title: StageI-Day8, H3K27ac, rep2

description: StageI-Day8_H3K27ac_zscore.bw (in bigwig_files_1.tar.gz)


title: StageI-Day8, H3K27ac, rep1

status: Public on Jun 22 2023

type: SRA

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

country: China

institute: Peking University

library_source: genomic

data_processing:
Quality control was performed using FastQC.
The reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:NexteraPE-PE.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using Bowtie2 with parameter ‘--very-sensitive’.
After converting and sorting the output SAM files to BAM files using Samtools, we removed the duplicated reads and reads with low mapping quality using Picard and Samtools.
The pileup signal intensity for each sample was z-score normalized by subtract mean value and divided by standard error calculated using 1kb bins along whole genome.
Assembly: hg19
Supplementary files format and content: .bw file containing normalized  signal intensity of each sample
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Approximately 1 x 10^5 cells of each sample were collected and analyzed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903-02) following the recommended protocol.
Briefly, harvest fresh cultures and count 1 x 10^5 cells for each sample. Then bind cells to Concanavalin A beads at room temperature for 10 min. Next, remove liquid and add primary antibody with ice-cold Antibody Buffer and incubate overnight at 4 oC. The next day, remove liquid and add Guinea Pig Anti-Rabbit Antibody secondary antibody with Dig-Wash Buffer and incubate at room temperature for 1 h. Then, wash sufficiently and bind CUT&Tag pA/G-Tn5 Transposomes at room temperature for 1 h. After gently but throughly wash, tagmentation at 37 oC for 1 h and then performed DNA extraction with DNA extraction beads.
Finally, combine i7 and i5 Indexed Primer for PCR amplification and perform clean-up for quantification and illumina sequencing

tag: cell line

tag: cell type

value: human somatic cells during chemical reprogramming stage I

tag: antibody


title: StageI-Day8, H3K4me3, rep2

description: StageI-Day8_H3K4me3_zscore.bw (in bigwig_files_1.tar.gz)


title: StageI-Day8, H3K9me3, rep1

description: StageI-Day8_H3K9me3_zscore.bw (in bigwig_files_1.tar.gz)


title: StageII-Day4, H3K9me3, rep2

description: StageII-Day4_H3K9me3_zscore.bw (in bigwig_files_1.tar.gz)

value: human somatic cells during chemical reprogramming stage II


title: DM6-11_Lumbar Spinal Cord

city: South San Francisco

first: Xianglong

last: Zhang

state: CA

address: 1120 Veterans Blvd

country: USA

institute: Amgen Inc

library_source: transcriptomic

data_processing:
All read files were processed by fastp (v0.19.8) to remove poor quality reads and to trim poor quality 3’ bases. The filtered and trimmed reads were aligned and quantified using OmicSoft’s (Cary, NC, USA) Array Studio software (https://www.omicsoft.com/publish-studio; Oshell.exe v10.0) to reference genome NCBI Macaca_fascicularis_5.0. The transcriptomic annotation NCBI Macaca fascicularis Annotation Release 101 was used as the transcript model reference. The alignment algorithm OSA is documented in an OmicSoft whitepaper (http://omicsoft.com/downloads/whitepaper/OmicsoftAligner.pdf), and the gene/transcript quantification module is an OmicSoft implementation of the RSEM algorithm.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: RNA-Seq data — gene name, read count

molecule: total RNA

organism: Macaca fascicularis

source_name: Lumbar Spinal Cord

extract_protocol:
Total RNA was extracted from 27 snap-froze tissues with RNeasy Micro/Mini Kit (QIAGEN, Germany, Cat. #74004/#74106), according to the manufacturer’s instructions. The quality of the isolated RNA was analyzed by Agilent Bioanalyzer 2100. Only the RNA samples with an RNA Integrity Number (RIN) value of 6.0 or higher were included for RNA sequencing.
RNA-seq libraries were constructed from RNA samples meeting QC criteria based on polyA+ selection of mRNA using a standard strand-specific protocol with VAHTS® Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme, China, Cat. #NR612). The quality of the sequencing libraries was analyzed by Agilent Bioanalyzer 4200 and the peak length ranged from 250~500 bp. Clusters were generated by cBot with the library diluted to 10 pM and then sequenced on Illumina HiSeq 2500 instruments with 2 × 150 bp paired-end sequencing. All libraries were sequenced to an average depth of 52 ± 8.8 (mean ± s.d.) million reads (corresponding to 26 ± 4.4 million paired-end reads).

tag: individual

tag: phenotype

tag: tissue

value: Lumbar Spinal Cord


title: DM6-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: StageI-Day8, H3K4me3, rep1


title: DM6-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: DM6-14_Esophagus

source_name: Esophagus

value: Esophagus


title: DM5-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: StageII-Day4, H3K4me1, rep1

description: StageII-Day4_H3K4me1_zscore.bw (in bigwig_files_1.tar.gz)


title: DM6-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: DM5-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: StageI-Day8, H3K4me1, rep2

description: StageI-Day8_H3K4me1_zscore.bw (in bigwig_files_1.tar.gz)


title: StageI-Day8, H3K4me1, rep1


title: DM6-10_Thalamus

source_name: Thalamus

value: Thalamus


title: StageI-Day4, H3K27me3, rep1

description: StageI-Day4_H3K27me3_zscore.bw (in bigwig_files_1.tar.gz)


title: StageI-Day4, H3K27me3, rep2


title: DM5-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: StageI-Day4, H3K27ac, rep2

description: StageI-Day4_H3K27ac_zscore.bw (in bigwig_files_1.tar.gz)


title: DM5-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: StageI-Day4, H3K27ac, rep1


title: StageI-Day4, H3K9me3, rep2

description: StageI-Day4_H3K9me3_zscore.bw (in bigwig_files_1.tar.gz)


title: DM5-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: DM5-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: StageI-Day4, H3K9me3, rep1


title: DM5-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: DM5-23_Salivary Gland

source_name: Salivary Gland

value: Salivary Gland


title: StageI-Day4, H3K4me3, rep2

description: StageI-Day4_H3K4me3_zscore.bw (in bigwig_files_1.tar.gz)


title: StageI-Day4, H3K4me1, rep2

description: StageI-Day4_H3K4me1_zscore.bw (in bigwig_files_1.tar.gz)


title: StageI-Day4, H3K4me3, rep1


title: DM5-21_Colon

source_name: Colon

value: Colon


title: StageI-Day4, H3K4me1, rep1

value: human somatic cells during chemical reprogramming stage I


title: DM5-20_Brain Stem


title: DM5-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: M.tuberculosis H37Rv transposon mutant rv0431_3

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

description: M.tuberculosis H37Rv transposon mutant of rv0431

data_processing:
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were filtered from the adapter sequences and  their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and  only are retained those  with at least 20 phred quality score.
Reads were mapped toM tuberculosis H37Rv strain reference genome using Tophat (https://ccb.jhu.edu/software/tophat/index.shtml) allowing two  mismatches (n = 2).
Resulting BAM aligment files were used in as input The resulting BAM alignment files for the samples were the input to Rsubread’s featureCounts function to generate a table of raw counts  required for the Differential Expression Analysis pipeline based on DESeq2 BioconductoR package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: M tuberculosis H37Rv - GCF_000195955.2_ASM19595v2
Supplementary_files_format_and_content: Tables of raw counts, obtained from the BAM files of the samples in each comparative. These tables are in tab separated plain text format.

organism: Mycobacterium tuberculosis H37Rv

source_name: Bacterial RNA

growth_protocol: Mtb strains were grown in MM supplemented with 0.05% Tyloxapol at 37 °C for 5 days or until they reached OD = 0.3  they reached an OD 595 nm 0.3, and harvested.

extract_protocol:
RNA isolated 5 with TRIzol Reagent using Ribozol kit (Zymo Research) following manufacturer’s instructions.
TruSeq Stranded mRNA library prep kit (Illumina Inc), following the Ribo-Zero rRNA Removal kit Reference guide and the “TruSeq Stranded mRNA Sample Preparation Guide."

tag: genotype

value: transposon mutation (rv0431)


title: hADSCs, H3K27ac, rep2

description: hADSCs_H3K27ac_zscore.bw (in bigwig_files_1.tar.gz)

value: adult human adipose derived mesenchymal stromal cells


title: M.tuberculosis H37Rv transposon mutant rv0431_2


title: hADSCs, H3K27me3, rep2

description: hADSCs_H3K27me3_zscore.bw (in bigwig_files_1.tar.gz)


title: DM5-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: hADSCs, H3K27ac, rep1


title: M.tuberculosis H37Rv transposon mutant rv0431_1


title: hADSCs, H3K9me3, rep1

description: hADSCs_H3K9me3_zscore.bw (in bigwig_files_1.tar.gz)


title: Wild type  M.tuberculosis H37Rv wt-4_1

description: Wild type  M.tuberculosis H37Rv

value: Wt


title: hADSCs, H3K9me3, rep2


title: hADSCs, H3K4me3, rep2

description: hADSCs_H3K4me3_zscore.bw (in bigwig_files_1.tar.gz)


title: DM5-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: hADSCs, H3K4me1, rep2

description: hADSCs_H3K4me1_zscore.bw (in bigwig_files_1.tar.gz)


title: M.tuberculosis H37Rv transposon mutant rv0431_4


title: Wild type  M.tuberculosis H37Rv wt-3_1

description: Wild type  M.tuberculosis H37Rv


title: hADSCs, H3K4me1, rep1


title: Wild type  M.tuberculosis H37Rv wt-1_1

description: Wild type  M.tuberculosis H37Rv


title: hADSCs, H3K4me3, rep1


title: DM5-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: hADSCs, H3K27me3, rep1


title: DM5-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: typeII lineage, RFP+, scRNA-seq

city: Stanford

first: Arjun

last: Rajan

state: California

address: 265 Campus Drive

department: Developmental Biology

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
Reads were mapped using Cell Ranger (6.0.1) to the Drosophila genome assembly provided by ENSEMBL, build BDGP6.32, with DsRed (Genbank: AY490568) added to the genome.
Assembly: dm6
Supplementary files format and content: Tab-separated values files and matrix files

organism: Drosophila melanogaster

source_name: Sorted Neural Progenitors and Neurons

extract_protocol:
UAS-dcr2; wor-gal4, ase-gal80; UAS-RFP::stinger larval brains (n=50) were dissected 96hr after larval hatching in ice cold Rinaldini’s solution during a 45-min interval. Dissected brains were transferred to Eppendorf tubes containing 30µL of Rinaldini’s solution. A total of 10µL of 20mg/mL papain, 10uL of 20mg/mL type-1 collagenase, and 1µL of 15µM ZnCl was added to the tube. Additional Rinaldini’s solution was added to adjust the final volume to be 100 µL. The tube was mixed gently by flicking, and them incubated on a heat block at 37°C for 1-hr, while covered with aluminum foil. During this incubation, the tube was flicked for mixing every 10 min.     After the 1-hr incubation, 5µL of 100µM E-64 was added to stop the papain digestion. Samples were incubated on ice for 2 min, and then centrifuged for 3 min at 500g. Supernatant was carefully removed, and chemical dissociated brains were resuspended in 100µL Schneider’s media with 10% fetal bovine serum (FBS). Mechanical dissociation was performed by setting a P100 pipette to 70µL and titrating 30 times at a frequency of ~1Hz. After titration, cells were diluted with 400µL Schneider’s media with 10% FBS, bringing the total volume to 500µL. A total of 1µL of DRAQ5 DNA stain (ThermoFisher Scientific) was added to label cells apart from debris.     A Sony MA900 FACS machine was used to select for RFP+, DRAQ5+ cells. Cells were sorted into a 1.5mL Eppendorf tube prefilled with 100µL of Schneider’s media with 10% FBS. Approximately 30,000 RFP+, DRAQ5 events were sorted. .
Cells were transported on ice to the University of Michigan’s Advanced Genomics Core and were loaded for 10X Chromium V3 sequencing following the manufacturer’s instructions.      The mRNA was subsequently reverse-transcribed, amplified, and sequenced on an IlluminaNovaSeq-6000 chip (University of Michigan Advanced Genomics Core). Then, 151-bp paired-end sequencing was performed, with a target of 100,000 reads/cell.

