title: CD45Plus, Pooled_cells, HTO

data_processing:
Library strategy: CITE-Seq
The Cell Ranger (v3.0.2) application (10x Genomics) was then used to demultiplex the BCL files into FASTQ files (cellranger mkfastq), to perform alignment (to Cell Ranger mouse genome references 3.0.2 GRCm38/build 97), filtering, UMI counting and to produce gene—barcode matrices (cellranger count).
CITE-seq-Count (Version 1.4.4) was used to cound the hashtags within each cell and produce the read counts table.
Filtered matrix files were used for further scRNAseq analyses with R Bioconductor (3.12) and Seurat (3.2.1).
Filtered matrices containing cell IDs and feature names in each sample were used to build a Seurat object. We performed a quality control by filtering out the cells with less than 200 detected genes, the genes detected in less than 3 cells and the cells exhibiting more than 10% of mitochondrial genes. Gene counts in each sample was normalized separately by default method “LogNormalize” with scale factor 10000 and log-transformation. Two thousands of highly variable features were identified with the “vst” method.
After merge cells from all samples, the contaminated cells were removed based on the expression of specific genes. Four clusters were identified in the remained cell using FindClusters functionand the differentially expressed genes were calculated using FindAllMarkers function (Seurat package).
Genome_build: GRCm38
Supplementary_files_format_and_content: Text counts table: counts of genes for all cells
Supplementary_files_format_and_content: Text counts table: counts of hashtags for all cells
Supplementary_files_format_and_content: makers_per_cluster.csv (DE genes in each cluster)
Supplementary_files_format_and_content: metadata_all_filtered_cells.csv (Metadata for all the filtered cells)
Supplementary_files_format_and_content: normalized_expression.csv (Normalized expression in all the filtered cells)
Supplementary_files_format_and_content: CD45Plus_NGS21_S229.HT6-12hDT.seuratObject.rds.counts_tbl.csv (counts table after hash-tag demultiplexing)
Supplementary_files_format_and_content: CD45Plus_NGS21_S229.HT7-24hDT.seuratObject.rds.counts_tbl.csv (counts table after hash-tag demultiplexing)
Supplementary_files_format_and_content: CD45Plus_NGS21_S229.HT8-48hDT.seuratObject.rds.counts_tbl.csv (counts table after hash-tag demultiplexing)
Supplementary_files_format_and_content: CD45Plus_NGS21_S229.HT6-12hDT.seuratObject.rds (Seurat Object for individual sample after hash-tag demultiplexing)
Supplementary_files_format_and_content: CD45Plus_NGS21_S229.HT7-24hDT.seuratObject.rds (Seurat Object for individual sample after hash-tag demultiplexing)
Supplementary_files_format_and_content: CD45Plus_NGS21_S229.HT8-48hDT.seuratObject.rds (Seurat Object for individual sample after hash-tag demultiplexing)

molecule: protein

source_name: FACS sorted lung interstitium macrophages and monocytes (HTO hashtag library)

extract_protocol:
Cells from each group were barcoded with different Biolegend anti-mouse Hastags:
GGTTGCCAGATGTCA:  HTO6 for group 12hDT
TGTCTTTCCTGCCAG:  HTO7 for group 24hDT
CTCCTCTGCAATTAC:  HTO8 for group 48hDT
After hashtag staining cells were pooled and approximately 18 000 cells suspended in PBS with 0.04% BSA were loaded into the Chromium Controller, in which they were partitioned, their polyA RNAs captured and barcoded using Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10X Genomics).
The cDNA were amplified and libraries compatible with Illumina sequencers were generated using Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10X Genomics). The libraries were sequenced on an Illumina NovaSeq sequencer on an SP100 cell flow (read1: 28 cycles; index: 8 cycles; read2: 80 cycles) at a depth of 50 000 reads per cell.
scRNA-Seq

value: Cx3cr1-LSL-DTR Tmem119-Cre

value: 50 ng diphtheria toxin treatment 12 hours (12hDT), 24 hours (24hDT) and 48 hours (48hDT) before sacrifice

value: lung


title: G401 E1 DMSO BiolRep 2

status: Public on Feb 07 2023

type: SRA

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

country: USA

institute: Memorial SLoan-Kettering Cancer Center

library_source: transcriptomic

data_processing:
Reads were adaptor and quality trimmed using ‘trim_galore’ (v0.4.4_dev)
Reads were mapped to hg19 using STAR v2.6.0a using default parameters.
Read counts were extracted using HTSeq.
Read counts tables were normalized using DESeq2
Assembly: hg19
Supplementary files format and content: tab-delimited text file containing normalized read counts

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: G401 malignant rhabdoid tumor cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, and penicillin/streptomycin s in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using RNeasy Mini, according to manufacturer’s instructions (Qiagen). After RiboGreen quantification and quality control by Agilent BioAnalyzer, 149-500ng of total RNA underwent Poly(A) selection
TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR
Samples were barcoded and run on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina)

treatment_protocol: 10µM tazemetostat or equivalent volume of DMSO for 11 days

tag: cell line

tag: cell type

value: Malignant Rhabdoid Tumor

tag: genotype

value: RB1 knockout

tag: clone

tag: treatment

value: DMSO


title: CD45Plus, Pooled_cells_chromium, GEX

city: Montpellier

first: Qiang

last: BAI

address: 371 Avenue du Doyen Gaston Giraud

country: France

institute: PhyMedExp INSERM U1046

organism: Mus musculus

source_name: FACS sorted lung interstitium macrophages and monocytes (Chromium scRNAseq library)

tag: strain

tag: tissue


title: Stage E6.5 embryo 6 section 4 region A

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

country: China

institute: Chinese Academy of Sciences

data_processing:
The reads for all samples are mapped to the mm10 using Tophat v2.0.8b with parameter: -p 20 -g 1 -N 4 --read-edit-dist 4 --microexon-search
The mapped reads were used to estimate transcriptomic alignment rates, and were also used as input in Cufflinks v2.1.1 (Trapnell et al., 2013) to quantify gene expression levels (fragment per kilobase per million, FPKM) with the default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each embryo

molecule: total RNA

source_name: Mouse embryonic cells

growth_protocol: Embryos from pre-gastrulation to late-gastrulation mouse were embedded with OCT and subjected to cryosection.

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit

treatment_protocol: Sample from sections were laser-microdissected and collected for single-cell based RNA sequencing.

tag: developmental stage

value: Early-gastrulation embryo (E6.5)

tag: tag


title: T47D siTLE3 biol rep 2

city: Cleveland

first: Ruth

last: Keri

state: OHIO

address: 9500 Euclid Ave

institute: Cleveland Clinic

description:
T47TLE2
T47TLEvsT47NS_DEG.xls

data_processing:
A non-directional, polyA selection library preparation was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina
paired end, cleaned reads were aligned to human genome (version hg19) using STAR (v2.5)
HTSeq v0.6.1 was used to count the read numbers mapped of each gene
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis between groups was preformed using DESeq2 (2_1.6.3). Genes considered signifcantly differentially expressed were determined by a corrected p-value of 0.05 (Benjamini & Hochberg method) and absolute fold change of 1
Assembly: hg19

source_name: Breast, Mammary Gland

growth_protocol: Cell lines were maintained as recommended by ATCC.

extract_protocol: RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) and processed as per manufacturer's instructions

treatment_protocol: cell were reverse transfected with either non-targting siRNA (siNS) or SMARTPOOL siRNAs targeting either TLE3 or FOXA1

value: Breast, Mammary Gland

value: Breast epithelial


title: T47D, INPUT, TLE3

library_source: genomic

data_processing:
Libraries were pooled and sequenced with Illumina technology with paired-end reads of 50bp length.
ChIP-seq reads were trimmed using TrimGalore!
ChIP-seq reads were aligned to the UCSC hg38 genome using BWA software v.0.7.5a and samples were filtered for regions blacklisted by the ENCODE project.
PCR duplicates and multimapping reads were removed using samtools
Peaks were called using MACS2
Assembly: hg38
Supplementary files format and content: bed files containing peaks (except for Input sample)

molecule: genomic DNA

growth_protocol: MDA-MB-453, T47D, and SKBR3 cell lines were maintained according to ATCC

extract_protocol:
Cells were fixed and immunopreciptated using Diagenode iDeal ChIP-seq kit for Transcription Factors per the manufacturers’ instructions. For TLE3 immunopreciptations, cells were crosslinked using Diagenode ChIP Cross-link Gold prior to formaldehyde fixation.
Library preparation was performed by Diagenode. Briefly, libraries were prepared using IP-Star Compact Automated System from both INPUT and ChIP DNA samples (starting amount of 3µg for IP and 1.5µg for INPUT) with the MIcroPlex Library Preparation Kit v2 (Diagenode #C05010013). Library amplification was assessed by qPCR, purified, and quantified with a Qubit dsDNA HS Assay Kit (Thermo Fisher Q32854). Fragment size was analyzed using High Sensitivity NGS Fragment Analysis Kit on an Agilent Fragment Analyzer.

tag: disease state

value: breast cancer

value: Human breast epithelial

tag: chip antibody


title: G401 E1 DMSO BiolRep 1


title: Plusplus, NoTreatment

data_processing:
The Cell Ranger (v3.0.2) application (10x Genomics) was then used to demultiplex the BCL files into FASTQ files (cellranger mkfastq), to perform alignment (to Cell Ranger mouse genome references 3.0.2 GRCm38/build 97), filtering, UMI counting and to produce gene—barcode matrices (cellranger count).
Filtered matrix files were used for further scRNAseq analyses with R Bioconductor (3.12) and Seurat (3.2.1).
Filtered matrices containing cell IDs and feature names in each sample were used to build a Seurat object. We performed a quality control by filtering out the cells with less than 200 detected genes, the genes detected in less than 3 cells and the cells exhibiting more than 10% of mitochondrial genes. Gene counts in each sample was normalized separately by default method “LogNormalize” with scale factor 10000 and log-transformation. Two thousands of highly variable features were identified with the “vst” method.
After merge cells from all samples, the contaminated cells were removed based on the expression of specific genes. Four clusters were identified in the remained cell using FindClusters functionand the differentially expressed genes were calculated using FindAllMarkers function (Seurat package).
Genome_build: GRCm38
Supplementary_files_format_and_content: Text counts table: counts of genes for all cells in each sample
Supplementary_files_format_and_content: Rds R-object: Seurat object containing gene expression and cell metatdata for all cells for each sample
Supplementary_files_format_and_content: Text normalized expression: normalized gene expression for all filtered cells merged from all samples
Supplementary_files_format_and_content: Text metadata table: metadata for all filtered cells merged from all samples.
Supplementary_files_format_and_content: makers_per_cluster.csv (DE genes in each cluster)
Supplementary_files_format_and_content: metadata_all_filtered_cells.csv (Metadata for all the filtered cells)
Supplementary_files_format_and_content: normalized_expression.csv (Normalized expression in all the filtered cells)

source_name: FACS sorted lung interstitium macrophages and monocytes

extract_protocol:
For each sample, approximately 3000 cells were suspended in PBS with 0.04% BSA and loaded into the Chromium Controller, in which they were partitioned, their polyA RNAs captured and barcoded using Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10X Genomics).
The cDNA were amplified and libraries compatible with Illumina sequencers were generated using Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10X Genomics). The libraries were sequenced on an Illumina NovaSeq sequencer on an SP100 cell flow (read1: 28 cycles; index: 8 cycles; read2: 80 cycles) at a depth of 50 000 reads per cell.
scRNA-Seq

value: No treatment


title: T47D, INPUT, FOXA1


title: T47D, TLE3, biol rep2

value: TLE3 (Proteintech (#11372-1AP)


title: Stage E6.5 embryo 6 section 3 region EP


title: Stage E6.5 embryo 6 section 3 region P


title: G401 WT TAZ BiolRep 3

value: WT

value: 10µM tazemetostat


title: G401 WT TAZ BiolRep 2


title: Pooled_cells, HTO

description:
Pooled with 4 different genotypes and genotype on the cells can be determinated with specific hashtag:
Control group: Hashtag-5
cMAF-KO group: Hashtag-6
MAFb-KO group: Hashtag-7
dKO group: Hashtag-8

