylvania

address: Public Health Building, 130 De Soto St,, 3121

department: Human Genetics

institute: University of Pittsburgh

data_processing:
The original data obtained from Illumina HiSeq platform are transformed to sequenced reads by base calling. Raw data are recorded in FASTQ files.
The reads were aligned to a concatenation of the human (GRCh38.90) and EBV Akata strain (KC207613.1) genomes and quantified using CellRanger (version 3.0.2). The Cell Ranger pipeline only counts reads that map to exons. In the original EBV genome annotation (KC207813.1) only 13 genes had exon annotations. Exon coordinates were added using available CDS coordinates (71 genes) in the EBV genome annotation (KC207813.1), and when unavailable (3 genes: BSLF1, BBLF2/BBLF3, BALF3) gene coordinates were used.
R package Seurat (3.1.4) was used to implement cell-wise cleaning. Cells that meet the following filtering criteria were used for downstream analysis: total number of detected genes > 500, percentage of mitochondrial genes < 25%, percentage of hemoglobin genes <  0.025%, percentage of ribosomal genes < 40%, and total number of reads count > 1000. 3328 out of 4553 sequenced cells met the filtering criteria.
Genome_build: Concatenation of the Human (GRCh38.90) and the EBV Akata strain (KC207613.1) genomes (https://github.com/TangLabGOT/Reference-Genomes)
Supplementary_files_format_and_content: h5 files generated by CellRanger (version 3.1.0) including the filtered count matrix

source_name: nasopharynx

extract_protocol:
fresh (never frozen) single cell suspension
10X Genomics 3'v3 chemistry

tag: cell type source

value: Primary nasopharynx-derived epithelial cells

tag: cell source

value: Donor NP-H10

value: infected with recombinant EBV (Akata strain)


title: P19_2F

tag: female parent

tag: male parent

tag: days after pollination

tag: number of nuclei


title: hibHSC79

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i707_i510


title: P19_2C

tag: fans peak

tag: plate/batch

tag: extra wash steps?

tag: control?


title: THP-1, ETS1, 24 h EtOH, replicate 2

description: Chromatin IP against ETS1

value: 24 h EtOH


title: hibHSC78

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i706_i510

tag: strain

tag: genotype

tag: batch


title: P19_2A


title: P19_2D


title: P19_1H

value: yes - two nuclei sorted in same well


title: P19_2B


title: hibHSC77

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i705_i510

tag: tissue

tag: age


title: THP-1, ETS1, 24 h EtOH, replicate 1

description: Chromatin IP against ETS1

tag: cell type

tag: chip antibody


title: P19_1G


title: THP-1, ETS1, 24 h 1,25(OH)2D3, replicate 1

description: Chromatin IP against ETS1

tag: treatment protocol


title: P19_1F


title: P19_1E


title: hibHSC76

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i704_i510


title: P19_1D


title: TEX_10d_WY332_25uM_3

city: Ann Arbor

first: Tomasz

last: Cierpicki

state: MI

address: 1150 W Medical Center Dr

department: Pathology

institute: University Of Michigan

description:
TEX10dWY33225uM3
TEX cells treated with 25uM WY332 for 10 days

data_processing:
Basecalls performed using CASAVA-1.8.2
Sequenced reads were aligned to the hg19 genome assembly using Tophat2 and Bowtie with default settings
Read count was generated using HTseq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

growth_protocol: TEX cells were plated in the 12-well plates at the initial concentration of 0.2x106 cells/ml and treated with 25μM RB-3 or DMSO (0.25%) in triplicates

extract_protocol:
Total RNA was isolated from cells using RNeasy kit (Qiagen), amplified, and quality was assessed using the TapeStation (Agilent).
Samples with RINs (RNA Integrity Numbers) of 8 or greater were prepped using the Illumina TruSeq mRNA kit (Illumina). RNA was converted to mRNA using a polyA purification. cDNA library was created using reverse transcriptase, barcoded and sequenced using 4 samples per lane on a HiSeq 2000 (Illumina) in High Output mode

treatment_protocol: After 4 days of treatment viable cell number was adjusted to the original concentration in the DMSO treated samples and the same dilution factor was used to adjust cell number in the RB-3 treated cells. Media was changed and compound or DMSO was re-supplied at that time. Cells were harvested after 6 and 10 days of incubation

tag: cell line

value: TEX

tag: treatment

tag: dose

tag: time

value: 10 days


title: TEX_10d_WY332_25uM_2

description:
TEX10dWY33225uM2
TEX cells treated with 25uM WY332 for 10 days


title: hibHSC91

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i707_i511

value: Bone marrow


title: P19_1B

tag: female parent

tag: male parent

tag: days after pollination

tag: number of nuclei


title: TEX_10d_WY332_25uM_1

description:
TEX10dWY33225uM1
TEX cells treated with 25uM WY332 for 10 days


title: P19_1C

tag: fans peak

tag: plate/batch

tag: extra wash steps?

