title: CD69_lo_24_C8

city: Bethesda

first: Jianfei

last: Hu

state: MD

address: BG NIHBC T40 RM 101A-09

department: VRC

institute: NIH

data_processing:
Illumina bcl2fastq-2.20 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mm10  genome using STAR v2.6.1c with parameters   --runThreadN 8 --readFilesCommand zcat --readFilesIn "$left" "$right" --outSAMtype BAM SortedByCoordinate --outFileNamePrefix $starDir --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --outFilterMismatchNmax 2 --outSAMstrandField intronMotif
Gene expression level was calculated by HTSeq (version 0.9.1)
Assembly: Mm10
Supplementary files format and content: Matrix of Raw reads Number mapped to each gene
Supplementary files format and content: Matrix of gene expression level (TPM)

organism: Mus

source_name: MCC CD69-lo,24 hour

extract_protocol:
Sorted cells were lysed and total RNA was extracted using RNAzol RT (Molecular Research Center Inc., Cincinnati, OH). Poly-adenylated RNA was purified using Dynabeads oligo (dT)25 (Invitrogen, Carlsbad, CA) and fragmented
cDNA was synthesized and Illumina-ready libraries were generated using a modified Illumina TruSeq mRNA Library preparation protocol (paired end NovaSeq 2x150 reads)

tag: strain

value: 5C.C7 TCR transgenic; B10.A-Rag2tm1FwaH2-T18aTg (Tcra5CC7,Tcrb5CC7)lwep

value: Lymph Node

tag: sorting phenotype

value: MCC CD69-lo

value: 24 hours


title: GP_CD69_lo_24_C7

status: Public on May 20 2025

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

source_name: MCC+GP CD69-lo,24 hour

tag: tissue

value: MCC+GP CD69-lo

tag: time


title: CD69_lo_1_A8

source_name: MCC CD69-lo,1 hour

value: 1 hour


title: GP_CD69_hi_1_B8

source_name: MCC+GP CD69-hi,1 hour

value: MCC+GP CD69-hi


title: PA14 ptsP and ptsN deleted cells, SCFM-2, biol rep 2

city: Stillwater

first: Matthew

last: Cabeen

state: Oklahoma

address: 307 Life Science East

department: Microbiology and Molecular Genetics

institute: Oklahoma State University

description: Library name: V2_S105

data_processing:
Sequence reads were processed and trimmed using FastQC and Cutadapt
Sequence reads were aligned to genome using Bowtie 2.
Differential gene expression analysis was processed using EdgeR.
All software was set using default parameters.
Assembly: NC_008463
Supplementary files format and content: Excel file includes gene list with log2 fold changes, P values, false discovery rate (FDR) P-values, log2 of read counts per million (CPM), and F-statistic.

organism: Pseudomonas aeruginosa

source_name: whole cells

growth_protocol: P. aeruginosa strains as noted were grown overnight in LB, washed 2X with PBS, then inoculated 1:1000 into liquid SCFM2 and grown at 37°C with shaking to an OD600 of 0.3 before extraction

extract_protocol:
Total RNA was extracted using the NEB Monarch total RNA extraction kit according to the manufacturer's protocol for gram-negative bacteria. Ribosomal RNA was removed using the Ribo-Zero kit.
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero plus kit was used according to the manufacturer's protocol

value: whole cells

tag: genotype

value: DptsP DptsN


title: Pseudogymnoascus destructans, Control3

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

description:
Library name: C3
Column names in 3.7.23.counttable.csv: C3

data_processing:
Sequencing reads trim using fastq_quality_trimmer (-t 30, -l 35); reads filter using fastq_quality_filter (-q30, -p 80); Genome mapping using Tophat2 (2.0.13); Read counting using subread (1.4.6)
Assembly: GCF_001641265.1_ASM164126v1_genomic
Supplementary files format and content: Read count per genome feature (gene); csv format; Each row is a gene, each column is a sample

organism: Pseudogymnoascus destructans

growth_protocol: The Pseudogymnoascus destructans (Pd) strain (MYA4855) was purchased from the American tissue culture collection (ATCC strain number 20631-21) and used for all experiments. The long-term propagation of Pd was carried out using solid Yeast extract-peptone and glucose (YPD) plates at 15ºC and consisted of 10 g/L of yeast extract, 20 g/L of peptone, 20 g/L glucose, and 15 g/L of agar. Metal growth studies were performed using chemically defined growth plates (SC-Ura) which were made using Milli-Q water and 1.8 g/L of yeast nitrogen base, 5g/L ammonium sulfate (NH4SO4), 20 g/L glucose, 100 mg/L histidine, 1.7 g/L of the SC-Ura-His amino acid supplement mixture, and 15 g/L agar

extract_protocol:
Transcriptomic studies were performed on Pd fungi grown for 10 days at 15 ºC on SC-Ura plates alone or supplemented with either copper chelator BCS (800 µM) or CuSO4 (500 µM). Fungal cells, including conidia and mycelium, were suspended in 2 ml of TE buffer by gently rubbing the mycelium mass with a sterile inoculating loop. The resulting cell suspension was transferred to a 2 mL microcentrifuge tube and pelleted for 5 minutes at 16,000 X g. The cells were washed twice with 1 ml of TE buffer. The resulting cell pellet was snap-frozen in dry ice and stored in – 80 C for later use. Total RNA was extracted from Pd cells using TRIZOL reagents using the manufacturer’s recommended procedure (Ref). Briefly, 1 ml of TIRZOL reagent was added to Pd cells along with approximately 100 μL of 0.5 μM zirconium beads (ZB-05; Next. Advanced) and homogenized at 4C in a bullet blender (SpeedXXX for 5 minutes). The resulting cell lysate was incubated on ice for 5 minutes. The cell lysates were then thoroughly mixed with 0.2 ml chloroform and incubated for 2 to 3 minutes before centrifugation at 12,000 X g for 15 minutes. The upper aqueous layer was transferred to a new microcentrifuge tube and 500 μL of isopropanol was added to the tube. After mixing, the solution was incubated on ice for 10 minutes and centrifuged at 12,000 X g at 4 °C. The supernatant was discarded, and 1 ml of 75% ethanol was added, vortex and centrifuged at 7,500 X g for 5 minutes at 4 ºC. The supernatant was discarded, and the white pellet was air-dried for 5–10 minutes. The RNA (pellet) was resuspended in 50 µl of 1X TE buffer and incubated for 15 minutes at 55 °C in a hot water bath. Finally, the concentration of the RNA was determined using nanodrop and analyzed using an Agilent bioanalyzer. Then RNA was stored at -80 ºC. All RNA samples were sent to Innomics, Inc, (Sunnyvale, CA) for the polyA mRNA enrichment, sequencing library construction, indexing and RNA sequencing.
polyA capture

treatment_protocol: Prior to autoclaving 1 pellet (~200 mg) of NaOH was added to the SC-Ura media prior to autoclave sterilization. The addition of sterile Cu-sulfate and Bathocuproine sulfonic acid sodium salt (BCS) was added to the SC-URA growth media using a 125 mM stock solution after autoclave sterilization at a temperature of approximately 50 ºC.

