title: Non-2

status: Public on Aug 08 2026

city: Fukuoka

first: Kei

last: Miyamoto

address: 744 Moto-oka, Nishi-ku

department: Faculty of Agriculture

country: Japan

institute: Kyushu University

data_processing:
Fastq files from Illumina sequencing were filtered for low quality reads by sliding window trimming (window size 10, <QV20), and low quality bases were trimmed from the ends of the reads (<QV20) using Trimmomatic. Reads less than 20 bases and unpaired reads were removed. Furthermore, adaptor, polyA, polyT and polyG sequences were removed using trim_galore and cutadapt.
The sequencing reads were then mapped to the mouse genome (mm10) using STAR. Reads on annotated genes were counted using featureCounts. FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample.

source_name: Embryo

growth_protocol: After in vitro fertilization, embryos were cultured in potassium simplex optimized medium (KSOM) at 37°C under 5% CO2 until the 2-cell stage (28 hours post insemination: 28 hpi).

extract_protocol:
After the removal of zona pellucida in acid Tyrode, embryos were washed with PBS containing 0.1% BSA, and then transferred to a 0.2 ml tube containing 9.5 μl of reaction buffer to make a final volume of 10.5 μl. After cell lysis in the buffer, 1 μl of the solution was removed and, instead, 1 μl of the diluted ERCC RNA Spike-In Mix was added (Thermo Fisher Scientific, 4456740). The lysed RNA solution with the spike-in RNA were subjected to reverse transcription.
SMART-seq library preparation was performed using SMART-Seq® HT Kit (Z4438N, Takara). The produced cDNA was amplified by PCR with 13 cycles. The amplified cDNA was purified using KAPA HyperPure Beads (KK8011, KAPA Biosystems). The purified cDNA was measured on the Bioanalyzer (Agilent) using High Sensitivity DNA Kit (5067-4626) and the normalized volume of DNA was subjected to library preparation using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096) by following the vendor’s instruction. The obtained library was quality-checked by Bioanalyzer and quantified using Qubit dsDNA HS Assay kit (Q32854, Thermo Scientific).

treatment_protocol: After insemination, fertilized embryos were collected at 12-14 hpi for mRNA injection. mRNAs were injected using a piezo manipulator (Prime Tech, Tsukuba, Japan).

value: Embryo

value: 2-cell embryo

value: Non injection control


title: BoneMarrow_DMSOforRU486_KO_rep3

status: Public on Aug 07 2026

type: SRA

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

country: China

institute: Zhejiang University School of Medicine

description:
Library name: BoneMarrow_DMSOforRU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

library_source: transcriptomic

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 or hg38 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

molecule: polyA RNA

organism: Mus musculus

source_name: BoneMarrow

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2–3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at −80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.

tag: tissue

value: BoneMarrow

tag: genotype

value: Mecp2 KO

tag: strain

tag: Sex

value: Male

tag: age

value: 2 months

tag: mouse id


title: NT2.5LV liver-preferential cell line, replicate 1

city: Los Angeles

first: Evanthia

middle: T

last: Roussos Torres

state: CA

country: USA

institute: University of Southern California

description: Library name: NT2.5LV_rep1

data_processing:
Base calling and demultiplexing were performed to generate paired-end FASTQ files (Novogene).
Reads were aligned to the mouse reference genome GRCm38 (mm10) using STAR v2.7.
Gene-level read counts were quantified using featureCounts (Subread package).
Counts were filtered with filterByExpr and normalized using the edgeR TMM method; normalized expression is reported as log2 counts per million (logCPM).
Assembly: GRCm38 (mm10)
Supplementary files format and content: raw_counts__featureCounts.tsv: tab-delimited text file of raw gene-level read counts (featureCounts); rows are Ensembl gene IDs, columns are the eight samples.
Supplementary files format and content: logCPM__edgeR_TMM__withGeneNames_corrected.tsv: tab-delimited text file of edgeR TMM-normalized log2 counts per million; columns are Ensembl gene ID, gene symbol, and the eight samples.

source_name: mammary tumor

growth_protocol: NT2.5, NT2.5LM, and NT2.5LV cells were maintained in RPMI-1640 supplemented with 20% fetal bovine serum, 100 U/mL penicillin, 100 U/mL streptomycin, 0.1% non-essential amino acids, 0.1% L-glutamine, and 10 mM HEPES, at 37 C in a humidified 5% CO2 incubator. Cells were harvested at 70-80% confluence.

extract_protocol:
Total RNA was extracted from cultured cells using a Qiagen RNA extraction kit according to the manufacturer's instructions, and RNA integrity and quantity were assessed prior to library preparation.
Messenger RNA was purified from total RNA by poly-T oligo-attached magnetic beads (poly(A) enrichment). Strand-specific paired-end libraries were prepared and sequenced as 2x150 bp reads on an Illumina NovaSeq X Plus to approximately 6 Gb of raw data per sample (Novogene).

value: mammary tumor

tag: cell line

tag: cell type

value: HER2-positive mammary carcinoma

value: neu-N transgenic (MMTV-neu)


title: K5

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: kidney biopsy

extract_protocol:
Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: kidney

value: kidney biopsy

value: 6 yo


title: TotalseqB_NEA2_cDNA_1

city: San Francisco

first: Gian Carlo

middle: L.

last: Baldonado

address: 2340 Sutter Street

department: Dermatology

institute: University of California San Francisco

description:
Library name: TotalseqB_NEA2_cDNA_1
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet

data_processing:
Raw FASTQ files were processed using Cell Ranger v8.0 (10x Genomics).
Cell Ranger count was run with the GRCh38 reference genome (refdata-gex-GRCh38-2020-A) and a custom TotalSeq-B antibody feature reference for ADT.
Donor demultiplexing was performed using Demuxlet with matched genotyping data.
Quality filtering, normalization, dimensionality reduction, and clustering performed using Seurat v5 with Weighted Nearest Neighbor (WNN) analysis for joint RNA and protein modalities.
Cell type annotation performed manually based on canonical marker gene and protein expression.
Assembly: GRCh38 (hg38)
Supplementary files format and content: MEX format: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene and ADT features), matrix.mtx.gz (count matrix) output by Cell Ranger v8.0. Each file prefixed with sample name for unique identification.
Supplementary files format and content: feature_reference.csv: TotalSeq-B antibody panel feature reference used by Cell Ranger.

source_name: peripheral blood

extract_protocol:
Gene expression and ADT libraries were prepared using the 10x Genomics Chromium Single Cell 5' Library & Gel Bead Kit with Feature Barcode Technology. Libraries were sequenced on an Illumina NovaSeq 6000.
PBMCs from multiple donors were multiplexed per sequencing batch using hashtag oligonucleotides (HTOs) and loaded onto the 10x Genomics Chromium Controller.

treatment_protocol: PBMCs were isolated from whole blood using Ficoll density gradient centrifugation and cryopreserved. Cells were thawed, washed, and stained with a TotalSeq-B antibody panel (BioLegend) per manufacturer protocol, then loaded onto the 10x Genomics Chromium Controller. Donors were multiplexed per batch using hashtag oligonucleotides (HTOs).

value: peripheral blood

value: PBMC

tag: batch


title: Lung, wildtype HH, male, rep2

city: Kansas City

first: Emily

last: Schueddig

state: KS

address: 2901 Rainbow Boulevard

department: Department of Biostatistics & Data Science

institute: University of Kansas Medical Center

description: Library name: RSB526-12

data_processing:
Read quality was assessed using FastQC (v0.12.1, RRID:SCR_014583). UMI-tools (v1.1.6, RRID:SCR_017048) was used for UMI and read extraction, then cutadapt (v5.0, RRID:SCR_011841) was used to retain reads with a minimum read length of 14 base pairs and maximum of 100 base pairs. BWA (v0.7.18, RRID:SCR_010910) with the aln algorithm was used for mapping with parameters set for no gaps (-o 0) and no mismatches (-n 0). Reads were aligned to the genomic sequence of aminoacetylated, mature mitochondrial mt-TR. Since there are known SNP in the mt-tRNA-Arg sequence for different mouse strains, each sample was mapped to its respective reference sequence. Aligned reads were deduplicated using UMI-tools. The resulting set of aligned reads were then mapped to the full mouse genome with the UCSC mm10 assembly as the reference using the bowtie (v1.3.1, RRID:SCR_005476) aligner. If the sequence mapped to another location, it was marked as a false positive and removed from downstream analysis. The number of reads for each unique sequence was extracted for each sample.
Assembly: NC_005089.1, CM004255.1, CM004184.1
Supplementary files format and content: counts.txt is a matrix of tRFs x samples that contains the extracted counts of sequences to the mt-tRNA-Arg gene

source_name: lung

extract_protocol:
Tissues were preserved in RNAlater (Invitrogen, AM7024) and frozen prior to RNA extraction. Small RNA was isolated using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific, AM1560) according to the manufacturer’s instructions with one exception: rather than being discarded, the corresponding large RNA fractions of small RNA isolations were retained, washed, and eluted to assess RNA integrity by visualization of 28S and 18S rRNA bands following agarose gel electrophoresis. Intact RNA samples were pooled by sodium acetate-propanol precipitation, followed by resuspension in nuclease-free water. RNA concentration was quantified using the Qubit microRNA Assay Kit (ThermoFisher Scientific, Q32881).
RNA isolated from mouse lungs using the mirVana miRNA Isolation Kit was sent to RealSeq (Santa Cruz, CA) for exploratory tRNA fragment sequencing using a single-adapter circularization-based library preparation approach.

value: lung

value: HH


title: BMM untreated 2

city: Berkeley

first: Stefan

middle: A

last: Fattinger

state: California

address: 415 Weill Hall

institute: UC Berkeley

description: Library name: Sample 2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36. Trimmed reads were mapped to the Mus musculus GRCm38 reference genome with STAR aligner v.2.5.2b. Analysis of raw counts was performed with DESeq2
Assembly: mm10
Supplementary files format and content: csv file including raw counts of each sample

source_name: Bone marrow derived macrphage (BMMs)

growth_protocol: Bone marrow-derived macrophages (BMMs) were differentiated from bone marrow and maintained in DMEM supplemented with 10% FBS, PenStrep, Glutamin, HEPES, and M-CSF in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were lysed with TRK lysis buffer (Omega Bio-Tek) and 2-mercaptoethanol followed by total RNA isolation using the E.Z.N.A Total RNA Kit I (Omega Bio-Tek)
RNA libraries for RNA-seq were prepared using an Illumina Poly(A) selection kit following manufacturer's protocols.