tag: control?


title: hibHSC88

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i704_i511

tag: strain

tag: tissue

value: 12-16 weeks

tag: genotype

tag: batch


title: P19_1A

value: yes - no nucleus sorted


title: P18_12H


title: P18_12G


title: TEX_10d_DMSO_3

description:
TEX10dDMSO3
TEX cells treated with DMSO for 10 days

value: DMSO


title: P18_12F

value: Cvi


title: hibHSC89

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i705_i511

tag: age

value: wild type


title: P18_12E

value: Col


title: TEX_10d_DMSO_1

description:
TEX10dDMSO1
TEX cells treated with DMSO for 10 days

tag: cell line


title: P18_12D

value: no


title: hibHSC86

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i702_i511


title: P18_12B


title: hibHSC87

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i703_i511


title: P18_12C


title: TEX_10d_DMSO_2

description:
TEX10dDMSO2
TEX cells treated with DMSO for 10 days

tag: treatment


title: hibHSC90

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i706_i511


title: TEX_6d_WY332_25uM_3

description:
TEX6dWY33225uM3
TEX cells treated with 25uM WY332 for 6 days

tag: dose

value: 6 days


title: TEX_6d_WY332_25uM_2

description:
TEX6dWY33225uM2
TEX cells treated with 25uM WY332 for 6 days

tag: time


title: P18_11G

tag: female parent


title: P18_11H

tag: male parent


title: hibHSC85

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i701_i511


title: P18_11F

tag: days after pollination


title: P18_11E

tag: number of nuclei


title: TEX_6d_DMSO_3

description:
TEX6dDMSO3
TEX cells treated with DMSO for 6 days


title: P18_11D

tag: fans peak


title: P18_11C

tag: plate/batch


title: fresh_HSC193

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i719_i513


title: TEX_6d_DMSO_2

description:
TEX6dDMSO2
TEX cells treated with DMSO for 6 days


title: P18_11B

tag: extra wash steps?


title: hibHSC96

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i715_i511


title: fresh_HSC192

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i718_i513


title: TEX_6d_DMSO_1

description:
TEX6dDMSO1
TEX cells treated with DMSO for 6 days


title: P18_11A

tag: control?


title: TEX_6d_WY332_25uM_1

description:
TEX6dWY33225uM1
TEX cells treated with 25uM WY332 for 6 days


title: hibHSC84

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i715_i510

tag: strain


title: P18_10H


title: fresh_HSC191

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i716_i513

tag: tissue


title: P18_10G


title: hibHSC94

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i712_i511

tag: genotype


title: P18_10C


title: P18_10E


title: P18_10D


title: hibHSC95

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i714_i511

tag: batch


title: hibHSC92

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i710_i511

tag: age


title: P18_10A

value: yes - only water used for Nextera library prep


title: P18_9H


title: 5hmC_tumor-3

city: Atlanta

first: Peng

last: Jin

state: Georgia

address: 615 Michael St., Rm 325

institute: Emory University

description: 5hmC Profiling (hMe-Seal)

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie version 0.12.9 with the standard parameters.
Peaks were called using MACS version 1.4.2 with the following setting: BW (200), GSIZE (hs).
Supplementary_files_format_and_content: Peaks called by MACS in bed format

source_name: Brain Tissues

extract_protocol:
DNA was isolated from brain tissues and used for 5hmC capture (hMe-Seal)
25ng of input genomic DNA or experimental enriched DNA were utilized for each library construction. 150-300 bp DNA fragments were selected by AMPure XP Beads (Beckman Coulter) after the adapter ligation. An Agilent 2100 BioAnalyzer was used to quantify the amplified DNA, qPCR was applied to accurately quantify the library concentration. libraries diluted to 6-8 pM were used for sequencing. 38-cycle single end sequencings were performed using Illumina HISeq 2000. Image processing and sequence extraction were done using the standard Illumina Pipeline.