tag: cell line

tag: treatment

tag: batch


title: GP_CD69_hi_24_B7

source_name: MCC+GP CD69-hi,24 hour


title: Pseudogymnoascus destructans, Control8

description:
Library name: C8
Column names in 3.7.23.counttable.csv: C8

source_name: Pseudogymnoascus destructans (Pd) strain (MYA4855)


title: Ewing2_GEX

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

library_source: transcriptomic single cell

data_processing:
Demultiplexing was performed using bcl2fastq v2.20.0.
Gene expression libraries were aligned to GRCh38 using CellRanger v7.0.1.
Assembly: GRCh38
Supplementary files format and content: Gzipped tar archive file containing tab-delimited barcodes, features, and matrix files.

molecule: polyA RNA

organism: Homo sapiens

source_name: tumor

extract_protocol:
Freshly resected Ewing sarcoma tumors were mechanically disrupted/ Single-cell RNAseq was performed using 10X Genomics and libraries were sequenced on an Illumina NovaSeq500 instrument.
The library generation strategy was as per the manufacturer's instructions for 10X Genomics 5' based chemistries.

value: tumor

tag: disease state

value: Ewing sarcoma


title: PA14 ptsP and ptsN deleted cells, SCFM-2, biol rep 1

description: Library name: V1_S104


title: Pseudogymnoascus destructans, Control4

description:
Library name: C4
Column names in 3.7.23.counttable.csv: C4

value: Pseudogymnoascus destructans (Pd) strain (MYA4855)


title: Sample_2909_KO

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Base calling and de-multiplexing was performed using CASAVA v1.8.2 and fastQC was used for quality control.
Subsequently, the reads were aligned to the mm10-based mouse Gencode reference transcriptome vM16 and quantified on gene level using star v2.7.1a. (Dobin et al., 2013).
Gene expression quantifications were imported to R 3.5.3 (2019-03-11) and DESeq2 v1.22.2 was used for downstream analyses (Love et al., 2014).
Lowly expressed genes (rowSums > 10) were filtered and variance stabilizing transformation was performed.
Subsequently, principal component analysis was conducted on all present genes using the prcomp function (R/stats 3.5.3).
Differential expression analysis was performed comparing WT and KO samples without pre-defined fold change threshold and using independent hypothesis weighting (IHW, v1.10.1) (Ignatiadis et al., 2016) as the multiple testing procedure.
Genes with an adjusted p-value < 0.05 and a fold change >1.5 were determined as significantly differentially expressed.
Functional enrichment analysis using the MSigDB data base (Liberzon et al., 2015) was performed on the DE gene sets using the R package ClusterProfiler v3.10.1 (Yu et al., 2012)).
Assembly: mm10 gencode vM16
Supplementary files format and content: rawexpression_unfiltered_231213.csv: comma separated file holding unfiltered quantifications of sequencing reads across all genes over all samples
Supplementary files format and content: normalized_expression_filtered_231213.csv: comma separated file holding filtered quantifications of sequencing reads across genes with at least 10 reads quantified over all samples

organism: Mus musculus

source_name: Spleen and lymph node

extract_protocol:
Total RNA was isolated from splenic CD4+ T naive cells lysed in QIAzol Lysis Reagent (Qiagen) using the miRNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
RNA quality and concentration was measured on the Agilent Tapestation 2200 (Agilent) using RNA screen tapes (Agilent) and further processed for barcoding, multiplexing and cDNA library construction using the TruSeq RNA Sample Preparation Kit v2 (Illumina). For indexing, barcoding indexes of Set A were used. cDNA library was measured in quality and quantity on Agilent Tapestation 2200 (Agilent) using High sensitivity Screen Tape (Agilent) and sequencing (single read, 75 bp) was performed on an Illumina HiSeq 1500 platform using the TruSeq SBS Kit v3 (Illumina) and TruSeq SR Cluster Kit v2 (Illumina) according to the manufacturer’s instruction.

value: Spleen and lymph node

tag: cell type

value: naive CD3+CD4+CD25-CD44low/-CD62L+ T cells

value: Satb1fl/fl x CD4-CreERT2wt/+

value: tamoxifen (KO)


title: Pseudogymnoascus destructans, Control2

description:
Library name: C2
Column names in 3.7.23.counttable.csv: C2


title: Sample_2908_KO


title: CD69_lo_24_H6


title: Pseudogymnoascus destructans, Control1

description:
Library name: C1
Column names in 3.7.23.counttable.csv: C1


title: PA14 cells, SCFM-2 + citrate, biol rep 4

description: Library name: S4_S92

value: WT


title: Sample_2907_KO


title: CD69_hi_24_G6

source_name: MCC CD69-hi,24 hour

value: 5C.C7 TCR transgenic; B10.A-Rag2tm1FwaH2-T18aTg (Tcra5CC7,Tcrb5CC7)lwep

value: MCC CD69-hi


title: Sample_2277_WT

description:
CountsPerPeak_unfiltered_231213.csv
PeakAnnotation_unfiltered_231213.csv