tag: tissue type

value: 3rd Instar Larval Brain

value: Sorted Neural Progenitors and Neurons

value: UAS-dcr2; wor-gal4, ase-gal80; UAS-dsRed::nls


title: human hepatic organoid derived from hiPSCs

city: Daejeon

first: Ilkyun

last: Im

address: 141 Gajeong-ro, Yuseong-gu

department: Department of Predictive Toxicology

country: South Korea

institute: Korea Institute of Toxicology

data_processing:
All preprocessing steps were performed using Cell Ranger (v3.1.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw UMI counts
Supplementary_files_format_and_content: Tab-delimited text file for cell barcodes and gene features

source_name: human hepatic organoid

extract_protocol:
Hepatic organoids were harvested and washed by DPBS followed by RNA extraction using NucleoZOL (MN)
single cell libraries were constructed using 10X genomics Single cell 3’ Reagent Kit v3

value: HiPSC-derived hepatic organoids


title: H3K27ac, brat_null-fruC_null, CUT&RUN 1

description:
H3K27ac-fruDF.bw
H3K27ac_fruDelvCntrl.tsv

data_processing:
Read quality was checked using FASTQC and FASTQ (Wingett and Andrews, 2018). Reads were trimmed using cutadapt (Martin, 2011), and aligned to BDGP6.32 using bowtie2 (Langmead and Salzberg, 2012) with the flags –local, --very-sensitive, --no-mixed, --no-discordant –dovetail, and -I 10 -X 700. Samtools (Li et al., 2009) was used to convert file formats and to mark fragments less than 120bp.
For transcription factor samples, only reads with a fragment size <120 bp were kept for downstream analysis. Peaks were called individually on each replicate by MACS version 2 (Zhang et al., 2008), using parameters specified in CUT&RUNTools2 (Yu et al. 2021).  and then merged using bedtools (Quinlan and Hall, 2010).     Bigwig files for transcription factors were generated using deeptools (Ramírez et al., 2016) bamcoverage with flags –ignoreDuplicates –maxFragmentLength 120 –normalizeUsing RPKM. For data visualization, z score-normalized bigwigs were generated by subtracting the mean read coverage (counts) from the merged replicate read counts in 10 bp bins across the entire genome and dividing by the standard deviation (Larson et al., 2021).
TMM (Trimmed Mean of M-Values) normalization was performed on histone mark samples to accurately account for differences in library composition and sequencing depth. First, peaks were called on control samples against IgG using gopeaks (Yashar et al., 2022). featureCounts (Liao et al., 2014) was then used to count reads from each replicate inside the peaks for each histone mark across control and fru-/- samples. EdgeR (Robinson et al., 2010) calcNormFactors(method = TMM) was called on each histone mark countMatrix, and the final normalization factor was calculated as 1,000,000/(normFactor * number of reads in peaks). Bigwig files were generated for individual replicates by using deeptools bamcoverage on aligned bam files with the –scaleFactor equal to the final normalization factor that was calculated. Bigwigs were then merged using deeptools bigWigCompare, and z score bigwig files for histone marks were generated
Differential enrichment for each histone marks between control (brat-/-) and (brat-/-; fruΔC/-) was performed using diffReps (Shen et al., 2013) with a 500bP sliding window and otherwise default parameters.
Assembly: dm6
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&RUN

source_name: 3rd Instar Larval Brain

growth_protocol: For CUT&RUN experiments, fly crosses were carried out in 30oz fly condos, and eggs were collected on 10mm apple caps in 12-hr intervals. Newly hatched larvae were genotyped and cultured on corn meal caps for ~5–6 days.

extract_protocol:
Larval brains were dissected in 45-min time windows in PBS and transferred to 0.5mL Eppendorf tubes. Dissected brains were then collected at the bottom of the tube, and supernatant was removed. CUTANATM  ChIC/CUT&RUN (Epicypher) was performed per the manufacturer’s protocol, with modifications. Brains were resuspended in 100µL wash buffer, and then homogenized by ~30-50 passes of a Dounce homogenizer. Homogenized samples were transferred to a 1.5mL Eppendorf tube, and then the cells were pelleted by centrifugation (600g for 3min). Next, then pellets were processed using the CUT&RUN kit.  A total of 0.5ng of antibody was used per sample, (or 0.5µL if antibody concentration was unknown). A total of 0.5 ng of Escherichia coli spike-in DNA was added into each sample as a spike-in control.     For control brains, antibodies used were goat anti-cMyc (abcam, ab9132), mouse anti-Su(H), rabbit anti-Trl, rabbit anti-Caf1 (Gift from J. Kadonaga, (Tyler et al., 1996)), rabbit anti-Su(z)12 (Gift from G. Cavalli, (Loubière et al., 2016)), rabbit anti-IgG (Epicypher), and rabbit anti-H3K9me3 (abcam, ab8898). For both control and fru-/- brains, antibodies used were rabbit anti-H3K4me3 (Active Motif: 39159), rabbit anti-H3K27me3 (Sigma Aldrich, 07-449), and rabbit anti-H3K27ac (Active Motif: 39136). A total of 50 brains were collected for transcription factor samples and 25 brains were collected for histone mark samples. All samples were performed in duplicate. Samples targeting acetylation had 100 mM of sodium butyrate (Sigma Aldrich) added to all buffers. Samples using mouse antibodies underwent an additional antibody incubation step, where samples were washed 2x with cell permeabilization buffer after primary antibody incubation, and then were incubated for 1 hr with 0.5ng of rabbit anti-mouse IgG.
Fragmented DNA was diluted to 50µL in 0.1X TE and library prepped using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645) with NEBNext® Multiplex Oligos for Illumina (E6440) per the manufacturer’s protocol with modifications. The adaptor was diluted 1:25, and bead clean-up steps were performed using 1.1x AMPure Beads without size selection. The PCR cycle was modified to match specifications provided by the CUTANATM  ChIC/CUT&RUN kit. DNA was eluted in 20µL 0.1X TE.
DNA samples were assessed for concentration and quality on an Agilent TapeStation. Samples with greater than 1% adaptor underwent an additional round of bead cleanup. Samples that passed quality control were sequenced on an IlluminaNovaSeq-6000 chip (University of Michigan Advanced Genomics Core). Then, 151-bp paired end sequencing was performed, with a target of at least 10,000,000 reads per replicate.

tag: replicate


title: DM5-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: H3K27ac, brat_null-fruC::myc, CUT&RUN 2

description:
H3K27ac.bw
H3K27ac_fruDelvCntrl.tsv

value: brat11/Df(2L)Exel8040; fruC::myc


title: DM5-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: SCC-15

city: Detroit

first: Jesse

last: Veenstra

address: One Ford Place

institute: Henry Ford Health

data_processing:
Raw fastq files were aligned using HISAT2 with default settings.
Assembly: GRCh38

source_name: FFPE pathology block

extract_protocol:
Total RNA was extracted from FFPE tissue curls using the RNeasy FFPE Kit (Qiagen) per manufacturer protocol
sequenced with TruSeq RNA Exome (Illumina) at 40M reads/sample following quality control (Novogene)

value: Skin

tag: age

tag: site

value: Left Preauricular region


title: H3K27ac, brat_null-fruC_null, CUT&RUN 2


title: SCC-14

value: Left helix


title: H3K27me3, brat_null-fruC_null, CUT&RUN 1

description:
H3K27me3-fruDF.bw
H3K27me3_fruDelvCntrl.tsv


title: H3K27me3, brat_null-fruC_null, CUT&RUN 2


title: DM5-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: H3K27ac, brat_null-fruC::myc, CUT&RUN 1

description:
H3K27ac.bw
H3K27ac_fruDelvCntrl.tsv


title: SCC-10

value: Right cheek


title: DM5-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: H3K27me3, brat_null-fruC::myc, CUT&RUN 2

description:
H3K27me3.bw
H3K27me3_fruDelvCntrl.tsv


title: SCC-9

value: Right eyebrow


title: SCC-13

value: Right post pinna


title: H3K4me3, brat_null-fruC_null, CUT&RUN 2

description:
H3K4me3-fruDF.bw
H3K4me3_fruDelvCntrl.tsv


title: DM5-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: H3K4me3, brat_null-fruC_null, CUT&RUN 1


title: H3K27me3, brat_null-fruC::myc, CUT&RUN 1

description:
H3K27me3.bw
H3K27me3_fruDelvCntrl.tsv


title: SCC-8

value: Left posterior ear


title: DM5-10_Thalamus

source_name: Thalamus

value: Thalamus


title: SCC-6

value: Right ear lobule


title: DM5-14_Esophagus

source_name: Esophagus

value: Esophagus


title: H3K4me3, brat_null-fruC::myc, CUT&RUN 1

description:
H3K4me3.bw
H3K4me3_fruDelvCntrl.tsv

value: 3rd Instar Larval Brain


title: H3K9me3, brat_null-fruC::myc, CUT&RUN 2


title: DM5-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: SCC-3

value: Right wrist


title: Caf-1, brat_null-fruC::myc, CUT&RUN 2

value: brat11/Df(2L)Exel8040; fruC::myc


title: SCC-2

value: Skin

value: Left index finger


title: DM4-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: Caf-1, brat_null-fruC::myc, CUT&RUN 1


title: Su(z)12, brat_null-fruC::myc, CUT&RUN 2


title: DM4-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: trl, brat_null-fruC::myc, CUT&RUN 2

description: GAF.bw

value: trl


title: SCC-1

value: Right chest


title: trl, brat_null-fruC::myc, CUT&RUN 1

description: GAF.bw


title: DM4-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: DM4-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: KA-15

value: Right hand


title: H3K4me3, brat_null-fruC::myc, CUT&RUN 2

description:
H3K4me3.bw
H3K4me3_fruDelvCntrl.tsv


title: Su(H), brat_null-fruC::myc, CUT&RUN 1

description: SuH.bw

value: Su(H)


title: Su(H), brat_null-fruC::myc, CUT&RUN 2

description: SuH.bw


title: DM4-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: fruCOM, brat_null-fruC::myc, CUT&RUN 2

