title: 2. GM0101 (AbpAB) T4 phage DNA

first: Amy

middle: Si-Ying

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

description: Library name: 2. GM0101 (AbpAB) T4 phage DNA

data_processing:
Paired-end reads were quality and adapter trimmed using Cutadapt to remove adapter sequences, poly-A/T, and low-quality bases (Q<30), retaining only reads ≥20 nt in length.
Cutom genome indices were built from FASTA files using bowtie2-build. Reads were aligned to either pGEM9z plasmid or T4 phage reference genomes using Bowtie2 to produce SAM alignment files.
SAM files were converted to sorted and indexed BAM format using Samtools (1.21)
Fragment lengths and strand-specific 5 prime end counts were extracted using the Bioconductor Rsamtools package in R (4.3.1).
The top 100 5 prime ends were used to extract ±10 nucleotide windows from the reference genome using Bsgenome and GenomicRanges R packages. Fasta sequences were saved for downstream WebLogo motif analysis.
Assembly: pGEM9z plasmid
Assembly: T4 phage
Supplementary files format and content: BigWig (.bw) files for each sample contain read coverage tracks generated from BAM files.

organism: Pseudomonas aeruginosa

source_name: bacteria

extract_protocol:
1 M Tris-HCl pH 8.0, 10% SDS, and 0.5 M EDTA pH 8.0 were added to the cleavage reaction followed by 10% SDS to reach 500 µL total volume. 500 µL of Phenol:Chlorofom:Isoamyl Alchol 25:24:1 Saturated with 10 mM Tris, pH 8.0, 1 mM EDTA (Sigma Aldrich) was added, vortexed, centrifuged, and the resulting aqueous phage was added to 50 µL 3M NaOAc and 1 µL 20 mg mL−1 glycogen. 1 mL of 100% ethanol was added, vortexed, and samples were stored at −20°C overnight. The following day, samples were pelleted and washed with 70% ethanol three times before resuspension in RNase-free dH2O.
Sequencing libraries were made from single stranded DNA fragments using a xGEN kit (IDT) and sequenced on a NextSeq500

treatment_protocol: Nuclease-NTPase protein concentrations were optimized to generate 100–600 bp DNA fragments required for DNA sequencing. 25 nM PaAbpAB, 75 nM BtHachiman, 1 µM EcPD-T4-8 were individually incubated with 400 ng pGEM9Z plasmid in a 40 µL reactions with DNA cleavage buffer (20 mM Tris-HCl pH 7.5, 150 mM KCl, 5 mM MgCl2, 1 mM MnCl2, 1 mM DTT). 25 nM PaAbpAB, 1 µM BmAzaca, 25 nM BtHachiman, and 1 µM EcPD-T4-8 were individually incubated with 400 ng phage T4 DNA in 40 µL reactions with DNA cleavage buffer. Proteins were diluted in gel filtration buffer supplemented with 10% glycerol. Reactions were incubated at 37°C for 30 min followed by 100 µg mL−1 Proteinase K treatment at 50°C for 30 min.

value: bacteria


title: LV, BZ, patch, 4wks, rep3

status: Public on Feb 18 2026

type: SRA

city: Suita

first: Kosuke

last: Torigata

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine, Department of Cardiovascular Surgery

country: Japan

institute: The University of Osaka

description:
Library name: LV_BZ_patch_4wks_rep3
ischemic border zone

library_source: transcriptomic

data_processing:
Whole transcriptome sequencing was applied to the RNA samples on an Illumina HiSeq 2500 platform in a 75-base single-end mode. Illumina Casava ver.1.8.2 software was used for base calling. Obtained reads were quality filtered by FastQC ver. 0.7.2 and Trim Galore ver. 0.5.0, then aligned to in silico combined human (GRCh38)-rat (Rattus norvegicus, Rnor_6.0) by HISAT2 ver.2.1.026 with default setting as described previously. The uniquely aligned reads were annotated to genes and calculated read-count by featureCounts function of Subread ver. 1.6.248 for human and rat, respectively. For data deposition, reads were aligned to the rat reference genome (Rnor_6.0), and uniquely mapped reads (MAPQ >= 60) were retained to ensure species-specificity. Gene-level count tables used in the published analyses are provided as processed data files to ensure reproducibility of the reported results.
Assembly: rat (Rattus norvegicus, Rnor_6.0) and human (GRCh38)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Rattus norvegicus

source_name: left ventricular

growth_protocol: Six to eight week old male nude rats (F344/NJcl-rnu/rnu) were anesthetized with endotracheal intubation using isoflurane (2%). A left thoracotomy was performed, and the left anterior descending artery was permanently ligated with a 5-0 nylon monofilament. Successful ligation was confirmed by the color change of the anterior left ventricular (LV) wall. After each surgery, all rats were allowed to recover in individual temperature-controlled cages. These rats were maintained in a specific pathogen-free room in our animal facility on a 12-hour light/12-dark cycle with free access to food and water. Rats were euthanized and the heart specimens were harvested at predetermined timepoints.

extract_protocol:
Each snap frozen heart tissue (timepoint; Day3, 1wk, 4wks, tissue; IZ, BZ, RZ for each group) were homogenized in Buffer RLT by disrupter MS-100R (TOMY). Total-RNA was extracted using RNeasy Mini Kit (74106, Qiagen) according to the manufacturer’s instructions. The quality of purified RNAs was assessed by Bioanalyzer 2100 (Agilent Technologies).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (RS-122-2101, Illumina) according to the manufacturer’s instructions.

treatment_protocol: After 1 week of LAD-ligation, rats underwent re-thoracotomy for the exposed pericardial space and were then randomly assigned into a control (without patch transplantation) group or a patch transplanted group. hiPSC-derived CM patches were transplanted over the epicardium of the anterior and lateral left-ventricular walls. hiPSC-derived CM patches were spread manually to cover both infarct and border areas of the heart and fixed by covering with pericardial membrane. The chest was closed with a 4-0 nylon monofilament.

tag: genotype

tag: tissue

value: left ventricular

tag: condition

value: myocaridal infarction

tag: treatment

value: hiPSC-derived CM patch

tag: time

value: 4 weeks


title: mesc_rad21_depletion_IAA-6h_104, Smart-seq3

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv

library_source: transcriptomic single cell

data_processing:
Smart-seq3 data were processed using zUMIs (https://github.com/sdparekh/zUMIs).
Bulk RNA-seq data were mapped to human reference genome using STAR and RSEM was used to calculate mRNA count for each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA counts for each cell and sample
Supplementary files format and content: tab-delimited text files include cell barcode and sample information for Smart-seq3

molecule: polyA RNA

organism: Mus musculus

source_name: mouse embryonic stem cell

extract_protocol:
Isolated single cell was lysed wih gentle lysis buffer (containing 0.45% NP-40), and the supernant was collected for the construction of sequencing library.
Collected supernant was amplified with standard Smart-seq3 protocol, then perform library preparation with homemade Tn5 transposase.
Smart-seq3 & bulk RNA-seq

tag: cell type

value: mouse embryonic stem cell

value: IAA (6h)


title: 1. GM0101 (AbpAB) pGEM9z

city: Boston

last: Lee

state: MA

country: USA

description: Library name: 1. GM0101 (AbpAB) pGEM9z

library_source: other

molecule: other

tag: strain


title: mesc_rad21_depletion_IAA-6h_103, Smart-seq3


title: Tetraploid ATAC-seq Replicate 1

city: Baoding

first: Haoyuan

last: Dong

state: Prof.

address: Lekai South Street

institute: Hebei Agricultural University

description: Library name: sample_29

library_source: genomic

data_processing:
Raw sequencing reads were trimmed using fastp (version 0.21.0) to remove adapters and low-quality bases.
fastp (v0.21.0) trimming; RNA-seq: HISAT2 (v2.2.1, --dta --very-sensitive) → SAMtools (v1.3.1, MAPQ>10) → Picard (v2.16.0) dedup → StringTie (v1.3.5) TPM + featureCounts (v2.0.1) counts; ChIP/ATAC: Bowtie2 (v2.11.1, -X1000) → SAMtools (v1.3.1, MAPQ>10) → Picard (v2.16.0) dedup → MACS2 (v2.2.7.1) peak calling → bigWig.
Assembly: B. rapa reference genome (B_rapa.fa).
Supplementary files format and content: FASTQ, BAM, TPM matrices, bigWig

molecule: genomic DNA

organism: Brassica rapa

source_name: leaf

growth_protocol: Monoploid, diploid, and autotetraploid Brassica rapa were propagated by tissue culture, transplanted to greenhouses (Hebei Agricultural Univ., Baoding, China).

extract_protocol:
RNA: TRIzol (Invitrogen). ChIP: chromatin crosslinking + sonication. ATAC: nuclei isolation + Tn5 transposition.
RNA-seq: Berry Genomics, standard Illumina protocol. ChIP-seq: antibodies H3K27me3 (Abcam), H3K4me3 (Millipore), H3K27ac (Abclonal); TransGen kit, Illumina NovaSeq PE150. ATAC-seq: standard protocol, Illumina NovaSeq PE150.

treatment_protocol: At 60 d after sowing (heading stage), 2nd–3rd inner young leaves were collected (10:00–11:00 am).

value: leaf


title: LV, RZ, control, 4wks, rep2

description:
Library name: LV_RZ_control_4wks_rep2
uninjured remote myocardium

value: untransplanted sham control


title: 00078A2478

city: La Jolla

first: Daniel

last: Munro

state: CA

address: 9500 Gilman Drive

department: Psychiatry

institute: UC San Diego

description: Library name: 00078A2478

data_processing:
Expression levels were quantified using kallisto
Assembly: GRCr8
Supplementary files format and content: Log2-transformed read counts per gene per sample in BED format. Start/end coordinates indicate only the gene's TSS coordinate.

source_name: whole brain hemisphere

growth_protocol: Naive outbred laboratory rats

extract_protocol:
RNA was extracted from frozen tissue microdissections using a TRIzol-based protocol after mechanical homogenization with a bullet blender to maximize tissue disruption and RNA yield.
RNA-seq libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina following polyA enrichment with the NEBNext Poly(A) mRNA Magnetic Isolation Module

treatment_protocol: No treatment

value: whole brain hemisphere


title: LV, BZ, patch, 4wks, rep2

description:
Library name: LV_BZ_patch_4wks_rep2
ischemic border zone


title: 00078A233D

description: Library name: 00078A233D


title: mesc_rad21_depletion_IAA-6h_102, Smart-seq3


title: Tetraploid ATAC-seq Replicate 2

description: Library name: sample_30


title: LV, RZ, control, 4wks, rep1

description:
Library name: LV_RZ_control_4wks_rep1
uninjured remote myocardium


title: 00078A25CF

description: Library name: 00078A25CF


title: mesc_rad21_depletion_IAA-6h_105, Smart-seq3


title: Diploid ATAC-seq Replicate 1

description: Library name: sample_16


title: 00078A22CE

description: Library name: 00078A22CE


title: Monoploid ATAC-seq Replicate 2

description: Library name: sample_5


title: Diploid ATAC-seq Replicate 2

description: Library name: sample_17


title: mesc_rad21_depletion_IAA-6h_101, Smart-seq3


title: LV, BZ, patch, 4wks, rep1

description:
Library name: LV_BZ_patch_4wks_rep1
ischemic border zone


title: LV, BZ, control, 4wks, rep2

description:
Library name: LV_BZ_control_4wks_rep2
ischemic border zone


title: LV, BZ, control, 4wks, rep3

description:
Library name: LV_BZ_control_4wks_rep3
ischemic border zone


title: ChIP-seq input Diploid_1

description: Library name: sample_24


title: 00078A22AF

description: Library name: 00078A22AF


title: mesc_rad21_depletion_IAA-6h_100, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_096, Smart-seq3


title: 00078A1C54

description: Library name: 00078A1C54


title: Monoploid ATAC-seq Replicate 1

description: Library name: sample_4


title: mesc_rad21_depletion_IAA-6h_098, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_099, Smart-seq3