library_source: genomic

data_processing:
Demultiplexing was perfomed using bcl2fastq2 v2.20
Adapter trimming was performed using Trimmomatic v0.36 with following parameters ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 MINLEN:36 CROP:48
Alignment was performed using bowtie2 v2.3.5 against the murine reference genome mm10.
Duplicated reads were removed using picard "dedup" function and the transposase-induced offset was removed using the deeptools v3.5.2 "alignmentSieve" function.
Sorting and indexing of bam files was done using samtools v1.9
Peak calling was performed using MACS2 v2.1.2.
After subsampling the reads for each sample to 5*10^6 reads using Sambamba v0.7.0, normalized bigwig files were produced using deeptools v3.3.0 for genomic visualization of the read coverage
After peak calling, bed files listing narrow peaks were imported to R 3.5.3 (2019-03-11) and consensus peak regions across all samples were generated with the ‘reduce’ function of the Bioconductor GenomicRanges package v1.34.0 and reads were counted per sample using the ‘summarizeOverlaps’ function of the Bioconductor GenomicAlignments package v1.18.1
Genomic regions on the ENCODE blacklist for mm10 were excluded from the analysis.
ChIPseeker v1.18.0 was used to annotate genomic regions (Yu et al., 2015) using the TxDb.Mmusculus.UCSC.mm10.knownGene data base v3.4.4.
Peak regions were filtered for a minimum sum of 10 counts across all samples and a minimum MACS2 detection rate of at least 2 samples per group.
Statistical analysis of the resulting peak counts was performed in R 3.5.3 using the DESeq2 package v1.22.2 (Love et al., 2014).
Assembly: mm10 gencode vM16
Supplementary files format and content: CountsPerPeak_unfiltered_231213.csv: comma separated file holding quantifications of sequencing reads in unified peak regions over all samples called using MACS2
Supplementary files format and content: PeakAnnotation_unfiltered_231213.csv:  comma separated file holding ChipSeeker annotations of all unified peak regions over all samples called using MACS2

molecule: genomic DNA

extract_protocol:
60000 naive CD4+ T cells were lysed in 50 µl cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500 g for 10 min.
Transposase reaction was performed with in-house Tn5 Transposase in tagmentation buffer (10 mM TAPS-NaOH (pH 8.5), 5 mM MgCl2, 10% DMF) for 30 minutes at 37°C and purified using the MinElute PCR Purification Kit (Qiagen) according the manufacturer’s protocol. Transposed DNA fragments were amplified using the NEBNext High-Fidelity PCR Master Mix (NEB) and customized Nextera PCR primers 1 and 2 (Primer sequences are listed in Table S4). The PCR products were purified using the MinElute PCR Purification Kit. Quality check and measurement of PCR concentration was performed on the Agilent Tapestation 2200 using High sensitivity D1000 Screen Tape (Agilent).
Libraries were sequenced (single read, 75 bp) on an Illumina HiSeq1500 using the TruSeq Rapid SBS Kit (Illumina) and TruSeq Rapid Cluster Kit (Illumina) according to the manufacturer’s instruction.

tag: cell number


title: PA14 cells, SCFM-2 + citrate, biol rep 3

description: Library name: S3_S91


title: Pseudogymnoascus destructans, Bathocuproine sulfonic acid sodium salt sampe6

description:
Library name: B6
Column names in 3.7.23.counttable.csv: B6

value: Bathocuproine sulfonic acid sodium salt


title: PA14 cells, SCFM-2 + citrate, biol rep 2

description: Library name: S2_S90


title: Pseudogymnoascus destructans, Bathocuproine sulfonic acid sodium salt sampe7

description:
Library name: B7
Column names in 3.7.23.counttable.csv: B7


title: GP_CD69_lo_6_E6

source_name: MCC+GP CD69-lo,6 hour

value: Lymph Node

value: 6 hours


title: Sample_2276_WT


title: Pseudogymnoascus destructans, Bathocuproine sulfonic acid sodium salt sampe5

description:
Library name: B5
Column names in 3.7.23.counttable.csv: B5


title: PA14 cells, SCFM-2 + citrate, biol rep 1

description: Library name: S1_S89


title: Sample_2910_KO


title: Sample_2275_WT


title: Pseudogymnoascus destructans, Bathocuproine sulfonic acid sodium salt sampe4

description:
Library name: B4
Column names in 3.7.23.counttable.csv: B4


title: GP_CD69_hi_6_D6

source_name: MCC+GP CD69-hi,6 hour


title: PA14 ptsN deleted cells, SCFM-2, biol rep 4

description: Library name: M4_S62

value: DptsN


title: PA14 cells, SCFM-2 + citrate, biol rep 5

description: Library name: S5_S93


title: Sample_2273_WT


title: PA14 ptsN deleted cells, SCFM-2, biol rep 5

description: Library name: M5_S63


title: Pseudogymnoascus destructans, Bathocuproine sulfonic acid sodium salt sampe3

description:
Library name: B3
Column names in 3.7.23.counttable.csv: B3


title: CD69_hi_6_C6

source_name: MCC CD69-hi,6 hour


title: Sample_2274_WT


title: GP_24_A7

source_name: GP,24 hour

value: GP

value: 24 hours


title: GP_CD69_lo_1_B6

source_name: MCC+GP CD69-lo,1 hour

value: MCC+GP CD69-lo

value: 1 hour


title: PA14 ptsN deleted cells, SCFM-2, biol rep 3

description: Library name: M3_S61

value: whole cells


title: Sample_2272_KO


title: PA14 ptsN deleted cells, SCFM-2, biol rep 2

description: Library name: M2_S60


title: GP_CD69_hi_1_A6

value: MCC+GP CD69-hi


title: Pseudogymnoascus destructans, Bathocuproine sulfonic acid sodium salt sampe1

description:
Library name: B1
Column names in 3.7.23.counttable.csv: B1

value: Pseudogymnoascus destructans (Pd) strain (MYA4855)


title: Pseudogymnoascus destructans, Bathocuproine sulfonic acid sodium salt sampe2

description:
Library name: B2
Column names in 3.7.23.counttable.csv: B2


title: NP_24_F6

source_name: No peptide (NP),24 hour

value: No peptide (NP)


title: Sample_2271_KO

value: Spleen and lymph node

value: naive CD3+CD4+CD25-CD44low/-CD62L+ T cells

value: Satb1fl/fl x CD4-CreERT2wt/+


title: GP_1_H5

source_name: GP,1 hour

value: 5C.C7 TCR transgenic; B10.A-Rag2tm1FwaH2-T18aTg (Tcra5CC7,Tcrb5CC7)lwep


title: PA14 ptsN deleted cells, SCFM-2, biol rep 1

description: Library name: M1_S59


title: Arabidopsis, INPUT, 12DAG, Rep2

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

country: China

institute: Northwest A&F University

description:
Library name: INPUT_Rep2,ChIP
The raw data are being used for peak-calling about H2A.Z and H3K9K14ac ChIP-seq data

data_processing:
ChIP-seq reads were trimmed using the fastp tool (version 0.23.4)  with a quality score threshold of 20 for the final base.Reads shorter than 35 bp after trimming were discarded.The clean reads were aligned to the TAIR 10 genome(https://www.arabidopsis.org/) using Bowtie2 with default parameters.
Assembly: TAIR 10
Supplementary files format and content: BigWig files of first processed data were generated by using the Deeptools  (version 3.5.2).The Merge BigWig files of second process data were  assessed by merging results from 'bigwigcompare' of two independent biological replicates, employing the 'mean' operation.NarrowPeak files of third processed data were from independent biological replicates by using the MACS2.NarrowPeak files of fourth processed data were obtained through IDR (Irreproducible Discovery Rate) analysis in the Columbia (WT).