description: fruCOM.bw

value: fruCOM


title: fruC-myc, brat_null-fruC::myc, CUT&RUN 2

description: fruC-myc.bw

value: c-Myc


title: fruCOM, brat_null-fruC::myc, CUT&RUN 1

description: fruCOM.bw

value: 3rd Instar Larval Brain


title: DM4-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: KA-9

value: Right arm


title: iGG, brat_null-fruC::myc, CUT&RUN 1

description: iGG.bw

value: brat11/Df(2L)Exel8040; fruC::myc

value: iGG


title: fruC-myc, brat_null-fruC::myc, CUT&RUN 1

description: fruC-myc.bw


title: Su(z)12, brat_null-fruC::myc, CUT&RUN 1


title: H3K9me3, brat_null-fruC::myc, CUT&RUN 1


title: nLN_T1n

city: Boston

first: Linglin

last: Huang

state: MA

address: 60 Fenwood Road, HBTM 10016F

department: Neurology

institute: Brigham and Women’s Hospital

description: 10x Genomics

data_processing:
Hashed scRNA-seq expression profiles were processed in Terra (https://app.terra.bio/) through the ‘demultiplexing’ workflow in scCloud/ Cumulus (v 0.8.070), a wrapper for cellranger_mkfastq, cellranger_count (v 3.0.2), and cumulus_adt. Profiles were mapped to the pre-built mouse reference mm10, cellranger reference v1.2.0 (Ensembl v84 gene annotation), specifying that the profiles were obtained with the 10x 5’ chemistry. After mapping, cell profiles were processed to remove ambient RNA with CellBender 71 through the Terra workflow ‘run_cellbender_remove_background_gpu’, with Docker image ‘us.gcr.io/broad-dsde-methods/cellbender:latest’ (as of Jan 30, 2020) with epochs = 300, low-count-threshold = Null
Next, cell profiles were matched with antibody derived tags (ADT) counts to assign their identity, as samples from different time points or locations had been associated with unique combinations of 2 hashing antibodies. Cells with incorrect combinations of hashing antibodies were discarded from the analysis. Separately, reads from the VDJ libraries (BCR and TCR) were processed with Cumulus, using the pre-built reference GRCm38_vdj_v3.1.0, part of cellranger reference 3.1.0, annotation built from Ensembl Mus_musculus.GRCm38.94.gtf. Filtered_contig annotations and filtered_contig.fasta from the two separate channels of each sample set (technical replicates) were merged before further processing.
Assembly: mm10
Supplementary files format and content: The MTX format is a sparse matrix format with genes on the rows and cells on the columns as output by Cell Ranger. Each MTX file has two TSV files with genes and barcode sequences corresponding to row and column indices, respectively
Supplementary files format and content: The CSV file for ADT is a dense matrix of UMI counts with antibody hashtags on the rows and  cells on the columns.
Supplementary files format and content: The CSV file for filtered contig annotations is output by Cell Ranger. Each row is one contig, columns are characteristics of contigs.
Supplementary files format and content: The CSV fiel for cell hashing ab to sampleID mapping contains relationship between hashing antibodies (first 2 columns) and samples (last column).
Supplementary files format and content: The CSV fiel for cell hashing barcode to antibody mapping contains relationship between hashing antibodies barcode sequencess (first column) and antibodies (last column).

molecule: polyA RNA

organism: Mus musculus

source_name: Non-draining lymph nodes

extract_protocol:
For the B cell atlas analysis or the examination of CD19cre/+ and TIM-1BKO mice, viable leukocytes were sorted by FACS-sorted from tumors (70% CD3e+ and CD19+ cells, 30% total CD45+ cells), dLN and ndLN (100% CD45+ cells) at three different time points as depicted in Extended Date Figure 2a. For the analysis of TIM-1-expressing B cells, viable B220+ CD19+ CD138+ and - cells derived from dLN, ndLN and spleen from C57Bl6/J mice were sorted by FACS. Cells were resuspended in PBS containing 2% FCS and stained with oligo tagged TotalSeq antibodies (BioLegend) for 30 minutes on ice. Cells were washed and pooled accordingly, centrifuged at 1,200 rcf for 5 minutes at 4°C and resuspended in PBS + 2% FCS.
For samples that did not include scBCR-seq and/or scTCR-seq and 5' feature barcoding, sorted cells were separated into droplet emulsions using the Chromium Single Cell 3′ Solution (v2) according to manufacturer’s instructions (10x Genomics). Samples that included scBCR-seq and/or scTCR-seq and 5' feature barcoding were separated into droplet emulsions using the Chromium Single Cell 5' V2 Solution, according to manufacturer’s instructions (10x Genomics). scBCR-seq, scTCR-seq and 5' feature barcoding libraries were prepared according to the manufacturer’s instructions (10x Genomics).

value: Non-draining lymph nodes

value: Tim-1 negative B cells

value: WT

tag: time


title: DM4-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: nLN_T1p

description: 10x Genomics

value: Tim-1 positive B cells


title: DM4-24_Bone Marrow, Femur

source_name: Bone Marrow

value: Bone Marrow


title: KA-4

value: Skin

value: Right leg


title: BKO_3_TCR

description: 10x Genomics

library_source: other

molecule: protein

source_name: Tumor and Lymph nodes

value: Tumor and Lymph nodes

value: Immune cells

value: WT and TIM-1BKO, hased


title: dLN_T1n

description: 10x Genomics

source_name: Draining lymph nodes

value: Draining lymph nodes


title: dLN_T1p

description: 10x Genomics


title: KA-5

source_name: FFPE pathology block

value: Left forearm


title: KA-14

value: Left shin


title: KA-10

value: Right thigh


title: BKO_3_BCR

description: 10x Genomics


title: DM4-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: KA-3

value: Left popliteal fossa


title: BKO_3_ADT

description:
10x Genomics
BKO_cell_hashing_ab_to_sampleID.csv
BKO_cell_hashing_barcode_to_ab.csv

molecule: other


title: KA-7

value: Right forearm


title: BKO_3

description: 10x Genomics


title: DM4-23_Salivary Gland

source_name: Salivary Gland

value: Salivary Gland


title: DM4-21_Colon

source_name: Colon

value: Colon


title: KA-2


title: BKO_2_BCR

description: 10x Genomics


title: KA-1

value: Left elbow


title: BKO_2_ADT


title: BKO_2

description: 10x Genomics


title: BKO_1_BCR

description: 10x Genomics


title: DM4-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: BKO_1_ADT


title: TimeCourse_6_TCR

description: 10x Genomics

value: WT

value: 3 time points, hashed


title: BKO_1

description: 10x Genomics


title: TimeCourse_6_BCR

description: 10x Genomics


title: TimeCourse_6_ADT

description:
10x Genomics
TimeCourse_cell_hashing_ab_to_sampleID.csv
TimeCourse_cell_hashing_barcode_to_ab.csv


title: DM4-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: DM4-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: TimeCourse_6_GEX

description: 10x Genomics

value: Tumor and Lymph nodes

value: Immune cells


title: DM4-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: BKO_2_TCR

description: 10x Genomics

value: WT and TIM-1BKO, hased


title: TimeCourse_5_TCR

description: 10x Genomics


title: TimeCourse_5_ADT


title: DM4-14_Esophagus

source_name: Esophagus

value: Esophagus


title: TimeCourse_4_TCR

description: 10x Genomics


title: DM4-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: TimeCourse_5_GEX

description: 10x Genomics


title: DM4-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: BKO_1_TCR

description: 10x Genomics


title: DM4-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: DM4-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: SHSY5Y Lamin A KO cells biol rep3

city: Gothenburg

first: Aishe

last: Sarshad

address: Medicinaregatan 9C

department: Dept.of Biochemistry & Cell Biology

country: Sweden

institute: University of Gothenburg

data_processing:
RNAseq data were preprocessed using the RNAseq nf-core pipeline  (https://nf-co.re/rnaseq)
Assembly: hg38
Supplementary files format and content: format: xlsx content: TPM

growth_protocol: A375 cells were cultured in DMEM media supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin, while SHSY5Y cells were  cultured in RPMI media supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin. Lamin A knockout cells were generated using PITCH-CRISPR-Cas9-microhomology-mediated end-joining. A375 and SHSY5Y Lamin A knock out cells were cultured with respective complete media complemented with 2 μg/ml puromycin and 350 μg/ml G418.

extract_protocol:
Total RNA was extracted using Quick-RNA Miniprep Kit (BioSite-R1055, Zymo Research).
Libraries was prepared from 300 ng RNA using the Illumina Stranded Total RNA library preparation kit, including Ribo-Zero Plus treatment (20040525/20040529, Illumina Inc.) according to manufacturer’s instructions. For indexing Unique Dual Indexes (20040553/20040554, Illumina Inc.) were used.

value: Lamin A KO

tag: treatment

value: no


title: TimeCourse_4_BCR

description: 10x Genomics


title: TimeCourse_4_ADT


title: SHSY5Y Lamin A KO cells biol rep2


title: SHSY5Y WT cells biol rep3


title: SHSY5Y Lamin A KO cells biol rep1


title: TimeCourse_4_GEX

description: 10x Genomics


title: DM4-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: TimeCourse_3_BCR

description: 10x Genomics


title: DM4-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: TimeCourse_5_BCR

description: 10x Genomics

source_name: Tumor and Lymph nodes

value: WT


title: TimeCourse_3_ADT

value: 3 time points, hashed


title: SHSY5Y WT cells biol rep1


title: TimeCourse_3_GEX

description: 10x Genomics


title: DM4-10_Thalamus

source_name: Thalamus

value: Thalamus


title: TimeCourse_2_BCR

description: 10x Genomics


title: DM4-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: TimeCourse_2_TCR

description: 10x Genomics

value: Tumor and Lymph nodes


title: TimeCourse_1_TCR

description: 10x Genomics

value: Immune cells


title: A375 Lamin A KO cells biol rep2


title: TimeCourse_2_GEX

description: 10x Genomics


title: A375 Lamin A KO cells biol rep3


title: DM3-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: A375 Lamin A KO cells biol rep1


title: TimeCourse_2_ADT


title: TimeCourse_1_BCR

description: 10x Genomics


title: TimeCourse_1_ADT


title: T3_ALL

data_processing:
Reads were extracted with Illumina’s Bcl2Fastq, run via the KCO (http://kcoserver.broadinstitute.org:8088/) Galaxy server 80. Reads were mapped and expression of genes was quantified using rsem-1.2.8 81, run from the KCO Galaxy server as above using as annotation “mm10_ucsc_genomestudio_genes”. Expression was quantified as gene-level TPMs (Transcripts Per Kilobase Million). Differential expression analysis and pathway enrichment analysis (Fig. 1l, Extended Data Figure 1D-G) were performed using iDEP 82 (v0.92) and DESeq2 (1.28.1), respectively.
Assembly: mm10
Supplementary files format and content: TPM.csv is a comma delimited file that contains a matrix of gene-level TPMs. Rows are genes, columns are samples.

