title: OvSaho.R2

status: Public on Oct 02 2020

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

data_processing:
RNA-Seq reads were mapped to the human genome (hg38, Genome Reference Consortium GRCh38)  using HISAT2 version 2.1.0.
Number of reads aligned to the exonic region of each gene were counted using htseq-count based on the Ensembl annotation.
Genes that achieved at least one read count per million reads (CPM) in at least 25% of the samples were kept.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: log2CPM.txt: Tab-delimited text file includes log2 cpm values for each Sample.

source_name: OvSaho cell line

growth_protocol: COV318 cells grown in DMEM, G33, Kuramochi, Ovkate, Ovsaho, Snu119 grown in RPMI (both media supplement with FBS). G164 grown in DMEM-F12 with human serum. FNE1/2 grown in FOMI media with cholera toxin.

extract_protocol: RNA extracted using RNeasy kit (Qiagen).

treatment_protocol: Cells growing in T-75 flasks, passaged once per week (FNE1/2 grown in Primaria surface modified flasks).

tag: cell line

value: OvSaho

tag: cell type

value: HGSC cancer cell line


title: Snu119.R1

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: Snu119 cell line


title: Snu119.R2


title: Breast cancer_45 cancer

status: Public on Oct 05 2020

type: RNA

city: New Taipei

first: Chih-Cheng

last: Chien

address: No 2, Ln 59, Jian-Cheng Rd, Sijhih Dist

country: Taiwan

institute: Sijhih Cathay General Hospital

description: Gene expression data from breast cancer tissues.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45 °C on GeneChip® Human Genome U133 Plus 2.0 expression arrays (Affymetrix, Inc., Santa Clara, CA).

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000.

data_processing: Scanned images processed by GeneChip® Operating Software and Affymetrix’s Microarray Suite software to generate detection p values. The Robust Multichip Average (RMA) algorithm, which consisted three steps of background adjustment, quantile normalization, and final summarization, was applied for perfect match probe signals within the study.

label: biotin

source_name: Breast cancer tumor tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA.

extract_protocol: Total RNA was extracted from frozen specimens using TRIzol® reagent (Invitrogen, Carlsbad, CA). RNA was purified using RNeasy® mini kits (Qiagen, Valencia, CA) and RNA integration was checked by gel electrophoresis.

treatment_protocol: Breast cancer samples were prospectively collected during surgery. Cancerous breast tissues were snap-frozen and stored in liquid nitrogen at -80 °C with RNAlaterTM reagent (Qiagen, Germantown, MD) within 30 minutes after surgery. Frozen samples were cut into 1~2-mm thick slices, and slices with more than 90% of cancer content were selected for microarray experiment.

tag: tissue

value: Breast

tag: dcis

value: With DCIS

tag: comed-dcis

value: Non-comedo DCIS

tag: microcalcification

value: With microcalcification

tag: relapse status

value: relapse

tag: survival time (years)

tag: er

value: negative

tag: pr

tag: grade

tag: her2 status

value: normal

tag: predicted risk

value: high


title: OvSaho.R1


title: Snu119.R3


title: OvKate.R2

source_name: OvKate cell line

value: OvKate


title: OvSaho.R3


title: OvKate.R1


title: Breast cancer_23 cancer

value: Without DCIS

value: Without microcalcification

value: non-relapse

value: positive

value: low


title: Kuramochi.R1

source_name: Kuramochi cell line

value: Kuramochi


title: Kuramochi.R3


title: OvKate.R4


title: Kuramochi.R2


title: Breast cancer_9 cancer


title: AOCS1.R3

source_name: AOCS1 cell line


title: G164.R3

source_name: G164 cell line


title: AOCS1.R1


title: Breast cancer_7 cancer


title: Breast cancer_8 cancer

value: Comedo DCIS

value: overexpression


title: G164.R2

value: HGSC cancer cell line


title: G164.R1


title: FNE1.R3

source_name: FNE1 cell line

value: hTERT immortalised Fallopian tube cell line


title: FNE2.R2

source_name: FNE2 cell line


title: FNE2.R1


title: FNE1.R2


title: FNE1.R1


title: Cov318.R1

source_name: Cov318 cell line


title: F107

status: Public on Sep 18 2020

city: Shanghai

first: rui

last: Dong

address: 399 Wan Yuan Road

country: China

institute: Department of Pediatric Surgery, Children’s Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defect

data_processing:
CellRanger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include normalized median scaling values for each cell.
Supplementary_files_format_and_content: Embryo_annotation.csv is related to F366 and F379.
Supplementary_files_format_and_content: Adrenal_gland_annotation.csv is related to F2, F7, F106, and F107.
Supplementary_files_format_and_content: Tumor_dataset_annotation.csv is related to T10, T19, T27, T34, T40, T44, T69, T71, T75, T92, T162, T174, T188, T200, T214, and T230.

source_name: fetal adrenal tissue

extract_protocol:
Tumor tissues were resected by surgery and transported in DMEM/F12 medium on ice to the laboratory within an hour. The fetal adrenal tissues were collected  and transported in DMEM/F12 medium on ice to the laboratory within an hour.
For scRNA-seq, the tissues were dissociated into single cells suspensions using digestion buffer (DMEM/F12 Medium+ 2 mg/ml of collagenase IV + 100 IU/ml DNase I), and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol.

tag: age

value: 13+2 PCW (post-conception wk)


title: F7

value: 8+3 PCW (post-conception wk)


title: F106

value: 14+4 PCW (post-conception wk)


title: T92

source_name: neuroblastoma tissue

tag: Sex

value: female


title: AOCS1.R2


title: T71

value: male


title: T75


title: T69


title: F2

value: 8+6 PCW (post-conception wk)


title: T34


title: T40


title: T27


title: T10


title: FNE2.R3


title: YS young spleen scRNA-seq

status: Public on Sep 11 2020

city: Beijing

first: Wei-Na

last: Jin

state: Beijing

address: NO.119, Southwest of the Fourth Ring Road, Fengtai District

department: China National Clinical Research Center for Neurological Diseases

institute: Beijing Tiantan Hospital, Capital Medical University

data_processing:
Raw FASTQ files were processed with Cell Ranger software (v1.3.1), which performs alignment, filtering, barcode counting and UMI counting
Reads were first simultaneously aligned with the Grch38 genomes, using CellRanger software (v1.3.1), for their assignment as murine sequences
Supplementary_files_format_and_content: EXCEL

organism: Mus musculus

source_name: young spleen

extract_protocol:
CD45hi single cells were sorted by flow cytometry for single-cell RNA sequencing.
10x Genomics Chromium single-cell 3’ v2 kit and protocol were used to prepare the libraries. HalioDx (Marseille, France) performed the RNA sequencing on a NextSeq500 machine with a sequencing depth of at least 50,000 reads per cell.

treatment_protocol: mice were injected with Tamoxifen and four weeks later, the bone marrow, spleen, blood, and brain tissues were obtained to measure tdTomato+ NK cells.

value: spleen

value: neuroblast


title: YB young brain scRNA-seq

source_name: young brain

value: brain


title: AS aged spleen scRNA-seq

source_name: aged spleen


title: AB aged brain scRNA-seq

source_name: aged brain


title: Cov318.R3


title: A3: aged sample 003

data_processing:
The clustering analysis of gene expression of all the samples in random sequence was performed with Cluster (v3.0) and Java Treeview software. Heatmaps were generated with the R heatmap package.
For prediction of the transcription factor (TF) families encoded by the DEGs, the open reading frame (ORF) of each DEG was detected with the Getorf software (http://emboss.sourceforge.net/apps/cvs/emboss/apps/getorf.html), and then mapped to the Animal TFDB databases with the DIAMOND software.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the instruction manual. About 60 mg of tissues were ground in liquid nitrogen in a 2 mL tube. After homogenization for 2 min, samples were rested horizontally for 5 min. The mix was centrifuged for 5 min at 12,000×g at 4°C, and then the supernatant was transferred into a new tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shaken vigorously for 15 sec, and then centrifuged at 12,000×g for 10 min at 4°C. After centrifugation, the upper aqueous phase was transferred into a new tube and an equal volume of isopropyl alcohol was added, then centrifuged at 13,600 rpm for 20 min at 4°C. After removing the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, and then the mix was centrifuged at 13,600 rpm for 3 min at 4°C to collect residual ethanol, followed by air drying for 5-10 min. Subsequently, RNA was resuspended in 25~100 μL DEPC water, and then qualified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo (dT)-attached magnetic beads were used to purify mRNA. Following purification, the mRNA was fragmented into small pieces using divalent cations at appropriate temperature. Then first-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added and incubated to end repair. The cDNA fragments obtained from the previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from the previous step were heated, denatured, and circularized by the splint oligo sequence to obtain the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library.


title: A1: aged sample 001


title: Y1: young sample 001


title: Y3: young sample 003


title: Y2: young sample 002


title: ATACseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc10)] replicate 2

status: Public on Sep 06 2020

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

country: USA

institute: Penn State University

library_source: genomic

data_processing:
Basecall conversion to fastq files was performed using Picard v 2.8.2
Alignment: Paired-end ATAC-seq reads were mapped to the mouse mm10 genome using Bowtie 2.2.2 (Langmead et al., 2009).
Domain Calls: Genome-wide ATAC-seq derived accessible domains were called using DomainFinder in the SeqCode project   (https://github.com/seqcode/seqcode-core/blob/master/src/org/seqcode/projects/seed/DomainFinder.java).
Genome_build: mm10
Supplementary_files_format_and_content: BED: Bed files with start and end co-ordinates corresponding to ATAC-seq domain boundaries

molecule: genomic DNA

source_name: ES-derived embryoid bodies+4D RA+SAG with induced transcription factors

growth_protocol: mESC lines were cultured in 2-inhibitors based medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), supplemented with 2.5% ESC-grade fetal bovine serum (vol/vol, Corning), N2 (Gibco), B27 (Gibco), 2mM L-glutamine (Gibco), 0.1 mM β-mercaptoethanol (Gibco), 1000 U/mL leukemia inhibitory factor (Millipore), 3μM CHIR (BioVision) and 1 μM PD0325901 (Sigma)) on 0.1% gelatin (Millipore) coated plates at 37 °C, 8% CO2.

extract_protocol:
Cells were collected prior to TF induction (day 2 of RA/SAG differentiation) and 48h after Doxycycline (Dox) treatment. 50,000 cells were aliquoted and washed twice in 1 × PBS (cold). Cell pellets were resuspended in 10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, and freshly added 0.1% NP-40 (vol/vol), and centrifuged at 4 °C. Pellets were resuspended in 25 µL of 2 × TD buffer, 2.5 µL TDE1 (Nextera DNA sample preparation kit, FC-121–1030) and 22.5 µL of water and incubated at 37 °C for 30 min. The sample was purified using the MinElute PCR purification kit (Qiagen, 28004).
A quantitative PCR reaction with 1 × SYBR Green (Invitrogen), custom-designed primers and 2 × NEB MasterMix (New England Labs, M0541) was performed to determine the optimal number of PCR cycles (one-third of the maximum measured fluorescence) (Buenrostro, Giresi, Zaba, Chang, & Greenleaf, 2013). PCR enrichment of the library was performed with custom-designed primers and 2 × NEB MasterMix (New England Labs, M0541). The libraries were purified using the MinElute PCR purification kit. High Sensitivity DNA ScreenTape (Agilent, 5067-5584) was used to verify the fragment length distribution of the library. Library quantification was performed using the KAPA library amplification kit on the Roche Lightcycler 480.

treatment_protocol: Embryoid bodies (EBs) were obtained by plating trypsinized (Gibco) mESCs in AK medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), 7% KnockOut SR (vol/vol) (Gibco), 2 mM L-glutamine, 0.1 mM ß-mercaptoethanol and penicillin–streptomycin (Gibco),) at 37 °C, 5% CO2 (day -2). On day 0, EBs were split 1:2 and AK medium was replenished and supplemented with 1 μM all-trans retinoic acid and 0.5 μM smoothened agonist (SAG) (Millipore, 566660). TF induction was performed by adding 3 μg/mL of Doxycycline (Sigma, D9891) on day 2. For ATAC-seq experiments, 3.5x10^5 mESCs were plated in 100mm suspension dishes (Corning).

