title: p12

value: Parkinson's Disease

value: HBRE

value: Male

tag: race

value: White

tag: ethnicity

value: Not Hispanic or  Latino

tag: postmortem interval hours

value: Stage II


title: Sample_chronic_4_CORT_ENZA

status: Public on Mar 28 2022

type: SRA

city: Leiden

first: Jacobus

middle: Cornelis

last: Buurstede

state: Zuid-Holland

address: Albinusdreef 2

department: Endocrinology

country: Netherlands

institute: Leiden University Medical Center

library_source: transcriptomic

data_processing:
Quality control was performed using FastQC and MultiQC
Reads were alligned to mm10 using STAR aligner (version 2.7.3a) settings: --runThreadN' '4' '--outSAMunmapped' 'Within KeepPairs' '--twopassMode' 'Basic’
Gene-read quantification was perfromed using HTSeq-count (version 0.12.4) settings: --format' 'bam' '--order' 'pos' '--stranded' 'reverse'
HTSeq-count output files were merged into the raw_gene_count_matrix.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every feature according to Ensembl97 for each sample.

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
NucleoSpin RNA kit (Macherey-Nagel)
Total RNA was isolated from the snap-frozen liver samples.
mRNA was enriched and purified and a stranded library was constructed for 100bp paired-end sequencing on BGI's DNBseq platform.

tag: strain

tag: tissue

value: liver

tag: treatment

value: Corticosterone + enzalutamide

tag: duration

value: chronic


title: s382-3_DLP_MYC_scRNA

city: Boston

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

country: USA

institute: Dana Faber Cancer Institute

description: Single-cell RNA-seq

data_processing:
Illumina Bcl2fastq v2.18.
Reads were aligned to mm10 using STAR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *h5: Cell gene barcode matrix in HD5 format.

molecule: polyA RNA

source_name: Hi-MYC dorsolateral prostate

growth_protocol: FVB Hi-MYC mice, expressing the human c-MYC transgene in prostatic epithelium, were obtained from the National Cancer Institute Mouse Repository at Frederick National Laboratory for Cancer Research. Upon weaning, male mice heterozygous for the transgene (MYC), together with their wild type littermates (WT), were fed a purified diet (Harlan Laboratories, TD.130838). Animals were kept on a 12-hour light / 12-hour dark cycle, and allowed free access to food and water at the Dana-Farber Cancer Institute (DFCI) Animal Resources Facility. The animal protocol was reviewed and approved by the DFCI Institutional Care and Use Committee (IACUC), and was in accordance with the Animal Welfare Act.

extract_protocol:
Fresh prostatic tissues from 12-week-old mice were dissociated to form a single cell suspension. Cell preparation for 3’ barcoded scRNA-seq (#120237, Chromium V2 assay) was performed according to the manufacturer’s protocol (10X Genomics) targeting 5000 cells from single-cell suspensions of freshly processed prostate lobes.
Library construction for 3’ barcoded scRNA-seq (#120237, Chromium V2 assay) was performed according to the manufacturer’s protocol (10X Genomics).

value: dorsolateral prostatic tissues

value: FVB

tag: genotype/variation

value: Hi-MYC

tag: Sex

tag: age

value: 12 weeks


title: D8

city: New York

first: Bin

last: Zhang

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequencing data were aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 3.1.0, 10x Genomics) against the provided GRCh38 reference genome using default parameters, including introns.
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

organism: Homo sapiens

source_name: Human postmortem brain sample

extract_protocol:
Nuclei were isolated from frozen tissue, as per 10x Genomics’ recommendations, using chilled, 0.1% Nonident P40 lysis buffer with gentle homogenization and washed.
Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (Thermofisher) analysis. Libraries were sequenced using a 2x100PE configuration on a NovaSeq instrument (Illumina, San Diego, CA), targeting a depth of 50,000-100,000 reads per nucleus.

value: Substanstia nigra

tag: disease state

value: Unaffected Control

tag: brain bank donor id

tag: gender

value: Female

tag: braak stage


title: Sample_chronic_3_CORT

value: Corticosterone


title: D33

value: Parkinson's Disease Dementia

value: HBNJ

value: Stage VI


title: Sample_chronic_2_CORT


title: intermediate_sCAD_rep1

type: RNA

city: Münster

first: Anika

last: Witten

address: Domagkstrasse 3

country: Germany

institute: Institute for Human Genetics

description: RNA isoated from flow cytometric isolated monocyte subpopulation

hyb_protocol: genechip hybridization wash and stain kit

scan_protocol: Affymetrix Fluidic Station 450, Gene Chip Scanner 3000 7G

data_processing: affymetrix expression console tm software and limma package

label: biotin

source_name: blood pbmc

label_protocol: affymetrix flashtag biotin hsr labeling kit

growth_protocol: patient blood samples

extract_protocol: Chloroform/Isopropanol isolation after cell lysis

treatment_protocol: total RNA was isolated from monocyte subpopulations separated by flow cytometry after antibody treatment

tag: group

value: male


title: s382-4_AP_WT_scRNA

description: Single-cell RNA-seq

source_name: WT anterior prostate

value: anterior prostatic tissues

value: WT

value: Male


title: s382-3_VP_MYC_scRNA

description: Single-cell RNA-seq

source_name: Hi-MYC ventral prostate

value: ventral prostatic tissues


title: D3

value: HctYM

value: White

value: Not Hispanic


title: classical_sCAD_rep1


title: s382-4_DLP_WT_scRNA

description: Single-cell RNA-seq

source_name: WT dorsolateral prostate

value: dorsolateral prostatic tissues

value: FVB


title: WT_1_3Pseq_noPAP

city: Aarhus C

first: William

last: Garland

address: C.F. Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description: QuantSeq 3'mRNA-Seq FW + UMI

data_processing:
RNA  3’end-seq data provided by Lexogen were already split by barcodes and UMI information was appended to read names, which were then quality controlled and trimmed using the bbduk.sh script from the BBMap software (v37.62) with parameters ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20. A-tails longer than 4 nucleotides on the 3’end of cleaned reads were trimmed off using a custom awk script and only reads with more than 20 nucleotides after this step were used for subsequent mapping.
A custom index, concatenating mouse genome mm10 and sequences for Lexogen ERCC and SIRV spike ins (SIRV-Set 3, Lexogen GmbH), was prepared. This merged genome was indexed using STAR (v.2.7.3a) with settings ‘--runMode genomeGenerate --genomeSAindexNbases 11’ and otherwise default settings. Reads were then mapped to this index using the STAR aligner (v2.7.3a) together with samtools (v.1.9) with settings ‘--outFilterType BySJout --outFilterMultimapNmax 1000’ to maintain multimapping reads.
Duplicate reads were removed via the included UMI information, using the dedup function from umi_tools (v1.0.1). Bam files were indexed using samtools and coverage of single mapping reads within last exons of RefSeq annotations were obtained using the multicov function from bedtools (v2.29.2) in strand-specific mode. Normalisation factors were obtained from those last exon counts using the estimateSizeFactors function from R package DESeq2 (v1.28.0), with at least a total of 100 reads summed over all libraries. Size factors were checked to be generally correlated with spike-in derived read numbers without indications for KO or EPAP treatment-specific biases.
genome build: mm10
processed data files format and content: Normalised coverage tracks were then produced using the genomecov function from bedtools with parameters ‘-bg -3 -scale 1/sizefactor’ and ‘-strand +’ or ‘-strand -’ for plus and minus strand coverage, respectively. Coverage for major mouse chromosomes was sorted using bedtools sort, the average of the 3 replicates computed and converted to bigwig format using bedGraphToBigwig function from UCSC tools (v357)

source_name: Embryonic stem cells

growth_protocol: ES cells were culturered on 0.2% gelatin coated plates in 2i/LIF containing medium

extract_protocol:
Total RNA for 3P-seq was isolated by Trizol extraction using standard procedures
3PS samples were either mock treated or incbated with E.coli Poly(A) polymerase (EPAP). rRNA was depleted using the RiboCop rRNA Depletion Kit (Lexogen). Libraries for QuantSeq 3'mRNA Seq FW + UMI were prepared by Lexogen and included the addition of spike-ins ERCC Mix1 and SIRV E0

tag: cell line

tag: genotype

value: Wildtype

tag: epap treatment

value: noPAP


title: D29

value: Substanstia nigra

value: HBIV

tag: race

tag: ethnicity

value: Not Hispanic or  Latino

value: Stage IV


title: non-classical_MI_rep3


title: s382-4_VP_WT_scRNA

description: Single-cell RNA-seq

source_name: WT ventral prostate

tag: strain

value: 12 weeks


title: Sample_chronic_1_CORT

tag: tissue

value: liver

value: Corticosterone

value: chronic


title: D27

value: Parkinson's Disease

value: HAAB

value: Male

value: Not Hispanic or Latino

tag: postmortem interval hours


title: an3_18h

city: Indianapolis

first: Stanley

middle: M

last: Spinola

state: Indiana

address: 635 Barnhill Dr., MS420

department: Department of Microbiology & Immunology

institute: Indiana University

data_processing:
Basecalling was performed with Illumina RTA v3.4.4 and bcl2fastq v2.20.
Sequenced reads were aligned to the Haemophilus ducreyi 35000HP genome (AE017143.1) using Bowtie2 v2.3.2.
A single count matrix was derived using the featureCounts function in Rsubread run in R v3.6.0 for matched pairs with a min MQS of 30 or higher.
Library normalization and statistical analysis was performed in R v4.0.0 with the edgeR package.
Genome_build: AE017143.1
Supplementary_files_format_and_content: txt file for the count matrix of the 24 samples

organism: [Haemophilus] ducreyi

source_name: Haemophilus ducreyi

growth_protocol: Overnight Haemophilus ducreyi cultures in GC broth plus hemin, FBS, and IsoVitalex (complete GC broth) were subcultured into complete GC broth plus either the commercial product Oxyrase or the buffer substrates to generate anaerobic or aerobic environments, respectively. Cultures were evenly aliquoted into glass tubes with rubber lined screw caps (7.5 mL/ea). The cap was screwed shut on anerobic cultures and loosely shut on aerobic cultures. Cultures were shaken at ~200 rpm and 33 degrees for the duration of the experiment. Four independent experiments were performed.

extract_protocol:
5 mL of culture was pelleted, media was removed and the pellet was resuspended in 1 mL of Trizol. Samples were stored at -80 until all samples were collected. RNA was extracted using the Zymo Directzol kit with both on-column DNase digestion as well as a subsequent DNase digestion of the eluate with TurboDNase.
Ribosomal RNA was removed with Qiagen FastSelect for bacteria. Libraries were prepared with a Roche KAPA kit.

treatment_protocol: Cells were grown either aerobically (buffer substrates) or anaerobically (with Oxyrase) for 4, 8, or 18 h.

tag: oxygen environment

value: anaerobic

tag: harvested

value: 18 hours


title: an4_18h


title: intermediate_MI_rep3

value: male


title: classical_MI_rep3


title: non-classical_MI_rep2


title: Pol2_MYC_2

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: Hi-MYC ventral prostates

growth_protocol: FVB Hi-MYC mice, expressing the human c-MYC transgene in prostatic epithelium, were obtained from the National Cancer Institute Mouse Repository at Frederick National Laboratory for Cancer Research. Upon weaning, male mice heterozygous for the transgene (MYC), together with their wild type littermates (WT), were fed a purified diet (Harlan Laboratories, TD.130838). Animals were kept on a 12-hour light / 12-hour dark cycle, and allowed free access to food and water at the Dana-Farber Cancer Institute (DFCI) Animal Resources Facility. The animal protocol was reviewed and approved by the DFCI Institutial Care and Use Committee (IACUC), and was in accordance with the Animal Welfare Act.