source_name: B16 tumor

extract_protocol:
1,000 live PAN-B cells (CD45+ CD3e- CD138+ CD19+/- cells) or TIM-1+ vs TIM-1- B cells were double-sorted by FACS and immediately lysed in TCL buffer (QIAGEN) supplemented with 1% ß-mercaptoethanol (Sigma).
Full-length RNA-seq libraries were prepared following a modified SMART-Seq2 protocol

value: B16 tumor

value: B cells

tag: strain

tag: disease

value: tumor


title: TimeCourse_1_GEX

description: 10x Genomics


title: DM3-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: A375 WT cells biol rep2


title: T2_ALL


title: TimeCourse_3_TCR

description: 10x Genomics


title: DM3-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: A375 WT cells biol rep3


title: T1_ALL


title: SHSY5Y WT cells biol rep2


title: A375 WT cells biol rep1


title: DM3-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: S3_plus

source_name: Spleen

value: Spleen

value: Tim-1 positive B cells


title: S3_ALL

value: All B cells


title: S3_min

value: Tim-1 negative B cells


title: DM3-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: Myometrial cells- MP365- scRNA-seq

city: Grand Rapids

first: Emmanuel

last: Paul

state: Michigan

address: 400 Monroe Ave NW

institute: MSU

description: 10x Genomics

data_processing:
Base calling was done by Illumina RTA3 and output was demultiplexed and converted to FastQ format with Cell Ranger (10X Genomics, v3.1.0)
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Human myometrium

extract_protocol:
Myometrial samples were washed with PBS, dissected away from non-myometrial tissue, and minced. Cells were isolated by incubation at 37°C in baffled flasks containing digestion media (DMEM/F12, 10% fetal bovine serum (FBS), collagenase type I, DNAse type I, and MgCl2) with agitation. The resulting cell suspensions were strained through 100- and 40-μm cell strainers, washed with warm media (DMEM/F12 containing 15% FBS), and centrifuged. Dead cells were removed from digested myometrial cells using the Dead Cell Removal Kit per manufacturer’s instructions
Libraries were generated and sequenced using the 10X Chromium Next GEM Single Cell 3ʹ GEM kit (10X Genomics, v2) platform according to the manufacturer’s instructions. 2 x 75 bp, paired end sequencing was performed on an Illumina NovaSeq 6000 sequencer using an S2 flow cell, 100 cycle sequencing kit (v1.5) to a minimum depth of 50K reads per cell (Illumina Inc., San Diego, CA, USA)

value: Human myometrium

value: Total myometrial cells

value: non-fibroid patient

tag: individual id

value: no previous hormonal treatment


title: DM3-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: Myometrial cells- MP363- scRNA-seq

description: 10x Genomics


title: S1_plus


title: S2_ALL


title: DM3-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: S2_min


title: S1_ALL


title: S2_plus


title: DM3-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: S1_min


title: Myometrial cells- MP356- scRNA-seq

description: 10x Genomics


title: DM3-23_Salivary Gland

source_name: Salivary Gland

value: Salivary Gland


title: N3_min

source_name: Non-draining lymph nodes

value: Non-draining lymph nodes

value: tumor


title: N3_plus


title: DM3-21_Colon

source_name: Colon

value: Colon


title: Myometrial cells- MP352- scRNA-seq

description: 10x Genomics


title: Myometrial cells- MP354- scRNA-seq

description: 10x Genomics


title: N3_ALL


title: N2_plus


title: DM3-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: Myometrial side population negative cells - MP398- Bulk RNA-seq

data_processing:
Reads were trimmed for quality and adapters using TrimGalore (version 0.6.5), and quality trimmed reads were assessed with FastQC (version 0.11.7). Trimmed reads were mapped to Homo sapiens genome assembly GRCh38 (hg38) using STAR (version 2.7.9a). Reads overlapping Ensembl annotations (version 99) were quantified with STAR prior to model-based differential expression analysis using the edgeR-robust method with paired samples. Genes with low counts per million (CPM) were removed using the filterByExpr function from edgeR
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text files include count per gene for each Sample

extract_protocol:
Myometrial samples were washed with PBS, dissected away from non-myometrial tissue, and minced. Cells were isolated by incubation at 37°C in baffled flasks containing digestion media (DMEM/F12, 10% fetal bovine serum (FBS), collagenase type I, DNAse type I, and MgCl2) with agitation. The resulting cell suspensions were strained through 100- and 40-μm cell strainers, washed with warm media (DMEM/F12 containing 15% FBS), and centrifuged. Live cells were incubated with 5 µg/mL of Hoechst 33342 dye for 90 min. As a negative control, separate aliquots of cells from the same patients were treated with 25 µg/ml of verapamil (Sigma) prior to addition of the Hoechst dye. PI was added to stained cells with and without verapamil treatment and analyzed in a MoFlo Astrios (Beckman Coulter) for side population gating by Hoechst red and blue filters and sorting in media (DMEM/F12) at 4 °C.
Total RNA was isolated from sorted cells using an RNeasy mini kit (Qiagen) and stored at −80 °C in nuclease-free water. RNA integrity values were determined with an Agilent 2100 Bioanalyzer (ThermoFisher), and values ≥7.5 were used for library preparation and paired-end (2 × 100 bp) RNA-sequencing on an Illumina NovaSeq 6000 instrument (Illumina). Libraries were prepared using a Kapa RNA HyperPrep kit with ribosomal reduction, pooled, and sequenced on flowcells to yield approximately 50–60 million reads/sample.

value: myometrial side population negative cells


title: Myometrial side population positive cells - MP398- Bulk RNA-seq

value: myometrial side population positive cells


title: N2_min


title: N2_ALL

value: All B cells


title: N1_plus

value: Tim-1 positive B cells


title: DM3-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: Myometrial side population positive cells - MP397- Bulk RNA-seq

value: Human myometrium


title: N1_min

value: Tim-1 negative B cells


title: D3_min

source_name: Draining lymph nodes

value: Draining lymph nodes


title: DM3-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: D3_plus


title: Myometrial side population negative cells - MP397- Bulk RNA-seq

value: non-fibroid patient

value: no previous hormonal treatment


title: DM3-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: D2_plus


title: D2_min


title: N1_ALL


title: Myometrial side population negative cells - MP371- Bulk RNA-seq


title: D1_ALL


title: D3_ALL


title: Myometrial SUSD2 positive cells - MP363- Bulk RNA-seq

extract_protocol:
Myometrial samples were washed with PBS, dissected away from non-myometrial tissue, and minced. Cells were isolated by incubation at 37°C in baffled flasks containing digestion media (DMEM/F12, 10% fetal bovine serum (FBS), collagenase type I, DNAse type I, and MgCl2) with agitation. The resulting cell suspensions were strained through 100- and 40-μm cell strainers, washed with warm media (DMEM/F12 containing 15% FBS), and centrifuged. Cells were then incubated with the primary antibody for 45 min at RT with SUSD2-PE anti-human (Miltenyi Biotec, #130-117-682). Stained myometrial cells were then wash with flow buffer and resuspend in 1 mL of flow buffer with 1 μg of 4′,6-diamidino-2-phenylindole (DAPI)  for live dead discrimination. Cells were sorted by the flow cytometry core using a FACSymphony S6 cytometer.
Total RNA was isolated from sorted cells using an RNeasy mini kit (Qiagen) and stored at −80 °C in nuclease-free water. RNA integrity values were determined with an Agilent 2100 Bioanalyzer (ThermoFisher), and values ≥7.5 were used for library preparation and paired-end (2 × 100 bp) RNA-sequencing on an Illumina NovaSeq 6000 instrument (Illumina). Libraries were prepared using a Kapa RNA HyperPrep kit with ribosomal reduction, pooled, and sequenced on flowcells to yield approximately 50–60 million reads/sample.

value: myometrial SUSD2 positive cells


title: DM3-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: D1_min

value: tumor


title: D1_plus


title: Myometrial SUSD2 negative cells - MP363- Bulk RNA-seq

value: myometrial SUSD2 negative cells


title: Myometrial SUSD2 positive cells - MP362- Bulk RNA-seq


title: scMultiome_sgPbrm1 [GEX]

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

description:
Single-Cell Multiome (RNA and ATAC) sequencing
sgPbrm1_GEX
mRNA

data_processing:
Reads were aligned to mouse reference genome mm10.
Assembly: mm10
Supplementary files format and content: Matrix files were generated using Cell Ranger (10x Genomics). GEX: h5 files; ATAC: fragments.tsv files.

source_name: CD8 T cells

extract_protocol: 10x Genomics; each sample generated one gene expression library (GEX) and one ATAC library (ATAC).

value: P14 CD8 T cells

value: Pbrm1 CRISPR knock out

value: sgPbrm1 RNP

tag: infection

value: Day 21 p.i.


title: D2_ALL

value: All B cells


title: DM3-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: scMultiome_sgArid2 [GEX]

description:
Single-Cell Multiome (RNA and ATAC) sequencing
sgArid2_GEX
mRNA

value: Arid2 CRISPR knock out

value: sgArid2 RNP


title: DM3-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: DM3-14_Esophagus

source_name: Esophagus

value: Esophagus


title: DM3-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: Myometrial SUSD2 negative cells - MP362- Bulk RNA-seq

source_name: Human myometrium

value: Human myometrium

value: non-fibroid patient

value: no previous hormonal treatment


title: tetOWapl_mCherry_omp_tta_F33_rep2

city: SAN FRANCISCO

first: Lea

last: Kiefer

address: 1651 4th Street, Weill Neurosci RM 471A

institute: UCSF

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20. HiC samples were aligned and processed using HiC-Pro (Servant et al. 2015 Genome Biology). 10x single cell RNA-seq was processed using cellranger.
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1).
For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Assembly: mm10
Supplementary files format and content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: Olfactory epithilium

extract_protocol:
For RNA-seq: RNA  was  isolated  from  tissue  using  TRIzol.  Cell  lysate  was  extracted  with  bromo-chloropropane and RNA was precipitated with 100% isopropanol supplemented with 10 μg of glycobluefor 10 min at room temperature and then pelleted at 16,000 x g for 30 min at  4°C.  The  RNA  pellet  was  washed  once  with  75%  ethanol  and  then  resuspended  in RNase-free water to a maximal concentration of 200 ng/μl. Genomic DNA contaminants were   removed   by   Turbo   DNase.   Removal   of   Turbo   DNase   was   performed   by phenol:chloroform  extraction  and  RNA  was  precipitated  as  described  above  and resuspended in RNase-free water and stored at -80°C.   For Raphe RNA-seq: RNA  was  isolated  from  coronal  sections  of  the  Raphe  (20  μm  thick)  obtainedfrom paraformaldehyde-fixed   brain   (described   in   more   detail   below,   see   paragraph “Preparation of Mouse Brain Tissue Sections”). After 3x 5 minutes washes of the slides with 1X PBS, a small portion of each section containing approximately the Raphe region was extracted. Then, the RNA was isolated using  RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Invitrogen) as instructed by the manufacturer.   For in situ HiC was carried out according to Rao et al. 2014.  For ChIP-seq: Cells were crosslinked with 1% formaldehyde for  10 minutes  at room  temperature. Formaldehyde  was  quenched  by  adding  glycine to  a  final concentration of 0.125 M for 5 minutes at room temperature. Cells were then washed with 1X cold PBS with protein inhibitors twice and pelleted. Cell pellets were stored at -80°C till use. Cells were lysed in lysis buffer (50 mM Tris pH 7.5, 140 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) for 10 minutes. Nuclei were spun for 10 minutes at 1000 x g and resuspended in the sonication buffer (10 mM Tris pH 7.5, 0.5% SDS) as 5million nuclei per 300 μl sonication buffer. Chromatin was sheared by Covaris (Peak power 105.0; Duty Factor 2.0; Cycle/Burst 200; Treatment 960 sec; Temperature 4-8°C). Following a spin at 13,000 x g for 10 minutes to remove debris, the sheared chromatin was diluted such that the final binding buffer concentration was 15 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS) and incubated for 2 hours with dynabeads G pre-equilibrated in the binding buffer for pre-clearing of the chromatin. Post-cleared chromatin was then incubated with the specific antibody overnight (1 μg of antibody was used per 5 million nuclei). The next day, dynabeads G were added to the chromatin-antibody mix for 2 hours. A total of four washes with 1X wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and one wash with TE buffer (10 mM Tris pH 7.5, 1 mM EDTA) were performed. The elution was performed at65°C for 1 hour in the elution buffer (1% SDS, 250 mM NaCl, 2 mM DTT).  All steps, with the exception of the elution, were performed at 4°C. All buffers, with the exception of the TE and elution buffer contained 1X protease inhibitors. The eluted chromatin was reverse-crosslinked overnight at 65°C and the DNA was purified with AMPure  XP  beads  (Beckman  Coulter).
For RNA-Seq experiments, raw FASTQ files were aligned with either Tophat or STAR using hg19 or mm10 reference genomes. When libraries were made following the SMARTer Stranded Total RNA-Seq, the initial 4 base pairs of both paired reads were trimmed prior to alignment.   For single cell RNA-seq, raw FASTQ files were analyzed using cellranger.    For in situ Hi-C experiments, raw FASTQ files were analyzed using HiC-Pro and hic files were generated (Servant et al. 2015).

