title: PDCs, IgG CUT&Tag, rep1

first: Chunlong

last: Zhong

address: 150 Jimo Road

department: Department of Neurosurgery

institute: Shanghai East Hospital, School of Medicine, Tongji University

description: Library name: IgG, rep1

data_processing:
Raw sequence reads underwent initial quality control using FastQC (v0.20.0)
Clean reads were obtained by removing adapter sequences, poly-N stretches, and low-quality reads. Quality-filtered reads were then mapped to the reference genome using BWA (v0.7.12)
Peak calling was performed using MACS2 (v2.1.0). Peaks were adjusted to a uniform size (500 bp) centered on peak summits
Motif discovery within these loci was conducted using HOMER (v4.9.1) with the command: findMotifsGenome.pl -len 8,10,12,14 -gc -size given -homer2 -dumpFasta.
Genomic annotation and identification of the nearest genes associated with peaks were performed using ChIPseeker.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

source_name: patient-derived glioma cells

growth_protocol: PDCs were maintained in DMEM/F12 medium supplemented with B27 (1:50, Gibco, USA), basic fibroblast growth factor (bFGF, PeproTech, USA) at 25 ng/mL, epidermal growth factor (EGF, PeproTech, USA) at 50 ng/mL, 10% fetal bovine serum (FBS, Gibco, USA), and 1% penicillin-streptomycin (Thermo, USA).

extract_protocol:
CUT&Tag was performed following previously established protocols using the CUT&Tag assay kit (Vazyme, TD904) (Kaya-Okur et al, 2019).
Approximately 1 × 105 PDCs were bound to ConA beads, followed by overnight incubation at 4°C with either a primary antibody or control IgG on a rotator. The next day, a secondary antibody was added and incubated for 60 minutes at room temperature, followed by pA/G-Tn5 transposome incubation and tagmentation in an activating buffer supplemented with magnesium. Adaptor-ligated DNA fragments were extracted and PCR-amplified using indexing primers (TD202, Vazyme). The amplified products were purified with VAHTS DNA Clean Beads (N411-01, Vazyme), and the DNA library's quantity and quality were assessed using a Qubit™ 4 Fluorometer and Bioanalyzer 2100 (Invitrogen). Libraries were sequenced on the Illumina platform by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China), generating 150 bp paired-end reads.

treatment_protocol: 5 μM CX5461 treated for 24 hours

tag: cut&tag antibody

value: Rabbit IgG (#2729, Cell Signaling)

value: patient-derived glioma cells

value: glioma cells

value: IDH/ATRX WT


title: pBUC_50lp2

status: Public on Aug 10 2026

type: SRA

city: Rehovot

first: Sharon

last: Schlesinger

address: Herzl 229

department: Animal Science

country: Israel

institute: Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem

description: Library name: P10_WJ

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor and polyA using Cutadapt
Trimmed sequence reads were mapped to Bos_taurus.ARS-UCD1.2 genome using STAR
Read count extraction to fatures using HTSeq
Normalization of the counts and differential expression analysis using DESeq
Assembly: Bos_taurus.ARS-UCD1.2
Supplementary files format and content: raw_counts_wj_sv40.xlsx
Library strategy: Bulk MARS-seq

molecule: polyA RNA

organism: Bos taurus

source_name: umbilical cord

growth_protocol: mesenchymal cells were maintained in low glucose Dulbecco's Modified Eagle's Medium, containing 10% Fetal Bovine Serum (FBS), penicillin-streptomycin solution 1% , Glutamine 1%, in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted via PureLink RNA Minikit
Library preparation was done by Weizmann Institute, Rehovot. Sequencing Libraries were prepared using Bulk MARS-Seq. SR reads were sequenced on 1 lane(s) of an Illumina NovaSeq Sp (100 cycles). The output was ~25 million reads per sample.

treatment_protocol: cells were immortalized by transient transfection of a plasmid carrying the SV40 large T antigen for the WJ-SV40 line

tag: tissue

value: umbilical cord

tag: cell line

value: primary cell culture

tag: cell type

value: mesenchymal stem cells

tag: breed

value: Holstein

tag: treatment

value: no treatment, 50 days culturing


title: SJRHB012_Y_DY8439_VT

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas

country: USA

institute: St. Jude Children's Research Hospital

description:
Library name: SJRHB000912_C7
2344266

data_processing:
https://wiki.stjude.org/display/CAB/RNAseq+differential+gene+expression+analysis#RNAseqdifferentialgeneexpressionanalysis-1.WorkflowSummary
Assembly: hg38
Supplementary files format and content: gene counts

molecule: total RNA

organism: Homo sapiens

source_name: Tumor

growth_protocol: Cells dissociated from O-PDX tumors were seeded onto PrimeSurface 96-well low-adhesion U-bottom plates at 25,000-50,000 cells/well (S-Bio, MS-9096UZ). Plates were centrifuged at 300xg for 3 minutes to aggregate the cells in each well. After 5-7 days, organoids had formed and were transferred to 0.5% geltrex- (Thermo, A14133-02) coated 10cm standard tissue culture plates. Cells that migrate from the organoid were considered a 2D culture and referred to as passage 0. Additional organoids were collected for downstream applications and cryopreserved in 90% FBS and 10% DMSO. After 7-10 days, 2D cells were passaged to fresh geltrex-coated 10cm dishes for 5-7 days and harvested for downstream molecular assays and cryopreserved stocks.

value: Tumor

value: VT

value: RMS

tag: batch


title: Multiome, Col-0 72h seedling, control, rep3, RNA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: Library name: 241001_ethylene_Ath_72h_seedling_air_3_1_multi_RNA

library_source: transcriptomic single cell

data_processing:
Cell by gene matrices and fragment files were generated with Cellranger-arc v2.0.2
Assembly: TAIR10 genome; Araport 11 transcriptome
Supplementary files format and content: harmony.rds, Seurat object that contains the snRNA-seq dataset of whole seedlings
Supplementary files format and content: apical_clusters.rds, Seurat object that contains cells that compose the apical seedling
Supplementary files format and content: spatial_multiome_imputed_250825.rds, Seurat object that contains cells related to the spatial multi-modal integration
Supplementary files format and content: GA_subclust26_multiome_imputed_250825.rds, Seurat object that contains the AHR (cluster 26) cells

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Arabidopsis seedlings were grown at 23C in complete darkness for 72h prior to harvest

extract_protocol:
Nuclei were extracted as described in (47), with slight modifications. Plants were grown as described previously, and nuclei were immediately extracted from air-grown seedlings following 28h, 48h, and 72h of growth and 72 h-old seedlings following 4h ET treatment in a green room. Purified nuclei were used as input for the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression kit.
Sequencing libraries were constructed following the manufacturer’s instructions and were sequenced with the Illumina NovaSeq X.

treatment_protocol: Control plants were treated with Zero grade air in sealed chambers at a rate of 30mL / min. Treated plants were exposed to 10 ppm ethylene gas at a flow rate of 30mL / min for the indicated treatment lengths.

value: Seedling

tag: genotype

value: Control

tag: developmental timepoint


title: pBUC_50pl1

description: Library name: P10_BUC


title: Multiome, Col-0 48h seedling, control, rep1, ATAC

description: Library name: 240111_ethylene_Ath_2do_seedling_air_1_1_multi_ATAC

library_source: genomic single cell

molecule: genomic DNA


title: pBUC_12pl3

description: Library name: P4_WJ_Male

value: no treatment, 12 days culturing


title: iBUC_165pl2

description: Library name: SV-40_2D-2

value: Immortalized SV-40

value: immortalized cells, 165 days culturing


title: KPCY cells, Scr_biol rep 3

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

data_processing:
Illumina base call files were de-multiplexed by bcl2fastq2 (v. 2.20) on Basespace. Adaptor sequences were trimmed and low-quality reads (< 35 base pairs) were discarded. Additionally, Bowtie was used to remove read pairs that aligned against abundant sequences. Demultiplexed read sequences were then aligned to the mm10 genome reference using STAR aligner. The number of aligned reads to each annotated gene was tallied with RnaReadCounter to generate read-count matrices for all samples, which were used as inputs for downstream analyses. Bowtie, STAR, and RnaReadCounter are tools built under RNA-Seq Alignment (v 1.1.1).
Genes with less than 20 read counts in at least 2 samples were filtered out and differential gene expression analysis and processed using DESeq2 (v1.36.0) in R (version 4.2.1)
Differential expression analysis was performed using DESeq2, and genes with fold-change ≥ 1.5 and p-value < 0.05 were considered as differentially expressed
Assembly: mm10
Supplementary files format and content: tab-delimited text file of raw read counts for each sample

organism: Mus musculus

source_name: KPCY pancreatic cancer cells

extract_protocol:
0.3x106 were seeded in a six-well plate and 24 hours later, the cells were trypsinized, and RNA was isolated using Qiazol/chloroform, and miRNeasy kit followed by RNA Seq
Samples with a RIN of 7 and above were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina). Sequencing was performed on the Illumina NextSeq 2000 using the P3 reagents (100 cycle; Illumina) to generate paired-end reads (59 x 59 base pairs).

treatment_protocol:
KPCY Scr and miR-27a KD cells were grown in DMEM media containing L-Glutamine, 4.5g/L Glucose, without Sodium Pyruvate, and 10% Fetal Bovine Serum using a six well plate.
miR-27a  stable cells were generated by transducing miR-27a lentiviral vectors inhibiting miR-27a-3p and scrambled sequence. Transduced cells were treated with 2 µg/mL of puromycin for 7 days and the puromycin resistant cells were further grown passaged and used for future experiments.

value: KPCY pancreatic cancer cells

tag: Sex

value: Male

value: Scrambled


title: RPMI8226, exp1, GFP-KRAS High, R6

status: Public on Aug 11 2026

city: Bethesda

first: Ryan

middle: M

last: Young

state: MD

address: 9000 Rockvill Pike, Bld. 10, rm. 6N105

department: LYMB

institute: NIH/NCI

description: Library name: RPMI8226_GFP_KRAS_6H

library_source: genomic

data_processing:
Demultiplexing was performed with DRAGEN (v3.7.4, Illumina), and sequencing reads were aligned to the reference sgRNA library using Bowtie2 (v2.2.9).
Assembly: hg19
Supplementary files format and content: Normalized readcounts for each sgRNA in the Brunello sgRNA library are found in KRAS-stability-norm-counts.txt
Library strategy: CRISPR Screen

source_name: multiple myeloma cell line

growth_protocol: XG7 and RPMI 8226 cells stably expressing Cas9(26) ectopically expressing mNG-KRASG12D were transduced in triplicate with the Brunello sgRNA library. Following transduction, cells were selected with 1 μg/mL puromycin, and Cas9 expression was induced by 100 ng/mL doxycycline treatment. Cells were expanded for 7 days, after which 5×10⁷ cells were harvested and stored as the baseline (input) sample. The remaining ~8×10⁷ cells were stained with anti-Lyt2 antibody (BioLegend) at a 1:1000 dilution in PBS supplemented with 0.5% FBS for 20 min on ice. Cells were washed, resuspended at ~2×10⁷ cells/mL in PBS with 0.5% FBS, and sorted on a Sony MA900 cell sorter to isolate the top and bottom 5% of mNG–KRAS-expressing populations, yielding ~2×10⁶ cells per fraction.  Each biological replicate was independently sorted in two technical replicates.

extract_protocol:
Genomic DNA from sorted populations was extracted using the QIAamp DNA FFPE Advanced Kit (QIAGEN) according to the manufacturer’s protocol.
Genomic DNA from CRISPR screens was processed using a nested PCR strategy. In the first round, sgRNA sequences were amplified from genomic DNA, followed by a second round of PCR to append Illumina-compatible sequencing adapters. Each PCR reaction was performed with ExTaq DNA polymerase (Takara) for 18–20 cycles per round. Amplified products were size-selected using a 2% E-Gel SizeSelect agarose gel (Invitrogen) and quantified with the Qubit dsDNA High-Sensitivity Assay (Thermo Fisher Scientific).

value: multiple myeloma cell line

value: Cas9 clone


title: SJRHB012_Y_DY8438_2D

description:
Library name: SJRHB000912_C5
2344265

source_name: Cells

value: Cells


title: pBUC_12pl2

description: Library name: P3_WJ

value: umbilical cord

value: primary cell culture

value: mesenchymal stem cells


title: Multiome, Col-0 72h seedling, 4h control, rep2, RNA

description: Library name: 241001_ethylene_Ath_72h_seedling_air_2_1_multi_RNA

value: 4h control


title: SJRHB010927_X1_DYE8740_T0

description:
Library name: SJRHB010927_X1
2364124

value: Tumor


title: pBUC_12pl1

description: Library name: P3_BUC_Mix

value: Holstein


title: SJRHB012_Y_DY8437_3D

description:
Library name: SJRHB000912_C2 Rep 1
2344264

value: RMS


title: Control (Ehmt1+/+, Ehmt2+/+, Rosa26 TdTomato/+, Wnt1-cre), biol rep3, IgG

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
Library name: df_9_Ig
Cut&Run for IgG

data_processing:
Adapters were trimmed from fastq files using TrimGalore with default parameters (ver. 0.6.4 using Cutadapt 4.2). The resulting reads were mapped with bowtie2 (ver. 2.5.0) with the parameters -X 2000 -N 1 --local --dovetail to the mm10 assembly. Only reads mapping to the 19 autosomal chromosomes were retained, and any reads mapping to the mm10 CUT&RUN blacklist were removed. Duplicates were marked using Picard.
Normalized bw files were produced for each sample using deeptools bamCoverage with the parameters --normalizeUsing CPM  --extendReads. H3K9me2 and H3K27ac samples were normalized to their matching IgG using deeptools bigwigCompare with the parameter --operation substract.
Z-scores for each bin were calculated from count files produced as above, ignoring any window with 0 counts in any sample, and rolling means incorporating the 5 windows flanking each window to each side were calculated from the z-scores.
Assembly: mm10
Supplementary files format and content: z-score bigwigs containing rolling means of z-scores from 1kb bins
Library strategy: CUT&Run

source_name: Branchial Arches

extract_protocol:
Branchial arches from E11.5 control (Ehmt1+/+, Ehmt2+/+, Rosa26 TdTomato/+, Wnt1-cre) were dissected in cold PBS. The tissues were then dissociated into single cell solutions with papain. Cells were washed twice in PBS, and then flow sorted on endogenous Td Tomato expression.
Td Tomato cells were collected processed for CUT&RUN via Epichypher CUT&ANA CUT&RUN kit instructions.