title: ChIP-seq input Monoploid_1

description: Library name: sample_12


title: ChIP-seq input Diploid_2

description: Library name: sample_25


title: LV, BZ, control, 4wks, rep1

description:
Library name: LV_BZ_control_4wks_rep1
ischemic border zone


title: LV, IZ, patch, 4wks, rep3

description:
Library name: LV_IZ_patch_4wks_rep3
middle of ischemic lesion


title: mesc_rad21_depletion_IAA-6h_097, Smart-seq3


title: 00078A1A70

description: Library name: 00078A1A70


title: 00079298CC

description: Library name: 00079298CC


title: ChIP-seq input Monoploid_2

description: Library name: sample_13


title: LV, IZ, patch, 4wks, rep2

description:
Library name: LV_IZ_patch_4wks_rep2
middle of ischemic lesion


title: 00078A1A62

description: Library name: 00078A1A62


title: LV, IZ, patch, 4wks, rep1

description:
Library name: LV_IZ_patch_4wks_rep1
middle of ischemic lesion


title: ChIP-seq input Tetraploid_2

description: Library name: sample_38


title: 00078A1A5D

description: Library name: 00078A1A5D


title: 00078A1A59

description: Library name: 00078A1A59


title: mesc_rad21_depletion_IAA-6h_094, Smart-seq3


title: ChIP-seq input Tetraploid_1

description: Library name: sample_37


title: LV, IZ, control, 4wks, rep2

description:
Library name: LV_IZ_control_4wks_rep2
middle of ischemic lesion


title: 00078A1A41

description: Library name: 00078A1A41


title: LV, IZ, control, 4wks, rep1

description:
Library name: LV_IZ_control_4wks_rep1
middle of ischemic lesion


title: LV, IZ, control, 4wks, rep3

description:
Library name: LV_IZ_control_4wks_rep3
middle of ischemic lesion


title: 00078A1A9A

description: Library name: 00078A1A9A


title: LV, RZ, patch, 1wk, rep3

description:
Library name: LV_RZ_patch_1wk_rep3
uninjured remote myocardium

value: 1 week


title: mesc_rad21_depletion_IAA-6h_093, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_095, Smart-seq3


title: 00078A19CC

description: Library name: 00078A19CC


title: mesc_rad21_depletion_IAA-6h_091, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_092, Smart-seq3


title: 00078A19AE

description: Library name: 00078A19AE


title: Tetraploid H3K27ac Replicate 2

description: Library name: sample_34


title: LV, RZ, patch, 1wk, rep2

description:
Library name: LV_RZ_patch_1wk_rep2
uninjured remote myocardium


title: Tetraploid H3K27me3 Replicate 1

description: Library name: sample_35


title: Tetraploid H3K27me3 Replicate 2

description: Library name: sample_36


title: LV, RZ, patch, 1wk, rep1

description:
Library name: LV_RZ_patch_1wk_rep1
uninjured remote myocardium


title: 00078A1936

description: Library name: 00078A1936


title: mesc_rad21_depletion_IAA-6h_089, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv


title: Tetraploid H3K4me3 Replicate 2

description: Library name: sample_32


title: mesc_rad21_depletion_IAA-6h_090, Smart-seq3


title: LV, RZ, control, 1wk, rep3

description:
Library name: LV_RZ_control_1wk_rep3
uninjured remote myocardium


title: 00078A1924

description: Library name: 00078A1924


title: Tetraploid H3K4me3 Replicate 1

description: Library name: sample_31


title: Tetraploid H3K27ac Replicate 1

description: Library name: sample_33


title: mesc_rad21_depletion_IAA-6h_088, Smart-seq3


title: 00078A190D

description: Library name: 00078A190D


title: LV, RZ, control, 1wk, rep2

description:
Library name: LV_RZ_control_1wk_rep2
uninjured remote myocardium


title: Diploid H3K27me3 Replicate 2

description: Library name: sample_23


title: LV, RZ, control, 1wk, rep1

description:
Library name: LV_RZ_control_1wk_rep1
uninjured remote myocardium


title: mesc_rad21_depletion_IAA-6h_087, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_086, Smart-seq3


title: 00078A18F6

description: Library name: 00078A18F6


title: LV, BZ, patch, 1wk, rep3

description:
Library name: LV_BZ_patch_1wk_rep3
ischemic border zone


title: Diploid H3K27ac Replicate 2

description: Library name: sample_21


title: mesc_rad21_depletion_IAA-6h_085, Smart-seq3


title: LV, BZ, patch, 1wk, rep2

description:
Library name: LV_BZ_patch_1wk_rep2
ischemic border zone


title: Diploid H3K27me3 Replicate 1

description: Library name: sample_22


title: mesc_rad21_depletion_IAA-6h_084, Smart-seq3


title: 00078A1900

description: Library name: 00078A1900


title: Diploid H3K27ac Replicate 1

description: Library name: sample_20


title: 00078A18EC

description: Library name: 00078A18EC


title: mesc_rad21_depletion_IAA-6h_083, Smart-seq3


title: LV, BZ, patch, 1wk, rep1

description:
Library name: LV_BZ_patch_1wk_rep1
ischemic border zone


title: 00078A18C8

description: Library name: 00078A18C8


title: mesc_rad21_depletion_IAA-6h_082, Smart-seq3


title: 00078A186F

description: Library name: 00078A186F


title: mesc_rad21_depletion_IAA-6h_081, Smart-seq3


title: 00078A18BA

description: Library name: 00078A18BA


title: Diploid H3K4me3 Replicate 1

description: Library name: sample_18


title: LV, BZ, control, 1wk, rep3

description:
Library name: LV_BZ_control_1wk_rep3
ischemic border zone


title: Diploid H3K4me3 Replicate 2

description: Library name: sample_19


title: LV, BZ, control, 1wk, rep1

description:
Library name: LV_BZ_control_1wk_rep1
ischemic border zone


title: 00078A1835

description: Library name: 00078A1835


title: LV, IZ, patch, 1wk, rep3

description:
Library name: LV_IZ_patch_1wk_rep3
middle of ischemic lesion


title: Monoploid H3K27me3 Replicate 1

description: Library name: sample_10


title: mesc_rad21_depletion_IAA-6h_071, Smart-seq3


title: 00078A184F

description: Library name: 00078A184F


title: Monoploid H3K27ac Replicate 2

description: Library name: sample_9


title: mesc_rad21_depletion_IAA-6h_072, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_070, Smart-seq3


title: LV, BZ, control, 1wk, rep2

description:
Library name: LV_BZ_control_1wk_rep2
ischemic border zone


title: Monoploid H3K27ac Replicate 1

description: Library name: sample_8


title: Monoploid H3K27me3 Replicate 2

description: Library name: sample_11


title: LV, IZ, patch, 1wk, rep1

description:
Library name: LV_IZ_patch_1wk_rep1
middle of ischemic lesion


title: 00078A17AE

description: Library name: 00078A17AE


title: mesc_rad21_depletion_IAA-6h_069, Smart-seq3


title: 00078A17F3

description: Library name: 00078A17F3


title: Monoploid H3K4me3 Replicate 2

description: Library name: sample_7


title: LV, IZ, control, 1wk, rep3

description:
Library name: LV_IZ_control_1wk_rep3
middle of ischemic lesion


title: LV, IZ, patch, 1wk, rep2

description:
Library name: LV_IZ_patch_1wk_rep2
middle of ischemic lesion


title: 00078A18A7

description:
Library name: 00078A18A7
Original label before genotype mismatch fix: 00078A17A8


title: Monoploid H3K4me3 Replicate 1

description: Library name: sample_6


title: mesc_rad21_depletion_IAA-6h_068, Smart-seq3


title: LV, IZ, control, 1wk, rep2

description:
Library name: LV_IZ_control_1wk_rep2
middle of ischemic lesion


title: 00078A17A5

description: Library name: 00078A17A5


title: mesc_rad21_depletion_IAA-6h_066, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_067, Smart-seq3


title: 00078A178C

description: Library name: 00078A178C


title: 00078A19B2

description: Library name: 00078A19B2


title: Tetraploid RNA-seq Replicate 3

description: Library name: sample_28


title: Tetraploid RNA-seq Replicate 2

description: Library name: sample_27


title: LV, RZ, patch, Day3, rep3

description:
Library name: LV_RZ_patch_Day3_rep3
uninjured remote myocardium

value: Day 3


title: 00078A1771

description: Library name: 00078A1771


title: Tetraploid RNA-seq Replicate 1

description: Library name: sample_26


title: mesc_rad21_depletion_IAA-6h_065, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv


title: mesc_rad21_depletion_IAA-6h_064, Smart-seq3


title: Diploid RNA-seq Replicate 2

description: Library name: sample_15


title: 00078A1765

description: Library name: 00078A1765


title: LV, RZ, patch, Day3, rep2

description:
Library name: LV_RZ_patch_Day3_rep2
uninjured remote myocardium


title: LV, RZ, patch, Day3, rep1

description:
Library name: LV_RZ_patch_Day3_rep1
uninjured remote myocardium


title: LV, IZ, control, 1wk, rep1

description:
Library name: LV_IZ_control_1wk_rep1
middle of ischemic lesion


title: 00078A1750

description: Library name: 00078A1750


title: Monoploid RNA-seq Replicate 3

description: Library name: sample_3


title: 00078A16D0

description: Library name: 00078A16D0


title: mesc_rad21_depletion_IAA-6h_063, Smart-seq3


title: LV, RZ, control, Day3, rep3

description:
Library name: LV_RZ_control_Day3_rep3
uninjured remote myocardium


title: mesc_rad21_depletion_IAA-6h_062, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_060, Smart-seq3


title: LV, RZ, control, Day3, rep2

description:
Library name: LV_RZ_control_Day3_rep2
uninjured remote myocardium


title: LV, BZ, patch, Day3, rep3

description:
Library name: LV_BZ_patch_Day3_rep3
ischemic border zone


title: 00078A16CF

description: Library name: 00078A16CF


title: Monoploid RNA-seq Replicate 2

description: Library name: sample_2


title: mesc_rad21_depletion_IAA-6h_059, Smart-seq3


title: 00078A16DB

description: Library name: 00078A16DB


title: LV, RZ, control, Day3, rep1

description:
Library name: LV_RZ_control_Day3_rep1
uninjured remote myocardium


title: Diploid RNA-seq Replicate 1

description: Library name: sample_14


title: 00078A09BB

description: Library name: 00078A09BB


title: X.laevis NF54-55 spinal cord replicate 4

city: Klosterneuburg

first: Yuri

last: Ignatyev

address: Am Campus

country: Austria

institute: ISTA Austria

description:
Library name: 136133
10x Genomics
NF54_raw_feature_bc_matrix.h5
NF54_output_FPR_0.01_filtered.h5

data_processing:
10X CellRanger v5.0.0 was used for gene alignment to obtain gene-barcode matrices. The genome used for the reference was Xenla 9.2 (X. laevis v9). For stages NF37-38, NF47-48 and NF54-55 samples were aggregated with the cellranger function aggr
Ambient RNA was removed with CellBender v0.3.2 with 150 epochs and fpr of 0.01 from the raw features matrices produced by the cellranger function count.
Assembly: Xenla 9.2 (X. laevis v9)
Supplementary files format and content: raw feature matrices in h5 format after the cellranger function count
Supplementary files format and content: filtered features matrices in h5 format after cellbender

organism: Xenopus laevis

source_name: spinal cord

extract_protocol:
For all stages, acquired tissue was dissociated with liberase to obtain single-cell suspension according to previously published methods, and FACS-sorted for the presence of GFP using a BD FACS Aria III Cell Sorter.  All animals, except for one replicate from NF57-58 batch, were transgenic Xla.Tg(tubb2b:maptGFP)Amaya (EXRC), expressing GFP under neuron-specific tubb2b transcriptional control, enabling us to enrich neuronal cells.
Cells were processed following the Chromium Single Cell 3’ v3.1 protocol and Chromium Reagent Kits were used to prepare single-cell libraries (10X Genomics). Sequencing was performed on a NovaSeq (Illumina).