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical)  and 500ng/mL DAPI (Invitrogen). For  HiC samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 10 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting.

value: Olfactory epithilium


title: DM3-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: Myometrial side population positive cells - MP371- Bulk RNA-seq

value: myometrial side population positive cells


title: Myometrial SUSD2 positive cells - MP361- Bulk RNA-seq

value: myometrial SUSD2 positive cells


title: DM3-10_Thalamus

source_name: Thalamus

value: Thalamus


title: tetOWapl_mCherry_omp_tta_F30_rep2


title: Myometrial SUSD2 negative cells - MP361- Bulk RNA-seq

value: myometrial SUSD2 negative cells


title: tetOWapl_mCherry_omp_tta_F30_rep1


title: DM3-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: tetOWapl_mCherry_omp_tta_F14_rep2


title: Myometrial SUSD2 positive cells - MP354- Bulk RNA-seq


title: tetOWapl_mCherry_omp_tta_F6_rep2


title: DM2-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: scMultiome_Control [GEX]

description:
Single-Cell Multiome (RNA and ATAC) sequencing
sgCtrl_GEX
mRNA

value: P14 CD8 T cells

value: CRISPR control

value: sgCtrl RNP

value: Day 21 p.i.


title: Myometrial SUSD2 negative cells - MP354- Bulk RNA-seq


title: tetOWapl_mCherry_omp_tta_F6_rep1


title: OmpGFP_rep5


title: Myometrial SUSD2 positive cells - MP352- Bulk RNA-seq


title: OmpGFP_rep3


title: DM2-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: DM2-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: HiC_SNU449_rep2

first: YEONWOO

last: KIM

address: 291 Daehak-ro, Yuseong-gu

department: Department of Biological Sciences

institute: Korea Advanced Institute of Science and Technology

data_processing:
HiC-Pro [16] was used to analyze the in situ Hi-C sequenced data.
Each raw file is aligned to the human genome (hg19) and filtered. Then we merged the replicates’ data.
Contact matrices are built from merged data, and iterative correction and eigenvector decomposition (ICE) normalization were done.
We generated various resolutions of ICE-normalized Hi-C matrices (10, 20, 40, 100, and 500-kb) and annotation files that indicate genomic bins.
Contact probability calculation and PCA analysis to define the compartment were done using cooltools at a 100-kb resolution
To define TAD boundaries, we calculated reciprocal insulation (RI) scores using CaTCH at 20-kb resolution.
For most of the Hi-C analysis, including relative contact probability (RCP), TAD insulation scores, aggregate TAD analysis (ATA), and aggregate peak analysis (APA), GENOVA was used.
We used the HiCUUPS algorithm of juicer tools with default parameters to identify chromatin loop interaction.
Assembly: hg19
Supplementary files format and content: hic
Supplementary files format and content: They are indexed binary-format contact matrix heatmaps. Their resolutions include 10, 20, 40, 100, and 500kb.

extract_protocol:
We followed the Arima-HiC protocol (Arima Genomics, Inc., Cat. No. A160259) to perform the in situ Hi-C with 1 million harvested cells.
We used the Arima-HiC kit (Arima Genomics, Inc., Cat. No. A510008) to generate the library.

tag: cell line

value: Hepatocellular carcinoma tumor


title: OmpGFP_rep4


title: tetOWapl_mCherry_omp_tta_F33_rep1


title: Myometrial SUSD2 negative cells - MP352 - Bulk RNA-seq

value: Human myometrium

tag: cell type

value: non-fibroid patient


title: DM2-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: OmpGFP_rep2

value: Olfactory epithilium


title: HiC_SNU449_rep1


title: OSN_Waplflfl_ompcre

data_processing:
For RNA-Seq experiments, raw FASTQ files were aligned with either Tophat or STAR using hg19 or mm10 reference genomes. When libraries were made following the SMARTer Stranded Total RNA-Seq, the initial 4 base pairs of both paired reads were trimmed prior to alignment.
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.3.2) with default parameters. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20. HiC samples were aligned and processed using HiC-Pro (Servant et al. 2015 Genome Biology). 10x single cell RNA-seq was processed using cellranger.
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq, bigWig files  were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Assembly: mm10
Supplementary files format and content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

extract_protocol: For RNA-seq: RNA  was  isolated  from  tissue  using  TRIzol.  Cell  lysate  was  extracted  with  bromo-chloropropane and RNA was precipitated with 100% isopropanol supplemented with 10 μg of glycobluefor 10 min at room temperature and then pelleted at 16,000 x g for 30 min at  4°C.  The  RNA  pellet  was  washed  once  with  75%  ethanol  and  then  resuspended  in RNase-free water to a maximal concentration of 200 ng/μl. Genomic DNA contaminants were   removed   by   Turbo   DNase.   Removal   of   Turbo   DNase   was   performed   by phenol:chloroform  extraction  and  RNA  was  precipitated  as  described  above  and resuspended in RNase-free water and stored at -80°C.   For Raphe RNA-seq: RNA  was  isolated  from  coronal  sections  of  the  Raphe  (20  μm  thick)  obtainedfrom paraformaldehyde-fixed   brain   (described   in   more   detail   below,   see   paragraph “Preparation of Mouse Brain Tissue Sections”). After 3x 5 minutes washes of the slides with 1X PBS, a small portion of each section containing approximately the Raphe region was extracted. Then, the RNA was isolated using  RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Invitrogen) as instructed by the manufacturer.   For in situ HiC was carried out according to Rao et al. 2014.  For ChIP-seq: Cells were crosslinked with 1% formaldehyde for  10 minutes  at room  temperature. Formaldehyde  was  quenched  by  adding  glycine to  a  final concentration of 0.125 M for 5 minutes at room temperature. Cells were then washed with 1X cold PBS with protein inhibitors twice and pelleted. Cell pellets were stored at -80°C till use. Cells were lysed in lysis buffer (50 mM Tris pH 7.5, 140 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) for 10 minutes. Nuclei were spun for 10 minutes at 1000 x g and resuspended in the sonication buffer (10 mM Tris pH 7.5, 0.5% SDS) as 5million nuclei per 300 μl sonication buffer. Chromatin was sheared by Covaris (Peak power 105.0; Duty Factor 2.0; Cycle/Burst 200; Treatment 960 sec; Temperature 4-8°C). Following a spin at 13,000 x g for 10 minutes to remove debris, the sheared chromatin was diluted such that the final binding buffer concentration was 15 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS) and incubated for 2 hours with dynabeads G pre-equilibrated in the binding buffer for pre-clearing of the chromatin. Post-cleared chromatin was then incubated with the specific antibody overnight (1 μg of antibody was used per 5 million nuclei). The next day, dynabeads G were added to the chromatin-antibody mix for 2 hours. A total of four washes with 1X wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and one wash with TE buffer (10 mM Tris pH 7.5, 1 mM EDTA) were performed. The elution was performed at65°C for 1 hour in the elution buffer (1% SDS, 250 mM NaCl, 2 mM DTT).  All steps, with the exception of the elution, were performed at 4°C. All buffers, with the exception of the TE and elution buffer contained 1X protease inhibitors. The eluted chromatin was reverse-crosslinked overnight at 65°C and the DNA was purified with AMPure  XP  beads  (Beckman  Coulter).

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical)  and 500ng/mL DAPI (Invitrogen). For Crosslinked-ChIP and HiC samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 10 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting.


title: OmpGFP_rep1


title: tetOWapl_mCherry_omp_tta_F14_rep1


title: DM2-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: OSN_Waplflwt_ompcre


title: HiC_Huh7_rep2


title: OmpGFP_rep7


title: DM2-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: OmpGFP_rep6


title: DM2-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: DM2-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: M21 scBCRseq

first: Carlos

last: Castrillon

address: 200 Longwood Ave, Warren Alpert Building

institute: Harvard Medical School / Boston Childrens Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and contig generation were made using the Cellranger software v5.0.1 with the multi function, including GEX and BCR fastq files. Gene expression count matrices were processed in R(4.0.1) using the OSCA workflow (https://bioconductor.org/books/release/OSCA/) as template and using the Single Cell Experiment (SCE) format. Scater and Scran were used for data QC and lognormalization. Cells were subset for less than 5% mitochondrial and 40 % ribosomal content. Ig genes were excluded from clustering and posterior expression analysis. Correction was done with fastMNN function from batchelor.
For Single cell BCR repertoire analysis, filtered contig fasta files from Cellranger were processed following the Immcantation workflow (https://immcantation.readthedocs.io/en/stable/). Genes were assigned using IgBlast and the IMGT reference sequence database. Clones were set using the DefineClones function from Change-O, with a 0.1691791 threshold defined using the findtThreshold function from Shazam
Assembly: modified mm10 including EYFP and CREREC transcripts

Supplementary files format and content: matrix files: produced by cellranger quantification
Supplementary files format and content: fasta files: all filtered contigs per cell after processing with cellranger
Supplementary files format and content: RDS file: SCE object used for analysis after cellular and gene level QC with all samples. Contains mouse_ID, Condition and Sex information in colData. Also MNN integration and UMAP in reducedDims.
Supplementary files format and content: Tab-separated values (.tsv) file

source_name: Spleen

extract_protocol:
Spleens from autoimmune and immunized chimeras were processed following viability recommendations for droplet-based Chromium single cell RNA-seq gene expression (10X). The full organs were dissociated in MACS buffer (PBS 1X, 0.5% BSA, 2nM EDTA) using syringe plungers and 70um cell strainers, spun down at 1000rpm for 5 min, resuspended in RBC lysis buffer and incubated on ice for 5 min. Samples were washed with MACS buffer and spun down 1000 rpm for min. Cells were enriched by negative selection with a Pan II B cell enrichment kit (Miltenyi) according to the provider specifications. During enrichment incubation cells were also stained for flow sorting
Barcoded RNA libraries for  gene expression and BCR vdj repertoire were processed according to the manufacturer's instructions (10x Genomics) for Chromium Single Cell Immune Profiling.