tag: strain genotype/variation

tag: treatment

value: EB + 4 Days RA + SAG, D2+48hours Dox

value: Embryoid Bodies


title: ATACseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc9)] replicate 2


title: T19


title: ATACseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc9)] replicate 1


title: ATACseq in EB_replicate2

source_name: ES-derived embryoid bodies

value: EB


title: ATACseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc6)] replicate 2


title: ATACseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc10)] replicate 1


title: rpb1-CTD-T4A29 rep3

status: Public on Sep 03 2020

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: STF_raw_counts; DESeq2_STF6_vs_T4A; DESeq2_STF9_vs_T4A

data_processing:
Base calls from Illumina NovaSeq 6000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Genome_build: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary_files_format_and_content: Matrix file for raw HTSeq counts; individual files for DESeq2 for comparison of each suppressor mutant with parent strain

molecule: polyA RNA

organism: Schizosaccharomyces pombe

growth_protocol: log phase cultures, 30ºC, YES medium

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina HiSeq 4000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Stranded polyA+ RNA Seq

tag: lab strain number

value: BS 1

tag: growth conditions

value: log phase culture, YES medium

tag: developmental stage

value: vegetative growth


title: ATACseq in EB-Day2[D0+RA+SAG]_replicate2

source_name: ES-derived embryoid bodies+2D RA+SAG

value: EB + 2 Days RA + SAG

tag: cell type


title: ATACseq in EB-Day2[D0+RA+SAG]_replicate1


title: ATACseq in EB_replicate1


title: rpb1-CTD-T4A29 rep2


title: ATACseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc6)] replicate 1


title: rpb1-CTD-T4A29 rep1


title: CH12: DDX3X knockdown (shDDX3X #2)

city: Washington

first: Hyeongjwa

last: Choi

state: DC

address: 3970 Reservoir Road NW

department: Oncology

institute: Georgetown University

description: shRNA were delivered to cells by transduction of lentiviral particles.

data_processing:
The alignment was doen using LifeScope.
The read numbers for mRNA were counted using "HTSeq".
mRNAs with read counts lower than 20 in all samples were filtered out.
"DESeq2" was used for the differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes DESeq2 normalized count for each sample

source_name: MCF7 Breast cancer cell line

growth_protocol: Cells were grown in DMEM supplemented with 10% heat-inactivated FBS, 1% Pen-Strep, and 2 ug/ml of puromycin.

extract_protocol:
RNA was extracted using QIAGEN Rneasy kits according to manufacturer's instructions.
RNA libraries were prepared for SOLiDTM sequencing using whole transcriptome library preparation (part num: 4409491)

tag: cell line

value: Breast cancer

tag: shRNA

value: DDX3X shRNA


title: A2: aged sample 002

tag: tissue


title: RAP aginst Xist containing the E-repeat

city: Los Angeles

first: Kathrin

last: Plath

state: CA

address: 615 Charles E. Young Drive South

department: Biological Chemistry

institute: UCLA

data_processing:
Adaptor trimming was performed using cutadapt version 1.15 in paired-end mode with the following parameters: "-a AGATCGGAAGAGC -A AGATCGGAAGAGC"
Read mapping was performed using bwa version 0.7.17-r1188 and samtools version 1.4 with the following command: "bwa mem -t 30 -T 0 ${INDEX} ${R1} ${R2} | samtools view -b - | samtools sort -O sam -T tmp -n - | samtools fixmate -O sam - - | samtools sort -O bam -T tmp - > ${BAM}"
Read filtereing was performed using samtools version 1.4 with the following command: "samtools view -b -q 30 ${BAM} | samtools rmdup - - | samtools view -b -L ${BED} - | samtools sort -O bam -T ${tmp} - > ${FILT_BAM}". The ${BED} variable is a path to a .bed file containing all entire chromosomes except for Xist locus (chrX:103460216-103483359)
Library-depth-normalised tracks were generated using bedtools v2.27.1 with the following commands: "bamToBed -i ${FILT_BAM} | sort -u -k 1,1 -k 2,2 -k 3,3 > ${FILT_BED} ; genomeCoverageBed -split -bga -scale `echo 1000000000/$(wc -l ${FILT_BED} | awk '{print $1}') | bc` -i ${FILT_BED} -g ${CHROM_SIZES} > ${BG} ; bedGraphToBigWig ${BG} ${CHROM_SIZES} ${BW}"
Sample library-depth-normalised tracks were divided by the library-depth-normalised input in R v3.5 using rtracklayer 1.42.2 to import the tracks as Rle and export the divided tracks as bigWig
Input-normalised tracks were smoothed using deeptools version 3.4.3 and bedtools version v2.27.1 with the following command: "multiBigwigSummary bins -b ${NORM_BW} -out res.npz -bs 1000 --outRawCounts ${NORM_BG} ; bedGraphToBigWig ${NORM_BG} ${CHROM_SIZES} ${SMOOTHED_NORM_BW}"
Genome_build: mm10
Supplementary_files_format_and_content: Sample processed data files (bw) represent RAPseq genomic profiles divided by a RAPseq input and smoothed with a 1kb window. Input processed data file (bw) is the input RAPseq genomic profile.

source_name: BstEii digested Xist cDNA in HPRT, male ESCs, 6h Dox

growth_protocol: ESC lines were cultured in knockout DMEM (Life Technologies) supplemented with 15% FBS (Omega), 2 mM L-glutamine (Life Technologies), 1× NEAA (Life Technologies), 0.1 mM Beta-Mercaptoethanol (Sigma), 1xPenicillin/Streptomycin (Life Technologies), and 1000 U/mL murine LIF (homemade) on 0.3% gelatinized plates (porcine skin gelatin, Sigma) pre-plated with irradiated male DR4 feeders (homemade from day 14.5 embryos with appropriate animal protocols in place). Xist expression was induced by adding 2 micrograms per milliliter (ug/mL) doxycycline at a defined time before harvesting cells.

extract_protocol:
RAP-seq and Input collection was performed as described in Engretiz et al. (PMID: 23828888 )
Illumina Tru-seq CHIP library preparation kit

value: 2mg/mL, 6h dox treatment

tag: cell lines

value: T20 male ESCs

tag: experiment

value: RAP-seq


title: CH10: DDX3X knockdown (shDDX3X #2)


title: CH19: DDX3X knockdown (shDDX3X #1)


title: RAP aginst Xist deleted of the E-repeat

source_name: SnaB1 digested Xist cDNA in HPRT, male ESCs, 6h dox

treatment_protocol: Xist expression was induced by adding 2 micrograms per milliliter (ug/mL) doxycycline at a defined time before harvesting cells.


title: CH18: DDX3X knockdown (shDDX3X #2)


title: Cov318.R2

value: HGSC cancer cell line


title: Breast cancer_133T

source_name: Breast cancer tumor tissue

value: Breast

tag: dcis

value: With DCIS

tag: comed-dcis

value: Comedo DCIS

tag: microcalcification

value: With microcalcification

tag: relapse status

value: non-relapse

tag: survival time (years)

tag: er

value: negative

tag: pr

value: overexpression

value: low


title: PTBP1chip_Dox_Xist

data_processing:
For ChIP experiments: Basecalls performed using CASAVA version 1.4, ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 (Langmead et al. 2012) with only those reads that aligned to a unique position with no more than two sequence mismatches were retained for further analysis.
For PTBP1 and MATR3 CLIP data: Basecalls performed using CASAVA version 1.4. Duplicate sequences removed (sequences contain 11nt Unique Molecular Identifiers) using the fastq-uniq program from the fastq-tools suite (v0.8). UMIs were removed using the fastx_clipper program from the FASTX-Toolkit (v0.7). Unique CLIP-seq reads were aligned to the mm9 genome assembly using TopHat2 (Kim et al. 2013) aligner with option -X1 (no mismatches allowed, multi-hits discarded).
For CELF1 CLIP and INPUT data: Raw sequencing read were pre-processed prior to alignment for removal of PCR duplicates, filtering of low-quality sequences, and trimming of the adapter a the 3’ end of reads. PCR duplicates are removed by collapsing molecules with identical 5' barcode sequences (11nt). Reads were mapped using TopHat2 (Kim et al. 2013) to the mouse reference genome (build mm9) using options: --b2-sensitive --library-type fr-unstranded --read-realign-edit-dist 0 --min-segment-intron 20 -x 20 --no-coverage-search. Reads containing less than 20 nucleotides were excluded for alignment. The alignment was visualized in bigWig format.
Genome_build: mm9
Supplementary_files_format_and_content: Data files represent the coverage of reads from CLIP-seq and ChIP-seq experiments that align to the Xist locus in bigWig format. Coverage is normalized by FPKM within non-overlapping genomic bins spanning 10 bps.

source_name: pSM33 20h Dox

extract_protocol:
RNA iCLIP-seq was performed as described in Damianov et al. (PMID: 27104978), RNA eCLIP-seq was performed as described in Van Nostrand et al. (PMID:28766298) and ChIIP-seq was performed as described in Chrois et al. (PMID:28111071)
Illumina Tru-seq CHIP library preparation kit

value: pSM33 male ESCs lacking Tsix

tag: induction

value: 2ug/mL dox, 20h

tag: experiment type

value: ChIP-seq

tag: fraction

value: Immunoprecipitated Genomic DNA

tag: antibody


title: CELF1_input_Xist

source_name: pSM33 6h Dox

value: pSM33 male ESCs

value: 2ug/mL dox, 6h

value: eCLIP-seq

value: Total RNA


title: PTBP1chip_NoDox_Xist

source_name: pSM33 no Dox treatment

value: No Dox treatment


title: CELF1_eclip_Xist

value: Immunoprecipitated RNA


title: MATR3_iclip_Xist

value: iCLIP-seq


title: T44

tag: Sex

value: female

tag: age


title: PTBP1_iclip_Xist

tag: cell line


title: CH11: DDX3X knockdown (shDDX3X #1)

tag: cell type

value: Breast cancer

tag: shRNA

value: DDX3X shRNA


title: MRISC - ATAC_rep1

status: Public on Aug 15 2020

first: Hongxiang

last: Sun

address: 280 South Chongqing Rd.

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University

data_processing:
Basecalls performed using Bcl2fastq
ATAC-seq reads were further Analyzed using esATAC
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated using esATAC
Supplementary_files_format_and_content: Bed files were generated using esATAC and BedTools

source_name: MRISC

extract_protocol:
Cells were isolated from mouse colon using Collagenase VIII and Dnase I, followed by AriaIII flow cytometer sorting with CD45/Epcam/CD31 negative, gp38 positive and cell subset specific Abs.
Libraries were prepared according to Novazyme's ATAC instructions accompanying the Kit TD501.

value: MRISC

tag: strain

value: 12 Week

value: male


title: CD138  - ATAC_rep1


title: MRISC - ATAC_rep2


title: CD138  - ATAC_rep2


title: CD34 SP- ATAC_rep2

source_name: CD34 SP

value: CD34 SP


title: CD34 SP- ATAC_rep1


title: Myofibroblast -ATAC_rep2

source_name: Myofibroblast

value: Myofibroblast


title: cardiac fibroblasts, P30 Tcf21 3

status: Public on Aug 05 2020

city: Cinicnnati

first: Katherine

middle: E

last: Yutzey

state: OH

address: 240 Albert Sabin Way

department: Divison of Molecular Cardiovascular Biology

institute: Cinicnnati Children's Hospital Medical Center

data_processing:
Raw fastq files obtained after sequencing were pre-processed with HTStream to extract the longest subsequence with no ambiguous sequence, identify and remove adapter sequences, polyA/T sequence, PCR duplicates, to identify and remove/keep/count contaminants, discreet trim of 5’ and/or 3’ basepairs, overlap paired end reads, assess quality score and to compute read stats. Resulting processed reads were mapped to the mouse genome (GRCm38.95) and raw gene counts were obtained using the aligner STAR(5).
Genome_build: GRCm38.95
Supplementary_files_format_and_content: raw_counts_all_samples.txt

source_name: Tcf21+ P30 cardiac cells

extract_protocol:
GFP+ cells were FACS sorted directly into Quizol and were frozen at -80C. The RNA was isolated using a RNAeasy micro kit.
RNA libraries were prepared for sequencing using Illumina HiSeq 2500 system

tag: tissue

value: cardiac

value: fibroblasts

tag: genotype

value: 30 days

tag: gender

value: Pooled Male and Female


title: cardiac fibroblasts, P30 Tcf21 1


title: cardiac fibroblasts, P7 Tcf21 2

source_name: Tcf21+ P7 cardiac cells

value: 7 days


title: Breast cancer_112T

value: Breast

tag: dcis

value: With DCIS

tag: comed-dcis

value: Non-comedo DCIS

tag: microcalcification

value: With microcalcification

tag: relapse status

value: non-relapse

value: positive

tag: grade

tag: her2 status

value: normal

tag: predicted risk

value: high


title: cardiac fibroblasts, P7 Periostin2

source_name: Postn+ P7 cardiac cells


title: cardiac fibroblasts, P7 Periostin1


title: WT cell with SKI ChIP

status: Public on Jul 28 2020

city: Chapel Hill

first: Yisong

last: Wan

state: NC

address: 125 Mason Farm Road

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill

data_processing:
Raw reads were first processed to remove adapter sequences using Trim Galore (version 0.4) with default parameters
Trimmed reads were mapped to mm10 Bowtie (version 1.2) with the parameters -m 1, -v 2 and –X 1500.
For all the data files, duplicated alignments were removed using Picard (version 1.115).
The findPeaks program from Homer (version 4.8.3) was applied to call all reported ChIP-seq peaks. Peak calling for all samples used its paired input sample as noise control. findPeaks was run using default parameters of “-F 4 -L 0 -C 2 -fdr 0.001”.
Genome_build: mm10
Supplementary_files_format_and_content: Bed coordinates for peaks generated by homer

source_name: activated CD8 T cells with TGFbR inhibitor

extract_protocol:
Lysates were cleared from sonicated nuclei. Smad4-DNA and Ski-DNA complexes were isolated with anti-Smad4 and anti-Ski antibody respectively.
The sequencing libraries were prepared following the protocol of MGI Easy DNAseq kit (MGI).