extract_protocol:
Fresh-frozen VP tissues from 12-week-old mice were pulverized (Cryoprep Impactor, Covaris), resuspended in PBS + 1% formaldehyde, and incubated at room temperature for 20 minutes. Fixation was stopped by the addition of 0.125 M glycine (final concentration) for 15 minutes at room temperature, then washing in ice cold PBS + EDTA-free protease inhibitor cocktail (PIC; #04693132001, Roche). Multiple biological replicates were combined for each condition in two distinct pools (replicates). Chromatin was isolated by the addition of lysis buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl (pH 7.4), 1 mM EDTA (pH 8.0), 0.1% NaDOC, 0.13 M NaCl, 1X PIC) + sonication buffer (0.25% sarkosyl, 1 mM DTT) to the samples, which were maintained on ice for 30 minutes. Lysates were sonicated (E210 Focused-ultrasonicator, Covaris) and the DNA was sheared to an average length of ~200-500 bp. Genomic DNA (input) was isolated by treating sheared chromatin samples with RNase (30 minutes at 37°C), proteinase K (30 minutes at 55°C), de-crosslinking buffer (1% SDS, 100 mM NaHCO3 (final concentration), 6-16 hours at 65°C), followed by purification (#28008, Qiagen). DNA was quantified on a NanoDrop spectrophotometer, using the Quant-iT High-Sensitivity dsDNA Assay Kit (#Q33120, Thermo Fisher Scientific). On ice,  AR (2 micrograms, #ab108341, Abcam), FOXA1 (6 micrograms, #ab23738, Abcam), RNA Pol II (4 micrograms, #sc899, Santa Cruz Biotechnology) or H3K27ac (10 microliters, #ab4729, Abcam) antibodies were conjugated to a mix of washed Dynalbeads protein A and G (Thermo Fisher Scientific), and incubated on a rotator (overnight at 4°C) with 5 micrograms (AR, FOXA1, RNA Pol II) or 1.5 micrograms (H3K27ac) of chromatin. ChIP’ed complexes were washed, sequentially treated with RNase (30 minutes at 37°C), proteinase K (30 minutes at 55°C), de-crosslinking buffer (1% SDS, 100 mM NaHCO3 (final concentration), 6-16 hours at 65°C), and purified (#28008, Qiagen). The concentration and size distribution of the immunoprecipitated DNA was measured using the Bioanalyzer High Sensitivity DNA kit (#5067-4626, Agilent).
Dana-Farber Cancer Institute Molecular Biology Core Facilities prepared libraries from 2 ng of DNA, using the ThruPLEX DNA-seq kit (#R400427, Rubicon Genomics), according to the manufacturer’s protocol; finished libraries were quantified by the Qubit dsDNA High-Sensitivity Assay Kit (#32854, Thermo Fisher Scientific), by an Agilent TapeStation 2200 system using D1000 ScreenTape (# 5067-5582, Agilent), and by RT-qPCR using the KAPA library quantification kit (# KK4835, Kapa Biosystems), according to the manufacturers’ protocols; ChIP-seq libraries were uniquely indexed in equimolar ratios, and sequenced to a target depth of 40M reads on an Illumina NextSeq500 run, with single-end 75bp reads.

value: ventral prostatic tissues

tag: antibody

tag: antibody manufacturer

value: Santa Cruz Biotechnology

tag: antibody catalog number

value: FVB


title: an2_18h


title: D20

value: Substanstia nigra

tag: disease state

value: Parkinson's Disease Dementia

tag: brain bank donor id

value: HBRR

tag: age

value: White

value: Stage VI


title: an1_18h


title: Pol2_MYC_1


title: D16

value: HBQH

tag: gender

value: Hispanic or Latino

tag: braak stage


title: Pol2_WT_2

source_name: WT ventral prostates


title: aero4_18h

value: aerobic


title: C8

value: Unaffected Control

value: Female

value: Not Hispanic or  Latino


title: classical_MI_rep2

tag: group


title: Pol2_WT_1


title: aero3_18h


title: C26

value: HBHD

value: Male

value: Stage II


title: C20

value: Parkinson's Disease

value: HBFS


title: C18

value: HBCX


title: aero1_18h

value: 18 hours


title: intermediate_MI_rep1

value: male


title: an4_8h

value: anaerobic

value: 8 hours


title: H3K27ac_WT_2

value: ventral prostatic tissues

value: Abcam

value: FVB


title: non-classical_MI_rep1


title: C11

value: Substanstia nigra

value: HBEH

value: White


title: H3K27ac_WT_1


title: an3_8h


title: classical_MI_rep1


title: an2_8h


title: intermediate_Ctrl_rep3


title: AR_MYC_2

value: anti-AR


title: non-classical_Ctrl_rep3


title: AR_MYC_1


title: B9

value: Unaffected Control

value: HctZZA

value: Not Hispanic


title: intermediate_MI_rep2


title: classical_Ctrl_rep3


title: B5

value: HctZZC

value: Female


title: AR_WT_2


title: non-classical_Ctrl_rep2


title: intermediate_Ctrl_rep2


title: aero4_8h

value: aerobic


title: an1_8h


title: B33

value: Parkinson's Disease Dementia

value: HBNN

value: Not Hispanic or  Latino

value: Stage VI


title: aero3_8h

value: 8 hours


title: aero2_8h


title: FOXA1_MYC_2

value: ventral prostatic tissues

value: Abcam


title: H3K27ac_MYC_2

value: FVB


title: AR_WT_1


title: B28

value: Substanstia nigra

value: HBIW

value: Male

value: Stage IV


title: aero2_18h

value: 18 hours


title: non-classical_Ctrl_rep1

value: male


title: H3K27ac_MYC_1


title: aero1_8h


title: classical_Ctrl_rep2


title: FOXA1_WT_2


title: an4_4h

value: anaerobic

value: 4 hours


title: B19

value: HBED

value: Female

value: White

value: Stage III


title: classical_Ctrl_rep1


title: B13

value: Parkinson's Disease Dementia

value: HBHP

value: Hispanic or Latino


title: FOXA1_WT_1

value: ventral prostatic tissues

value: Abcam


title: an3_4h


title: A38

value: Substanstia nigra

value: HBOQ

value: Not Hispanic or  Latino

value: Stage VI


title: NF cells_rep3

city: Nanjing

first: Junlong

last: Zhuang

address: 321# Zhongshan Road

country: China

institute: Institute of Urology, Drum Tower hospital

description: NFs from normal bladder tissues pairing with cancers

hyb_protocol: Labeled miRNA was hybridized to the array for 16 hours at 48 “C and 60 rpm as described in the protocol.

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

data_processing: The data were analyzed with Robust Multi-chip Average (RMA) algorithm as normalization method.

source_name: NFs from human normal bladder tissues

label_protocol: Per RNA sample, 1 ug were used as input into the procedure as recommended by protocol (Genisphere FlashTagTM Biotin RNA Labeling for Affymetrix GeneChip miRNA arrays).

growth_protocol: cells were maintained in DMEM/F12 supplemented with 10% FBS, 100 units/ml penicillin and 100g/ml streptomycin at 37℃

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

tag: cell type

value: fibroblasts

value: normal bladder

tag: patient id


title: NF cells_rep2


title: an2_4h

value: anaerobic


title: A18

value: HBBC

value: Male

tag: race

tag: ethnicity

value: Not Hispanic or Latino

value: Stage IV


title: B25

tag: tissue

value: Parkinson's Disease

value: HBHV

value: Female

value: White

value: Stage III


title: aero3_4h

value: aerobic

value: 4 hours


title: s382-4_AP_WT_bulk

data_processing:
Illumina Bcl2fastq v2.18
Reads were aligned to mm10 using STAR
For fpkm calculation cufflinks was used.
Genome_build: mm10
Supplementary_files_format_and_content: csv file of FPKM table

extract_protocol:
Fresh prostatic tissues from 12-week-old mice were dissociated to form a single cell suspension. RNA from an equal number of cells was extracted using the miRNeasy Micro Kit (#217084, Qiagen) coupled with on-column DNAse treatment (#79254, Qiagen). RNA sample concentration was measured and subjected to quality evaluation, using a Bioanalyzer RNA 6000 Nano kit (#5067-1511, Agilent).
The Dana-Farber Cancer Institute Molecular Biology Core Facilities prepared libraries from 500 ng of purified total RNA, using TruSeq Stranded mRNA sample preparation kits (#RS-122-2101, Illumina) according to the manufacturer’s protocol; finished libraries were quantified by the Qubit dsDNA High-Sensitivity Assay Kit (#32854, Thermo Fisher Scientific), by an Agilent TapeStation 2200 system using D1000 ScreenTape (# 5067-5582, Agilent), and by RT-qPCR using the KAPA library quantification kit (# KK4835, Kapa Biosystems), according to the manufacturers’ protocols; pooled uniquely indexed RNA-seq libraries in equimolar ratios, and sequenced these to a target depth of 40M reads on an Illumina NextSeq500 run with single-end 75bp reads.

value: anterior prostatic tissues

tag: strain

value: FVB


title: an1_4h

tag: oxygen environment


title: WGBS_sgNSD1

city: Santiago de Compostela

first: Carmen

last: Rivas

address: Avda Barcelona

department: CIMUS

country: Spain

institute: Universidad de Santiago de Compostela

description: According to manufacturer's protocol

data_processing:
Raw ChIP sequencing reads were aligned using BWA version 0.7.17 with default parameters
Raw RNA sequencing reads were aligned using STAR version 2.5.3a with default parameters
Whole-Genome Bisulfite Sequencing (WGBS) raw reads were submitted to Bismark(version 0.22.3) for mapping and methylation calling, against mouse genome version mm10/GRCm38, discarding duplicate reads. Briefly, the methylation level at a CpG (similarly for CHH) site was the number of reads with that site methylated divided by the total number of reads covering the site. To ensure comparability of region DNA methylation levels across all samples, CpGs that overlapped with SNPs from dbSNPs or were located within the ENCODE blacklisted regions, termed DER (Duke excluded regions) were excluded and only CpGs covered by ≥ 5x in all samples were retained for the computation of DNA methylation levels. We defined the average methylation for a genomic region as the coverage-weighted mean of the methylation levels of the individual CpGs within the region.
Genome_build: mm10 and dm6 for mouse and drosophila data, respectively
Supplementary_files_format_and_content: bigWig, tdf

source_name: Mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells were maintained on gelatin-coated plates in Knockout DMEM (Gibco) supplemented with 15% ES-cell-qualified FBS (Gemini), 0.1 mM 2-mercapoethanol, 2mM L-glutamine (Life technologies) and LIF. Drosophila S2 cells were cultured in Schneider’s Drosophila Medium (Invitrogen) containing 10% heat-inactivated FBS.