value: AID-EYFP+ cells

value: Spleen

tag: Sex

value: female

tag: condition

value: autoimmune


title: M17 scBCRseq

description: 10x Genomics

value: male


title: M34 scBCRseq

description: 10x Genomics


title: M23 scBCRseq

description: 10x Genomics

value: immunized


title: M24 scBCRseq

description: 10x Genomics


title: M14 scBCRseq

description: 10x Genomics


title: HiC_Huh1_rep1

value: Liver


title: DM2-23_Salivary Gland

source_name: Salivary Gland

extract_protocol:
Total RNA was extracted from 27 snap-froze tissues with RNeasy Micro/Mini Kit (QIAGEN, Germany, Cat. #74004/#74106), according to the manufacturer’s instructions. The quality of the isolated RNA was analyzed by Agilent Bioanalyzer 2100. Only the RNA samples with an RNA Integrity Number (RIN) value of 6.0 or higher were included for RNA sequencing.
RNA-seq libraries were constructed from RNA samples meeting QC criteria based on polyA+ selection of mRNA using a standard strand-specific protocol with VAHTS® Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme, China, Cat. #NR612). The quality of the sequencing libraries was analyzed by Agilent Bioanalyzer 4200 and the peak length ranged from 250~500 bp. Clusters were generated by cBot with the library diluted to 10 pM and then sequenced on Illumina HiSeq 2500 instruments with 2 × 150 bp paired-end sequencing. All libraries were sequenced to an average depth of 52 ± 8.8 (mean ± s.d.) million reads (corresponding to 26 ± 4.4 million paired-end reads).

tag: individual

tag: phenotype

value: Salivary Gland


title: DM2-21_Colon

source_name: Colon

tag: tissue

value: Colon


title: M13 scBCRseq

description: 10x Genomics


title: M11 scBCRseq

description: 10x Genomics


title: HiC_Hep3B_rep2

value: Hepatocellular carcinoma tumor


title: M34 scRNAseq

description: 10x Genomics


title: M24 scRNAseq

description: 10x Genomics


title: M23 scRNAseq

description: 10x Genomics


title: DM2-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: M21 scRNAseq

description: 10x Genomics


title: HiC_Hep3B_rep1


title: DM2-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: HiC_Huh7_rep1


title: M14 scRNAseq

description: 10x Genomics


title: M17 scRNAseq

description: 10x Genomics


title: HiC_HMEC_rep1

source_name: Breast

value: Breast

value: HMEC

value: primary mammary epithelial cells


title: HiC_Huh1_rep2


title: M13 scRNAseq

description: 10x Genomics


title: DM2-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: DM2-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: HiC_HMEC_rep2


title: M11 scRNAseq

description: 10x Genomics

value: AID-EYFP+ cells


title: NFO136-9: NFO136-9_HD#9_RNA-Seq

city: Copenhagen

first: Nicolas

last: Fossat

address: Blegdamsvej 3B

country: Denmark

institute: University of Copenhagen

description: Paired-end 2 x 75 bp

data_processing:
CLIP-Seq: Removal of poor quality sequence and adaptors using Trimmomatic. Mapping to the mm10 mouse reference genome using bowtie. PCR duplicates collapsed using tools developed in-house or found in galaxy. Collapsed mapped reads were then grouped into clusters depending on their location, followed by quantification of the number of reads for each region for each sample. Clusters were then annotated, and their size normalised to the sample size before subsequent analyses and comparisons between samples. Significance of overlap was assessed by Fisher’s exact test.
RNA-Seq: Removal of poor quality sequence and adaptors using Trimmomatic. Mapping to the mm10 mouse reference genome using RNA STAR (v2.7.3) following the two-pass alignment protocol. BAM files were imported in SeqMonk (v 1.45.4,  Babraham Institute) where data was assessed for data integrity (RNA-Seq QC pipeline), and quantified using the RNA-Seq quantitation pipeline to generate raw counts to mRNA and setting library type to “opposing strand specific”. Differentially expressed genes were calculated using SeqMonk edgeR via the “statistical test on replicated data” script as generated via SeqMonk. For differentially expressed exons and introns we quantified data in SeqMonk to a collapsed exon reference and then performed edgeR analysis.
Genome_build: mm10

source_name: Brain

extract_protocol:
Whole brains were collected as fast as possible from euthanasied mice, bissected longitudinally, then cells were gently dissociated and processed as described in the "overall design" section above. For RNA-Seq, total RNA was extracted using RNAeasy micro kit (Qiagen #74004).
For CLIP-Seq, library was constructed following a custom-made protocol (see PMID: 24407355). For RNA-Seq, library was constructed following protocol described chapter 2 of NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB #E7760S).

value: 12 weeks old

value: Male

tag: genotype

value: R6/2 (Huntington's disease)

tag: animal id

value: Brain

tag: experiment

value: Total-RNA-Seq

tag: antibody


title: ATAC_SNU449_rep1

data_processing:
The adaptors of raw reads were trimmed with cutadapt.
They were mapped to the human genome (hg19) via Bowtie2 (version 2.5.0) with default parameters.
The aligned bam files are merged and sorted with samtools.
We used the bam2wig tool of the RseQC tool to make bigwig files.
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: Describe the positions of the peaks in ATAC-seq.

extract_protocol:
The pelleted nuclei were incubated in 25 μl fresh TD buffer (10 mM Tris-HCl, pH 8.0, 5 mM MgCl2, and 10% dimethylformamide) with 2.5 μl Tn5 transposase for 30 min at 37℃. Purify DNA fragments using a QIAquick PCR purification kit (Qiagen, Cat. No. 28106).
The library was amplified as described in the provided manual using the KAPA HiFi HotStart ReadyMix (Roche, KK2061). There was additional purification with a QIAquick PCR purification kit.

value: Liver


title: DM2-17_White Adipose Tissue

data_processing:
All read files were processed by fastp (v0.19.8) to remove poor quality reads and to trim poor quality 3’ bases. The filtered and trimmed reads were aligned and quantified using OmicSoft’s (Cary, NC, USA) Array Studio software (https://www.omicsoft.com/publish-studio; Oshell.exe v10.0) to reference genome NCBI Macaca_fascicularis_5.0. The transcriptomic annotation NCBI Macaca fascicularis Annotation Release 101 was used as the transcript model reference. The alignment algorithm OSA is documented in an OmicSoft whitepaper (http://omicsoft.com/downloads/whitepaper/OmicsoftAligner.pdf), and the gene/transcript quantification module is an OmicSoft implementation of the RSEM algorithm.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: RNA-Seq data — gene name, read count

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: NFO136-4: NFO136-4_WT#4_RNA-Seq

description: Paired-end 2 x 75 bp

tag: age

value: Wild-type


title: DM2-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: NFO136-3: NFO136-3_WT#3_RNA-Seq

description: Paired-end 2 x 75 bp


title: ATAC_Huh7_rep2

source_name: Liver

value: Hepatocellular carcinoma tumor


title: NFO136-2: NFO136-2_WT#2_RNA-Seq

description: Paired-end 2 x 75 bp


title: DM2-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: ATAC_Huh7_rep1


title: FF-EV_24

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

data_processing:
CLC Genomics Workbench version 9.5.3 program
Sequence reads were trimmed and mapped to theto the miRbase 22 database allowing up to two mismatches
Reads per million mapped reads (RPM) method was used for normalization.
Assembly: the miRbase 22
Supplementary files format and content: txt, miRNA profile

source_name: follicular fluid

extract_protocol:
Approximately 1 mL of each FF sample was centrifuged at 10,000 g for 40 min at 4 ℃ in the Kubota Model 7000 ultra-centrifuge (KUBOTA Co., Tokyo, Japan). The supernatant was filtered using a 0.22 µm filter (Millex-GV 33 mm, Millipore) and then ultracentrifuged at 110,000 g for 70 min at 4 ℃ using an MLS50 rotor (Beckman Coulter Inc., USA). The pellet was washed with PBS, ultracentrifuged with the same conditions, and resuspended in PBS to extract small EVs. Then, total RNAs were extracted using the miRNeasy Plus Mini Kit (QIAGEN, Hilden, Germany).
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA). Then, PCR products were separated by electrophoresis (120 V, 60 min), and DNA fragments corresponding to 140–160 bp (the length of small non-coding RNA plus the adaptors) were recovered.

value: follicular fluid

tag: type

value: EV

tag: group

value: non-pregnant


title: FF-EV_23


title: DM2-14_Esophagus

source_name: Esophagus

value: Esophagus


title: FF-EV_22

value: pregnant


title: ATAC_Huh1_rep2


title: FF-EV_21


title: DM2-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: FF-EV_20


title: ATAC_Huh1_rep1


title: FF-EV_19


title: ATAC_Hep3B_rep2


title: DM2-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: FF-EV_18


title: ATAC_SNU449_rep2


title: DM2-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: ATAC_Hep3B_rep1


title: FF-EV_17


title: NFO136-8: NFO136-8_HD#8_RNA-Seq

description: Paired-end 2 x 75 bp

tag: strain

value: 12 weeks old

value: Male

value: R6/2 (Huntington's disease)


title: FF-EV_15


title: DM2-10_Thalamus

source_name: Thalamus

value: Thalamus


title: FF-EV_14


title: NCI-H82 Xenograft HW_TR1421

city: Sioux Falls

first: Michael

last: Kareta

state: SD

address: 2301 East 60th Street North

department: Genetics & Genomics

institute: Sanford Research

description: NCI-H82 Xenograft

data_processing:
The data was processed using CellRanger  (10X Genomics, version 6.0.1). Initially CellRanger count was run on each sample followed by CellRanger aggregate to generate one expression matrix, a vector of genes and a vector of barcodes. CellRanger was run with the –expect-cells parameter set to the expected number of cells.
Assembly: Mus_musculus_GRCm39 or Homo_sapiens_GRCh38, both appended with the sequence for eGFP.

source_name: Xenograft

growth_protocol: Cell lines were grown in RPMI with 10% BGS and penicillin/streptomycin. All cell lines were validated and regularly tested for mycoplasma.

extract_protocol:
Samples were harvested and processed according to either the mouse or human tumor dissociation kit (Miltenyi Biotec).
Performed on a 10X Chromium Controller using standard protocol (version 3 chemistry).

treatment_protocol: For cell lines, cisplatin = 2.876 uM and etoposide = 0.110 uM. For mice, cisplatin = 5 mg/kg and etoposide = 10 mg/kg on day one. On days two and three they were treated with etoposide = 10 mg/kg.