organism: Arabidopsis thaliana

source_name: 12DAG seedling

growth_protocol: For H2A.Z, H3K9K14ac, H3K27ac, H3K36ac and H3 ChIP-Seq analyses, we collected 12 DAG (days after germination) seedlings that were grown on 1x MS plates supplemented with 1% sucrose at 22 °C under long-day conditions (16 h light and 8 h dark).

extract_protocol:
The plants were cross-linked in a 1% formaldehyde solution under intermittent vacuum for approximately 10 minutes..After nuclear lysis,chromatin was sonicated using using Bioruptor® Pico with the following conditions:sonication ON for 10 seconds, sonication OFF for 30 seconds, 14 cycles, using 1.5-ml tubes at 4°C.
ChIP-Seq libraries were prepared using Ovation® Ultralow System V2 Library Preparation Kit (PART NO. 0344, 0344NB).

value: 12DAG seedling


title: PA14 ptsO deleted cells, SCFM-2, biol rep 5

description: Library name: L5_S58

value: DptsO


title: Sample_2270_KO

value: tamoxifen (KO)


title: Sample_2269_KO


title: CD69_hi_1_F5

source_name: MCC CD69-hi,1 hour

value: Lymph Node

value: MCC CD69-hi


title: Arabidopsis, gcn5-7,nrp1-1,nrp2-2_H3, 12DAG, Rep2

description: Library name: gcn5-7,nrp1-1,nrp2-2_H3_Rep2,ChIP

tag: chip antibody


title: PA14 ptsO deleted cells, SCFM-2, biol rep 4

description: Library name: L4_S57


title: Sample_2268_KO


title: NP_1_E5

source_name: No peptide (NP),1 hour


title: GP_CD69_lo_24_D5

source_name: MCC+GP CD69-lo,24 hour


title: Arabidopsis, gcn5-7,nrp1-1,nrp2-2_H3, 12DAG, Rep1

description: Library name: gcn5-7,nrp1-1,nrp2-2_H3_Rep1,ChIP


title: Arabidopsis, nrp1-1,nrp2-2_H3, 12DAG, Rep2

description: Library name: nrp1-1,nrp2-2_H3_Rep2,ChIP


title: PA14 ptsO deleted cells, SCFM-2, biol rep 3

description: Library name: L3_S56

source_name: whole cells


title: Arabidopsis, nrp1-1,nrp2-2_H3, 12DAG, Rep1

description: Library name: nrp1-1,nrp2-2_H3_Rep1,ChIP


title: ChIP-seq-Hbo1 KO, +Dox: H3K14ac

city: Boston

first: Wei-Chien

last: Yuan

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts
Paired-end reads were aligned to mm10 using bowtie or STAR.
Duplicate reads were removed using picard.
Peaks were called using MACS2
For the CRISPR screen, reads were trimmed and then mapped to a custom-built index of the library using bowtie 2. The mapped counts were first normalized within each library (total counts = 10E6 reads), averaged across experimental replicates, and then divided by the average normalized reads of the respective sequenced plasmid libraries (BC1-BC4) to calculate the final fold-enrichment for each guide in each mouse.
Genome_build: mm10
Supplementary_files_format_and_content: For RNA-seq, gene count was generted using featurecounts. For bulk ATAC-seq and ChIP-seq, algined reads are converted to bigwig tracks. For scATAC, peak-cell matrix is generated using ChromVAR. For the CRISPR-screening, processed data are tab separated text files for each mouse (biological replicate), showing, for each sgRNA, the fold enrichment over its abundance in the corresponding plasmid library (BC1-BC4).

source_name: TetO-YAP S127A

extract_protocol:
Hepatocytes were cross-linked in 1% formaldehyde for 10 min at room temperature after which the reaction was stopped by addition of 0.125M glycine. Cells were then lysed in ChIP buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100, and 5 mM EDTA) and the chromatin was sheared with a Diagenode Bioruptor sonicator UCD-200 to obtain fragments of average size of 200-500 bp.
Libraries for ChIP-sequencing were generated by using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) and barcoded using NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, 2 or 3) (NEB) according to the manufacturer’s instructions.

value: hepatocytes

value: Col:YAP/+, R26:sr/Tom

value: Dox

tag: antibody


title: GP_CD69_hi_24_C5

source_name: MCC+GP CD69-hi,24 hour

value: 24 hours


title: PA14 ptsO deleted cells, SCFM-2, biol rep 2

description: Library name: L2_S55

value: whole cells


title: ChIP-seq-Hbo1 KO, +Dox: TEAD4


title: PA14 ptsP deleted cells, SCFM-2, biol rep 5

description: Library name: G5_S33

value: DptsP


title: GP_24_B5

value: GP


title: Arabidopsis, gcn5-7_H3, 12DAG, Rep2

description: Library name: gcn5-7_H3_Rep2,ChIP


title: CD69_lo_24_A5

source_name: MCC CD69-lo,24 hour

value: MCC CD69-lo


title: Arabidopsis, INPUT, 12DAG, Rep1

description:
Library name: INPUT_Rep1,ChIP
The raw data are being used for peak-calling about H3K27ac and H3K36ac ChIP-seq data