data_processing:
Library strategy: CITE-Seq
The Cell Ranger (v3.0.2) application (10x Genomics) was then used to demultiplex the BCL files into FASTQ files (cellranger mkfastq), to perform alignment (to Cell Ranger mouse genome references 3.0.2 GRCm38/build 97), filtering, UMI counting and to produce gene—barcode matrices (cellranger count).
CITE-seq-Count (Version 1.4.4) was used to cound the hashtags within each cell and produce the read counts table.
Filtered matrix files were used for further scRNAseq analyses with R Bioconductor (3.12) and Seurat (3.2.1).
Filtered matrices containing cell IDs and feature names in each sample were used to build a Seurat object. We performed a quality control by filtering out the cells with less than 200 detected genes, the genes detected in less than 3 cells and the cells exhibiting more than 10% of mitochondrial genes. Gene counts in each sample was normalized separately by default method “LogNormalize” with scale factor 10000 and log-transformation. Two thousands of highly variable features were identified with the “vst” method.
After merge cells from all samples, the contaminated cells were removed based on the expression of specific genes.  Ly6C- patrolling monocytes, CD206+ IMs, CD206- Ims subsets were identified in the remained cells after clustering and expression of specific markers (Seurat package).
Genome_build: GRCm38
Supplementary_files_format_and_content: Text counts table: counts of genes for all cells
Supplementary_files_format_and_content: Text counts table: counts of hashtags for all cells
Supplementary_files_format_and_content: metadata_all_filtered_cells.csv (Metadata for all the filtered cells)
Supplementary_files_format_and_content: normalized_expression.csv (Normalized expression in all the filtered cells)
Supplementary_files_format_and_content: IM_mono.HT5-Control.seuratObject.rds.counts_tbl.csv (counts table after hash-tag demultiplexing)
Supplementary_files_format_and_content: IM_mono.HT6-cMAF-KO.seuratObject.rds.counts_tbl.csv (counts table after hash-tag demultiplexing)
Supplementary_files_format_and_content: IM_mono.HT7-MAFb-KO.seuratObject.rds.counts_tbl.csv (counts table after hash-tag demultiplexing)
Supplementary_files_format_and_content: IM_mono.HT8-dKO.seuratObject.rds.counts_tbl.csv (counts table after hash-tag demultiplexing)
Supplementary_files_format_and_content: IM_mono.HT5-Control.seuratObject.rds (Seurat Object for individual sample after hash-tag demultiplexing)
Supplementary_files_format_and_content: IM_mono.HT6-cMAF-KO.seuratObject.rds (Seurat Object for individual sample after hash-tag demultiplexing)
Supplementary_files_format_and_content: IM_mono.HT7-MAFb-KO.seuratObject.rds (Seurat Object for individual sample after hash-tag demultiplexing)
Supplementary_files_format_and_content: IM_mono.HT8-dKO.seuratObject.rds (Seurat Object for individual sample after hash-tag demultiplexing)

extract_protocol:
Cells from each group were barcoded with different Biolegend anti-mouse Hastags:
CTTTGTCTTTGTGAG:  HT5_Control
!Sample_extract_protocol_ch1 = TATGCTGCCACGGTA:  HT6_cMAF_KO
GAGTCTGCCAGTATC:  HT7_MAFb_KO
TATAGAACGCCAGGC:  HT8_dKO
After hashtag staining cells were pooled and approximately 20 000 cells suspended in PBS with 0.04% BSA were loaded into the Chromium Controller, in which they were partitioned, their polyA RNAs captured and barcoded using Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10X Genomics).
The cDNA were amplified and libraries compatible with Illumina sequencers were generated using Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10X Genomics). The libraries were sequenced on an Illumina NovaSeq sequencer on an SP100 cell flow (read1: 28 cycles; index: 8 cycles; read2: 80 cycles) at a depth of 50 000 reads per cell.
scRNA-Seq

value: Control, cMAF-KO, MAFb-KO, dKO

value: lung interstitium macrophages and monocytes


title: T47D, TLE3, biol rep1


title: T47D siNS biol rep 1


title: Stage E6.5 embryo 6 section 3 region EA


title: Stage E6.5 embryo 6 section 4 region EA


title: Pooled_cells_chromium, GEX

extract_protocol:
Cells from each group were barcoded with different Biolegend anti-mouse Hastags:
CTTTGTCTTTGTGAG:  HT5_Control
TATGCTGCCACGGTA:  HT6_cMAF_KO
GAGTCTGCCAGTATC:  HT7_MAFb_KO
TATAGAACGCCAGGC:  HT8_dKO
After hashtag staining cells were pooled and approximately 20 000 cells suspended in PBS with 0.04% BSA were loaded into the Chromium Controller, in which they were partitioned, their polyA RNAs captured and barcoded using Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10X Genomics).
The cDNA were amplified and libraries compatible with Illumina sequencers were generated using Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10X Genomics). The libraries were sequenced on an Illumina NovaSeq sequencer on an SP100 cell flow (read1: 28 cycles; index: 8 cycles; read2: 80 cycles) at a depth of 50 000 reads per cell.
scRNA-Seq


title: T47D, FOXA1, biol rep2


title: T47D, FOXA1, biol rep1


title: Stage E6.5 embryo 6 section 3 region A


title: Stage E6.5 embryo 6 section 2 region P


title: SKBR3, INPUT, TLE3


title: Rep3d_SNC Ips 2

city: St. Louis

first: Rui

last: Feng

state: Missouri

address: 660 South Euclid Avenue

institute: Washington University in St louis

description: single cell

data_processing:
A digital expression matrix was obtained using the 10X Genomics Cell Ranger pipeline.
Quantification and statistical analysis were done with Partek Flow package (https://www.partek.com/partek-flow/).
Genome_build: mus musculus mm10
Supplementary_files_format_and_content: csv files containing the UMI count matrix

source_name: L4-L5 repopulated ipsliterial  DRG after sciatic nerve injury

extract_protocol:
L4 and L5 DRG’s from 8-weeks-old female mice were collected into cold HBSS with 10% 1M HEPES, then transferred to fresh made pre-warmed dissociation medium (15U/mL Papain suspension, 20mg/mL L-cysteine, 10mg/mL Deoxyribonuclease I , 10% 1M HEPES in HBSS) incubated in 37oC for 20 min. Samples were incubated with collagenase (150µg/mL) in 37oC for 20 min after washing with pre-warmed HBSS twice. After washing with pre-warmed HBSS twice, the single cell suspension was resuspend by gently triturating in complete medium (Neurobasal™-A Medium, with B-27™ Plus Supplement ; GlutaMAX™ Supplement) following by passing through 70-micron cell strainers. Single cell suspension was resuspend in HBSS with 10% 1M HPEPS and 0.1% Fetal Bovine Serum following by staining with LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit (ThermoFisher; Catalog# L34965). Live single cells were sorted by MoFlo. Sorted cells were washed in DPBS+0.04%BSA solution and manually counted using a hemocytometer. Solution was adjusted to a concentration of 700-1000cell/microliter
single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 3′ Gel Bead and Library Kit (10x Genomics). polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform.

treatment_protocol: 6-weeks-old female mice were feded with PLX73086  for 14 days period to injury. PLX73086 was removed immediately after injury. Samples were collected at 3 days post injury. Completely naive sample were collected from untreated, uninjuried age matched female mice. 6-weeks-old female mice were feded with PLX73086 for 14 days, and then PLX73086 was removed for 3 days. DRGs were collected as repopulated naive group.

value: Dorsal root ganglion (L4-L5)

value: fedded with PLX73086 diet 14 days at 6 weeks-old, then control diet (AIN-76A) 3 days

tag: surgery

value: sciatic nerve crush

tag: age

tag: gender

value: female


title: G401 WT DMSO BiolRep 2

value: Malignant Rhabdoid Tumor


title: Stage E6.5 embryo 6 section 2 region EP


title: Cplus, DT96h

value: Cx3cr1-LSL-DTR Tmem119-Cre

value: 50 ng diphtheria toxin treatment 4 days before

value: lung


title: SKBR3, TLE3, biol rep2


title: SKBR3, INPUT, FOXA1


title: G401 WT TAZ BiolRep 1


title: Stage E6.5 embryo 6 section 2 region A

value: Early-gastrulation embryo (E6.5)


title: PBAT_CiPSK_P25_2

city: Beijing

first: Jiansen

last: Lu

address: No. 5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

institute: Peking University

data_processing:
Library strategy: PBAT
For scRNA-seq data, We firstly extracted cell barcodes and UMI sequences from read 2 of raw fastq data by UMItools (v1.0.0) (Smith et al., 2017) and attached them after the read name of read 1. After TSO and polyA sequences removal by local scripts, the “clean” reads were aligned to the mouse mm10 reference genome using STAR (2.7.2b) (Dobin et al., 2013), gene features were assigned by featureCounts (v2.0.0) (Liao et al., 2014). We used UMItools to generate UMI count expression matrix. For the quality control of scRNA-seq data, cells with detected gene numbers fewer than 2,000 or the fraction of mitochondrial reads more than 5% were excluded from further analysis, besides, genes expressed in fewer than 3 cells were filtered out for analysis.
For bisulfite sequencing data, trim_galore (v0.6.4) were used to remove low quality reads and adaptor sequence, and 9 bp of random primers from 5’ end of both read 1 and read 2 were also trimmed. Clean reads were then mapped to mm10 genome using Bismark (v0.23.0) with paired-end mode and ‘--non_directional’ option. Unmapped reads were outputted and mapped again by single-end mode. Aligned bam files were merged and sorted by samtools (v 1.11) and PCR duplicates were marked by picard MarkDuplicates (v2.23.6). Methylation calls for each CpG site were extracted by ‘bismark_methylation_extractor’ of Bismark. The thresholds for CpG sites coverage were 1X and 3X for single-cell- and bulk DNA methylation, respectively. Only methylation levels less than 10% or greater than 90% were retained for single-cell methylation data. Bisulfite conversion rate (BSCR) was estimated by methylation ratio of lambda DNA, samples with BSCR greater than 98% and detected CpG sites greater than 1,000,000 were kept for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix: matrix of UMI counts for all genes in each cell
Supplementary_files_format_and_content: bismark coverage: genome-wide cytosine report outputs of Bismark methylation extractor

source_name: CiPS cell line

growth_protocol: SSCs were cultured in StemPro-34 SFM (Gibico, USA) supplemented with 20 ng/ml EGF, 10 ng/ml bFGF, 10 ng/ml GDNFand 1000 U/ml ESGRO. gPSC were cultured in N2B27 medium supplemented with 2iL.

extract_protocol:
For modified STRT-seq and scTrio-seq2, RNA and DNA are extracted with lysis buffer.  For PBAT and WGBS, genomic DNA was extracted using FastPure Cell/Tissue DNA Isolation Mini Kit.
The libraries for modified STRT-seq, Trio-seq2, PBAT and WGBS are performed according to the previously reported studies (Dong et al., 2018) (Bian et al., 2018) (Smallwood et al., 2014) (Li et al., 2010)

treatment_protocol: The reprogramming process is induced with- or without five mechanicals in 24-well culture plates.

value: CiPS


title: Stage E6.5 embryo 6 section 2 region EA


title: SKBR3, FOXA1, biol rep2

value: breast cancer

value: Human breast epithelial


title: SKBR3, TLE3, biol rep1

value: TLE3 (Proteintech (#11372-1AP)


title: G401 WT DMSO BiolRep 3

value: WT

value: DMSO


title: SKBR3, FOXA1, biol rep1


title: Stage E6.5 embryo 6 section 1 region EA/EP


title: Stage E6.5 embryo 5 section 8 region P


title: Stage E6.5 embryo 6 section 1 region A/P


title: MDA-MB-453, INPUT, TLE3


title: Rep3d_SNC Contra 2

description: single cell

source_name: L4-L5 repopulated contraliterial  DRG after sciatic nerve injury


title: Rep3d_SNC Contra 1

description: single cell


title: Rep3d_SNC Ips 1

description: single cell


title: G401 WT DMSO BiolRep 1


title: intima HCD PANDORA-seq rep 1

city: Riverside

first: Changcheng

last: Zhou

state: California

address: 900 University Avenue

department: Biomedical Sciences

institute: The University of California Riverside

description:
intima_HCD_pandora_1
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
15-50 nt RNA

data_processing:
Sequence reads that fit any of the following parameters were removed with following standard quality control criteria: 1) the reads containing “N”; 2) the reads containing more than four bases with quality score <10; 3) the reads containing more than six bases with quality score is <13; 4) the reads with 5’ primer contaminants or without 3’ primer; 5) The reads without the insert tag; 6) the reads with poly A.; and 7) the reads shorter than 15 nt and longer than 45 nt. The sequencing data analyses were performed upon the clean reads after data filtration.
Assembly: mm10
Supplementary files format and content: *.txt: Tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: Intima

growth_protocol: 3-week-old LDLR-/- male mice were fed a low cholesterol or high cholesterol diet for 9 weeks.