treatment_protocol: BMMs were left untreated, stimulated with 10ng/ml of IFNβ, IFNγ, TNF, or TGFβ for 6 hours or preexposed to 10ng/ml IFNβ for 24h before adding 10ng/ml IFNγ for 6h.

value: Bone marrow derived macrphage (BMMs)

value: B6 WT

tag: treatment

value: Untreated


title: S131 scTCR-seq

city: Houston

first: Moran

last: Amit

address: 1515 Holcombe Blvd

department: Head & Neck Surgery

institute: University of Texas - MD Anderson Cancer Center

description:
Library name: cohort2_10
10x TCR 5' V2 HT (High Throughput)

data_processing:
TCR contigs and V(D)J annotations were generated using the Cell Ranger V(D)J v7.1.0 workflow from 10x Genomics.
Sequencing data was aligned to the Human (GRCh38) 2020-A reference sequence.
Assembly: Human GRCh38
Supplementary files format and content: filtered_contig_annotations.csv: TCR contig annotations with cell barcodes
Library strategy: TCR-Seq

source_name: Tumor

extract_protocol:
After collection, specimens were immediately dissociated by using Human whole skin dissociation kit and Red Blood Cell Lysis Solution (10×) from Military Biotech. Dissociated cells were stained with APC conjugated CD45 (H130) mouse mAb from Cell Signaling. Then CD45 positive cells were sorted by using CytoFLEX SRT Cell Sorter for single cell sequencing.
T-cell receptor (TCR) single cell libraries were generated using the 10X Genomics Chromium Single Cell 5' v2 HT workflow with Feature Barcode technology.

value: Tumor

tag: pathology

value: SCC

value: IS

tag: patient


title: TotalseqB_NEA1_ADT3

description:
Library name: TotalseqB_NEA1_ADT3
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet

library_source: other

molecule: other


title: Lung, wildytpe CC, male, rep5

description: Library name: RSB526-09

value: CC


title: S70 scTCR-seq

description:
Library name: cohort2_6
10x TCR 5' V2 HT (High Throughput)


title: BoneMarrow_RU486_KO_rep6

description:
Library name: BoneMarrow_RU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: BoneMarrow

value: Mecp2 KO

value: Male

value: 2 months


title: Lung, wildytpe CC, male, rep4

description: Library name: RSB526-08


title: TotalseqB_NEA1_ADT2

description:
Library name: TotalseqB_NEA1_ADT2
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: S75 scTCR-seq

description:
Library name: cohort2_5
10x TCR 5' V2 HT (High Throughput)


title: Heart_RU486_KO_rep1

description:
Library name: Heart_RU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

source_name: Heart

value: Heart


title: TotalseqB_NEA2_ADT2

description:
Library name: TotalseqB_NEA2_ADT2
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: Lung, wildtype FF, male, rep2

description: Library name: RSB526-20

value: FF


title: TotalseqB_NEA2_ADT1

description:
Library name: TotalseqB_NEA2_ADT1
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet

value: peripheral blood


title: iPSC-derived OPCs, control_2, CT24, differtiation 1

city: Palo Alto

first: Erin

middle: M

last: Gibson

address: 3165 Porter Drive

department: Psychiatry and Behavioral Sciences

institute: Stanford University

description: Library name: TDR72Z_4_CT24_659_1

data_processing:
Data quality control and comparisons were conducted by the Plasmidsaurus online analysis platform in November 2025.  In short, quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR. Optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file. Differential expression was done with edgeR v4.0.16 using standard practice including filtering for low-expressed genes with edgeR::filterByExprwith default values and FDR values were used for further analysis. Samples CT24_300_3, CT24_021_3, CT30_300_3, CT30_021_3, CT36_300_3, CT36_021_3, CT42_300_3, CT42_021_3, CT42_008_3 were excluded from the analysis.
Assembly: GRCh38
Supplementary files format and content: Expression_matrix.tsv includes counts and CPM values for every sample

growth_protocol: Human inducible pluripotent stem cells (hiPSC) from RRMS (relapsing remitting, early-stage MS, n=3) and SPMS (secondary progressive, late-stage MS, n=3) MS patients, and age/sex-matched healthy controls (n=3 control) were acquired from the New York Stem Cell Foundation (see Suppl. Fig. 12A for line details) and differentiated towards OPCs, as previously described132. In short, iPSCs were cultured in 6-well plates coated with matrigel (Corning 354230, 1:100) in iPSC culture media comprising Miltenyi StemMACS iPS-brew XF with supplement (Miltenyi 130-104-368) and 1% Antibiotic Antimycotic Solution (Sigma). ROCK inhibitor Y-27632 (10 µM, Tocris) was added to the iPSC media for the first 24 hours. Once the iPSCs reached 70–80% confluency, cells were detached with pre-warmed EDTA (0.5 mM) for passaging, or pre-warmed accutase (SIGMA A6964) for embryoid bodies (EBs) formation. To form EBs, cells were resuspended in iPSC media supplemented with ROCK inhibitor and seeded (~ 1.5 × 10⁶ cells) in AggreWell™400 microwell culture plates (Stem Cell Technologies 34815) overnight. The EBs were then transferred to 10-cm petri dishes (Falcon 351029), placed on a rotary shaker, and cultured for 7 days in a chemically defined medium (CDM): 1:1 mix of F12 and Iscove’s modified Dulbecco’s medium (Invitrogen) with chemically defined Lipid concentrate 100 (Invitrogen), monothioglycerol (450 µM, Sigma), BSA (5 mg/ml, Sigma), transferrin (15 mg/ml, Roche), insulin (7 mg/ml, Roche), and 1% Antibiotic Antimycotic Solution. N-acetyl cysteine (1 mM, Sigma), Activin inhibitor SB 431542 (10 µM, Sigma), and LDN193189 (0.1 µM, Stratech) were added for neural induction. Next, the neurospheres formed from the EBs were caudalized for 7 days in CDM supplemented with N-acetyl cysteine (1 mM, Sigma), heparin (5 µg/ml, Sigma), retinoic acid (0.1 µM, Sigma), and basic fibroblast growth factor (FGF-2; 10 ng/ml, PeproTech). For morphological assessment of neural conversion, the cells were plated on plates coated with laminin (10 μg/ml, Sigma). Post-neural induction, the spheres were cultured in advanced DMEM medium containing 0.5% GlutaMAX (Invitrogen), 5 µg/ml heparin (Sigma), 1% N2 (Invitrogen), 1% B27 (Invitrogen), and 1% Antibiotic Antimycotic Solution. To initiate ventralization, purmorphamine (1 µM, Calbiochem), retinoic acid (1 µM, Sigma), and FGF-2 (10 ng/ml, PeproTech) were added to the media for 7 days, after which FGF-2 was removed for 14 days. hOPC proliferation was then promoted by supplementing the medium with FGF-2 (10 ng/mL), T3 (60 ng/mL, Sigma), PDGFα (20 ng/mL, PeproTech), SAG (1 µM, Calbiochem), purmorphamine (1 µM, Sigma), and IGF-1 (10 ng/mL, PeproTech). After 14 days, spheres were dissociated using the Worthington papain dissociation system (LK003150 per manufacturer’s instructions) and single cells were seeded in matrigel-coated T-75 Flasks (CELLTREAT 229341). After 24 hours, cells were purified for PDGFRα by MACS using PE-conjugated CD140a antibody (Miltenyi 130-115-238) and Anti-PE MicroBeads (Miltenyi 130-048-801) according to the manufacturer’s instructions.

extract_protocol:
Bulk RNA sequencing was performed by Plasmidsaurus using Illumina Sequencing Technology.
1.Poly-A mRNA capture and reverse transcription for cDNA synthesis: oligo-dT primer to capture just the mRNA (contains sample barcode, UMI, and Read 1 sequences). 2. Second strand synthesis and tagmentation: double stranded-cDNA is generated. Tagmentation creates fragments and incorporates Read 2 sequence. 3.Illumina library amplification: adds unique dual indices (UDI = i5, i7) and P5/P7 sequences.

treatment_protocol: PDGFRα+ cells were seeded in matrigel-coated 6-well plates and allowed to recover for 24 hours before synchronization with dexamethasone (100nM, 1h, Sigma-Aldrich D4902). Following complete media change, cells were harvested at 24h (CT24), 30h (CT30), 36h (CT36), or 42h (CT42). Cells lysates were preserved in Zymo DNA/RNA Shield (ZYMO RESEARCH R1100-50) for bulk RNA sequencing performed by Plasmidsaurus.