title: ChIP-seq-Hbo1 KO, +Dox: YAP

value: YAP


title: Arabidopsis, gcn5-7_H3, 12DAG, Rep1

description: Library name: gcn5-7_H3_Rep1,ChIP


title: ChIP-seq-Hbo1 KO, +Dox: input


title: CD69_lo_1_G5

source_name: MCC CD69-lo,1 hour

value: 1 hour


title: PA14 ptsP deleted cells, SCFM-2, biol rep 4

description: Library name: G4_S32


title: ChIP-seq-Hbo1 KO, -Dox: H3K14ac

value: no Dox


title: Arabidopsis, Columbia_H3, 12DAG, Rep2

description: Library name: Columbia_H3_Rep2,ChIP


title: NP_24_G4

value: 5C.C7 TCR transgenic; B10.A-Rag2tm1FwaH2-T18aTg (Tcra5CC7,Tcrb5CC7)lwep

value: No peptide (NP)


title: ChIP-seq-Hbo1 KO, -Dox: TEAD4


title: Arabidopsis, Columbia_H3, 12DAG, Rep1

description: Library name: Columbia_H3_Rep1,ChIP

value: 12DAG seedling


title: CD69_hi_24_H4

source_name: MCC CD69-hi,24 hour


title: PA14 ptsP deleted cells, SCFM-2, biol rep 3

description: Library name: G3_S31


title: PA14 ptsO deleted cells, SCFM-2, biol rep 1

description: Library name: L1_S54

value: DptsO


title: GP_CD69_lo_6_F4

source_name: MCC+GP CD69-lo,6 hour

value: Lymph Node

value: MCC+GP CD69-lo

value: 6 hours


title: ChIP-seq-Hbo1 KO, -Dox: YAP

value: hepatocytes

value: Col:YAP/+, R26:sr/Tom


title: PA14 ptsP deleted cells, SCFM-2, biol rep 1

description: Library name: G1_S29


title: ChIP-seq-Hbo1 KO, -Dox: input


title: GP_CD69_hi_6_E4

source_name: MCC+GP CD69-hi,6 hour

value: MCC+GP CD69-hi


title: GP_6_D4

source_name: GP,6 hour


title: ChIP-seq-ctrl, +Dox: H3K27ac

value: Dox


title: Arabidopsis, nrp1-1,nrp2-2_H3K36ac, 12DAG, Rep2

description: Library name: nrp1-1,nrp2-2_H3K36ac_Rep2,ChIP

value: Active Motif:39379


title: PA14 cells, SCFM-2, biol rep 5

description: Library name: B5_S109

value: whole cells

value: WT


title: ChIP-seq-ctrl, +Dox: HBO1


title: Arabidopsis, gcn5-7,nrp1-1,nrp2-2_H3K36ac, 12DAG, Rep1

description: Library name: gcn5-7,nrp1-1,nrp2-2_H3K36ac_Rep1,ChIP


title: CD69_hi_6_B4

source_name: MCC CD69-hi,6 hour

value: MCC CD69-hi


title: PA14 cells, SCFM-2, biol rep 2

description: Library name: B2_S7


title: PA14 cells, SCFM-2, biol rep 3

description: Library name: B3_S8


title: CD69_lo_6_C4

source_name: MCC CD69-lo,6 hour

value: MCC CD69-lo


title: Arabidopsis, gcn5-7_H3K36ac, 12DAG, Rep2

description: Library name: gcn5-7_H3K36ac_Rep2,ChIP


title: ChIP-seq-ctrl, +Dox: TEAD4


title: Arabidopsis, nrp1-1,nrp2-2_H3K36ac, 12DAG, Rep1

description: Library name: nrp1-1,nrp2-2_H3K36ac_Rep1,ChIP


title: ChIP-seq-ctrl, +Dox: H3K14ac


title: NP_6_A4

source_name: No peptide (NP),6 hour


title: PA14 cells, SCFM-2, biol rep 1

description: Library name: B1_S6


title: PA14 ptsP deleted cells, SCFM-2, biol rep 2

description: Library name: G2_S30

value: DptsP


title: Arabidopsis, gcn5-7,nrp1-1,nrp2-2_H3K36ac, 12DAG, Rep2

description: Library name: gcn5-7,nrp1-1,nrp2-2_H3K36ac_Rep2,ChIP


title: ChIP-seq-ctrl, +Dox: YAP

value: YAP


title: GP_CD69_lo_1_H3

source_name: MCC+GP CD69-lo,1 hour

value: 5C.C7 TCR transgenic; B10.A-Rag2tm1FwaH2-T18aTg (Tcra5CC7,Tcrb5CC7)lwep

value: 1 hour


title: Arabidopsis, Columbia_H3K36ac, 12DAG, Rep2

description: Library name: Columbia_H3K36ac_Rep2,ChIP

source_name: 12DAG seedling

value: 12DAG seedling


title: 3077_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_male_IP_Rep1

city: Beijing

first: Kun

last: Li

address: HaiDian

institute: Tsinghua University

description: Library name: Sample1

data_processing:
Sequencing reads were aligned to the UCSC mm10 reference genome with STAR (version 2.3.0e_r291). Aligned reads were quantified by the ‘htseq-count’ module of ‘HTSeq’ framework (version 0.6.0). Differential gene expression analysis was performed by using DESeq2 (version 1.34.0). Genes were identified as differentially expressed with a false discovery rate (FDR) adjusted p value < 0.05 and log2Fold Change > 1.2 or < -1.2.
Assembly: mm10
Supplementary files format and content: text file includes raw counts

source_name: mPFC

extract_protocol:
The mPFC cortices were dissected in dissection buffer (1X HBSS, 2.5 mM HEPES-KOH 35 mM Glucose, 4 mM NaHCO3, RNase-free water, freshly added 100 μg/mL cycloheximide) using a brain matrix one month after retrograde viral infection. The tissues were immediately homogenized in an ice-cold homogenization buffer (150 mM KCl, 10 mM HEPES pH 7.4, 5 mM MgCl2, 0.5 mM dithiothreitol (Sigma-Aldrich, D9779), 100 μg/mL cycloheximide (Inalco, 1758-9310), 20 U/μL SUPERase-In RNase Inhibitor (Ambion, AM2696), 40 U/μL RNasin Ribonuclease Inhibitor (Promega, N2515), and EDTA-free protease inhibitors) in the cold room using a motor-driven Teflon glass homogenizer. Polyribosomes were immunoprecipitated by monoclonal anti-EGFP antibodies (MSKCC Antibody & Bioresource Core Facility. a mixture of clones 19C8 and 19F7) that have been conjugated to Dynabeads MyOne Streptavidin T1 (Thermo Fisher Scientific, 65601), which were pre-incubated with Recombinant Protein L (Pierce, 29997) for 16 hours at 4°C on an end-over-end rotator. The RNeasy Plus Micro Kit (QIAGEN, 74034) was used to extract and purify RNAs from ribosomes according to the manufacturer's instructions. The RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
cDNA was synthesized and further amplified using the Oviation RNA-seq System V2 Kit (NuGEN,7102-32). cDNA fragments of 200 bp were end-repaired and ligated with adapters for NextSeq 500 technology using NEBNext Ultra™ II DNA Library Prep Kit (New England Biolabs, E7645L) and NEBNext® Multiplex Oligos (New England Biolabs, E7500S) for Illumina. The cDNA libraries were sequenced on the NextSeq 500 System (Ilumina Inc., San Diego, CA, USA). The quality of libraries was evaluated by using Bioanalyzer High Sensitivity DNA Analysis (Agilent, 5067-4626) on the Aglient 2200 TapeStation system.