value: Xenograft

tag: treatment

value: Cisplatin/Etoposide


title: FF-EV_13


title: DM2-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: NCI-H82 Xenograft HW_TL1421

description: NCI-H82 Xenograft


title: FF-EV_11


title: FF-EV_10


title: FF-EV_9


title: NCI-H82 Xenograft HW_T1430

description: NCI-H82 Xenograft


title: FF-EV_8


title: DM1-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: NCI-H82 Xenograft HW_T1429

description: NCI-H82 Xenograft


title: DM1-7_Left Lobe of the Liver

value: Liver


title: FF-EV_7

value: follicular fluid


title: FF-EV_6

value: EV


title: FF-EV_16

value: non-pregnant


title: NCI-H82 Xenograft HW_T1426

description: NCI-H82 Xenograft


title: FF-EV_5


title: FF-EV_4


title: NCI-H82 Xenograft HW_R1424

description: NCI-H82 Xenograft

value: Untreated


title: FF-EV_3

value: pregnant


title: DM1-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: FF-EV_2


title: NFO136-7: NFO136-7_HD#7_RNA-Seq

description: Paired-end 2 x 75 bp

value: Brain

value: Total-RNA-Seq


title: DM1-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: FF-EV_12


title: DM1-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: NCI-H82 Xenograft HW_L1424

description: NCI-H82 Xenograft


title: DM1-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: FF-EV_1


title: DM1-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: NCI-H82 Xenograft HW_R1422

description: NCI-H82 Xenograft

value: Xenograft


title: HFF KO P53 ABRAXAS2 transfected clone

type: genomic

city: Bordeaux

first: Julian

last: Boutin

state: Nouvelle Aquitaine

address: 146 rue Leo Saignat

country: France

institute: INSERM U1312 BRIC

description:
Test 1
Agilent 60K CGH 021924

hyb_protocol: Labeled DNAs were hybridized onto Agilent oligonucleotide microarrays (8x60K Agilent Genetisure) according to the manufacturer’s instructions (Agilent Technologies)

scan_protocol: Scanning of the microarrays was performed using a G5761A scanner (Agilent Technologies).

data_processing:
Data analysis was carried out with Agilent Technologies software, namely Feature Extraction for Cytogenomics Algorithm v5.0 for the fluorescence ratio calculation and Agilent CytoGenomics v5.2 for the localization of chromosomal imbalances.
Deletions and duplications in the heterozygous state were characterized by values of the log2 ratio of fluorescence intensities (cyanine5/cyanine3) below -0.5 and above +0.3, respectively, with the statistical algorithm ADM2 used at a threshold of five.

source_name: CGH ABRAXA

label_protocol: DNA (minimum 125ng) was labeled  (cyanine 3 or cyanine 5) using the Genomic DNA ULS Labeling Kit from Agilent Technologies (Agilent Technologies, Santa Clara, USA)

growth_protocol: HFF cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM with glucose (4.5 g.L-473 1), L-Glutamine (1 g.L-1) and pyruvate supplemented with 20% fetal bovine serum, MEM non-essential 474 amino acids 100X (Gibco® by ThermoFisher scientific, Carlsabad, CA, USA), 100 U/mL penicillin, and 475 100μg/mL streptomycin (all from Eurobio, Courtaboeuf, France)

extract_protocol: DNA was extracted from cultivated cells using the Wizard manual kit (Promega Corporation, Madison, USA).

treatment_protocol: HFF cells were transfected with 16.9 μg Cas9 RNP and 5 μM of Alt-R® Cas9 Electroporation Enhancer by electroporation using the AMAXA™ 4D-499 Nucleofector™ device (Lonza®, Bale, Switzerland) with P3 Primary Cell Line and CZ-167

value: HFF

source_name: KOTP53 NUC FAM FLUO NEG


title: HFF KO P53 SORSC1 transfected clone

description:
Test 2
Agilent 60K CGH 021924

source_name: CGH SORSC1

source_name: KOTP53 SORC1 FLUO NEG


title: HFF PLEKHA1 transfected CGH bulk

description:
Test 5
Agilent 60K CGH 021924

source_name: CGH PLEKHA1

source_name: A1-HFF WT Clone 6


title: DM1-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: HFF VCL transfected CGH bulk

description:
Test 4
Agilent 60K CGH 021924

source_name: CGH VCL


title: HFF TRUB1 transfected CGH bulk

description:
Test 3
Agilent 60K CGH 021924

source_name: CGH TRUB1


title: NCI-H82 Cell Line HW_H82

description: NCI-H82 Cell Line

source_name: Cell Line

value: Cell Line


title: HFF CPXM2 transfected CGH bulk

description:
Test 2
Agilent 60K CGH 021924

source_name: CGH CPXM2


title: HFF ADRA2A transfected CGH bulk

description:
Test 1
Agilent 60K CGH 021924

source_name: CGH ADRA2A


title: NCI-H209 Xenograft HW_T1624

description: NCI-H209 Xenograft

source_name: Xenograft

value: Cisplatin/Etoposide


title: DM1-23_Salivary Gland

source_name: Salivary Gland

value: Salivary Gland


title: HFF ABRAXAS2 transfected CGH bulk

description: Test 1

hyb_protocol: Labeled DNAs were hybridized onto Agilent oligonucleotide microarrays (8x60K Agilent Genetisure or 180K CGH + SNP) according to the manufacturer’s instructions (Agilent Technologies)

data_processing:
Data analysis was carried out with Agilent Technologies software, namely Feature Extraction for Cytogenomics Algorithm v5.0 for the fluorescence ratio calculation and Agilent CytoGenomics v5.2 for the localization of chromosomal imbalances and LOH.
Deletions and duplications in the heterozygous state were characterized by values of the log2 ratio of fluorescence intensities (cyanine5/cyanine3) below -0.5 and above +0.3, respectively, with the statistical algorithm ADM2 used at a threshold of five. LOH was evaluated with the statistical algorithm ADM2 used at a threshold of 6 (Default Analysis Method v2)

source_name: ABRAXAS2 CGH bulk

source_name: Control HFF WT


title: WT_1

city: Erlangen

first: Mark

last: Dedden

state: Bayern

address: Schwabachanlage 12

department: Department of Medicine 1

country: Germany

institute: Universitätsklinikum Erlangen

data_processing:
The reads were aligned with Star v2.5.4b against the GRCm38 reference genome.
Reads were counted with featureCounts of the Rsubread package v2.8.1
.
Assembly: GRCm38
Supplementary files format and content: comma separated values

source_name: Thymus

extract_protocol:
RNA of mouse thymocytes was isolated with the NucleoSpin RNA Kit for RNA isolation (Machery Nagel).
Sequencing libraries were generated from RNA samples using the TruSeq Stranded mRNA Kit (Illumina).

value: Thymus

value: Thymocytes


title: DM1-21_Colon

first: Xianglong

last: Zhang

address: 1120 Veterans Blvd

institute: Amgen Inc

source_name: Colon

value: Colon


title: WT_3


title: WT_2


title: IL3RAKO_2


title: NCI-H209 Xenograft HW_T1620

description: NCI-H209 Xenograft


title: NCI-H82 Xenograft HW_L1422

description: NCI-H82 Xenograft

value: Untreated


title: DM1-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: DM1-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: IL3RAKO_3


title: IL3RAKO_1


title: NCI-H209 Xenograft HW_T1623

description: NCI-H209 Xenograft


title: NCI-H209 Xenograft HW_R1420

description: NCI-H209 Xenograft


title: DM1-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: NCI-H209 Xenograft HW_L1420

description: NCI-H209 Xenograft


title: NCI-H209 Xenograft HW_R1419

description: NCI-H209 Xenograft


title: DM1-24_Bone Marrow, Femur

source_name: Bone Marrow

value: Bone Marrow


title: NCI-H209 Xenograft HW_L1419

description: NCI-H209 Xenograft


title: PGCLCday2 OSMI-1, rep2

city: Sendai

first: Yohei

last: Hayashi

state: Miyagi

address: 4-1 Seiryo-machi, Aobaku

department: Institute of Development, Aging and Cancer

institute: Tohoku University

description:
OSMI_kallisto_res.txt
PGCLCOSMI_2

data_processing:
Sequenced reads then were trimmed using fastp software.
For gene expression analysis, reads were mapped to the mouse genome (UCSC mm10 genome assembly and NCBI RefSeq database) using kallisto software with an estimated average fragment length of 50, followed by calculation of read counts and TPM (transcripts per million).
For analyses of differentially expressed genes (DEGs), only genes with a mean TPM exceeding 1 were analyzed.
Functional enrichment analysis of DEGs was performed using the Metascape (https://metascape.org/gp/index.html#/main/step1) (Zhou et al, 2019).
Calculation and drawing of Venn diagrams were performed on the website of Bioinformatics & Evolutionary Genomics (https://bioinformatics.psb.ugent.be/webtools/Venn/).
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing TPM value for each sample.

source_name: BVSC Escells

extract_protocol:
RNA was harvested using with Rneasy micro kit (QIAGEN). 100ng of total RNA was used for the construction of sequence libraries.
Each library was constructed using a TruSeq RNA Library Preparation Kit (Illumina).

value: BVSC Escells

tag: agent

value: WT

value: PGC induction


title: PGCLCday2 DMSO, rep2

description:
OSMI_kallisto_res.txt
PGCLCDMSO_2

tag: cell line

value: DMSO


title: PGCLCday2 glucose-, rep2

description:
glucose_kallisto_res.txt
PGCLCG0_3


title: PGCLCday2 OSMI-1 rep1

description:
OSMI_kallisto_res.txt
PGCLCOSMI_1


title: PGCLCday2 glucose+, rep2

description:
glucose_kallisto_res.txt
PGCLCG25_3

value: glucose


title: NCI-H209 Cell Line HW_H209

description: NCI-H209 Cell Line


title: PGCLCday2 glucose+, rep1

description:
glucose_kallisto_res.txt
PGCLCG25_2


title: DM1-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: StageII-Day16_scRNA

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

data_processing:
The clean single-cell RNA-seq reads were mapped to human reference genome hg19 using Cell Ranger v3.1.0.
Assembly: hg19
Supplementary files format and content: .tar.gz files containing cellranger output

extract_protocol:
Using single cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, cells at different time points throughout chemical reprogramming process were harvested and resuspended at 1 x 106 cells per milliliter in 1 x PBS with 0.04% BSA. About 1 x 104 cells were added to each channel, and the target cell will be recovered was estimated to be about 5 x 103 cells. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53 ℃ for 45 min, followed by 85 ℃ for 5 min, and hold at 4 ℃. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200.
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 The libraries were finally sequenced using an IlluminaNovaseq6000 sequencer with a sequencing depth of at least 1 x 105 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

tag: cell type

value: human somatic cells during chemical reprogramming stage II


title: Neuron, motor, WT, rep3

city: Mississauga

first: Ho Sung

last: Rhee

state: ON

address: 3359 Mississauga Rd

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

data_processing:
To remove adapter sequences from the sequencing data, raw sequencing reads were trimmed using Trim Galore (www.bioinformatics.babraham.ac.uk/).
The raw trimmed reads were aligned to the mm10 mouse genome using the RNA STAR using Galaxy (www.usegalaxy.org).
BAM files were generated using Galaxy (www.usegalaxy.org)
FPKM values were generated using Cufflinks using Galaxy (www.usegalaxy.org)
Tabular files were generated using Galaxy (www.usegalaxy.org)
Assembly: mm10
Supplementary files format and content: FPKM (Fragments Per Kilobase per Million mapped fragments)
Supplementary files format and content: Tabular file format (FPKM values are sorted in a raw and column format)

source_name: mESC-derived motor neuron

growth_protocol: Motor neuron differentiation of mouse embryonic stem (ES) cells was performed as described previously (Jaura and Yeh et al., Nat. Commun, 2022) with some modifications.