extract_protocol:
DNA was extracted from 4M cell pelets using DNeasy Blood and Tissue (Qiagen). 1000 ng of genomic DNA was spiked with 0.1% (w/w) unmethylated λ DNA (Roche Diagnostics) previously fragmented to 300–400 bp peak sizes using the Covaris focused-ultrasonicator E210. Fragment size was controlled on a Bioanalyzer High Sensitivity DNA Chip (Agilent)
NxSeq AmpFREE Low DNA Library Kit (Lucigen)and bisulfite converted using the EZ-DNA Methylation Gold Kit (Zymo Research)

tag: cell line

value: ESC line V6.5 1A

value: C57BL/6 x 129S4/SvJae F1 embryo-derived embryonic stem cells

tag: genotype


title: NF cells_rep1

value: fibroblasts

value: normal bladder


title: A29

value: Substanstia nigra

value: Parkinson's Disease Dementia

value: HBOX

value: Not Hispanic or  Latino

tag: postmortem interval hours

value: Stage VI


title: CAF cells_rep3

description: CAFs from human bladder cancer tissues

source_name: CAFs from human bladder cancer tissues

value: bladder cancer


title: WGBS_Parental_wt

description: According to manufacturer's protocol

value: wild-type


title: s382-3_AP_MYC_bulk

source_name: Hi-MYC anterior prostate


title: A15

value: HBGK

value: Male

value: White

value: Hispanic or Latino

value: Stage II


title: aero1_4h

value: aerobic

tag: harvested

value: 4 hours


title: FOXA1_MYC_1

value: ventral prostatic tissues

tag: antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number

value: FVB


title: CAF cells_rep1

description: CAFs from human bladder cancer tissues

value: fibroblasts


title: s382-4_VP_WT_bulk

tag: age


title: aero2_4h


title: s382-3_VP_MYC_bulk


title: CAF cells_rep2

description: CAFs from human bladder cancer tissues


title: A31

value: Substanstia nigra

tag: disease state

value: Parkinson's Disease Dementia

tag: brain bank donor id

value: HBQF

tag: gender

value: Female

tag: braak stage


title: s382-4_DLP_WT_bulk

value: dorsolateral prostatic tissues


title: 18log_rep2

status: Public on Mar 27 2022

city: Istanbul

first: Hande

last: Morgil

state: Fatih

address: Beyazit St.

department: Biology

country: Turkey

institute: Istanbul University

description: polyA RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor contamination and low-quality reads (Phred score < 20) were removed by Trimmomatic (v0.35) (Bolger et al. 2014) with the argument sliding window 4:20.
De novo assembly was performed using Trinity tool with the default parameters using all sample sequences.
The Bowtie aligner was used to map the reads to the de novo transcriptome assembly with default parameters.
Functional annotation of the trinity assembled de novo transcripts, we used the custom pipeline of Trinotate using the Swiss-Prot (SP) and UniRef90 (version: April 2018) for the blastp against proteins with the following arguments: word_size = 4; evalue = 10−5; num_descriptions = 5; num_alignments = 5; threshold = 18. Finding specific genes Annocript annotation tool were used.
Genome_build: Trinity assembled de novo transcripts Trinity.fasta file
Supplementary_files_format_and_content: Trinity_assembly_N_Aquatica.fasta.gz (Trinity assembled de novo transcripts Trinity.fasta file)
rpstblastn_out.gff.gz (Annocript annotation file)
Neochloris_trans_counts.TMM.EXPR.matrix.gz (Normalized expression matrix)

organism: Neochloris aquatica

growth_protocol: The microalgae Neochloris aquatica (Accession number: KF803402) was obtained from the Algal Biotechnology Laboratory, Mehmet Akif Ersoy University (Burdur, Turkey). The cells were maintained in BG11 medium at 22°C in a germination chamber under a 12/12 h (light/dark) photoperiod.

extract_protocol:
TRIzol (Invitrogen, USA) protocol
Poly(A) mRNA Magnetic Isolation Module kit (New England  Biolabs, USA)

treatment_protocol: The experiment was performed in four different modified media and BG11 medium with 18 mmol/L NaNO 3 concentration was used as a control group. Other media were (1) Medium (3 mmol/L); (2) Medium (9 mmol/L); (3) Medium (27 mmol/L).

tag: treatment

value: 18mmol/L nitrogen (control)

tag: phase

value: Logarithmic phase


title: intermediate_Ctrl_rep1

tag: group

value: male


title: 27log_rep2

description: polyA RNA

value: 27mmol/L nitrogen


title: 18log_rep1

description: polyA RNA


title: s382-3_DLP_MYC_bulk

tag: tissue

tag: strain


title: aero4_4h

tag: oxygen environment


title: A10

value: Unaffected Control

value: HctZZT

value: Male

tag: race

value: White

tag: ethnicity

value: Not Hispanic


title: 3log_rep2

description: polyA RNA

value: 3mmol/L nitrogen


title: 3log_rep1

description: polyA RNA


title: 9log_rep2

description: polyA RNA

value: 9mmol/L nitrogen


title: MDAMB231_WSS_rep3

city: Houston

first: Pamela

middle: L

last: Wenzel

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharmacology

institute: University of Texas Health Science Center at Houston

data_processing:
Raw reads were checked with FASTQC for quality and trimmed with Trimmomatic
Reads were mapped using RNA STAR (Galaxy Version 2.7.8a)
Mapping quality was verified by SAMtools idxstats, Picard tools MarkDuplicates, and MultiQC
Gene counts were produced with featureCounts assuming reverse strandness
Normalization was conducted using limma-voom
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw_counts.xlsx excel file contains a matrix table with raw counts generated from featureCounts of mapped reads. The first column contains official gene symbol and all remaining columns contain counts grouped first by cell line, then force, then replicate.
Supplementary_files_format_and_content: Norm_counts.xlsx excel file contains a matrix table with normalized abundance measurements generated from limma-voom. The first column contains EntrezID, the second column contains official gene symbol, and all remaining columns contain counts grouped first by cell line, then force, then replicate.

source_name: breast cancer cell line

growth_protocol: MCF-7 was cultured in DMEM with 10% FBS. HCC1187, EFM-19, and MDA-MB-231 were grown in RPMI with 10% FBS. All culture media contained 1% penicillin and streptomycin antibiotics, and cell lines were cultured at 37°C in 5% CO2 (v/v). Cells were routinely passaged on tissue culture plastic and transferred into microfluidic channels 20 hr prior to application of WSS.

extract_protocol:
Cells were lysed directly on microfluidic channels in RLT lysis buffer and total RNA was isolated (RNeasy Micro kit, Qiagen), according to the manufacturer’s instructions.
RNA was measured using a Qubit RNA high sensitivity assay and an Agilent Bioanalyzer total RNA 6000 Pico chip. A KAPA mRNA HyperPrep protocol for Illumina platforms was used for poly(A) mRNA capture and construction of reverse-stranded mRNA-Seq libraries. Briefly, mRNA was captured using oligo-dT beads, fragmented with heat and magnesium, and cDNA synthesized according to manufacturer guidelines. Libraries were ligated to KAPA adapter sequences and amplified. cDNA was quality checked on an Agilent Bioanalyzer high sensitivity DNA assay chip. Equimolar amounts of each sequencing library were pooled and purified with magnetic KAPA Pure Beads. Pool was sequenced on the Illumina NextSeq 550 using the NextSeq500/550 High Output kit v2.5 (2x75 paired end cycles).

treatment_protocol: Following an overnight culture period in 50 μg/ml Type I Collagen-coated microfluidic IBIDI channels, unidirectional media flow was introduced through the channel at a constant flow rate using a programmable syringe pump. Based upon viscosity of media and the dimensions of the culture channels, we applied flow rates corresponding to 0.05 dyne cm-2 WSS for 6 hr. Comparisons were conducted in parallel with static cultures on equivalent microfluidic devices.

tag: force

value: WSS

tag: response

value: Positive

tag: cancer type

value: breast

tag: cell line


title: 9log_rep1

description: polyA RNA


title: MDAMB231_WSS_rep2


title: LSCs-YBX1cKO_rep1

city: wuhan

first: Qifan

last: Wang

address: donghu road

institute: wuhan university

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low quality sequances, then pseudoaligned to GRCm38 whole transcriptome using hisat2(version 2.1.0) with default parameters
FeatureCounts were used to summary raw counts from bam files
rlog normalized  and  differential expression analysis were performed by  DESeq2
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalzied reads each Sample

source_name: Leukemia cells

extract_protocol:
leukemia cells were collect from bone marrow.Total RNA were extracted with Trizol and mRNA were isolated with Oligo dT beads.
Libraries were prepared according to VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Part# NR601). Briefly, mRNA was interrupted with metal ions in interrupted buffer , cDNA synthesis using random primers for reverse transcription of mRNA. The cDNA strands in the hybrid double strands were digested by RNaseH to synthesize cDNA complementary strands for cDNA second strand synthesis. Repair sticky ends were repaired to blunt ends   add A-tail,and connection connector.After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: bone marrow

tag: genotype


title: LSCs-YBX1cKO_rep2


title: MDAMB231_Static_rep1

value: Static


title: HCC1187_WSS_rep2

value: Negative


title: EFM19_Static_rep1


title: HCC1187_Static_rep3


title: MDAMB231_WSS_rep1


title: LSCs-WT_rep1

value: LSCs-WT


title: EFM19_WSS_rep1


title: HCC1187_Static_rep2


title: EFM19_WSS_rep3


title: HCC1187_WSS_rep3


title: EFM19_Static_rep2


title: MDAMB231_Static_rep3


title: P10.r3

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Reads were Illumina adapter trimmed using Cutadapt v1.16 (Martin, 2011) and aligned against GRCh38 and Ensembl release 86 transcript annotations using STAR v2.5.2b (Dobin et al., 2013) via the transcript quantification software RSEM v1.3.0 (Li and Dewey, 2011).
Genome_build: GRCh38
Supplementary_files_format_and_content: RSEM gene-level abundance estimates based on Ensembl 86.

source_name: Human embryonic stem cells

growth_protocol: WA09 hESCs were maintained in feeder-free cultures, plated on Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix (Corning Incorporated, 354230) and grown in mTESR1 (STEMCELL technologies, 85850). Cells were passaged as aggregates at a ratio of 1:10/15 using Gibco Versene Solution (Thermo Fisher Scientific, 15040066).

extract_protocol:
RNA was extracted using RNEasy mini kit (Qiagen) following the manufacturer’s instructions including recommended DNase digestion step.
RNA concentration was measured on a on a GloMax (Promega Corporation) and RNA integrity on TapeStation (Agilent Technologies). Libraries were prepared using KAPA mRNA (PolyA) HyperPrep Kit (Roche Holding AG, KK8581) using 500 ng RNA per sample according to manufactorers instructions. Libraries were sequenced using a HiSeq 4000 (Illumina Biotechnology) as follows: pooled to 4 nM, 75bp single end sequencing and up to 38 million reads per sample.

treatment_protocol: WA09 hESCs were treated with N2B27 (-vitamin A) supplemented with CHIR-99021, rhFGF2, AGN193109 and Y-27632 for 36h to generate hESC-derived NMP-like cells. Human ESC-derived NMP-like cells were collected at 36h for RNA-seq analysis. To generate PNP/NC cells, cells at 36h were dissociated using TrypLE express and re-plated at a ratio of 1:6 into N2B27 (-vitamin A) supplemented with CHIR-99021, rhFGF2, AGN193109 and Y-27632. PNP/NC cells were subsequently passaged every 3-4 days when 80-90% confluent and collected for RNA-seq analysis at each passage (P1-10). At passage 5 and passage 8, TrypLE express was used to selectively detach mesenchymal (MES, NC cells) and epithelial (EPI, PNPs) cells from the differentiated cultures.  Samples enriched for either EPI and MES cells were collected for RNA-seq analysis.