value: spinal cord

tag: developmental stage


title: X.laevis NF54-55 spinal cord replicate 3

description:
Library name: 136132
10x Genomics
NF54_raw_feature_bc_matrix.h5
NF54_output_FPR_0.01_filtered.h5


title: 00078A097C

description: Library name: 00078A097C


title: LV, BZ, patch, Day3, rep1

description:
Library name: LV_BZ_patch_Day3_rep1
ischemic border zone


title: Monoploid RNA-seq Replicate 1

description: Library name: sample_1


title: mesc_rad21_depletion_IAA-6h_057, Smart-seq3


title: 00078A093C

description: Library name: 00078A093C


title: LV, BZ, control, Day3, rep3

description:
Library name: LV_BZ_control_Day3_rep3
ischemic border zone


title: mesc_rad21_depletion_IAA-6h_056, Smart-seq3


title: X.laevis NF54-55 spinal cord replicate 1

description:
Library name: 136130
10x Genomics
NF54_raw_feature_bc_matrix.h5
NF54_output_FPR_0.01_filtered.h5


title: 00078A0841

description: Library name: 00078A0841


title: 00078A072C

description: Library name: 00078A072C


title: mesc_rad21_depletion_IAA-6h_058, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_055, Smart-seq3


title: LV, BZ, patch, Day3, rep2

description:
Library name: LV_BZ_patch_Day3_rep2
ischemic border zone


title: LV, BZ, control, Day3, rep2

description:
Library name: LV_BZ_control_Day3_rep2
ischemic border zone


title: X.laevis NF54-55 spinal cord replicate 2

description:
Library name: 136131
10x Genomics
NF54_raw_feature_bc_matrix.h5
NF54_output_FPR_0.01_filtered.h5


title: LV, IZ, patch, Day3, rep3

description:
Library name: LV_IZ_patch_Day3_rep3
middle of ischemic lesion


title: LV, BZ, control, Day3, rep1

description:
Library name: LV_BZ_control_Day3_rep1
ischemic border zone


title: mesc_rad21_depletion_IAA-6h_054, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv


title: X.laevis NF47-48 spinal cord replicate 4

description:
Library name: 133939
10x Genomics
NF47_raw_feature_bc_matrix.h5
NF47_output_FPR_0.01_filtered.h5


title: X.laevis NF47-48 spinal cord replicate 3

description:
Library name: 133938
10x Genomics
NF47_raw_feature_bc_matrix.h5
NF47_output_FPR_0.01_filtered.h5


title: mesc_rad21_depletion_IAA-6h_053, Smart-seq3


title: X.laevis NF47-48 spinal cord replicate 2

description:
Library name: 133937
10x Genomics
NF47_raw_feature_bc_matrix.h5
NF47_output_FPR_0.01_filtered.h5


title: 00078A02B6

description: Library name: 00078A02B6


title: LV, IZ, patch, Day3, rep2

description:
Library name: LV_IZ_patch_Day3_rep2
middle of ischemic lesion


title: X.laevis NF47-48 spinal cord replicate 1

description:
Library name: 133936
10x Genomics
NF47_raw_feature_bc_matrix.h5
NF47_output_FPR_0.01_filtered.h5


title: mesc_rad21_depletion_IAA-6h_052, Smart-seq3


title: 00078A0264

description: Library name: 00078A0264


title: 00078A0295

description: Library name: 00078A0295


title: 00078A02C3

description: Library name: 00078A02C3


title: LV, IZ, patch, Day3, rep1

description:
Library name: LV_IZ_patch_Day3_rep1
middle of ischemic lesion


title: X.laevis NF37-38 dorsal trunk replicate 4

description:
Library name: 162002
10x Genomics
NF38_raw_feature_bc_matrix.h5
NF38_output_FPR_0.01_filtered.h5

source_name: dorsal trunk

value: dorsal trunk


title: 00078A0222

description: Library name: 00078A0222


title: LV, IZ, control, Day3, rep3

description:
Library name: LV_IZ_control_Day3_rep3
middle of ischemic lesion


title: X.laevis NF37-38 dorsal trunk replicate 3

description:
Library name: 162001
10x Genomics
NF38_raw_feature_bc_matrix.h5
NF38_output_FPR_0.01_filtered.h5


title: LV, IZ, control, Day3, rep2

description:
Library name: LV_IZ_control_Day3_rep2
middle of ischemic lesion


title: mesc_rad21_depletion_IAA-6h_049, Smart-seq3


title: 00078A020C

description: Library name: 00078A020C


title: X.laevis NF37-38 dorsal trunk replicate 2

description:
Library name: 162000
10x Genomics
NF38_raw_feature_bc_matrix.h5
NF38_output_FPR_0.01_filtered.h5


title: mesc_rad21_depletion_IAA-6h_050, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_051, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_048, Smart-seq3


title: LV, IZ, control, Day3, rep1

description:
Library name: LV_IZ_control_Day3_rep1
middle of ischemic lesion


title: 00078A01F1

description: Library name: 00078A01F1


title: X.laevis NF37-38 dorsal trunk replicate 1

description:
Library name: 161999
10x Genomics
NF38_raw_feature_bc_matrix.h5
NF38_output_FPR_0.01_filtered.h5


title: 00078A01D3

description: Library name: 00078A01D3


title: mesc_rad21_depletion_IAA-6h_047, Smart-seq3


title: SAP_rep 2

city: Jinan

first: Shulei

last: Zhao

state: China

address: Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jingwu Weiqi Rd, Jinan 250021, China.

department: Gastroenterology

description:
Library name: Sample4
stRNA-seq library, ileum tissue.

data_processing:
Spatial transcriptomics: Reads were mapped to the mRatBN7.2 genome using STAR, counted and annotated with SAW (v8.1), and analyzed using Stereopy (v1.6.0). Bin50 spots (50×50 DNBs; 25 μm) were generated. Low-quality spots (UMI <500, genes <100, or percent.mt >15%) and genes detected in fewer than 3 spots were excluded. Batch correction was performed using Stereopy integration, clustering was performed using Leiden, and visualization was conducted with Scanpy. Spatially variable genes were identified using SPARK-X (FDR <0.05), and spatial neighborhood/co-occurrence analyses were performed using squidpy.
Assembly: Rattus norvegicus reference genome mRatBN7.2 (GCF_015227675.2).
Supplementary files format and content: Stereo-seq bin50 spot-by-gene expression matrices and spot-level metadata with cell-type annotation. Additional analysis outputs include differential expression results, GO/KEGG enrichment results, CellChat inferred ligand–receptor interaction matrices, and SCENIC regulon activity (AUC) matrices.
Library strategy: Spatial Transcriptomics

source_name: ileum

extract_protocol:
For spatial transcriptomics, ileal tissues were embedded in OCT within 30 min after resection, snap-frozen on dry ice, stored at −80°C, sectioned at 10 μm on a cryostat, and mounted onto Stereo-seq chips for downstream permeabilization and reverse transcription.
For Stereo-seq, libraries were generated following the STOmics Gene Expression Set-S1 protocol. After tissue staining and imaging, cDNA was released from the chip following permeabilization (6–24 min optimized per sample), reverse transcription was performed, and indexed libraries were constructed per the manufacturer’s instructions.

value: ileum

value: wild type

value: SAP

tag: batch


title: AAB_CD8_S5a_RV_2

city: Maimi

first: Alejandro

last: Villarino

state: Florida

address: 1600 NW 10th Ave, Rosenstiel Medical Science Building (RMSB), Room 3152A

institute: University of Miami

description:
Library name: Ristin_RNAseq_68
Ristin_GEO_CD8_RV_RNAseq_counts.txt

data_processing:
FASTQ alignment with Tophat2
Assembly with cufflinks
Gene expression read count data  generated using htseq-count
Assembly: mm9
Supplementary files format and content: Tab delimited text of RNA-seq gene-level expression count data

source_name: pooled LN and spleen

growth_protocol: 20-100K viable cells were sorted and cultured for 12-16 hours, then lysed and stored in Trizol

extract_protocol:
Total RNA isolated from TRIzol by phenol/chloroform extraction, then mRNA enriched with NEBNext Poly(A) mRNA Magnetic Isolation Module
NEBNext Ultra II Library Prep Kit for Illumina (E7645L, New England Biolabs)

treatment_protocol: 20-100K viable cells were sorted and cultured with IL-7 or IL-15, then lysed and stored in Trizol

value: pooled LN and spleen

tag: cell line

value: CD8+ T cells activated in vitro and transduced with retrovirus

value: In vitro activated CD8+ T cell

value: Stat5a-/- Stat5b+/- (AAB)

value: transduced with retrovirus


title: 00078A0162

description: Library name: 00078A0162


title: AAB_CD8_Ctl_RV_

description:
Library name: Ristin_RNAseq_67
Ristin_GEO_CD8_RV_RNAseq_counts.txt


title: mesc_rad21_depletion_IAA-6h_046, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv

value: mouse embryonic stem cell


title: SAP_rep 1

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

description:
Library name: Sample3
stRNA-seq library, ileum tissue.


title: CON_rep 2

description:
Library name: Sample2
stRNA-seq library, ileum tissue.

value: Control


title: 00078A0129

description: Library name: 00078A0129


title: 00078A0121

description: Library name: 00078A0121


title: AAB_CD8_S5a_RV_1

description:
Library name: Ristin_RNAseq_66
Ristin_GEO_CD8_RV_RNAseq_counts.txt


title: AAB_CD8_Ctl_RV_2

description:
Library name: Ristin_RNAseq_69
Ristin_GEO_CD8_RV_RNAseq_counts.txt


title: mesc_rad21_depletion_IAA-6h_061, Smart-seq3

value: IAA (6h)


title: BBA_CD8_Tem_IL15_2

description:
Library name: Ristin_RNAseq_65
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Effector CD8+ T cells +IL-15 (12-16 hrs)

value: Effector CD8+ CD44 high, CD62L low T cell

value: Stat5a+/- Stat5b-/- (BBA)


title: AAB_CD8_Tem_IL15_2

description:
Library name: Ristin_RNAseq_64
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: mesc_rad21_depletion_IAA-6h_043, Smart-seq3


title: CON_rep 1

description:
Library name: Sample1
stRNA-seq library, ileum tissue.


title: 00078A00E5

description: Library name: 00078A00E5

value: whole brain hemisphere


title: SAP_3

description:
Library name: Sample6
snRNA-seq library, ileum tissue.

data_processing:
snRNA-seq: Raw sequencing data were processed using dnbc4tools (v2.1.3) to generate the gene expression (UMI count) matrix. Quality control and downstream analyses were performed in Seurat (v4.3.0). Low-quality nuclei (UMI <1200, genes <500, or percent.mt >5%) and genes detected in fewer than 10 nuclei were excluded. Samples were merged and integrated using Harmony; clustering was performed using the top 30 PCs and resolution 0.8, and cell types were annotated using marker genes and ScType.
Assembly: Rattus norvegicus reference genome mRatBN7.2 (GCF_015227675.2).
Supplementary files format and content: Processed data include (1) snRNA-seq gene-by-nucleus UMI count matrices, cell metadata tables (cell type/cluster/group annotations), and marker gene lists;

molecule: nuclear RNA

growth_protocol: Male Sprague–Dawley rats (6 weeks old, SPF grade) were housed under SPF conditions (22–26°C, 50–60% humidity, 12 h light/dark cycle) with free access to water and acclimatized for 7 days before experimentation.

extract_protocol:
For snRNA-seq, ileal tissue (~100 mg) was processed for nuclei isolation using the Boyou® Cell Nucleus Isolation Kit (SHBIO, 52009-10, China) according to the manufacturer’s protocol. Nuclei were counted and quality assessed using a fluorescence cell analyzer (Countstar® Rigel S2/Mira FL) and microscopy. For spatial transcriptomics, ileal tissues were embedded in OCT within 30 min after resection, snap-frozen on dry ice, stored at −80°C, sectioned at 10 μm on a cryostat, and mounted onto Stereo-seq chips for downstream permeabilization and reverse transcription.
snRNA-seq libraries were prepared using the DNBelab C High-throughput Single-cell RNA Library Preparation Kit V3.0 (MGI Tech). Single nuclei were co-encapsulated with barcoded gel beads and reverse transcriptase mix into droplets using the DNBelab C-TaiM 4 system, followed by cDNA synthesis, emulsion breakage, cDNA purification and amplification, fragmentation, end repair/A-tailing, adaptor ligation, size selection (300–600 bp), PCR amplification, and library purification.

treatment_protocol: Severe acute pancreatitis (SAP) was induced by retrograde infusion of 3% sodium taurocholate (0.1 mL/100 g, 0.1 mL/min) into the pancreatic duct under anesthesia (3% pentobarbital sodium, 40 mg/kg, i.p.), followed by clamping for 5 min. Control animals underwent sham laparotomy without infusion. Animals were sacrificed 24 h after induction, and ileal tissues were harvested and processed for downstream assays.