treatment_protocol: CD8+ T cells were isolated from WT and Cd4Cre;Smad4fl/fl mice and activated with TGFbR inhibitor for 2 days. Live cells were collected for further ChIP analysis.

value: CD8+ T cells

value: Wild type

tag: chip antibody

value: anti-mouse SKi


title: S4 KO cell with S4 ChIP

value: S4 KO

value: anti-mouse Smad4


title: WT cell with S4 ChIP


title: WT input DNA rep1


title: WT input DNA rep2


title: Myofibroblast -ATAC_rep1

value: Myofibroblast

value: 12 Week

tag: Sex

value: male


title: dd09

status: Public on Jul 09 2020

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

data_processing:
align with cellranger
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: h5

source_name: Trachea+proximal airway

extract_protocol:
10x genomics chromium 3' single cell RNAseq kit v2 or v3
follow 10x genomics instruction

value: Trachea+proximal airway

tag: group

value: Donor


title: dd39

source_name: Trachea

value: Trachea


title: dd10


title: dd49


title: Sc_Isopu_run2

city: Fribourg

first: Jules

last: Duruz

state: Fribourg

address: Ch. du Musée 10

department: Biology

country: Switzerland

institute: University of Fribourg

data_processing:
Sequenced libraries with processed with cell ranger pipeline (10X Genomics)
Single datasets were later aggregated with cell ranger (v3.0.2) aggr pipeline.
Transcriptome build: From Brauchle et al., 2018 (NCBI accession number: SAMN07276911)
Supplementary_files_format_and_content: Matrix files originated with cell ranger pipeline (v3.0.2).  Isopu_nonred_transcriptome.fasta (Reference transcriptome used for single-cell RNA sequencing analysis).

organism: Isodiametra pulchra

source_name: All cells

growth_protocol: Animals were kept at 20°C in a 12h/12h light-dark cycle in glass petri dishes and were fed diatoms (Nitzschia curvilineata)

extract_protocol:
Cell dossiciation is done with collagenase (1mg/ml) for 1h at 25°C. mRNAs were obtained by applying 10X Genomics protocol for scRNAseq, Chromium Single Cell 3’ Library & Gel Bead Kit v3.
Libraries were constructed accoring to the manufacturer's guideline, for sequencing on a Illumina NovaSeq 6000
Libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v2&3 (10X Genomics)

tag: Stage

value: Hatchling


title: Sc_Isopu_run1

data_processing:
Sequenced libraries with processed with cell ranger pipeline (10X Genomics)
Single datasets were later aggregated with cell ranger (v3.0.2) aggr pipeline.
Transcriptome build: From Brauchle et al., 2018 (NCBI accession number: SAMN07276911)
Supplementary_files_format_and_content: Matrix files originated with cell ranger pipeline (v3.0.2). Isopu_nonred_transcriptome.fasta (Reference transcriptome used for single-cell RNA sequencing analysis).


title: cardiac fibroblasts, P30 Tcf21 2

value: cardiac

tag: cell type

value: fibroblasts

tag: age

value: 30 days

value: Pooled Male and Female


title: cc05


title: cc04


title: cardiac fibroblasts, P7 Tcf21 1

value: 7 days


title: 4CBS_H3K4me3_rep1

status: Public on Jul 06 2020

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
Inserted sequence was add to the mm10 genome. And a customized mm10 genome was indexed by bowtie2-build
ChIP-seq sequencing data was trimmed and aligned to mm10 by bowtie2. Unmapped, multimapped and PCR duplicates were removed.
Genome_build: mm10
Supplementary_files_format_and_content: Signal tracks were generated by bamCoverage with parameters "--normalizeUsingRPKM -bs 50 --smoothLength 150" (deepTools)

source_name: embryonic stem cells

growth_protocol: Cells were cultured on feeder-free, serum free 2i condition (Serum free mouse ES medium supplemented with 1uM PD03259010, 3uM CHIR99021, 2mM glutamine, 0.15uM Monothioglycerol, 1000U/ml LIF). The growth medium was changed every day. Cells were dissociated by Accutase (AT104) and passaged to onto 0.2% gelatin-coated plates every 2-3 days.

extract_protocol: Crosslinked cells were processed by Covaris truChIP Chromatin Shearing kit and chromatin were sonicated to 300-500bp by Covaris M220. ChIP DNA and Input DNA were constucted into illumina Tru-seq libraries as previously described (Jian Yan et al., 2013), followed by size selection for 300-500bp.

tag: cell line

value: F123 ESC

tag: strain

value: F1 hybrid (castaneus x S129/SvJae)

value: Millipore, 04-745


title: 4CBS_Input_rep1

tag: genotype


title: 4CBS_CTCF_rep1


title: WT_Input_rep2

value: Wild-type


title: WT_Input_rep1


title: 4CBS_H3K4me3_rep2


title: 4CBS_CTCF_rep2


title: WT_CTCF_rep2


title: 4CBS_RAD21_rep2


title: WT_CTCF_rep1


title: 4CBS_H3K27ac_rep2

value: Active Motif,39685


title: WT_H3K27ac_rep1


title: WT_H3K27ac_rep2


title: 4CBS_RAD21_rep1


title: 4CBS_H3K27ac_rep1


title: WT_RAD21_rep2


title: WT_RAD21_rep1


title: WT_H3K4me3_rep1


title: Syn1-6_Input_rep1


title: Syn1-6_Input_rep2


title: WT_H3K4me3_rep2


title: 4CBS_Input_rep2


title: nbd_Syn-15_Input_rep2


title: Syn1-6_RAD21_rep2


title: nbd_Syn-15_RAD21_rep2


title: nbd_Syn-6_Input_rep2


title: nbd_Syn-15_Input_rep1


title: nbd_Syn-6_CTCF_rep1


title: nbd_Syn-15_CTCF_rep1


title: nbd_Syn-15_RAD21_rep1


title: F0_C3_hippocampus_normal

status: Public on Jun 28 2020

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

data_processing:
RNA-sequencing reads were aligned to the mouse genome GRChM38 (mm10) using HISAT2 (Kim et al., 2015). The gene expression profile was generated by Cufflinks 2.2.1 (Trapnell et al., 2010). Low and non-expressed genes with less than an average of 10 fragments per kilobase of exon model per million mapped reads (FPKM) in all samples were omitted from the analysis.
Differential analysis was performed using Student’s t test. Significance was set at an uncorrected p < 0.05 for broad pattern identification. A fold-change threshold was set at > 1.3. Heatmaps were generated using pheatmap R package and GO analysis was performed using DAVID Bioinformatics Resource 6.8 (Huang et al., 2009a, b).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Normal mice

extract_protocol:
Hippocampal samples collected from 3 independent mice of the F0-Ctl, F0-Dep and F1-Dep groups were processed for RNA extraction. Transcriptome libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: hippocampus

value: 8 week


title: F1_D3_hippocampus_depressed_offspring

source_name: offspring born to stress-induced depressed male mice


title: nbd_Syn-15_CTCF_rep2


title: nbd_Syn-6_RAD21_rep1


title: nbd_Syn-6_RAD21_rep2


title: nbd_Syn-6_CTCF_rep2


title: F1_D2_hippocampus_depressed_offspring


title: F1_D1_hippocampus_depressed_offspring


title: F0_D3_hippocampus_depressed

source_name: Stress-induced depressed mice


title: F0_D1_hippocampus_depressed


title: Syn1-6_CTCF_rep2


title: Syn1-6_CTCF_rep1


title: Syn1-6_RAD21_rep1


title: F0_C2_hippocampus_normal


title: CENP-A_ChIP_rep1_2

status: Public on Jun 24 2020

city: Stanford

first: Owen

middle: Kabnick

last: Smith

address: 279 Campus Drive

department: Biochemistry

institute: Stanford University School of Medicine

data_processing:
Remove PCR duplicates with BBtools Clumpify, bbmap v38.06
Trim adapters with trimmomatic, v0.38
Generate k-mers with KMC, v3.1.1
Identify CENP-A enriched k-mers
Align genome segments with enriched k-mers with bowtie2 v2.3.5
Align enriched k-mers with bowtie v1.2.2 with parameters -v 0 -a
Generate, sort ,index bam with Samtools, v1.9
Generate bigWig with deeptools, v2.5.7, -bs 5
Genome_build: X. laeivs v10.3
Supplementary_files_format_and_content: bigWig displaying mapping of CENP-A enriched k-mers
Supplementary_files_format_and_content: xla_v10.2_cen.bed: Bed file from the CENP-A ChIP dataset used in the analysis.
Supplementary_files_format_and_content: FCR_monomers.fa: FASTA file from the CENP-A ChIP dataset used in the analysis.

organism: Xenopus laevis

source_name: Red Blood Cells

extract_protocol:
Nuclei were isolated from cells through dounce nuclear extraction, incubated with MNase (300U 30min RT). Soluble mononucleosomes were extracted and precleared prior to use as input for antibody pulldowns.
Sequencing libraries were prepared with the NEBNext Ultra II DNA Library prep kit (E7645) with up to 1µg of input or ChIP eluate DNA following the manufacturer’s protocol

treatment_protocol: no treatement conditions

value: J-strain

value: Red Blood Cells

value: X. laevis Rb-anti-CENP-A (Straight)


title: F0_C1_hippocampus_normal


title: CENP-A_ChIP_rep3


title: Sequin Mix B replicate 2

status: Public on Jun 18 2020

city: PARKVILLE

first: Xueyi

state: VIC

address: 1G ROYAL PARADE

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
MinKNOW version 3.6.0 with Bream version 4.3.12.
Base calling and quality scoring: Guppy version 4.0.11
Trimming and de-multiplexing: Guppy version 4.0.11
Sequenced reads were mapped using minimap2 version 2.17 with arguments -ax splice --MD.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.34.4) using the RNA sequin annotation 2.4 GTF file with arguments isGTFAnnotationFile = TRUE, isLongRead = TRUE, primaryOnly=TRUE.
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.26.5, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise linear models (Smyth, SAGMB 2004) with observational level weights (Law et al. Genome Biology 2014) were fitted to summarise the values from replicates samples using functionality from the limma package (version 3.40.6, Smyth, 2005).
Genome_build: RNA sequin decoy chromosome 2.4
Supplementary_files_format_and_content: *.tsv: Tab-delimited text files with columns representing Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

organism: synthetic construct

source_name: Neat RNA Sequins Mix B

extract_protocol:
Refer to Hardwick et al. 2016.
cDNA libraries were constructed with the cDNA-PCR (SQK-PCS109) sequencing and PCR Barcoding (SQK-PBK004) kits using the supplied protocol. RNA sequins are provided in two mixes (A and B), which contain the same transcripts, but at variable molar ratios to parallel differences in gene expression and alternative splicing. Briefly, duplicate libraries of each mix (A1, A2, B1, B2), were constructed using 15 ng as input for cDNA synthesis. Samples were barcoded (1 – 4) using the supplied PCR barcodes (ONT). Transcripts were amplified by 14x cycles of PCR with a 6 min extension time. Sequencing libraries were individually purified using 0.8x AMPure XP beads (Beckman Coulter) and quantified using a Qubit 4.0 (ThermoFisher Scientific). Equimolar amounts of each sample were pooled to a total of approximately 160 fmol (assuming median transcript size = 1 kb), and the pooled library QC’d using a TapeStation 4200 (Agilent Technologies). The final library was loaded onto a R9.4.1 MinION flow cell and sequenced for 65 hrs, with a buffer refuel at 24 hrs with 250 uL buffer FB.