value: Branchial Arches

value: Neural Crest Cells

value: Ehmt1f/f, Ehmt2f/f, Rosa26 TdTomato/+, Wnt1-cre

tag: antibody

value: IgG


title: Control (Ehmt1+/+, Ehmt2+/+, Rosa26 TdTomato/+, Wnt1-cre), biol rep3, H3K9me2

description:
Library name: df_9_me2
Cut&Run for H3K9me2


title: SJRHB011_X_DY8436_VT

description:
Library name: SJRHB000911_C5
2344263

value: VT


title: Control (Ehmt1+/+, Ehmt2+/+, Rosa26 TdTomato/+, Wnt1-cre), biol rep2, IgG

description:
Library name: df_7_IG
Cut&Run for IgG


title: Multiome, Col-0 48h seedling, control, rep1, RNA

description: Library name: 240111_ethylene_Ath_2do_seedling_air_1_1_multi_RNA

value: Seedling

value: Control


title: SJRHB011_X_DY8435_2D

description:
Library name: SJRHB000911_C3
2344262


title: Multiome, Col-0 72h seedling, 4h ethylene, rep1, RNA

description: Library name: 220422_multiRNA_Ath_3do_seedling_4ET_1_1

value: 4h ethylene


title: Control (Ehmt1+/+, Ehmt2+/+, Rosa26 TdTomato/+, Wnt1-cre), biol rep1, IgG

description:
Library name: df_6_IG
Cut&Run for IgG


title: Control (Ehmt1+/+, Ehmt2+/+, Rosa26 TdTomato/+, Wnt1-cre), biol rep3

description: Library name: control.b3

data_processing:
Adapters were trimmed from fastq files using TrimGalore with default parameters. Reads were mapped to the mm10 genome using STAR version 2.7.10a with the parameters --peOverlapNbasesMin 5 --alignIntronMax 100000 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16. Duplicates were marked by Picard and ignored for further analysis. Read counts on genes were calculated using an in-house R script utilizing the GenomicRanges functions summarizeOverlaps.
Assembly: mm10
Supplementary files format and content: count table, number of reads on genes

extract_protocol:
Qiagen Rneasy Plus Mini Kit
Illumina Stranded mRNA Prep, Ligation


title: SJRHB011_X_DY8434_3D

description:
Library name: SJRHB000911_C1
2344261


title: Multiome, Col-0 72h seedling, 0h control, rep1, RNA

description: Library name: 220422_multiRNA_Ath_3do_seedling_0ET_1_1

value: 0h control


title: Control (Ehmt1+/+, Ehmt2+/+, Rosa26 TdTomato/+, Wnt1-cre), biol rep2

description: Library name: control.b2


title: SJRHB013_X_DY8433_2D

description:
Library name: SJRHB000913_C2
2344260

value: Cells


title: Control (Ehmt1+/+, Ehmt2+/+, Rosa26 TdTomato/+, Wnt1-cre), biol rep1

description: Library name: control.b1


title: Kidney 8M single-cell ATAC library

city: Guangzhou

first: Yage

last: Nie

address: No.74 Zhongshan Rd.2, Guangzhou

country: China

institute: Sun Yat-sen University

description:
Library name: KIDNEY_8M_ATAC
10x Genomics single-cell multiome chromatin accessibility library from kidney tissue.

data_processing:
Raw base call files were demultiplexed to FASTQ files.
FASTQ files were processed with Cell Ranger ARC pipelines to generate gene expression matrices, chromatin accessibility matrices, peak calls, and fragment files.
Filtered Feature Barcode matrices were exported in MEX format with uniquely named barcodes, features, and matrix files for each sample.
H5/HDF5 archives and aggregation.csv files are provided when available from Cell Ranger output.
mm10
Assembly: Processed scRNA-seq data are cell-level Feature Barcode MEX matrices and H5 files from Cell Ranger filtered feature-barcode outputs.
Supplementary files format and content: Processed scRNA-seq data are cell-level Feature Barcode MEX matrices and H5 files from Cell Ranger filtered feature-barcode outputs.
Supplementary files format and content: Processed scATAC-seq data are cell-level Feature Barcode MEX matrices and H5 files from Cell Ranger filtered feature-barcode outputs.

source_name: kidney

growth_protocol: Tissues were collected from 8-month-old POLG F1 mice and processed for cell isolation.

extract_protocol:
Single-cell suspensions were prepared from lung and kidney tissues following the 10x Genomics single-cell multiome workflow.
10x Genomics Chromium single-cell multiome gene expression and chromatin accessibility libraries were prepared according to the manufacturer's protocol and sequenced using paired-end Illumina sequencing.

value: kidney

value: POLG F1


title: DKO (Ehmt1f/f, Ehmt2f/f, Rosa26 TdTomato/+, Wnt1-cre), biol rep3

description: Library name: DKO.b3


title: DKO (Ehmt1f/f, Ehmt2f/f, Rosa26 TdTomato/+, Wnt1-cre), biol rep2

description: Library name: DKO.b2


title: Kidney 8M single-cell gene expression library

description:
Library name: KIDNEY_8M_GEX
10x Genomics single-cell multiome gene expression library from kidney tissue.


title: DKO (Ehmt1f/f, Ehmt2f/f, Rosa26 TdTomato/+, Wnt1-cre), biol rep1

description: Library name: DKO.b1


title: SJRHB012_X_DY8431_2D

description:
Library name: SJRHB000912_C4
2344258


title: PHOX2A.W137C.Rep2

type: protein

city: Boston

first: Stephen

last: Gisselbrecht

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

hyb_protocol: First, microarrays were double stranded by on-slide primer extension, as described in Berger et al. (Berger et al. Nat Biotechnol. 2006 (PMID 16998473)). The primer extension mixture contains Cy3-conjugated dUTP, to allow for quantification of the relative amount of double stranded DNA on each spot. Double stranded microarrays were pre-wetted in standard phosphate buffered saline (PBS) (10mM PO43-, 137 mM NaCl, 2.7 mMKCl, pH7.4) / 0.01% Triton-X 100 for 5 minutes. PBS / 2% (wt/vol) nonfat dried milk (Sigma) was applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarray was incubated for 1 hour at room temperature. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% (vol/vol) Triton X-100 for 2 min. Proteins were diluted in a 75-μl protein binding mixture containing PBS / 2% (wt/vol) milk, 51.3 ng/μl salmon testes DNA (Sigma), 0.2 μg/μl bovine serum albumin (New England Biolabs). Pre-incubated protein binding mixtures were applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 hour at room temperature. Microarrays were again washed once with PBS/ 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS/ 0.01% (vol/vol) Triton X-100 for 2 minutes. Alexa-488-conjugated rabbit polyclonal anti-GST antibody (Invitrogen) was diluted to 50μg/ml in PBS / 2% (wt/vol) milk and applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 30 minutes at room temperature. Microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each incubation step, microarrays and cover slips were disassembled in a staining dish filled with the first wash solution. All washes were performed in Coplin jars at room temperature on an orbital shaker at 125 rpm. Following each series of washes, microarrays were rinsed in PBS and slowly removed to ensure removal of detergent and uniform drying.

scan_protocol: Cy3 signal was scanned to assess double-stranding efficiency and Alexa488 signal was scanned at multiple photomultiplier tube gain settings on a Molecular Devices GenePix 4400A microarray scanner.

data_processing: The scanned images were analyzed with GenePix software to produce separate .gpr files for each chamber associating background-subtracted median signal intensity at a probe to probe sequence; scans were combined with Masliner and the resulting file was normalized to Cy3 signal and analyzed with the Universal PBM Analysis Suite (Berger et al., Nature Biotechnology 2006) to report Enrichment scores for each 8-mer.

molecule: protein

source_name: in vitro trancription and translation

label_protocol: Agilent microarrays (AMADID #030236) containing all 10-nt sequences were made double-stranded by primer annealing and on-array extension with Cy3-labelled nucleotides to monitor double-stranding efficiency; GST-tagged proteins were detected with Alexa488-labelled anti-GST antibody.

extract_protocol: GST fusion proteins were expressed by in vitro transcription and translation.

treatment_protocol: Variants of human transcription factor DBDs were generated by site-directed mutagenesis of cDNA and Gateway cloned into pDEST15.

tag: protein detail

value: isolated DNA-binding domain

tag: protein allele

value: putative pathogenic variant


title: Lung 8M single-cell ATAC library

description:
Library name: LUNG_8M_ATAC
10x Genomics single-cell multiome chromatin accessibility library from lung tissue.

source_name: lung

value: lung


title: SJRHB012_X_DY8430_3D

description:
Library name: SJRHB000912_C1 Rep 1
2344257


title: PHOX2A.Ref.Rep2

value: reference allele


title: PHOX2A.W137C.Rep1


title: Lung 8M single-cell gene expression library

description:
Library name: LUNG_8M_GEX
10x Genomics single-cell multiome gene expression library from lung tissue.


title: OLIG2.R156L.Rep2


title: Mouse cervix, postnatal day 15, biol rep 2

city: Columbia

first: Andrew

last: Kelleher

state: MO

address: 1030 Hitt Street

department: Ob, Gyn Womens Health

institute: University of Missouri

description:
Library name: PND15_2_cvx
Postnatal day 15 mouse cervix, biol rep 2; 10x Genomics Chromium Fixed RNA Profiling (Flex); Flex barcode BC004; EpCAM-sorted prior to library preparation

library_source: other

data_processing:
Raw FASTQ files were processed using Cell Ranger multi (v9.0.1; 10x Genomics) configured via per-timepoint CSV files specifying the Chromium Mouse Transcriptome Probe Set v1.0.1 (mm10-2020-A) and default parameters. Reads were aligned to the mouse reference genome (refdata-gex-mm10-2020-A; mm10/GRCm38) and filtered feature-barcode count matrices (.h5) were generated for each demultiplexed sample.
Ambient RNA contamination was removed from raw Cell Ranger count matrices using CellBender (v0.3.2) with default parameters to produce denoised gene expression count matrices.
Denoised count matrices were imported into R and quality-controlled using Seurat (v5.3.0). Cells were retained if they had 200-15,000 detected genes (nFeature_RNA), 0-100,000 total UMIs (nCount_RNA), and mitochondrial read fraction below 10%.
Doublets were identified and removed using scDblFinder (v1.20.2) with default parameters prior to downstream analysis.
Filtered count matrices from all timepoints were merged and integrated using Harmony (where indicated) for batch correction. Unsupervised clustering, UMAP dimensionality reduction, and cell type annotation were performed in Seurat (v5.3.0). Loupe Browser files (.cloupe) were generated using LoupeR (10x Genomics).
Assembly: mm10 (GRCm38); 10x Genomics reference package refdata-gex-mm10-2020-A
Supplementary files format and content: HDF5 (.h5) — Cell Ranger filtered feature-barcode matrix output by cellranger multi, one per demultiplexed sample. Contains a sparse UMI count matrix (genes x cell barcodes). Naming: {sample_id}_filtered_feature_bc_matrix.h5
Supplementary files format and content: HDF5 (.h5) — CellBender-denoised count matrix, one per sample, generated from Cell Ranger raw output with ambient RNA removed. These serve as input for downstream Seurat-based analysis.

molecule: other

source_name: cervix

growth_protocol: C57BL/6J female mice were housed under standard conditions. For fetal collections, a vaginal plug was defined as embryonic day 0.5 (E0.5) and developmental stage confirmed by Theiler staging at dissection. For neonatal collections, the day of birth was designated postnatal day 0 (PND0). Uterine and cervical tissues were collected at embryonic day 16.5 (E16.5) and postnatal days 1, 5, 12, and 15, with 90-125 (PND1), 85-100 (PND5), 45-60 (PND12), and 36-45 (PND15) uteri pooled per timepoint.