title: mesc_rad21_depletion_IAA-6h_045, Smart-seq3


title: SAP_2

description:
Library name: Sample5
snRNA-seq library, ileum tissue.


title: BBA_CD8_Tem_IL15_1

description:
Library name: Ristin_RNAseq_63
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: mesc_rad21_depletion_IAA-6h_042, Smart-seq3


title: SAP_1

description:
Library name: Sample4
snRNA-seq library, ileum tissue.


title: 00078A00AD

description: Library name: 00078A00AD


title: mesc_rad21_depletion_IAA-6h_041, Smart-seq3


title: AAB_CD8_Tem_IL15_1

description:
Library name: Ristin_RNAseq_62
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: CON_3

description:
Library name: Sample3
snRNA-seq library, ileum tissue.


title: mesc_rad21_depletion_IAA-6h_044, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_040, Smart-seq3


title: BBA_CD8_Tem_NC_2

description:
Library name: Ristin_RNAseq_61
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Effector CD8+ T cells (No Cytokine)

value: No Cytokine (NC)


title: 00078A0055

description: Library name: 00078A0055


title: CON_2

description:
Library name: Sample2
snRNA-seq library, ileum tissue.

value: ileum


title: AAB_CD8_Tem_NC_2

description:
Library name: Ristin_RNAseq_60
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: 00078A00E6

description: Library name: 00078A00E6


title: BBA_CD8_Tem_NC_1

description:
Library name: Ristin_RNAseq_59
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: 00078A0057

description: Library name: 00078A0057


title: 00078A0039

description: Library name: 00078A0039


title: mesc_rad21_depletion_IAA-6h_038, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv


title: VUMC02634

type: RNA

city: Nashville

first: Hui

last: Cai

state: TN

address: 2525 West End Ave.

institute: VUMC

hyb_protocol: The samples from the miRNA Sample Preparation Protocol were denatured at 85°C for 5 minutes, then 5ul of each sample were hybridized with NanoString CodeSet chemistry (consists of a Reporter CodeSet and a Capture ProbeSet) at 65°C for 20-22 hours.

scan_protocol: After hybridization, the samples were proceeded immediately to post-hybridization on the nCounter Prep Station, where excess probes were removed, and target-probe complexes were immobilized and aligned on the cartridge. Their barcodes are then counted on an nCounter Digital Analyzer.

data_processing:
The tabulated barcodes from the nCounter Digital Analyzer were analyzed using r package nanostringr (R/Bioconductor Packages) for normalization analysis
Normalized barcode counts

organism: Homo sapiens

source_name: nested case-control study

label_protocol: From 20 µL of total RNA yield, 3 µL was used for miRNA expression analysis. The unique oligonucleotide tags were annealed and subsequently ligated with miRNAs of interest via a target specific bridge oligo. Sequence specificity between each miRNA and its appropriate tag was ensured by careful, stepwise control of annealing and ligation temperatures, following NanoString’s miRNA Sample Preparation Protocol.

extract_protocol: Total RNA, including miRNA, was extracted and purified from plasma samples using Qiagen's miRNeasy Serum/Plasma Kit, following the manufacturer’s protocol. To minimize cellular contamination, plasma samples were centrifuged at 16,000 × g for 10 minutes at 4°C, and 200 µL of the supernatant was used for RNA extraction. To control for variability in starting material and extraction efficiency, 5 µL each of three synthetic spike-in RNA oligonucleotides—osa-miR414 (2 pg/µL), cel-miR248 (1 pg/µL), and ath-miR159a (4 pg/µL)—were added to each sample.

value: plasma


title: CON_1

description:
Library name: Sample1
snRNA-seq library, ileum tissue.

value: wild type


title: 00078A0031

description: Library name: 00078A0031


title: mesc_rad21_depletion_IAA-6h_037, Smart-seq3


title: AAB_CD8_Tem_NC_1

description:
Library name: Ristin_RNAseq_58
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: pooled LN and spleen


title: Cohort3-ED_grp_682-sample-GEX

city: New York

first: Patrick

last: Wilson

state: NY

address: 413 E 69th St

department: Drukier Institute

institute: Weill Cornell Medicine

description:
Library name: sample-GEX
10x Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger (v7.1.0) functions (mkfastq, count, vdj)
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of cell barcode sequences
Supplementary files format and content: features.tsv.gz: list of gene IDs + names
Supplementary files format and content: matrix.mtx.gx: gene expression count data in Market Exchange Format
Supplementary files format and content: consenus.fasta: the consensus sequence of each assembled contig in FASTA format
Supplementary files format and content: filtered_contig_annotations.csv: high-level annotations of each high-confidence contigs from cell associated barcodes

source_name: B cells

extract_protocol:
Single-cell suspensions of FACS-sorted B cells were processed using the 10x Genomics Chromium Single Cell 5' Immune Profiling workflow. Cells were loaded onto the Chromium Controller for partitioning and barcoding, followed by reverse transcription, cDNA amplification, and library construction according to the manufacturer’s protocol [10x Genomics Single Cell V(D)J Reagent Kits v2].
The sorted single cells were processed according to 10x Genomics 5’ gene expression and B cell Immunoglobulin (Ig) enrichment protocol to prepare the libraries for sequencing.

value: B cells

tag: library type

value: GEX


title: Cohort3-ED_grp_682-sample-VDJ

description:
Library name: sample-VDJ
10x Genomics

value: VDJ


title: mesc_rad21_depletion_IAA-6h_036, Smart-seq3


title: 000789FFF2

description: Library name: 000789FFF2


title: BBA_CD8_Tcm_IL7_2

description:
Library name: Ristin_RNAseq_57
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Memory CD8+ T cells +IL-7 (12-16 hrs)

value: Memory CD8+ CD44 high, CD62L high T cell


title: 000789FFC6

description: Library name: 000789FFC6


title: mesc_rad21_depletion_IAA-6h_035, Smart-seq3

value: mouse embryonic stem cell


title: Cohort3-ED_grp_682-sample-ADT

description:
Library name: sample-ADT
10x Genomics

value: ADT


title: BBA_CD8_Tcm_IL7_1

description:
Library name: Ristin_RNAseq_55
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: AAB_CD8_Tcm_IL7_2

description:
Library name: Ristin_RNAseq_56
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Stat5a-/- Stat5b+/- (AAB)


title: 000789FFB3

description: Library name: 000789FFB3


title: 000789FFB4

description: Library name: 000789FFB4


title: mesc_rad21_depletion_IAA-6h_034, Smart-seq3

value: IAA (6h)


title: mesc_rad21_depletion_IAA-6h_033, Smart-seq3


title: Cohort1-A-5mice_igGpo_SARS2-YB5-RNA

description:
Library name: YB5-RNA
10x Genomics

value: RNA


title: AAB_CD8_Tcm_IL7_1

description:
Library name: Ristin_RNAseq_54
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: 000789FFAE

description: Library name: 000789FFAE

value: whole brain hemisphere


title: Cohort1-A-5mice_igGpo_SARS2-YB5-ADT

description:
Library name: YB5-ADT
10x Genomics


title: mesc_rad21_depletion_IAA-6h_032, Smart-seq3


title: BBA_CD8_Tcm_IL15_2

description:
Library name: Ristin_RNAseq_53
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Memory CD8+ T cells +IL-15 (12-16 hrs)

value: Stat5a+/- Stat5b-/- (BBA)


title: AAB_CD8_Tcm_IL15_2

description:
Library name: Ristin_RNAseq_52
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: 000789FF9E

description: Library name: 000789FF9E


title: mesc_rad21_depletion_IAA-6h_030, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_031, Smart-seq3


title: Cohort1-O-repeat_XBB-YB-mouse-RNA

description:
Library name: YB-mouse-RNA
10x Genomics


title: 000789FF72

description: Library name: 000789FF72


title: Cohort1-A-5mice_igGpo_SARS2-YB5-VDJ

description:
Library name: YB5-VDJ
10x Genomics


title: mesc_rad21_depletion_IAA-6h_029, Smart-seq3


title: BBA_CD8_Tcm_IL15_1

description:
Library name: Ristin_RNAseq_51
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: Cohort1-O-repeat_XBB-YB-mouse-ADT

description:
Library name: YB-mouse-ADT
10x Genomics


title: 000789FF64

description: Library name: 000789FF64


title: Cohort1-O-repeat_XBB-YB-mouse-VDJ

description:
Library name: YB-mouse-VDJ
10x Genomics


title: mesc_rad21_depletion_IAA-6h_028, Smart-seq3


title: BBA_CD8_Tcm_NC_2

description:
Library name: Ristin_RNAseq_49
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Memory CD8+ T cells (No Cytokine)

value: No Cytokine (NC)


title: 00078999AE

description: Library name: 00078999AE


title: Cohort1-O-XBB1-YB3-VDJ

description:
Library name: YB3-VDJ
10x Genomics


title: mesc_rad21_depletion_IAA-6h_027, Smart-seq3


title: AAB_CD8_Tcm_IL15_1

description:
Library name: Ristin_RNAseq_50
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: 000789FF60

description: Library name: 000789FF60


title: Cohort1-O-XBB1-YB3-RNA

description:
Library name: YB3-RNA
10x Genomics


title: Cohort1-O-XBB1-YB3-ADT

description:
Library name: YB3-ADT
10x Genomics


title: BBA_CD8_Tcm_NC_1

description:
Library name: Ristin_RNAseq_47
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: 0007899981

description: Library name: 0007899981


title: mesc_rad21_depletion_IAA-6h_026, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_025, Smart-seq3


title: AAB_CD8_Tcm_NC_2

description:
Library name: Ristin_RNAseq_48
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: Cohort2-6mice_bolus_immu_PB-VDJ

description:
Library name: PB-VDJ
10x Genomics


title: mesc_rad21_depletion_IAA-6h_039, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_024, Smart-seq3


title: AAB_CD8_Tcm_NC_1

description:
Library name: Ristin_RNAseq_46
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: 0007899974

description: Library name: 0007899974


title: 000789998B

description: Library name: 000789998B


title: AAB_CD8_Nv_IL7_2

description:
Library name: Ristin_RNAseq_44
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Naive CD8+ T cells +IL-7 (12-16 hrs)

value: Naive CD8+ CD44 low, CD62L high T cell


title: 0007899963

description:
Library name: 0007899963
Removed: no matching genotype sample


title: mesc_rad21_depletion_IAA-6h_023, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv


title: Cohort2-6mice_bolus_immu_AS-VDJ

description:
Library name: AS-VDJ
10x Genomics

value: B cells


title: BBA_CD8_Nv_IL7_2

description:
Library name: Ristin_RNAseq_45
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: pooled LN and spleen


title: mesc_rad21_depletion_IAA-6h_022, Smart-seq3


title: 0007899919

description: Library name: 0007899919


title: Cohort2-6mice_bolus_immu_AS-GEX

description:
Library name: AS-GEX
10x Genomics

value: GEX


title: 000792A080

description:
Library name: 000792A080
Original label before genotype mismatch fix: 000789990A


title: BBA_CD8_Nv_IL7_1

description:
Library name: Ristin_RNAseq_43
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: Cohort2-6mice_bolus_immu_AS-ADT

description:
Library name: AS-ADT
10x Genomics


title: mesc_rad21_depletion_IAA-6h_021, Smart-seq3


title: BBA_CD8_Nv_IL15_2

description:
Library name: Ristin_RNAseq_41
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Naive CD8+ T cells +IL-15 (12-16 hrs)


title: AAB_CD8_Nv_IL7_1

description:
Library name: Ristin_RNAseq_42
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: Cohort1-A-5mice_pool-YB2-VDJ

description:
Library name: YB2-VDJ
10x Genomics

value: VDJ


title: AAB_CD8_Nv_IL15_2

description:
Library name: Ristin_RNAseq_40
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: mesc_rad21_depletion_IAA-6h_019, Smart-seq3

value: mouse embryonic stem cell


title: mesc_rad21_depletion_IAA-6h_020, Smart-seq3


title: 00078998A8

description: Library name: 00078998A8


title: BBA_CD8_Nv_IL15_1

description:
Library name: Ristin_RNAseq_39
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: 00078998E4

description: Library name: 00078998E4


title: mesc_rad21_depletion_IAA-6h_017, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_018, Smart-seq3


title: AAB_CD8_Nv_IL15_1

description:
Library name: Ristin_RNAseq_38
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: 0007899826

description: Library name: 0007899826


title: BBA_CD8_Nv_NC_2

description:
Library name: Ristin_RNAseq_37
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Naive CD8+ T cells (No Cytokine)


title: mesc_rad21_depletion_IAA-6h_016, Smart-seq3


title: 00078998C8

description: Library name: 00078998C8


title: Cohort1-A-7mice_pool-YB-RNA

description:
Library name: YB-RNA
10x Genomics


title: 0007899884

description: Library name: 0007899884


title: AAB_CD8_Nv_NC_2

description:
Library name: Ristin_RNAseq_36
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Stat5a-/- Stat5b+/- (AAB)


title: Cohort1-A-7mice_pool-YB-ADT

description:
Library name: YB-ADT
10x Genomics

value: ADT


title: Cohort1-A-5mice_pool-YB2-RNA

description:
Library name: YB2-RNA
10x Genomics

value: RNA


title: Cohort1-A-5mice_pool-YB2-ADT

description:
Library name: YB2-ADT
10x Genomics


title: BBA_CD8_Nv_NC_1

description:
Library name: Ristin_RNAseq_35
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: mesc_rad21_depletion_IAA-6h_014, Smart-seq3

value: IAA (6h)


title: 000789980F

description: Library name: 000789980F

value: whole brain hemisphere


title: Cohort1-A-7mice_pool-YB-VDJ

description:
Library name: YB-VDJ
10x Genomics


title: P7_Ctrl_NE_0_1_AAAYVHJHV

city: Cleveland

first: Davin

middle: J

last: Marro

state: Ohio

address: 2210 Circle Dr

department: Neurosciences

institute: Case Western Reserve University

description:
Library name: L60078
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software.
Assembly: mouse mm10
Supplementary files format and content: Processed h5 files containing gene counts per cell barcode.