tag: cell type

value: hESC-derived neural progenitors

value: WA09 Human embryonic stem cells

tag: time

tag: replicate


title: LSCs-WT_rep2


title: MDAMB231_Static_rep2


title: MCF7_WSS_rep1


title: HCC1187_WSS_rep1


title: HCC1187_Static_rep1


title: P8.r3


title: EFM19_Static_rep3


title: P8_EPI.r3

value: Enriched hESC-derived neural progenitors (epithelial)


title: MCF7_WSS_rep3


title: P8_MES.r3

value: Enriched hESC-derived neural crest (mesenchymal)


title: 27log_rep1

description: polyA RNA

value: 27mmol/L nitrogen

value: Logarithmic phase


title: MCF7_WSS_rep2


title: P7.r3


title: EFM19_WSS_rep2


title: MCF7_Static_rep3


title: P5_MES.r3


title: P5.r3


title: P5_EPI.r3


title: P4.r3


title: N1014M-4 [lncRNA-seq]

city: Shanghai

first: Xiang

last: Liping

address: 180 Fenglin Road, Xuhui, Shanghai

institute: Fudan university

data_processing:
lncRNA-Seq:
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Library quality was assessed on the Agilent Bioanalyzer 2100 system. The sequencing libraries were sequenced on an Illumina Hiseq2500/X platform. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
Cuffquant and cuffnorm (v2.2.1) was used to calculate FPKMs of genes in each sample.
Assembly: mm9
Supplementary files format and content: Raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Total RNAs were extracted using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: disease state

value: NASH


title: RNASeq_E13.5_Stomach_Replicate #1

city: Charlottesville

first: Hongpan

state: VA

address: 1300 Jefferson Park Avenue

department: Center for Public Health Genomics

institute: University of Virginia

description: RNASeq_E13.5_Stomach_Replicate #1

data_processing:
The trimmed pair-end reads were aligned to mouse reference genome (GRCm38) with STAR (version 2.4.2a), and gene expression was then quantified using the reads per kilobase per million mapped reads (RPKM) method.
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing the gene expression matrix

source_name: Mouse E13 embryonic tissue

growth_protocol: All animal husbandry was conducted in adherence to the standards proposed by the Canadian Council on Animal care and approved by the institutional animal care committees, The Centre for Phenogenomics, Toronto.

extract_protocol:
For E13.5 mouse experiments, ShhCre; R26YFP/+ embryos were used for downstream high-throughput experiments. After dissection, the stomach and intestinal organs were isolated, separated, washed in cold PBS and digested in 4ml of a 3:1 solution of Trypsin LE: 1x PBS at 37˚C. After 10 minutes, tissue was vigorously pipetted, until the organs broke down into a single cell suspension, which was confirmed using brightfield microscopy. The enzymatic reaction was then inhibited with 10% FBS. After washing cells in cold PBS, the single cells were re-suspended in 400µl of 1:5000 Sytox Blue (ThermoFisher Scientific, S34857) in cold 1x PBS, filtered through a 30µm mesh and submitted for sorting. Sorted cells were washed again and processed for ATAC-seq (50,000 cells from 3-4 YFP+ embryos) using the previously published protocol (44).    For E16.5 experiments, whole organ digestion using Trypsin was detrimental to epithelial cell viability; thus, an alternative isolation approach was employed. Given strict cell numbers are required for ATAC-seq, gut epithelium was isolated from ShhCre;R26YFP/+ embryos prior to single cell dissociation. In more detail, the E16.5 embryonic stomach, the proximal small intestine and the colon were dissected and opened longitudinally using a 0.5 cm tungsten needle. The forestomach was separated from the hindstomach along the squamous-glandular border under a dissecting microscope, and incubated in Dispase solution for 15 minutes at 37˚C. Following, the epithelial layer was manually separated from the mesenchyme and flash frozen for RNA isolation or collagenase digested for sorting. The hindstomach, proximal small intestine and colon were incubated in 10mM EDTA, 5mM EDTA and 5mM EDTA in 1x PBS, respectively, for 30-40 minutes at 4˚C on a shaker. Tissues were then moved to fresh 1x PBS and shaken vigorously for 2-3 minutes, or until epithelial glands/villi/crypts were observed in suspension. Isolated epithelial cells were immediately frozen and RNA isolation was conducted using an RNA isolation kit (Qiagen, Cat No. 74104). To prepare for sorting for ATAC-seq experiments, the fresh epithelial pellets of the forestomach, hindstomach, intestine and colon were then digested in collagenase-based solution for 20 mins at 37˚C. The resulting single cell suspension was washed in cold 1x PBS, re-suspended in 500µl of 1:5000 Sytox Blue and submitted for sorting. Sorted cells were then used for ATAC-seq using the same protocol as mentioned above.
Whole transcriptome sequencing libraries were prepared using TruSeq® Stranded mRNA Library Prep Kit (RS-122-2101, Illumina, San Diego, CA, USA) by following the manufacturer’s instructions.

treatment_protocol: No treatment

tag: age


title: RNASeq_E13.5_Intestine_Replicate #2

description: RNASeq_E13.5_Intestine_Replicate #2


title: N1014M-3 [lncRNA-seq]


title: RNASeq_E13.5_Stomach_Replicate #2

description: RNASeq_E13.5_Stomach_Replicate #2


title: RNASeq_E13.5_Intestine_Replicate #1

description: RNASeq_E13.5_Intestine_Replicate #1


title: N1014M-2 [lncRNA-seq]


title: P1.r3


title: 36h.r3

value: hESC-derived neuromesodermal progenitor-like cells


title: N1014C-4 [lncRNA-seq]

value: Normal


title: t0.r3

value: Undifferentiated hESCs


title: P9.r2


title: N610M-4 [lncRNA-seq]

value: NAFL


title: P8_MES.r2


title: N1014C-3 [lncRNA-seq]


title: MCF7_Static_rep1

value: breast


title: VBNC 2

city: Columbus

first: Devin

last: Sindeldecker

state: OH

department: MI&I

institute: The Ohio State University

data_processing:
Data trimmed using Trimmomatic v0.38
Alignment to the reference genome was done using STAR v2.7.10a
Transcript counts obtained with HTSeq v0.12.4
Differential gene expression processed by edgeR v3.24.3
Assembly: GCF_000006765.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Pseudomonas aeruginosa

source_name: VBNC

extract_protocol:
RNA extraction from each sample was completed following the manufacturer's protocol for the Direct-zol RNA Miniprep Kit (Zymo).
rRNA was removed from samples following the manufacturer's protocol for the RiboZero Bacteria Kit (Illumina). Barcoded RNAseq libraries were generated following the manufacturer's protocol for the ScriptSeq v2 Kit (Illumina).

tag: treatment

value: Tobramycin

tag: treatment time

value: 96 hr


title: VBNC 3


title: P6.r3


title: MCF7_Static_rep2

value: Static

value: Negative


title: N610M-3 [lncRNA-seq]

tag: tissue


title: N610M-2 [lncRNA-seq]

tag: strain


title: P8_EPI.r2


title: P8.r2

value: hESC-derived neural progenitors


title: VBNC 1


title: N610C-8 [lncRNA-seq]


title: Outer 3

source_name: Outer


title: Outer 2


title: P2.r3

value: WA09 Human embryonic stem cells


title: P3.r3


title: P7.r2


title: P6.r2


title: N610C-7 [lncRNA-seq]


title: Outer 1


title: Edge 3

source_name: Edge

value: 72 hr


title: N610C-4 [lncRNA-seq]


title: Edge 2


title: Phoenix Colony 3

source_name: Phoenix Colony


title: Edge 1


title: P5_MES.r2

value: Enriched hESC-derived neural crest (mesenchymal)


title: Phoenix Colony 2


title: E13.5_lung_RNA_r2

data_processing:
ScATAC-seq data were pre-processed using the cellranger-atac package (genome version mm10). The ArchR package was used for QC and basic analysis.
Bulk RNA-seq data were aligned to the mouse reference genome mm10 using hisat2 with default parameters. Mapped reads were further filtered by MAPQ (>=30) using samtools, and chimeric reads were discarded. The gene expression index was summarized using htseq (count) and stringtie (rpkm).
Bulk ATAC-seq data were aligned to the mouse reference genome mm10 using bowtie2 (with additional parameters '-X 2000 -3 76'). Mapped reads were further filtered by MAPQ (>=30), and chimeric reads were discarded. Bulk ATAC-seq peaks were detected using MACS2 (with additional parameters '-q 0.01 --keep-dup all --nomodel --extsize 100').
Genome_build: mm10
Supplementary_files_format_and_content: Barcoded and aligned fragment file (in tsv format), barcode file (in tsv format), filtered peak barcode matrix (in MEX format) and peak file (in bed format) were all generated by 10X Cell Ranger ATAC for each scATAC-seq sample. Tab-delimited text files (generated by HT-seq) include raw reads count of genes for each RNA-seq sample. Normalized signal track (in bigwig format) for each ATAC-seq sample.

source_name: E13.5 lung

growth_protocol: All mice used in this study were handled in accordance with the rules and regulations of the Canadian Council on Animal Care Guidelines for Use of Animals in Research and Laboratory Animal Care under protocols approved by the Animal Care Committee at The Centre for Phenogenomics (protocol: 19-0276H).

extract_protocol:
For E9.5 mouse experiments, gut tubes were micro-dissected, washed in cold PBS and digested in 4ml of a 2:1 solution of Trypsin LE: 1x PBS at 37˚C. After 10 minutes, tissue was vigorously pipetted, until the organs broke down into a single cell suspension, which was confirmed using brightfield microscopy. The enzymatic reaction was then inhibited with 10% FBS. After washing cells in cold PBS, the single cells were re-suspended in 400µl of 1:5000 Sytox Blue (ThermoFisher Scientific, S34857) and 1:200 EPCAM (Abcam, ab95641) in cold 1x PBS, filtered through a 30µm mesh and submitted for sorting. For E13.5 mouse experiments, Pdx1Cre/+;R26mTmG/+ and ShhCre/+;R26mTmG/+ embryos were used for downstream high-throughput experiments. After dissection, the pancreas and lung were isolated, separated, washed in cold PBS and digested in 4ml of a 2:1 solution of Trypsin LE: 1x PBS at 37˚C. After 10 minutes, tissue was vigorously pipetted, until the organs broke down into a single cell suspension, which was confirmed using brightfield microscopy. The enzymatic reaction was then inhibited with 10% FBS. After washing cells in cold PBS, the single cells were re-suspended in 400µl of 1:5000 Sytox Blue (ThermoFisher Scientific, S34857) in cold 1x PBS, filtered through a 30µm mesh and submitted for sorting. Sorted cells were washed again and processed for either ATAC-seq (50,000 cells from 3-4 GFP+ embryos, using the previously published protocol) or RNA-seq (all isolated epithelial cells were processed using an RNA isolation kit, Qiagen, Cat No. 74034).
All protocols to generate scATAC-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://support.10xgenomics.com/single-cell-atac.
Nextera DNA Flex Library Prep Kit
Whole transcriptome sequencing libraries were prepared using TruSeq® Stranded mRNA Library Prep Kit (RS-122-2101, Illumina, San Diego, CA, USA) by following the manufacturer’s instructions.