extract_protocol:
Uterine and cervical tissues were enzymatically dissociated in Liberase (0.2 mg/mL; Roche, 643505) diluted in phenol red-free RPMI 1640 supplemented with DNase I (0.5 mg/mL; Roche, 10104159001) for 45 min at 4°C, then 45 min at 37°C on an orbital shaker (50 RPM). To achieve an approximately 50:50 epithelial-to-non-epithelial ratio, dissociated cells from PND1-PND15 were subjected to EpCAM-based magnetic separation using anti-CD326 (EpCAM) MicroBeads (Miltenyi Biotec, 130-105-958). E16.5 cells did not meet the viability threshold (<30%) and were processed without magnetic sorting. Cell viability was assessed using a Cellometer K2 Fluorescent Cell Counter (Revvity). 250,000 cells per sample were fixed for 22 h at 4°C per the 10x Genomics Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling protocol (CG000478) and stored at -80°C.
Fixed cells were processed using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (PN-1000414; 10x Genomics). Approximately 200,000 cells per sample were hybridized with the Chromium Mouse Whole Transcriptome (WTA) probe set (PN-1000496; 10x Genomics), pooled and washed per the Chromium Fixed RNA Profiling Reagent Kit protocol (CG000527; 10x Genomics). Multiplexed samples were labeled using Flex probe barcodes (BC001-BC004): BC001 = replicate 1 uterus, BC002 = replicate 1 cervix, BC003 = replicate 2 uterus, BC004 = replicate 2 cervix. GEMs were generated on the Chromium X instrument using Next GEM Chip Q (PN-1000422; 10x Genomics), targeting >=20,000 cells per GEM well (10,000 epithelial:10,000 non-epithelial). All libraries were sequenced in paired-end mode on a NovaSeq X Plus (Illumina).

treatment_protocol: No exogenous treatment was applied to developmental atlas samples. For hormone-perturbation experiments (not included in this dataset), C57BL/6J female neonates received daily subcutaneous injections of 17beta-estradiol (E2; 8 ug/kg body weight; Sigma E8875), progesterone (P4; 50 ug/g body weight; Sigma P0130), or sesame oil vehicle from PND1 through PND5.

value: cervix

tag: strain

tag: developmental stage


title: OLIG2.Ref.Rep2


title: SJRHB031691_X3_DY8428_3D

description:
Library name: SJRHB031691_C3
2344255

value: RMS


title: Mouse uterus, postnatal day 15, biol rep 2

description:
Library name: PND15_2_ute
Postnatal day 15 mouse uterus, biol rep 2; 10x Genomics Chromium Fixed RNA Profiling (Flex); Flex barcode BC003; EpCAM-sorted prior to library preparation

source_name: uterus

value: uterus


title: MAFB.E223K.Rep2


title: MAFB.Ref.Rep2


title: SJRHB031691_X2_DY8427_VT

description:
Library name: SJRHB031691_C7
2344254

value: Tumor


title: OLIG2.R156L.Rep1


title: Mouse uterus, postnatal day 15, biol rep 1

description:
Library name: PND15_1_ute
Postnatal day 15 mouse uterus, biol rep 1; 10x Genomics Chromium Fixed RNA Profiling (Flex); Flex barcode BC001; EpCAM-sorted prior to library preparation


title: OLIG2.Ref.Rep1


title: SJRHB031691_X2_DY8426_2D

description:
Library name: SJRHB031691_C5
2344253


title: Mouse cervix, postnatal day 12, biol rep 2

description:
Library name: PND12_2_cvx
Postnatal day 12 mouse cervix, biol rep 2; 10x Genomics Chromium Fixed RNA Profiling (Flex); Flex barcode BC004; EpCAM-sorted prior to library preparation


title: MAFB.Ref.Rep1


title: SJRHB031691_X2_DY8425_3D

description:
Library name: SJRHB031691_C2
2344252


title: OTS964 C

city: Rochester

first: Clara

last: Kielkopf

state: New York

address: 601 Elmwood Ave

department: Biochemistry & Biophysics

institute: University of Rochester

description: Library name: OTS964_C

data_processing:
Performed by URGRC: raw reads were trimmed and filtered with fastp 0.23.1 (--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y -r). Reads were then aligned using STAR 2.7.9a (--twopassMode Basic --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical).
Read counts quantified by subread 2.0.3 (featureCounts -t exon -s 2 -p --countReadPairs -B -C).
Assembly: GRCh38 Primary Assembly
Supplementary files format and content: raw_counts.txt: Tab-delimited text file containing ENSEMBL gene IDs, gene symbols, and raw counts per gene for each sample.
Supplementary files format and content: *_SJ.out.tab (output from STAR): Tab-delimited text files for each sample containing splice junction counts. Column descriptions: 1. chromosome; 2. first base of junction (1-based); 3. last base of junction (1-based); 4. strand, 0 = undefined, 1 = +, 2 = -; 5. intron motif, 0 = noncanonical, 1 = GT/AG, 2 = CT/AC, 3 = GC/AG, 4 = CT/GC, 5 = AT/AC, 6 = GT/AT; 6. inclusion in annotation file, 0 = absent, 1 = present; 7. number of uniquely mapping reads spanning the junction; 8. number of multimapping reads spanning the junction; 9. maximum spliced alignment overhang.

source_name: HEK 293T

growth_protocol: Human embryonic kidney epithelial cells (HEK 293T, ATCC CRL-3216) were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNAs were extracted from transfected cells in biological triplicates using an RNeasy Mini kit (Qiagen) and further purified with an RNA Clean & Concentrator kit (Zymo Research).
siRNA and plasmid-transfected cells: the University of Rochester Genomics Research Center (URGRC) prepared polyA-selected libraries using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) according to the manufacturer’s instructions. DMSO and OTS964-treated cells: URGRC prepared polyA-selected libraries using the Illumina Stranded mRNA Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Transfections: Cells were transfected with nonspecific or SF3B1-targeting Stealth siRNAs (Thermo Fisher Sci.) and empty vector or plasmids containing wildtype, phospho-dead, or phospho-mimic SF3B1 constructs. Cells were harvested 2 days after transfection. Drug treatment: Cells were treated with 50 nM OTS964 or 0.1% DMSO for 4 hours prior to harvest.

value: HEK 293T

value: 50 nM OTS964


title: HMC3_WT_Rep4

city: Houston

first: Yi-Lan

last: Weng

state: Texas

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

description: polyA-seletion

data_processing:
Sequence read were trimmed using Trimmomatic.
The sequence reads were aligned to the human genome (hg38) using the STAR aligner.
Read count tables were then generated based on the STAR alignment to the hg39 transcriptome and subsequently normalized using DESeq2.
Assembly: hg38
Supplementary files format and content: METTL3KO_DEG.txt
Supplementary files format and content: METTL3KO_rRNAfree.TPM.txt

extract_protocol:
Total RNA was extracted using the Trizol reagent, followed by purification with Zymo RNA Clean and Concentrator.
The Smart-seq2 protocol (poly-A selection) was then applied to 100 ng of this RNA for sequencing library construction.  For rRNA-depleted RNA-seq, rRNA was depleted from 100 ng total RNA, followed by library construction using the NEBNext Ultra II Directional RNA Library Prep Kit.

value: microglial cell

value: WT


title: Mouse uterus, postnatal day 12, biol rep 2

description:
Library name: PND12_2_ute
Postnatal day 12 mouse uterus, biol rep 2; 10x Genomics Chromium Fixed RNA Profiling (Flex); Flex barcode BC003; EpCAM-sorted prior to library preparation


title: OTS964 B

description: Library name: OTS964_B


title: SJRHB071779_X2_DY8424_2D

description:
Library name: SJRHB071779_C4
2344251


title: OTS964 A

description: Library name: OTS964_A


title: Mouse uterus, postnatal day 12, biol rep 1

description:
Library name: PND12_1_ute
Postnatal day 12 mouse uterus, biol rep 1; 10x Genomics Chromium Fixed RNA Profiling (Flex); Flex barcode BC001; EpCAM-sorted prior to library preparation


title: DMSO C

description: Library name: DMSO_C

value: 0.1% DMSO


title: DMSO B

description: Library name: DMSO_B


title: SJRHB071779_X2_DY8423_3D

description:
Library name: SJRHB071779_C2
2344250


title: Multiome, Col-0 28h seedling, control, rep1, RNA

description: Library name: 240206_ethylene_Ath_28h_seedling_air_1_1_multi_RNA

value: Seedling

value: Control


title: MAFB.E223K.Rep1


title: Mouse cervix, postnatal day 5, biol rep 2

description:
Library name: PND5_2_cvx
Postnatal day 5 mouse cervix, biol rep 2; 10x Genomics Chromium Fixed RNA Profiling (Flex); Flex barcode BC004; EpCAM-sorted prior to library preparation


title: DMSO A

description: Library name: DMSO_A


title: Control (Ehmt1+/+, Ehmt2+/+, Rosa26 TdTomato/+, Wnt1-cre), biol rep2, H3K9me2

description:
Library name: df_7_me2
Cut&Run for H3K9me2

value: Branchial Arches

value: Neural Crest Cells

value: Ehmt1f/f, Ehmt2f/f, Rosa26 TdTomato/+, Wnt1-cre


title: SJRHB071779_X1_DY8422_VT

description:
Library name: SJRHB071779_C5
2344249

value: VT


title: HeLa, +DOX, day1

city: Lanzhou

first: Wenyuan

last: Zhu

state: Gansu

address: South Tianshui Road

institute: Lanzhou University

description: Library name: HeLa_+DOX_day1

data_processing:
Upon receipt of the sequencing data, bioinformatics analysis was performed. Raw reads were processed using Trim Galore (v0.6.10) (https://github.com/FelixKrueger/TrimGalore) to remove adapter sequences and low-quality bases.
Trimmed reads were aligned to human hg38 and mouse mm10 using STAR(v2.5.2b) with “--outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.02”.
Normalization factors were estimated based on mouse spike in using multiBamSummary function from deeptools(v3.5.5).
Assembly: hg38
Supplementary files format and content: bigwig files include spike-in normalized signals for each sample

source_name: Cervix

growth_protocol: HeLa cells was cultured in Dulbecco’s Modified Eagle’s Media (G4511, Servicebio, Wuhan, China) supplemented with 10% fetal calf serum (G8003, Servicebio, Wuhan, Chin) and pen/strep. cells were maintained at 37°C, 90% humidity, and 5% CO2.

extract_protocol:
Approximately 107 cells were metaboliclabelling with 500 mM 4-thiouridine (4sU) for 10 min, followed by being lysed in 5 mL TRIzol (Sangon) to extract total RNA. 100 mg total RNA was mixed with 4sU-labeled HT-22 total RNA (500 ng, as spike-in). The mixed RNA was fragmented using NaOH (final concentration is 0.2 M) for 14 min and neutralized with Tris-HCl (pH 6.8, final concentration is 0.5 M). Subsequently, RNA was purified by isopropanol and ethanol. Labelled RNA was biotinylated in 150 mL biotinylation mix (fragmented total RNA, 10 mM HEPES pH 7.5, 1 mM EDTA, 0.167 mg/mL MTSEA-biotin) for 30min at room temperature and purified by chloroform extraction.The biotinylated RNA (after denatured at 65℃ for 5min) was incubated with 50 mL Beaver Beads (blocked with 40 ng/mL glycogen for 1 h) for 15 min at RT. The 4sU-labeled RNA was eluted with 100 mM DTT and purified with the RNA clean beads (Beyotime).
DNA libraries were prepared using the Stranded mRNA-seq Lib Prep Module for Illumina (Abclonal, RK20349) according to the manufacturer’s instructions.

treatment_protocol: The control group was not induced by Dox, and the experimental group was induced by Dox(1 μg/mL) for 1 day. Dox could induce nGDOWN1.

value: Cervix

value: HeLa

value: Epithelial cell

value: inducible nGDOWN1

value: doxycycline induced, day1


title: Mouse uterus, postnatal day 5, biol rep 2

description:
Library name: PND5_2_ute
Postnatal day 5 mouse uterus, biol rep 2; 10x Genomics Chromium Fixed RNA Profiling (Flex); Flex barcode BC003; EpCAM-sorted prior to library preparation

value: uterus


title: Control (Ehmt1+/+, Ehmt2+/+, Rosa26 TdTomato/+, Wnt1-cre), biol rep1, H3K9me2

description:
Library name: df_6_me2
Cut&Run for H3K9me2


title: HeLa, control

description: Library name: HeLa_control

value: uninduced


title: Mouse uterus, postnatal day 5, biol rep 1

description:
Library name: PND5_1_ute
Postnatal day 5 mouse uterus, biol rep 1; 10x Genomics Chromium Fixed RNA Profiling (Flex); Flex barcode BC001; EpCAM-sorted prior to library preparation


title: SJRHB071779_X1_DY8421_2D

description:
Library name: SJRHB071779_C3
2344248

value: Cells

value: RMS


title: ChIP, HeLa, Input, +DOX, day1

description: Library name: ChIP_HeLa_Input_+DOX_day1

data_processing:
Sequencing data were processed as follows: trimmed reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.3.5.1) with the parameters “--end-to-end --very-sensitive --no-mixed --no-discordant -I 10 -X 700”.
Peak calling was performed using MACS3 (v3.0.1) with the settings “--format BAMPE -g hs --qvalue 0.01”.
Normalized bigWig files were generated using bamCoverage from deepTools (v3.5.5), with genomic regions from the ENCODE blacklist (hg38) excluded to minimize artifacts.
Peak annotation was carried out using the R package ChIPseeker (v1.38.0), defining promoter regions as ±1,000 bp relative to the transcription start site (TSS).
Assembly: hg38
Supplementary files format and content: bigWig files include normalized ChIP-seq signals for each sample
Supplementary files format and content: narrowPeak files include macs3 peaks for each sample (except for Input)

extract_protocol:
Approximately 3×107 cells were used per immunoprecipitation.  The following antibodies were used: anti-Flag (14793, CST), anti-RPB1-Total (14958S, CST), anti-RPB1-S2P (61084, Proteintech), and anti-RPB1-S5P (904001, BioLegend).  Protein A/G magnetic beads (22204, Beaver) were used for immunoprecipitation.  ChIP-enriched DNA was treated sequentially with RNase A (T3018-2, New England Biolabs) and Proteinase K (P8107S, New England Biolabs) to remove RNA and proteins prior to library construction.
DNA libraries were prepared using the Rapid Plus DNA Lib Prep Kit for Illumina V2 (Abclonal) according to the manufacturer’s instructions.