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

treatment_protocol: Small RNA-seq processed with PANDORA-seq were treated with AlkB and PNK4.

value: Intima

value: LDLRKO

tag: Sex

value: Male

value: high-cholesterol diet

tag: time

value: 9 weeks

tag: method

value: PANDORA-seq


title: intima HCD PANDORA-seq rep 5

description:
intima_HCD_pandora_5
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
15-50 nt RNA


title: MDA-MB, 453, INPUT, FOXA1

tag: cell line


title: intima HCD PANDORA-seq rep 4

description:
intima_HCD_pandora_4
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
15-50 nt RNA


title: intima HCD PANDORA-seq rep 3

description:
intima_HCD_pandora_3
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
15-50 nt RNA


title: intima HCD PANDORA-seq rep 2

description:
intima_HCD_pandora_2
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
15-50 nt RNA


title: Stage E6.5 embryo 5 section 8 region EP


title: Stage E6.5 embryo 5 section 8 region EA


title: Intima HCD traditional rep 5

description:
intima_HCD_traditional_5
RNAs were sequenced with standard protocols.
15-50 nt RNA

value: traditional


title: PBAT_CiPSD_P25_2


title: PBAT_CiPSK_P5_2


title: MDA-MB-453, TLE3, biol rep2

tag: cell type


title: PBAT_CiPSD_P25_1


title: Stage E6.5 embryo 5 section 8 region A


title: Intima HCD traditional rep 4

description:
intima_HCD_traditional_4
RNAs were sequenced with standard protocols.
15-50 nt RNA

tag: genotype


title: MDA-MB-453, FOXA1, biol rep2


title: PBAT_CiPSK_P5_1


title: PBAT_F1ES5_P10_1

source_name: F1 4-5 mESC

value: C57BL/6[female] X DBA[male]


title: PBAT_CiPSD_P5_1


title: PBAT_F1ES5_P10_2


title: Stage E6.5 embryo 5 section 7 region EP


title: Hantavirus kidney (Sample H5)

city: Paris

first: Pierre

last: Isnard

address: 156-160, rue de Vaugirard

institute: INEM

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_105

data_processing:
The quality of reads was assessed using FastQC and aligned to the GRCh38 human reference genome with HISAT2
Gene expression was quantified by htseq-count (version 0.13.5)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include htseq-count values for each sample

source_name: Kidney

extract_protocol:
RNA was extracted from nitrogen-frozen and Optimal Cutting Temperature embedded kidneys using the miRNeasy Kit (QIAGEN) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using “Ovation Universal RNA-Seq System” (Nugen, Tecan) following manufacturer's protocols.

value: Kidney

value: Hantavirus

tag: virus


title: Intima HCD traditional rep 2

description:
intima_HCD_traditional_2
RNAs were sequenced with standard protocols.
15-50 nt RNA

tag: treatment


title: Stage E6.5 embryo 5 section 7 region EA

value: Early-gastrulation embryo (E6.5)


title: MDA-MB-453, FOXA1, biol rep1


title: Intima HCD traditional rep 3

description:
intima_HCD_traditional_3
RNAs were sequenced with standard protocols.
15-50 nt RNA


title: Stage E6.5 embryo 5 section 7 region P


title: Intima HCD traditional rep 1

description:
intima_HCD_traditional_1
RNAs were sequenced with standard protocols.
15-50 nt RNA


title: intima LCD PANDORA-seq rep 4

description:
intima_LCD_pandora_4
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
15-50 nt RNA

value: low-cholesterol diet


title: PBAT_5C_gPSC_P25_4

source_name: Cells induced from SSC

tag: strain


title: Stage E6.5 embryo 5 section 7 region A


title: MDA-MB-453, TLE3, biol rep1

value: breast cancer


title: Hantavirus kidney (Sample H3)

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_103

tag: tissue


title: intima LCD PANDORA-seq rep 2

description:
intima_LCD_pandora_2
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
15-50 nt RNA


title: intima LCD PANDORA-seq rep 3

description:
intima_LCD_pandora_3
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
15-50 nt RNA


title: Stage E6.5 embryo 5 section 6 region EP

tag: developmental stage


title: Stage E6.5 embryo 5 section 6 region P

tag: tag


title: PBAT_5C_gPSC_P25_3


title: PBAT_5C_gPSC_P25_2


title: Hantavirus kidney (Sample H2)

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_102

tag: disease state


title: Hantavirus kidney (Sample H1)

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_101


title: PBAT_CiPSD_P5_2

value: CiPS


title: intima LCD PANDORA-seq rep 1

description:
intima_LCD_pandora_1
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
15-50 nt RNA


title: Stage E6.5 embryo 5 section 6 region EA


title: FISH positive Kidney (Sample 29 Bis)

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_29

value: SARS-CoV-2 FISH positive


title: PBAT_5C_gPSC_P25_1


title: PBAT_CiPSK_P25_1


title: Intima LCD traditional rep 4

description:
intima_LCD_traditional_4
RNAs were sequenced with standard protocols.
15-50 nt RNA


title: PBAT_5C_gPSC_P5_4


title: FISH positive Kidney (Sample 27 Bis)

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_27


title: Stage E6.5 embryo 5 section 6 region A


title: PBAT_5C_gPSC_P5_3


title: Stage E6.5 embryo 5 section 5 region P


title: FISH positive Kidney (Sample 22 Bis)

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_22


title: Stage E6.5 embryo 5 section 5 region EP


title: FISH positive Kidney (Sample 4 Bis)

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_4


title: Intima LCD traditional rep 1

description:
intima_LCD_traditional_1
RNAs were sequenced with standard protocols.
15-50 nt RNA


title: PBAT_5C_gPSC_P5_2


title: Stage E6.5 embryo 5 section 5 region EA


title: Non-COVID-19 ATI kidney (Sample 13  Bis)

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_13

value: Non-COVID-19 ATI kidneys


title: PBAT_5C_gPSC_P5_1


title: PBAT_gPSC_P25_4


title: Stage E6.5 embryo 5 section 5 region A


title: Non-COVID-19 ATI kidney (Sample 11  Bis)

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_11


title: LSC

city: Stanford

first: Feng

last: Pan

state: CA

address: 265 Campus Drive

department: Pathology

institute: Stanford University School of Medicine

data_processing:
RNA-seq reads were mapped with STAR against the mouse genome (mm9).
Differential expression analysis were carried out with raw counts using RSEM/EBseq
Assembly: mm9
Supplementary files format and content: raw gene counts for every gene and every sample

source_name: bone marrow

growth_protocol: Murine MLL-AF10 leukemia cells were grown in RPMI 1640 supplemented with 20% fetal bovine serum (FBS), 20% WEHI-conditioned medium, and 1% penicillin-streptomycin.

extract_protocol:
RNA was extracted using RNeasy Plus Kits from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LSCs were treated with A-485 for 0h, 8h, 24h, 48h, and 72h.

value: Tumor

value: leukemia stem cell


title: Stage E6.5 embryo 5 section 4 region P


title: Non-COVID-19 ATI kidney (Sample 8  Bis)

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_8


title: Non-COVID-19 ATI kidney (Sample 2  Bis)

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_2


title: PBAT_gPSC_P25_3


title: Stage E6.5 embryo 5 section 4 region EP


title: PBAT_gPSC_P25_2


title: GMP

value: WT

value: granulocyte-monocyte progenitors


title: CAGE_xrn1D_Replicate_2

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: Maryland

address: 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institutes of Health

data_processing:
As described earlier (Martin-Marcos et al. 2017), Illumina sequencing reads were trimmed to remove the constant adapter sequence, mixed sample sequences were separated by the sample barcodes followed by removal of PCR duplicates using a custom Python (3.7) script. The sequences aligned to yeast non-coding RNAs were removed using bowtie (Langmead et al., 2009) and non-rRNA reads (unaligned reads) were then mapped to the S. cerevisiae genome (R64-1-1 S288C Saccer3 Genome Assembly) using TopHat (Trapnell et al., 2009). Only uniquely mapped reads from the final genomic alignment were used for subsequent analyses. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
The sequenced CAGE reads of each sample were aligned to the reference genome of S. cerevisiae S288c (Assembly version: sacCer3) using HISAT2. CAGE reads mapped to rRNA genes were identified using rRNAdust (http://fantom.gsc.riken.jp/5/sstar/Protocols:rRNAdust), and were excluded from subsequent TSS analyses. CAGE reads with a mapping quality score (MAPQ) > 20 were considered uniquely mapped reads and were used for subsequent analyses. CAGE signals of biological replicates were then merged as a single sample. The transcription abundance of each TSS was quantified as the numbers of CAGE tags/reads supporting the TSS per million mapped reads (TPM). For RNA-Seq samples in parallel with CAGE-Seq, Fastq files after passing the QC and the adapter content check they were mapped to yeast genome (sacCer3) with STAR aligner, then PCR duplicates were removed by samtools.
Assembly: sacCer3
Supplementary files format and content: Processed data (csv) files contain raw reads for each file. For ribosome profiling and parallel RNA-Sequencing, Raw_counts_Ribo (Ribo-sequencing) and Raw_counts_RNA (RNA-sequencing), each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. Foe CAGE-sequencing and parallel RNA-Sequencing, each file contains two columns providing: systemmatic gene name (Gene_ID), total reads.

organism: Saccharomyces cerevisiae

source_name: Whole cells

extract_protocol: CAGE libraries were constructed from 5µg of total RNA isolated from two biological replicates of each strain using the nAnT-iCAGE protocol (Murata et al. 2014) by DNAFORM in Yokohama, Japan. After first strand cDNAs were transcribed to the 5’ end of capped RNAs, cap structure of mRNA was chemically biotinylated to allow streptavidin capture, RNase1 digested, captured using avidin magnetic beads and attached to CAGE “barcode” tags. Each CAGE library used linkers with specific barcodes and was sequenced using Illumina NextSeq


title: PBAT_gPSC_P25_1


title: Intima LCD traditional rep 3

description:
intima_LCD_traditional_3
RNAs were sequenced with standard protocols.
15-50 nt RNA

value: Intima

value: LDLRKO

value: Male


title: Healthy Kidney (Sample 14  Bis)

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_14

value: Healthy Kidney


title: Intima LCD traditional rep 2

description:
intima_LCD_traditional_2
RNAs were sequenced with standard protocols.
15-50 nt RNA

value: 9 weeks

value: traditional


title: PBAT_gPSC_P5_2

value: C57BL/6[female] X DBA[male]


title: PBAT_gPSC_P5_1


title: Healthy Kidney (Sample 12  Bis)

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_12

value: Kidney


title: Stage E6.5 embryo 5 section 4 region A

value: Early-gastrulation embryo (E6.5)


title: Stage E6.5 embryo 5 section 4 region EA


title: Stage E6.5 embryo 5 section 3 region P


title: CAGE_dcp2D_Replicate_2


title: mAML

value: mature AML cells


title: Stage E6.5 embryo 5 section 3 region EP


title: Healthy Kidney (Sample 5 Bis)