value: iPSC-derived OPCs

value: differentiation 1


title: Lung, wildytpe CC, male, rep3

description: Library name: RSB526-07

value: lung


title: TotalseqB_NEA1_ADT1

description:
Library name: TotalseqB_NEA1_ADT1
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet

value: PBMC


title: TotalseqB_NEA2_cDNA_3

description:
Library name: TotalseqB_NEA2_cDNA_3
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: S130 scTCR-seq

description:
Library name: cohort2_2
10x TCR 5' V2 HT (High Throughput)


title: BoneMarrow_RU486_KO_rep4

description:
Library name: BoneMarrow_RU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: Lung, wildytpe CC, male, rep2

description: Library name: RSB526-06


title: TotalseqB_NEA1_cDNA4

description:
Library name: TotalseqB_NEA1_cDNA4
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: S110 scTCR-seq

description:
Library name: cohort2_24
10x TCR 5' V2 HT (High Throughput)

value: BCC


title: BoneMarrow_RU486_KO_rep3

description:
Library name: BoneMarrow_RU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: S128 scTCR-seq

description:
Library name: cohort2_20
10x TCR 5' V2 HT (High Throughput)


title: BoneMarrow_RU486_KO_rep2

description:
Library name: BoneMarrow_RU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: Lung, MNX CF, male, rep4

description: Library name: RSB526-04

value: CF


title: S112 scTCR-seq

description:
Library name: cohort2_19
10x TCR 5' V2 HT (High Throughput)

value: Tumor


title: BoneMarrow_RU486_KO_rep1

description:
Library name: BoneMarrow_RU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: Lung, MNX CF, male, rep3

description: Library name: RSB526-03


title: TotalseqB_NEA1_cDNA1

description:
Library name: TotalseqB_NEA1_cDNA1
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: S129 scTCR-seq

description:
Library name: cohort2_7
10x TCR 5' V2 HT (High Throughput)


title: Lung, wildtype HH, male, rep1

description: Library name: RSB526-11

value: HH


title: Bone_DMSOforRU486_KO_rep6

description:
Library name: Bone_DMSOforRU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

source_name: Bone

value: Bone


title: TotalseqB_NEA1_ADT4

description:
Library name: TotalseqB_NEA1_ADT4
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: BoneMarrow_DMSOforRU486_KO_rep1

description:
Library name: BoneMarrow_DMSOforRU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: Lung, MNX CF, male, rep2

description: Library name: RSB526-01


title: Peritoneal cavity, CARNKT

first: Yichen

last: Zhu

address: 610 Charles E Young Drive S

institute: University of California, Los Angeles

description:
Library name: Sample_02
10x Genomics

library_source: transcriptomic single cell

data_processing:
For cell clustering and annotation, the merged digital expression matrix generated by Cellranger was analyzed using an R package Seurat (v.4.0.0) following the guidelines. Briefly, after filtering the low-quality cells, the expression matrix was normalized using NormalizeData function, followed by selecting variable features across datasets using FindVariableFeatures and SelectIntegrationFeatures functions. To correct the batch effect, FindIntegrrationAnchors and IntegrateData functions were used based on the selected feature genes. The corrected dataset was subjected to standard Seurat workflow for dimension reduction and clustering. In this study, clusters of human therapeutic cells were manually merged and annotated based on gene signatures reported from Human Protein Atlas (proteinatlas.org) and previous studies. Clusters of mouse immune cells were manually merged and annotated based on immune cell lineage markers. AddModuleScore was used to calculate module scores of each list of gene signatures, and FeaturePlot function was used to visualize the expression of each signature in the UMAP plots.
Assembly: Human (GRCh38) 2024-A
Supplementary files format and content: matrix.mtx.gz: Matrix Market Format, with rows representing genes and columns representing cells.
Supplementary files format and content: barcode.tsv.gz: Tab-separated values, where each row represents a unique identifier for a cell.
Supplementary files format and content: features.tsv.gz: Tab-separated values, where each row represents a gene.

source_name: Peritoneal cavity

extract_protocol:
Using the in vivo CRS model, human therapeutic cells were subjected to scRNA-seq analysis. At 3 days post–therapeutic cell injection, mice were euthanized, and six tissues were harvested, including peritoneal fluid, blood, liver, lung, spleen, and bone marrow. Single-cell suspensions were prepared from each tissue and subjected to fluorescence-activated cell sorting (FACS). Cells from the peritoneal fluid were further sorted to isolate human therapeutic cells (CD45⁺CD3⁺CAR⁺), corresponding to CAR-T and CAR-NKT cells.
Sorted cells were immediately delivered to the UCLA Technology Center for Genomics & Bioinformatics (TCGB) core facility for library preparation and subsequent scRNA-seq analysis. Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 20,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3’ Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: Peritoneal cavity

value: T cells


title: S144_2 scTCR-seq

description:
Library name: cohort1_53B_53C
10x TCR 5' V2 HT (High Throughput)

value: SCC

value: IS


title: Bone_DMSOforRU486_KO_rep5

description:
Library name: Bone_DMSOforRU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Mecp2 KO

value: Male

value: 2 months


title: Lung, MNX CF, male, rep1

description: Library name: RSB528-23


title: Peritoneal cavity, CART

description:
Library name: Sample_01
10x Genomics


title: Bone_DMSOforRU486_KO_rep4

description:
Library name: Bone_DMSOforRU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: 3D-VET-GEX

city: Parkville

first: Michael

last: See

state: VIC

address: Royal Children's Hospital, 50 Flemington Rd

country: Australia

institute: MCRI

description:
Library name: 3D-Valve-Cells
10x Genomics

data_processing:
Data were processed with Cellranger 9.0.0 which performed alignment and gene quantification per-cell
Assembly: GRCh38 2020-A from 10x
Supplementary files format and content: filtered and raw h5 files produced by Cellranger
Supplementary files format and content: filtered h5 files produced by CellBender

source_name: valve engineered tissue

growth_protocol: stem cell-derived valve cells were cultured as 3D constructs in RPMI 1640 supplemented with L-Ascorbic acid, Dexamethasone, L-Proline, 1X ITS and 10% Fetal Bovine Serum for 30 days

extract_protocol:
After 30 days in culture, cells were isolated from macroVETs using Miltenyi Cell Isolation Kit - Umbilical cord kit (130-105-737) as per manufacturers instructions and cells were sorted with flow cytometry
10X  Chromium Next GEM Single Cell 3' protocol

value: valve engineered tissue

value: PSC-derived valve cells


title: Lung, MNX CH, male, rep4

description: Library name: RSB528-21

value: CH


title: S142 scTCR-seq

description:
Library name: cohort1_46
10x TCR 5' V2 HT (High Throughput)


title: Bone_DMSOforRU486_KO_rep3

description:
Library name: Bone_DMSOforRU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: S144_1 scTCR-seq

description:
Library name: cohort1_53A
10x TCR 5' V2 HT (High Throughput)


title: Lung, MNX CH, male, rep3

description: Library name: RSB528-19

value: lung


title: 2D-Valve-Cells-GEX

description:
Library name: 2D-Valve-Cells
10x Genomics


title: BoneMarrow_RU486_KO_rep5

description:
Library name: BoneMarrow_RU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: BoneMarrow


title: S143 scTCR-seq

description:
Library name: cohort1_44
10x TCR 5' V2 HT (High Throughput)


title: Bone_DMSOforRU486_KO_rep1

description:
Library name: Bone_DMSOforRU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: RNAseq_Safe7608_R3

city: Montreal

first: Guillaume

last: Lettre

state: Quebec

address: 5000 Belanger

country: Canada

institute: Montreal Heart Institute

description: Library name: RNAseq_sample_21

data_processing:
FASTQ files were aligned on an index genome using Kallisto to generate raw count. ENSEMBL IDs were replaced by gene names using EnsDb.Hsapiens.v86 using gene level setting. Data filtered for counts >10.
Assembly: Homo_sapiens.GRCh38.cdna.all
Supplementary files format and content: Raw count for each gene with count >10. First column: gene name, second column: raw count.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Mini Kit.
Total RNA samples were sent at genome Quebec facilities fo rRNA depleted libraries preparation.

value: erythropoietic

value: gRNA transduction


title: Bone_RU486_KO_rep6

description:
Library name: Bone_RU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: Lung, MNX CH, male, rep1

description: Library name: RSB528-17


title: Lung, MNX CH, male, rep2

description: Library name: RSB528-18


title: RNAseq_Safe7608_R2

description: Library name: RNAseq_sample_20


title: S132_2 scTCR-seq

description:
Library name: cohort1_19C
10x TCR 5' V2 HT (High Throughput)

value: Tumor


title: Bone_RU486_KO_rep5

description:
Library name: Bone_RU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: Lung, MNX HC, male, rep4

description: Library name: RSB528-14

value: HC


title: RNAseq_Safe7608_R1

description: Library name: RNAseq_sample_19


title: S132_1 scTCR-seq

description:
Library name: cohort1_18
10x TCR 5' V2 HT (High Throughput)


title: TotalseqB_NEA1_cDNA3

description:
Library name: TotalseqB_NEA1_cDNA3
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet

value: peripheral blood

value: PBMC


title: Lung, MNX HC, male, rep3

description: Library name: RSB528-12


title: Bone_RU486_KO_rep4

description:
Library name: Bone_RU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Bone


title: Lung, wildytpe CC, male, rep1

description: Library name: RSB526-05

value: CC


title: RNAseq_Ch19_229_R4

description: Library name: RNAseq_sample_18


title: S138 scTCR-seq

description:
Library name: cohort1_32
10x TCR 5' V2 HT (High Throughput)

value: SCC

value: IS


title: Bone_RU486_KO_rep3

description:
Library name: Bone_RU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Mecp2 KO

value: Male


title: TotalseqB_NEA1_cDNA2

description:
Library name: TotalseqB_NEA1_cDNA2
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: RNAseq_Ch19_229_R3

description: Library name: RNAseq_sample_17


title: Lung, MNX HC, male, rep2

description: Library name: RSB528-11


title: Bone_RU486_KO_rep2

description:
Library name: Bone_RU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: 2 months


title: Lung, MNX HC, male, rep1

description: Library name: RSB528-10


title: S115 scTCR-seq

description:
Library name: cohort1_45
10x TCR 5' V2 HT (High Throughput)

value: BCC


title: Bone_RU486_KO_rep1

description:
Library name: Bone_RU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: S117 scTCR-seq

description:
Library name: cohort1_12
10x TCR 5' V2 HT (High Throughput)


title: iPSC-derived OPCs, RRMS_2, CT24, differtiation 1

description: Library name: TDR72Z_13_CT24_021_1

value: iPSC-derived OPCs

value: differentiation 1


title: Lung, wildtype FF, female, rep5

description: Library name: RSB528-09

value: lung

value: FF


title: RNAseq_Ch19_229_R2

description: Library name: RNAseq_sample_16

value: erythropoietic

value: gRNA transduction


title: RNAseq_Ch19_199_R4

description: Library name: RNAseq_sample_15


title: Heart_DMSOforRU486_KO_rep3

description:
Library name: Heart_DMSOforRU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Heart


title: S118 scTCR-seq

description:
Library name: cohort1_11
10x TCR 5' V2 HT (High Throughput)

value: Tumor


title: S108 scTCR-seq

description:
Library name: cohort1_20
10x TCR 5' V2 HT (High Throughput)