treatment_protocol: HeLa cells inducibly expressing nGDOWN1 were harvested in the absence or presence of 1 μg/mL Dox for 24 hours.


title: ChIP, HeLa, Input, +DOX, day4

description: Library name: ChIP_HeLa_Input_+DOX_day4

value: doxycycline induced, day4


title: SJRHB071779_X1_DY8420_3D

description:
Library name: SJRHB071779_C1
2344247


title: SJRHB013_X_DY8432_3D

description:
Library name: SJRHB000912_C1 Rep 2
2344259


title: Mouse cervix, postnatal day 1, biol rep 2

description:
Library name: PND1_2_cvx
Postnatal day 1 mouse cervix, biol rep 2; 10x Genomics Chromium Fixed RNA Profiling (Flex); Flex barcode BC004; EpCAM-sorted prior to library preparation

value: cervix


title: ChIP, HeLa, Input, control

description: Library name: ChIP_HeLa_Input_control


title: ChIP, HeLa, Pol II-nGDOWN1-Flag, +DOX, day4

description: Library name: ChIP_HeLa_Pol II-nGDOWN1-Flag_+DOX_day4


title: SJRHB031412_X1_DY8418_3D

description:
Library name: SJRHB031412_C1
2344245


title: Mouse uterus, postnatal day 1, biol rep 2

description:
Library name: PND1_2_ute
Postnatal day 1 mouse uterus, biol rep 2; 10x Genomics Chromium Fixed RNA Profiling (Flex); Flex barcode BC003; EpCAM-sorted prior to library preparation


title: ChIP, HeLa, Pol II-nGDOWN1-Flag, +DOX, day1

description: Library name: ChIP_HeLa_Pol II-nGDOWN1-Flag_+DOX_day1


title: ChIP, HeLa, Pol II-nGDOWN1-Flag, control

description: Library name: ChIP_HeLa_Pol II-nGDOWN1-Flag_control


title: SJRHB031320_X1_DY8417_2D

description:
Library name: SJRHB031320_C1
2344244


title: ChIP, HeLa, Pol II-pSer5, +DOX, day4

description: Library name: ChIP_HeLa_Pol II-pSer5_+DOX_day4


title: Mouse uterus, postnatal day 1, biol rep 1

description:
Library name: PND1_1_ute
Postnatal day 1 mouse uterus, biol rep 1; 10x Genomics Chromium Fixed RNA Profiling (Flex); Flex barcode BC001; EpCAM-sorted prior to library preparation


title: ChIP, HeLa, Pol II-pSer5, +DOX, day1

description: Library name: ChIP_HeLa_Pol II-pSer5_+DOX_day1


title: ChIP, HeLa, Pol II-pSer5, control

description: Library name: ChIP_HeLa_Pol II-pSer5_control


title: SJRHB031320_X1_DY8416_3D

description:
Library name: SJRHB031320_C2
2344243


title: Mouse uterus, E16.5, biol rep B2

description:
Library name: E16.5_Ute_B2
Embryonic day 16.5 mouse uterus, biol rep B2; 10x Genomics Chromium Fixed RNA Profiling; not EpCAM-sorted (viability <30%); not Flex multiplexed

value: Pool 4


title: ChIP, HeLa, Pol II-pSer2, +DOX, day4

description: Library name: ChIP_HeLa_Pol II-pSer2_+DOX_day4


title: SJRHB030680_X1_DY8415_2D

description:
Library name: SJRHB030680_C2 Rep 2
2344242


title: ChIP, HeLa, Pol II-pSer2, +DOX, day1

description: Library name: ChIP_HeLa_Pol II-pSer2_+DOX_day1


title: Mouse uterus, E16.5, biol rep B1

description:
Library name: E16.5_Ute_B1
Embryonic day 16.5 mouse uterus, biol rep B1; 10x Genomics Chromium Fixed RNA Profiling; not EpCAM-sorted (viability <30%); not Flex multiplexed


title: ChIP, HeLa, Pol II-pSer2, control

description: Library name: ChIP_HeLa_Pol II-pSer2_control


title: SJRHB030680_X1_DY8414_3D

description:
Library name: SJRHB030680_C1 Rep 2
2344241


title: ChIP, HeLa, Pol II-NTD, +DOX, day4

description: Library name: ChIP_HeLa_Pol II-NTD_+DOX_day4


title: Mouse cervix, E16.5, biol rep B

description:
Library name: E16.5_Cvx_B
Embryonic day 16.5 mouse cervix, biol rep B; 10x Genomics Chromium Fixed RNA Profiling; not EpCAM-sorted (viability <30%); not Flex multiplexed

value: Pool 3


title: SJRHB031691_X3_DY8429_2D

description:
Library name: SJRHB031691_C6
2344256


title: PHOX2A.Ref.Rep1

value: isolated DNA-binding domain

value: reference allele


title: SJRHB031117_X1_DY8412_3D

description:
Library name: SJRHB031117_C1
2344239


title: ChIP, HeLa, Pol II-NTD, control

description: Library name: ChIP_HeLa_Pol II-NTD_control


title: Mouse cervix, E16.5, biol rep A

description:
Library name: E16.5_Cvx_A
Embryonic day 16.5 mouse cervix, biol rep A; 10x Genomics Chromium Fixed RNA Profiling; not EpCAM-sorted (viability <30%); not Flex multiplexed


title: ChIP, HeLa, Pol II-NTD, +DOX, day1

description: Library name: ChIP_HeLa_Pol II-NTD_+DOX_day1


title: FAPs, KPC- Day 14 biol rep 4

description:
231G3
FAPs_Day_14_raw_counts.txt

source_name: Hindlimb muscle

growth_protocol: KPCY cell line was grown in DMEM media containing L-Glutamine, 4.5g/L Glucose, without Sodium Pyruvate, and 10% Fetal Bovine Serum.

extract_protocol:
FAPs were sorted using an Influx cell sorter (Becton Dickinson) with the following gating strategy: CD31-/ CD45-/ α7-integrin-/ PI-/ SCA-1+/ Hoechst 33342+. RNA of sorted FAPs was isolated using a combination of Qiazol/chloroform, and miRNeasy kit.
Samples with a RIN of 7 and above were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina). Sequencing was performed on the Illumina NextSeq 2000 using the P3 reagents (100 cycle; Illumina) to generate paired-end reads (59 x 59 base pairs).

treatment_protocol: 2 million cells in 50uL were injected into the pancreas. Control mice received sham surgery

value: Hindlimb muscle

value: Freshly sorted FAPs

value: Male

value: Orthotopic implantation of KPCY cells

tag: time

value: Day 14


title: CUT&Tag, HeLa, IgG, rep2

description: Library name: CUT_Tag_HeLa_IgG_+DOX_day1_rep2

data_processing:
Upon data delivery, bioinformatics analysis was carried out as follows: trimmed reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.3.5.1) with the parameters “--end-to-end --very-sensitive --no-mixed --no-discordant -I 10 -X 700”.
Peak calling was performed using MACS3 (v3.0.1) with the settings “-f BAMPE -g hs --keep-dup all -q 1e-5”.
Normalized bigWig files were generated using bamCoverage from deepTools (v3.5.5), with genomic regions in the ENCODE blacklist (hg38) excluded to reduce technical artifacts.
Peak annotation was conducted using the R package ChIPseeker (v1.38.0), defining promoter regions as ±1,000 bp relative to the transcription start site (TSS).
Assembly: hg38
Supplementary files format and content: bigWig files include normalized CUT&Tag signals for each sample
Supplementary files format and content: narrowPeak files include macs3 peaks for each sample (except for IgG)
Library strategy: CUT&Tag

extract_protocol: Approximately 107 cells were used per assay, and all procedures were performed strictly according to the manufacturer’s instructions for the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech).

treatment_protocol: HeLa cells inducibly expressing nGDOWN1 were harvested either in the absence or presence of 1 μg/mL Dox for 24 hours.

value: Cervix

value: HeLa

value: Epithelial cell

value: inducible nGDOWN1


title: Mouse uterus, E16.5, biol rep C

description:
Library name: E16.5_Ute_C
Embryonic day 16.5 mouse uterus, biol rep C; 10x Genomics Chromium Fixed RNA Profiling; not EpCAM-sorted (viability <30%); not Flex multiplexed

value: uterus


title: SJRHB030451_X1_DY8411_2D

description:
Library name: SJRHB030451_C2
2344238

value: Cells

value: RMS


title: CUT&Tag, HeLa, IgG, rep1

description: Library name: CUT_Tag_HeLa_IgG_+DOX_day1_rep1

value: doxycycline induced, day1


title: CUT&Tag, HeLa, nGDOWN1-Flag, +DOX, day1, rep2

description: Library name: CUT_Tag_HeLa_nGDOWN1-Flag_+DOX_day1_rep2


title: SJRHB030451_X1_DY8410_3D

description:
Library name: SJRHB030451_C1
2344237


title: CUT&Tag, HeLa, nGDOWN1-Flag, +DOX, day1, rep1

description: Library name: CUT_Tag_HeLa_nGDOWN1-Flag_+DOX_day1_rep1


title: Mouse uterus, E16.5, biol rep A

description:
Library name: E16.5_Ute_A
Embryonic day 16.5 mouse uterus, biol rep A; 10x Genomics Chromium Fixed RNA Profiling; not EpCAM-sorted (viability <30%); not Flex multiplexed


title: Limb_KKK_4

city: Seattle

first: Yuzuru

last: Sasamoto

state: WA

address: 750 Republican St

department: Ophthalmology

institute: University of Washington

description: Library name: Sample 32

data_processing:
Trimmed reads were aligned to the reference genome using STAR v2.6.1d. Differential gene expression (DEG) analysis was achieved using g:Profiler python API v1.0.0.
Assembly: hg38
Supplementary files format and content: Matrix table with normalized counts for every gene and every sample

source_name: Cultured limbal epithelial cells

growth_protocol: Human donor eyes were obtained from eye banks. The eyes were dissected into three tissues: conjunctiva, limbus and central cornea. Epithelial cells from each tissue were obtained by Dispase II. After dissociation by TrypLE, the cells were used for cell sheet formation.

extract_protocol:
Total RNA was isolated using the miRVana miRNA Isolation Kit, with phenol.
Libraries were prepared using Zymo-Seq RiboFree Total RNA Library Prep Kit according to the manufacturer's instruction manual.

value: Cultured limbal epithelial cells

value: In vitro human limbal epithelial cells

value: Sample 4, limbus, KKK


title: SJRHB030549_X1_DY8409_VT

description:
Library name: SJRHB030549_C3
2344236

value: Tumor

value: VT


title: Limb_EKK_4

description: Library name: Sample 31

value: Sample 4, limbus, EKK


title: CT26 Mlh1 KO B2m KO Isotype CTRL Rep4

city: Oxford

first: David

last: Church

address: Roosevelt Drive

department: Centre for Human Genetics

country: United Kingdom

institute: University of Oxford

description: Library name: Tumor_157

data_processing:
Base calling using CASAVA
Raw reads were filtered as follows: Remove reads containing adaptors; Remove reads containing N > 10% (N represents base that could not be determined);  Qscore (Quality value) of over 50% bases of the read is <= 5
Following filtering, clean reads were mapped to the GRCm39 (ensembl_103_mus_musculus_grcm39_toplevel) genome using HISAT2 (v2.0.5)
StringTie (v1.3.3b) was used to assemble reads into transcripts and quantify them
Assembly: GRCm39 (ensembl_103_mus_musculus_grcm39_toplevel)
Supplementary files format and content: tab-delimted file includes raw counts per sample

source_name: Tumour

extract_protocol:
Tissue digestion was performed as first step, then the RNA was extracted using the AllPreP DNA/RNA Micro Kit (Qiagen)
Sequencing libraries were generated using RNA Library Prep Kit for Illumina following manufacturer’s recommendations