tag: mix

value: B

tag: molecule subtype

value: Neat RNA spike-in (no natural RNA)

tag: sequencing protocol

value: single-end


title: CENP-A_ChIP_rep2


title: Sequin Mix B replicate 1


title: Sequin Mix A replicate 2

source_name: Neat RNA Sequins Mix A

value: A


title: CENP-A_ChIP_rep4


title: CENP-A_ChIP_rep1


title: Sequin Mix A replicate 1


title: nbd_Syn-6_Input_rep1


title: F0_D2_hippocampus_depressed


title: CND_RNA_CTR_18H_3

city: Bethesda

first: Kathleen

middle: Shaindel Metz

last: Reed

state: MD

address: 41 Medlars Dr, B507

department: Genetics and Molecular Biology

institute: National Cancer Institute, NIH

data_processing:
Adapters and low-quality reads were trimmed using Trim Galore! (version 0.4.3; parameters: --paired)
Trimmed reads were quantified using Salmon in mapping-based mode (version 0.8.2; parameters: -l A)
Gene-level summaries of counts were compiled using tximport (version 1.2.0)
Differential analysis was conducted in R (version 3.5.1) with DESeq2 (version 1.22.2; design: LRT, full= ~patient+treatment, reduced= ~ patient, lfcShrink (apeglm),  LFC threshold = 1, pval threshold = 0.01)
Genome_build: hg19
Supplementary_files_format_and_content:  CND_RNA_<TRMT>_<TIME>_<DONOR>_quant.sf (Salmon output; transcript-level quantification; tab-delimited file listing transcript name, length, effective length, TPM, and estimated number of reads mapped); CRFT_differentialAnalysisFullData.txt (formatted DESeq2 output; gene-level quantification and differential analysis statistics; tab-separated table listing gene ENSEMBL ID, HGNC ID, cluster assignment, LRT p-value, LFC at 3, 6, and 18 hours, average (among three donors) difference in z-score normalized counts between treated and control samples at 3, 6, and 18 hours, and gene-summarized raw counts from the 'NumReads' in quant.sf files for each sample)

source_name: Normal femoral cartilage

growth_protocol: Primary femoral chondrocytes were isolated from normal donor ankles using enzymatic digestion. Cells were cultured to conlfuency in DMEM/F12 with 10% fetal bovine serum, and then serum-starved for 2 hours prior to treatment.

extract_protocol:
RNA was extracted using a Qiagen RNeasy kit. RIN were checked with Tapestation RNA HS tape and confirmed to be in range of 8.5-10
Ribosomal RNA was removed using the NEBNext rRNA Depletion Kit. Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit and NEBNext Multiplex Oligos for Illumina.

treatment_protocol: Cells were treated with either purified endotoxin-free recombinant FN-f (1 uM in PBS), or PBS alone as a control. The 42 kDa FN-f used here consists of domains 7-10 in native fibronectin and contains the RGD cell binding domain recognized by the ɑ5β1 integrin. Cells were left for 3, 6, or 18 hours prior to RNA extraction.

tag: donor

tag: treatment

value: PBS, 18 hours

value: Primary articular chondrocytes


title: CND_RNA_CTR_18H_2


title: CND_RNA_CTR_18H_1


title: CND_RNA_FNF_18H_3

value: FNF, 18 hours


title: CND_RNA_CTR_03H_3

value: PBS, 3 hours


title: CND_RNA_CTR_03H_1


title: CND_RNA_FNF_18H_2


title: CND_RNA_FNF_03H_3

value: FNF, 3 hours


title: CND_RNA_FNF_06H_1

value: FNF, 6 hours


title: CND_RNA_FNF_03H_2


title: CND_RNA_FNF_03H_1


title: Smchd1 null replicate 3

data_processing:
PromethION software version 18.02.6 (batch 1) and 19.01.6 (batch 2).
Base calling and quality scoring: Guppy version 4.0.11
Trimming and de-multiplexing: Guppy version 4.0.11
Sequenced reads were mapped using minimap2 version 2.17 with arguments -ax splice -uf -k14 --junc-bed.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.34.4) using GENCODE vM23 annotation.
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.26.5, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise linear models (Smyth, SAGMB 2004) with observational level weights (Law et al. Genome Biology 2014) were fitted to summarise the values from replicates samples using functionality from the limma package (version 3.40.6, Ritchie et al. NAR, 2015).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.tsv: tab-delimited text files with columns representing Ensembl Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: Neural stem cell

growth_protocol: NSCs were derived as previously described (Chen et al., 2015). Cells were grown in NeuroCult Stem Cell medium (StemCell Technologies #05702) with cytokines: ◦ 45ml NeuroCult NSC Basal Medium (Mouse) (StemCell Technologies #05700) ◦ 5ml NeuroCult Proliferation Supplement (Mouse) (StemCell Technologies #05701) ◦ 4μl (0.25mg/ml) rh EGF (StemCell Technologies #02633) ◦ 4μl (0.25mg/ml) rh bFGF (StemCell Technologies #02634).

extract_protocol:
We extracted total RNA with Trizol and purified polyA RNA with the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490).
We prepared direct cDNA nanopore libraries with the DCS108 kit (batch 1) and DCS109 kit (batch 2) and barcoded libraries with the native barcoding kit (NB103 and 114). Samples were sequenced on two FLO-PRO002 PromethION flow cells.
Single-end

value: FVB/N

value: Neural stem cell

tag: batch


title: Wild-type replicate 4

value: Smchd1 Wild-type


title: Wild-type replicate 3


title: Smchd1 null replicate 2


title: Smchd1 null replicate 1


title: Wild-type replicate 1

value: 1 and 2


title: Wild-type replicate 2


title: P3_EM

status: Public on Jun 11 2020

city: Stockholm

first: Marcus

last: Buggert

address: C2:94; Karolinska Universitetssjukhuset Huddinge

department: Microbiology

country: Sweden

institute: Karolinska Institutet

data_processing:
Sequencing reads were aligned to the hg38 reference genome using STAR 2.5.2a
Data was normalized using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated text file include normalized read counts for each sample

source_name: Donor 3, Effector memory CD8+ T cell

growth_protocol: Cells were thawed and rested overnight at 37C in RPMI + 10% FBS + 1% L-glut + 1% Pen/Strep media

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

treatment_protocol: Cells were not treated with any compound

value: Donor 3

value: Effector memory CD8+ T cell


title: CND_RNA_CTR_06H_3

value: PBS, 6 hours


title: CND_RNA_CTR_06H_1


title: P3_Naive

source_name: Donor 3, Naïve CD8+ T cell

value: Naive CD8+ T cell


title: CND_RNA_CTR_06H_2


title: P2_CM

source_name: Donor 2, Central memory CD8+ T cell

value: Donor 2

value: Central memory CD8+ T cell


title: P2_EM

source_name: Donor 2, Effector memory CD8+ T cell


title: CND_RNA_FNF_18H_1


title: CND_RNA_FNF_06H_2


title: P2_EMRA

source_name: Donor 2, Effector (RA+) CD8+ T cell

value: Effector (RA+) CD8+ T cell


title: CND_RNA_CTR_03H_2


title: P2_Naive

source_name: Donor 2, Naïve CD8+ T cell


title: P1_EMRA

source_name: Donor 1, Effector (RA+) CD8+ T cell

value: Donor 1


title: P1_CM

source_name: Donor 1, Central memory CD8+ T cell


title: CND_RNA_FNF_06H_3

value: Primary articular chondrocytes


title: P1_Naive

source_name: Donor 1, Naïve CD8+ T cell


title: P1_EM

source_name: Donor 1, Effector memory CD8+ T cell


title: 1Yr-Sham-N3

status: Public on May 26 2020

city: Minneapolis

first: Laura

last: Stone

address: 420 Delaware Street SEMMC 294

institute: University of Minnesota

data_processing:
Data was processed according to the Canadian Centre for Computational Genomic GenPipes Methyl-Seq pipeline http://www.computationalgenomics.ca/about_genpipes/
Read Trimming and Quality filtering - Trimmomatic 0.36. trailing 30, minlen 50
Read alignment - Bismark 0.18.1  -N 0 -L 20 -X 500 -p 2 --multicore 3 / bowtie2 2.3.1 / samtools 1.4
Add Read groups -  Picard 2.9.0
Merge SAM files - Picard 2.9.0
Remove Duplicates - Picard 2.9.0
Methylation call - Bismark 0.18.1 bismark_methylation_extractor --no_overlap --comprehensive --gzip --multicore 5 --no_header --bedGraph --buffer_size 20G --cytosine_report
Genome_build: mm10
Supplementary_files_format_and_content: bedgraphs were generated depicting CpG position and scores represent methylation values

source_name: Prefrontal Cortex

extract_protocol:
PFC tissue was homogenized and genomic DNA was extracted using the Qiagen DNEasy Blood and Tissue Kit protocol
DNA was bisulfite converted according to the Roche SeqCap Epi Developer M Enrichment system and standard Illumina protocols
Custom Probe Capture Bisulfite Sequencing

value: Prefrontal Cortex

tag: timepoint

value: One Year post-injury

tag: injury

value: Sham


title: P3_EMRA

source_name: Donor 3, Effector (RA+) CD8+ T cell


title: M6-Sham-7.3

value: Six Months post-injury


title: 1Yr-SNI-L4

value: SNI


title: 1Yr-Sham-N1


title: 1Yr-SNI-O4


title: 1Yr-Sham-J1


title: 1Yr-SNI-O3


title: P3_CM

source_name: Donor 3, Central memory CD8+ T cell


title: 1Yr-SNI-O5


title: M6-Sham-7.2


title: M6-Sham-7.1


title: M6-SNI-6.2


title: M6-Sham-3.2


title: M6-Sham-11.1


title: M6-Sham-3.3


title: M6-SNI-4.3


title: M6-SNI-6.1


title: M6-SNI-20.2


title: M6-SNI-10.2


title: W2-Sham-5.2

value: Two Weeks post-injury


title: W2-Sham-5.3


title: M6-SNI-10.1


title: W2-Sham-9.3


title: W2-Sham-9.1


title: W2-Sham-5.1


title: W2-SNI-8.3


title: 1Yr-SNI-L1


title: W2-Sham-9.2


title: 1Yr-SNI-L2


title: W2-SNI-8.1


title: W2-SNI-16.3


title: W2-SNI-16.2


title: W2-SNI-8.2


title: D1-Sham-2.2

value: One Day post-injury


title: D1-Sham-1.1


title: D1-Sham-1.2


title: D1-Sham-1.3


title: W2-SNI-16.1


title: D1-SNI-4.1


title: D1-SNI-3.3


title: D1-SNI-3.2


title: 1Yr-Sham-N2


title: 36_FGF1 single-cell from the hypothalamus of 1 mouse

status: Public on Apr 21 2020

city: Copenhagen

first: Tune

middle: Hannes

last: Pers

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Basic Metabolic Research

country: Denmark

institute: University of Copenhagen

description:
wholecell_normdata.csv.gz
wholecell_metadata.csv.gz

data_processing:
Read alignment: Cell Ranger version 1.2 (10X Genomics, USA) was used to de-multiplex and quantify unique molecular identifiers (UMI). A count matrix was generated for each sample with default parameters and genes were mapped to the 10x reference for GRCm38 (mm10; for the scRNA-seq data set) or an adapted reference from 10x mm10-premrna to include introns (for the snRNA-seq data set), following the steps outlined on the 10x Genomics website  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references).
Barcode filtering: Barcodes were filtered to include those with a total UMI count >10% of the 99th percentile of the expected recovered cells.
Quality control: The Scrublet tool was run with default parameters to identify likely doublets (this step was omitted for the snRNA-seq data) which were subsequently removed from the expression matrix. Further processing was performed using the Seurat50 R package (version 2.3). Cells in which <500 or >4,000 (>5,500 for the snRNA-seq data) expressed genes were detected, as well any cell with >20% (>5% for snRNA-seq) mitochondrial and/or ribosomal transcripts were discarded. Genes detected in <10 cells (<3 cells in the snRNA-seq data) were also removed.
Normalization: Counts were normalized using Seurat SCTransform
Genome_build: Mus Musculus reference genome build Grch38 – release 77
Supplementary_files_format_and_content: nuclei_normdata.csv.gz: comma-separated, gzip archived. Contents: gene*nuclei matrix containing the filtered and normalized nuclei counts
Supplementary_files_format_and_content: nuclei_metadata.csv.gz: comma-separated, gzip archived. Contents: nuclei metadata. Columns nCount_RNA,nFeature_RNA,nCount_SCT,nFeature_SCT,sample,batch,trt,number,day,group,pred_ID,pred_CONF,ref,celltype
Supplementary_files_format_and_content: wholecell_normdata.csv.gz: comma-separated, gzip archived. Contents: gene*cell matrix containing the filtered and normalized cell counts
Supplementary_files_format_and_content: wholecell_metadata.csv.gz: comma-separated, gzip archived. Contents: cell metadata. Columns: orig.ident,nCount_RNA,nFeature_RNA,percent.mito,percent.ribo,nCount_SCT,nFeature_SCT,SCT_snn_res.0.1,seurat_clusters,trt,sample,batch,SCT_snn_res.0.6
Supplementary_files_format_and_content: nuclei_rawdata.csv.gz: comma-separated, gzip archived. Contents: gene*nuclei matrix containing the filtered nuclei counts
Supplementary_files_format_and_content: wholecell_rawdata.csv.gz: comma-separated, gzip archived. Contents: gene*cell matrix containing filtered cell counts