title: TotalseqB_NEA3_ADT3

description:
Library name: TotalseqB_NEA3_ADT3
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet

value: peripheral blood

value: PBMC


title: iPSC-derived OPCs, RRMS_1, CT24, differtiation 3

description: Library name: TDR72Z_12_CT24_029_3

value: differentiation 3


title: Heart_DMSOforRU486_KO_rep1

description:
Library name: Heart_DMSOforRU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: Heart_RU486_KO_rep6

description:
Library name: Heart_RU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: WhiteFat_DMSOforRU486_WT_rep6

description:
Library name: WhiteFat_DMSOforRU486_WT_rep6_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

source_name: WhiteFat

value: WhiteFat

value: WT

value: 3 months


title: RNAseq_Ch19_199_R3

description: Library name: RNAseq_sample_14


title: Lung, wildtype FF, female, rep4

description: Library name: RSB528-08


title: Lung, MNX CH, female, rep6

description: Library name: Sample-13

value: CH


title: S111 scTCR-seq

description:
Library name: cohort1_17
10x TCR 5' V2 HT (High Throughput)

value: IS


title: Lung, wildtype FF, female, rep3

description: Library name: RSB528-07


title: RNAseq_Ch19_199_R1

description: Library name: RNAseq_sample_13


title: WhiteFat_DMSOforRU486_WT_rep5

description:
Library name: WhiteFat_DMSOforRU486_WT_rep5_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

value: Male


title: S39 scTCR-seq

description:
Library name: cohort1_1
10x TCR 5' V2 HT (High Throughput)

value: SCC

value: IC


title: RNAseq_Ch16_633_R4

description: Library name: RNAseq_sample_12


title: WhiteFat_DMSOforRU486_WT_rep4

description:
Library name: WhiteFat_DMSOforRU486_WT_rep4_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: S17 scTCR-seq

description:
Library name: cohort1_10
10x TCR 5' V2 HT (High Throughput)


title: Lung, wildtype FF, female, rep2

description: Library name: RSB528-06

value: lung


title: Lung, wildtype FF, female, rep1

description: Library name: RSB528-05

value: FF


title: WhiteFat_DMSOforRU486_WT_rep3

description:
Library name: WhiteFat_DMSOforRU486_WT_rep3_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: RNAseq_Ch16_633_R3

description: Library name: RNAseq_sample_11

value: erythropoietic


title: Lung, wildtype HH, female, rep5

description: Library name: RSB528-02

value: HH


title: RNAseq_Ch16_633_R1

description: Library name: RNAseq_sample_10

value: gRNA transduction


title: S7 scTCR-seq

description:
Library name: cohort1_4
10x TCR 5' V2 HT (High Throughput)

value: Tumor


title: TotalseqB_NEA3_cDNA_2

description:
Library name: TotalseqB_NEA3_cDNA_2
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet

value: peripheral blood


title: S15 scTCR-seq

description:
Library name: cohort1_50
10x TCR 5' V2 HT (High Throughput)


title: WhiteFat_DMSOforRU486_WT_rep2

description:
Library name: WhiteFat_DMSOforRU486_WT_rep2_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: Lung, wildtype HH, female, rep4

description: Library name: RSB528-01


title: WhiteFat_DMSOforRU486_WT_rep1

description:
Library name: WhiteFat_DMSOforRU486_WT_rep1_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: RNAseq_Ch8_821_R3

description: Library name: RNAseq_sample_9


title: S49 scTCR-seq

description:
Library name: cohort1_5a
10x TCR 5' V2 HT (High Throughput)

value: BCC


title: WhiteFat_RU486_WT_rep6

description:
Library name: WhiteFat_RU486_WT_rep6_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: Lung, wildtype HH, female, rep3

description: Library name: RSB527-23


title: S56 scTCR-seq

description:
Library name: cohort1_6
10x TCR 5' V2 HT (High Throughput)


title: WhiteFat_RU486_WT_rep5

description:
Library name: WhiteFat_RU486_WT_rep5_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: RNAseq_Ch8_821_R1

description: Library name: RNAseq_sample_7


title: Lung, wildtype HH, female, rep2

description: Library name: RSB527-22


title: Lung, wildtype HH, female, rep1

description: Library name: RSB527-21


title: S51 scTCR-seq

description:
Library name: cohort1_23
10x TCR 5' V2 HT (High Throughput)


title: RNAseq_Ch6_809_R3

description: Library name: RNAseq_sample_6


title: WhiteFat_RU486_WT_rep3

description:
Library name: WhiteFat_RU486_WT_rep3_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: Lung, wildtype CC, female, rep6

description: Library name: RSB527-20

value: CC


title: RNAseq_Ch6_809_R2

description: Library name: RNAseq_sample_5


title: Lung, wildtype CC, female, rep5

description: Library name: RSB527-19


title: S47 scTCR-seq

description:
Library name: cohort1_7
10x TCR 5' V2 HT (High Throughput)


title: S53 scTCR-seq

description:
Library name: cohort1_24
10x TCR 5' V2 HT (High Throughput)


title: Lung, wildtype CC, female, rep4

description: Library name: RSB527-18


title: RNAseq_Ch6_809_R1

description: Library name: RNAseq_sample_4


title: WhiteFat_RU486_WT_rep1

description:
Library name: WhiteFat_RU486_WT_rep1_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

value: WhiteFat


title: Thymus_DMSOforRU486_WT_rep6

description:
Library name: Thymus_DMSOforRU486_WT_rep6_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

source_name: Thymus

value: Thymus

value: WT


title: RNAseq_Ch1_764_R4

description: Library name: RNAseq_sample_3


title: S46 scTCR-seq

description:
Library name: cohort1_8
10x TCR 5' V2 HT (High Throughput)


title: RNAseq_Ch1_764_R3

description: Library name: RNAseq_sample_2


title: Lung, wildtype CC, female, rep3

description: Library name: RSB527-17


title: Lung, wildtype CC, female, rep2

description: Library name: RSB527-16


title: Thymus_DMSOforRU486_WT_rep5

description:
Library name: Thymus_DMSOforRU486_WT_rep5_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

value: 3 months


title: S55 scTCR-seq

description:
Library name: cohort1_9
10x TCR 5' V2 HT (High Throughput)


title: RNAseq_Ch1_764_R1

description: Library name: RNAseq_sample_1


title: Thymus_DMSOforRU486_WT_rep4

description:
Library name: Thymus_DMSOforRU486_WT_rep4_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: Lung, wildtype CC, female, rep1

description: Library name: RSB527-15


title: VS_Cas9_R3_fraction_5

description: Library name: VS_sample_16

library_source: genomic

data_processing:
Using gRNA list, gRNA counts were establsihed from fastq files. The raw counts were normalized without suppervision to remove sequenciing batch effect to create normalized counts.
Assembly: Homo_sapiens.GRCh38.cdna.all
Supplementary files format and content: Unsuppervised normalized count for each gRNA in the given Percoll gradient fraction. Each file contain the data for 1 fraction. First column: gRNA name, second column: normalized count (relative gRNA abundance in the fraction)
Library strategy: CRISPR Screen

molecule: genomic DNA

growth_protocol: HUDEP-2 were culture in StemSpan medium supplemented with 1 µg/ml doxycycline, 0.4 µg/ml dexamethasone, 0.1 µg/ml Stem Cell Factor, 3 units/ml erythropoietin, 2 mM L-glutamine, 200 IU penicillin, 200 µg/ml streptomycin and incubated at 37°C and 5% CO2.

extract_protocol:
The gDNA was extracted using the Qiagen DNeasy blood and tissue kit. PCR products from gDNA was purified with either the Qiagen QIAquick PCR Purification Kit or SPRISelect reagen. 2 µg of purified PCR product was purified on agarose gel using Qiagen QIAquick gel extraction kit.
The PCR amplification was adding the Illumina TruSeq LT adapator and sample index.

treatment_protocol: gRNA either librairies or single gRNA were transduced in HUDEP-2 cells using lentivirus. The MOI for gRNA librarie was 0.3, while 200 Kcells were infected with 300 µl of viral suspension for single gRNA. Selection with appropriate antibiotic was performed 6 days for Cas9, 5 days for dCas9-KRAB, and 4 days for dCas9-VP64

value: VS


title: GM12878_Direct_CAD-C_M_2x250_TR2

city: New York

first: Viviana

middle: I

last: Risca

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description: Library name: GM12878_Direct_CAD-C_M_2x250_TR2

data_processing:
Paired-end reads were aligned to the human reference genome (hg38) using bwa-mem2, converted to BAM format, and processed with a pairtools-based pipeline to parse contacts, correct orientation, sort, remove duplicates, and generate final high-confidence contact pairs for downstream analysis.
Assembly: hg38
Supplementary files format and content: cool, bw

growth_protocol: GM12878 cells were cultured in the media and conditions recommended by Coriell Institute for Medical Research.

extract_protocol:
For CADwalk, crosslinked cells were processed by CAD digestion and in situ proximity ligation without end repair or biotin labeling; proximity-ligation concatemer DNA was isolated after crosslink reversal and protein digestion, size-selected by agarose gel electrophoresis, and recovered by gel extraction.
Purified DNA was either sonicated and subjected to streptavidin-based enrichment followed by Illumina library preparation, processed directly with the NEBNext UltraExpress FS kit, or converted into long-read PacBio libraries via ligation-based adapter construction, followed by PCR amplification and sequencing.