value: Tumour

value: CT26, Mlh1 KO, b2m KO

value: Mlh1 KO, b2m KO

value: Isotype CTRL


title: Limb_EEK_4

description: Library name: Sample 30

value: Sample 4, limbus, EEK


title: SJRHB030549_X1_DY8408_2D

description:
Library name: SJRHB030549_C2
2344235


title: Limb_EEE_4

description: Library name: Sample 29

value: Sample 4, limbus, EEE


title: Conj_KKK_4

description: Library name: Sample 28

source_name: Cultured conjunctival epithelial cells

value: Cultured conjunctival epithelial cells

value: In vitro human conjunctivall epithelial cells

value: Sample 4, conjunctiva, KKK


title: CT26 Mlh1 KO B2m KO Isotype CTRL Rep3

description: Library name: Tumor_156


title: FAPs, KPC- Day 21 biol rep 1

description:
273A3
FAPs_Day_21_raw_counts.txt

value: Hindlimb muscle

value: Freshly sorted FAPs

value: Male

value: Orthotopic implantation of KPCY cells

value: Day 21


title: SJRHB030549_X1_DY8407_3D

description:
Library name: SJRHB030549_C1
2344234

value: Cells

value: RMS


title: Conj_EKK_4

description: Library name: Sample 27

value: Sample 4, conjunctiva, EKK


title: CT26 Mlh1 KO B2m KO Isotype CTRL Rep2

description: Library name: tumor_155

value: Tumour


title: Conj_EEK_4

description: Library name: Sample 26

value: Sample 4, conjunctiva, EEK


title: SJRHB071775_X1_DY8406_2D

description:
Library name: SJRHB071775_C2
2344233


title: CT26 Mlh1 KO B2m KO Isotype CTRL Rep1

description: Library name: Tumor_148

value: CT26, Mlh1 KO, b2m KO

value: Mlh1 KO, b2m KO


title: Conj_EEE_4

description: Library name: Sample 25

value: Sample 4, conjunctiva, EEE


title: Limb_KKK_3

description: Library name: Sample 24

value: Cultured limbal epithelial cells

value: In vitro human limbal epithelial cells

value: Sample 3, limbus, KKK


title: SJRHB071775_X1_DY8405_3D

description:
Library name: SJRHB063831_C1 Rep 2
2344232


title: Limb_EKK_3

description: Library name: Sample 23

value: Sample 3, limbus, EKK


title: CT26 Mlh1 KO B2m KO aPD1 aCTLA4 Rep4

description: Library name: Tumor_154


title: Limb_EEK_3

description: Library name: Sample 22

value: Sample 3, limbus, EEK


title: SJRHB063831_X1_DY8404_VT

description:
Library name: SJRHB063831_C4
2344231

source_name: Tumor

value: Tumor

value: VT


title: Limb_EEE_3

description: Library name: Sample 21

value: Sample 3, limbus, EEE


title: CT26 Mlh1 KO B2m KO aPD1 aCTLA4 Rep3

description: Library name: Tumor_152


title: Conj_KKK_3

description: Library name: Sample 20

value: Cultured conjunctival epithelial cells

value: In vitro human conjunctivall epithelial cells

value: Sample 3, conjunctiva, KKK


title: SJRHB063831_X1_DY8403_2D

description:
Library name: SJRHB063831_C2
2344230

value: Cells

value: RMS


title: Conj_EKK_3

description: Library name: Sample 19

value: Sample 3, conjunctiva, EKK


title: CT26 Mlh1 KO B2m KO aPD1 aCTLA4 Rep2

description: Library name: Tumor_147

value: Tumour

value: CT26, Mlh1 KO, b2m KO


title: Conj_EEK_3

description: Library name: Sample 18

value: Sample 3, conjunctiva, EEK


title: Conj_EEE_3

description: Library name: Sample 17

value: Sample 3, conjunctiva, EEE


title: SJRHB063831_X1_DY8402_3D

description:
Library name: SJRHB063831_C1 Rep 1
2344229


title: CT26 Mlh1 KO B2m KO aPD1 aCTLA4 Rep1

description: Library name: Tumor_146

value: Mlh1 KO, b2m KO


title: Limb_KKK_2

description: Library name: Sample 16

value: Cultured limbal epithelial cells

value: In vitro human limbal epithelial cells

value: Sample 2, limbus, KKK


title: Limb_EKK_2

description: Library name: Sample 15

value: Sample 2, limbus, EKK


title: SJRHB030765_X1_DY8401_2D

description:
Library name: SJRHB030765_C1
2344228


title: Apc Het Mlh1 WT Polyp Rep4

description: Library name: MGWX111g_P

source_name: Intestinal Polyp

value: Intestinal Polyp

value: Apc:Het| Mlh1:WT


title: Limb_EEK_2

description: Library name: Sample 14

value: Sample 2, limbus, EEK


title: SJRHB030765_X1_DY8400_3D

description:
Library name: SJRHB030765_C2
2344227


title: Apc Het Mlh1 WT Normal Rep4

description: Library name: MGWX111g_N

source_name: Normal Intestine

value: Normal Intestine


title: Conj_KKK_2

description: Library name: Sample 12

value: Cultured conjunctival epithelial cells

value: In vitro human conjunctivall epithelial cells

value: Sample 2, conjunctiva, KKK


title: Conj_EKK_2

description: Library name: Sample 11

value: Sample 2, conjunctiva, EKK


title: SJRHB063830_X1_DY8399_2D

description:
Library name: SJRHB063830_C2
2344226

value: Cells

value: RMS


title: Apc Het Mlh1 WT Polyp Rep3

description: Library name: MGWW105g_P


title: Conj_EEK_2

description: Library name: Sample 10

value: Sample 2, conjunctiva, EEK


title: Conj_EEE_2

description: Library name: Sample 9

value: Sample 2, conjunctiva, EEE


title: SJRHB063830_X1_DY8398_3D

description:
Library name: SJRHB063830_C1
2344225


title: Apc Het Mlh1 WT Normal Rep3

description: Library name: MGWW105g_N


title: Limb_KKK_1

description: Library name: Sample 8

value: Sample 1, limbus, KKK


title: SJRHB030730_X1_DY8397_2D

description:
Library name: SJRHB030730_C2 Rep 1
2344224


title: Limb_EKK_1

description: Library name: Sample 7

value: Cultured limbal epithelial cells

value: Sample 1, limbus, EKK


title: Apc Het Mlh1 WT Polyp Rep2

description: Library name: MGWW102b_P


title: SJRHB030730_X1_DY8396_3D

description:
Library name: SJRHB030730_C1
2344223


title: Limb_EEK_1

description: Library name: Sample 6

value: In vitro human limbal epithelial cells

value: Sample 1, limbus, EEK


title: Limb_EEE_1

description: Library name: Sample 5

value: Sample 1, limbus, EEE


title: Apc Het Mlh1 WT Normal Rep2

description: Library name: MGWW102b_N

value: Apc:Het| Mlh1:WT


title: SJRHB030705_X1_DY8395_2D

description:
Library name: SJRHB030705_C2 Rep 2
2344222


title: Conj_KKK_1

description: Library name: Sample 4

value: Sample 1, conjunctiva, KKK


title: Conj_EKK_1

description: Library name: Sample 3

value: Sample 1, conjunctiva, EKK


title: Apc Het Mlh1 WT Polyp Rep1

description: Library name: MGWX181f_P

value: Intestinal Polyp


title: iBUC_21pl3

description: Library name: SV40_AM-3

data_processing:
Sequence reads were trimmed for adaptor and polyA using Cutadapt
Trimmed sequence reads were mapped to Bos_taurus.ARS-UCD1.2 genome using STAR
Read count extraction to fatures using HTSeq
Normalization of the counts and differential expression analysis using DESeq
Assembly: Bos_taurus.ARS-UCD1.2
Supplementary files format and content: raw_counts_wj_sv40.xlsx
Library strategy: Bulk MARS-seq

source_name: umbilical cord

extract_protocol:
Total RNA was extracted via PureLink RNA Minikit
Library preparation was done by Weizmann Institute, Rehovot. Sequencing Libraries were prepared using Bulk MARS-Seq. SR reads were sequenced on 1 lane(s) of an Illumina NovaSeq Sp (100 cycles). The output was ~25 million reads per sample.

value: umbilical cord

value: Immortalized SV-40

value: mesenchymal stem cells

value: Holstein

value: immortalized cells, 21 days culturing


title: Conj_EEK_1

description: Library name: Sample 2

value: Cultured conjunctival epithelial cells

value: In vitro human conjunctivall epithelial cells

value: Sample 1, conjunctiva, EEK


title: SJRHB030705_X1_DY8394_3D

description:
Library name: SJRHB030705_C1 Rep 2
2344221

data_processing:
https://wiki.stjude.org/display/CAB/RNAseq+differential+gene+expression+analysis#RNAseqdifferentialgeneexpressionanalysis-1.WorkflowSummary
Assembly: hg38
Supplementary files format and content: gene counts

source_name: Cells

value: Cells

value: RMS


title: Conj_EEE_1

description: Library name: Sample 1

value: Sample 1, conjunctiva, EEE


title: Apc Het Mlh1 WT Normal Rep1

description: Library name: MGWX181f_N

value: Normal Intestine


title: SJRHB063825_X1_DY8393_VT

description:
Library name: SJRHB063825_C4
2344220

value: Tumor

value: VT


title: EMC10, Input, rep3

city: Chicago

first: Qianru

last: Li

state: IL

address: 303 E. Superior Street

institute: Northwestern University

description: Library name: Sample 13

data_processing:
RNase footprinting reads were trimmed to remove the first 7 nucleotides and A-tail adaptor sequence using Cutadapt v4.1. Trimmed reads were aligned to ribosome RNA sequences (downloaded from Ensembl) using Bowtie v2.2.6, and matched reads were discarded. The remaining reads were then mapped to the human hg38 genome and transcriptome using TopHat v2.1.0, with transcriptome annotations based on RefSeq. Uniquely mapped reads were selected for calculating ribosome occupancy.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Library strategy: Ribo-Seq

source_name: Embryonic kidney

growth_protocol: Flp-In T-REx 293 cells were maintained in DMEM supplemented with 10% FBS, 100 U/mL penicillin, and 0.1 mg/mL streptomycin mixture at 37 °C and 5% CO2.

extract_protocol:
Cells were lysed, and microsomes were isolated. After treatmnet with 10,000 U micrococcal nuclease for 30 min at 37 °C, microsomes were pelleted and solubilized. The cleared supernatant was used as input, after M2 Flag affinity beads binding, immunoprecipitated material was used as IP. To prepare RNase footprints, input and IP samples were digested with RNase 1 at 0.5 - 1 U/µl within a 90 µl reaction at RT for 1.5 h. RNase footprints were extracted by adding 400 µl TRIzol followed by 100 µl of chloroform. RNA in the aqueous layer was separated by centrifugation at 12000 g for 15 min at 4 ℃ and then precipitated overnight by adding 0.1 volume of 3 M sodium acetate, 10 mg of glycoblue, and 1.2 volumes of isopropanol.
Purified RNase footprints were used for library preparation. RNase footprints were resuspended in 5 µl TNK reaction mixture (1x PNK buffer, 10 U PNK (NEB), and 10 U SUPERase·In) and end-repaired at 37 ℃ for 1 h. The reaction was added with 5 µl of polyadenylation mix containing 10 U E. coli poly (A) polymerase (NEB), 2 µl of 5x first-strand buffer (250 mM Tris-HCl (pH 8.3), 375 mM KCl, 15 mM MgCl2), 0.25 mM ATP, and 10 U SUPERase·In and incubated at 37 ℃ for 2 h. The resulting polyadenylated RNA was then reverse transcribed by a SMART-RT reaction. The reaction mixture was first added with 2.5 µl of RT primer (10 µM, 5’-ACGTGTGCTCTTCCGATCTNNNNNNNNNNNNNNNTTTTTTTTTTTTTTTVN-3’, where “N” is any base and “V” is either “A”, “C” or “G”) and annealed by heating to 72 °C for 5 min and cooled on ice, and then supplemented with SMAT-RT mixture (2.5 µl dNTP (10 mM), 400 U Superscript II reverse transcriptase (Invitrogen), 10 U SUPERase·In, 4 µl Superscript II first-strand buffer (5x), 1.5 µl DTT (100 mM), 6 µl Betaine (5 mM), 0.12 µl MgCl2 (1 M), 0.5 µl template-switching oligos (100 µM 5’-CTCTTTCCCTACACGACGCTCTTCCGATCTNNNNrGrG+G-3’, where “N” is any base and “+G'' is a locked nucleic acid guanylate), and 0.5 µl nuclease-free water. Reverse transcription was carried out with incubation at 42 ℃ for 1 h, followed by 10 cycles of heating at 50 °C for 2 min and then incubating at 42 ℃ for 2 min. The reverse transcriptase was inactivated by heating at 70 ℃ for 10 min. RNA footprints hybridized to DNA were removed by incubating at 37 ℃ for 15 min with 5 U of RNase H. The resultant cDNA was then amplified by a first round of PCR with seven cycles, purified, and subjected to another four cycles of PCR using extended primers. The DNA library was visualized and separated in a 4% agarose gel. DNA with a 15-35 bp insert was excised and recovered using a DNA gel recovery kit (Zymo). Equal amounts of barcoded libraries were pooled and then sequenced with Illumina NovoSeq.

treatment_protocol: Cells were seeded in ten 15-cm dishes, induced with 0.5-1.0 ng/mL doxycycline and harvested after 72 hours (~80% confluency) with ice-cold PBS containing 0.1 mg/mL CHX.