source_name: hypothalamus

growth_protocol: Individually housed under specific-pathogen free conditions in a temperature-controlled room with a 12:12h light:dark cycle and provided with ad libitum (ad-lib) access to water and Altromin 1310 chow (Brogaarden, Denmark)

extract_protocol:
Tissue dissociation with Neural Tissue Dissociation Kit (Miltenyi Biotec) and fire-polished Pasteur pipettes. See article for details
Single-cells cDNA libraries were generated using Chromium Single-cell platform and 3’ v2 Reagent Kit according to manufacturer’s protocol (10x Genomics, USA). Single-cell libraries were sequenced on a NextSeq 500 platform (3 samples (whole single-cells) and 2 samples (single-nuclei) on one flow cell)

treatment_protocol: 3 ug intracerebral ventricular injection of FGF1. Euthanized 5d post injection

value: ob/ob

tag: Sex

value: male

value: 11 weeks

tag: number of mice

value: hypothalamus


title: 21_FGF1 single-cell from the hypothalamus of 1 mouse


title: 22_PF single-cell from the hypothalamus of 1 mouse

treatment_protocol: intracerebral ventricular injection of PBS. Pair-fed to amount eaten by FGF1 injected mice. Euthanized 5d post injection


title: 20_PF single-cell from the hypothalamus of 1 mouse


title: 10_FGF1 single-cell from the hypothalamus of 1 mouse


title: 6_FGF1 single-cell from the hypothalamus of 1 mouse


title: 25_PF single-cell from the hypothalamus of 1 mouse


title: D1-SNI-3.1


title: 35_FP single-cell from the hypothalamus of 1 mouse


title: 45_FGF Single-nucleus from the hypothalamus of 1 mouse

description:
nuclei_normdata.csv.gz
nuclei_metadata.csv.gz

growth_protocol: Individually housed under specific-pathogen free conditions in a temperature-controlled room with a 12:12h light:dark cycle and provided with ad libitum (ad-lib) access to water and Purina 5008 chow (Animal Specialties, Inc., CA, USA)

extract_protocol:
Nuclei extraction with EZ buffer (Sigma) and dounce tissue grinders followed by Nuclei PURE Prep Isolation Kit (Sigma). See article for details
Single-cells cDNA libraries were generated using Chromium Single-cell platform and 3’ v2 Reagent Kit according to manufacturer’s protocol (10x Genomics, USA). Single-cell libraries were sequenced on a NextSeq 500 platform (3 samples (whole single-cells) and 2 samples (single-nuclei) on one flow cell)


title: 38_PF Single-nucleus from the hypothalamus of 1 mouse


title: 7_FGF1 single-cell from the hypothalamus of 1 mouse


title: 37_FGF Single-nucleus from the hypothalamus of 1 mouse


title: PF_3 Single-nucleus from the hypothalamus of 1 mouse

treatment_protocol: intracerebral ventricular injection of PBS. Pair-fed to amount eaten by FGF1 injected mice. Euthanized 24h post injection


title: 28_PF Single-nucleus from the hypothalamus of 1 mouse


title: 28_FGF1 single-cell from the hypothalamus of 1 mouse


title: 1_FGF Single-nucleus from the hypothalamus of 1 mouse

treatment_protocol: 3 ug intracerebral ventricular injection of FGF1. Euthanized 24h post injection


title: FGF_3 Single-nucleus from the hypothalamus of 1 mouse


title: FGF_2 Single-nucleus from the hypothalamus of 1 mouse


title: PF_2 Single-nucleus from the hypothalamus of 1 mouse


title: PDAC-B ST1

status: Public on Jan 13 2020

first: Itai

last: Yanai

state: NY

address: 435 E. 30th Street, 8th Floor

institute: Institute for Computational Medicine, NYU Langone Health

data_processing:
Illumina RTA v2 software was used for basecalling and quality determination.
Raw sequencing data obtained from the inDrop method were processed using a custom-built pipeline, available online (https://github.com/flo-compbio/singlecell). Briefly, the “W1” adapter sequence of the inDrop RT primer was located in the barcode read (the second read of each fragment), by comparing the 22-mer sequences starting at positions 9-12 of the read with the known W1 sequence (“GAGTGATTGCTTGTGACGCCTT”), allowing at most two mismatches. Reads for which the W1 sequence could not be located in this way were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read, which can range from 8-11 bp, as well as the start position of the second part of the inDrop cell barcode, which always consists of 8 bp. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read, allowing at most one mismatch. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally, the UMI sequence was extracted (included in Read 1 together with transcript), and reads with low-confidence base calls for the six bases comprising the UMI sequence (minimum PHRED score less than 20) were discarded. The reads containing the mRNA sequence (the first read of each fragment) were mapped by STAR 2.5.1 with parameter “—outSAMmultNmax 1” and default settings otherwise36. Mapped reads were split according to their cell barcode and assigned to genes by testing for overlap with exons of protein-coding genes.
Raw sequencing data obtained from the ST method were processed using a custom-built pipeline, available online (https://github.com/yanailab/celseq2). The pipeline was adapted to ST sequencing data using the following three steps: 1) Tagging and demultiplexing: the left-most 25 nucleotides (nt) of the R1 sequence contains the 18 nt for the spot-specific barcode and then 7 nt for UMI. The R2 sequence contains the transcript sequence, and its left-most 35 nt are used. The name of every read in the R2 file is tagged with the spot-specific barcode and UMI sequence that are extracted from the paired R1 read. The R2 file is demultiplexed to create the 1007 spot-specific FASTQ files. If the detected spot-specific barcode of a read is not present in the pre-defined barcodes list, the read is excluded from the downstream analysis. 2) Alignment of demultiplexed FASTQ files using Bowtie2. 3) Counting UMI using HTSeq. The reads that are aligned to a user-defined feature (by default: “gene_name”) are collapsed to count only once if they have same UMI. Here we used the version 2.3.1 of Bowtie2 with default parameters and the 0.9.1 version of HTSeq in the “union” mode. For demultiplexing spatial barcodes, PDAC-A ST1 was demultiplexed using the lot10001 barcode file, and PDAC-B ST1 was demultiplexed using the lot10003 barcode file (barcode files included in submission, and is also available at https://spatialtranscriptomics.com/resources/
Genome_build: hg38
Supplementary_files_format_and_content: for inDrop data: tab-delimited files with genes as rows and cells as columns.  Cell ID is composed of the word "cell" followed by two numbers which represent the sequence number of the barcodes available in the files inDrop_gel_barcode*txt. For example, cell_004-028 is represented by the 4th barcode sequence in inDrop_gel_barcode1_list.txt  and the 28th sequence in inDrop_gel_barcode2_list.txt.
Supplementary_files_format_and_content: For ST data: tab-delimited files with spots as rows (with first column is the coordinate of each spot along the array) and genes are columns.

source_name: pancreatic adenocarcinoma tissue

extract_protocol:
For single-cell RNA-seq (inDrop platform), cell suspension was generated by incubating minced pancreatic cancer tissue with trypsin for 15' at 37C prior to droplet encapsulation and individual barcoding of cells using the inDrop platform. Cell lysis was performed in droplets to release RNA, and reverse transcription and barcoding took place in droplets at 50C for 2h. For spatial transcriptomics of pancreatic cancer tissue, 10 µm cryosections were mounted onto spatially barcoded arrays where reverse transcription of cellular transcripts took place in situ after tissue permeabilisation.
For single-cell RNA-seq library construction, we followed the inDrop library construction protocol detailed by Klein et al,  Cell 2015, with minor changes. Briefly, RNA was reverse transcribed (RT) with SuperScript III (Invitrogen) in droplets. Droplet emulsions were broken, and post-RT material underwent second strand syntehsis and in vitro transcription using the T7 High Yield Enzyme mix (New England Biolabs). RNA was fragmented for 105 seconds with 1X fragmentation reagent (1CellBio) prior to RT with random hexamers, eliminating the need for an adaptor ligation step. Cycles required for final library amplification was assessed by quantitative PCR (qPCR) with KAPA HiFi Hot Start PCR Mix (KAPA Biosystems) and EvaGreen dye (Biotium). Final libraries were amplified with KAPA HiFi Hot Start PCR mix for 9 to 13 cycles. inDrop library size assessed on a DNA BioAnalyzer chip following the manufacturer's instructions (Agilent).   For spatial transcriptomics (ST) library construction, we followed the previously published ST protocol from Stahl et al. Science 2016, with minor changes. Briefly, after brightfield imaging of stained tissue, tissue was permeabilized with collagenase and 0.1% pepsin prior to an overnight RT step with SuperScript III on the ST slide. Tissue was digested away with proteinase K and 1% 2-mercaptoethanol prior to cleavage of probes from the slide surface with USER enzyme. Second strand synthesis was performed with DNA Pol I and RNase H (New england biolabs) followed by an in vitro transcription amplification step with the MEGAScript T7 kit (Thermofisher). Amplified RNA then underwent a second RT with random hexamers and SuperScript II (Invitrogen), eliminating the need for an adaptor ligation step. Cycles required for final library amplification was assessed by quantitative PCR (qPCR) with KAPA HiFi Hot Start PCR Mix (KAPA Biosystems) and EvaGreen dye (Biotium). Final libraries were amplified with KAPA HiFi Hot Start PCR mix for 9 to 13 cycles. inDrop library size assessed on a DNA BioAnalyzer chip following the manufacturer's instructions (Agilent).

value: pancreatic adenocarcinoma

tag: tissue preparation

value: tissue cryosections


title: 1_PF Single-nucleus from the hypothalamus of 1 mouse


title: Saos2_DNase-seq

status: Public on Jan 03 2020

first: Matthew

middle: T

last: Maurano

address: 435 East 30th Street

department: Institute for Systems Genetics

institute: NYU School of Medicine

data_processing:
Illumina adapters were trimmed using Trimmomatic v. 0.38
Reads were aligned to the hg38 human reference using BWA v.0.7.15
Peak calling was performed using hotspot2 with a cutoff of 5% false discovery rate
Genome_build: hg38
Supplementary_files_format_and_content: bed.gz files contain peak calls; bw files contain read mapping density data

extract_protocol:
Nuclei were extracted from cells and incubated with limiting concentrations of the DNA endonuclease DNase I (Sigma) supplemented with Ca2+ and Mg2+ for 3 min at 37 °C.
DNA fragments isolated from DNaseI digestions were end-repaired, A-tailed, and then Illumina adapters were ligated during an overnight digestion at 16C. The resulting libraries were PCR amplified for 8-10 cycles.