value: B lymphoblastoid cell line


title: Lung, MNX CF, female, rep5

description: Library name: RSB527-14

value: CF


title: VS_Cas9_R3_fraction_4

description: Library name: VS_sample_15


title: Thymus_DMSOforRU486_WT_rep3

description:
Library name: Thymus_DMSOforRU486_WT_rep3_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

value: Male


title: Thymus_DMSOforRU486_WT_rep2

description:
Library name: Thymus_DMSOforRU486_WT_rep2_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: GM12878_Direct_CAD-C_M_2x250_TR1

description: Library name: GM12878_Direct_CAD-C_M_2x250_TR1


title: Lung, MNX CF, female, rep4

description: Library name: RSB527-13

value: lung


title: VS_Cas9_R3_fraction_3

description: Library name: VS_sample_14


title: GM12878_Direct_CAD-C_S_2x250_TR2

description: Library name: GM12878_Direct_CAD-C_S_2x250_TR2


title: Thymus_DMSOforRU486_WT_rep1

description:
Library name: Thymus_DMSOforRU486_WT_rep1_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: GM12878_Direct_CAD-C_S_2x250_TR1

description: Library name: GM12878_Direct_CAD-C_S_2x250_TR1


title: Thymus_RU486_WT_rep6

description:
Library name: Thymus_RU486_WT_rep6_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: VS_Cas9_R3_fraction_1

description: Library name: VS_sample_12


title: Thymus_RU486_WT_rep5

description:
Library name: Thymus_RU486_WT_rep5_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: Lung, MNX CF, female, rep1

description: Library name: RSB527-09


title: VS_Cas9_R2_fraction_5

description: Library name: VS_sample_11


title: Thymus_RU486_WT_rep4

description:
Library name: Thymus_RU486_WT_rep4_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: K562_Classic_TR1

description: Library name: K562_Classic_TR1

data_processing:
Paired-end reads were aligned to the human reference genome (hg38) using bwa-mem2, converted to BAM format, and processed with a pairtools-based pipeline to parse contacts, correct orientation, sort, remove duplicates, and generate final high-confidence contact pairs for downstream analysis.
Assembly: hg38
Supplementary files format and content: cool

growth_protocol: K562 cells were cultured in Iscove’s Modified Dulbecco’s Medium supplemented with 10 % fetal bovine serum and 1 % penicillin–streptomycin. hTERT RPE-1 and GM12878 cells were cultured in the media and conditions recommended by ATCC and Coriell Institute for Medical Research, respectively.

extract_protocol:
For Classic CAD-C, crosslinked cells were subjected to RNase treatment and CAD digestion, followed by in situ end repair, biotin fill-in, and proximity ligation; nuclei were then treated with Exonuclease III, crosslinks were reversed by proteinase K digestion, and DNA was purified by phenol–chloroform extraction with ethanol precipitation or by column-based cleanup. For Express CAD-C, DNA extraction followed the Classic CAD-C workflow through CAD digestion, end repair, biotin fill-in, proximity ligation, Exonuclease III treatment, and crosslink reversal, yielding purified CAD-C DNA that was subsequently used directly as input for library preparation. For Direct CAD-C, crosslinked cells were processed by CAD digestion and in situ proximity ligation without end repair or biotin labeling; proximity-ligation concatemer DNA was isolated after crosslink reversal and protein digestion.
Purified DNA was either sonicated and subjected to streptavidin-based enrichment followed by Illumina library preparation, processed directly with the NEBNext UltraExpress FS kit, followed by PCR amplification and sequencing.

value: myelogenous leukemia cell


title: Lung, MNX HC, female, rep7

description: Library name: RSB527-04

value: HC


title: GM12878_Express_P3_S4

description: Library name: GM12878_Express_P3_S4


title: VS_Cas9_R2_fraction_4

description: Library name: VS_sample_10

value: erythropoietic


title: Lung, MNX HC, female, rep6

description: Library name: RSB527-03


title: GM12878_Express_P3_S3

description: Library name: GM12878_Express_P3_S3


title: Thymus_RU486_WT_rep2

description:
Library name: Thymus_RU486_WT_rep2_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: Thymus_RU486_WT_rep1

description:
Library name: Thymus_RU486_WT_rep1_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: Lung, MNX HC, female, rep5

description: Library name: RSB527-02


title: Lung, MNX HC, female, rep4

description: Library name: RSB527-01


title: GM12878_Express_P3_S1

description: Library name: GM12878_Express_P3_S1


title: Telencephalon_DMSOforRU486_WT_rep6

description:
Library name: Telencephalon_DMSOforRU486_WT_rep6_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

source_name: Telencephalon

value: Telencephalon


title: VS_Cas9_R1_fraction_5

description: Library name: VS_sample_6

value: gRNA transduction


title: Telencephalon_DMSOforRU486_WT_rep5

description:
Library name: Telencephalon_DMSOforRU486_WT_rep5_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: GM12878_Classic_P1_TR4

description: Library name: GM12878_Classic_P1_TR4


title: VS_Cas9_R1_fraction_4

description: Library name: VS_sample_5


title: GM12878_Classic_P1_TR3

description: Library name: GM12878_Classic_P1_TR3


title: Lung, MNX CH, female, rep1

description: Library name: RSB491-04

value: CH


title: VS_Cas9_R1_fraction_3

description: Library name: VS_sample_4


title: Telencephalon_DMSOforRU486_WT_rep4

description:
Library name: Telencephalon_DMSOforRU486_WT_rep4_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: Telencephalon_DMSOforRU486_WT_rep3

description:
Library name: Telencephalon_DMSOforRU486_WT_rep3_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: GM12878_Classic_P1_TR2

description: Library name: GM12878_Classic_P1_TR2


title: VS_Cas9_R1_fraction_2

description: Library name: VS_sample_3


title: GM12878_Classic_P1_TR1

description: Library name: GM12878_Classic_P1_TR1


title: Lung, MNX HC, female, rep2

description: Library name: RSB491-02


title: VS_Cas9_R1_fraction_1

description: Library name: VS_sample_2


title: RPE1_Classic_P3_S4

description: Library name: RPE1_Classic_P3_S4

value: Retinal Pigment Epithelial cell


title: Thymus_RU486_WT_rep3

description:
Library name: Thymus_RU486_WT_rep3_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: Telencephalon_DMSOforRU486_WT_rep1

description:
Library name: Telencephalon_DMSOforRU486_WT_rep1_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: VS_Cas9_R2_fraction_3

description: Library name: VS_sample_9


title: Lung, MNX HC, female, rep1

description: Library name: RSB491-01


title: VS_Cas9_R2_fraction_2

description: Library name: VS_sample_8


title: VS_plasmid_pHKO

description: Library name: VS_sample_1


title: RPE1_Classic_P3_S3

description: Library name: RPE1_Classic_P3_S3


title: WT_fin_distal_tip_7_dpa_rep3

city: Madison

first: Jianhong

last: Ou

state: Wisconsin

address: 330 N Orchard Street

institute: Morgridge Institute For Research

description: Library name: day7_REP3

data_processing:
RNA-seq reads were trimmed by Trim Galore (v 0.6.7, with cutadapt v 3.5) and counted by salmon (v 1.4.0) by supplying the UCSC danRer11 annotation
The counts were normalized to transcripts per million (TPM)
Assembly: danRer11
Supplementary files format and content: csv file with TPM counts

organism: Danio rerio

source_name: Fin tip

extract_protocol:
Tissue was homogenized with a stainless-steel bead (5mm, Cat. No. 69989) in Tri-Reagent. RNA was extracted by cholorform followed by an isopropanol precipitation. Remaining DNA was digested by DNase. RNA was purified with a Zymo RNA Clean & Concentrator Kit.
Library preparation was performed by BGI Genomics.

value: Fin tip

tag: time point


title: RPE1_Classic_P3_S2

description: Library name: RPE1_Classic_P3_S2


title: DS_VP64_R4_fraction_5

description: Library name: DS_sample_62


title: Telencephalon_RU486_WT_rep5

description:
Library name: Telencephalon_RU486_WT_rep5_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: WT_fin_distal_tip_7_dpa_rep2

description: Library name: day7_REP2


title: DS_VP64_R4_fraction_4

description: Library name: DS_sample_61


title: WT_fin_distal_tip_7_dpa_rep1

description: Library name: day7_REP1


title: Telencephalon_RU486_WT_rep4

description:
Library name: Telencephalon_RU486_WT_rep4_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: DS_VP64_R4_fraction_3

description: Library name: DS_sample_60


title: RPE1_Classic_P2_TR4

description: Library name: RPE1_Classic_P2_TR4


title: DS_VP64_R4_fraction_2

description: Library name: DS_sample_59


title: Telencephalon_RU486_WT_rep2

description:
Library name: Telencephalon_RU486_WT_rep2_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: WT_fin_distal_tip_3_dpa_rep2

description: Library name: day3_REP2


title: Telencephalon_RU486_WT_rep6

description:
Library name: Telencephalon_RU486_WT_rep6_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: S48 scTCR-seq

description:
Library name: cohort1_29
10x TCR 5' V2 HT (High Throughput)

value: Tumor

value: BCC

value: IC


title: WhiteFat_RU486_WT_rep4

description:
Library name: WhiteFat_RU486_WT_rep4_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

value: WhiteFat

value: WT

value: 3 months


title: RNAseq_Ch8_821_R2

description: Library name: RNAseq_sample_8


title: DS_VP64_R4_fraction_1

description: Library name: DS_sample_58


title: RPE1_Classic_P2_TR2

description: Library name: RPE1_Classic_P2_TR2


title: WhiteFat_RU486_WT_rep2

description:
Library name: WhiteFat_RU486_WT_rep2_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: S54 scTCR-seq

description:
Library name: cohort1_25
10x TCR 5' V2 HT (High Throughput)


title: Telencephalon_RU486_WT_rep1

description:
Library name: Telencephalon_RU486_WT_rep1_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: WT_fin_distal_tip_3_dpa_rep1

description: Library name: day3_REP1


title: DS_VP64_R3_fraction_5

description: Library name: DS_sample_57


title: RPE1_Classic_P3_S1

description: Library name: RPE1_Classic_P3_S1


title: RPE1_Classic_P2_TR1

description: Library name: RPE1_Classic_P2_TR1


title: Muscle_DMSOforRU486_WT_rep6

description:
Library name: Muscle_DMSOforRU486_WT_rep6_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

source_name: Muscle

value: Muscle


title: DS_VP64_R3_fraction_4

description: Library name: DS_sample_56


title: S123

description:
Library name: cohort2_11
10x Genomics Gene Expression 5' V2 HT (High Throughput)

data_processing:
Cell Ranger software version 7.1.0 was used to generate gene expression count matrices.
Sequencing data was aligned to the Human (GRCh38) 2020-A reference sequence.
Assembly: Human GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of cell barcodes
Supplementary files format and content: features.tsv.gz: list of feature IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data

extract_protocol:
After collection, specimens were immediately dissociated by using Human whole skin dissociation kit and Red Blood Cell Lysis Solution (10×) from Military Biotech. Dissociated cells were stained with APC conjugated CD45 (H130) mouse mAb from Cell Signaling. Then CD45 positive cells were sorted by using CytoFLEX SRT Cell Sorter for single cell sequencing.
Gene expression (GEX) single cell libraries were generated using the 10X Genomics Chromium Single Cell 5' v2 HT workflow with Feature Barcode technology.