tag: tissue type

value: medulloblastoma tumor


title: 5hmC_tumor-2

description: 5hmC Profiling (hMe-Seal)


title: 5hmC_tumor-1

description: 5hmC Profiling (hMe-Seal)


title: hibHSC93

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i711_i511


title: P18_9G


title: P18_9F


title: hibHSC36

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i715_i505


title: P18_9E


title: P18_12A


title: P18_9C


title: P18_10F


title: 5hmC_normal-1

description: 5hmC Profiling (hMe-Seal)

value: normal brain


title: hibHSC38

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i702_i506


title: P18_8H


title: P18_9A


title: P18_9B


title: MuSC_d21_Aged_bulkATACseq_Rep1

first: Sundari

last: Chetty

state: MA

address: 185 Cambridge Street

department: Harvard Medical School

institute: Massachusetts General Hospital, Harvard University

description:
MuSCs, Post-injury Day 21, Aged
PE ATAC-seq

data_processing:
In according with the NextSeq500 analysis, protocol, base calling and quality scoring are performed by an updated implementation of Real-Time Analysis (RTA), called RTA v2
FASTQ reads are processed with the ENCODE-DCC ATAC-seq pipeline, v 1.0
A merged ATAC-seq peak set across samples was generated by applying the bedtools merge command across the sample naive overlap optimal peak sets
Read counts for each peak for each sample were obtained with the bedtools coverage command over the merged ATAC-seq peak set
Technical replicates with pearson correlation < 0.9 across peak CPM values were excluded from analysis
Genome_build: mm10
Supplementary_files_format_and_content: tagAlign files, bigWig files, and peak calls files (narrowPeak) were generated for each technical replicate via the ENCODE ATAC-seq data processing pipeline ()
Reads were aligned to mm10 reference genome using STAR (v 2.5.0a)
Transcript and gene abundance was quantified via RSEM (v 1.3.0)
Technical replicates with pearson correlation < 0.9 across gene TPM values were excluded from analysis
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimeted text file include FPKM, TPM, and expected read count values for each technical replicate

source_name: Muscle stem cells

extract_protocol:
Hind limb muscles (tibialis anterior and gastrocnemius) of control and experimental mice were dissected using sterile surgical tools,  tissues were minced and transferred into 50 mL conical tubes containing 20 mL of digest solution. Cell sorting was done using a BD FACSAria III Cell Sorter.
RNA libraries were prepared for sequencing using standard Illumina protocols for the NextSeq 500.

tag: cell type

value: Flow sorted muscle stem cells

value: Aged

tag: timecourse


title: P18_10B


title: MuSC_d21_Young_bulkATACseq_Rep1

description:
MuSCs, Post-injury Day 21, Young
PE ATAC-seq


title: P18_8G


title: MuSC_d21_Young_bulkATACseq_Rep2


title: hibHSC37

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i701_i506


title: P18_8F


title: MuSC_d21_Aged_bulkRNAseq_Rep2

description:
MuSCs, Post-injury Day 21, Aged
SE RNA-seq


title: hibHSC40

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i704_i506


title: MuSC_d21_Aged_bulkRNAseq_Rep1


title: P18_8C


title: MuSC_d21_Aged_bulkATACseq_Rep2


title: P18_9D


title: P18_8D


title: MuSC_d21_Young_bulkRNAseq_Rep3

description:
MuSCs, Post-injury Day 21, Young
SE RNA-seq

value: Young


title: hibHSC42

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i706_i506


title: hibHSC35

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i714_i505


title: hibHSC39

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i703_i506


title: P18_8B


title: MuSC_d21_Young_bulkRNAseq_Rep2


title: hibHSC41

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i705_i506


title: P18_7F


title: P18_7G


title: P18_7D


title: P18_8A


title: MuSC_d21_Young_bulkRNAseq_Rep1


title: hibHSC44

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i710_i506


title: P18_7C


title: hibHSC43

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i707_i506


title: E9.5 P-Sp V+61+E+ sort

city: Seattle

first: Brandon

last: Hadland

state: WA

address: 1100 Fairview Avenue N., D2-115, P.O. Box 19024

institute: Fred Hutchinson Cancer Research Center

description: scRNA-seq (10X V2)

data_processing:
The Cell Ranger 2.1.1 pipeline (10X Genomics) was used to align reads to the mm10 reference genome and generate feature barcode matrix, filtering low-quality cells using default parameters.
The Monocle (v.3.2.3.0) platform was used for downstream analysis, combining read-depth normalized data across samples where applicable
Genome_build: mm10
Supplementary_files_format_and_content: 10X Cell Ranger output files in filtered feature-barcode matrix: "genes.tsv" contains gene information, "barcodes.tsv" contains cellular barcodes, and "matrix.mtx" contains a sparse matrix of UMIs
Supplementary_files_format_and_content: Monocle vs3 cell data set files: "SampleX.RDS" contains monocle cell data sets for sample(s) X imported from 10Xoutput files; "Sample1-2_P.RDS" contains cell data set for combined sample 1-2 following pre-processing, batch correction, dimensionality reduction, and clustering steps