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_5


title: PBAT_SSC_P20_2


title: CAGE_dcp2D_Replicate_1


title: CAGE_WT_Replicate_2


title: PBAT_SSC_P20_1


title: Stage E6.5 embryo 5 section 3 region A


title: CAGE_xrn1D_Replicate_1


title: Stage E6.5 embryo 5 section 3 region EA


title: Stage E6.5 embryo 5 section 2 region P


title: FISH positive Kidney (Sample 29)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_29


title: scTrioseq2Met_5C_sc35

data_processing:
Library strategy: Trio-seq2 (DNAme)
For scRNA-seq data, We firstly extracted cell barcodes and UMI sequences from read 2 of raw fastq data by UMItools (v1.0.0) (Smith et al., 2017) and attached them after the read name of read 1. After TSO and polyA sequences removal by local scripts, the “clean” reads were aligned to the mouse mm10 reference genome using STAR (2.7.2b) (Dobin et al., 2013), gene features were assigned by featureCounts (v2.0.0) (Liao et al., 2014). We used UMItools to generate UMI count expression matrix. For the quality control of scRNA-seq data, cells with detected gene numbers fewer than 2,000 or the fraction of mitochondrial reads more than 5% were excluded from further analysis, besides, genes expressed in fewer than 3 cells were filtered out for analysis.
For bisulfite sequencing data, trim_galore (v0.6.4) were used to remove low quality reads and adaptor sequence, and 9 bp of random primers from 5’ end of both read 1 and read 2 were also trimmed. Clean reads were then mapped to mm10 genome using Bismark (v0.23.0) with paired-end mode and ‘--non_directional’ option. Unmapped reads were outputted and mapped again by single-end mode. Aligned bam files were merged and sorted by samtools (v 1.11) and PCR duplicates were marked by picard MarkDuplicates (v2.23.6). Methylation calls for each CpG site were extracted by ‘bismark_methylation_extractor’ of Bismark. The thresholds for CpG sites coverage were 1X and 3X for single-cell- and bulk DNA methylation, respectively. Only methylation levels less than 10% or greater than 90% were retained for single-cell methylation data. Bisulfite conversion rate (BSCR) was estimated by methylation ratio of lambda DNA, samples with BSCR greater than 98% and detected CpG sites greater than 1,000,000 were kept for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix: matrix of UMI counts for all genes in each cell
Supplementary_files_format_and_content: bismark coverage: genome-wide cytosine report outputs of Bismark methylation extractor


title: CAGE_WT_Replicate_1


title: Stage E6.5 embryo 5 section 2 region EP


title: scTrioseq2Met_5C_sc34


title: FISH positive Kidney (Sample 4)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_4


title: FISH positive Kidney (Sample 22)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_22


title: Rhino Kdm3 GLKD sisters (control) biol rep 1

city: PARIS

first: Antoine

last: Boivin

address: 9 quai St Bernard

department: IBPS

institute: Sorbonne Universite CNRS

data_processing:
small RNA-seq
Sequence reads in fastq format were trimmed from the adapter sequence 5’-TGGAATTCTCGGGTGCCAAG-3’ and matched to the D. melanogaster genome release 6 (dm6) using Bowtie
Sequence length distributions, small RNA mapping and small RNA overlap signatures were generated from bowtie alignments using Python and R (http://www.r- project.org/) scripts, which were wrapped and run in Galaxy instance publicly from ARTbio platform available at http://mississippi.fr.
For library comparisons, read counts were normalized to one million reads
unique mapper reads were obtained using sR_Bowtie -m0 (Galaxy Version 2.1.1)
For alignments we used a cleaned version of r6.36 version of Drosophila melanogaster genome (dm6, Flybase) in which sequences corresponding to unmapped (chrU), Y chromosome (chrY) and mitochondrial chromosome (chrM) were removed (dm6_clean).
Assembly: dm6_clean
Supplementary files format and content: bigWig, DEseq2 result for biological triplicates as a tab-delimited text file
RNA-seq
A DeSEq2 analyze on all D. mel. genes (release 6.36) was performed using the three biological replicates for each genotype, control or Kdm3 GLKD.
Assembly: dm6_clean
Supplementary files format and content: bigWig, DEseq2 result for biological triplicates as a tab-delimited text file
ChIP-Seq
reads were mapped on dm6_clean reference genome with BWA (Galaxy Version 0.7.17.4).
PCR duplicates were discarded using Picard tool (Galaxy Version 2.18.2.1)
Peak calling was made on mapped reads with MACS2 (Galaxy Version 2.1.1.20160309.6) using following parameters : --gsize ‘120000000’ --keep-dup ‘1’ --qvalue ‘0.05’ --nomodel --extsize ‘200’ --shift ‘0’. Narrowpeak was used for libraries obtained with Rhino antibody and broadpeak calling was used for libraries obtained with H3K9me2 and H3K9me3 antibodies ( --broad --broadcutoff=’0.1’).
Assembly: dm6_clean
Supplementary files format and content: bigWig and MACS2 files, broadpeak for H3K9me2 and H3K9me3, narrowpeak for Rhino

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: Flies were raised at 25°C on cornmeal medium.

extract_protocol:
ChIP-seq: Chromatin immunoprecipitation (ChIP) was performed as described in Lee et al., 2006. Briefly, 100 ovary pairs were manually dissected into Schneider media and cross-linked in 1% formaldehyde/PBS for 10 min at room temperature with agitation. The cross-linking reaction was quenched by STOP buffer (PBS 1X, Triton 0.1%, Glycine 1 M) and ovaries were washed in PBS and homogenized in a glass douncer: first slightly dounced in PBST 0.1% and centrifugated 1 min 400g, followed by strong douncing in cell lysis buffer buffer (KCL 85 mM, HEPES 5 mM, NP-40 0.5% , Sodium butyrate 10 mM, EDTA free protease inhibitor cocktail Sigma) following by 5 min centrifugation at 2000g. We performed 2 washes with cell lysis buffer. The homogenates were then lysed on ice for 30 min in nucleus lysis buffer (HEPES 50 mM, EDTA 10 mM, N lauryl sarkosyl 0.5%, sodium butyrate 10 mM, EDTA free protease inhibitor cocktail Sigma). DNA was sheared using a Bioruptor pico from Diagenode for 10 cycles (30 sec on, 30 sec off). The sonicated lysates were cleared by centrifugation and then incubated overnight at 4°C with anti-Rhino antibody. Then 40 µL of Protein A Dynabeads was then added and allowed to bind antibody complexes by incubation for 1 h at 4°C. For H3K9me2 and me3 ChIP, 50 µL of Protein A Dynabeads were first coated with the anti-H3K9me3 or me2 antibodies and then incubated with the chromatin overnight at 4°C. Following four washing steps with high salt buffer (Tris pH 7.5 50 mM, NaCl 500 mM, Triton 0.25% , NP-40 0.5% , BSA 0.5% , EDTA pH 7.5 5 mM), DNA-protein complexes were eluted and de-cross-linked 10 h at 65°C. RNA and protein was digested by RNase A and Proteinase K treatments, respectively, before purification using Phenol/Chloroform protocol.
Barcoded libraries were prepared using Illumina technology

value: ovary

value: germinal + somatic

value: wild type for Kdm3


title: Rhino Kdm3 GLKD sisters (control) biol rep 2


title: Healthy Kidney (Sample 7 Bis)

description:
Processed data file: table_htseq-counts_sequencing_2.txt
count_7


title: FISH negative Kidney (Sample 28)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_28

value: SARS-CoV-2 FISH negative


title: Stage E6.5 embryo 5 section 2 region EA


title: scTrioseq2Met_5C_sc33


title: scTrioseq2Met_5C_sc32


title: Rhino Kdm3 GLKD biol rep 2

value: Kdm3 germline knock down


title: Rhino Kdm3 GLKD biol rep 1


title: Stage E6.5 embryo 5 section 2 region A


title: FISH negative Kidney (Sample 25)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_25


title: scTrioseq2Met_5C_sc31


title: Stage E6.5 embryo 5 section 1 region EA


title: FISH negative Kidney (Sample 19)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_19


title: Input Kdm3 GLKD, 2


title: scTrioseq2Met_5C_sc30


title: FISH positive Kidney (Sample 27)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_27

value: SARS-CoV-2 FISH positive


title: FISH negative Kidney (Sample 17)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_17


title: Stage E6.5 embryo 5 section 1 region A/P


title: scTrioseq2Met_5C_sc29


title: Inpiut Kdm3 GLKD sisters (control)


title: H3K9me3 Kdm3 GLKD biol rep 2


title: FISH negative Kidney (Sample 16)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_16


title: Stage E6.5 embryo 4 section 7 region P


title: Non-COVID-19 ATI kidney (Sample 13)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_13

value: Non-COVID-19 ATI kidneys


title: scTrioseq2Met_5C_sc28


title: Stage E6.5 embryo 4 section 7 region A


title: H3K9me3 Kdm3 GLKD biol rep 1


title: scTrioseq2Met_5C_sc27


title: Stage E6.5 embryo 4 section 6 region P


title: Non-COVID-19 ATI kidney (Sample 11)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_11


title: Stage E6.5 embryo 4 section 6 region A


title: Non-COVID-19 ATI kidney (Sample 10)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_10


title: H3K9me3 Kdm3 GLKD sisters (control) biol rep 2


title: scTrioseq2Met_5C_sc25


title: H3K9me3 Kdm3 GLKD biol rep 3


title: scTrioseq2Met_5C_sc26


title: H3K9me3 Kdm3 GLKD sisters (control) biol rep 1


title: Stage E6.5 embryo 4 section 5 region P


title: H3K9me2 Kdm3 GLKD biol rep 3


title: scTrioseq2Met_5C_sc23


title: Non-COVID-19 ATI kidney (Sample 9)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_9


title: Stage E6.5 embryo 4 section 5 region A


title: scTrioseq2Met_5C_sc24


title: Non-COVID-19 ATI kidney (Sample 2)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_2


title: Non-COVID-19 ATI kidney (Sample 8)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_8


title: Stage E6.5 embryo 4 section 4 region P


title: H3K9me2 Kdm3 GLKD biol rep 2


title: scTrioseq2Met_5C_sc22


title: H3K9me3 Kdm3 GLKD sisters (control) biol rep 3


title: scTrioseq2Met_5C_sc36


title: Stage E6.5 embryo 4 section 4 region A


title: scTrioseq2Met_5C_sc21


title: H3K9me2 Kdm3 GLKD biol rep 1


title: Healthy Kidney (Sample 15)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_15


title: Stage E6.5 embryo 4 section 3 region P


title: Healthy Kidney (Sample 14)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_14


title: scTrioseq2Met_5C_sc20


title: Stage E6.5 embryo 4 section 3 region A


title: Healthy Kidney (Sample 12)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_12


title: Stage E6.5 embryo 4 section 2 region P


title: Healthy Kidney (Sample 7)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_7


title: H3K9me2 Kdm3 GLKD sisters (control) biol rep 1


title: Healthy Kidney (Sample 5)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_5


title: scTrioseq2Met_5C_sc18


title: Input Kdm3 GLKD, 1


title: Stage E6.5 embryo 4 section 1 region A/P


title: scTrioseq2Met_5C_sc17


title: H3K9me2 Kdm3 GLKD sisters (control) biol rep 3


title: scTrioseq2Met_5C_sc16


title: Kdm3 GLKD sisters (control) biol rep 3 [rna-seq]

extract_protocol:
long RNA-seq: Total RNA was extracted with TRIzol from hand dissected ovaries in 1X PBS and 1 µg was treated with DNase (Fermentas).
Libraries were prepared using the RNA RiboZero Stranded protocol by Fasteris.