source_name: Olfactory Epithelium

extract_protocol:
Animals were euthanized with standard protocols in Stowers Institute for Medical Research, olfactory epithelium was dissected and bones were removed in the ice cold HBSS. Dissected epitheliums were dissociated in papain solution (20 mg/mL papain and 3 mg/mL L-cysteine in HBSS) with RNase-free DNase I (10unit) at 37 °C for 15–20 mins. 0.01% BSA in PBS was added to the digestion solution before filtering with 70 µm and 30 µm filters (pluriSelect).  Dissociated cells were washed twice in 0.01% BSA with final volume 1 mL, followed by Draq5 (25 µM) and DAPI (0.5 µg/mL) staining 5 min on ice. Draq5+/DAPI- cells (live/nucleated cells) were sorted on BD Influx cytometer (BD Bioscience) with 100 µm nozzle.
Note: Library protocol will be specified for each batch present in study.  MOLNG-2453: Cells deemed to be 45-85% viable were loaded based on live cell concentration onto a Chromium Controller instrument (10x Genomics) and libraries prepared using the Chromium Single Cell 3' Library & Gel Bead Kit v2 (10x Genomics) according to manufacturer’s directions.  Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer (Agilent Technologies) and Qubit Fluorometer (Thermo Fisher Scientific).  With cells captured estimated at ~1,300-9,000 cells per sample, libraries were pooled and sequenced to a depth necessary to achieve at least 19,000 mean reads per cell on an Illumina HiSeq 2500 instrument in Rapid Run mode utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 26*8*98bp
MOLNG-2407: Cells deemed to be at least 69% viable were loaded based on live cell concentration onto a Chromium Controller instrument (10x Genomics) and libraries prepared using the Chromium Single Cell 3' Library & Gel Bead Kit v2 (10x Genomics) according to manufacturer’s directions.  Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer (Agilent Technologies) and Qubit Fluorometer (Thermo Fisher Scientific).  With cells captured estimated at ~1,500-4,000 cells per sample, libraries were pooled and sequenced to a depth necessary to achieve at least 20,000 mean reads per cell on an Illumina HiSeq 2500 instrument in Rapid Run mode utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 26*8*98bp.
MOLNG-3334: Cells deemed to be at least 90% viable were loaded on a Chromium Single Cell Controller (10x Genomics), based on live cell concentration.  Libraries were prepared using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) according to manufacturer’s directions.  Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer (Agilent Technologies) and Qubit Fluorometer (Thermo Fisher Scientific).  With cells captured estimated at ~3,100-7,400 cells per sample, libraries were pooled as needed and sequenced to a depth necessary to achieve at least 38,000 mean reads per cell on an Illumina NovaSeq 6000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 28*10*10*90bp.
MOLNG-3650: Dissociated, sorted cells were assessed for concentration and viability using a Luna-FL cell counter (Logos Biosystems).   Cells deemed to be at least 95% viable were loaded based on live cell concentration onto a Chromium X Series instrument (10x Genomics) and libraries prepared using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) according to manufacturer’s directions.  Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer (Agilent Technologies) and Qubit Fluorometer (Thermo Fisher Scientific).  With cells captured estimated at ~4,000-10,000 cells per sample, libraries were pooled and sequenced to a depth necessary to achieve at least 30,000 mean reads per cell on an Illumina NextSeq 2000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 28*10*10*90bp.

value: Olfactory Epithelium

value: Multiple

value: Wt/Ctrl


title: 0007899866

description: Library name: 0007899866


title: 0007899800

description: Library name: 0007899800


title: mesc_rad21_depletion_IAA-6h_013, Smart-seq3


title: P7_Fzd1KO_NE_0_1_AAAYVHJHV

description:
Library name: L60077
10x Genomics


title: AAB_CD8_Nv_NC_1

description:
Library name: Ristin_RNAseq_34
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: No Cytokine (NC)


title: mesc_rad21_depletion_IAA-6h_015, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_012, Smart-seq3


title: P3_Ctrl_NE_0_1_AAAYVHJHV

description:
Library name: L60076
10x Genomics


title: 00078997E9

description: Library name: 00078997E9


title: mesc_rad21_depletion_IAA-6h_011, Smart-seq3


title: P3_Fzd1KO_NE_0_1_AAAYVHJHV

description:
Library name: L60075
10x Genomics


title: WT_CD8_Tem_IL15_1

description:
Library name: Ristin_RNAseq_32
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Effector CD8+ T cells +IL-15 (12-16 hrs)

value: Effector CD8+ CD44 high, CD62L low T cell

value: Stat5a+/+ Stat5b+/+ (WT)


title: WT_CD8_Tem_NC_2

description:
Library name: Ristin_RNAseq_31
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: pooled LN and spleen

value: Effector CD8+ T cells (No Cytokine)


title: 00078997FE

description: Library name: 00078997FE


title: 00078997C9

description: Library name: 00078997C9


title: P7_Fzd1KO_stim_0_1_AAAYVHJHV

description:
Library name: L59806
10x Genomics

value: Odor Stimulation


title: mesc_rad21_depletion_IAA-6h_010, Smart-seq3

value: mouse embryonic stem cell


title: mesc_rad21_depletion_IAA-6h_009, Smart-seq3


title: WT_CD8_Tem_NC_1

description:
Library name: Ristin_RNAseq_30
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: WT_CD8_Tcm_IL15_2

description:
Library name: Ristin_RNAseq_29
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Memory CD8+ T cells +IL-15 (12-16 hrs)

value: Memory CD8+ CD44 high, CD62L high T cell


title: P3_Ctrl_stim_0_1_AAAYVHJHV

description:
Library name: L59805
10x Genomics


title: P3_Fzd1KO_stim_0_1_AAAYVHJHV

description:
Library name: L59804
10x Genomics


title: WT_CD8_Tem_IL15_2

description:
Library name: Ristin_RNAseq_33
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: mesc_rad21_depletion_IAA-6h_008, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv


title: WT_CD8_Tcm_IL15_1

description:
Library name: Ristin_RNAseq_28
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: 0007899781

description:
Library name: 0007899781
Original label before genotype mismatch fix: 00078997BF


title: mesc_rad21_depletion_IAA-6h_007, Smart-seq3


title: 00078997C4

description: Library name: 00078997C4


title: 00078997BB

description: Library name: 00078997BB


title: mesc_rad21_depletion_IAA-6h_006, Smart-seq3


title: 00078997D2

description: Library name: 00078997D2


title: 00078997B9

description: Library name: 00078997B9


title: Cohort2-6mice_bolus_immu_PB-GEX

description:
Library name: PB-GEX
10x Genomics

value: B cells

value: GEX


title: 00078997AC

description: Library name: 00078997AC


title: brain, Het1

city: Bronx

first: Deyou

last: Zheng

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: Library name: het83470

data_processing:
Sample demultiplexing, barcode processing and single-cell transcript counting were performed using Cell Ranger (10X Genomics; version 5.0)
The snRNA-seq data analysis was performed with the RISC software (v1.0) . In each sample, nuclei with Unique Molecular Identifiers (UMIs) between 500 and 50,000, > 200 detected genes and <5% mitochondrial reads were kept. After this filtering, data from all four samples were integrated by the Reference Principal Component Integration (RPIC) method in the RISC package and then clustered with Louvain algorithm using 15 principal components and otherwise default parameters.
Assembly: Mouse mm10-2020-A
Supplementary files format and content: tab-separated value files and matrix files

source_name: brain

growth_protocol: Csf1r+/- mice were generated, maintained and genotyped as described previously (Dai et al., 2002, PMID: 11756160). Mouse strain is C57/BL6.

extract_protocol:
Brain cell nuclei were isolated from 2-month-old wt and Csf1r+/- female mice using a detergent-free nuclei isolation kit (Invent Biotechnologies). Briefly, mice were anesthetized and perfused with 50ml of ice-cold, RNase-free PBS containing 50U/ml Heparin. The nuclei were separated according to the manufacturer’s instructions. Myelin debris were removed using Myelin depletion immunomagnetic beads (Miltenyi). After the final centrifugation, nuclei were resuspended in 0.5 ml nuclei suspension buffer (2% BSA and 0.2U/μl RNase inhibitor in RNase-free molecular biology-grade PBS) and filtered through a 40-μm FlowMi Cell Strainer.
Droplet-based isolation of single nuclei and subsequent preparation of the snRNA-seq libraries were performed using the 10× Genomics platform and kit, according to the manufacturer’s specifications.

treatment_protocol: no treatment was applied

value: brain


title: mesc_rad21_depletion_IAA-6h_005, Smart-seq3

value: IAA (6h)


title: brain, Het2

description: Library name: het83471


title: mesc_rad21_depletion_IAA-6h_004, Smart-seq3


title: WT_CD8_Tcm_NC_2

description:
Library name: Ristin_RNAseq_25
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Memory CD8+ T cells (No Cytokine)


title: brain, WT1

description: Library name: wt83468

value: WT


title: brain, WT2

description: Library name: wt83469


title: WT_CD8_Tcm_IL7_2

description:
Library name: Ristin_RNAseq_27
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Memory CD8+ T cells +IL-7 (12-16 hrs)


title: 00078997A0

description: Library name: 00078997A0

value: whole brain hemisphere


title: mesc_rad21_depletion_IAA-6h_003, Smart-seq3


title: 00078997BF

description:
Library name: 00078997BF
Original label before genotype mismatch fix: 0007899781


title: WT_CD8_Nv_IL15_2

description:
Library name: Ristin_RNAseq_23
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Naive CD8+ T cells +IL-15 (12-16 hrs)

value: Naive CD8+ CD44 low, CD62L high T cell


title: WT_CD8_Tcm_NC_1

description:
Library name: Ristin_RNAseq_24
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Stat5a+/+ Stat5b+/+ (WT)

value: No Cytokine (NC)