title: PDAC-A ST1

data_processing:
Illumina RTA v2 software was used for basecalling and quality determination.
Raw sequencing data obtained from the inDrop method were processed using a custom-built pipeline, available online (https://github.com/flo-compbio/singlecell). Briefly, the “W1” adapter sequence of the inDrop RT primer was located in the barcode read (the second read of each fragment), by comparing the 22-mer sequences starting at positions 9-12 of the read with the known W1 sequence (“GAGTGATTGCTTGTGACGCCTT”), allowing at most two mismatches. Reads for which the W1 sequence could not be located in this way were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read, which can range from 8-11 bp, as well as the start position of the second part of the inDrop cell barcode, which always consists of 8 bp. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read, allowing at most one mismatch. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally, the UMI sequence was extracted, and reads with low-confidence base calls for the six bases comprising the UMI sequence (minimum PHRED score less than 20) were discarded. The reads containing the mRNA sequence (the first read of each fragment) were mapped by STAR 2.5.1 with parameter “—outSAMmultNmax 1” and default settings otherwise36. Mapped reads were split according to their cell barcode and assigned to genes by testing for overlap with exons of protein-coding genes.
Raw sequencing data obtained from the Spatial Transcriptomics (ST) method were processed using a publicly available pipeline (https://github.com/jfnavarro/st_pipeline). Briefly, quality trimming is performed to remove low quality bases and reads with long nucleotide stretches (> 15). Read 2 (transcript sequence) is mapped with STAR 2.5.1 and Read 1 (spatial barcode) is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq-count; to get a final read count annotated reads are grouped by spatial barcode.
Genome_build: hg38
Supplementary_files_format_and_content: for inDrop data: tab-delimited files with genes as rows and cells as columns. For ST data: tab-delimited files with spots as rows (with first column is the coordinate of each spot along the array) and genes are columns.


title: U2OS_DNase-seq


title: F23

status: Public on Sep 19 2019

city: Austin

first: Anna

last: Battenhouse

state: TX

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

institute: The University of Texas at Austin

description: RNAseq of SEC fraction 23

data_processing:
Illumina Casava software used for basecalling.
After performing quality control on the sequencing fastq files using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/), 3' adapter contamination was removed using Cutadapt (v1.10) (Martin, 2011).
Alignment of the 8 RNA fraction datasets was then performed with the Hisat2 transcriptome-aware aligner (v2.1.0) (Kim et al., 2015), against a Hisat2 reference index built using GRCh38 primary assembly genome fasta from Gencode (v27, Ensembl release 90) (Harrow et al., 2012) annotated with the corresponding v27 GTF (General Transfer Format) annotations.
The Hisat suite Stringtie program (v1.3.3b) (Pertea et al., 2016) was used to quantify gene-level expression from the alignment files.
TPM (Transcripts Per Million, a sequencing-depth-normalized estimate of reads mapping to the gene), output files from Stringtie were used for further analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files provide TPM (Transcript Per Million) gene expression values for each Sample.

source_name: embryonic kidney cells

growth_protocol: HEK293T cells (ATCC CRL3216) cultured in DMEM (Gibco) supplemented with 10 % (v/v) FBS (Life Technologies) were continually split over 7 days to give four 10-cm dishes of adherent cells.

extract_protocol:
Cells (approximately 0.1 g wet weight) were lysed on ice (5 min) by resuspension in Pierce IP Lysis Buffer (0.8 mL; 25 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% NP-40 and 5% glycerol; Thermo Fisher) containing 1x protease inhibitor cocktail III (Calbiochem). The resulting lysate was clarified (17,000g, 10 min, 4 °C) and left at room temperature (30 min). The sample was filtered (Ultrafree-MC filter unit (Millipore); 12,000g, 2 min, 4 °C) to remove insoluble aggregates.
All lysates were subject to size exclusion chromatography (SEC) using an Agilent 1100 HPLC system (Agilent Technologies, ON, Canada) with a multi-phase chromatography protocol as previously described (Havugimana et al., 2012). Fractions from a biological replicate SEC separation corresponding to higher molecular weight species (approximately >1.5 MDa; fractions 16-23 in Figure 1B) were analyzed by total RNA sequencing. Total RNA was isolated from each fraction (0.375 mL) by addition of Trizol (1.125 mL; Thermo Fisher) and the sample (1.4 mL) was transferred to a Phasemaker tube (Thermo Fisher). Total RNA was extracted following the protocol supplied by the manufacturer and further cleaned up using a RNeasy MinElute Cleanup Kit (Qiagen). RNA integrity number (RIN) was measured using an Agilent Bioanalyzer and samples were ribo-depleted using a RiboZero Gold (Human/Mouse/Rat) kit (Illumina) to remove rRNAs. RNA libraries were prepared for sequencing according to vendor protocols using NEBNext R Small RNA Library Prep Set for Illumina R (Multiplex Compatible), Cat #E7330L, according to the protocol described by Podnar et al. (Podnar et al., 2014). RNA was fragmented using elevated temperature in carefully controlled buffer conditions to yield average fragment sizes of 200 nucleotides. These fragments were directionally ligated to 5' and 3' adaptors so that sequence orientation is preserved throughout sequencing. Reverse transcription and PCR were performed to complete the DNA sequencing libraries, which were sequenced using an Illumina NextSeq 500 instrument (75-nt single reads) at the Genomic Sequencing and Analysis Facility at the University of Texas at Austin.

tag: cell type

value: ATCC CRL3216

value: embryonic kidney 293 cells


title: F22

description: RNAseq of SEC fraction 22


title: 27_PF single-cell from the hypothalamus of 1 mouse

tag: age


title: 29_PF single-cell from the hypothalamus of 1 mouse


title: F21

description: RNAseq of SEC fraction 21


title: F19

description: RNAseq of SEC fraction 19


title: F18

description: RNAseq of SEC fraction 18


title: F20

description: RNAseq of SEC fraction 20


title: Renca Responder rep11 [RZ69]

status: Public on Jul 18 2019

city: Crawley, Perth

first: Emma

last: de Jong

state: WA

address: 35 Stirling Hwy

institute: University of Western Australia

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3. RTA performs real-time base calling on the HiSeq instrument computer
The Illumina bcl2fastq 2.18.0.12 pipeline was used to generate the sequence data
Read libraries were mapped to the GRCh37 (hg19) Human genome using HISAT2 (v2.0.4)
Gene-level quantitation (counts) of HISAT2 alignments was performed using SummarizeOverlaps
Transcript discovery and quantification (FPKM) of HISAT2 alignments was performed using StringTie (v1.3.0) and Ballgown
Genome_build: hg19
Supplementary_files_format_and_content: genecounts.csv file contains a matrix of raw gene counts (unfiltered and un-normalised data)

growth_protocol: AB1 or Renca tumour cells were subcutaneously injected into Balb/c mice, and whole tumour surgically removed 8 or 10 days after (respectively)"

extract_protocol:
Frozen tumours were dissociated in Trizol using a TissueRuptor, total RNA was extracted using chloroform and purified on Rneasy MiniElute columns.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: host strain

value: balb/c

tag: host mouse age

value: 8-9 weeks

tag: host mouse gender

value: female

tag: tumor cells

value: Renca

tag: tumor type

value: kidney cancer

value: anti-CTLA4 plus anti-PDL-1

value: day 0 - pretreatment

tag: response to immunotherapy

value: Responder


title: Renca Non-responder rep8 [RZ58]

value: Non-responder


title: Renca Non-responder rep10 [RZ68]


title: Renca Responder rep12 [RZ71]


title: Renca Responder rep9 [RZ65]


title: Renca Responder rep10 [RZ67]


title: Renca Non-responder rep11 [RZ70]


title: Renca Non-responder rep9 [RZ66]


title: Renca Non-responder rep6 [RZ42]


title: Renca Responder rep6 [RZ41]


title: Renca Non-responder rep12 [RZ72]


title: Renca Responder rep5 [RZ33]


title: Renca Responder rep8 [RZ57]


title: Renca Non-responder rep7 [RZ50]


title: F17

description: RNAseq of SEC fraction 17

tag: strain

tag: tissue


title: Renca Responder rep7 [RZ49]

tag: treatment


title: Renca Non-responder rep4 [RZ26]


title: Renca Non-responder rep2 [RZ10]


title: Renca Non-responder rep5 [RZ34]


title: Renca Responder rep4 [RZ25]


title: Renca Responder rep1 [RZ01]


title: Renca Non-responder rep1 [RZ02]


title: AB1 Non-responder rep12 [AB72]

value: mesothelioma


title: AB1 Responder rep12 [AB71]


title: AB1 Non-responder rep11 [AB70]


title: AB1 Non-responder rep10 [AB68]


title: AB1 Responder rep11 [AB69]


title: AB1 Non-responder rep8 [AB58]


title: AB1 Responder rep8 [AB57]


title: AB1 Non-responder rep9 [AB66]


title: AB1 Responder rep7 [AB49]


title: AB1 Responder rep10 [AB67]


title: AB1 Non-responder rep6 [AB42]


title: Renca Responder rep3 [RZ17]


title: AB1 Responder rep9 [AB65]


title: AB1 Non-responder rep5 [AB34]


title: Renca Responder rep2 [RZ09]


title: F16

description: RNAseq of SEC fraction 16


title: AB1 Non-responder rep7 [AB50]


title: AB1 Responder rep4 [AB25]


title: AB1 Non-responder rep2 [AB10]


title: AB1 Responder rep6 [AB41]


title: AB1 Responder rep3 [AB17]


title: AB1 Non-responder rep4 [AB26]


title: Renca Non-responder rep3 [RZ18]


title: AB1 Non-responder rep1 [AB02]


title: AB1 Responder rep5 [AB33]


title: AB1 Responder rep2 [AB09]


title: AB1 Responder rep1 [AB01]


title: AB1 Non-responder rep3 [AB18]


title: hESC-HNF1A-KO2: ES_797365

status: Public on Apr 12 2019

city: New York

first: Dieter

last: Egli

address: 701 West 168th Street

institute: Columbia University

description: Differentiation day 25. Experiment number A34. Genotype HNF1A KO2

data_processing:
Single cell RNA-Seq data from total of 271 hESC-derived cells (113 for WT and 158 for KO) were obtained. Raw reads were aligned to the hg19 reference genome using STAR (2.5.2b) and gene quantification were performed using FeatureCounts (1.5.2).
Quality control was conducted as follows: cells with low mapped reads (<1,000,000), low exon count (<100,000), low exon mapped rate (<0.2), high intergenic mapped rate (>0.3), low detected gene count (<1,000) and with more than 10% Mitochondria genes' count were removed. In addition, genes with <10 non-zero counts across all the cells were eliminated. All the downstream analysis was done with in R-3.4.1. Filtered raw count data were normalized and scaled by Seurat package and only variable genes generated by Seurat were used to do PCA and t-SNE. n=3 for each genotype.
Genome_build: GRCh37
Supplementary_files_format_and_content: .txt files are the processed raw count files of each cell with label information.

source_name: Endocrine cells

growth_protocol: The initial stages of differentiation were conducted in planar culture (d0-d11). For definitive endoderm stage (d1-d3) cells were cultured using STEMdiffTM Definitive Endoderm Differentiation Kit (Stemcell Technologies, 05110). For primitive gut stage (d4-d6), cells were cultured in RPMI containing GlutaMAX (Life Technology, 61870-127), 1% (v/v) Penicillin-Streptomycin (PS) (Thermo Fisher Scientific, 15070-063), 1% (v/v) B27 Serum-Free Supplement (50x) (Life Technology, 17504044) and 50 ng/ml FGF7 (R&D System, 251-KG). For posterior foregut stage (d7-d8), cells were cultured in DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 0.25 μM KAAD-Cyclopamine (Stemgent, 04-0028), 2 μM Retinoic acid (Stemgent, 04-0021) and 0.25 μM LDN193189 (Stemgent, 04-0074). For pancreatic progenitor stage (d9-d11), cells were cultured in DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27 and 50 ng/ml EGF (R&D System, 236-EG). Cells were then dissociated using TrypLE™ Express (Life Technology, 12605036) and seeded into low-attachment 96 well-plates (Corning, 7007) (1 well of 6 well-plate to 60 wells of 96-well-plate) for clustering step to form aggregates or clusters of endocrine cells in DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 0.25 μM Cyclopamine, 1 μM thyroid hormone (T3) (Sigma, T6397), 10 μM Alk5i, 10 μM Zinc sulfate (Sigma-Aldrich, Z4750) and 10 μg/ml Heparin (Sigma-Aldrich, H3149) for 2 days (d12-d13). For pancreatic endocrine stage (d14-20) cells were cultured using DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 100 nM LDN, 1 μM T3, 10 μM Alk5i, 10 μM Zinc sulfate, 10 μg/ml Heparin and 100 nM gamma-secretase inhibitor (DBZ) (EMD Millipore, 565789). For mature pancreatic endocrine stage (d21-d27) cells were cultured using DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 1 μM T3, 10 μM Alk5i, 10 μM Zinc sulfate, 10 μg/ml Heparin, 1 mM N-acetyl cysteine (N-Cys) (Sigma-Aldrich, A9165-5G), 10 μM Trolox (EMD Millipore, 648471-500MG) and 2 μM R428 (Tyrosine kinase receptor AXL inhibitor) (ApexBio, A8329). From d1 to d11 media was changed every day and from d12 to d27 media was changed every other day. All differentiations were done for 27 to 30 days.