title: SAMP-1606_RNA

city: La Jolla

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

data_processing:
Alignment to the genome and initial processing were performed using the 10x Genomics Cell Ranger multiome ARC v.2.0.0 pipelines
Assembly: hg19
Supplementary files format and content: h5ad objects include raw count matrix of RNA (multiome_RNA_raw.h5ad) and ATAC (multiome_ATAC_raw.h5ad) data
Supplementary files format and content: h5ad objects include cell clustering results of RNA (multiome_RNA_final.h5ad) and ATAC (multiome_ATAC_final.h5ad) data

source_name: Islets

extract_protocol:
Islets were resuspended in 1 mL wash buffer (10mM Tris-HCL (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 1% fatty acid-free BSA (Proliant, 68700), 1 mM DTT (Sigma), 1x protease inhibitors (Thermo Fisher Scientific, PIA32965), 1U/µl RNAsin (Promega, N2515) in molecular biology-grade water) and homogenized using 1 mL glass dounce homogenizer with a tight-fitting pestle (Wheaton, EF24835AA) for 10-20 strokes until the solution was homogeneous. Homogenized islets were filtered with 30 µm filter (CellTrics, Sysmex) and pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). Nuclei were resuspended in 400 µL of sort buffer (1% fatty acid-free BSA, 1x protease inhibitors (Thermo Fisher Scientific, PIA32965), 1U/µl RNAsin (Promega, N2515) in PBS) and stained with 7-AAD (1 µM; Thermo Fisher Scientific, A1310). 120,000 nuclei were sorted using an SH800 sorter (Sony) into 87.5 μl of collection buffer (1U/µl RNAsin (Promega, N2515), 5% fatty acid-free BSA (Proliant, 68700) in PBS). Nuclei suspension was mixed in a ratio of 4:1 with 5x permeabilization buffer (50 mM Tris-HCL (pH 7.4), 50 mM NaCl, 15 mM MgCl2, 0.5% Tween-20 (Sigma),  0.5% IGEPAL-CA630 (Sigma), 0.05% Digitonin (Promega), 5% fatty acid-free BSA (Proliant, 68700), 5 mM DTT (Sigma), 5x protease inhibitors (Thermo Fisher Scientific, PIA32965), 1U/µl RNAsin (Promega, N2515) in molecular biology-grade water) and incubated on ice for 1 min before pelleting with a swinging-bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). Supernatant was gently removed and ~50 µl were left behind to increase nuclei recovery. 650 µl of wash buffer (10mM Tris-HCL (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 1% fatty acid-free BSA (Proliant, 68700), 1 mM DTT (Sigma), 1x protease inhibitors (Thermo Fisher Scientific, PIA32965), 1U/µl RNAsin (Promega, N2515) in molecular biology-grade water) were added without disturbing the pellet and nuclei were pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). Supernatant was gently removed without disturbing the pellet and leaving ~2-3 µl behind. 7-10 µl of 1x Nuclei Buffer (10x Genomics) was added and nuclei gently resuspended. Nuclei were counted using a hemocytometer, and 16,550-18,000 nuclei were used as input for tagmentation.
Single Cell Multiome ATAC + Gene Expression libraries were generated following manufacturer instructions (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 1000283; Chromium Next GEM Chip J Single Cell, 1000234; Dual Index Kit TT Set A, 1000215; Single Index Kit N Set A, 1000212; 10x Genomics) with these PCR cycles: 7 cycles for ATAC index PCR, 7 cycles for cDNA amplification, 13-16 cycles for RNA index PCR. Final libraries were quantified using a Qubit fluorimeter (Life Technologies) and the size distribution was checked using a Tapestation (High Sensitivity D1000, Agilent). Libraries were sequenced on NextSeq 500 and NovaSeq 6000 sequencers (Illumina) with following read lengths (Read1 + Index1 + Index2 + Read2): ATAC (NovaSeq 6000) 50 + 8 + 24 + 50; ATAC (NextSeq 500 with custom recipe) 28 + 10 + 10 + 90;  RNA (NextSeq 500, NovaSeq 6000): 50 + 8 + 16 + 50.

value: Non-diabetic

tag: bmi

tag: islet index

tag: library id

tag: sample id

value: M

tag: race

value: White

tag: purity


title: scTrioseq2Met_5C_sc15


title: SAMP-1503_RNA

tag: age

tag: gender


title: Kdm3 GLKD sisters (control) biol rep 2 [rna-seq]

tag: cell line

tag: cell type


title: H3K9me2 Kdm3 GLKD sisters (control) biol rep 2

tag: genotype


title: SAMP-1498_RNA

value: Hispanic Latino


title: Kdm3 GLKD sisters (control) biol rep 1 [rna-seq]

tag: treatment


title: scTrioseq2Met_5C_sc19

tag: strain


title: scTrioseq2Met_5C_sc14


title: Stage E6.0 embryo 2 section 5 region A

description: E6.0_Reference_all.samples.genes.fpkm.txt

value: Pre-gastrulation embryo (E6.0)


title: Stage E6.0 embryo 2 section 4 region P


title: SAMP-1612_RNA

value: Caucasian


title: scTrioseq2Met_5C_sc13

value: C57BL/6[female] X DBA[male]


title: Stage E6.0 embryo 2 section 4 region A


title: Stage E6.5 embryo 4 section 2 region A


title: Kdm3 GLKD biol rep 3 [rna-seq]

tag: tissue


title: SAMP-1609_RNA

value: F

value: Black or African American


title: scTrioseq2Met_5C_sc12


title: Kdm3 GLKD biol rep 2 [rna-seq]


title: scTrioseq2Met_5C_sc11


title: Healthy Kidney (Sample 1)

description:
Processed data file: table_htseq-counts_sequencing_1.txt
count_1

value: Kidney

value: Healthy Kidney

tag: virus


title: Stage E6.0 embryo 2 section 3 region VE

tag: developmental stage

tag: tag


title: Stage E6.0 embryo 2 section 5 region P


title: SAMP-1501_RNA

tag: disease state

tag: bmi


title: Kdm3 GLKD biol rep 1 [rna-seq]

value: ovary

value: germinal + somatic


title: SAMP-1499_RNA

tag: islet index

tag: library id


title: Kdm3 GLKD biol rep 3

extract_protocol:
small RNA-seq: Total RNA was extracted from 10-20 pairs of ovaries using TRIzol (Life Technologies). A small RNA fraction of 15 nt to 30 nt in length was obtained following separation of total RNA on a denaturing polyacrylamide gel.
This fraction was used to generate multiplexed libraries with Illumina TruSeq Small RNA library preparation kits (RS-200-0012, RS200-0024, RS-200-036 or RS-200-048) at Fasteris (http://www.fasteris.com).
A house protocol based on TruSeq, which reduces 2S RNA (30 nt) contamination in the final library, was performed.


title: scTrioseq2Met_5C_sc10


title: SAMP-1500_RNA

tag: sample id

tag: race

value: Hispanic


title: Stage E6.0 embryo 2 section 2 region VE


title: Stage E6.0 embryo 2 section 3 region P


title: SAMP-1142_RNA

tag: age

tag: purity


title: scTrioseq2Met_5C_sc9


title: Input Kdm3 GLKD sisters (control)

tag: cell line

value: wild type for Kdm3


title: Kdm3 GLKD biol rep 2

tag: cell type

value: Kdm3 germline knock down


title: Kdm3 GLKD biol rep 1

tag: genotype


title: SAMP-1141_RNA

tag: gender


title: Kdm3 GLKD sisters (control) biol rep 3

tag: treatment


title: scTrioseq2Met_5C_sc7

tag: strain


title: Stage E6.0 embryo 2 section 2 region A


title: scTrioseq2Met_5C_sc6


title: scTrioseq2Met_5C_sc5


title: Stage E6.0 embryo 2 section 1 region VE


title: SAMP-1139_RNA


title: Kdm3 GLKD sisters (control) biol rep 2

tag: tissue


title: Stage E6.0 embryo 2 section 3 region A

tag: developmental stage


title: Kdm3 GLKD sisters (control) biol rep 1


title: scTrioseq2Met_5C_sc4


title: SAMP-1145_RNA


title: Kdm3 GLKD sisters (control)


title: Stage E6.0 embryo 2 section 1 region A/P

tag: tag


title: scTrioseq2Met_5C_sc8


title: SAMP-1134_RNA

tag: disease state


title: Stage E6.0 embryo 2 section 4 region VE


title: Stage E6.0 embryo 2 section 2 region P


title: scTrioseq2Met_5C_sc3


title: Kdm3 GLKD


title: scTrioseq2Met_5C_sc2


title: SAMP-1138_RNA

tag: bmi


title: SAMP-1150_RNA

tag: islet index


title: hfp GLKD nieces (control daughters)

value: wild type for hfp


title: Stage E6.0 embryo 1 section 4 region P


title: Stage E6.0 embryo 1 section 5 region A


title: hfp GLKD sisters (control)


title: scTrioseq2Met_DMSO_sc21

value: DMSO


title: SAMP-1696_RNA

value: Non-diabetic

tag: library id

value: M


title: Stage E6.0 embryo 1 section 4 region A


title: SAMP-1605_RNA

tag: sample id

value: Hispanic Latino


title: hfp GLKD daughters


title: SAMP-1695_RNA

tag: race

value: Hispanic/Latino


title: hfp GLKD

value: hfp germline knock down


title: Stage E6.0 embryo 1 section 3 region A

value: Pre-gastrulation embryo (E6.0)


title: SAMP-1608_RNA

tag: age


title: Stage E6.0 embryo 1 section 5 region P


title: Stage E6.0 embryo 1 section 2 region P


title: scTrioseq2Met_DMSO_sc18

value: C57BL/6[female] X DBA[male]


title: H00200

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
Illumina standard primers were trimmed
Paired reads were mapped to the human reference genome (b37) using STAR
Number of reads for each gene was counted using HTSeq
Assembly: b37
Supplementary files format and content: raw read count matrix (genes x samples)

source_name: skin

extract_protocol:
5mm skin punch biopsies were stored in PaxGene tissue containers (PreAnalytiX) at -80°C until isolation of total RNA with the Qiagen AllPrep DNA/RNA Mini Kit preceded by an additional disruption/homogenization step with innuSPEED Lysis Tubes W (Analytik Jena) and Qiagen QIAshredder spin-columns.
RNA samples were prepared for sequencing using the Illumina Truseq® Stranded total RNA Protocol in combination with the RiboZero rRNA removal Kit and sequenced on the HiSeq2500 with 2x125bp.

value: skin

tag: skin type

value: non-lesional

tag: patient id


title: scTrioseq2Met_5C_sc1


title: H00191

value: acute lesion


title: Stage E6.0 embryo 1 section 2 region A

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit


title: scTrioseq2Met_DMSO_sc17


title: SAMP-1613_RNA

value: F

value: Caucasian

tag: purity


title: H00199

value: chronic lesion


title: SAMP-1606_ATAC

value: White


title: scTrioseq2Met_DMSO_sc16


title: Stage E6.0 embryo 1 section 1 region A/P


title: H00202


title: SAMP-1503_ATAC


title: scTrioseq2Met_DMSO_sc15


title: Stage E5.5 embryo 2 section 6 region P

description: E5.5_Reference_all.samples.genes.fpkm.txt

value: Pre-gastrulation embryo (E5.5)