title: Middle phalanx (P2) cells, FGF8 treated

city: Bryan

first: Andreea

last: Trache

state: TX

address: 402 John Sharp Pkwy

department: Medical Physiology

institute: Texas A&M University

description:
Library name: Sample 2
10X Genomics

data_processing:
FASTQ formatted sequencing reads were processed using CellRanger (v9.0.0) (10x Genomics, Pleasanton, CA) with default parameters and the GRCm39-2024-A transcriptome reference for UMI and gene expression quantification
Ambient and doublet captures were removed from the count matrcies using Seurat by applying filters: 200 < nFeatures < 7500 and mitochondrial gene count < 15%.
BSA and FGF8 treated samples were merged and gene counts normalized using the SCTransform algorithm. The datasers were then integrated using the Canonical Correlation Analysis (CCA) method. Clustering was performed at a resolution of 0.05, identifying nine distinct clusters. Uniform Manifold Approximation and Projection (UMAP) was used for dimensionality reduction, and the resutling embeddings were visualized in 2D space.
Cluster-specific and shared markers were identified using the FindConservedMarkers function in Seurat. Conserved markers were ranked by the difference in percentage of of cells expressing each marker between clusters (pct.diff = pct.1 - pct.2), averaged across both samples. The resulting unique, conserved, and highly expressed markers were cross-referenced against the PangloaDB to assign cell types.
To identify fibroblast sub-populations, the integrated Seurat object was subset to include only cells identified as fibroblasts. This subset was re-clustered at a resolution of 0.2, revealing six sub-populations.
The Seurat FindMarkers function was used to identify differentially expressed genes (DEGs). DEGs were defined as genes having a p (Benjamini-Hochberg corrected p-values) < 0.05 and |log2FoldChange| > 1. Pathway enrichment was conducted using both the GO and  KEGG enrichment databses with the clusterProfiler package.
Assembly: Mouse mm10
Supplementary files format and content: Tab-seperated files
Supplementary files format and content: Count and UMI matrix files
Supplementary files format and content: RDS files of Seurat integrated object

source_name: Middle phalanx

extract_protocol:
Cell collection was carried out by removing the surrounding epithelium from the amputated digits and dissecting the tissue distal to the P2 stump, followed by placing the tissue into ice-cold PBS. Enzymatic dissociation was perform using 2U/ml Liberase Blendzyme (37°C, 4h; Sigma-Aldrich Co.), with manual pipet trituration every 2 hours. Cells were filtered to remove aggregates, washed and resuspended in 0.8% BSA in PBS.
Single cells were captured in Gel Beads-in-Emulsion (GEMs) using the Chromium Controller with Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10X Genomics, Pleasanton, CA). Barcoded cDNA was generated through reverse transcription, followed by amplification and fragmentation. Dual-indexed sequencing libraries were constructed according to the 10X Genomics Single Cell 3' v3.1 protocol.

value: Middle phalanx

tag: age

tag: Sex

value: pooled male and female

value: bead implant


title: mesc_rad21_depletion_IAA-6h_002, Smart-seq3

value: mouse embryonic stem cell


title: Middle phalanx (P2) cells, BSA treated

description:
Library name: Sample 1
10X Genomics


title: WT_CD8_Tcm_IL7_1

description:
Library name: Ristin_RNAseq_26
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: pooled LN and spleen

value: Memory CD8+ CD44 high, CD62L high T cell


title: mesc_rad21_depletion_IAA-6h_001, Smart-seq3


title: WT_CD8_Nv_IL15_1

description:
Library name: Ristin_RNAseq_22
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: 000789977D

description: Library name: 000789977D


title: mesc_rad21_depletion_IAA-3h_192, Smart-seq3

value: IAA (3h)


title: ESC, SETb OE, rep 2

city: Jerusalem

first: Eran

last: Meshorer

address: Institute of Life Sciences, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram

department: Department of Genetics

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Sequenced reads were aligned with STAR (v2.5.4b) using default parameters to the mouse genome and transcriptome from ENSEMBL (GRCm38.97)
Gene counts were obtained using featureCounts (Subread package v2.0.0) with default parameters
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts for each gene in every sample

source_name: KH2 pBS31-HA-SETb

growth_protocol: Mouse ESCs were cultured on MEF coated plates, in DMEM (Sigma) supplemented with 15% FBS (Biological Industries), L‐glutamine, 1X MEM non‐essential amino acids, Sodium Pyruvate, 1x Penstrep, 0.2 mM β-ME and LIF.

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen).
500ng of RNA was used to generate libraries with QuantSeq 3’ mRNASeq Kit (Lexogen) according to the manufacturer's instructions.

value: KH2 pBS31-HA-SETb

value: Embryonic Stem Cells

value: WT + SETb

value: 1ug/ml doxycycline, 24h


title: WT_CD8_Nv_IL7_2

description:
Library name: Ristin_RNAseq_21
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Naive CD8+ T cells +IL-7 (12-16 hrs)


title: ESC, SETb OE, rep 1


title: 0007899761

description: Library name: 0007899761

value: whole brain hemisphere


title: WT_CD8_Nv_IL7_1

description:
Library name: Ristin_RNAseq_20
Ristin_GEO_CD8_RNAseq_gene_counts.txt


title: mesc_rad21_depletion_IAA-3h_191, Smart-seq3


title: 000789975D

description: Library name: 000789975D


title: mesc_rad21_depletion_IAA-3h_190, Smart-seq3


title: ESC, SETb OE, rep 3


title: ESC, WT SETb, rep 3

value: WT

value: no dox


title: WT_CD8_Nv_NC_2

description:
Library name: Ristin_RNAseq_19
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: Naive CD8+ T cells (No Cytokine)

value: Naive CD8+ CD44 low, CD62L high T cell

value: Stat5a+/+ Stat5b+/+ (WT)


title: 0007899758

description: Library name: 0007899758


title: WT_CD8_Nv_NC_1

description:
Library name: Ristin_RNAseq_18
Ristin_GEO_CD8_RNAseq_gene_counts.txt

value: No Cytokine (NC)


title: 0007899751

description: Library name: 0007899751


title: mesc_rad21_depletion_IAA-3h_188, Smart-seq3


title: BBA_CD4_Nv_IL7_3

description:
Library name: Ristin_RNAseq_17
Ristin_GEO_CD4_RNAseq_gene_counts.txt

value: Naive CD4+ T cells +IL-7 (12-16 hrs)

value: Naive CD4+ CD44 low, CD62L high T cell

value: Stat5a+/- Stat5b-/- (BBA)


title: ESC, WT SETb, rep 2


title: ESC, WT SETb, rep 1


title: mesc_rad21_depletion_IAA-3h_189, Smart-seq3

value: mouse embryonic stem cell


title: mesc_rad21_depletion_IAA-3h_187, Smart-seq3

value: IAA (3h)


title: 000789973F

description: Library name: 000789973F


title: WT_CD4_Nv_IL7_3

description:
Library name: Ristin_RNAseq_15
Ristin_GEO_CD4_RNAseq_gene_counts.txt

value: pooled LN and spleen


title: mesc_rad21_depletion_IAA-3h_186, Smart-seq3


title: AAB_CD4_Nv_IL7_3

description:
Library name: Ristin_RNAseq_16
Ristin_GEO_CD4_RNAseq_gene_counts.txt

value: Stat5a-/- Stat5b+/- (AAB)


title: 0007899734

description: Library name: 0007899734


title: ESC, SETa OE, rep 2

source_name: KH2 pBS31-HA-SETa

value: KH2 pBS31-HA-SETa

value: Embryonic Stem Cells

value: WT + SETa


title: mesc_rad21_depletion_IAA-3h_185, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv


title: BBA_CD4_Nv_IL7_2

description:
Library name: Ristin_RNAseq_14
Ristin_GEO_CD4_RNAseq_gene_counts.txt


title: ESC, SETa OE, rep 1

value: 1ug/ml doxycycline, 24h


title: 0007899718

description: Library name: 0007899718

value: whole brain hemisphere


title: AAB_CD4_Nv_IL7_2

description:
Library name: Ristin_RNAseq_13
Ristin_GEO_CD4_RNAseq_gene_counts.txt


title: ESC, SETa OE, rep 3


title: ESC, WT SETa, rep 3

value: WT

value: no dox


title: mesc_rad21_depletion_IAA-3h_184, Smart-seq3


title: WT_CD4_Nv_IL7_2

description:
Library name: Ristin_RNAseq_12
Ristin_GEO_CD4_RNAseq_gene_counts.txt


title: mesc_rad21_depletion_IAA-3h_183, Smart-seq3


title: 00078996CE

description: Library name: 00078996CE


title: ESC, WT SETa, rep 2


title: 00079FAA78

description:
Library name: 00079FAA78
Original label before genotype mismatch fix: 0007899712


title: BBA_CD4_Nv_IL7_1

description:
Library name: Ristin_RNAseq_11
Ristin_GEO_CD4_RNAseq_gene_counts.txt


title: ESC, WT SETa, rep 1


title: mesc_rad21_depletion_IAA-3h_182, Smart-seq3


title: 000789972A

description: Library name: 000789972A


title: 00078996BD

description: Library name: 00078996BD


title: BBA_CD4_Nv_NC_3

description:
Library name: Ristin_RNAseq_9
Ristin_GEO_CD4_RNAseq_gene_counts.txt


title: mesc_rad21_depletion_IAA-3h_180, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_181, Smart-seq3


title: ESC, KO C2 SETb, beta 4h addback experiement 4h rep2

source_name: KH2 SET-KO pBS31-HA-SETb

value: KH2 SET-KO pBS31-HA-SETb

value: SET KO clone 2 + SETb

value: 1ug/ml doxycycline, 4h


title: WT_CD4_Nv_IL7_1

description:
Library name: Ristin_RNAseq_10
Ristin_GEO_CD4_RNAseq_gene_counts.txt

value: Naive CD4+ T cells +IL-7 (12-16 hrs)

value: Stat5a+/+ Stat5b+/+ (WT)


title: 00078996AC

description: Library name: 00078996AC


title: ESC, KO C2 SETb, beta 4h addback experiement 2h rep2

value: SET KO clone 2

value: 1ug/ml doxycycline, 2h


title: ESC, KO C2 SETb, beta 4h addback experiement 4h rep1


title: 0007899695

description: Library name: 0007899695


title: 00078996A6

description: Library name: 00078996A6


title: AAB_CD4_Nv_NC_3

description:
Library name: Ristin_RNAseq_8
Ristin_GEO_CD4_RNAseq_gene_counts.txt

value: Naive CD4+ CD44 low, CD62L high T cell


title: WT_CD4_Nv_NC_3

description:
Library name: Ristin_RNAseq_7
Ristin_GEO_CD4_RNAseq_gene_counts.txt

value: pooled LN and spleen

value: Naive CD4+ T cells (No Cytokine)

value: No Cytokine (NC)


title: mesc_rad21_depletion_IAA-3h_178, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: 0007899688

description: Library name: 0007899688


title: ESC, KO C2 SETb, beta 4h addback experiement 2h rep1

value: Embryonic Stem Cells


title: BBA_CD4_Nv_NC_2

description:
Library name: Ristin_RNAseq_6
Ristin_GEO_CD4_RNAseq_gene_counts.txt

value: Stat5a+/- Stat5b-/- (BBA)


title: mesc_rad21_depletion_IAA-3h_176, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_177, Smart-seq3


title: 000789963D

description: Library name: 000789963D

value: whole brain hemisphere


title: AAB_CD4_Nv_NC_2

description:
Library name: Ristin_RNAseq_5
Ristin_GEO_CD4_RNAseq_gene_counts.txt

value: Stat5a-/- Stat5b+/- (AAB)


title: 0007899629

description: Library name: 0007899629


title: ESC, KO C1 SETb, beta 4h addback experiement 4h rep1

value: KH2 SET-KO pBS31-HA-SETb

value: SET KO clone 1 + SETb


title: mesc_rad21_depletion_IAA-3h_175, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_179, Smart-seq3


title: 0007899607

description: Library name: 0007899607


title: ESC, KO C1 SETb, beta 4h addback experiement 2h rep1

value: SET KO clone 1


title: WT_CD4_Nv_NC_2

description:
Library name: Ristin_RNAseq_4
Ristin_GEO_CD4_RNAseq_gene_counts.txt


title: BBA_CD4_Nv_NC_1

description:
Library name: Ristin_RNAseq_3
Ristin_GEO_CD4_RNAseq_gene_counts.txt


title: 0007899778

description: Library name: 0007899778


title: ESC, WT SETb, beta 4h addback experiement 4h rep2

value: WT

value: 1ug/ml doxycycline, 4h


title: 0007899605

description: Library name: 0007899605


title: mesc_rad21_depletion_IAA-3h_174, Smart-seq3


title: ESC, KO C1 SETb, beta 4h addback experiement 2h rep2


title: AAB_CD4_Nv_NC_1

description:
Library name: Ristin_RNAseq_2
Ristin_GEO_CD4_RNAseq_gene_counts.txt


title: 00078995FC

description: Library name: 00078995FC


title: WT_CD4_Nv_NC_1

description:
Library name: Ristin_RNAseq_1
Ristin_GEO_CD4_RNAseq_gene_counts.txt

value: Stat5a+/+ Stat5b+/+ (WT)


title: ESC, WT SETb, beta 4h addback experiement 4h rep1


title: mesc_rad21_depletion_IAA-3h_173, Smart-seq3


title: 00077EAD3C

description: Library name: 00077EAD3C


title: ESC, WT SETb, beta 4h addback experiement 2h rep1

value: 1ug/ml doxycycline, 2h


title: mesc_rad21_depletion_IAA-3h_171, Smart-seq3


title: ESC, KO C2 SETb, beta 4h addback experiement 1h rep2

value: SET KO clone 2 + SETb

value: 1ug/ml doxycycline, 1h


title: 00077E90D8

description: Library name: 00077E90D8


title: ESC, KO C2 SETb, beta 4h addback experiement 1h rep1


title: 00077E9063

description: Library name: 00077E9063


title: mesc_rad21_depletion_IAA-3h_169, Smart-seq3


title: hiPSC-derived dental organoid at Week5-3

city: Seattle

first: YANG

last: Zhou

state: WA

address: 1410 NE Campus Pkwy

institute: university of washington

description: Library name: sample-6

data_processing:
soapnuke version 1.5.6
Reads containing adapters (adapter contamination)
Reads with an unknown base 'N' content greater than 0.1%
Low-quality reads (reads with a percentage of bases with a quality value less than 15 exceeding
20% of the total bases in the read) The filtered data, referred to as clean data, were subsequently analyzed, visualized, and mined using Online Multi-Omics Data Mining System
Assembly: hisat2 version 2.21
Supplementary files format and content: CSV files containing TPM values for each sample

source_name: skin

extract_protocol:
RNA was harvested using QIAGEN Rneasy plus kits.
mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized doublestranded DNA was then end-repaired and 5' phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control.