value: mPFC

value: total cell

tag: Sex

value: male


title: GP_CD69_hi_1_G3

source_name: MCC+GP CD69-hi,1 hour

value: Lymph Node


title: ChIP-seq-ctrl, +Dox: input

value: hepatocytes

value: Col:YAP/+, R26:sr/Tom


title: PA14 cells, SCFM-2, biol rep 4

description: Library name: B4_S9


title: ChIP-seq-ctrl, -Dox: HBO1

value: no Dox


title: GP_1_F3

source_name: GP,1 hour

value: GP


title: Cep83/Flrt1/3 TKO replicate1

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: 10x genomics

data_processing:
Transcriptome and barcode libraries were sequenced either on an Illumina NextSeq 500 and NovaSeq 6000 at the Next Generation Sequencing Facility of the Max Planck Institute of Biochemistry. Then, the sequencing data was processed with cellranger (version 7.0.1, reference 'refdata-gex-mm10-2020').
Assembly: mm10
Supplementary files format and content: filtered feature barcode matrix output of cellranger, zipped

source_name: neocortex

extract_protocol:
E15.5 of mutant embryos were removed from the uterus of mutant females, and stored in ice-cold in Leibowitz medium with 5% FBS. Brains were isolated and cut in 300 μm using a vibratome (Leica VT1000S, Germany) in cutting buffer, Leibowitz medium with 5% FBS. Then, brain sections were manually dissected for both hemisphere of cortical primordium of cortex. Meanwhile, genotyping was performed. Then, collected tissues were transferred into a dissociation Buffer, EBSS. Dissociation was performed with Worthington Kit and manually Papain dissociation system was carried out according to the recommended protocol (Worthington, #LK003163).
For experiments utilizing the 10x Genomics platform, the following reagents were used Chromium Single Cell Next GEM Single Cell 3’ GEM kit v3.1 (PN-1000130), Library Construction Kit (PN-1000196), Chromium Next GEM Single Cell 3′ Gel Bead Kit v3.1 (PN-1000129) and Single Index Kit T Set A (PN-1000213) and Dual Index Kit TT Set A (PN-1000215) were used according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits v3.1 User Guide.

value: neocortex

value: Cortical neurons

tag: chemistry

value: Single Index Kit T


title: Arabidopsis, gcn5-7,nrp1-1,nrp2-2_H3K9K14ac, 12DAG, Rep2

description: Library name: gcn5-7,nrp1-1,nrp2-2_H3K9K14ac_Rep2,ChIP


title: CD69_lo_1_E3

value: MCC CD69-lo


title: Arabidopsis, gcn5-7,nrp1-1,nrp2-2_H3K9K14ac, 12DAG, Rep1

description: Library name: gcn5-7,nrp1-1,nrp2-2_H3K9K14ac_Rep1,ChIP


title: ChIP-seq-ctrl, -Dox: H3K14ac

source_name: TetO-YAP S127A


title: CNS_Satb1_WT_EAE_Rhapsody

description:
BD Rhapsody, targeted panel of genes
satb1_ko_eae_230905.rds

data_processing:
Demultiplexing was perfomed using bcl2fastq2 v2.20
Adapter trimming was performed using cutadapt 1.16 with following parameters NexteraPE-PE.fa --minimum-length 15 --cores=10 --overlap 6 -o Running on 10 cores MINLEN:36 CROP:48
Alignment was performed using STAR version 2.7.3a against a custom genome comprising a targeted 400-gene panel in addition to the sequences of the hashtag oligos (HTO) used to multiplex the samples
A UMI-corrected gene expression matrix (gene by barcode matrix) was generated using a custom adaptation of the dropSeqPipe (https://github.com/Hoohm/dropSeqPipe) based on the DropSeq Cookbook (https://github.com/broadinstitute/Drop-seq/blob/v2.5.0/doc/Drop-seq_Alignment_Cookbook.pdf)
UMI-corrected count matrix was imported into R version 4.1.2 using readMM function from the Matrix package version 1.4-0
Inflection point was computed using the barcodeRanks function from the DropletUtils package (https://rdrr.io/bioc/DropletUtils/man/barcodeRanks.html)
HTO demultiplexing, quality control, principal component analysis, clustering, and differential expression analysis were performed using Seurat version 4.1.0
Assembly: mm10 + sequences corresponding to the HTO barcodes
Supplementary files format and content: barcodes.tsv files list the cell barcodes detected in the scRNA-seq libraries.
Supplementary files format and content: genes.tsv files list the genes detected in the scRNA-seq libraries.
Supplementary files format and content: matrix.mtx files hold gene expression counts across all barcodes and genes detected in the scRNA-seq libraries.
Supplementary files format and content: satb1_ko_eae_230905.rds is a seurat object of the analysis including raw, normalized and scaled data as well as cell annotation and dimension reductions.

source_name: Brain and spinal cord

extract_protocol:
After perfusion of mice with ice-cold phosphate buffered saline (PBS), brain and spinal cord were isolated, cut into small pieces and digested in 5 ml DMEM supplemented with 10% FCS and 200 µg/ml Collagenase Type IV (Merck) for 45 minutes at 37°C followed by digesting with 170 µg/ml DNaseI (Merck) for 45 minutes at 37°C under slow rotation. The homogenized tissue was passed through a 100 µm cell strainer and lymphocytes were isolated using density gradient centrifugation (20 min, 900 g, room temperature). Cells were collected from the 30%/70% interphase of the percoll gradient, washed in PBS, and stained with fluorescently labelled antibodies, prior to sorting using a BD FACSAria instrument.
Library preparation followed the BD Rhapsody manufacturer's instructions: targeted priming of a panel of 400 genes, followed by index PCR to ligate sequencing indices.