value: Embryonic kidney

value: Flp-In T-REx 293

value: Input

value: replicate 3


title: Limb_EEE_2

description: Library name: Sample 13

value: Cultured limbal epithelial cells

value: In vitro human limbal epithelial cells

value: Sample 2, limbus, EEE


title: EMC10, IP, rep3

description: Library name: Sample 14

value: IP


title: Apc Het Mlh1 Hom Tumour Rep5

description: Library name: MGWX113a2_P

source_name: Intestinal Tumour

value: Intestinal Tumour

value: Apc:Het| Mlh1:Hom


title: EMC10, IP, rep2

description: Library name: Sample 12

value: replicate 2


title: iBUC_165pl5

description: Library name: SV-40_2D-5

value: umbilical cord

value: Immortalized SV-40

value: mesenchymal stem cells

value: Holstein

value: immortalized cells, 165 days culturing


title: SJRHB063825_X1_DY8392_2D

description:
Library name: SJRHB063825_C2
2344219

value: Cells

value: RMS


title: EMC10, Input, rep2

description: Library name: Sample 11

value: Embryonic kidney

value: Flp-In T-REx 293


title: Apc Het Mlh1 Hom Polyp Rep5

description: Library name: MGWX113a_P

value: Intestinal Polyp


title: EMC10, IP, rep1

description: Library name: Sample 10

value: replicate 1


title: SJRHB063825_X1_DY8391_3D

description:
Library name: SJRHB063825_C1
2344218


title: EMC10, Input, rep1

description: Library name: Sample 9

value: Input


title: EMC7, IP, rep2

description: Library name: Sample 8


title: Apc Het Mlh1 Hom Normal Rep5

description: Library name: MGWX113a_N

value: Normal Intestine


title: EMC7, Input, rep2

description: Library name: Sample 7


title: Apc Het Mlh1 Hom Polyp Rep4

description: Library name: MGWW123a_P


title: SJRHB063823_X1_DY8390_2D

description:
Library name: SJRHB063823_C2
2344217


title: EMC7, IP, rep1

description: Library name: Sample 6

value: IP


title: SJRHB063823_X1_DY8389_3D

description:
Library name: SJRHB063823_C1
2344216


title: EMC7, Input, rep1

description: Library name: Sample 5


title: Apc Het Mlh1 Hom Normal Rep4

description: Library name: MGWW123a_N


title: EMC6, IP, rep2

description: Library name: Sample 4

value: EMC6 knockout, doxycycline-inducible 3Flag-EMC6 expressing


title: SJRHB049189_X1_DY8388_2D

description:
Library name: SJRHB049189_C2
2344215


title: EMC6, Input, rep2

description: Library name: Sample 3


title: Apc Het Mlh1 Hom Polyp Rep3

description: Library name: BTFM124c_P

value: Apc:Het| Mlh1:Hom


title: EMC6, IP, rep1

description: Library name: Sample 2


title: SJRHB049188_X1_DY8386_2D

description:
Library name: SJRHB049188_C2
2344213


title: EMC6, Input, rep1

description: Library name: Sample 1


title: Apc Het Mlh1 Hom Normal Rep3

description: Library name: BTFM124c_NI


title: SJRHB013758_X2_DYE3650_RA-CCLF-VT

description:
Library name: SJRHB013758_C11 Rep 2
3360165

value: Tumor

value: RA-CCLF-VT


title: SJOS030605_X2_DYE3651_RA-CCLF-VT

description:
Library name: SJEWS063826_C6
3360166

value: EWS


title: SJNBL046148_X1_DYE3649_CCLF-VT

description:
Library name: SJNBL046148_C4
3360164

value: CCLF-VT

value: NBL


title: SJRHB046156_X2_DY8384_VT

description:
Library name: SJRHB046156_C5
2344211

value: VT


title: Apc Het Mlh1 Hom Polyp Rep2

description: Library name: BTFM121a_P


title: SJNBL012407_X1_DYE3648_CCLF

description:
Library name: SJNBL012407_C3 Rep 4
3360163

value: Cells

value: CCLF


title: Apc Het Mlh1 Hom Normal Rep2

description: Library name: BTFM121a_N


title: SJRHB013759_X15_DYE3616_CCLF-VT

description:
Library name: SJRHB013759_C16
3357284

value: RMS


title: SJRHB049188_X1_DY8385_3D

description:
Library name: SJRHB049188_C1
2344212


title: SJRHB012_Z_DY8441_2D

description:
Library name: SJRHB000912_C6
2344268


title: SJRHB046156_X2_DY8383_2D

description:
Library name: SJRHB046156_C3 Rep 2
2344210


title: SJEWS063826_X1_DYE3615_CCLF-VT

description:
Library name: SJEWS063826_C5
3357283


title: Apc Het Mlh1 Hom Polyp Rep1

description: Library name: MGWX171d_P


title: SJEWS030393_X1_DYE3614_CCLF-VT

description:
Library name: SJEWS030393_C6
3357282


title: SJRHB046156_X2_DY8382_3D

description:
Library name: SJRHB046156_C2
2344209


title: SJRHB000026_X1_DYE2568_RA-CCLF

description:
Library name: SJRHB000026_C6
3309723

value: RA-CCLF


title: SJNBL012407_X1_DYE2820_CCLF

description:
Library name: SJNBL012407_C3 Rep 3
3300210


title: Apc Het Mlh1 Hom Tumour Rep1

description: Library name: MGWX171d2_P

value: Intestinal Tumour


title: Apc Het Mlh1 Hom Normal Rep1

description: Library name: MGWX171d_N


title: SJNBL012407_X1_DYE2819_CCLF

description:
Library name: SJNBL012407_C3 Rep 2
3300209


title: SJRHB046156_X1_DY8381_2D

description:
Library name: SJRHB046156_C3 Rep 1
2344208


title: SJRHB013758_X2_DYE2802_RA-CCLF-VT

description:
Library name: SJRHB013758_C11 Rep 1
3292222


title: SJRHB046156_X1_DY8380_3D

description:
Library name: SJRHB046156_C1
2344207


title: SJNBL031239_X1_DYE2801_CCLF-VT

description:
Library name: SJNBL031239_C6
3292221


title: d32_04_08.2.RNA

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

description: Library name: HI_464_2

data_processing:
Demultiplexing, barcode processing, read counting, and aggregation were carried out using Cell Ranger Arc 2.0.2 with the mouse 2020-A transcriptome reference from 10X Genomics.
Read counts were analyzed using Seurat and Signac. Processed counts, cell type annotations, and other metadata were stored as a Seurat object in an RDS file.
Assembly: mm10
Supplementary files format and content: brain.so.rds: RDS file containing Seurat object with annotated single-cell data

source_name: cerebellum

extract_protocol:
Cerebellum from E14.5 litters were manually dissected in ice-cold PBS and flash-frozen in either a dry ice methanol bath (1 pair) or liquid nitrogen (3 pairs). Nuclei were prepared and processed through the 10X Multiome ATAC + Gene Expression protocol.
Sequencing libraries were constructed according to the 10X Genomics Multiome protocol.

value: cerebellum

tag: mouse strain

value: FVB

value: WT

value: Female

tag: mouse id


title: SJNBL013762_X1_DYE2800_CCLF-VT

description:
Library name: SJNBL013762_C5
3292220

tag: tissue


title: SJRHB013759_X15_DY8379_2D

description:
Library name: SJRHB013759_C2
2344206

tag: cell line


title: d32_04_05.2.RNA

description: Library name: HI_462_2

value: Mut


title: SJNBL012407_X1_DYE2799_CCLF

description:
Library name: SJNBL012407_C3 Rep 1
3292219

tag: cell type


title: SJRHB000026_X1_DYE2798_RA-CCLF-VT

description:
Library name: SJRHB000026_C10 Rep 2
3292218


title: SJNBL046148_X1_DYE2796_CCLF

description:
Library name: SJNBL046148_C3
3292216


title: SJRHB013759_X15_DY8378_3D

description:
Library name: SJRHB013759_C6
2344205


title: SJRHB013759_X14_DY8377_VT

description:
Library name: SJRHB013759_C13
2344204


title: SJEWS063826_X1_DY2698_RA-CCLF

description:
Library name: SJEWS063826_C4
3277851


title: SJNBL013762_X1_DYE2797_CCLF

description:
Library name: SJNBL013762_C3
3292217


title: d32_04_01.2.RNA

description: Library name: HI_458_2

value: Male


title: SJRHB013758_X2_DY2697_RA-CCLF

description:
Library name: SJRHB013758_C7
3277850


title: d32_04_04.2.RNA

description: Library name: HI_460_2


title: SJRHB013759_X14_DY8375_3D

description:
Library name: SJRHB013759_C5
2344202


title: SJNBL031239_X1_DY2696_CCLF

description:
Library name: SJNBL031239_C5
3277849


title: mj2_02_02.2.RNA

description: Library name: HI_456_2

value: BKS


title: SJEWS056156_X1_DY2695_RA-CCLF-VT

description:
Library name: SJEWS056156_C6
3277848

value: Tumor

value: RA-CCLF-VT


title: SJRHB013759_X1_DY8374_VT

description:
Library name: SJRHB013759_C12
2344201


title: SJNBL030721_X4_DY2694_CCLF-VT

description:
Library name: SJNBL030721_C16
3277847

value: CCLF-VT


title: mj2_02_06.2.RNA

description: Library name: HI_454_2


title: SJRHB013758_X2_DY2693_CCLF-VT

description:
Library name: SJRHB013758_C10
3277846


title: SJOS030605_X2_DYE2433_RA-CCLF

description:
Library name: SJOS030605_C4
3240767

value: OST


title: SJRHB013759_X1_DY8373_2D

description:
Library name: SJRHB013759_C11
2344200


title: SJEWS056156_X1_DYE2432_RA-CCLF

description:
Library name: SJEWS056156_C4
3240766

value: EWS


title: SJRHB013759_X1_DY8372_3D

description:
Library name: SJRHB013759_C4
2344199

value: Cells


title: SJEWS030393_X1_DYE2431_RA-CCLF

description:
Library name: SJEWS030393_C4
3240765


title: mj2_02_03.2.RNA

description: Library name: HI_452_2


title: SJEWS063826_X1_DYE2429_CCLF

description:
Library name: SJEWS063826_C3
3240763

value: CCLF


title: mj2_12_05.2.RNA

description: Library name: HI_450_2


title: SJRHB010928_X1_DY8371_2D

description:
Library name: SJRHB010928_C2
2344198

value: RMS


title: SJOS030605_X2_DYE2428_RA-CCLF-VT

description:
Library name: SJOS030605_C5
3240762


title: SJEWS030393_X1_DYE2427_RA-CCLF-VT

description:
Library name: SJEWS030393_C7
3240761


title: mj2_12_03.2.RNA

description: Library name: HI_448_2


title: SJRHB010928_X1_DY8370_3D

description:
Library name: SJRHB010928_C1
2344197


title: SJRHB000026_X1_DYE2426_RA-CCLF-VT

description:
Library name: SJRHB000026_C10 Rep 1
3240760


title: SJEWS056156_X1_DYE2425_CCLF-VT

description:
Library name: SJEWS056156_C5
3240759


title: d32_04_08.2.ATAC

description: Library name: HI_451_2


title: SJRHB010468_X1_DY8369_2D

description:
Library name: SJRHB010468_C2 Rep 2
2344196


title: SJRHB063831_X1_DYE2424_CCLF-VT

description:
Library name: SJRHB063831_C5
3240758


title: d32_04_05.2.ATAC

description: Library name: HI_449_2


title: SJNBL030721_X4_DYE2421_CCLF

description:
Library name: SJNBL030721_C14
3240755

value: NBL


title: SJRHB013759_X15_DYE2423_CCLF

description:
Library name: SJRHB013759_C10
3240757


title: SJRHB010468_X1_DY8368_3D

description:
Library name: SJRHB010468_C1 Rep 2
2344195


title: d32_04_04.2.ATAC

description: Library name: HI_447_2


title: SJNBL013762_X1_DYE7974_2D

description:
Library name: SJNBL013762_C2
2323350


title: SJRHB013758_X2_DYE2420_CCLF

description:
Library name: SJRHB013758_C6
3240754


title: SJRHB013759_X15_DYE2142_CCLF

description:
Library name: SJRHB013759_C10 Rep 2
3156894


title: d32_04_01.2.ATAC

description: Library name: HI_445_2


title: SJNBL013762_X1_DYE7973_3D

description:
Library name: SJNBL013762_C1
2323349


title: SJRHB010928_X1_DYE2066_CCLF-VT

description:
Library name: SJRHB010928_C5 Rep 1
3131662


title: SJOS030605_X2_DYE1990_CCLF

description:
Library name: SJOS030605_C3
3112609


title: SJRHB010928_X1_DYE2067_CCLF-VT

description:
Library name: SJRHB010928_C5 Rep 2
3131663


title: mj2_02_02.2.ATAC

description: Library name: HI_443_2


title: SJNBL013762_X1_DYE7972_T0

description:
Library name: SJNBL013762_X1
2323348


title: SJEWS056156_X1_DYE1989_CCLF

description:
Library name: SJEWS056156_C3
3112608


title: mj2_02_06.2.ATAC

description: Library name: HI_541_2


title: SJEWS030393_X1_DYE1988_CCLF

description:
Library name: SJEWS030393_C3
3112607


title: SJNBL046_X_DYE7971_2D

description:
Library name: SJNBL006105_C4
2323347


title: SJRHB063831_X1_DYE1987_CCLF

description:
Library name: SJRHB063831_C3
3112606


title: mj2_02_03.2.ATAC

description: Library name: HI_539_2


title: SJRHB013759_X15_DYE1986_CCLF

description:
Library name: SJRHB013759_C10 Rep 1
3112605


title: SJNBL046_X_DYE7970_3D

description:
Library name: SJNBL006105_C1
2323346


title: SJRHB000026_X1_DYE1804_CCLF-VT

description:
Library name: SJRHB000026_C9 Rep 2
2673598


title: mj2_12_05.2.ATAC

description: Library name: HI_537_2


title: SJRHB000026_X1_DYE1803_CCLF-VT

description:
Library name: SJRHB000026_C9 Rep 1
2673597


title: SJNBL046_X_DYE7969_T0

description:
Library name: SJNBL046_X
2323345


title: SJRHB010928_X1_DYE1698_CCLF

description:
Library name: SJRHB010928_C3
2654601


title: mj2_12_03.2.ATAC

description: Library name: HI_535_2


title: SJRHB000026_X1_DYE1678_CCLF

description:
Library name: SJRHB000026_C5
2634532


title: SJRHB000026_X2_DYE 6211_2D

description:
Library name: SJRHB000026_C4
2169855


title: SJOS030597_X1_DYE2812_T0

description:
Library name: SJOS030597_X1
3297271


title: SJNBL030721_X2_DYE2811_T0

description:
Library name: SJNBL030721_X2
3297270


title: PolIIS5P-CUTandTag_24h-WT_rep2

city: Beijing

first: Mingzhao

address: 15 Da Tun Rd, Chaoyang District

department: Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

description:
Library name: PolIIS5P-CUTandTag_24h-WT2
PolIIS5P-CUTandTag_24h-WT.bw

data_processing:
Raw sequencing data were trimmed and filtered by using Trim Galore v0.6.7.
Bowtie2 v2.5.1 was used to align reads to the mouse genome with default parameters and then sorted using the Samtools v1.15.
MACS2 v2.2.7.1 was used to call peaks.
bamCoverage v3.5.1 was used to generate bigwig files from bam files.
Assembly: mm10
Supplementary files format and content: bigWig files
Library strategy: CUT&Tag

source_name: spleen

extract_protocol:
Naïve CD8+ T (CD62L+CD44lo) cells were purified from spleens of  WT and H2AZ-cKO. The sorted naïve T cells were stimulated with anti-CD3 and anti-CD28 antibodies (Abs) for 6 or 24 h.  Then the naive CD8 T or activated CD8 T cells were collected for ATAC-seq and CUT&Tag assay. ATAC-seq library was constructed by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, #TD501-01),  following the manufacturer’s instructions. DNA for CUT&Tag-seq was cleavaged Under Target & Tagmentation by H2A.Z, H3K4me3, H3K27me3, H3K27ac and PolII S5P antibody in T cells. Genomic DNA was extracted using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, #TD904).
CUT&Tag libraries was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, #TD904), following the manufacturer’s instructions.