value: skin

value: hiPSC

tag: group

value: hiPSC-derived dental organoid at week 5


title: mesc_rad21_depletion_IAA-3h_168, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: mesc_rad21_depletion_IAA-3h_172, Smart-seq3


title: ESC, KO C2 SETb, beta 4h addback experiement 0h rep2

value: Embryonic Stem Cells

value: SET KO clone 2

value: no dox


title: E12.5+18h ureter cultures, NOGGIN treated vs control, rep2

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended for 4-plex Microarray-Slides in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 2500ng of each fluorescently labelled cRNA were used for hybridization.

scan_protocol: Slides were scanned using the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE2_107_Sep09.xml’.  Measurements of on-chip replicates were averaged using the geometric mean of ‘ProcessedSignal’ (PS) values (for each channel independently) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:  normalized PSArray i = PSArray i x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized PS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

source_name: control 2

label_protocol: 200ng of total RNA were used to synthesize AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#AM1753, Thermo Fisher Scientific) according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1) and reaction volumes were halved, and just one round of T7 amplification was conducted.

extract_protocol: Extraction of total RNA was performed using peqGOLD RNAPure (VWR Peqlab) according to the manufacturer’s recommendations.

treatment_protocol: Ureters were mechanically dissected from E12.5 embryos and cultured on transwell membranes for 18h in medium containing 10 µg/ml NOGGIN or inmedium without NOGGIN.

value: NMRI

value: wildtype

value: mixed

tag: culture time

value: ureter

source_name: NOGGIN treated 2

value: 10 µg/ml NOGGIN


title: hiPSC-derived dental organoid at Week5-2

description: Library name: sample-5


title: E12.5+18h ureter cultures, NOGGIN treated vs control, rep1

source_name: control 1

source_name: NOGGIN treated 1


title: ESC, KO C1 SETb, beta 4h addback experiement 1h rep2

value: KH2 SET-KO pBS31-HA-SETb

value: SET KO clone 1 + SETb


title: mesc_rad21_depletion_IAA-3h_170, Smart-seq3

source_name: mouse embryonic stem cell


title: 00077E8E43

description: Library name: 00077E8E43

source_name: whole brain hemisphere

value: whole brain hemisphere


title: hiPSC-3

description: Library name: sample-3


title: mesc_rad21_depletion_IAA-3h_166, Smart-seq3


title: 00077EA94E

description: Library name: 00077EA94E


title: hiPSC-derived dental organoid at Week5-1

description: Library name: sample-4


title: mesc_rad21_depletion_IAA-3h_167, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_164, Smart-seq3


title: 00077E8CD3

description: Library name: 00077E8CD3


title: 00077E8CCF

description: Library name: 00077E8CCF


title: hiPSC-2

description: Library name: sample-2


title: ESC, KO C1 SETb, beta 4h addback experiement 1h rep1

value: 1ug/ml doxycycline, 1h


title: mesc_rad21_depletion_IAA-3h_165, Smart-seq3


title: hiPSC-1

description: Library name: sample-1

value: skin


title: 00077E8EB8

description: Library name: 00077E8EB8


title: 00077E8653

description: Library name: 00077E8653


title: ESC, WT SETb, beta 4h addback experiement 1h rep2

value: WT


title: mesc_rad21_depletion_IAA-3h_163, Smart-seq3


title: GM04521, 3D-3

description: Library name: sample-6

source_name: conjuctiva

value: conjuctiva

value: fibroblast

value: 3D scaffold culture condition


title: mesc_rad21_depletion_IAA-3h_162, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: ESC, WT SETb, beta 4h addback experiement 1h rep1

value: Embryonic Stem Cells


title: mesc_rad21_depletion_IAA-3h_161, Smart-seq3


title: 00077E82F7

description: Library name: 00077E82F7


title: ESC, KO C1 SETb, beta 4h addback experiement 0h rep2

value: SET KO clone 1

value: no dox


title: 00077E8223

description: Library name: 00077E8223


title: 00077E82E3

description:
Library name: 00077E82E3
Original label before genotype mismatch fix: 00077E83E3


title: GM04521, 3D-2

description: Library name: sample-5


title: GM04521, 2D-3

description: Library name: sample-3

value: 2D culture condition


title: GM04521, 3D-1

description: Library name: sample-4


title: ESC, WT SETb, beta 4h addback experiement 0h rep1


title: ESC, WT SETb, beta 4h addback experiement 0h rep2


title: mesc_rad21_depletion_IAA-3h_160, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv


title: mesc_rad21_depletion_IAA-3h_159, Smart-seq3


title: 00077E7819

description: Library name: 00077E7819


title: 00077E7879

description: Library name: 00077E7879


title: mesc_rad21_depletion_IAA-3h_158, Smart-seq3


title: GM04521, 2D-1

description: Library name: sample-1


title: ESC, KO C2 SETa, alpha 4h addback experiement 4h rep2

source_name: KH2 SET-KO pBS31-HA-SETa

value: KH2 SET-KO pBS31-HA-SETa

value: SET KO clone 2 + SETa

value: 1ug/ml doxycycline, 4h


title: ESC, KO C2 SETa, alpha 4h addback experiement 2h rep2

value: SET KO clone 2

value: 1ug/ml doxycycline, 2h


title: GM04521, 2D-2

description: Library name: sample-2


title: 00077E7666

description: Library name: 00077E7666

value: whole brain hemisphere


title: 00077E76EB

description: Library name: 00077E76EB


title: ESC, KO C2 SETa, alpha 4h addback experiement 4h rep1


title: ESC, KO C2 SETa, alpha 4h addback experiement 2h rep1


title: 00077E75DE

description: Library name: 00077E75DE


title: ESC, KO C1 SETa, alpha 4h addback experiement 4h rep2

value: SET KO clone 1 + SETa


title: mesc_rad21_depletion_IAA-3h_157, Smart-seq3


title: E13.75+18h ureter cultures, NOGGIN treated vs control, rep1

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended for 4-plex Microarray-Slides in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 2300ng of each fluorescently labelled cRNA were used for hybridization.

treatment_protocol: Ureters were mechanically dissected from E13.75 embryos and cultured on transwell membranes for 18h in medium contraining 10 µg/ml NOGGIN or in medium without NOGGIN.

value: NMRI

value: wildtype

value: mixed

value: ureter

value: 10 µg/ml NOGGIN


title: 00077E669E

description: Library name: 00077E669E


title: mesc_rad21_depletion_IAA-3h_156, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: mesc_rad21_depletion_IAA-3h_154, Smart-seq3


title: E13.75+18h ureter cultures, NOGGIN treated vs control, rep2


title: ESC, KO C1 SETa, alpha 4h addback experiement 4h rep1

value: Embryonic Stem Cells


title: E14.5 ureters, Smad4cKO (UE) vs control, rep2

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol V6.7’, except that 2500ng of each fluorescently labelled cRNA were used for hybridization.

label_protocol: 150ng of total RNA were used as input. Synthesis of Cy3- or Cy5-labeled cRNA was performed in ¾ reaction volumes with the ‘Low Input Quick Amp Labeling Kit, Two Color’ (#5190-2944, Agilent Technologies) according to the manufacturer’s recommendations.

treatment_protocol: Ureters were mechanically dissected from E14.5 embryos.

value: male

source_name: Smad4cKO (UE) 2


title: mesc_rad21_depletion_IAA-3h_155, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_152, Smart-seq3


title: ESC, KO C1 SETa, alpha 4h addback experiement 2h rep2

value: SET KO clone 1


title: mesc_rad21_depletion_IAA-3h_153, Smart-seq3


title: 050924 siSet8 PE1h M3

city: San Diego

first: Yuliang

last: Tan

address: 9500 Gilman Dr.

institute: UCSD

description:
Library name: Sample 16
H4K20me3

data_processing:
Basecalls performed using CASAVA version 1.4
The sequencing reads were aligned to rn7 using Bowtie2 using very sensitive parameters.
The common artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data.
CUT&RUN enriched region identification, and quality control were performed using Samtools and HOMER, as described in our previously published methods.Briefly, we created tag directories for each individual sample, allowing no more than 2 tags per base pair and the combined replicates of each treatment, and then normalized each directory to the total number of mapped tags, ensuring each directory contained 10 million tags. We next made peak calls with a very low threshold, as required for IDR (findPeaks -style histone -o auto), for the individual samples, combined replicates, individual pseudo-replicates, and combined pseudo-replicates.
We then applied the HOMER-IDR program to format the data for the IDR R package, determined the IDR threshold and identified the top peaks above that threshold.
Assembly: rn7
Supplementary files format and content: Bedgraph
Library strategy: CUT&Run

source_name: Heart

growth_protocol: Six-week-old male Sprague–Dawley rats were anesthetized with Ketamine (45–90 mg/kg i.p.) and Xylazine (5–13 mg/kg i.p.). Hearts were extracted and perfused using a Langendorff system with calcium depletion perfusion buffer (mmol/L: 120 NaCl, 5.4 KCl, 1.2 NaH2PO4·7H2O, 20 NaHCO3, 1.6 MgCl2·6H2O, 5 taurine, 5.6 glucose, and 10 2,3-butanedione monoxime [BDM]), followed by type II collagenase digestion at 37 °C. The ventricular tissue was cut using sterilized scissors, and the cells were disassociated by pipetting and then filtered using 250 µm pore-size mesh. Ventricular myocytes were collected by centrifugation at 50 xg for 1 min. Myocytes were then washed and purified using perfusion buffer containing 0.1% fatty acid-free bovine serum albumin (BSA), 1 mmol/L ATP (pH 7.2), and 1 mmol/L glutamine with CaCl2 added gradually until reaching a Ca2+ concentration of 1.8 mmol/L. The purified myocytes were then resuspended in a defined Minimal Medium [Medium 199 (11150059, ThermoFisher, United States) supplemented with (mmol/L) 5 creatine, 2 l-carnitine, 5 taurine, 25 HEPES, 0.2% fatty acid-free BSA, 10 BDM and 1x insulin-transferrin-selenium (ITS) supplement] and seeded onto square cover slips (22 mm × 22 mm) coated with mouse laminin (10 μg/mL diluted in phosphate-buffered saline [PBS]) in 6-well plates (100,000 cells per well).