value: Brain and spinal cord

value: CD45+ CD3+ CD4+ T cells

value: Satb1fl/fl x CD4-CreERT2+/+

value: Tamoxifen


title: CD69_hi_1_D3

source_name: MCC CD69-hi,1 hour

value: 5C.C7 TCR transgenic; B10.A-Rag2tm1FwaH2-T18aTg (Tcra5CC7,Tcrb5CC7)lwep

value: MCC CD69-hi

value: 1 hour


title: Arabidopsis, nrp1-1,nrp2-2_H3K9K14ac, 12DAG, Rep2

description: Library name: nrp1-1,nrp2-2_H3K9K14ac_Rep2,ChIP

value: 12DAG seedling


title: ChIP-seq-ctrl, -Dox: YAP

value: YAP


title: Arabidopsis, nrp1-1,nrp2-2_H3K9K14ac, 12DAG, Rep1

description: Library name: nrp1-1,nrp2-2_H3K9K14ac_Rep1,ChIP


title: RRBS_ApcMin_Rep2_Ileum_tumor4

city: Berlin

first: Sara

last: Hetzel

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

description: Methylation profiling of control and tumor tissue from the ApcMin mouse model.

data_processing:
Raw reads were subjected to adapter and quality trimming using cutadapt (version 4.1; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter), followed by NuGEN diversity adapter trimming (https://github.com/nugentechnologies/NuMetRRBS).
The trimmed reads were aligned to the mouse genome (mm10) using BSMAP (version 2.90; parameters: -v 0.1 -s 12 -q 20 -w 100 -S 1 -u -R -D C-CGG).
Aligned reads were deduplicated based on unique molecular identifiers (UMIs) using NuDup (https://github.com/nugentechnologies/nudup; parameters: --start 6 --length 6).
Methylation rates were called using mcall from the MOABS package (version 1.3.9.6; default parameters).
All analyses were restricted to autosomes and only CpGs covered by at least 5 and at maximum 150 reads were considered for downstream analyses.
Assembly: mm10
Bigwig file containing methylation rates for CpGs covered by at least 5 and at most 150 reads: <chr> <start> <end> <methylation rate>

source_name: Ileum

growth_protocol: Two C57BL6/J-ApcMin strain mice (Jackson Labs, Cat # 002020) were euthanized at 6 months of age, after the expected emergence of early adenomas within the small intestine.

extract_protocol:
The full intestine was dissected, cleared of waste, and divided into three (Duodenum, Jejunum, Ileum) and two (Cecum and Colon) fractions for the small and large intestine, respectively. Samples were then bisected longitudinally to confirm the presence of macroscopic adenomas in the range of ~1-5 mm, after which the tumors were carefully dissected and the position from the cecum and diameter of the tumor were measured. Following isolation of visible benign tumors, the bulk epithelial tissue was purified to provide a matched non-cancer tissue control. Both primary “tumors” and isolated epithelia were briefly inspected for purity prior to snap freezing on dry ice. Then, isolated tissue were purified using QIAmp DNA Blood and Tissue Kit with an extended 6 hour Proteinase K incubation to improve the bisulfite conversion efficiency.
Concentration of genomic DNA (gDNA) was quantified using a Qubit 3.0 Fluorometer. RRBS was performed on 100 ng gDNA of each sample using the Swift Biosciences ACCEL-NGS Methyl-Seq DNA Library Kit (#30024) following the manufacturer’s recommendations with the following modifications: The DNA was fragmented using Covaris S2 and purified with Agencourt RNAclean XP beads (Beckman Coulter, #A63987) (1.8X). After the final repair step, the bisulfite conversion of DNA was conducted using the Qiagen EpiTect Fast Bisulfite Conversion kit (Qiagen, #59824) following the manufacturer’s recommendations, eluting the bisulfite converted DNA in 22 µl EB. Libraries were amplified with 10 cycles of PCR. Amplified library purification with Agencourt RNAclean XP beads (Beckman Coulter, #A63987) was performed twice (1.2X). The purified libraries were sequenced for 76 bp single-end reads on a NextSeq 500  platform (Illumina).

value: Ileum

tag: tissue type

value: tumor

value: Apc(Min/+)


title: NP_1_C3

source_name: No peptide (NP),1 hour

value: Lymph Node

value: No peptide (NP)


title: Arabidopsis, gcn5-7_H3K36ac, 12DAG, Rep1

description: Library name: gcn5-7_H3K36ac_Rep1,ChIP

value: Active Motif:39379


title: ChIP-seq-ctrl, -Dox: input

value: hepatocytes

value: Col:YAP/+, R26:sr/Tom

value: no Dox


title: GP_CD69_lo_24_B3

source_name: MCC+GP CD69-lo,24 hour

value: MCC+GP CD69-lo

value: 24 hours


title: 3085_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_female_IP_Rep1

description: Library name: Sample2

value: mPFC

value: total cell

value: WT

value: female


title: RRBS_ApcMin_Rep2_Ileum_tumor3


title: RNA-seq-Hbo1 KO, +Dox rep2

extract_protocol:
RNA was harvested using Trizol reagent.
RNA-seq libraries were generated using TruSeq RNA Sample Prep Kit v2 (Illumina) according to manufacturer’s recommendations.