extract_protocol:
Around 100 cells per genotype at day 27 of differentiation are dissociated and sorted for GFP using BD FACS Aria II cell sorter.
Human embryonic stem cells with different HNF1A genotypes (WT, KO1 and KO2) were differentiated into islet-like clusters of endocrine cells for 25 days in vitro. Clusters of islet-like cells were dissociated into single cells and insulin producing cells were purified by FACS sorting for INS-GFP. Cells were analyzed by single cell RNA sequencing. There are three WT and three KO.

treatment_protocol: Cells are untreated

value: hES-derived endocrine cells

tag: passages

tag: clone

tag: genotype

tag: days

value: Differentiation day 25

tag: batch


title: hESC-HNF1A-KO2: ES_797366


title: hESC-HNF1A-KO2: ES_797363


title: hESC-HNF1A-KO2: ES_797364


title: hESC-HNF1A-KO2: ES_797362


title: hESC-HNF1A-KO2: ES_797361


title: hESC-HNF1A-KO2: ES_797360


title: hESC-HNF1A-KO2: ES_797355


title: hESC-HNF1A-KO2: ES_797354


title: hESC-HNF1A-KO2: ES_797353


title: hESC-HNF1A-KO2: ES_797350


title: hESC-HNF1A-KO2: ES_797348


title: hESC-HNF1A-KO2: ES_797352


title: hESC-HNF1A-KO2: ES_797356


title: hESC-HNF1A-KO2: ES_797343


title: hESC-HNF1A-KO2: ES_797342


title: hESC-HNF1A-KO2: ES_797340


title: hESC-HNF1A-KO2: ES_797347


title: hESC-HNF1A-KO2: ES_797349


title: hESC-HNF1A-KO2: ES_797339


title: hESC-HNF1A-KO2: ES_797337


title: hESC-HNF1A-KO2: ES_797341


title: hESC-HNF1A-KO2: ES_797335


title: hESC-HNF1A-KO2: ES_797336


title: hESC-HNF1A-KO2: ES_797338


title: hESC-HNF1A-KO2: ES_797358


title: hESC-HNF1A-KO2: ES_797357


title: hESC-HNF1A-KO2: ES_797345


title: hESC-HNF1A-KO2: ES_797332


title: hESC-HNF1A-KO2: ES_797359


title: hESC-HNF1A-KO2: ES_797334


title: hESC-HNF1A-KO2: ES_797351


title: hESC-HNF1A-KO2: ES_797344


title: hESC-HNF1A-KO2: ES_797331


title: hESC-HNF1A-KO2: ES_797330


title: hESC-HNF1A-KO2: ES_797329


title: hESC-HNF1A-KO2: ES_797327


title: hESC-HNF1A-KO2: ES_797346


title: hESC-HNF1A-KO2: ES_797328


title: hESC-HNF1A-KO2: ES_797324


title: hESC-HNF1A-KO2: ES_797325


title: hESC-HNF1A-KO2: ES_797322


title: hESC-HNF1A-KO2: ES_797326


title: hESC-HNF1A-KO2: ES_797321


title: hESC-HNF1A-KO2: ES_783369

description: Differentiation day 25. Experiment number A7. Genotype HNF1A KO2


title: hESC-HNF1A-KO2: ES_783370


title: hESC-HNF1A-KO2: ES_783366


title: hESC-HNF1A-KO2: ES_783367


title: hESC-HNF1A-KO2: ES_783371


title: hESC-HNF1A-KO2: ES_783368


title: hESC-HNF1A-KO2: ES_797320


title: hESC-HNF1A-KO2: ES_783362


title: hESC-HNF1A-KO2: ES_783365


title: hESC-HNF1A-KO2: ES_783363


title: hESC-HNF1A-KO2: ES_783361


title: hESC-HNF1A-KO2: ES_783360


title: hESC-HNF1A-KO2: ES_783357


title: hESC-HNF1A-KO2: ES_783358


title: hESC-HNF1A-KO2: ES_783359


title: hESC-HNF1A-KO2: ES_797323


title: hESC-HNF1A-KO2: ES_783355


title: hESC-HNF1A-KO2: ES_783351


title: hESC-HNF1A-KO2: ES_783354


title: hESC-HNF1A-KO2: ES_783353


title: hESC-HNF1A-KO2: ES_783350


title: hESC-HNF1A-KO2: ES_783348


title: hESC-HNF1A-KO2: ES_783347


title: hESC-HNF1A-KO2: ES_783346


title: hESC-HNF1A-KO2: ES_783345


title: hESC-HNF1A-KO2: ES_783344


title: hESC-HNF1A-KO2: ES_783339


title: hESC-HNF1A-KO2: ES_783343


title: hESC-HNF1A-KO2: ES_783336


title: hESC-HNF1A-KO2: ES_783337


title: hESC-HNF1A-KO2: ES_783338


title: hESC-HNF1A-KO2: ES_783342


title: hESC-HNF1A-KO2: ES_783335


title: hESC-HNF1A-KO2: ES_783356


title: hESC-HNF1A-KO2: ES_783340


title: hESC-HNF1A-KO2: ES_783334


title: hESC-HNF1A-KO2: ES_783331


title: hESC-HNF1A-KO2: ES_783333


title: hESC-HNF1A-KO2: ES_783329


title: hESC-HNF1A-KO2: ES_783330


title: hESC-HNF1A-KO2: ES_783328


title: hESC-HNF1A-KO2: ES_783332


title: hESC-HNF1A-KO2: ES_783352


title: hESC-HNF1A-KO2: ES_783349


title: hESC-HNF1A-KO2: ES_783327


title: hESC-HNF1A-KO2: ES_783324


title: hESC-HNF1A-KO2: ES_783325


title: hESC-HNF1A-KO2: ES_783326


title: hESC-HNF1A-KO2: ES_783323


title: hESC-HNF1A-KO2: ES_783321


title: hESC-HNF1A-KO2: ES_783322


title: hESC-HNF1A-KO2: ES_783320


title: hESC-HNF1A-KO2: ES_783319


title: hESC-HNF1A-KO2: ES_783318


title: hESC-HNF1A-KO2: ES_783317


title: hESC-HNF1A-KO2: ES_783315


title: hESC-HNF1A-KO2: ES_783316


title: hESC-HNF1A-KO2: ES_783310


title: hESC-HNF1A-KO2: ES_783313


title: hESC-HNF1A-KO2: ES_783312


title: hESC-HNF1A-KO2: ES_783311


title: hESC-HNF1A-KO2: ES_783314


title: hESC-HNF1A-KO2: ES_783307


title: hESC-HNF1A-KO2: ES_783309


title: hESC-HNF1A-KO2: ES_783308


title: hESC-HNF1A-KO1: ES_797448

description: Differentiation day 25. Experiment number A38. Genotype HNF1A KO1


title: hESC-HNF1A-KO2: ES_783306


title: hESC-HNF1A-KO2: ES_783303


title: hESC-HNF1A-KO1: ES_797447


title: hESC-HNF1A-KO2: ES_783304


title: hESC-HNF1A-KO1: ES_797446


title: hESC-HNF1A-KO1: ES_797445


title: hESC-HNF1A-KO1: ES_797444


title: hESC-HNF1A-KO1: ES_797442


title: hESC-HNF1A-KO1: ES_797441


title: hESC-HNF1A-KO1: ES_797440


title: hESC-HNF1A-KO1: ES_797439


title: hESC-HNF1A-KO1: ES_797443


title: hESC-HNF1A-KO1: ES_797437


title: hESC-HNF1A-KO1: ES_797438


title: hESC-HNF1A-KO1: ES_797436


title: hESC-HNF1A-KO1: ES_797434


title: hESC-HNF1A-KO2: ES_783305


title: hESC-HNF1A-KO1: ES_797433


title: hESC-HNF1A-KO1: ES_797435


title: hESC-HNF1A-KO1: ES_797430


title: hESC-HNF1A-KO1: ES_797429


title: hESC-HNF1A-KO1: ES_797427


title: hESC-HNF1A-KO1: ES_797420


title: hESC-HNF1A-KO1: ES_797423


title: hESC-HNF1A-KO1: ES_797425


title: hESC-HNF1A-KO1: ES_797426


title: hESC-HNF1A-KO1: ES_797422


title: hESC-HNF1A-KO1: ES_797424


title: hESC-HNF1A-KO1: ES_797419


title: hESC-HNF1A-KO1: ES_797421


title: hESC-HNF1A-KO1: ES_797418


title: hESC-HNF1A-KO1: ES_797417


title: hESC-HNF1A-KO1: ES_797416


title: hESC-HNF1A-KO1: ES_797414


title: hESC-HNF1A-KO1: ES_797415


title: hESC-HNF1A-KO1: ES_797411


title: hESC-HNF1A-KO1: ES_797432


title: hESC-HNF1A-KO1: ES_797412


title: hESC-HNF1A-KO1: ES_797431


title: hESC-HNF1A-KO1: ES_797413


title: hESC-HNF1A-KO1: ES_797428


title: hESC-HNF1A-WT: ES_797319

description: Differentiation day 25. Experiment number A34. Genotype HNF1A WT

value: WT


title: hESC-HNF1A-KO1: ES_797408


title: hESC-HNF1A-KO1: ES_797406


title: hESC-HNF1A-KO1: ES_797407


title: hESC-HNF1A-KO1: ES_797409


title: hESC-HNF1A-WT: ES_797317


title: hESC-HNF1A-WT: ES_797316


title: hESC-HNF1A-WT: ES_797311


title: hESC-HNF1A-WT: ES_797312


title: hESC-HNF1A-WT: ES_797313


title: hESC-HNF1A-WT: ES_797310


title: hESC-HNF1A-WT: ES_797309


title: hESC-HNF1A-WT: ES_797306


title: hESC-HNF1A-WT: ES_797307


title: hESC-HNF1A-WT: ES_797315


title: hESC-HNF1A-WT: ES_797305


title: hESC-HNF1A-KO1: ES_797410


title: hESC-HNF1A-WT: ES_797304


title: hESC-HNF1A-WT: ES_797303


title: hESC-HNF1A-KO1: ES_797405


title: hESC-HNF1A-WT: ES_797301


title: hESC-HNF1A-WT: ES_797297


title: hESC-HNF1A-WT: ES_797299


title: hESC-HNF1A-WT: ES_797318


title: hESC-HNF1A-WT: ES_797314


title: hESC-HNF1A-WT: ES_797296


title: hESC-HNF1A-WT: ES_797295


title: hESC-HNF1A-WT: ES_797294


title: hESC-HNF1A-WT: ES_797293


title: hESC-HNF1A-WT: ES_797292


title: hESC-HNF1A-WT: ES_797308


title: hESC-HNF1A-WT: ES_797287


title: hESC-HNF1A-WT: ES_797288


title: hESC-HNF1A-WT: ES_797285


title: hESC-HNF1A-WT: ES_797284


title: hESC-HNF1A-KO2: ES_797333


title: hESC-HNF1A-WT: ES_797283


title: hESC-HNF1A-WT: ES_797282


title: hESC-HNF1A-WT: ES_797286


title: hESC-HNF1A-WT: ES_797281


title: hESC-HNF1A-WT: ES_797280


title: hESC-HNF1A-WT: ES_797298


title: hESC-HNF1A-WT: ES_797302


title: hESC-HNF1A-WT: ES_783445

description: Differentiation day 25. Experiment number A7. Genotype HNF1A WT


title: hESC-HNF1A-WT: ES_783443


title: hESC-HNF1A-WT: ES_783442


title: hESC-HNF1A-WT: ES_797300


title: hESC-HNF1A-WT: ES_783441


title: hESC-HNF1A-WT: ES_783439


title: hESC-HNF1A-WT: ES_783440


title: hESC-HNF1A-WT: ES_797291


title: hESC-HNF1A-WT: ES_797290


title: hESC-HNF1A-WT: ES_783437


title: hESC-HNF1A-WT: ES_783438


title: hESC-HNF1A-WT: ES_797289


title: hESC-HNF1A-WT: ES_783434


title: hESC-HNF1A-WT: ES_783433


title: hESC-HNF1A-WT: ES_783436


title: hESC-HNF1A-WT: ES_783432


title: hESC-HNF1A-WT: ES_783431


title: hESC-HNF1A-WT: ES_783429


title: hESC-HNF1A-WT: ES_783430


title: hESC-HNF1A-WT: ES_783427


title: hESC-HNF1A-WT: ES_783428


title: hESC-HNF1A-WT: ES_783426


title: hESC-HNF1A-WT: ES_783425


title: hESC-HNF1A-WT: ES_783423


title: hESC-HNF1A-WT: ES_783422


title: hESC-HNF1A-WT: ES_783421


title: hESC-HNF1A-WT: ES_783415


title: hESC-HNF1A-WT: ES_783417


title: hESC-HNF1A-WT: ES_783416


title: hESC-HNF1A-WT: ES_783418


title: hESC-HNF1A-WT: ES_783419


title: hESC-HNF1A-WT: ES_783435


title: hESC-HNF1A-WT: ES_783413


title: hESC-HNF1A-WT: ES_783414


title: hESC-HNF1A-WT: ES_783420


title: hESC-HNF1A-WT: ES_783409


title: hESC-HNF1A-WT: ES_783411


title: hESC-HNF1A-WT: ES_783412


title: hESC-HNF1A-WT: ES_783410


title: hESC-HNF1A-WT: ES_783408


title: hESC-HNF1A-WT: ES_783407


title: hESC-HNF1A-WT: ES_783405


title: hESC-HNF1A-WT: ES_783406


title: hESC-HNF1A-WT: ES_783404


title: hESC-HNF1A-WT: ES_783403


title: hESC-HNF1A-WT: ES_783402


title: hESC-HNF1A-WT: ES_783424


title: hESC-HNF1A-WT: ES_783400


title: hESC-HNF1A-WT: ES_783397

description: Differentiation day 25. Experiment number A3. Genotype HNF1A WT


title: hESC-HNF1A-WT: ES_783399


title: hESC-HNF1A-WT: ES_783398


title: hESC-HNF1A-WT: ES_783396


title: hESC-HNF1A-WT: ES_783394


title: hESC-HNF1A-WT: ES_783393


title: hESC-HNF1A-WT: ES_783388


title: hESC-HNF1A-WT: ES_783386


title: hESC-HNF1A-WT: ES_783387


title: hESC-HNF1A-WT: ES_783389


title: hESC-HNF1A-WT: ES_783385