value: spleen

value: naive CD8+ T cell

tag: cell subset


title: SJRHB013758_X2_DYE 6193_2D

description:
Library name: SJRHB013758_C4
2169837


title: PolIIS5P-CUTandTag_24h-WT_rep1

description:
Library name: PolIIS5P-CUTandTag_24h-WT1
PolIIS5P-CUTandTag_24h-WT.bw

tag: treatment


title: SJNBL031668_X1_DYE2809_T0

description:
Library name: SJNBL031668_X1
3293597

tag: batch


title: SJNBL063820_X1_DYE2810_T0

description:
Library name: SJNBL063820_X1
3297269


title: PolIIS5P-CUTandTag_24h-H2AZKO_rep2

description:
Library name: PolIIS5P-CUTandTag_24h-H2AZKO2
PolIIS5P-CUTandTag_24h-H2AZKO.bw

tag: genotype


title: SJNBL031232_X1_DYE2808_T0

description:
Library name: SJNBL031232_X1 Rep 2
3293596


title: SJRHB030680_X1_DYE 6191_2D

description:
Library name: SJRHB030680_C2 Rep 1
2169835


title: SJNBL030721_X7_DYE2806_T0

description:
Library name: SJNBL030721_X7
3293594


title: SJRHB013758_X2_DYE 6192_3D

description:
Library name: SJRHB013758_C2
2169836


title: PolIIS5P-CUTandTag_24h-H2AZKO_rep1

description:
Library name: PolIIS5P-CUTandTag_24h-H2AZKO1
PolIIS5P-CUTandTag_24h-H2AZKO.bw


title: SJNBL031239_X2_DYE2807_T0

description:
Library name: SJNBL031239_X2
3293595


title: SJNBL030721_X6_DYE2805_T0

description:
Library name: SJNBL030721_X6
3293593


title: SJRHB030680_X1_DYE 6190_3D

description:
Library name: SJRHB030680_C1 Rep 1
2169834


title: PolIIS5P-CUTandTag_0h-WT_rep2

description:
Library name: PolIIS5P-CUTandTag_0h-WT2
PolIIS5P-CUTandTag_0h-WT.bw

value: unstimulated


title: SJNBL030721_X5_DYE2804_T0

description:
Library name: SJNBL030721_X5
3293592


title: SJNBL030721_X1_DYE2803_T0

description:
Library name: SJNBL030721_X1
3293591


title: SJRHB000026_X1_DYE 6189_2D

description:
Library name: SJRHB000026_C3
2169833


title: SJNBL031239_X1_DYE2740_2D

description:
Library name: SJNBL031239_C3
3284118


title: PolIIS5P-CUTandTag_0h-WT_rep1

description:
Library name: PolIIS5P-CUTandTag_0h-WT1
PolIIS5P-CUTandTag_0h-WT.bw

value: WT


title: SJNBL031239_X1_DYE2739_3D

description:
Library name: SJNBL031239_C1
3284117


title: SJNBL031239_X1_DYE2738_T0

description:
Library name: SJNBL031239_X1
3284116


title: SJRHB000026_X1_DYE 6188_3D

description:
Library name: SJRHB000026_C1
2169832


title: SJRHB010927_X1_DYE 6187_2D

description:
Library name: SJRHB010927_C2
2169831


title: SJNBL031232_X1_DYE2736_T0

description:
Library name: SJNBL031232_X1 Rep 1
3284114


title: PolIIS5P-CUTandTag_0h-H2AZKO_rep1

description:
Library name: PolIIS5P-CUTandTag_0h-H2AZKO1
PolIIS5P-CUTandTag_0h-H2AZKO.bw


title: PolIIS5P-CUTandTag_0h-H2AZKO_rep2

description:
Library name: PolIIS5P-CUTandTag_0h-H2AZKO2
PolIIS5P-CUTandTag_0h-H2AZKO.bw


title: SJNBL031232_X1_DYE2737_3D

description:
Library name: SJNBL031232_C2
3284115


title: SJNBL030513_X1_DYE2735_3D

description:
Library name: SJNBL030513_C2
3284113


title: SJRHB010927_X1_DYE 6186_3D

description:
Library name: SJRHB010927_C1
2169830


title: SJNBL030513_X1_DYE2734_T0

description:
Library name: SJNBL030513_X1
3284112


title: H3K4me3-CUTandTag_CD8_24h_WT_rep2

description:
Library name: H3K4me3-CUTandTag_CD8_24h_WT2
H3K4me3-CUTandTag_CD8_24h_WT.bw


title: SJNBL063821_X1_DYE2733_3D

description:
Library name: SJNBL063821_C1
3284111


title: SJRHB015720_X1_DYE 6185_2D

description:
Library name: SJRHB015720_C2
2169829


title: SJNBL063821_X1_DYE2732_T0

description:
Library name: SJNBL063821_X1
3284110


title: SJNBL046148_X1_DYE2731_2D

description:
Library name: SJNBL046148_C2
3284109


title: SJRHB015720_X1_DYE 6184_3D

description:
Library name: SJRHB015720_C1
2169828


title: H3K4me3-CUTandTag_CD8_24h_WT_rep1

description:
Library name: H3K4me3-CUTandTag_CD8_24h_WT1
H3K4me3-CUTandTag_CD8_24h_WT.bw


title: H3K4me3-CUTandTag_CD8_24h_IgG-Ctr

description:
Library name: H3K4me3-CUTandTag_CD8_24h_IgG
H3K4me3-CUTandTag_CD8_24h_IgG.bw


title: SJRHB013758_X1_DYE 6182_2D

description:
Library name: SJRHB013758_C3 Rep 2
2169826


title: SJNBL046148_X1_DYE2730_3D

description:
Library name: SJNBL046148_C1
3284108


title: SJNBL046148_X1_DYE2729_T0

description:
Library name: SJNBL046148_X1
3284107


title: SJRHB046156_X1_DYE1851_T0

description:
Library name: SJRHB046156_X1
2685948


title: SJRHB010928_X1_DYE1852_T0

description:
Library name: SJRHB010928_X1
2685949


title: H3K4me3-CUTandTag_CD8_24h_H2AZ-cKO_rep2

description:
Library name: H3K4me3-CUTandTag_CD8_24h_H2AZ-cKO2
H3K4me3-CUTandTag_CD8_24h_H2AZ-cKO.bw


title: SJRHB013758_X1_DYE 6180_3D

description:
Library name: SJRHB013758_C1 Rep 2
2169824


title: SJRHB011_X_DYE1850_T0

description:
Library name: SJRHB011_X
2685947


title: H3K4me3-CUTandTag_CD8_24h_H2AZ-cKO_rep1

description:
Library name: H3K4me3-CUTandTag_CD8_24h_H2AZ-cKO1
H3K4me3-CUTandTag_CD8_24h_H2AZ-cKO.bw


title: SJRHB013759_X14_DYE1849_T0

description:
Library name: SJRHB013759_X14
2685946


title: SJRHB013757_X2_DYE 6177_2D

description:
Library name: SJRHB013757_C1 Rep 1
2169821


title: SJOS031478_X4_DYE1794_VT

description:
Library name: SJOS031478_C4
2671601

value: VT


title: H3K4me3-CUTandTag_CD8_0h_WT_rep2

description:
Library name: H3K4me3-CUTandTag_CD8_0h_WT-N2
H3K4me3-CUTandTag_CD8_0h_WT-N2.bw


title: SJRHB013757_X2_DYE 6176_3D

description:
Library name: SJRHB013757_C2 Rep 1
2169820


title: H3K4me3-CUTandTag_CD8_0h_WT_rep1

description:
Library name: H3K4me3-CUTandTag_CD8_0h_WT-N1
H3K4me3-CUTandTag_CD8_0h_WT-N1.bw


title: SJOS016015_X1_DYE1792_3D

description:
Library name: SJOS016015_C1
2671599


title: SJOS016015_X1_DYE1793_2D

description:
Library name: SJOS016015_C2
2671600


title: Parental HeLa cells treated with palmitate for 18 h

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

description: Library name: W6

data_processing:
Basecalling was performed with RTAVersion ver. 3.4.4
The seuqence data was mapped to the genome sequence with STAR ver. 2.7.1a.
Assembly: GRCh38
Supplementary files format and content: Expression values of refseq gene models were calculated with RSEM ver. 1.3.0

source_name: HeLa

growth_protocol: Parental and RNF213-knockout HeLa cells, derived from cervical cancer, were obtained from American Type Culture Collection (ATCC, VA, USA), and cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Nacalai Tesque, Kyoto, Japan) supplemented with 10 % fetal bovine serum, 100 U/mL penicillin, and 100 µg/mL streptomycin (Nacalai Tesque). All cells were maintained in an incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from HeLa cells using Sepasol®-RNA I Super G (Nacalai Tesque). PolyA(+) RNA was purified using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, MA, USA).
RNA libraries were constructed using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs).

treatment_protocol: HeLa cells are treated with 0.5 mM sodium palmitate (Nacalai Tesque) for 0, 1, 3, 6, 12, or 18 h.

value: HeLa

value: cervical cancer cell line

value: wild-type

value: treated with palmitate for 18 h


title: SJOS071782_X1_DYE1790_2D

first: Michael

address: 262 Danny Thomas

institute: St. Jude Children's Research Hospital

description:
Library name: SJOS071782_C2
2671597


title: H3K4me3-CUTandTag_CD8_0h_IgG-Ctr

description:
Library name: H3K4me3-CUTandTag_CD8_0h_IgG
H3K4me3-CUTandTag_CD8_0h_IgG.bw


title: SJOS071782_X1_DYE1788_T0

description:
Library name: SJOS071782_X1
2671595

value: Tumor


title: Parental HeLa cells treated with palmitate for 12 h

description: Library name: W5

value: treated with palmitate for 12 h


title: SJOS016015_X1_DYE1791_T0

description:
Library name: SJOS016015_X1
2671598

value: OST


title: Mouse uterus, postnatal day 12, Visium HD spatial transcriptomics

description:
Library name: PND12
Visium HD probe-based spatial transcriptomics of PND12 mouse uterus

data_processing:
Raw sequencing data were processed using Space Ranger v4.0.1 (10x Genomics)
Sequencing reads were aligned to the mouse reference genome (refdata-gex-mm10-2020-A) using Space Ranger default settings
The Space Ranger software was used to align the barcoded spot pattern to the H&E tissue image and to differentiate tissue from background
Cell segmentation and downstream spatial analysis and visualization were performed in Seurat (v5.3.0), following the recommended workflow for Visium HD data with cell segmentation outputs
Spot-level gene expression matrices were generated at 8 µm bin resolution
Assembly: mm10 (refdata-gex-mm10-2020-A)
Supplementary files format and content: filtered_feature_cell_matrix.h5: gene expression count matrix containing spatial barcodes, gene IDs, and UMI counts at 8 µm bin resolution in HDF5 format
Supplementary files format and content: PND5.tiff: full-resolution CytaAssist brightfield image for PND5; PND5_tissue_hires_image.tiff: high-resolution H&E tissue image for PND5 generated by Space Ranger; A1.json: Loupe Browser fiducial alignment file for PND5 capture area; PND12.tiff: full-resolution CytaAssist brightfield image for PND12; PND12_tissue_hires_image.tiff: high-resolution H&E tissue image for PND12 generated by Space Ranger; D1.json: Loupe Browser fiducial alignment file for PND12 capture area
Library strategy: Spatial Transcriptomics

source_name: uterus

growth_protocol: C57BL/6J mice were maintained under standard housing conditions at the University of Missouri. Uterine horns from postnatal day 5 (PND5) and postnatal day 12 (PND12) female mice (n=5 per timepoint) were collected.