title: scTrioseq2Met_DMSO_sc14


title: H00197


title: scTrioseq2Met_DMSO_sc20


title: Stage E5.5 embryo 2 section 6 region A


title: scTrioseq2Met_DMSO_sc19


title: Stage E6.0 embryo 1 section 3 region P


title: scTrioseq2Met_DMSO_sc13


title: Stage E5.5 embryo 2 section 5 region P


title: SAMP-1609_ATAC

value: Black or African American


title: SAMP-1612_ATAC


title: H00192


title: Stage E5.5 embryo 2 section 5 region A


title: SAMP-1501_ATAC


title: scTrioseq2Met_DMSO_sc11

value: DMSO


title: scTrioseq2Met_DMSO_sc12


title: SAMP-1499_ATAC


title: H00195


title: SAMP-1498_ATAC


title: SAMP-1500_ATAC

value: Hispanic


title: scTrioseq2Met_DMSO_sc10


title: SAMP-1142_ATAC

value: M


title: scTrioseq2Met_DMSO_sc9


title: Stage E5.5 embryo 2 section 4 region A


title: scTrioseq2Met_DMSO_sc8


title: SAMP-1141_ATAC


title: H00193


title: H00194


title: H00204


title: scTrioseq2Met_DMSO_sc7


title: Stage E5.5 embryo 2 section 3 region A


title: SAMP-1139_ATAC


title: Stage E5.5 embryo 2 section 2 region A


title: scTrioseq2Met_DMSO_sc6


title: H00196


title: SAMP-1145_ATAC


title: scTrioseq2Met_DMSO_sc5


title: Stage E5.5 embryo 2 section 4 region P


title: Stage E5.5 embryo 2 section 1 region A/P


title: H00201


title: SAMP-1134_ATAC

value: Non-diabetic


title: Stage E5.5 embryo 2 section 3 region P


title: SAMP-1138_ATAC


title: F03750


title: H00190


title: Stage E5.5 embryo 2 section 2 region P


title: SAMP-1150_ATAC


title: scTrioseq2Met_DMSO_sc3


title: F03749


title: Stage E5.5 embryo 1 section 6 region A

description: E5.5_Embryo19_all.samples.genes.fpkm.txt


title: F03748


title: scTrioseq2Met_DMSO_sc1


title: Stage E5.5 embryo 1 section 5 region A

description: E5.5_Embryo16_all.samples.genes.fpkm.txt


title: H00198


title: scTrioseq2Rna_5C_8

data_processing:
Library strategy: Trio-seq2 (RNA)
For scRNA-seq data, We firstly extracted cell barcodes and UMI sequences from read 2 of raw fastq data by UMItools (v1.0.0) (Smith et al., 2017) and attached them after the read name of read 1. After TSO and polyA sequences removal by local scripts, the “clean” reads were aligned to the mouse mm10 reference genome using STAR (2.7.2b) (Dobin et al., 2013), gene features were assigned by featureCounts (v2.0.0) (Liao et al., 2014). We used UMItools to generate UMI count expression matrix. For the quality control of scRNA-seq data, cells with detected gene numbers fewer than 2,000 or the fraction of mitochondrial reads more than 5% were excluded from further analysis, besides, genes expressed in fewer than 3 cells were filtered out for analysis.
For bisulfite sequencing data, trim_galore (v0.6.4) were used to remove low quality reads and adaptor sequence, and 9 bp of random primers from 5’ end of both read 1 and read 2 were also trimmed. Clean reads were then mapped to mm10 genome using Bismark (v0.23.0) with paired-end mode and ‘--non_directional’ option. Unmapped reads were outputted and mapped again by single-end mode. Aligned bam files were merged and sorted by samtools (v 1.11) and PCR duplicates were marked by picard MarkDuplicates (v2.23.6). Methylation calls for each CpG site were extracted by ‘bismark_methylation_extractor’ of Bismark. The thresholds for CpG sites coverage were 1X and 3X for single-cell- and bulk DNA methylation, respectively. Only methylation levels less than 10% or greater than 90% were retained for single-cell methylation data. Bisulfite conversion rate (BSCR) was estimated by methylation ratio of lambda DNA, samples with BSCR greater than 98% and detected CpG sites greater than 1,000,000 were kept for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix: matrix of UMI counts for all genes in each cell
Supplementary_files_format_and_content: bismark coverage: genome-wide cytosine report outputs of Bismark methylation extractor


title: SAMP-1605_ATAC

value: Hispanic Latino


title: Stage E5.5 embryo 1 section 4 region P

description: E5.5_Embryo13_all.samples.genes.fpkm.txt


title: F03747


title: F03746


title: Stage E5.5 embryo 1 section 4 region A

description: E5.5_Embryo11_all.samples.genes.fpkm.txt


title: scTrioseq2Met_DMSO_sc4


title: scTrioseq2Rna_5C_7


title: SAMP-1608_ATAC


title: Stage E5.5 embryo 1 section 3 region P


title: SAMP-1613_ATAC


title: scTrioseq2Rna_5C_6


title: F03745


title: Stage E5.5 embryo 1 section 6 region P

description: E5.5_Embryo21_all.samples.genes.fpkm.txt


title: SAMP-1606

data_processing:
Alignment to the genome and initial processing were performed using the 10x Genomics Cell Ranger ATAC v1.1.0 pipeline
We used ‘clean_barcode_multiplets_1.1.py’ script from 10x to identify barcode multiplets for each donor
We called peaks for each cluster using the MACS2 call peak command using parameters ‘--nomodel --extsize 200 –shift 0 --keep-dup all -q 0.05’
Genome_build: hg19
Supplementary_files_format_and_content: h5ad object includes raw barcode-by-peak (500bp) count matrix (snATAC_all_500bp_raw.h5ad)
Supplementary_files_format_and_content: h5ad object includes cell clustering results (snATAC_all_final.h5ad)
Supplementary_files_format_and_content: Detailed information of each cell (barcode_snATAC_UMAP.csv)
Supplementary_files_format_and_content: Subtype information of each beta cell (AI_beta_subtype.csv)

extract_protocol:
Approximately 1,000 islet equivalents (~1,000 cells per IEQ) were resuspended in 1 ml nuclei permeabilization buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 0.1% IGEPAL-CA630 (Sigma) and 0.01% Digitonin (Promega) in water) and homogenized using 1ml glass dounce homogenizer with a tight-fitting pestle for 15 strokes. Homogenized islets were incubated for 10 min at 4°C and filtered with 30 µm filter (CellTrics). Nuclei were pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf) and washed twice with Wash buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, and 1% BSA (Proliant 7500804) in molecular biology-grade water). Nuclei were pelleted and resuspended in 30 µL of 1X Nuclei Buffer (10x Genomics). Nuclei were counted using a hemocytometer, and 15,360 nuclei were used for tagmentation.
Single nucleus ATAC-seq libraries were generated using the (Chromium Chip E Single Cell ATAC kit (10x Genomics, 1000086) and indexes (Chromium i7 Multiplex Kit N, Set A, 10x Genomics, 1000084) following manufacturer instructions. Final libraries were quantified using a Qubit fluorimeter (Life technologies) and the nucleosomal pattern was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries were sequenced on NextSeq 500 and HiSeq 4000 sequencers (Illumina) with following read lengths: 50 + 8 + 16 + 50 (Read1 + Index1 + Index2 + Read2).

tag: diagnosis

value: Islets


title: scTrioseq2Rna_5C_4


title: scTrioseq2Rna_5C_5


title: F03743


title: Stage E5.5 embryo 1 section 2 region P

data_processing:
The reads for all samples are mapped to the mm10 using Tophat v2.0.8b with parameter: -p 20 -g 1 -N 4 --read-edit-dist 4 --microexon-search
The mapped reads were used to estimate transcriptomic alignment rates, and were also used as input in Cufflinks v2.1.1 (Trapnell et al., 2013) to quantify gene expression levels (fragment per kilobase per million, FPKM) with the default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each embryo


title: Stage E5.5 embryo 1 section 3 region A


title: SAMP-1503

tag: gender


title: Stage E5.5 embryo 1 section 2 region A


title: F03741


title: scTrioseq2Rna_5C_3

tag: treatment


title: scTrioseq2Rna_5C_2

tag: strain


title: F03742

tag: tissue


title: Stage E5.5 embryo 1 section 1 region A/P

tag: developmental stage


title: SAMP-1498


title: SAMP-1612


title: scTrioseq2Rna_5C_1


title: E00482


title: F03744


title: E00481


title: SAMP-1609


title: Replicate 5, scRNAseq

city: Durham

first: Gayathri

last: Viswanathan

state: NC

address: 0150, Carl building, 130 Research Drive

department: Cardiology

institute: Duke University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: Human NCBI genome build 36
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Distal Thrombus removed from pulmonary artery of CTEPH patient

extract_protocol:
The segmental/subsegmental fibrothrombotic material isolated from CTEPH patients were cut into ~ 3 mm pieces and digested using collagenase A for 1 hour. Cells were strained using 70 µM cell strainer. To remove red blood cells, cells were washed with ice cold DPBS and incubated with ACK (red blood cells lysis buffer) on ice for 5 mins. Cells were washed with DPBS and resuspended in cation-free HBSS that contains 10% FBS, 3 mM EDTA and 10 mM HEPES. Viable cells were counted manually using a hemocytometer. Cells were washed in DPBS and stained with Aqua (cell viability dye) (1:500). The stained cells were washed with ice cold DPBS and fixed with 80% of methanol for 15 mins. The viable cells were sorted using flow cytometry.
After rehydration of methanol-fixed cells, scRNAseq libraries were prepared using the 10X Genomics Single Cell Protocol in collaboration with the Duke Human Vaccine Institute Genetics Analysis Core. Live cells were barcoded with cell-specific barcodes and unique molecular identifier (UMI) based on the Chromium Single Cell 3’ library with Gel Bead Kit version 2 protocol. ScRNAseq libraries was obtained and RNA sequencing was performed that passed quality control (Novogene).


title: SAMP-1610


title: Replicate 4, scRNAseq

description: 10x Genomics

value: Distal Thrombus removed from pulmonary artery of CTEPH patient


title: F03740


title: scTrioseq2Rna_DMSO_5

value: C57BL/6[female] X DBA[male]


title: scTrioseq2Rna_DMSO_4


title: Replicate 3, scRNAseq

description: 10x Genomics


title: SAMP-1501


title: scTrioseq2Rna_DMSO_3


title: Replicate 2, scRNAseq

description: 10x Genomics


title: F03739

value: skin


title: SAMP-1499


title: F03738

value: non-lesional


title: SAMP-1500


title: F03737

value: acute lesion


title: Replicate 1, scRNAseq

description: 10x Genomics


title: scTrioseq2Rna_DMSO_1

data_processing:
Library strategy: modified STRT-seq
For scRNA-seq data, We firstly extracted cell barcodes and UMI sequences from read 2 of raw fastq data by UMItools (v1.0.0) (Smith et al., 2017) and attached them after the read name of read 1. After TSO and polyA sequences removal by local scripts, the “clean” reads were aligned to the mouse mm10 reference genome using STAR (2.7.2b) (Dobin et al., 2013), gene features were assigned by featureCounts (v2.0.0) (Liao et al., 2014). We used UMItools to generate UMI count expression matrix. For the quality control of scRNA-seq data, cells with detected gene numbers fewer than 2,000 or the fraction of mitochondrial reads more than 5% were excluded from further analysis, besides, genes expressed in fewer than 3 cells were filtered out for analysis.
For bisulfite sequencing data, trim_galore (v0.6.4) were used to remove low quality reads and adaptor sequence, and 9 bp of random primers from 5’ end of both read 1 and read 2 were also trimmed. Clean reads were then mapped to mm10 genome using Bismark (v0.23.0) with paired-end mode and ‘--non_directional’ option. Unmapped reads were outputted and mapped again by single-end mode. Aligned bam files were merged and sorted by samtools (v 1.11) and PCR duplicates were marked by picard MarkDuplicates (v2.23.6). Methylation calls for each CpG site were extracted by ‘bismark_methylation_extractor’ of Bismark. The thresholds for CpG sites coverage were 1X and 3X for single-cell- and bulk DNA methylation, respectively. Only methylation levels less than 10% or greater than 90% were retained for single-cell methylation data. Bisulfite conversion rate (BSCR) was estimated by methylation ratio of lambda DNA, samples with BSCR greater than 98% and detected CpG sites greater than 1,000,000 were kept for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix: matrix of UMI counts for all genes in each cell
Supplementary_files_format_and_content: bismark coverage: genome-wide cytosine report outputs of Bismark methylation extractor


title: F03736


title: Nugen Control 2

city: Boston

first: Stefan

last: Halvorsen

state: MA

address: 185 Cambridge Street

department: Center for Computational and Integrative Biology

institute: Massachusetts General Hospital

data_processing:
Reads mapping to human rRNA (using Bowtie 0.12.7) were removed
Reads mapped using STAR (version 2.7.10a)
Gene read counts generated using STAR (--quantMode GeneCounts), unstranded RNA-seq read counts shown in processed files
Assembly: GRCh38 primary assembly and Gencode v40 annotations
Supplementary files format and content: Tab-delimited text file exported from STAR; Column 1: Gene ID; Column 2: Read counts

source_name: Nugen Total RNA Control

extract_protocol:
None
Nugen Ovation Pico WTA kit followed by WT-Ovation Exon Module then Illumina DNA Sample Prep Kit

value: Nugen Total RNA Control


title: SAMP-1602


title: F03735


title: Nugen Control 1


title: SAMP-1137


title: OE_25_Input

city: 杭州市

first: Mingyue

last: Guo

state: 浙江省

address: 浙江大学紫金港校区

institute: 浙江大学

data_processing:
The library was constructed by Novogene Corporation (Beijing, China).
Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina). Library quality was assessed on the Agilent Bioanalyzer 2100 system.
For ChIP-Seq data analysis, raw data of fastq format were firstly processed using fastp (version 0.19.11) software
Clean data were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
After mapping reads to the reference genome, we used the MACS2 (v 2.1.0) peak calling software to identify regions of IP enrichment over background. A adjuested P-value threshold of 0.05 was used for all data sets.
Assembly: Reference genome and gene model annotation files were downloaded from tomato genome website (https://solgenomics.net/) directly.
Supplementary files format and content: bigWig

organism: Solanum lycopersicum

source_name: leaves

extract_protocol:
ChIP experiments were performed using the EpiQuiK Plant ChIP kit (Epigentek) as described in the manufacturer’s protocol. Approximately 1.5 g of leaf tissue was harvested from transgenic plants and WT plants, respectively. Chromatin was immunoprecipitated with an HA antibody, and a goat anti-mouse IgG antibody was used as the negative control.
The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: leaves