source_name: Hemogenic/endothelial cells

growth_protocol: NA, primary cells sorted by FACS from dissected murine embryos were used directly for scRNAseq on 10X platform

extract_protocol:
FACS-isolated primary cells were washed with PBS/0.04% ultrapure BSA, and resuspended in PBS/BSA for loading into the 10X Genomics Chromium Single Cell B Chip, and processed in the Chromium single cell controller
The 10X Genomics Version 2 single cell 3’ kit was used to prepare single cell mRNA libraries with the Chromium i7 Multiplex Kit, according to manufacturer protocols.  Sequencing was performed for pooled libraries from each sample on an Illumina NextSeq 500 using the 75 cycle, high output kit

tag: cell type(s)

value: Hemogenic/endothelial cells-primary

tag: cell fraction


title: hibHSC46

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i712_i506


title: P18_8E

tag: female parent

tag: male parent


title: P18_7A

tag: days after pollination

tag: number of nuclei


title: E9 P-Sp V+61+E+ sort

description: scRNA-seq (10X V2)


title: P18_6H

tag: fans peak

tag: plate/batch


title: P18_7B

tag: extra wash steps?

tag: control?


title: P18_6G


title: P18_6F


title: BRI-308: S961

data_processing: Raw sequencing data were demultiplexed, aligned to the mouse genome (mm10) and UMI-collapsed using CellRanger.

source_name: pumps with S961

extract_protocol:
Islets were treated with 1 mL of TrypLE Express for 10 minutes at 37C,with vortexing every 3 minutes. Digestion was stopped with media with serum. After filtering, single cells were lysed in droplets using the 10X Chromium instrument.
Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit.

tag: strain

tag: tissue

value: pancreas islets

tag: gender

value: male

tag: barcode suffix


title: P18_6E

source_name: seed nuclei


title: P18_7H


title: hibHSC48

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i715_i506

value: Bone marrow

tag: age

value: 12-16 weeks

tag: genotype

tag: batch


title: BRI-307: CTRL

source_name: control (pumps with no S961)


title: P18_6D


title: hibHSC47

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i714_i506

source_name: Bone marrow


title: P18_7E


title: P18_6C


title: P18_6B


title: P18_6A


title: hibHSC50

description:
HTSeq_counts_SLX16045_batch3.txt.gz
SLX_16045.i702_i507


title: P18_5G


title: ARH77.DNA.WGS

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: DNA sequencing EBV positive ARH77 cell line

data_processing:
Library strategy: Whole genome sequencing
Whole genome sequencing raw reads were aligned against EBV genome version NC_001345.1 using BWA algorithm and A/T/C/G counts were obtained for every coordinates
Genome_build: NC_001345.1
Supplementary_files_format_and_content: Prosessed files contains A/T/C/G counts for every coordinates

source_name: Multiple myeloma ARH77 cell line

extract_protocol:
Genomic DNA was purified with Wizard® Genomic DNA Purification Kit (Promega, A1120).
Sequencing library preparation was then completed using the Illumina DNA prep kit according to the manufacturer’s instructions

tag: cell line

tag: ebv

value: positive

tag: cell type

value: Multiple myeloma


title: IM9.DNA.WGS

description: DNA sequencing EBV positive IM9 cell line

source_name: Multiple myeloma IM9 cell line


title: IM9, shBLRF2 sh4, replicate 2

data_processing:
RNA-Seq data analyzing was done with rsem (ver. 1.2.3) and hg19 genome with Ensemble transcriptome information
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

extract_protocol:
Total RNA was isolated from 1.5 x 106 cells using the Direct-zol microprep kit following the manufacturer’s protocol (Zymo Research)
Sequencing library preparation was then completed using QuantSeq library preparation kit

tag: blrf2 condition

tag: replicate


title: BRI-309: S961 RECOVERED

source_name: recovered (mice with pumps removed)