tag: patient id

value: SCC

value: IS


title: WT_fin_distal_tip_14_dpa_rep1

description: Library name: day14_REP1


title: Muscle_DMSOforRU486_WT_rep5

description:
Library name: Muscle_DMSOforRU486_WT_rep5_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

value: Male


title: WT_fin_distal_tip_3_dpa_rep3

description: Library name: day3_REP3


title: DS_VP64_R3_fraction_3

description: Library name: DS_sample_55


title: Telencephalon_RU486_WT_rep3

description:
Library name: Telencephalon_RU486_WT_rep3_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: Lung, MNX CF, female, rep3

description: Library name: RSB527-12

value: lung

value: CF


title: S131

description:
Library name: cohort2_10
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: VS_Cas9_R3_fraction_2

description: Library name: VS_sample_13

value: erythropoietic

value: VS


title: K562_Classic_TR2

description: Library name: K562_Classic_TR2

value: myelogenous leukemia cell


title: Muscle_DMSOforRU486_WT_rep4

description:
Library name: Muscle_DMSOforRU486_WT_rep4_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: S140

description:
Library name: cohort2_9
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: DS_VP64_R3_fraction_2

description: Library name: DS_sample_54

value: gRNA transduction


title: WT_fin_distal_tip_10_dpa_rep2

description: Library name: day10_REP2

value: Fin tip


title: Muscle_DMSOforRU486_WT_rep3

description:
Library name: Muscle_DMSOforRU486_WT_rep3_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: DS_VP64_R3_fraction_1

description: Library name: DS_sample_53


title: S70

description:
Library name: cohort2_6
10x Genomics Gene Expression 5' V2 HT (High Throughput)

value: Tumor


title: Muscle_DMSOforRU486_WT_rep2

description:
Library name: Muscle_DMSOforRU486_WT_rep2_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: DS_VP64_R2_fraction_5

description: Library name: DS_sample_52


title: WT_fin_distal_tip_10_dpa_rep1

description: Library name: day10_REP1


title: S75

description:
Library name: cohort2_5
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: Muscle_DMSOforRU486_WT_rep1

description:
Library name: Muscle_DMSOforRU486_WT_rep1_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: Muscle_RU486_WT_rep6

description:
Library name: Muscle_RU486_WT_rep6_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: WT_fin_distal_tip_0_dpa_rep3

description: Library name: day0_REP3


title: DS_VP64_R2_fraction_4

description: Library name: DS_sample_51


title: Muscle_RU486_WT_rep5

description:
Library name: Muscle_RU486_WT_rep5_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: DS_VP64_R2_fraction_3

description: Library name: DS_sample_50


title: S110

description:
Library name: cohort2_24
10x Genomics Gene Expression 5' V2 HT (High Throughput)

value: BCC


title: WT_fin_distal_tip_0_dpa_rep1

description: Library name: day0_REP1


title: WT_fin_distal_tip_10_dpa_rep3

description: Library name: day10_REP3


title: S128

description:
Library name: cohort2_20
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: DS_VP64_R2_fraction_2

description: Library name: DS_sample_49


title: Muscle_RU486_WT_rep4

description:
Library name: Muscle_RU486_WT_rep4_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: Sprague Dawley hypothalamus SD

city: Dalian

first: Yanxiang

last: Qu

address: No.9 West Section, Lvshun South Road, Dalian, Liaoning Province

institute: Dalian Medical University

description:
Library name: XQN-2
10X genomics

data_processing:
Raw BCL files were converted to FASTQ using bcl2fastq. After quality filtering (reads with >3 N bases, >20% bases with Q<5, or adapter sequences removed), clean reads were aligned to the mRatBN7.2_V2 rat reference genome using Cell Ranger (v7.0.0) with default parameters. Cell Ranger count generated raw and filtered feature-barcode matrices for each sample. Doublets were removed using Scrublet (expected_doublet_rate = 0.07). High-quality cells were retained (genes >200, UMI counts >400, mitochondrial reads <20%) using Seurat. Downstream analysis was performed with Seurat (v3.1.5): data were normalized (LogNormalize, scale factor 10,000), and the top 2,000 variable genes were selected. PCA (30 PCs), UMAP visualization, and clustering (FindClusters, resolution = 1, SNN graph) were applied. Batch effects were corrected using FindIntegrationAnchors and IntegrateData. Differentially expressed genes were identified using FindAllMarkers (only.pos = TRUE, Wilcoxon test, min.pct = 0.25), with P values and adjusted P values computed. Cell types were annotated using SingleR against the Human Cell Landscape reference (Guo et al., 2020). GO, KEGG, and Reactome enrichment analyses were performed using ClusterProfiler (adjusted P < 0.05).
Assembly: mRatBN7.2_V2-
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: hypothalamus

extract_protocol:
The fresh hypothalamus tissue was homogenized using a Dounce homogenizer in ice-cold lysis buffer. The nuclei suspension was filtered through a 35-μm cell strainer to remove debris and aggregates. Nuclei were counted using a hemocytometer, and the concentration was adjusted to the target required for the 10x Genomics Chromium assay (approximately 1,000 nuclei/µL).
Single-nucleus libraries were prepared using the Chromium Single Cell 3' Reagent Kits (10x Genomics, v3.1) according to the manufacturer's protocol. Briefly, 10,000 nuclei were loaded onto the Chromium Controller to generate single-cell gel beads in emulsion (GEMs). The captured cells were lysed, and the released RNA was reverse-transcribed with primers containing poly-T, barcode, unique molecular identifiers (UMIs), and read 1 primer sequence in GEMs. Barcoded cDNA was purified and amplified by PCR. Adapter ligation was performed to add sample index and read 2 primer sequence. After quality control, the libraries were sequenced on the Illumina NovaSeq platform in 150 bp paired-end mode (Berry Genomics Corporation, Beijing, China).

value: hypothalamus

value: Sprague Dawley

value: SD


title: Muscle_RU486_WT_rep3

description:
Library name: Muscle_RU486_WT_rep3_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 or hg38 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2–3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at −80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.

value: WT

value: 3 months


title: Sprague Dawley hypothalamus Ctrl

description:
Library name: XQN-1
10X genomics

value: Ctrl


title: DS_VP64_R1_fraction_5

description: Library name: DS_sample_47


title: S129

description:
Library name: cohort2_7
10x Genomics Gene Expression 5' V2 HT (High Throughput)

value: IS


title: f2_24h_rep4

city: Geneva

first: Hongrui

last: Wang

address: 630 W. North Street

department: School of Integrative Plant Science, Horticulture section

institute: Cornell University

description: Library name: Sample 95

data_processing:
FastQC for quality control
BBDuk for removing adaptors and poly-A following the pipeline suggested by the manufacturer (https://www.lexogen.com/quantseq-data-analysis/)
STAR for gene level quantification using ‘-quantMode GeneCounts’
Low count gene filterig based on 'total gene count greater than sample number*10'
DESeq2 for variance stabilization transformation and gene expression normalization
WGCNA for gene co-expression analysis, noise gene filtering, module eigengene visualization and contrast generation
ORA for pathway enrichment analysis
Assembly: Vitis vinifera 12X.v2 genome with VCost.v3 annotation
Supplementary files format and content: One matrix table with raw gene counts for every gene and every sample without any filtering

organism: Vitis vinifera

source_name: bud

extract_protocol:
Total RNA was extracted using SpectrumTM Plant Total RNA Kit (Sigma Aldrich, St Louis, MO, USA) following the protocol suggested by the manufacturer
Libraries were constructed with Lexogen QuantSeq 3’mRNA-Seq Prep Kit (Lexogen, Greenland, NH, USA) following standard practices as a service provided by Cornell University Institute of Genomic Diversity (Ithaca, NY, USA). Sequencing of the libraries was accomplished using NextSeq500 (Illumina, Inc., San Diego, CA, USA) with 95 samples per lane at Cornell University Institute of Biotechnology (Ithaca, NY, USA). The read length was 85 bp.

value: bud

value: Cabernet Sauvignon

tag: field collection_date

tag: field chilling_(nc_model)

tag: field collection_id


title: DS_VP64_R1_fraction_4

description: Library name: DS_sample_46


title: S114

description:
Library name: cohort2_3
10x Genomics Gene Expression 5' V2 HT (High Throughput)

tag: tissue


title: f4_2h_rep3

description: Library name: Sample 94

tag: genotype


title: DS_VP64_R1_fraction_3

description: Library name: DS_sample_45


title: Muscle_RU486_WT_rep1

description:
Library name: Muscle_RU486_WT_rep1_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

value: Muscle

tag: strain

value: Male


title: f3_3d_rep3

description: Library name: Sample 93


title: Bone_DMSOforRU486_WT_rep6

description:
Library name: Bone_DMSOforRU486_WT_rep6_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

value: Bone

tag: Sex


title: DS_VP64_R1_fraction_2

description: Library name: DS_sample_44

value: erythropoietic


title: S144_1

description:
Library name: cohort1_53A
10x Genomics Gene Expression 5' V2 HT (High Throughput)

value: SCC


title: f3_7d_rep3

description: Library name: Sample 92


title: DS_VP64_R1_fraction_1

description: Library name: DS_sample_43

value: gRNA transduction


title: Bone_DMSOforRU486_WT_rep4

description:
Library name: Bone_DMSOforRU486_WT_rep4_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

tag: age


title: f4_4h_rep3

description: Library name: Sample 91


title: DS_KRAB_R4_fraction_5

description: Library name: DS_sample_42


title: S143

description:
Library name: cohort1_44
10x Genomics Gene Expression 5' V2 HT (High Throughput)

value: Tumor


title: Bone_DMSOforRU486_WT_rep3

description:
Library name: Bone_DMSOforRU486_WT_rep3_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz

tag: mouse id


title: Bone_DMSOforRU486_WT_rep2

description:
Library name: Bone_DMSOforRU486_WT_rep2_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: S108

description:
Library name: cohort1_20
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: DS_KRAB_R4_fraction_3

description: Library name: DS_sample_40

tag: cell line


title: f1_2h_rep3

description: Library name: Sample 89


title: S132_2

description:
Library name: cohort1_19C
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: WT_fin_distal_tip_14_dpa_rep2

description: Library name: day14_REP2

value: Fin tip


title: Bone_DMSOforRU486_WT_rep1

description:
Library name: Bone_DMSOforRU486_WT_rep1_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: DS_KRAB_R4_fraction_2

description: Library name: DS_sample_39

tag: cell type


title: S132_1

description:
Library name: cohort1_18
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: f1_24h_rep4

description: Library name: Sample 88


title: Bone_RU486_WT_rep6

description:
Library name: Bone_RU486_WT_rep6_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: f2_3d_rep4

description: Library name: Sample 87


title: WT_fin_distal_tip_0_dpa_rep2

description: Library name: day0_REP2


title: DS_KRAB_R4_fraction_1

description: Library name: DS_sample_38

tag: batch


title: S130

description:
Library name: cohort2_2
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: S138

description:
Library name: cohort1_32
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: Bone_RU486_WT_rep5

description:
Library name: Bone_RU486_WT_rep5_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: DS_VP64_R2_fraction_1

description: Library name: DS_sample_48

tag: treatment


title: DS_KRAB_R3_fraction_5

description: Library name: DS_sample_37


title: f2_7d_rep4

description: Library name: Sample 86


title: S115

description:
Library name: cohort1_45
10x Genomics Gene Expression 5' V2 HT (High Throughput)

tag: pathology

value: BCC


title: S112

description:
Library name: cohort2_19
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: Muscle_RU486_WT_rep2

description:
Library name: Muscle_RU486_WT_rep2_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: Bone_RU486_WT_rep4

description:
Library name: Bone_RU486_WT_rep4_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: f2_3d_rep3

description: Library name: Sample 85


title: DS_KRAB_R3_fraction_4

description: Library name: DS_sample_36


title: S117

description:
Library name: cohort1_12
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: f4_7d_rep3

description: Library name: Sample 84


title: S144_2

description:
Library name: cohort1_53B_53C
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: DS_KRAB_R3_fraction_3

description: Library name: DS_sample_35


title: Bone_RU486_WT_rep2

description:
Library name: Bone_RU486_WT_rep2_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: S118

description:
Library name: cohort1_11
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: f4_3d_rep2

description: Library name: Sample 83


title: DS_KRAB_R3_fraction_2

description: Library name: DS_sample_34


title: Bone_RU486_WT_rep1

description:
Library name: Bone_RU486_WT_rep1_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: S111

description:
Library name: cohort1_17
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: Bone_DMSOforRU486_WT_rep5

description:
Library name: Bone_DMSOforRU486_WT_rep5_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: f2_7d_rep3

description: Library name: Sample 82


title: DS_KRAB_R3_fraction_1

description: Library name: DS_sample_33


title: S39

description:
Library name: cohort1_1
10x Genomics Gene Expression 5' V2 HT (High Throughput)

value: IC


title: Bone_RU486_WT_rep3

description:
Library name: Bone_RU486_WT_rep3_RNA-seq
RU486 versus DMSO in WT mice (five tissues)
RNAseq_WT_RU486_vs_DMSO_count.txt.gz


title: Correlation_WhiteFat_WT_female_rep3

description:
Library name: Correlation_WhiteFat_WT_female_rep3_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz

value: WhiteFat

value: Female

value: 6.5 months


title: S142

description:
Library name: cohort1_46
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: f4_7d_rep2

description: Library name: Sample 81


title: DS_KRAB_R2_fraction_5

description: Library name: DS_sample_32


title: Correlation_WhiteFat_WT_female_rep2

description:
Library name: Correlation_WhiteFat_WT_female_rep2_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz

value: WT

value: 4 months


title: f1_4h_rep3

description: Library name: Sample 80

value: bud


title: S17

description:
Library name: cohort1_10
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: DS_KRAB_R2_fraction_4

description: Library name: DS_sample_31


title: S15

description:
Library name: cohort1_50
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: f2_2h_rep3

description: Library name: Sample 79

value: Cabernet Sauvignon


title: Correlation_WhiteFat_WT_female_rep1

description:
Library name: Correlation_WhiteFat_WT_female_rep1_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz

value: 3.5 months


title: DS_KRAB_R2_fraction_3

description: Library name: DS_sample_30


title: S7

description:
Library name: cohort1_4
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: Correlation_WhiteFat_KO_female_rep3

description:
Library name: Correlation_WhiteFat_KO_female_rep3_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz

value: Mecp2 KO


title: f6_24h_rep3

description: Library name: Sample 78


title: DS_KRAB_R2_fraction_2

description: Library name: DS_sample_29


title: S49

description:
Library name: cohort1_5a
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: Correlation_WhiteFat_KO_female_rep2

description:
Library name: Correlation_WhiteFat_KO_female_rep2_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz


title: f3_3d_rep2

description: Library name: Sample 77


title: f4_3d_rep3

description: Library name: Sample 90


title: DS_KRAB_R2_fraction_1

description: Library name: DS_sample_28


title: DS_KRAB_R4_fraction_4

description: Library name: DS_sample_41


title: Correlation_WhiteFat_KO_female_rep1

description:
Library name: Correlation_WhiteFat_KO_female_rep1_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz


title: DS_KRAB_R1_fraction_5

description: Library name: DS_sample_27


title: S56

description:
Library name: cohort1_6
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: f3_0h_rep3

description: Library name: Sample 76


title: Lung, MNX CH, female, rep2

description: Library name: RSB491-05

value: lung

value: CH


title: S48

description:
Library name: cohort1_29
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: Correlation_Thymus_WT_male_rep3

description:
Library name: Correlation_Thymus_WT_male_rep3_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz

value: Thymus

value: Male

value: 8 weeks


title: f2_0h_rep3

description: Library name: Sample 75


title: DS_KRAB_R1_fraction_4

description: Library name: DS_sample_26

value: erythropoietic

value: gRNA transduction


title: S51

description:
Library name: cohort1_23
10x Genomics Gene Expression 5' V2 HT (High Throughput)

value: Tumor

value: BCC

value: IC


title: Correlation_Thymus_WT_male_rep2

description:
Library name: Correlation_Thymus_WT_male_rep2_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz


title: f2_24h_rep3

description: Library name: Sample 74


title: DS_KRAB_R1_fraction_3

description: Library name: DS_sample_25


title: S47

description:
Library name: cohort1_7
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: Correlation_Thymus_WT_male_rep1

description:
Library name: Correlation_Thymus_WT_male_rep1_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz


title: f2_0h_rep2

description: Library name: Sample 73


title: DS_KRAB_R1_fraction_2

description: Library name: DS_sample_24


title: f4_2h_rep2

description: Library name: Sample 72


title: S53

description:
Library name: cohort1_24
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: Correlation_Thymus_KO_male_rep3

description:
Library name: Correlation_Thymus_KO_male_rep3_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz


title: Correlation_Thymus_KO_male_rep2

description:
Library name: Correlation_Thymus_KO_male_rep2_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz


title: S54

description:
Library name: cohort1_25
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: DS_KRAB_R1_fraction_1

description: Library name: DS_sample_23


title: f6_0h_rep3

description: Library name: Sample 71


title: DS_Cas9_R4_fraction_5

description: Library name: DS_sample_22


title: Correlation_Thymus_KO_male_rep1

description:
Library name: Correlation_Thymus_KO_male_rep1_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz


title: S46

description:
Library name: cohort1_8
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: 35_BCC_IS_Cohort2

type: RNA

first: Veena

last: Kochat

state: TX

address: 1901 East Road

department: Genomic Medicine

institute: The University of Texas MD Anderson Cancer Center

description: XENIUM

data_processing:
Raw images were processed using Xenium software to generate spatially resolved transcript maps for downstream analysis.
Raw Xenium images were processed with 10x Genomics Xenium software to detect transcripts and generate spatially resolved gene expression matrices. Low-confidence spots were filtered, and background correction was applied. Spatial transcriptomic analyses, including transcript density mapping, cell type annotation, and niche composition analysis, were performed in R using standard packages and custom scripts. Data visualization was performed using ggplot2 and Xenium overlays.
cell_boundaries.csv.gz : Polygon coordinates defining the boundaries of each segmented cell. Used for assigning transcripts to cells and generating cell-level features.
cell_feature_matrix.h5 : Cell-by-feature matrix (containing counts of transcripts per cell and other computed features.
cells.csv.gz : Metadata for each cell, including cell IDs, centroids to link transcripts to cell boundaries.
gene_panel.json : List of genes targeted in the Xenium panel, including probe sequences and gene IDs for mapping transcript counts to gene names.
morphology.ome.tif : High-resolution tissue morphology image (OME-TIFF format). Used for overlaying transcript and cell data on tissue morphology.
transcripts.parquet : Coordinates and gene assignments for individual transcripts for spatial plotting and cell-level assignment.
transcripts.csv.gz : Coordinates and gene assignments for individual transcripts  in compressed CSV format

extract_protocol:
TMA samples were embedded into FFPE blocks and 5um sections were prepared. Frozen tissues were OCT embedded and 10um cryosections were prepared.
Tissue specimens were sectioned at 5–10 µm thickness and mounted onto Xenium-compatible slides (10x Genomics). Sections were fixed in 4% paraformaldehyde, permeabilized using a tissue-optimized buffer, and hybridized with target-specific probes according to the manufacturer’s instructions (10x Genomics Xenium User Guide). Signal amplification and labeling were performed in situ, followed by high-resolution imaging on the Xenium instrument.