title: hESC-HNF1A-WT: ES_783390


title: hESC-HNF1A-WT: ES_783392


title: hESC-HNF1A-WT: ES_783391


title: hESC-HNF1A-WT: ES_783382


title: hESC-HNF1A-WT: ES_783401


title: hESC-HNF1A-WT: ES_783380


title: hESC-HNF1A-WT: ES_783383


title: hESC-HNF1A-WT: ES_783384


title: hESC-HNF1A-WT: ES_783381


title: hESC-HNF1A-WT: ES_783375


title: hESC-HNF1A-WT: ES_783373


title: hESC-HNF1A-WT: ES_783376


title: hESC-HNF1A-WT: ES_783377


title: hESC-HNF1A-WT: ES_783374


title: hESC-HNF1A-WT: ES_783378


title: hESC-HNF1A-WT: ES_783379


title: hESC-HNF1A-WT: ES_783372


title: hESC-HNF1A-WT: ES_783395


title: healthy_mouse_2 [mouse_h_2_1]

status: Public on Apr 09 2019

city: Vilnius

first: Rapolas

last: Zilionis

state: LT

address: Sauletekis av 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

data_processing:
All  processing steps from fastq files to count matrixes were performed using a custom pipeline for inDrops data analysis (github.com/indrops). The following steps are provided as an overview on the internal workings of inDrops.py. FASTQ files and processing steps are provided for mouse only.
inDrops.py first filters reads  for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index.
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, parameters: -n 1 -l 12 -e 70 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene.
Subsequent steps are performed using the output of inDrops.py to generate the final normalized counts files provided here. Individual cell barcodes were filtered for: i) total counts > 600; ii) mitochondrial gene content <15.  Counts were total counts normalized as described in methods, and combined into a single genes x cells normalized filtered matrix per species. Putative cell doublets were identified using Scrublet (Wolock et al., 2018) and removed from further analysis. The resulting count matrixes are provided as mouse_counts_normalized_15939x28205.mtx and human_counts_normalized_54773x41861.mtx
Genome_build: GRCm38/91 (mouse) and GRCh38/81 (human)
Supplementary_files_format_and_content: human_counts_normalized_54773x41861.mtx contains filtered normalized counts from human samples.  human_cell_metadata_54773x25.tsv contains per-cell meta data for human samples, such as cell subset labels, xy coordinates for scatterplot shown in the publication, percentage of mitochondrial counts, total counts.  gene_names_human_41861.tsv contains the list of human gene names.  mouse_counts_normalized_15939x28205.mtx contains filtered normalized counts from mouse samples.  mouse_cell_metadata_15939x12.tsv contains per-cell meta data for mouse samples, such as cell subset labels, xy coordinates for scatterplot shown in the publication, percentage of mitochondrial counts, total counts.  gene_names_mouse_28205.tsv contains the list of mouse gene names.  human_*_raw_counts.tsv.gz contain unfiltered raw counts from human samples prior to normalization; one file per sequencing library.  mouse_*_raw_counts.tsv.gz contain unfiltered raw counts from mouse samples prior to normalization; one file per sequencing library.

source_name: lung

extract_protocol:
Single cell suspensions were obtained from lung tissue of C57BL/6 male mice which were perfused with PBS. Small tissue pieces were generated from perfused lungs using scissors and digested (RPMI containing 0.2 mg/ml collagenase type I, Worthington Biochemical Corporation) for 15min at 37°C while shaking (700rpm). Digested lung tissue was gently meshed through 70µM cell strainers using a plunger. Single cell suspensions were then stained with a fluorescent conjugated antibody specific to CD45 (clone 30-F11, Biolegend) for 45min at 4°C. The cells were washed with staining buffer (PBS containing 0.5% BSA and 2 mM EDTA) and CD45+ live cells were sorted on a FACS Aria cell sorter (BD) into FBS containing tubes which were kept on ice until the cells were further processed for scRNASeq. 7-aminoactinomycin (7AAD, Sigma) positivity was used to exclude dead cells.
Single cell barcoding and library preparation were performed using the inDrops protocol as described in Zilionis et 2017, Nature Protocols.

tag: gender

value: M

tag: treatment received prior to surgery (1= treated; 0=untreated)

tag: purification

value: RBC-depletion; CD45+ cells

tag: age at sacrifice (weeks)


title: healthy_mouse_2 [mouse_h_2_3]


title: healthy_mouse_2 [mouse_h_2_2]


title: healthy_mouse_1 [mouse_h_1_1]

description: Analyses in the publication (Zilionis et al. 2019) use h_1_1 library counts (GSM3635304_mouse_h_1_1_raw_counts.tsv.gz) generated from one sequencing run (SRR8646217). Additional reads were obtained for the library h_1_1 [SRR10097588] and are made available on SRA for completeness.


title: healthy_mouse_1 [mouse_h_1_2]


title: P28 AT2 RPKM 1

status: Public on Apr 01 2019

city: Cincinnati

first: LungMAPP

last: DCC

address: 3333 Burnet Ave

institute: LungMAP DCC

data_processing:
Next-generation sequencing of equimolar pools of cDNA libraries was performed using a single read 75 rapid flow cell on a HiSeq 2500 sequencing platform (Illumina), generating greater than 30 million raw reads per sample. The raw sequenced reads were aligned from FASTQ files to the human genome build GRCm38/mm10 and the UCSC reference transcriptome (http://ccb.jhu.edu/software/tophat/index.shtml) using Tophat 2.0.9.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: type II pneumocyte

growth_protocol: Embryos and mice for this study were collected from timed pregnant mice.

extract_protocol: Total RNA was extracted from cells using the QIAamp Circulating Nucleic Acid Kit (QIAGEN). RNA was quality checked, transcribed into complementary DNA using the Verso complementary DNA synthesis kit (AB-1453; LifeTechnologies, Carlsbad, CA), sheared, amplified, adaptor ligated and sequenced for pair-end RNA-Seq reads (Illumina Inc. San Diego, CA, USA). Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina).

treatment_protocol: Whole lungs were surgically dissected at embryonic (E) days 16.5, 18.5 and postnatal days (PND) 1, 3, 7, 14, and 28

tag: age


title: P07 AT2 RPKM 1


title: Epi-18.5-Rep1

status: Public on Mar 29 2019

data_processing:
Next-generation sequencing of equimolar pools of cDNA libraries was performed using a single read 75 rapid flow cell on a HiSeq 2500 sequencing platform (Illumina), generating greater than 30 million raw reads per sample.  The raw sequenced reads were aligned from FASTQ files to the human genome build GRCm38/mm10 and the UCSC reference transcriptome (http://ccb.jhu.edu/software/tophat/index.shtml) using Tophat 2.0.9.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

extract_protocol:
Total RNA was extracted from cells using the QIAamp Circulating Nucleic Acid Kit (QIAGEN). RNA was quality checked, transcribed into complementary DNA using the Verso complementary DNA synthesis kit (AB-1453; LifeTechnologies, Carlsbad, CA), sheared, amplified, adaptor ligated and sequenced for pair-end RNA-Seq reads (Illumina Inc. San Diego, CA, USA)
Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina).

treatment_protocol: Whole lungs were surgically dissected at embryonic (E) days 16.5, 18.5 and postnatal days (PND) P7 and P28 wild-type C57BL6 mice

tag: genotype/variation

value: lung

tag: cell type

value: epithelial cell


title: Immune-P07-Rep1

description: run1245_lane1_indexN710-S517=9_15.62A_CD45_plus_ve-mouse10_align

value: immune cell


title: Endo-18.5-Rep2

value: endothelial cell


title: Epi-18.5-Rep2


title: Epi-P07-Rep2

description: run1462_lane12_indexN701-S508=15_68A_CD326ve_PND7_15848~mouse10_align


title: P28 Pdgfra+ fibroblasts

data_processing:
Next-generation sequencing of equimolar pools of cDNA libraries was performed using a single read 75 rapid flow cell on a HiSeq 2500 sequencing platform (Illumina), generating greater than 30 million raw reads per sample.
The raw sequenced reads were aligned from FASTQ files to the human genome build GRCm38/mm10 and the UCSC reference transcriptome (http://ccb.jhu.edu/software/tophat/index.shtml) using Tophat 2.0.9."
Genome_build: mm10
Supplementary_files_format_and_content: FPKM abundance measuements

source_name: mesenchymal derived cell

value: Pdgfra+ fibroblasts


title: E16.5 Pdgfra+ fibroblasts


title: P07 Pdgfra+ fibroblasts


title: Epi-P28-Rep2

description: run1233_lane12_indexN704-S504=4_15.57A_CD326_plus_ve-mouse10_align


title: Endo-P07-Rep2

description: run1462_lane12_indexN702-S517=15_68A_CD31ve_PND7_15849~mouse10_align


title: Endo-P28-Rep2

description: run1233_lane12_indexN705-S505=5_15.57A_CD31_plus_ve-mouse10_align


title: Immune-E16.5-Rep2

description: run1449_lane12_indexN704-S508=16_112_113_CD45ve_E16_15840~mouse10_align


title: Immune-P07-Rep2

description: run1462_lane12_indexN712-S507=15_68A_CD45ve_PND7_15847~mouse10_align


title: Endo-P07-Rep1

description: run1245_lane1_indexN708-S508=8_15.62A_CD31_plus_ve-mouse10_align


title: E18.5 Pdgfra+ fibroblasts


title: Immune-E16.5-Rep1

description: run1449_lane12_indexN701-S505=16_110_111_CD45ve_E16_5_15837-mouse10_align


title: Immune-P28-Rep1

description: run1233_lane12_indexN703-S503=3_15.52A_CD45_plus_ve-mouse10_align


title: Epi-P07-Rep1

description: run1233_lane12_indexN707-S507=7_15.62A_CD326_plus_ve-mouse10_align


title: Endo-P28-Rep1

description: run1233_lane12_indexN702-S502=2_15.52A_CD31_plus_ve-mouse10_align


title: Epi-E16.5-Rep2

description: run1449_lane12_indexN702-S506=16_110_111_CD326ve_E16_15838-mouse10_align


title: Endo-E16.5-Rep1

description: run1449_lane12_indexN703-S507=16_110_111_CD31ve_E16_15839-mouse10_align


title: Epi-E16.5-Rep1

description: run1449_lane12_indexN705-S517=16_112_113_CD326ve_E17_15841~mouse10_align


title: Endo-E16.5-Rep2

description: run1449_lane12_indexN706-S502=16_112_113_CD31ve_E18_15842~mouse10_align