title: P18_5E

data_processing:
Reads were trimmed and quality-filtered using Trim Galore v.0.4.1 and aligned using STAR v.2.7.1a. Reads from Col- Cvi crosses were mapped to a Col-Cvi 'metagenome' (TAIR10 sequence appended to a Cvi 'pseudogenome' generated by substituting the Cvi allele at 576,697 Col-Cvi SNPs). Reads from Col-Ler crosses were mapped to a Col-Ler 'metagenome'. Sequences from ThermoFisher ERCC RNA spike-ins were also appended to the metagenome. Reads that mapped uniquely to the ERCC sequences were extracted and omitted from the rest of the analysis. Procedures and scripts for mapping with the metagenome are available in Picard and Gehring (Methods Mol Biol 2020). Reads overlapping a SNP were identified  using a custom script (Picard and Gehring, 2020) and assigned to parent- of-origin. PCR duplicates were removed using MarkDuplicates from the Picard Toolkit (Broad Institute). Total and allele-specific counts over genes were then obtained using htseq-count v.0.9.1 and the Araport11 gene annotations (excluding new Araport11 annotations antisense to existing TAIR10 genes). Single-nuclei samples with a total of at least 1,500 genes detected (≥ 1 overlapping read) and 1,000 genes well-detected (≥ 5 overlapping reads) prior to removing PCR duplicates were considered high quality and kept for subsequent analyses. Raw total expression counts were normalized to CPM (counts per million) while allelic count data for Col,Cvi reciprocal crosses at 4 DAP were normalized using the same procedure used in DESingle (Miao et al. 2018, Bioinformatics).
Genome_build: Araport 11 (excluding new Araport11 annotations antisense to existing TAIR10 genes)
Supplementary_files_format_and_content: Processed files for each library are tab-delimited with four fields: locus_name, all_counts, [parent1]_counts, [parent2]_counts, corresponding to raw counts of total reads, parent1-derived reads, and parent2-derived reads respectively. Additionally, three matrices are provided: CPM_total_expression.txt contains CPM-normalized total expression data for all 1,437 libraries that passed QC checks (and were not controls). norm_maternal_counts.txt and norm_paternal_counts.txt contain maternal and paternal counts for the 4 DAP Col, Cvi dataset (excluding libraries with few allelic counts; N=748 total), respectively; this subset of the data was used for imprinting analyses. Maternal and paternal counts were normalized according to the procedure used in DESingle (Miao et al. 2018, Bioinformatics), separately for the Col x Cvi and the Cvi x Col dataset.

extract_protocol:
Seeds were manually removed from siliques (~ 2 siliques per sample) into 50 uL Partec nuclei extraction buffer (Partec CyStain UV Precise P system), ground to release nuclei, DAPI stained by adding 400 uL Partec staining buffer, and filtered through a 30 um mesh. For the last four batches, nuclei were then washed 2x in 1:8 Partec extraction buffer:Partec staining buffer. Other batches did not include this was step. Single nuclei from the 3C or 6C peaks were sorted into a 96 well plate using fluorescence-activated nuclei sorting (FANS); each plate also included at least one negative control (no nucleus sorted into the well).
Libraries were prepared according the Smart-seq v2 protocol with a few minor variations and carried out at reduced volume. Nuclei were sorted into 1 μL lysis buffer (0.19% vol/vol Triton-X 100, 2U SUPERase RNase inhibitor, ERCC RNA spike-ins (ThermoFisher). 1 μL poly-A hybridization mix (final conc. 2.5mM/ea. dNTPs + 2.5 μM oligo-dT primer) was added to each well and the plate was incubated at 72°C 3 min before putting back on ice. 2.85 μL RT reaction mix (final concentration 1μM TSO, 1x Maxima RT buffer (Life Technologies), 1M betaine, 5 mM DTT, 6 mM MgCl2, 0.5 U SUPERase RNase-inhibitor, 2 U Maxima RT) was added and RT reaction was performed either in thermocycler with program 42°C 90', 10 x [50°C 2', 42°C 2'], 70°C 15' or in thermomixer. 7.5 μL pre-amp PCR mix (final conc. 1x KAPA HiFi HotStart Readymix (Kapa Biosystems), 0.1 μM IS PCR primer) was added and plate was incubated in thermocycler: 3' 98°C, [cycle #] x [98°C 20'', 67°C 15'', 72°C 6'], 72°C 5'. Number of pre- amplification cycles used varied between 18-21. cDNA was cleaned up using a 0.8x Ampure XP protocol (Beckman Coulter). Final libraries were built from successful cDNA preps using the Nextera XT kit (Illumina) with reduced volume (1/4 or 1/5 standard volumes). Up to 384 libraries were multiplexed together and sequenced on an Illumina HiSeq 2000 using a 40bp single-end protocol, or on an Illumina NextSeq using a 40x40bp paired-end protocol.

tag: female parent

value: Cvi

tag: male parent

tag: days after pollination

tag: number of nuclei