tag: developmental stage

value: embryonic day 13.5

value: Mouse lung


title: P10.r2


title: N1014C-1 [lncRNA-seq]

value: liver


title: P5_EPI.r2

value: Enriched hESC-derived neural progenitors (epithelial)


title: E13.5_lung_RNA_r1


title: P5.r2


title: Lawn Control 2

source_name: Lawn Control

value: Untreated


title: Phoenix Colony 1


title: E13.5_panc_RNA_r2

source_name: E13.5 pancreas

value: Mouse pancreas


title: Lawn Control 3


title: P4.r2


title: E13.5_panc_RNA_r1


title: P3.r2


title: SL_H3

city: Nijmegen

first: Ivo

last: Rieu

state: Gelderland

address: Heyendaalseweg 135

department: Plant Systems & Physiology

institute: Radboud University

description: strigolactone biosynthesis antisense transgenic line

data_processing:
Illumina Casava1.8 software was used for basecalling.
Raw reads were filtered to remove reads with adaptor contamination, when uncertain nucleotides constitute more than 10 percents of either read, or when low quality nucleotides (base quality less than 5) constitute more than 50 percents of the read.
Mapping to reference genome was performed using hisat2 v2.0.5, using the following parameters: --dta --phred33
FeatureCounts v1.5.0-p3 software was used to analyze the gene expression levels, using default parameters.
Genome_build: ITAG3.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Solanum lycopersicum

source_name: anther

growth_protocol: Solanum lycopersicum (cv. Micro-Tom) plants were grown on potting soil (No.4, Horticoop, Lentse Potgrond, Slingerland Potgrond) with 4 g/L Osmocote® Exact Standard 3–4 M (Everris), in climate-controlled cabinets (MC1600, Snijders Labs), using a 12/12-hour photoperiod (Philips Green Power LED DR/B/FR 120, ~250 µmol m-2s-1 at plant height), at 25°C during day-time, and 19°C during the night and 50% relative humidity (RH) ("CT conditions").

extract_protocol:
RNA was isolated via TRI-reagent extraction with clean-up on Qiagen Plant RNeasy (catalog no. 74104) columns. All RNAs were treated with DNaseI using the Plant RNeasy Kit. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and MMuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.  The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and 125 bp/150 bp paired-end reads were generated.

treatment_protocol: Plants were moved into LTMH conditions upon flowering, with 34°C during day-time, and 28°C during the night and 68% RH, or left in CT conditions for control samples. Anther were isolated approximately 5 hours into the light period after after eight days and immediately frozen in liquid nitrogen. Six anthers were pooled per replicate.

tag: temperature

value: LTMH


title: SL_H2


title: P2.r2


title: SL_C4

value: CT


title: SL_H1


title: P1.r2


title: E13.5_lung_ATAC_r1


title: E13.5_lung_ATAC_r3


title: E13.5_lung_ATAC_r2


title: SL_C3


title: 36h.r2

value: hESC-derived neuromesodermal progenitor-like cells


title: E13.5_panc_ATAC_r2


title: SL_C1


title: SA_H3

description: salicylic acid-deficient transgenic line


title: t0.r2

value: Undifferentiated hESCs


title: SA_H2


title: P10.r1


title: SA_H4


title: SA_C4


title: E9.5_gut_endoderm_scATAC_r2

source_name: E9.5 gut endoderm

value: embryonic day 9.5

value: Mouse gut endoderm


title: SA_C2


title: SA_C3


title: P9.r1


title: SA_C1


title: SL_H4


title: Lawn Control 1


title: NR_H4

description: ethylene-insensitive mutant

value: Never ripe


title: E9.5_gut_endoderm_scATAC_r1


title: P8_MES.r1


title: P8.r1

value: hESC-derived neural progenitors


title: P8_EPI.r1

value: WA09 Human embryonic stem cells


title: SL_C2


title: NR_H1

description: ethylene-insensitive mutant


title: NR_C3

description: ethylene-insensitive mutant


title: NR_C2

description: ethylene-insensitive mutant


title: NR_C4

description: ethylene-insensitive mutant


title: NR_C1

description: ethylene-insensitive mutant


title: P7.r1


title: E13.5_panc_ATAC_r1


title: P6.r1


title: Input library rep1

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description:
sgRNAs from Calu-3 cells 2 days after seeding (uninfected).
PCR amplicon

data_processing:
MAGeCK v0.5.6 was used to count sgRNA from FASTQ files.
MAGeCK v0.5.6 was used to analyze the selection effect of genes based on the change in sgRNA distribution, using the robust rank aggregation (RRA) algorithm with normalization to total reads.
Genome_build: The GeCKO library was used as reference for sgRNA counts.
Supplementary_files_format_and_content: sgRNA_counts.txt: Matrix table with raw counts for every sgRNA and every sample.

source_name: Calu 3

growth_protocol: Calu-3 cells (ATCC HTB-55) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% heat-inactivated fetal bovine serum (FBS), 10 mM non-essential amino acids (NEAA), 2 mM L-Glutamine, 1 mM Sodium pyruvate and 1% Penicillin/Streptomycin (all from Biological Industries, Israel) at 37◦C, 5% CO2.

extract_protocol:
Cell pellets were dissolved in 10% triton and boiled for 30 minutes. Genomic DNA was extracted using a QIAamp DNA mini kit.
sgRNA sequences were amplified by one-step PCR using primers with Illumina adapters and the gDNA as a template.

treatment_protocol: Calu-3 cells were transduced with lentivirus of human Brunello Human CRISPR library, two days post-transduction, 5 ug/ml puromycin was added to the media and transduced cells were selected for seven days. Twenty-four hours prior to infection with SARS-CoV-2, 1.5*10^7 Calu-3 library-cells were seeded in 75-cm2 flasks. For viability screen, mock cells were harvested 7 days after seeding and served as a control for the depletion of genes that are essential for cell survival. Three screens, using 3 variants of SARS-CoV-2, were performed with 3*10^7 cells in each screen which is sufficient for the representation of each sgRNA into ~400 unique cells. For SARS-CoV-2 infection cells were washed once with RPMI without FBS and infected with SARS-CoV-2 virus, at a MOI of 0.02 to 0.04, in the presence of 20 μg per ml TPCK trypsin and 2% FBS. Flasks were incubated for 1 hour at 37 °C to allow viral adsorption. Then, RPMI medium supplemented with 2% FBS, was added to each well. Nine days post infection with SARS-CoV-2 cells were collected. All screens were performed in duplicate.

value: Calu 3 (ATCC HTB-55)

tag: infection

value: Uninfected

tag: crispr library

value: GeCKO


title: WT_H3

description: wild-type

value: wild-type


title: P5_MES.r1

value: Enriched hESC-derived neural crest (mesenchymal)


title: WT_H2

description: wild-type


title: WT_C4

description: wild-type


title: P5_EPI.r1

value: Enriched hESC-derived neural progenitors (epithelial)


title: P5.r1


title: WT_C3

description: wild-type


title: NR_H3

description: ethylene-insensitive mutant


title: Cd3e-/-SCLtgLMO1tg T-ALL_rep3

city: Montreal

first: mathieu

last: tremblay

state: QC

address: 2950 Chemin de Polytechnique, pav marcelle-coutu 1432

country: Canada

institute: Université de Montréal/IRIC

hyb_protocol: Hybridization to the probe array Mouse Genome 430A 2.0 (Affymetrix) was performed by the Ottawa Genome Center.

scan_protocol: Scanning performed by the Ottawa Genome Center.

data_processing: Normalization and summarization were performed using Bioconductor packages in the R environment, according to the following pipeline: (i) probesets were summarized and normalized using the RMA procedure implemented in the Affy package [115]; (ii) absent/present probesets were detected using the MAS5 implementation of the Affy package, and probesets deemed absent were removed from downstream analysis; and (iii) detection of differentially expressed genes was carried out using the Rank Products package.

source_name: CD3e-/- primary thymocytes from SCLtg-LMO1tg, ectopically expressing SCL (under Sil promoter) and LMO1 (under Lck promoter)

label_protocol: The extract was labelled using the GeneChip Eukaryotic Small Sample Target Labelling protocol (Affymetrix)

growth_protocol: Thymocytes were collected from untreated mice.

extract_protocol: RNA was extracted and purified using Qiagen RNeasy Mini Kit (P/N 741104) and resuspended in 5 ml of RNase free water at a concentration of 0.05 mg/ul.

treatment_protocol: Thymi from mice were dissected out and kept in cold PBS 2% fetal bovine serum for RNA extraction.

value: Thymus

value: CD3e-/- Sil-SCL Lck-LMO1

tag: Stage

value: leukemic

value: primary thymocytes


title: WT_C2

description: wild-type

value: CT


title: Cd3e-/-SCLtgLMO1tg T-ALL_rep1


title: Cd3e+/+SCLtgLMO1tg T-ALL_rep3

value: CD3e+/+ Sil-SCL Lck-LMO3


title: Cd3e-/-SCLtgLMO1tg T-ALL_rep2


title: Cd3e+/+SCLtgLMO1tg T-ALL_rep1

value: CD3e+/+ Sil-SCL Lck-LMO1


title: PK-1 cells, transient GFP overexpression

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

country: Japan

institute: Kobe University

data_processing:
Raw sequence files (fastq) were aligned to the human genome build 38 (hg38) reference sequences using the Strand NGS software program with default parameters.
All aligned reads were normalized using Transcripts per million (TPM).
TPM values were log2-transformed with an offset value of 1.0. Baseline transformation was not performed.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include Gene Symbol, Entrez Gene ID and TPM values (log2-transformed with an offset value of 1.0) for each Sample.

source_name: Transient GFP-overexpression in PK-1

extract_protocol:
Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacture's instruction.
RNA libraries were prepared for TruSeq Stranded mRNA Sample Preparation Guide (Part#15031047 Rev.3).

value: human pancreatic cancer cells

value: Transient GFP-overexpression


title: Uninfected screen rep1

description:
sgRNAs from Calu-3 cells 7 days after seeding (uninfected).
PCR amplicon


title: Cd3e-/-SCLtgLMO1tg pre-leukemic_rep2

value: preleukemic


title: P3.r1

value: hESC-derived neural progenitors

value: WA09 Human embryonic stem cells


title: Cd3e+/+SCLtgLMO1tg T-ALL_rep2

value: CD3e+/+ Sil-SCL Lck-LMO2


title: Cd3e-/-SCLtgLMO1tg pre-leukemic_rep1


title: Cd3e-/-SCLtgLMO1tg pre-leukemic_rep3


title: WT_C1

description: wild-type


title: PK-1 cells, transient SPRR1A overexpression

source_name: Transient SPRR1A-overexpression in PK-1

value: Transient SPRR1A-overexpression


title: scRNA-seq of spleen group 1 ILCs liver2

city: 合肥市

first: yawen

last: chen

state: 蜀山区

address: 稻香村街道

institute: USTC

data_processing:
Data were mapped to the mouse genome mm10 using Cell Ranger 2.1.1 (10X Genomics)
Gene-barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell-associated barcodes.
The output for a gene-barcode matrix containing the barcoded cells and gene expression counts was then imported into the Seurat (v3.0) R toolkit for quality control and downstream analysis.
The Seurat object was first generated using the following criteria: each gene was expressed by at least 50 cells, and at least 500 genes were expressed per cell.
We further filtered out cells that had unique feature counts greater than 3,000 or fewer than 500 and >4% mitochondrial counts.
The principal component analysis was performed using variable genes. Clusters and t-SNE plots were generated based on selected principal component analysis dimensions. Marker genes were identified by the Seurat function FindVariableFeatures.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Purified group 1 ILCs  from adult mouse liver2

extract_protocol:
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation. After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription.
The library construction were performed according to the standard manufacturer's protocol.