extract_protocol:
Cells were collected, poly(A)+ RNA was homogenized in a phenol-containing solution, and the sample was isolated by standard ethanol precipitation.
RNA-seq libraries were prepared according to the standard Illumina protocols. Briefly, cDNA was synthesized from RNA, end-repaired, and ligated to sequencing adaptors, then PCR amplified and gel purified. The purified DNA libraries were sequenced following the manufacturer's protocols.

treatment_protocol: ES cells were trypsinized and seeded at 8 x 10^4 cells per mL on day 0. 1 uM retinoic acid and 0.25 uM Sonic Hedgehog Agonist were added to the medium on day 2. 5 uM gamma-secretase inhibitors were added on days 4 and 5.

value: mESC-derived motor neuron


title: Neuron, motor, WT, rep2


title: DM1-15_Pituitary Gland

city: South San Francisco

source_name: Pituitary Gland

value: Pituitary Gland


title: StageII-Day12_scRNA


title: Neuron, motor, WT, rep1


title: iBAT, HFD, Wild-Type, Rep5

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

data_processing:
bcl2Fastq used for demultiplexing + basecalling
Trimmomatic v0.36 used for trimming low quality reads and adapter sequences
STAR v2.6.1c used for read alignments with options: --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --alignEndsProtrude 3 ConcordantPair
Rsubread 1.32.1 used for feature quantification
Differential expression analysis: DESeq2
Assembly: Ensembl/GRCm38.p5/Annotation/Release_91-2018-02-26
Supplementary files format and content: Tab-separated raw counts

source_name: interscapular brown adipose tissue (iBAT)

growth_protocol: Mice were on ad lib HFD and non-restricted access to water, standard room temperature and humidity conditions

extract_protocol: Libraries were constructed using TruSeq RNA Sample preparation kit (Illumina)

treatment_protocol:
Different genotype, we compare Wild-Type Controls to whole-body constitutive Axl KO mice
iBAT was dissected and snap-frozen. Total RNA was extracted using the Trizol-chloroform method and was Dnase treated for genomic DNA removal.

value: Wild-Type

value: HFD Challenge

tag: replicate


title: iBAT, HFD, Wild-Type, Rep3

value: interscapular brown adipose tissue (iBAT)


title: DM1-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: PGCLCday2 DMSO, rep1

description:
OSMI_kallisto_res.txt
PGCLCDMSO_1


title: StageII-Day8_scRNA


title: iBAT, HFD, Wild-Type, Rep2


title: DM1-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: StageII-Day4_scRNA


title: PGCLCday2 glucose-, rep1

description:
glucose_kallisto_res.txt
PGCLCG0_2


title: iBAT, HFD, Axl KO, Rep5

value: Axl KO


title: iBAT, HFD, Wild-Type, Rep1


title: DM1-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: iBAT, HFD, Axl KO, Rep4


title: iBAT, HFD, Axl KO, Rep3


title: StageI-Day8_scRNA

value: human somatic cells during chemical reprogramming stage I


title: StageI-Day4_scRNA


title: iBAT, HFD, Axl KO, Rep2


title: iBAT, HFD, Axl KO, Rep1


title: hADSCs_scRNA

value: adult human adipose derived mesenchymal stromal cells


title: DM1-10_Thalamus

source_name: Thalamus

value: Thalamus


title: DM1-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: KO_bis_Rep2

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to the mouse reference genome (mm10) using meRanGh from meRanTK
The m5C sites were determined using meRanTK
Assembly: mm10
Supplementary files format and content: tab separated text file from meRanCompare

source_name: NRAS/AE9a leukemic cells

growth_protocol: Cells were cultured in RPMI 1640 medium supplied with murine 50 ng/ml SCF, 10 ng/ml IL-3 and IL-6, 1 mg/mL G418, and 2 µg/mL puromycin

extract_protocol:
The total RNA were extracted with QIAzol lysis reagent.
RNA library preparation was conducted usingKAPA Stranded mRNA-Seq Kit (Illumina Platforms) following manufacturer's protocols.

value: NRAS/AE9a leukemic cells

value: AML cells

value: Tet2 KO

value: Bisulfite-conversion


title: DM1-14_Esophagus

source_name: Esophagus

value: Esophagus


title: iBAT, HFD, Wild-Type, Rep4


title: AC4-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: WT_bis_Rep2

value: WT


title: StageII-Day16_ATAC

data_processing:
The single-cell RNA-seq reads were mapped to human reference genome hg19 using Cell Ranger v3.1.0.
The single-cell ATAC-seq reads were mapped to human reference genome hg19 using Cell Ranger ATAC v1.2.0.
Assembly: hg19
Supplementary files format and content: .tar.gz files containing cellranger and cellranger-ATAC output

extract_protocol:
The nuclei were isolated and washed according to the methods supplied by 10x Gemomics: Nuclei Isolation for Single Cell ATAC + Gene Expression Sequencing (CG000365). Then the nuclei were resuspended in chilled Diluted Nuclei Buffer (10x Genomics, PN2000153). The volume of Diluted Nuclei Buffer used was based on the number of starting cells and the final target nuclei concentration. Nuclei were counted using Countstar (Rigel S2) and then subjected to single-cell multiome libraries construction immediately.
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338) using Chromium Next GEM Chip J Single Cell Kit (PN-1000234) and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (PN-1000283). Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. The transposed nuclei in bulk samples were then loaded into a microfluidic chip and run in the Chromium Controller to be partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs). A pool of ~736,000 10x Barcodes is sampled to separately and uniquely index the transposed DNA and cDNA of each individual nucleus.
ATAC and gene expression (GEX) libraries were generated from the same pool of pre-amplified transposed DNA/cDNA (performed by CapitalBio Technology, Beijing). The ATAC libraries were sequenced using an Illumina Novaseq sequencer with a sequencing depth of at least 25,000 read pairs per nucleus with pair-end 50bp (PE50) reading strategy, while GEX libraries were sequenced with pair-end 150bp (PE150) reading strategy and a sequencing depth of at least 20,000 read pairs per nucleus.

value: human somatic cells during chemical reprogramming stage II


title: KO_bis_Rep1


title: KO_mouse_Rep2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to the  mouse mm10 using the STAR aligner. The aligned reads were then assigned to genes using RSEM
Assembly: mm10
Supplementary files format and content: table delimited text file containing the expression of genes

source_name: spleen

extract_protocol:
The total RNA were extracted with QIAzol lysis reagent.
RNA library preparation was conducted using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) following manufacturer's protocols.

treatment_protocol: NRAS/AE9a leukemic cells were transplanted into lethally irradiated (900 cGy) 6- to 8-week-old NCI C57 B6.SJL (CD45.1+) recipient mice.

value: spleen

value: The cells were isolated from speen of  NRAS/AE9a mouse and the CD45.2 cells were enriched.


title: WT_bis_Rep1


title: KO_mouse_Rep1


title: DM1-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: StageII-Day8_ATAC


title: StageI-Day9_ATAC


title: WT_mouse_Rep2


title: AC4-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: AC4-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: WT_mouse_Rep1


title: KO_model 2_Rep1

description: KO_model 2_Rep1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to the mouse mm10 using the STAR aligner. The aligned reads were then assigned to genes using RSEM
Assembly: mm10
Supplementary files format and content: table delimited text file containing the expression of genes


title: WT_model 2_Rep2

description: WT_model 2_Rep2


title: StageII-Day16_RNA


title: hADSCs_ATAC


title: WT_model 2_Rep1

description: WT_model 2_Rep1


title: DM1-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: KO_model 1_Rep2

description: KO_model 1_Rep2


title: StageII-Day8_RNA


title: StageI-Day9_RNA

value: human somatic cells during chemical reprogramming stage I


title: WT_model 1_Rep2

description: WT_model 1_Rep2


title: WT_model 1_Rep1

description: WT_model 1_Rep1


title: hADSCs_RNA

value: adult human adipose derived mesenchymal stromal cells


title: KO_model 2_Rep2

description: KO_model 2_Rep2


title: WT_rep3

city: Duarte

first: Hung Ping

last: Shih

address: 1500 East Duarte Road

institute: City of Hope

data_processing:
fastq files were aligned to version 79 of mouse reference genome GRCm38 using the STAR aligner.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the TMM function in the edgeR package in R
Differentially expressed genes (³1.5-fold and <5% FDR-adjusted p values) were identified by generalized linear modeling using the edgeR package
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

source_name: pancreas

extract_protocol:
Islets were harvested by perfusing pancreta with collagenase P from wildtype and Itgb1 mutant mice
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the  KAPA RNA HyperPrep Kit with RiboErase (HMR) according to the manufacturer’s instructions.

value: pancreas

tag: background strain

value: wild-type

value: islets


title: Mut_rep3

value: Ngn3-Cre, itgb1-/-


title: Mut_rep4


title: Mut_rep1


title: Mut_rep2


title: WT_rep4


title: AC4-6_Renal Medulla

source_name: Renal Medulla

tag: individual

value: Renal Medulla


title: WT_rep1


title: AC4-23_Salivary Gland

source_name: Salivary Gland

tag: phenotype

value: Salivary Gland


title: AC4-21_Colon

source_name: Colon

tag: tissue

value: Colon


title: AC4-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: AC4-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: AC4-24_Bone Marrow, Femur

source_name: Bone Marrow

value: Bone Marrow


title: lncap_p53_ca_c1

city: Shanghai

first: Hanling

last: Wang

address: Shanghai

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Science

description:
LNCap_6group_gene_exp.txt
p53_ca_c1_RPKM

data_processing:
The mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA). And then fragmented to approximately 200bp. Subsequently, the RNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligaion and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina.
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher  Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).
HISAT2 was used to align the clean reads to the mouse reference genome mm10 with default parameters.
HTSeq was subsequently employed to convert aligned short reads into read counts for each gene
Differential expression was assessed by DESeq2 using read counts as input.
Assembly: hg19, mm10
Supplementary files format and content: tab-delimited text files include RPKM or TPM values for each Sample

source_name: LNCap cell line

growth_protocol: LNCap were cultured in RPM1640 media supplemented with 10% FBS at 37°C under 5% CO2. Cancer associated fibroblasts were cultured in DMEM media supplemented with 10% FBS at 37°C under 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. Total RNA was subjected to Hiseq RNA-Seq, performed by RiboBio Co., Ltd.
RNA libraries for RNA-seq were prepared according to instructions of NEBNext® Ultra™ RNA LibraryPrep Kit for Illumina (NEB, USA)

treatment_protocol: For LNCap, enzalutamide (1μM) was added into different conditions, treatment was performed in two biological replicates. For cancer assocciated fibroblasts, enzalutamide (1 μM) and TGF-β1 (5 ng/ml) was added into different conditions, treatment was performed in two biological replicates.

value: LNCap cell line

value: epithelial

tag: genotype

value: WT

value: DMSO

value: cocultured with CRPCCAFs

tag: time

value: Day 7


title: lncap_p53_ca_c2

description:
LNCap_6group_gene_exp.txt
p53_ca_c2_RPKM