extract_protocol:
Uterine horns from PND5 and PND12 female C57BL/6J mice (n=5 per timepoint) were collected, fixed in 4% paraformaldehyde for 16 hours at 4°C, and processed for paraffin (FFPE) embedding. FFPE blocks were sectioned at 5 µm and mounted onto Visium HD H1 capture area slides.
Spatial Gene Expression library preparation and sequencing were performed by the Genome Technology Access Center at Washington University in St. Louis. 5-µm FFPE paraffin sections were deparaffinized, stained with hematoxylin and eosin, and imaged to capture tissue morphology. Sections were processed using the Visium HD H1 Slide with HD probe-based v1 chemistry and the Visium Mouse Transcriptome Probe Set v2.0 (10x Genomics), following the manufacturer's instructions.

treatment_protocol: No hormonal or pharmacological treatment. Tissue collected at standard postnatal timepoints.

value: uterus


title: H3K4me3-CUTandTag_CD8_0h_H2AZ-cKO_rep2

description:
Library name: H3K4me3-CUTandTag_CD8_0h_H2AZ-cKO-N2
H3K4me3-CUTandTag_CD8_0h_H2AZ-cKO-N2.bw


title: SJOS030876_X2_DYE1787_2D

description:
Library name: SJOS030876_C4
2671594

value: Cells


title: Parental HeLa cells treated with palmitate for 6 h

description: Library name: W4

value: treated with palmitate for 6 h


title: SJOS030876_X2_DYE1785_T0

description:
Library name: SJOS030876_X2
2671592


title: pooled samples (WT untx, WT Caur, IFNg KO untx, IFNg KO Caur, IL17 KO Caur, YETI Caur), CMO

city: San Francisco

first: Charlotte

last: Hurabielle

address: 513 Parnassus Avenue

institute: University of California, San Francisco

description:
Library name: pooled samples, CMO
10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cellranger software version 8.1.0 (10X genomics)
using cellranger, data was demultiplexed so that each of the individual conditions (WT untreated, WT Caur topical, IFNg KO untreated, IFNg KO Caur topical, IL17 KO Caur topical, YETI Caur topical; 3 technical replicates each) could be retrieved
all the samples were represented in the libraries and demultiplexed using the CMO barcodes: skin, WT untreated, WT Caur topical, IFNg KO untreated, IFNg KO Caur topical, IL17 KO Caur topical, YETI Caur topical, 3 technical replicates
Assembly: Mouse mm10
Supplementary files format and content: Matrix files

source_name: skin

extract_protocol:
After tissue digestion of back skin and single cell solution formation, CD45+ and CD45- cells were sorted using in a 1:1 ratio from mock or C. auris colonized B6 mice, mock or C. auris colonized IFNg-/- mice, C. auris colonized IFNgKO and C. auris colonized IL-17-/- mice.  Prior to sorting, 3-4 mice per condition were pooled. After sorting, 1 replicate per group was multiplexed in equal ratios
Library preparation was performed according to the manufacturer's instructions using single cell 3’ CellPlex kit (10X genomics). 3 gene expression and associated multiplexing libraries were created with all 6 conditions being present in each library (3 technical replicates)

treatment_protocol: Candida auris colonization versus untreated mice

value: skin

value: various, see data processing step

value: pooled after barcoding:wild type untreated, wild type treated with Candida auris skin colonization, IFNg KO untreated, IFNg KO treated with Candida auris skin colonization, IL17 KO treated with Candida auris skin colonization, YETI treated with Candida auris skin colonization)

tag: library type

value: CMO


title: Mouse uterus, postnatal day 5, Visium HD spatial transcriptomics

description:
Library name: PND5
Visium HD probe-based spatial transcriptomics of PND5 mouse uterus


title: H3K27me3-CUTandTag_CD8_24h_WT

description:
Library name: H3K27me3-CUTandTag_CD8_24h-WT
H3K27me3-CUTandTag_CD8_24h_WT.bw

value: spleen

value: naive CD8+ T cell


title: Parental HeLa cells treated with palmitate for 3 h

description: Library name: W3

value: treated with palmitate for 3 h


title: H3K4me3-CUTandTag_CD8_0h_H2AZ-cKO_rep1

description:
Library name: H3K4me3-CUTandTag_CD8_0h_H2AZ-cKO-N1
H3K4me3-CUTandTag_CD8_0h_H2AZ-cKO-N1.bw

value: unstimulated


title: SJNBL030721_X4_DYE1784_VT

city: Memphis

last: Dyer

description:
Library name: SJNBL030721_C15
2671591

value: VT

value: NBL


title: H3K27me3-CUTandTag_CD8_24h_H2AZ-cKO

description:
Library name: H3K27me3-CUTandTag_CD8_24h-H2AZ-cKO
H3K27me3-CUTandTag_CD8_24h_H2AZ-cKO.bw


title: pooled samples (WT untx, WT Caur, IFNg KO untx, IFNg KO Caur, IL17 KO Caur, YETI Caur), GEX

description:
Library name: pooled samples, GEX
10X genomics

value: GEX


title: Parental HeLa cells treated with palmitate for 1 h

description: Library name: W2

value: HeLa

value: cervical cancer cell line

value: wild-type

value: treated with palmitate for 1 h


title: SJNBL012407_X1_DYE1783_VT

description:
Library name: SJNBL012407_C4
2671590

value: Tumor


title: Parental HeLa cells treated with palmitate for 0 h

description: Library name: W1

value: treated with palmitate for 0 h


title: pooled samples (untreated, Calb topical, Caur topical)

description:
Library name: pooled samples
10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cellranger software version 8.1.0 (10X genomics)
all the samples were linked with barcodes (CMO) and then pooled, ie all the samples were represented in the libraries and demultiplexed using the CMO barcodes
using cellranger, data was demultiplexed so that each of the individual conditions (WT untx, biol rep 1; WT untx, biol rep 2; WT Calb, biol rep 1; WT Calb, biol rep 2; WT Caur, biol rep 1; WT Caur, biol rep 2) could be retrieved
all the samples were represented in the libraries and demultiplexed using the CMO barcodes:skin, WT mice, untreated, 3 technical replicates, biol rep 1 and 2; WT treated with topical Calb, 3 technical replicates, biol rep 1 and 2; WT treated with topical Caur, 3 technical replicates, biol rep 1 and 2)
Assembly: Mouse mm10
Supplementary files format and content: Matrix files

extract_protocol:
After tissue digestion of back skin and single cell solution formation, CD45+ and CD45- cells were sorted using in a 1:1 ratio from mock colonized B6 mice, C. auris colonized B6 mice and C. albicans colonized B6 mice (4 applications on days 0,2,4,6 and harvest on day 14). Prior to sorting 2 mice per condition were pooled. After sorting, 2 biological replicates per group (2x Untreated, 2x C. auris colonized, 2x C. albicans colonized) were multiplexed in equal ratios
Library preparation was performed according to the manufacturer's instructions using single cell 3’ CellPlex kit (10X genomics). 3 gene expression and associated multiplexing libraries were created with all 6 conditions being present in each library (3 technical replicates)

treatment_protocol: Candida albicans colonization versus Candida auris colonization versus mock colonization (untreated) mice

value: skin

value: WT

value: pooled after barcoding:2 groups of untreated mice; 2 groups of WT mice treated with Candida albicans skin colonization; 2 groups of WT mice treated with Candida auris skin colonization)

value: GEX and CMO


title: H3K27me3-CUTandTag_CD8_0h_WT_rep2

description:
Library name: H3K27me3-CUTandTag_CD8_0h_WT-N2
H3K27me3-CUTandTag_CD8_0h_WT.bw

value: spleen


title: SJWLM046152_X1_DYE1782_2D

description:
Library name: SJWLM031558_C2
2671589

value: Cells


title: RNF213-knockout HeLa cells treated with palmitate for 18 h

description: Library name: B6

value: RNF213 knockout

value: treated with palmitate for 18 h


title: H3K27me3-CUTandTag_CD8_0h_WT_rep1

description:
Library name: H3K27me3-CUTandTag_CD8_0h_WT-N1
H3K27me3-CUTandTag_CD8_0h_WT.bw

value: naive CD8+ T cell

value: unstimulated


title: RNF213-knockout HeLa cells treated with palmitate for 12 h

description: Library name: B5

value: treated with palmitate for 12 h


title: SJWLM046152_X1_DYE1780_T0

description:
Library name: SJWLM046152_X1
2671587


title: Col-0 whole seedling, 4h ethylene treated, rep5, lane1

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

description:
Library name: 220316_Ath_SC_Ath_3do_col_4ET_5_1_10xHTRNA
10x Genomics

data_processing:
Cell by gene matrices were generated with Cellranger v3.1.0
Assembly: TAIR10 genome; Araport 11 transcriptome
Supplementary files format and content: harmony.rds, Seurat object that contains the snRNA-seq dataset of whole seedlings
Supplementary files format and content: apical_clusters.rds, Seurat object that contains cells that compose the apical seedling
Supplementary files format and content: spatial_multiome_imputed_250825.rds, Seurat object that contains cells related to the spatial multi-modal integration
Supplementary files format and content: GA_subclust26_multiome_imputed_250825.rds, Seurat object that contains the AHR (cluster 26) cells

source_name: Whole seedling

extract_protocol:
1.5g pulverized frozen tissue was extracted in 10 mL nuclei purification buffer (NPB; 20 mM MOPS pH 7, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, 1X protease inhibitors (Sigma), 1:1000 SUPERase (Thermo), at 4 oC for 10 min with gentle agitation. The nuclei-containing extract was sequentially filtered through 70 µm (Fisher) and 30 µm (Miltenyi) filters at 4 oC. The filtered extract was then homogenized using a pre-chilled Dounce homogenizer with 10 loose pestle strokes followed by 10 tight pestle strokes. Nuclei were pelleted by centrifugation at 700 x g for 5 min at 4 °C and resuspended in 3 mL NPB. A discontinuous gradient of 15% / 45% optiprep was prepared by diluting 60% Optiprep (Sigma) to 50% with 120 mM Tris-Cl, pH 8.0, 150 mM KCl, 30 mM MgCl2, and further diluted to 15% or 45% with NPB containing 1:1000 SUPERase. The nuclear pellet was resuspended in 3 mL NPB, gently layered onto the 15%/45% OptiPrep gradient, and centrifuged at 1500 × g for 15 min at 4 oC. Following centrifugation, the nuclei were collected from the 15%/45% OptiPrep interface, washed with 10 mL of 1X PBS (Corning), and pelleted by centrifugation at 500 × g for 5 min at 4 oC. The nuclei were resuspended in 1 mL of PBS, stained with 3 µg of Hoechst 33342, placed on ice, and taken to the Flow Cytometry Core for Fluorescence-Activated Nuclei Sorting (FANS). A BD Influx sorter with a 100-μm nozzle was used to sort nuclei in 1x PBS with sheath fluid at 20 PSI; nuclei were kept at 4 °C during the purification process. Debris was excluded first by gating using forward and side scatter pulse area parameters (FSC-A and SSC-A in log scale), then exclusion of aggregates using pulse width parameters (FSC-W and SSC-W), and finally gating on Hoechst-positive nuclei. Hoechst was excited with a 405nm laser at 100mW and detected using the 460/50BP filter. The Hoechst-positive nuclei were sorted using the '1-drop pure' mode directly into 1.5mL Eppendorf tubes containing 1x PBS, 0.5% BSA, and 1:1,000 SUPERase.
Following FANS, nuclei were centrifuged at 500 × g for 5 min; the supernatant was aspirated, and the nuclei were resuspended in 50 µl of PBS, BSA, and RNase inhibitors and quantified using a hemocytometer (Incyto). 10,000 nuclei, or the total nucleus suspension if fewer than 10,000 nuclei were collected, were used as input for the 10x Genomics Single Cell 3’ Gene Expression v3 reagents. Sequencing libraries were constructed following the manufacturer’s instructions and were sequenced with the Illumina NovaSeq 6000.

value: Whole seedling

value: 4h ethylene


title: Col-0 whole seedling, 4h ethylene treated, rep5, lane2

description:
Library name: 220316_Ath_SC_Ath_3do_col_4ET_5_2_10xHTRNA
10x Genomics


title: H3K27me3-CUTandTag_CD8_0h_H2AZ-cKO_rep2

description:
Library name: H3K27me3-CUTandTag_CD8_0h_H2AZ-cKO-N2
H3K27me3-CUTandTag_CD8_0h_H2AZ-cKO.bw


title: SJWLM071786_X2_DYE1779_2D

description:
Library name: SJWLM071786_C2
2671586


title: Col-0 whole seedling, 4h control, rep5, lane2

description:
Library name: 220316_Ath_SC_Ath_3do_col_4air_5_2_10xHTRNA
10x Genomics

value: 4h control


title: RNF213-knockout HeLa cells treated with palmitate for 6 h

description: Library name: B4

value: HeLa

value: cervical cancer cell line

value: treated with palmitate for 6 h


title: H3K27me3-CUTandTag_CD8_0h_H2AZ-cKO_rep1

description:
Library name: H3K27me3-CUTandTag_CD8_0h_H2AZ-cKO-N1
H3K27me3-CUTandTag_CD8_0h_H2AZ-cKO.bw


title: SJWLM071786_X2_DYE1778_3D

description:
Library name: SJWLM071786_C1
2671585


title: Col-0 whole seedling, 4h control, rep5, lane1

description:
Library name: 220316_Ath_SC_Ath_3do_col_4air_5_1_10xHTRNA
10x Genomics


title: RNF213-knockout HeLa cells treated with palmitate for 3 h

description: Library name: B3

value: treated with palmitate for 3 h