value: normal


title: SAMP-1151


title: OE_4_Ip

value: cold


title: OE_25_Ip


title: Notochord Sample 2

source_name: Notochord

extract_protocol:
Laser Capture Microscopy followed by PicoPure RNA Isolation
Nugen Ovation Pico WTA kit followed by WT-Ovation Exon Module then Illumina DNA Sample Prep Kit

value: Notochord

tag: cell type

value: Normal Tissue


title: Stage E5.5 embryo 1 section 5 region P

description: E5.5_Embryo17_all.samples.genes.fpkm.txt

source_name: Mouse embryonic cells

value: Pre-gastrulation embryo (E5.5)

tag: tag


title: OE_4_Input


title: Notochord Sample 3


title: scTrioseq2Rna_DMSO_2

value: DMSO


title: Notochord Sample 1


title: SAMP-1142

value: M

value: Black or African American

tag: bmi


title: Chordoma Sample 98

source_name: Chordoma

extract_protocol:
RNA extracted with Trizol and a bead beater
Nugen Ovation Pico WTA kit followed by WT-Ovation Exon Module then Illumina DNA Sample Prep Kit

value: Chordoma

value: Tumor


title: SAMP-1141

value: Islets

value: F

value: White

tag: islet index


title: scRNAseq_mES

extract_protocol:
For modified STRT-seq and scTrio-seq2, RNA and DNA are extracted with lysis buffer.  For PBAT and WGBS, genomic DNA was extracted using FastPure Cell/Tissue DNA Isolation Mini Kit.
The libraries for modified STRT-seq, Trio-seq2, PBAT and WGBS are performed according to the previously reported studies (Dong et al., 2018) (Bian et al., 2018) (Smallwood et al., 2014) (Li et al., 2010)

value: C57BL/6[female] X DBA[male]


title: jeko2um2

city: Shanghai

first: Ji

last: Zhang

state: Select a State or Province

address: 197 Ruijin 2nd Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
RNA-Seq reads were mapped to human reference genome (hg19) using hisat2 with default parameters
FPKM value for each gene was calculated by StringTie
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each gene

growth_protocol: B-NHL cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RN Awas isolated by RNeasy Mini Kit (Qiagen, Germantown, MD, USA) using the manufacturer’s instructions. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

value: Mantle cell lymphoma

value: CBL0137 2um

tag: time

value: 24 hours


title: scRNAseq_gPSC_N2B27_P15


title: jeko2um3


title: TXNIP-null in MDA-MB-231 cells, rep 1

city: Salt Lake City

first: Donald

last: Ayer

state: Utah

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

data_processing:
Sequencing reads were aligned to hg19 using Bowtie (Langmead et al., 2009) with the following parameters: -m 1 -t–best -q -S -l 32 -e 80 -n 2. SAM files were converted to BAM files and sorted using samtools (Li et al., 2009).
Assembly: hg 19
Supplementary files format and content: bigwig

growth_protocol: Parental MDA-MB-231 and TXNIP knockout MDA-MB-231 (231:TKO) cells were cultured in DMEM (Gibco; 1195073) with 10% Fetal Bovine Serum (FBS) (Gibco; A3160506), 1X MEM Non-Essential Amino Acids Solution (Gibco; 11140076) and 1X Penicillin-streptomycin (Gibco; 15140148).

extract_protocol:
Briefly, 250,000 cells were trypsinized and pelleted, washed once with cold 1X PBS, resuspended, and lysed in 50µL of ATAC-lysis buffer (ATAC Resuspension buffer: 10mM Tris-HCl pH 7.4, 3mM MgCl2, 10mM NaCl containing 0.1% NP40, 0.1% Tween-20 and 0.1% Digitonin), and incubated for 3 to 4 minutes on ice. Lysis was quenched with 1mL of wash buffer (ATAC-resuspension buffer containing 0.10% Tween-20), lysed nuclei were counted using Countess II cell counter.
Nuclei were pelleted and resuspended in transposition mixture using an in-house prepared Tn5 transposase as described by Picellie et al. 2014.

treatment_protocol: 231:TKO cells were generated using human TXNIP CRISPR/Cas9 KO plasmid with TXNIP-specific guide RNA sequences from GeCKO (v2) library (Santa Cruz; sc-400664).

value: triple-negative breast cancer

tag: genotype

value: TXNIP knockout


title: Parental 231 cells, rep 1

value: wild-type


title: Chordoma Sample 4


title: jeko2um1


title: SAMP-1139

tag: age

tag: race

value: Hispanic


title: scRNAseq_gPSC_N2B27_P1


title: jekocon3


title: SAMP-1145


title: Chordoma Sample 3


title: scRNAseq_SSCR_D8_1


title: SAMP-1148


title: Chordoma Sample 1


title: SAMP-1134

value: Non-diabetic

value: Caucasian


title: jekocon2


title: jekocon1


title: scRNAseq_SSCR_D27_5


title: scRNAseq_SSCR_D27_4


title: Chordoma Sample 11


title: Chordoma Sample 10


title: Raji2um3

source_name: Raji

value: Raji

value: Burkitt Lymphoma


title: H00203

value: skin

tag: skin type

value: acute lesion

tag: patient id


title: scRNAseq_SSCR_D27_3


title: SAMP-1138

tag: diagnosis

value: Islets

value: M

tag: purity


title: USB1 mut D30,  rna-seq 3

city: boulder

first: Roy

last: parker

address: colorado ave

institute: university of colorado boulder

data_processing:
Adapters were trimmed and low quality reads were removed using Trimmomatic 0.36
Trimmed reads were aligned to Ensembl GRCh38 V99 transcriptome release using Salmon 0.13.1
Salmon abundances were converted to gene level abundance using tx2gene
Salmon abundances were inputted to DESeq2 and differential expression was calculated at each time point (D0, D16, D30) between control and USB1 mut
Assembly: hg38
Supplementary files format and content: CSV file containing gene level abundance and normalized abundance output from DESeq2

extract_protocol:
Cells were collected and lysed with Trizol (Invitrogen)
Libraries were prepared using NextFlex Rapid Directional RNA-seq kit 2.0

value: Mature blood cells

value: USB1 mut

tag: time point

value: Day 30 post-hematopoiesis


title: USB1 mut D30,  rna-seq 2


title: scRNAseq_SSCR_D27_2

tag: strain

value: C57BL/6[female] X DBA[male]

tag: treatment


title: Raji2um1

value: CBL0137 2um

value: 24 hours


title: Rajicon3


title: scRNAseq_SSCR_D27_1


title: scRNAseq_SSCR_D23_7


title: SAMP-1697

tag: tissue

tag: gender

value: Hispanic/Latino


title: Rajicon2

tag: cell type


title: USB1 mut D30,  rna-seq 1


title: SAMP-1150

value: F

value: White

tag: bmi


title: Raji2um2


title: Control D30,  rna-seq 3

value: WT


title: Control D30,  rna-seq 2


title: SAMP-1696

value: Non-diabetic

tag: islet index


title: SAMP-1136

value: Hispanic


title: Control D30,  rna-seq 1

tag: cell line


title: SAMP-1149


title: SAMP-1605

value: Hispanic Latino


title: su2um3

value: Diffuse large B-cell lymphoma

tag: time


title: SAMP-1696_ATAC

tag: disease state

tag: library id

tag: sample id


title: USB1 mut D16,  rna-seq 3

value: Hematopoietic progenitors

tag: genotype

value: Day 16 post-hematopoiesis


title: SAMP-1607

value: Islets

tag: age

value: M

tag: race

value: Black or African American


title: scRNAseq_SSCR_D23_4


title: scRNAseq_SSCR_D23_6


title: scRNAseq_SSCR_D23_5


title: scRNAseq_SSCR_D23_3


title: USB1 mut D16,  rna-seq 2

value: USB1 mut


title: SAMP-1611

tag: diagnosis

tag: purity


title: scRNAseq_SSCR_D23_2

tag: strain

value: C57BL/6[female] X DBA[male]


title: USB1 mut D16,  rna-seq 1

tag: time point


title: su2um1

tag: treatment

value: CBL0137 2um


title: sucon3

value: 24 hours


title: SAMP-1097

tag: tissue

tag: gender


title: Rajicon1

value: Raji

tag: cell type

value: Burkitt Lymphoma


title: Control D16,  rna-seq 3


title: scRNAseq_SSCR_D23_1


title: SAMP-1695

value: Hispanic/Latino

tag: bmi

tag: islet index


title: sucon2

tag: cell line

tag: time


title: Control D16,  rna-seq 2

value: WT


title: SAMP-1608


title: su2um2


title: scRNAseq_SSCR_D20_8


title: Control D16,  rna-seq 1


title: TKO cells, rep 2

data_processing:
STAR was used to align the reads to GRCh38/hg38. FeatureCounts was used to obtain read counts for each gene.
Assembly: hg38
Supplementary files format and content: counts

growth_protocol: Parental MDA-MB-231 and TXNIP knockout MDA-MB-231 (TKO) cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco; 1195073) with 10% Fetal Bovine Serum (FBS) (Gibco; A3160506), 1X MEM Non-Essential Amino Acids Solution (Gibco; 11140076) and 1X Penicillin-streptomycin (Gibco; 15140148).

extract_protocol:
Total RNA was extracted from 3X106 cells using the Zymo Research Quick RNA miniprep kit (Zymo Research; R1055).
500 ng of total RNA was used to capture mRNA and construct library using KAPA Stranded mRNA-Seq Kit (KAPA Biosystems; KK8420) according to the manufacturer’s protocol. Briefly, after mRNA capturing and fragmentation, cDNA was synthesized. Sequencing adaptors were ligated to the cDNA fragments. The adaptor-ligated cDNA fragments were amplified with library PCR primers that contain barcodes for about 10 cycles.

treatment_protocol: 231:TKO cells were generated using human TXNIP CRISPR/Cas9 KO plasmid with TXNIP-specific guide RNA sequences from GeCKO (v2) library (Santa Cruz; sc-400664). Myc was knocked down in parental 231 and 231:TKO cells using siRNA approach for 48 hours.

value: triple-negative breast cancer

value: TXNIP knockout


title: SAMP-1613

value: F

value: Caucasian


title: scRNAseq_SSCR_D20_7


title: USB1 mut D0,  rna-seq 3

value: Human embryonic stem cells

value: Day 0 post-hematopoiesis


title: USB1 mut D0,  rna-seq 2


title: scRNAseq_SSCR_D20_6


title: SAMP-689

value: Islets

value: Hispanic


title: TKO cells, rep 1


title: SAMP-1144


title: SAMP-692

value: Non-diabetic

value: M


title: NEG_6

city: Oulu

first: Antti

last: Haapalainen

address: Aapistie 5A

department: CRC

country: Finland

institute: University of Oulu

data_processing:
Base-calling was done with bcl2fastq2 conversion software (NovaSeq 6000)
Read alignment and counting was done using Rsubread package (v. 2.0) using in-built RefSeq gene annotation.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data file rsubread_featureCounts.csv is tab delimited text file containing the genewise read counts for each sample.

source_name: cell

growth_protocol: The HTR-8/Svneo cells were cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum, 100 U/ml penicillin, 100 mg/ml streptomycin, 2 mM glutamine and 1 mM sodium pyruvate.

extract_protocol:
RNA was isolated by using RNeasy Micro Kit
TruSeq® Stranded mRNA Sample Preparation, Illumina (15031047)

treatment_protocol: The transfection with siRNA was done either with 10 nM siRNA pair or 10 nM siRNA universal negative control and using approximately 100 000 cells and duoble transfection. The first transfection was done in suspension and the second transfection in adherent cells.

value: trophoblast

value: placenta

value: siRNA universal negative control


title: parental 231 cells, rep 1

value: wild-type


title: scRNAseq_SSCR_D20_9

value: C57BL/6[female] X DBA[male]


title: USB1 mut D0,  rna-seq 1

value: USB1 mut


title: Control D0,  rna-seq 3

value: WT


title: sucon1

value: Diffuse large B-cell lymphoma

value: 24 hours


title: NEG_4


title: Control D0,  rna-seq 2


title: TKO, Input

data_processing:
ChIP-seq reads were aligned to human genome (hg19) using NovoAlign 3.08.02 with the following arguments: --NonC -r Random -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
Peaks were called using macs2 2.1.1.20160309 with the following arguments: macs2 callpeaks -g 3.1e9 -B --qvalue cutoff = 1.00e-02 --mfold=5 50
Assembly: hg19
Supplementary files format and content: BigWig files; pileup values for reads
Supplementary files format and content: Excel files; chromosome, start, stop, length, summits, p-value, fold enrichment, q-value, name value of peaks called by macs

growth_protocol: Parental MDA-MB-231 and TXNIP knockout MDA-MB-231 (TKO) cells were cultured in DMEM (Gibco; 1195073) with 10% Fetal Bovine Serum (FBS) (Gibco; A3160506), 1X MEM Non-Essential Amino Acids Solution (Gibco; 11140076) and 1X Penicillin-streptomycin (Gibco; 15140148).