value: Liver

tag: cells

value: 6-8 weeks


title: scRNA-seq of spleen group 1 ILCs spleen

source_name: Purified group 1 ILCs  from adult mouse spleen

value: Spleen


title: WT_H4

description: wild-type

value: wild-type

value: LTMH


title: Input library rep2

tag: cell line

value: Calu 3 (ATCC HTB-55)

value: Uninfected

value: GeCKO


title: P2.r1

source_name: Human embryonic stem cells


title: Cd3e-/- control_rep3

source_name: CD3e-/- primary thymocytes

value: Thymus

tag: genotype

value: normal

value: primary thymocytes


title: PK-1 cells, stable DsRed overexpression

source_name: Stable DsRed-overexpression in PK-1

tag: cell type

value: human pancreatic cancer cells

value: Stable DsRed-overexpression


title: Uninfected screen rep2


title: Cd3e-/- control_rep2


title: 36h.r1

value: hESC-derived neuromesodermal progenitor-like cells

tag: time


title: Cd3e-/- control_rep1


title: P1.r1

value: hESC-derived neural progenitors

value: WA09 Human embryonic stem cells

tag: replicate


title: P4.r1


title: E+

data_processing:
Illumina Casava1.8 software used for basecalling. Raw data of fastq format were firstly processed through in-house perl scripts. In this step, clean data were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver ILC1s

extract_protocol:
Liver Ly49E+ or Ly49E− ILC1s from WT adult mice were sorted, and RNA was isolated using TRIzol  and Direct-zolTM RNA Miniprep kit.  A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: liver

value: Ly49E+  ILC1


title: scRNA-seq of liver group 1 ILCs liver1

source_name: Purified group 1 ILCs  from adult mouse liver1

value: Liver

value: 6-8 weeks


title: Beta screen rep1

description:
sgRNAs from Calu-3 cells 7 days post infection with Beta SARS-CoV-2.
PCR amplicon

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: Calu 3 + SARS-CoV-2

value: Beta SARS-CoV-2

tag: days post infection


title: Alpha screen rep2

description:
sgRNAs from Calu-3 cells 7 days post infection with Alpha SARS-CoV-2.
PCR amplicon

value: Alpha SARS-CoV-2


title: HT29-sgCtrl_rep1

city: Boston

first: Marios

last: Giannakis

state: Massachusetts

address: Brookline Ave 450

institute: Dana Farber Cancer Institute

description:
Control
RNA-seq.txt

data_processing:
Raw reads were trimed by trimmomatic. Then clean reads were aligned to a bowtie2 indexed human genome (hg19 sourced from UCSC) using STAR (v2.5.2a)
Gene expression levels were quantified as read counts generated by counts per million reads (CPM), with default settings. Raw tag counts were normalized for GC content using EDASeq (v2.8.0)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Matrix table with counts per million reads (CPM) for each sample

source_name: human colorectal cancer cell line

growth_protocol: Cells were maintained in the McCoy's 5A Medium and supplemented with 10% fetal bovine serum, 100 units/ml penicillin, and 100 mg/ml streptomycin in a 5% CO2 atmosphere at 37°C.

extract_protocol:
Total RNA was isolated using RNeasy RNA isolation kit (Qiagen) following supplier’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transduced with Lenti_Guide_puro-control_sgRNA or Lenti_Guide_puro-RNF43_659mutant_sgRNA via lentiviral infection to generate control or isogenic RNF43 mutant cell lines respectively, then the stable cell lines were selected for 7 days with 1 ug/mL puromycin

value: colorectal

value: human colorectal cancer cells

tag: age

value: APC, TP53, BRAF mutation

value: Control


title: S4

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Library strategy: CITE-seq
Sequencing files of cDNA and ADT libraries were processed using the Cell Ranger Single Cell Software (v3.1.0) to perform quality control, sample de-multiplexing, barcode processing, alignment to mm10 genome with STAR (version 2.6.1.a), counting of reads and UMIs, and counting of CITE-seq antibody barcodes. We followed the "Feature Barcoding Analysis" instructions (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis). Default parameters were used for Cell Ranger, except for the STAR parameters outSAMmultNmax set to 1 and alignIntronMax set to 10000.
A custom reference was built, adding the sequences of the YFP, human CD4 and iCre constructs from the mouse strain to the reference refdata-cellranger-mm10-3.0.0 (available at https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) using Ensembl 93 gene models.
Filtering for high-quality cells was done using the cells library sizes, the number of detected genes and the percentage of reads mapping to mitochondrial genes, based on the distribution observed across cells. Low-abundance genes were filtered out. After quality filtering, the resulting dataset consisted of 12,165 genes and 20,595 cells across the 4 samples. The filtered UMI counts matrix for these genes and cells is provided in file UMIsMatrix.txt.gz.
Further quality controls and analyses were performed using R (version 3.6), and Bioconductor (version 3.10) packages, notably dropletUtils (version 1.6.1), scran (v1.14.6) and scatter (v1.14.6), mostly following the steps of the simpleSingleCell Bioconductor workflow (https://osca.bioconductor.org/).
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw UMI counts for filtered Ensembl release 93 gene models (rows 1 to 12165), mice constructs YFP, hCD4 and iCre transcripts (rows 12166 to 12168), and CITE-seq antibodies (rows 12169 to 12179); the first column corresponds to ENSEMBL ID/construct/antibody, and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID separated by a dash (e.g., "AATGCCAAGATTGGGC-1")

source_name: bone-marrow LSK cells

extract_protocol:
Bone marrow cells from four TdT[hCD4]-TdT[iCre]-Rosa26[YFP] double reporter mice were isolated and enriched for progenitor cells by MACS (Magnetic-activated cell sorting) using antibodies directed against CD3, CD19, B220, Ter119, and Ly6G. Subsequently cells were stained with antibodies directed against additional lineage markers (CD11b, CD11c, NK1.1, GR-1), Sca-1, and CD117 in order to identify LSK cells.
For CITE-seq, cells were stained with antibodies coupled to oligonucleotides directed against hCD4, Flt3, CD48, CD150, CD9, CD41, CD55, CD105, CD115, CXCR4, and ESAM (Biolegend)
LSK cells were sorted and an estimate of 4000 cells per mouse were loaded on one well each of a 10x Genomics Chromium Single Cell Controller. Single-cell capture and cDNA and library preparation were performed at the Genomics Facility Basel of the ETH Zurich, Basel, with a Single-Cell 3’ v3 Reagent Kit (10x Genomics) according to the manufacturer’s instructions, with the changes as described in (Stoeckius et al., 2017. Simultaneous epitope and transcriptome measurement in single cells. Nat Methods 14:865-868.) to capture cDNA and produce libraries from antibody derived oligos (ADT).
Sequencing was performed on 4 lanes (2 flow-cells) of an Illumina NovaSeq 6000 instrument, with a mix of 90% cDNA library and 10% ADT library for the 2 first lanes, and 95% cDNA library and 5% ADT library for the 2 last lanes.

value: Lineage-Sca1+cKit+ (LSK) cells

tag: Sex

value: male


title: E- 2

value: Ly49E-  ILC1s


title: HT29_RNF43_G659 mutations_rep3

description:
RNF43_G659 mutations
RNA-seq.txt

value: RNF43, APC, TP53, BRAF mutation

tag: treatment

value: RNF43_G659 mutations


title: PK-1 cells, stable SPRR1A overexpression

source_name: Stable SPRR1A-overexpression in PK-1

value: human pancreatic cancer cells

value: Stable SPRR1A-overexpression


title: E- 1

tag: tissue

value: liver


title: Beta screen rep2

value: Calu 3 (ATCC HTB-55)

value: GeCKO


title: Knockout LT-HSC at 3 weeks, biological rep3

first: Qingsong

last: Qiu

address: Ruijin er road No.197

institute: SIH

description: SAMPLE 6

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: RMA expression value derived from Expression Console software, and analysis was performed using Partek Genomics Suite.  affymetrix-algorithm-name = rma-gene-default, affymetrix-algorithm-version = 1.0, program-name = Expression Console, program-version = 1.1.2800.28061

label: Biotin

source_name: Knockout LT-HSC at 3 weeks,  #3

label_protocol: Total RNA were amplified, labeled and purified by using Ovation® Pico WTA System V2(Cat#3302， NuGEN, San Carlos, CA, US)and FL-Ovation™ cDNA Biotin Module V2(Cat#4200， NuGEN, San Carlos, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Murine bone marrow lineage- Sca-1+ c-kit+ CD48- CD150+ cells were sorted directly into buffer RLT (Qiagen) with 1% β-Mercaptoethanol.

extract_protocol: Total RNA was extracted and purified using RNeasy micro kit(Cat#74004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: Bone marrow

value: knockout


title: Wildtype LT-HSC at 3 weeks, biological rep3

description: SAMPLE 3

source_name: Wildtype LT-HSC at 3 weeks,  #3

value: wildtype


title: Wildtype LT-HSC at 3 weeks, biological rep2

description: SAMPLE 2

source_name: Wildtype LT-HSC at 3 weeks,  #2


title: MET4-C-004a EOT

status: Public on Mar 26 2022

city: Guelph

first: Kyla

last: Cochrane

state: ntario

address: 488 Gordon Street

institute: NuBiyota

data_processing:
Library strategy: 16S rRNA DNA-seq
Reads in which more than 70% of bases had a Phred score of 30 or more were retained and trimmed using DADA2 [v1.14.1].
Taxonomy was assigned with a naive implementation of the naive Bayesian classifier method and trained with the Silva database [v132].
Amplicon sequence variants were assigned and collates to the closest related taxon using NCBI BLAST.
Supplementary files format and content: MET4denoised.csv (abundance data (denoised 16S))
Supplementary files format and content: MET4IO_NCBI_merged.csv (abundance data (full taxonomy))

organism: human feces metagenome

source_name: human fecal tissue

extract_protocol:
DNA was extracted from from the fecal material using the Quick-DNA Fecal/Soil Microbe Kits (Zymo Research).
The 16S rRNA gene V4 variable region was amplified with PCR using primers 515F and 806R with the barcode on the forward primer. After PCR amplification samples were pooled in equal proportions, on the basis of molecular weight and DNA concentration and purified with calibrated Ampure XP beads. Pooled and purified PCR product was used to prepare an Illumina Nextera DNA library using the MiSeq version 3 reagents.
Amplicon Sequencing of the 16S rRNA gene for bacterial identification

value: human fecal tissue

value: Post microbial therapy

tag: strain

value: fecal bacterial strains -mixed

tag: sample type

value: human gut microbiome


title: Wildtype LT-HSC at 3 weeks, biological rep1

description: SAMPLE 1

source_name: Wildtype LT-HSC at 3 weeks,  #1


title: HT29-sgCtrl_rep3

description:
Control
RNA-seq.txt

value: colorectal

value: human colorectal cancer cells

value: APC, TP53, BRAF mutation

value: Control


title: HT29-sgCtrl_rep2

description:
Control
RNA-seq.txt


title: HT29_RNF43_G659 mutations_rep2

description:
RNF43_G659 mutations
RNA-seq.txt

value: RNF43, APC, TP53, BRAF mutation

value: RNF43_G659 mutations


title: Alpha screen rep1

value: Alpha SARS-CoV-2


title: MET4-C-004a Wk 3-4 (Post MET)