value: IS

value: Cohort 2


title: Lung, MNX HC, female, rep3

description: Library name: RSB491-03

value: HC


title: f6_3d_rep4

description: Library name: Sample 70

value: bud


title: DS_Cas9_R4_fraction_4

description: Library name: DS_sample_21


title: f3_7d_rep2

description: Library name: Sample 69

value: Cabernet Sauvignon


title: SC9-54_BCC_IC_scRNA-seq

description: Library name: SC9-54_scRNA-seq

data_processing:
Initially, the raw multiome data comprising both gene expression and chromatin accessibility fragments were processed using 10x Genomics Cell Ranger ARC. The scRNAseq data from multiple samples were imported using import10xFeatureMatrix. For the ATAC modality, low-quality cells defined as those with TSS enrichment less than 5, fewer than 2,500 fragments, or missing RNA UMIs were filtered out. Cell barcodes were used to match and integrate scRNA-seq and scATAC-seq data in ArchR, retaining only shared cells using subsetArchRProject(). Gene expression data were incorporated with matched RNA constraints, and iterative LSI was applied separately to both RNA and ATAC matrices for dimensionality reduction. A combined low-dimensional embedding was then generated followed by UMAP visualization and clustering. Differential gene activity gene score matrix and chromatin accessibility peak matrix were identified, peaks calling was performed using MACS2. Subsequently, motif enrichment analysis was conducted using ENCODE and HOMER annotations to identify transcription factor binding patterns across clusters.
Assembly: GRCh38
Supplementary files format and content: atac_fragments.tsv.gz
Supplementary files format and content: atac_fragments.tsv.gz.tbi
Supplementary files format and content: filtered_feature_bc_matrix.h5

extract_protocol:
From frozen tissues nuclei were isolated using the Chromium Nuclei Isolation Kit from 10X genomics (PN-1000493) based on the manufacturer's protocol.
Single nuclei suspensions were processed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (10x Genomics, PN: 1000283) platform following the manufacturer’s protocol, generating paired ATAC and gene expression libraries for each sample.


title: DS_Cas9_R4_fraction_3

description: Library name: DS_sample_20


title: DS_Cas9_R4_fraction_2

description: Library name: DS_sample_19


title: Correlation_Muscle_WT_male_rep3

description:
Library name: Correlation_Muscle_WT_male_rep3_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz

value: Muscle

value: WT


title: S55

description:
Library name: cohort1_9
10x Genomics Gene Expression 5' V2 HT (High Throughput)


title: f1_7d_rep3

description: Library name: Sample 68


title: Correlation_Muscle_WT_male_rep2

description:
Library name: Correlation_Muscle_WT_male_rep2_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz


title: SC8-4R_BCC_IC_scRNA-seq

description: Library name: SC8-4R_scRNA-seq


title: Correlation_Muscle_WT_male_rep1

description:
Library name: Correlation_Muscle_WT_male_rep1_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz


title: DS_Cas9_R4_fraction_1

description: Library name: DS_sample_18


title: f6_0h_rep2

description: Library name: Sample 67


title: Correlation_Muscle_KO_male_rep3

description:
Library name: Correlation_Muscle_KO_male_rep3_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz

value: Mecp2 KO


title: f6_3d_rep3

description: Library name: Sample 66


title: SC7-19_SCC_IS_scRNA-seq

description: Library name: SC7-19_scRNA-seq

value: SCC


title: DS_Cas9_R3_fraction_5

description: Library name: DS_sample_17


title: SC6-68_BCC_IS_scRNA-seq

description: Library name: SC6-68_scRNA-seq


title: Correlation_Muscle_KO_male_rep2

description:
Library name: Correlation_Muscle_KO_male_rep2_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz


title: f4_0h_rep3

description: Library name: Sample 65


title: DS_Cas9_R3_fraction_4

description: Library name: DS_sample_16


title: f3_4h_rep3

description: Library name: Sample 64


title: DS_Cas9_R3_fraction_3

description: Library name: DS_sample_15


title: SC5-60_SCC_IS_scRNA-seq

description: Library name: SC5-60_scRNA-seq


title: SC4-25_BCC_IC_scRNA-seq

description: Library name: SC4-25_scRNA-seq


title: Correlation_Muscle_KO_male_rep1

description:
Library name: Correlation_Muscle_KO_male_rep1_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz


title: Correlation_Bone_WT_male_rep3

description:
Library name: Correlation_Bone_WT_male_rep3_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz

value: Bone


title: f6_4h_rep3

description: Library name: Sample 63


title: DS_Cas9_R3_fraction_2

description: Library name: DS_sample_14


title: SC3-38_BCC_IC_scRNA-seq

description: Library name: SC3-38_scRNA-seq


title: Correlation_Bone_WT_male_rep2

description:
Library name: Correlation_Bone_WT_male_rep2_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz

value: Male


title: f4_0h_rep2

description: Library name: Sample 62


title: DS_Cas9_R3_fraction_1

description: Library name: DS_sample_13


title: SC10-64_BCC_IS_scRNA-seq

description: Library name: SC10-64_scRNA-seq


title: Correlation_Bone_WT_male_rep1

description:
Library name: Correlation_Bone_WT_male_rep1_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz

value: 8 weeks


title: f1_24h_rep3

description: Library name: Sample 61


title: 23_SCC_IS_Cohort2

description: XENIUM


title: DS_Cas9_R2_fraction_5

description: Library name: DS_sample_12

value: erythropoietic


title: LymphNode_RU486_KO_rep5

description:
Library name: LymphNode_RU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

source_name: LymphNode

value: LymphNode

value: 2 months


title: SC9-54_BCC_IC_scATAC-seq

description: Library name: SC9-54_scATAC-seq

library_source: genomic single cell

value: Tumor

value: BCC


title: Correlation_Bone_KO_male_rep3

description:
Library name: Correlation_Bone_KO_male_rep3_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz


title: DS_Cas9_R2_fraction_4

description: Library name: DS_sample_11

value: gRNA transduction


title: f3_7d_rep1

description: Library name: Sample 60


title: SC8-4R_BCC_IC_scATAC-seq

description: Library name: SC8-4R_scATAC-seq

value: IC


title: Correlation_Bone_KO_male_rep2

description:
Library name: Correlation_Bone_KO_male_rep2_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz


title: f1_7d_rep2

description: Library name: Sample 59


title: SC7-19_SCC_IS_scATAC-seq

description: Library name: SC7-19_scATAC-seq

value: IS


title: DS_Cas9_R2_fraction_3

description: Library name: DS_sample_10


title: Correlation_Bone_KO_male_rep1

description:
Library name: Correlation_Bone_KO_male_rep1_RNA-seq
KO versus WT (four tissues for correlation analysis with pathological indicators)
RNAseq_correlation_KO_vs_WT_count.txt.gz


title: f1_7d_rep1

description: Library name: Sample 58

value: bud


title: DS_Cas9_R2_fraction_2

description: Library name: DS_sample_9


title: SC6-68_BCC_IS_scATAC-seq

description: Library name: SC6-68_scATAC-seq


title: f6_24h_rep2

description: Library name: Sample 57

value: Cabernet Sauvignon


title: NR3C1_Telencephalon_WTforOE

description:
Library name: NR3C1_Telencephalon_WTforOE_CUTnTag
CUT&Tag

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were aligned to mm10 using bowtie2 (v2.5.2). Reads with quality > 2 were selected and sorted by query names. BAM files were converted to BEDPE files then to fragment files (sorted BED files). Fragments in the blacklist regions of mm10 (https://www.encodeproject.org/files/ENCFF547MET/) were removed. BED files were converted to BW files for subsequent visualization.
The raw sorted BED files (blacklist regions were not removed) are supported as supplementary files for individual samples.
Assembly: mm10
Supplementary files format and content: BED  files including sorted fragments
Library strategy: CUT&Tag

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at −80°C.
Concanavalin A (ConA) coated magnetic beads were freshly activated with Ca²⁺ and Mn²⁺. Nuclei were extracted and a total of 10,000 nuclei were incubated with activated ConA beads. Supernatant was next removed, and beads were incubated with antibody (1:50) on a rotator at 4°C overnight, followed by incubated with secondary antibody (1:100) for 1 hr at room temperature. Beads were washed three times and suspended in dig300-wash buffer pre-mixed with pG-Tn5 (1:100), incubated for 1 hr at room temperature. After washing beads for three times, tag buffer was added to each well, then incubated on a rotator at 37 °C for 1 hr. After centrifugation, beads were washed once and resuspended. Lysis buffer was added to each well, and incubated for 2 hr at 65 °C. After adding 10% Tween20, TruePrep CUT&Tag Amplification Mix (Vazyme), 10 mM MGI-P5 (or ilu-P5), and 10 mM MGI-P7 (or ilu-i7) primers were added. Then PCR program was performed. Finally, 1.5 × VAHTS DNA Clean Beads were used to purify the library.

value: Telencephalon

tag: antibody

value: FVB/NJ

value: 3 months


title: NR3C1_Telencephalon_OE

description:
Library name: NR3C1_Telencephalon_OE_CUTnTag
CUT&Tag

value: MECP2 OE


title: DS_Cas9_R2_fraction_1

description: Library name: DS_sample_8


title: SC5-60_SCC_IS_scATAC-seq

description: Library name: SC5-60_scATAC-seq

value: SCC


title: DS_Cas9_R1_fraction_5

description: Library name: DS_sample_7


title: f4_4h_rep2

description: Library name: Sample 56


title: SC4-25_BCC_IC_scATAC-seq

description: Library name: SC4-25_scATAC-seq


title: NR3C1_Pituitary_WTforOE

description:
Library name: NR3C1_Pituitary_WTforOE_CUTnTag
CUT&Tag

source_name: Pituitary

value: Pituitary

value: WT

value: Male


title: f2_0h_rep1

description: Library name: Sample 55


title: DS_Cas9_R1_fraction_4

description: Library name: DS_sample_6

value: erythropoietic


title: SC3-38_BCC_IC_scATAC-seq

description: Library name: SC3-38_scATAC-seq


title: DS_Cas9_R1_fraction_3

description: Library name: DS_sample_5


title: f6_7d_rep3

description: Library name: Sample 54


title: NR3C1_Pituitary_OE

description:
Library name: NR3C1_Pituitary_OE_CUTnTag
CUT&Tag


title: SC10-64_BCC_IS_scATAC-seq

description: Library name: SC10-64_scATAC-seq