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and then were treated with 0.125M glycine for 5 min to stop cross-linking reaction. Cross-linked cells were washed with 1X cold PBS and scraped for harvest. Myc-DNA complexes were isolated using Myc antibody (Cell signaling).
ChIP library was generated as described in Reddy et al. 2009. Briefly, blunted DNA fragments were ligated with sequencing adapters. The ligated DNA fragments were amplified with library PCR primers that contain barcodes (NEBNext ChIP-Seq Library Prep Reagent for Ilumina) for 15 cycles. Amplified DNA libraries from the anti-Myc ChIP were sequenced using Illumina HiSeq Sequencing with 50 cycles of single read.

value: triple-negative breast cancer

tag: chip antibody


title: Parental231, Input


title: scRNAseq_SSCR_D20_4


title: scTrioseq2Met_DMSO_sc2

data_processing:
Library strategy: Trio-seq2 (DNAme)
For scRNA-seq data, We firstly extracted cell barcodes and UMI sequences from read 2 of raw fastq data by UMItools (v1.0.0) (Smith et al., 2017) and attached them after the read name of read 1. After TSO and polyA sequences removal by local scripts, the “clean” reads were aligned to the mouse mm10 reference genome using STAR (2.7.2b) (Dobin et al., 2013), gene features were assigned by featureCounts (v2.0.0) (Liao et al., 2014). We used UMItools to generate UMI count expression matrix. For the quality control of scRNA-seq data, cells with detected gene numbers fewer than 2,000 or the fraction of mitochondrial reads more than 5% were excluded from further analysis, besides, genes expressed in fewer than 3 cells were filtered out for analysis.
For bisulfite sequencing data, trim_galore (v0.6.4) were used to remove low quality reads and adaptor sequence, and 9 bp of random primers from 5’ end of both read 1 and read 2 were also trimmed. Clean reads were then mapped to mm10 genome using Bismark (v0.23.0) with paired-end mode and ‘--non_directional’ option. Unmapped reads were outputted and mapped again by single-end mode. Aligned bam files were merged and sorted by samtools (v 1.11) and PCR duplicates were marked by picard MarkDuplicates (v2.23.6). Methylation calls for each CpG site were extracted by ‘bismark_methylation_extractor’ of Bismark. The thresholds for CpG sites coverage were 1X and 3X for single-cell- and bulk DNA methylation, respectively. Only methylation levels less than 10% or greater than 90% were retained for single-cell methylation data. Bisulfite conversion rate (BSCR) was estimated by methylation ratio of lambda DNA, samples with BSCR greater than 98% and detected CpG sites greater than 1,000,000 were kept for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix: matrix of UMI counts for all genes in each cell
Supplementary_files_format_and_content: bismark coverage: genome-wide cytosine report outputs of Bismark methylation extractor

value: DMSO


title: Control D0,  rna-seq 1

value: Human embryonic stem cells


title: scRNAseq_SSCR_D20_2


title: SAMP-1695_ATAC

extract_protocol:
Islets were resuspended in 1 mL wash buffer (10mM Tris-HCL (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 1% fatty acid-free BSA (Proliant, 68700), 1 mM DTT (Sigma), 1x protease inhibitors (Thermo Fisher Scientific, PIA32965), 1U/µl RNAsin (Promega, N2515) in molecular biology-grade water) and homogenized using 1 mL glass dounce homogenizer with a tight-fitting pestle (Wheaton, EF24835AA) for 10-20 strokes until the solution was homogeneous. Homogenized islets were filtered with 30 µm filter (CellTrics, Sysmex) and pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). Nuclei were resuspended in 400 µL of sort buffer (1% fatty acid-free BSA, 1x protease inhibitors (Thermo Fisher Scientific, PIA32965), 1U/µl RNAsin (Promega, N2515) in PBS) and stained with 7-AAD (1 µM; Thermo Fisher Scientific, A1310). 120,000 nuclei were sorted using an SH800 sorter (Sony) into 87.5 μl of collection buffer (1U/µl RNAsin (Promega, N2515), 5% fatty acid-free BSA (Proliant, 68700) in PBS). Nuclei suspension was mixed in a ratio of 4:1 with 5x permeabilization buffer (50 mM Tris-HCL (pH 7.4), 50 mM NaCl, 15 mM MgCl2, 0.5% Tween-20 (Sigma),  0.5% IGEPAL-CA630 (Sigma), 0.05% Digitonin (Promega), 5% fatty acid-free BSA (Proliant, 68700), 5 mM DTT (Sigma), 5x protease inhibitors (Thermo Fisher Scientific, PIA32965), 1U/µl RNAsin (Promega, N2515) in molecular biology-grade water) and incubated on ice for 1 min before pelleting with a swinging-bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). Supernatant was gently removed and ~50 µl were left behind to increase nuclei recovery. 650 µl of wash buffer (10mM Tris-HCL (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 1% fatty acid-free BSA (Proliant, 68700), 1 mM DTT (Sigma), 1x protease inhibitors (Thermo Fisher Scientific, PIA32965), 1U/µl RNAsin (Promega, N2515) in molecular biology-grade water) were added without disturbing the pellet and nuclei were pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). Supernatant was gently removed without disturbing the pellet and leaving ~2-3 µl behind. 7-10 µl of 1x Nuclei Buffer (10x Genomics) was added and nuclei gently resuspended. Nuclei were counted using a hemocytometer, and 16,550-18,000 nuclei were used as input for tagmentation.
Single Cell Multiome ATAC + Gene Expression libraries were generated following manufacturer instructions (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 1000283; Chromium Next GEM Chip J Single Cell, 1000234; Dual Index Kit TT Set A, 1000215; Single Index Kit N Set A, 1000212; 10x Genomics) with these PCR cycles: 7 cycles for ATAC index PCR, 7 cycles for cDNA amplification, 13-16 cycles for RNA index PCR. Final libraries were quantified using a Qubit fluorimeter (Life Technologies) and the size distribution was checked using a Tapestation (High Sensitivity D1000, Agilent). Libraries were sequenced on NextSeq 500 and NovaSeq 6000 sequencers (Illumina) with following read lengths (Read1 + Index1 + Index2 + Read2): ATAC (NovaSeq 6000) 50 + 8 + 24 + 50; ATAC (NextSeq 500 with custom recipe) 28 + 10 + 10 + 90;  RNA (NextSeq 500, NovaSeq 6000): 50 + 8 + 16 + 50.

tag: disease state

tag: library id

tag: sample id

value: Hispanic/Latino


title: HSPA5_3

value: silenced with siRNA of HSPA5


title: TKO, Myc, rep2

value: Myc (Cell signaling, D3N8F)


title: USB1 mut D30, 3

data_processing:
Adapters were trimmed and reads shorter than 19nt were dropped using Cutadapt 2.5
Trimmed reads were aligned to human mature miRNA release from miRbase 22 using Bowtie2 2.2.9
Aligned reads were co-ordinate shorted to BAM files using Samtools 1.3.1
miRNA counts were extracted from BAM files
Differential expression between WT and USB1 mutant miRome was calculated using DEseq2
Assembly: miRbase 22
Supplementary files format and content: CSV file containing counts of miRNA reads

extract_protocol:
Cells were collected and lysed using Trizol
Lexogen Small RNA-seq library prep kit

tag: genotype

value: Hematopoietic differentiation


title: scRNAseq_SSCR_D20_1


title: USB1 mut D30, 2


title: TKO, Myc, rep1


title: scRNAseq_SSCR_D18_7


title: scRNAseq_SSCR_D20_5


title: HSPA5_2


title: scRNAseq_SSCR_D18_6


title: parental 231 cells, rep 2


title: Parental231, Myc, rep2


title: NEG_5


title: scRNAseq_SSCR_D20_3


title: USB1 mut D30, 1


title: Parental231, Myc, rep1


title: scRNAseq_SSCR_D18_5


title: Control D30, 3


title: RNAseq, ganglion_neurons_IL17A_96h, rep4

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

description: RNAseq_counts_dorsal_ganglion_neurons.txt

data_processing:
RNA-seq samples were mapped to the mm10 mouse genome with STAR. Gene expression was assessed using HOMER’s analyze Repeats with parameters rna, mm10, -count exons, -condenseGenes. Raw data are shown as transcripts per million (TPM). Differential expression was calculated using DESeq2. Genes were considered differentially expressed with FDR < 0.05 and FC > 2. Gene ontology analysis was done with Metascape or IPA (Qiagen).
Genome_build: mm10
Supplementary_files_format_and_content: TPMs

source_name: dorsal root ganglion neurons exposed to IL17-A in vitro for 96 hours

extract_protocol:
For S. aureus RNA-seq: Ear pinna skin was split into the dorsal and the ventral sheets and placed in RPMI 1640 media supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 1 mM non-essential amino acids, 50 μM β-mercaptoethanol, 20 mM HEPES, 100 U/ml of penicillin, 100 mg/ml of streptomycin, 0.5 mg/ml of DNAse I (Sigma-Aldrich) and 0.25 mg/ml of Liberase TL purified enzyme blend (Roche) for 90 minutes at 37C and 5% CO2. Digested ear skin sheets were homogenized using the Medicon/Medimachine tissue homogenizer system. T cells were FACsorted (BD FACS Aria, Becton Dickinson) from Foxp3-GFP reporter mice. The RNA from the sorted T cells was extracted using the RNeasy Plus Micro Kit (Qiagen) as per manufacturer instructions. Libraries were prepared using the Clontech SMARTer Ultra low input mRNA-Seq sequence kit and samples were sequenced paired end on one lane of NextSeq 550.
For DRG RNA-seq: Supernatant was removed from cells, cells were lysed with RLT Plus buffer (Qiagen) and the RNA was extracted to perform bulk RNA sequencing. Libraries were prepared using the Clontech SMARTer Ultra low input mRNA-Seq sequence kit and samples were sequenced paired end on one lane of NextSeq 550.
Libraries were prepared using the Clontech SMARTer Ultra low input mRNA-Seq sequence kit and samples were sequenced paired end on one lane of NextSeq 550.

treatment_protocol:
For S. aureus treatment: Staphyloccocus aureus (42F02) was cultured in tryptic soy broth for 4 hours at 37oC with shaking at 200 rpm. For commensal colonization, each mouse was topically associated by applying up to 5 mL of a culture of S. aureus (approximately 10^9 CFU/mL) across the entire skin surface, or by applying 1 mL in each ear skin, using a sterile cotton swab. Unless otherwise noted, associations were repeated every other day for a total of 4 times. For infections, mice were intradermally injected in the ear pinnae with 2x10^7 CFU of S. aureus (42F02).
For dorsal ganglion neuron treatment: 5000 cells were seeded into flat-bottom 96-well plates coated with laminin (Thermo Fisher) and allowed to attach to the bottom of the wells for 2 hours, then the medium was removed and replaced with neurobasal medium containing 50 ng/ul nerve growth factor (Thermo Fisher). Following an overnight incubation, the supernatant was removed and replaced with neurobasal medium containing 50 ng/ul nerve growth factor, 10 uM cytosine arabinoside (Sigma), and 100 ng/ml IL17-A. Culture medium was replaced daily for the duration of the experiment.

value: dorsal ganglion neurons


title: Control D30, 2


title: RNAseq, ganglion_neurons_IL17A_96h, rep3


title: RNAseq, ganglion_neurons_IL17A_96h, rep2


title: Control D30, 1


title: USB1 mut D16, 3