title: S3

value: Lineage-Sca1+cKit+ (LSK) cells

value: TdT[hCD4]-TdT[iCre]-Rosa26[YFP] double reporter mice

value: male


title: MET4-C-004a Screening

value: No treatment


title: S1


title: MET4-C-002a Wk 3-4 (Post MET)


title: Knockout LT-HSC at 3 weeks, biological rep2

description: SAMPLE 5

source_name: Knockout LT-HSC at 3 weeks,  #2

value: Bone marrow

value: knockout


title: MET4-C-002a EOT

value: human fecal tissue


title: Knockout LT-HSC at 3 weeks, biological rep1

description: SAMPLE 4

source_name: Knockout LT-HSC at 3 weeks,  #1


title: WT screen

description:
sgRNAs from Calu-3 cells 7 days post infection with WT SARS-CoV-2.
PCR amplicon

value: Calu 3 (ATCC HTB-55)

value: WT SARS-CoV-2

value: GeCKO


title: MET4-C-003b Day 10-16

value: Post immunotherapy

value: fecal bacterial strains -mixed

value: human gut microbiome


title: HT29_RNF43_G659 mutations_rep1

description:
RNF43_G659 mutations
RNA-seq.txt

value: colorectal

value: human colorectal cancer cells


title: MET4-C-004a Day 10-16


title: MET4-C-002a Screening


title: S2


title: MET4-C-003b Screening


title: MET4-C-003b Wk 3-4 (Post MET)

value: Post microbial therapy


title: MET4-C-002a Day 10-16


title: t0.r1

value: Undifferentiated hESCs

value: WA09 Human embryonic stem cells


title: MET4-C-001b EOT


title: MET4-C-002a Wk 24 (Post MET)


title: MET4-C-001b Wk 3-4 (Post MET)


title: MET4-C-001b Wk 24 (Post MET)


title: MET4-B-030 Screening


title: MET4-C-001b Screening


title: MET4-C-001b Day 10-16


title: MET4-B-030 Week 3-4 (Pre-MET4)


title: MET4-B-029a Week 3-4 (Pre MET4)


title: MET4-B-029a Wk 6-8 (Post-MET)


title: MET4-B-029a Screening


title: MET4-B-029a Day 10-16 (Post MET)


title: MET4-B-028a EOT


title: MET4-B-027a EOT


title: MET4-B-027a Screening


title: MET4-B-028a Screening


title: MET4-B-026b Day 10-16 (Post MET)


title: MET4-B-026b Wk 6-8 (Post-MET)


title: MET4-B-027a Wk 3-4 (Pre-MET)


title: MET4-B-027a Day 10-16 (Post MET)


title: MET4-B-026b Wk 3-4 (Pre-MET)


title: MET4-B-025a Wk 6-8 (Post-MET)


title: MET4-B-025a EOT


title: MET4-B-025a Screening


title: MET4-B-025a Wk 3-4 (Pre-MET)


title: MET4-B-025a Day 10-16 (Post MET)


title: MET4-B-024b EOT


title: MET4-B-026b Screening


title: MET4-B-024b Wk 6-8 (Post-MET)


title: MET4-B-024b Wk 3-4 (Pre-MET)


title: MET4-B-024b Screening


title: MET4-B-024b Day 10-16 (Post MET)


title: MET4-B-023a Wk 6-8 (Post-MET)


title: MET4-B-023a Day 10-16 (Post MET)


title: MET4-B-023a Screening


title: MET4-B-023a Wk 24 (Post-MET)


title: MET4-B-022a EOT


title: MET4-B-022a Screening


title: MET4-B-021a Day 10-16 (Post MET)


title: MET4-B-020b EOT


title: MET4-B-020b Wk 3-4 (Pre-MET)


title: MET4-B-021a Screening


title: MET4-B-022a Wk 3-4 (Pre-MET)


title: MET4-B-021a EOT


title: MET4-B-022a Wk 6-8 (Post-MET)


title: MET4-B-020b Wk 6-8 (Post-MET)


title: MET4-B-020b Screening


title: MET4-B-021a Wk 3-4 (Pre-MET)


title: MET4-B-018a Unscheduled


title: MET4-B-019a Screening


title: MET4-B-019a Day 10-16 (Post MET)


title: MET4-B-019a Wk 3-4 (Pre-MET)


title: MET4-B-018a Day 10-16 (Post MET)


title: MET4-B-017a Wk 24


title: MET4-B-018a Wk 3-4 (Pre-MET)


title: MET4-B-019a EOT


title: MET4-B-021a Wk 6-8 (Post-MET)


title: MET4-B-020b Day 10-16 (Post MET)


title: MET4-B-017a Unscheduled2


title: MET4-B-017a Wk 6-8 (Post-MET)


title: MET4-B-018a Wk 6-8 (Post-MET)


title: MET4-B-017a Day 10-16 (Post MET)


title: MET4-B-016a EOT


title: MET4-B-017a Wk 3-4 (Pre-MET)


title: MET4-B-016a Wk 6-8 (Post-MET)


title: MET4-B-016a Screening


title: MET4-B-023a Wk 3-4 (Pre-MET)


title: MET4-B-014b Screening


title: MET4-B-013a Wk 3-4 (Pre-MET)


title: MET4-B-015a Screening


title: MET4-B-016a Wk 3-4 (Pre-MET)


title: MET4-B-013a EOT


title: MET4-B-016a Day 10-16 (Post MET)


title: MET4-B-011a Wk 3-4 (Pre-MET)


title: MET4-B-010b EOT


title: MET4-B-012a Wk 24


title: MET4-B-010b Day 10-16 (Post MET)


title: MET4-B-012a Day 10-16 (Post MET)


title: MET4-B-012a Wk 6-8 (Post-MET)


title: MET4-B-010b Screening


title: MET4-B-010b Wk 6-8 (Post-MET)


title: MET4-B-012a Wk 3-4 (Pre-MET)


title: MET4-B-011a Screening


title: MET4-B-018a Screening


title: MET4-B-009b Screening


title: MET4-B-010b Wk 3-4 (Pre-MET)


title: MET4-B-017a Unscheduled1


title: MET4-B-009 EOT


title: MET4-B-009a Wk 6-8 (Post-MET)


title: MET4-B-017a Screening


title: MET4-B-009a Wk 3-4 (Pre-MET)


title: MET4-B-008a EOT


title: MET4-B-009a Screening


title: MET4-B-008a Day 10-16 (Post MET)


title: MET4-B-008a Wk 3-4 (Pre-MET)


title: MET4-B-008a Screening


title: MET4-B-007b Day 10-16 (Post MET)


title: MET4-B-007b Wk 3-4 (Pre-MET)


title: MET4-B-013a Screening


title: MET4-B-007b Screening


title: MET4-B-006a Wk 6-8 (Post-MET)


title: MET4-B-012a Screening


title: MET4-B-006a EOT


title: MET4-B-006a Wk 3-4 (Pre-MET)


title: MET4-B-011a EOT


title: MET4-B-006a Day 10-16 (Post MET)


title: MET4-B-006a Screening


title: MET4-B-005a EOT


title: MET4-B-011a Unscheduled


title: MET4-B-005a Wk 6-8 (Post-MET)


title: MET4-B-005a Wk 24


title: MET4-B-004a Wk 24


title: MET4-B-004a EOT


title: MET4-B-005a Day 10-16 (Post MET)


title: MET4-B-005a Wk 3-4 (Pre-MET)


title: MET4-B-005a Screening


title: MET4-B-004a Wk 3-4 (Pre-MET)


title: MET4-B-004a Day 10-16 (Post MET)


title: MET4-B-003b Wk 6-8 (Post-MET)


title: MET4-B-003b Wk 3-4 (Pre-MET)


title: MET4-B-004a Screening


title: MET4-B-003b Screening


title: MET4-B-003b Day 10-16 (Post MET)


title: MET4-B-002a Wk 3-4 (Pre-MET)


title: MET4-B-002a EOT


title: MET4-B-002a Wk 6-8 (Post-MET)


title: MET4-B-008a Wk 6-8 (Post-MET)


title: MET4-B-001a Wk 3-4 (Pre-MET)


title: MET4-B-001a Screening


title: MET4-B-001a EOT


title: MET4-B-001a Wk 6-8 (Post-MET)


title: MET4-B-001a Day 10-16 (Post MET)


title: MET4-B-001a Wk 24


title: MET4-A-006 WK 24


title: MET4-A-006 EOT


title: MET4-A-006 Day 10-16


title: MET4-A-006 Wk 3-4


title: MET4-A-006 Screening


title: MET4-A-004 Screening


title: MET4-A-005 Day 10-16


title: MET4-A-005 Wk 3-4


title: MET4-A-005 Screening


title: MET4-A-003 EOT


title: MET4-A-003 Wk 3-4


title: MET4-B-004a Wk 6-8 (Post-MET)


title: MET4-A-003 Day 10-16


title: MET4-A-003 Screening


title: MET4-A-002 EOT


title: MET4-A-002 Unscheduled


title: MET4-A-002 Screening


title: MET4-A-002 Wk 3-4


title: MET4-A-001 EOT


title: MET4-B-002a Day 10-16 (Post MET)


title: MET4-A-002 Day 10-16


title: MET4-B-002a Screening


title: MET4-A-001 Wk 3-4


title: MET4-A-001 Screening


title: MET4-A-001 Day 10-16


title: Hep3B sh Con H3K9 Me3

city: Winston-Salem

first: zhen

last: cai

state: NC

address: 391 Technology way

institute: wake forest baptist medical center

data_processing:
Briefly, sequencing data (.fastq.gz) were imported to local galaxy platform (https://usegalaxy.org/). After concatenating sequences of each sample, Bowtie2 was applied to align the processed data to both hg19 (human) and mm9 (Canonical) (Mouse) assembly. BamCoverage tool in DeepTools was used to generate the ChIP-seq peak profiles for each sample by normalizing the ChIP-seq reads to the percentage of reference genome (Mouse) reads in the same sample. Then incorporate the data with UCSC genome browser to generate custom track hubs and visualize data.
Genome_build: hg19,    mm9 (canonical)
Supplementary_files_format_and_content: bigwig files were generated by bamcoverage in Deeptools and normalized the ChIP-seq reads to the percentage of reference genome (Mouse) reads in the same sample

source_name: Hep3B cells

growth_protocol: All cells were cultured in normal DMEM medium supplied with 10%FBS

extract_protocol:
ChIP-IT High Sensitivity kit (Active motif) according to the manufacturer’s manual
Prepared using DNA Library preparation kit (KAPA, KK8232), as per the manufacturer’s protocol. In brief, DNA was fragmented to a median size of 150bp by sonication. Fragmented DNA ends were polished and 5′-phosphorylated. After addition of 3′-A to the ends, indexed Y-adapters were ligated and the samples were PCR amplified.

tag: shRNA

value: control

tag: antibody

value: H3K9 Me3 (Active Motif, Cat No 39161)

tag: spike in reference

value: 3/200 mouse genome


title: Hep3B sh AMPK 1# H3K9 Me3

value: sh AMPK 1#


title: Hep3B sh AMPK 2# H3K4 Me3

value: sh AMPK 2#

value: H3K4 Me3 (Active Motif, Cat No 39159)


title: Hep3B sh AMPK 1# H3K4 Me3


title: Hep3B sh AMPK 2# H3K36 Me3

value: H3K36 Me3 (Active Motif, Cat No 61101)


title: Hep3B sh Con H3K4 Me3


title: Hep3B sh AMPK 2# H3K9 Me3


title: Hep3B sh Con H3K36 Me3


title: Hep3B sh AMPK 2# H3K27 Me3

value: H3K27 Me3 (Active Motif, Cat No 39155)


title: Sh AMPK 2#-rep2

description:
replicate 2
Hep3BShAMPK4-2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were normalized with average signal from housekeeping genes