extract_protocol:
Ventricular myocytes were cultured in six well plates at 100,000 per well. Myocytes were treated with control or KMT5A siRNA as indicated for 48 hours and/or treated with phenylephrine (20 µmol/L) for 1 h before harvest. CUT&RUN was performed using the CUTANA™ CUT&RUN Kit (EpiCypher, 14-1048) and K-MetStat Panel (EpiCypher, 19-1002) according to the manufacturer’s instructions with minor modification.55 Cells were immobilized on concanavalin A coated magnetic beads (EpiCypher catalog no. 21-1401) and incubated overnight (4 °C with gentle rocking) with 1 µg antibody per sample. CUTANA pAG-MNase was then added to samples to cleave DNA selectively at antibody-bound chromatin.
10 ng genomic DNA was used to prepare sequencing libraries with the KAPA HTP/LTP Library Preparation Kits (Roche catalog no. 07961880001). Libraries were sequenced with NovaSeq 6000 system according to the manufacturer’s instructions. Paired-end fastq files were aligned to the rn7 reference genome using the Bowtie v.2 algorithm.

treatment_protocol: One hour after isolation, myocytes were washed with 2 mL medium, infected with adenovirus (multiplicity of infection = 10-200) or transfected with 25 nmol/L each of 4 pooled target-plus siRNA (Smartpool siRNA) or 100 nmol/L individual siRNAs using Dharmafect1 (Dharmacon, T-2001-01) overnight, and then cultured for another 24 hrs in Minimal Medium with or without phenylephrine (20 µmol/L) as indicated.

value: Heart

value: Ventricular myocytes

value: Primary Cells

value: prague Dawley rats

value: siSet8 PE1h


title: 050924 siCtrl PE1h M3

description:
Library name: Sample 15
H4K20me3

value: siCtrl PE1h


title: 050924 siSet8 M3

description:
Library name: Sample 14
H4K20me3


title: ESC, KO C1 SETa, alpha 4h addback experiement 2h rep1

value: KH2 SET-KO pBS31-HA-SETa

value: 1ug/ml doxycycline, 2h


title: E14.5 ureters, Smad4cKO (UE) vs control, rep1

value: NMRI

value: female

source_name: Smad4cKO (UE) 1


title: mesc_rad21_depletion_IAA-3h_151, Smart-seq3


title: NBL tumor, histotripsy treated, histotripsy side rep2

city: Chicago

first: Yuqing

last: Xue

state: IL

address: 900 E 57th St

institute: University of Chicago

description: Library name: SHW-07

library_source: genomic single cell

data_processing:
Data processing and quality control. Barcoded libraries sequenced with 80 bp paired-end reads (barcode: 12 bp cell barcode, 8 bp UMI) and 60 bp (3′ end of transcript) served as the input for data processing. The Cell Ranger package (v8.1.0; 10x Genomics, Pleasanton, CA) was used to process the scRNA-seq FASTQ files. The “cellranger count” function, with default command settings, aligned FASTQ files to the mouse GRCm39 (refdata-cellranger-arc-GRCm39-2024-A) reference genome and generated an expression matrix with gene read counts per cell. The filtered count matrices were read into the R package Seurat (v5.3.0; Satija Lab, New York, NY). Cells with less than 200 or more than 7,500 expressed genes, or more than 10% mitochondrial content were removed. Samples that had abnormal cell density distributions (more than 30% low-quality cells) were discarded. The data were normalized using the “NormalizeData” function with the “LogNormalize” method. To reduce background signals before integration, “FindVariableFeatures” was used to identify the top 2,000 feature genes with the highest variability. Samples were then integrated with the “IntegrateData” function using these feature genes to remove batch effects. The “ScaleData” function with default settings was applied to the integrated dataset, followed by Principal Component Analysis (PCA) using the “RunPCA” function.
Assembly: GRCm39
Supplementary files format and content: .rds file generated using Seurat (R package). The .rds file contains a Seurat object including the gene expression matrix, cell-level metadata (e.g., sample identity, quality control metrics, clustering results, and manual cell type annotations)， and dimensionality reduction embeddings (e.g., PCA and UMAP).. Expression values are stored as normalized counts within the RNA assay.

source_name: Neuro-2a subcutaneous tumor

extract_protocol:
. Upon sacrifice, tumors were excised and the skin tissue was dissected away. Scissors were used to mince the tumor into chunks before mixing with 3 to 4 mL of PBS within a Falcon tube on ice strained through a 40 µm nylon mesh cell strainer (Thermo Fisher Scientific, Waltham, MA; cat. no. 08-771-1). The tumor chunks were collected and placed into a Falcon tube with freshly prepared 4 mL of RPMI with 5% FBS with 1 mg/mL collagenase A (Sigma-Aldrich, St. Louis, MO; cat. no. C9891) and 100 µL of 1 mg/mL DNase I (Roche, Basel, Switzerland; cat. no. 10104159001). This mixture was incubated for 30 minutes at 37°C. The Falcon tube was gently inverted every 5 minutes. After incubation, the solution was filtered through a 40 µm nylon mesh cell strainer and centrifuged for 4 minutes at 1000 rpm. The pellet was resuspended in 2.5 mL of PBS. 2.5 mL of ACK Lysing Buffer (Quality Biological, Gaithersburg, MD; cat. no. 118-156-101) for 30 seconds and incubated at room temperature for 30 seconds to remove red blood cells. After centrifugation, the supernatant was removed, and the pellet was resuspended in PBS. Trypan Blue was used to check cell viability and cell count before proceeding with Dead Cell Removal Kit (Miltenyi Biotec, Bergisch Gladbach, Germany; cat. no. 130-090-101) per manufacturer’s instructions. Cell preparations with under 70% cell viability were excluded from analysis
Library preparation and sequencing were performed by the University of Chicago Genomics Core (RRID:SCR_019196). Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (10x Genomics, Pleasanton, CA) were used for library generation and NovaSeq X-10B-100 (Illumina, San Diego, CA) for sequencing.

value: Neuro-2a subcutaneous tumor

value: Histotripsy


title: 042524 siSet8 PE1h M3

description:
Library name: Sample 12
H4K20me3


title: ESC, WT SETa, alpha 4h addback experiement 4h rep2

value: WT

value: 1ug/ml doxycycline, 4h


title: 050924 siCtrl M3

description:
Library name: Sample 13
H4K20me3

value: siCtrl


title: mesc_rad21_depletion_IAA-3h_149, Smart-seq3

city: Beijing

last: Xie

data_processing:
Smart-seq3 data were processed using zUMIs (https://github.com/sdparekh/zUMIs).
Bulk RNA-seq data were mapped to human reference genome using STAR and RSEM was used to calculate mRNA count for each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA counts for each cell and sample
Supplementary files format and content: tab-delimited text files include cell barcode and sample information for Smart-seq3

extract_protocol:
Isolated single cell was lysed wih gentle lysis buffer (containing 0.45% NP-40), and the supernant was collected for the construction of sequencing library.
Collected supernant was amplified with standard Smart-seq3 protocol, then perform library preparation with homemade Tn5 transposase.
Smart-seq3 & bulk RNA-seq

value: mouse embryonic stem cell

value: IAA (3h)


title: mesc_rad21_depletion_IAA-3h_150, Smart-seq3


title: NBL tumor, histotripsy treated, contralateral side

description: Library name: SHW-05

value: Contralateral


title: ESC, WT SETa, alpha 4h addback experiement 4h rep1

value: Embryonic Stem Cells


title: NBL tumor, histotripsy treated, histotripsy side

description: Library name: SHW-06


title: NBL tumor, histotripsy treated, contralateral side rep2

description: Library name: SHW-08


title: ESC, WT SETa, alpha 4h addback experiement 2h rep2


title: mesc_rad21_depletion_IAA-3h_148, Smart-seq3


title: ESC, KO C2 SETb, beta 4h addback experiement 0h rep1

value: KH2 SET-KO pBS31-HA-SETb

value: SET KO clone 2

value: no dox


title: NBL tumor, untreated rep3

description: Library name: LWU-3

value: Untreated control


title: ESC, WT SETa, alpha 4h addback experiement 2h rep1


title: 042524 siCtrl PE1h M3

description:
Library name: Sample 11
H4K20me3

value: Heart

value: Ventricular myocytes

value: Primary Cells

value: prague Dawley rats

value: siCtrl PE1h


title: mesc_rad21_depletion_IAA-3h_147, Smart-seq3


title: ESC, KO C2 SETa, alpha 4h addback experiement 1h rep2

value: KH2 SET-KO pBS31-HA-SETa

value: SET KO clone 2 + SETa

value: 1ug/ml doxycycline, 1h


title: 042524 siCtrl M3

description:
Library name: Sample 9
H4K20me3

value: siCtrl


title: 042524 siSet8 M3

description:
Library name: Sample 10
H4K20me3


title: NBL tumor, untreated rep2

description: Library name: LWU-2

value: Neuro-2a subcutaneous tumor


title: mesc_rad21_depletion_IAA-3h_146, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: mesc_rad21_depletion_IAA-3h_145, Smart-seq3


title: ESC, KO C2 SETa, alpha 4h addback experiement 0h rep2

value: Embryonic Stem Cells


title: Uninfected-iSLK-ALT-C

city: Gainesville

first: Rolf

last: Renne

state: FL

address: 1200 Newell Dr.

institute: University of Florida

description: Library name: Sample 6

data_processing:
Paired-end reads were quality checked using FastQC.
The reads in each sample were trimmed using fastp to remove adapter sequences.
Assembly: hg38 + NC_009333.1
Supplementary files format and content: alignment-Results of STAR alignment to hg38plusKSHV
Supplementary files format and content: deseq2-gene-level differential expression results

source_name: iSLK

growth_protocol: Cells were grown at 37°C and 5% CO2 in a humidified incubator and were cultured in RPMI 1640 plus 10% fetal bovine serum and 1% Penicillin-Streptomycin.

extract_protocol:
Total RNA was isolated from cultured cells using the TRIzol reagent (Ambion) as per manufacturer's protocol. Ribosomal RNA was depleted from total RNA using the NEB rRNA depletion kit (E6310)
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760) was used to prepare stranded RNA-Seq libraries.

treatment_protocol: Transfection with pcDNA empty vector od pcDNA-ALT using X-tremeGENE reagent

value: iSLK

value: Renal carcinoma cells

value: WT

value: Transfection with ALT plasmid (pcDNA-ALT)


title: 040424 siSet8 PE1h M1

description:
Library name: Sample 8
H4K20me1

value: Heart

value: siSet8 PE1h


title: mesc_rad21_depletion_IAA-3h_144, Smart-seq3

first: Xiaoliang

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University


title: NBL tumor, untreated

description: Library name: LWU-1

value: Untreated control


title: ESC, KO C1 SETb, beta 4h addback experiement 0h rep1

value: KH2 SET-KO pBS31-HA-SETb

value: SET KO clone 1

value: no dox


title: 040424 siCtrl PE1h M1

description:
Library name: Sample 7
H4K20me1

value: Ventricular myocytes

value: Primary Cells

value: prague Dawley rats

value: siCtrl PE1h


title: 040424 siSet8 M1

description:
Library name: Sample 6
H4K20me1


title: ESC, KO C2 SETa, alpha 4h addback experiement 0h rep1

value: KH2 SET-KO pBS31-HA-SETa

value: SET KO clone 2


title: ESC, KO C2 SETa, alpha 4h addback experiement 1h rep1

value: Embryonic Stem Cells

value: SET KO clone 2 + SETa

value: 1ug/ml doxycycline, 1h


title: Uninfected-iSLK-ALT-A

description: Library name: Sample 4

value: iSLK

value: Renal carcinoma cells

value: WT


title: Uninfected-iSLK-Control-C

description: Library name: Sample 3

value: Transfection with control plasmid (pcDNA empty vector)


title: Uninfected-iSLK-ALT-B

description: Library name: Sample 5

value: Transfection with ALT plasmid (pcDNA-ALT)


title: ESC, KO C1 SETa, alpha 4h addback experiement 1h rep2

value: SET KO clone 1 + SETa


title: ESC, KO C1 SETa, alpha 4h addback experiement 0h rep2

value: SET KO clone 1


title: ESC, KO C1 SETa, alpha 4h addback experiement 1h rep1


title: mesc_rad21_depletion_IAA-3h_141, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: 040424 siCtrl M1

description:
Library name: Sample 5
H4K20me1

value: Heart

value: Ventricular myocytes

value: Primary Cells

value: siCtrl


title: Uninfected-iSLK-Control-A

description: Library name: Sample 1


title: Uninfected-iSLK-Control-B

description: Library name: Sample 2


title: mesc_rad21_depletion_IAA-3h_142, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_140, Smart-seq3