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

extract_protocol: RNA was extracted with Trizol reagent, followed by purification with QIAGEN RNeasy mini kit

value: Sh AMPK 2#


title: MET4-A-002 WK 24

value: human fecal tissue


title: Hep3B sh AMPK 1# H3K27 Me3


title: Hep3B sh Con H3K27 Me3


title: Sh Luc-rep3

description:
replicate 3
Hep3BshLuc-3


title: Sh AMPK 1#-rep2

description:
replicate 2
Hep3BShAMPK3-2

value: Sh AMPK 1#


title: 16-DLD1-p53-rep1

city: Saugus

first: Michael

last: Raabe

address: 3214 Founders Way

institute: Massachusetts General Hospital

data_processing:
reads trimmed and quality checked using skewer
aligned to hg38 and repeat elements using STAR
reads assigned to genes and repeats (Gencode and repeat masker) using featureCounts
unassigned reads remapped to Repbase consensus sequence
Assembly: GRCH38; REP
Supplementary files format and content: rawcounts in .tsv format

source_name: cell line

growth_protocol: For 3D culture (tumorspheres), serum-free media (RPMI, DMEM, or DMEM/F12) was supplemented with 20 μl/ml B27+ 20 ng/ml EGF + 20 ng/ml bFGF (ThermoFisher). Cells were plated in ultra-low attachment plates (Corning). For xenografts, SW620 or HCT116 cell lines stably transduced with Luciferase (1 x 106) were injected in the flank of six-week old female nude mice (Charles River Laboratories) at a 1:1 ratio with Matrigel (Sigma Aldrich).

extract_protocol:
RNA was isolated using Trizol reagent (ThermoFisher) or the AllPrep DNA/RNA/protein mini kit (Qiagen #80004) according to manufacturer recommendations. For ChIP-seq, HCT116, HCT8, DLD1, and SW620 cells were cross-linked with formaldehyde (1% final) for 10 min at room temperature. Cross-linked cells were quenched with glycine (125 mM final) for 5 min, followed by two washes in cold PBS. Nuclei were then isolated from 20 million cells as previously described (67), and chromatin was sheared to 250-bp average size using a Covaris S220. Immunoprecipitations were performed using 1000 μg of sheared chromatin lysate and 5 μg of p53 antibody (p53 D07; Santa Cruz, sc-47698) preconjugated to protein G beads (Invitrogen). ChIP reactions were incubated for 16 hours at 4°C with rotation and then washed four times in wash buffer [50 mM Hepes-HCl (pH 8), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, and 0.5% N-laurylsarcosine], followed by one wash in ChIP final wash buffer (1× tris-EDTA (TE) Buffer and 50 mM NaCl). Immunoprecipitated DNA was eluted from washed beads, reverse cross-linked overnight, purified, and used to construct libraries.
Clontech/Takara SMARTer Stranded Total RNA-seq PICO v2 kit (Clontech/Takara 634414) for RNA-seq. For ChIP-seq, libraries were prepared using NEBNext Ultra reagents (New England Biolabs).

treatment_protocol: For cell lines in 3D culture, cell lines were treated with DMSO or 1-10 micromolar 3TC for 1 or 7 days before extraction. For Xenografts, mice were randomized and divided into treatment arms: Control (PBS), and Lamivudine (3TC).  3TC was solubilized in PBS and administered intraperitoneally at a dosage of 50 mg/kg 3 times a week. In the control group, PBS was administered intraperitoneally. Mice were treated for 20 days, and tumor volume was measured every 5 days through IVIS imaging. At 20 days mice were euthanized according to IACUC guidelines.

tag: sequencing pool

value: ChIP Pool2

value: p53 IP


title: 22-HCT116-dmso-p53-rep1


title: 23-HCT116-dmso-p53-rep2


title: 19-HCT8-dmso-p53-rep2


title: Sh AMPK 1#-rep1

description:
replicate 1
Hep3BShAMPK3-1


title: 18-DLD1-p53-rep2


title: Sh AMPK 2#-rep1

description:
replicate 1
Hep3BShAMPK4-1


title: 13-SW620-p53-rep1


title: 15-SW620-p53-rep2


title: HK12 putified isolate B

type: genomic

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing:
The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio. The Whole genome arrays were completed with Agilent platform with Design ID Agilent-027438 was used. Sectored colonies were mapped using Agilent platforsm with Design IDs Agilent-031671, which contains probes specific only to chromosome IV, and Agilent-047217, which contains many probes on chromsome IV, but few probes near the telomere and centromere of all chromosomes.
Processed data: Ratio of the medians (635 nm/532 nm).

organism: Saccharomyces cerevisiae

source_name: cell culture of strain HK12B

label_protocol: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC24) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Yeast cells were grown at 30 degree.

extract_protocol: Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)

treatment_protocol: Isolates were grown in liquid YPD medium and the genomic DNA from independent isolates was extracted and analyzed by the whole-genome microarrays.

tag: type

value: diploid strain

source_name: cell culture of JSC24

value: control strain JSC24


title: 10-HCT116-dmso-input-rep2

tag: cell line

value: input


title: 4-DLD1-input-rep2


title: Sh AMPK 1#-rep3

description:
replicate 3
Hep3BShAMPK3-3


title: HK12 putified isolate A

source_name: cell culture of strain HK12A


title: 6-HCT8-dmso-input-rep2


title: 9-HCT116-dmso-input-rep1


title: 3-DLD1-input-rep1


title: Sh Luc-rep2

description:
replicate 2
Hep3BshLuc-2


title: 5-HCT8-dmso-input-rep1


title: Hep3B sh AMPK 1# H3K36 Me3


title: Sh Luc-rep1

description:
replicate 1
Hep3BshLuc-1


title: 1-SW620-input-rep1


title: HK10 putified isolate B

source_name: cell culture of strain HK10B


title: 25-HCT8-dmso-p53-rep1


title: 2-SW620-input-rep2


title: Cross of MD893-2 with LSY3454-2 Zygote2

source_name: cell culture of strain MD892_2


title: 9N_HCT116_PBS

source_name: xenograft

value: PBS


title: Sh AMPK 2#-rep3

description:
replicate 3
Hep3BShAMPK4-3


title: 9R_HCT116_3TC


title: HK10 putified isolate A

source_name: cell culture of strain HK10A


title: 8R_HCT116_AZA

value: AZA


title: Cross of MD893-2 with LSY3454-2 Zygote1

source_name: cell culture of strain MD892_1


title: 9B_HCT116_3TC


title: 9L_HCT116_AZA


title: Cross of MD893-1 with LSY3454-2 Zygote4

source_name: cell culture of strain MD891_4


title: Cross of MD893-1 with LSY3454-2 Zygote1

source_name: cell culture of strain MD891_1


title: Cross of MD893-1 with LSY3454-2 Zygote3

source_name: cell culture of strain MD891_3


title: Cross of MD893-1 with LSY3454-2 Zygote2

source_name: cell culture of strain MD891_2


title: 6R_HCT116_3TC


title: IS_24h_male_rep2

city: St. Louis

first: Lite

last: Yang

state: MO

address: 4922 Parkview Place

institute: Washington University in St. Louis

data_processing:
Raw fastq files are prepared by demultiplexing Illumina Nextseq runs using v3 indrops python scripts (github/indrops). Barcoded nuclei in a biological sample are divided into 2-3 tubes and their libararies are prepared and sequenced separately, which are then added together for each sample informatically after mapping.
All  subsequent processing steps from fastq files to count matrixes were performed using a custom pipeline for inDrops data analysis (github.com/indrops), using the default version 3 parameters.
inDrops.py first filters reads based on information present in read files 2,3, and 4, for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index. inDrops.py demultiplexes by Illumina library index (read 3).  For read 3, the library indices provided to the indrop.py custom pipeline are given in the yaml files. Libraries called "not_included_in_study_*" were not included in the study, but their indexes should be specified when using the indrop.py pipeline for demultiplexing.
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 (revealed by Read 2 and 4) 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 15 -e 70 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.81 or GRCh38.85) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes). The reference index is assembled using inDrops.py as described in the manual.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene. Resulting raw count files are provided and called  *.counts.tsv.gz.
10X Genomics gene expression assay data were demultiplexed and mapped using cellranger
10X Genomics ATAC assay data were demultiplexed and mapped using cellranger-atac
Assembly: mm10
Supplementary files format and content: Raw counts tables from each sample were then combined by their respective experiment into the raw counts files available in GEO

source_name: Trigeminal ganglia

extract_protocol:
For snRNA-seq data, mouse trigeminal ganglia were dissociated into a single nuclei suspension as described in Renthal et al. 2020 and Yang et al. 2021. Briefly, tissue was dissociated by dounce homogenization and clarified by ultracentrifugation through a Optiprep gradient based on a protocol (Mo et al. Neuron 2015) and modified in Renthal et al. 2020. For snATAC-seq samples, TG were collected using a non-gradient protocol described previously (Slyper et al., 2020), and GFP+ nuclei were sorted and collected using FACS.
inDrops libraries were constructued as described in Zilionis et al., Nat. Protoc. 2017. 10X Genomics gene expression assay and ATAC assay were prepared according to the user manuals.
single-nucleus RNA-seq

value: Trigeminal ganglia

value: Male

tag: assay

value: inDrops

tag: headache model

value: IS

tag: hours after treatment


title: PBS_1h_female_rep1

value: Female

value: 10X Genomics gene expression assay


title: 8L_HCT116_PBS

state: MA


title: IS_6h_male_rep2


title: 21R_SW620_3TCAZA


title: 6N_HCT116_PBS


title: IS_1h_male_rep3


title: PBS_1h_male_rep1


title: IS_6h_male_rep1


title: 21B_SW620_3TCAZA


title: 6B_HCT116_PBS


title: 8B_HCT116_3TCAZA

value: 3TC + AZA


title: 20N_SW620_3TCAZA


title: 20L_SW620_PBS


title: 20B_SW620_3TCAZA


title: 19R_SW620_3TC


title: 19L_SW620_AZA


title: 19N_SW620_PBS


title: IS_1h_female_rep1


title: CSD_6h_male_rep1

value: CSD


title: CSD_6h_male_rep2


title: 18R_SW620_3TCAZA


title: 18B_SW620_3TC


title: 6L_HCT116_3TC


title: Naive_male_rep10

value: Naive


title: CSD_1.5h_male_rep1


title: 17N_SW620_3TC


title: 17R_SW620_3TCAZA


title: 17L_SW620_3TC


title: IS_24h_male_rep1


title: 18N_SW620_3TC


title: Naive_male_rep9


title: Naive_male_rep8


title: Naive_male_rep6


title: Naive_male_rep7


title: 16N_SW620_AZA


title: 16R_SW620_3TC


title: Naive_male_rep5


title: IS_1h_male_rep2


title: Naive_male_rep4


title: IS_1h_male_rep1


title: IS_1h_female_rep2


title: Naive_male_rep3


title: Naive_male_rep2


title: 16L_SW620_3TCAZA


title: CSD_1.5h_male_rep2


title: 16B_SW620_AZA


title: 15N_SW620_PBS


title: 18L_SW620_PBS


title: 15B_SW620_3TCAZA