value: Col:YAP/+, R26:sr/Cas9

value: Dox


title: GP_CD69_hi_24_A3

source_name: MCC+GP CD69-hi,24 hour

value: 5C.C7 TCR transgenic; B10.A-Rag2tm1FwaH2-T18aTg (Tcra5CC7,Tcrb5CC7)lwep

value: MCC+GP CD69-hi


title: Arabidopsis, gcn5-7_H3K9K14ac, 12DAG, Rep2

description: Library name: gcn5-7_H3K9K14ac_Rep2,ChIP

value: 12DAG seedling


title: Arabidopsis, Columbia_H3K36ac, 12DAG, Rep1

description: Library name: Columbia_H3K36ac_Rep1,ChIP


title: Arabidopsis, gcn5-7_H3K9K14ac, 12DAG, Rep1

description: Library name: gcn5-7_H3K9K14ac_Rep1,ChIP


title: GP_24_H2

source_name: GP,24 hour

value: Lymph Node

value: GP


title: RNA-seq-Hbo1 KO, +Dox rep1


title: Arabidopsis, Columbia_H3K9K14ac, 12DAG, Rep2

description: Library name: Columbia_H3K9K14ac_Rep2,ChIP


title: RRBS_ApcMin_Rep2_Colon_tumor1

source_name: Colon

value: Colon

value: tumor

value: Apc(Min/+)


title: RNA-seq-Hbo1 KO, -Dox rep2

value: hepatocytes

value: no Dox


title: CD69_hi_24_F2

source_name: MCC CD69-hi,24 hour

value: MCC CD69-hi

value: 24 hours


title: Arabidopsis, Columbia_H3K9K14ac, 12DAG, Rep1

description: Library name: Columbia_H3K9K14ac_Rep1,ChIP


title: ChIP-seq-ctrl, -Dox: TEAD4

value: Col:YAP/+, R26:sr/Tom


title: CNS_Satb1_KO_EAE_Rhapsody

value: Brain and spinal cord

value: CD45+ CD3+ CD4+ T cells

value: Satb1fl/fl x CD4-CreERT2wt/+

value: Tamoxifen


title: NP_24_E2

source_name: No peptide (NP),24 hour

value: 5C.C7 TCR transgenic; B10.A-Rag2tm1FwaH2-T18aTg (Tcra5CC7,Tcrb5CC7)lwep

value: No peptide (NP)


title: RRBS_ApcMin_Rep2_Ileum_control

value: Ileum

value: control


title: RNA-seq-ctrl, +Dox rep2

value: Col:YAP/+, R26:sr/Cas9

value: Dox


title: GP_CD69_lo_6_D2

source_name: MCC+GP CD69-lo,6 hour

value: Lymph Node

value: MCC+GP CD69-lo

value: 6 hours


title: Arabidopsis, gcn5-7,nrp1-1,nrp2-2_H3K27ac, 12DAG, Rep1

description: Library name: gcn5-7,nrp1-1,nrp2-2_H3K27ac_Rep1,ChIP

source_name: 12DAG seedling

value: 12DAG seedling

value: Active Motif:39135


title: RRBS_ApcMin_Rep2_Cecum_control

source_name: Cecum

value: Cecum

value: Apc(Min/+)


title: RNA-seq-ctrl, +Dox rep1

value: hepatocytes


title: GP_CD69_hi_6_C2

source_name: MCC+GP CD69-hi,6 hour

value: MCC+GP CD69-hi


title: Arabidopsis, nrp1-1,nrp2-2_H3K27ac, 12DAG, Rep2

description: Library name: nrp1-1,nrp2-2_H3K27ac_Rep2,ChIP


title: GP_6_B2

source_name: GP,6 hour

value: GP


title: RRBS_ApcMin_Rep2_Ileum_tumor2

value: tumor


title: RNA-seq-ctrl, -Dox rep2

value: no Dox


title: Arabidopsis, nrp1-1,nrp2-2_H3K27ac, 12DAG, Rep1

description: Library name: nrp1-1,nrp2-2_H3K27ac_Rep1,ChIP


title: RRBS_ApcMin_Rep1_Duodenum_tumor9

source_name: Duodenum

value: Duodenum


title: RNA-seq-ctrl, -Dox rep1


title: RRBS_ApcMin_Rep1_Duodenum_tumor8


title: CD69_hi_6_H1

source_name: MCC CD69-hi,6 hour

value: 5C.C7 TCR transgenic; B10.A-Rag2tm1FwaH2-T18aTg (Tcra5CC7,Tcrb5CC7)lwep

value: MCC CD69-hi


title: Arabidopsis, gcn5-7_H3K27ac, 12DAG, Rep1

description: Library name: gcn5-7_H3K27ac_Rep1,ChIP


title: ATAC-seq-HBO1 KO, Dox 28 days rep3

extract_protocol: Hepatocytes were suspended in lysis and transposition buffer (10 mM Tris-HCl (pH 7.5), 5 mM MgCl2, 1% DMF, 0.5% NP-40, and 1X illumina Tn5) for 30 min on a thermomixer at 37 °C and mixed at 300 rpm. After the reaction, the samples were placed on ice briefly and cleaned up by a QIAquick PCR purification kit following the instructions of the kit. PCR was performed to amplify the libraries for 18 cycles using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, and 72 °C for 90 s; following by 72 °C 5 min. After the PCR reaction, libraries were purified with the AMPure (Beckman) beads.

value: Col:YAP/+, R26:sr/Cas9

tag: time point

value: 28 days


title: RNA-seq-Hbo1 KO, -Dox rep1


title: RRBS_ApcMin_Rep2_Duodenum_control

value: control


title: CD69_lo_6_A2

source_name: MCC CD69-lo,6 hour

tag: strain

value: Lymph Node

value: MCC CD69-lo


title: ATAC-seq-HBO1 KO, Dox 28 days rep2

value: Dox


title: Arabidopsis, gcn5-7,nrp1-1,nrp2-2_H3K27ac, 12DAG, Rep2

description: Library name: gcn5-7,nrp1-1,nrp2-2_H3K27ac_Rep2,ChIP

value: 12DAG seedling

value: Active Motif:39135


title: RRBS_ApcMin_Rep1_Jejunem_tumor6

source_name: Jejunem

value: Jejunem

value: Apc(Min/+)


title: Arabidopsis, Columbia_H3K27ac, 12DAG, Rep2

description: Library name: Columbia_H3K27ac_Rep2,ChIP


title: RRBS_ApcMin_Rep1_Duodenum_tumor7


title: NP_6_G1

source_name: No peptide (NP),6 hour

tag: sorting phenotype

value: No peptide (NP)

value: 6 hours


title: GP_CD69_lo_1_E1

source_name: MCC+GP CD69-lo,1 hour

tag: tissue

value: MCC+GP CD69-lo

value: 1 hour


title: Arabidopsis, Columbia_H3K27ac, 12DAG, Rep1

description: Library name: Columbia_H3K27ac_Rep1,ChIP


title: GP_1_D1

source_name: GP,1 hour

value: GP

tag: time


title: ATAC-seq-HBO1 KO, Dox 14 days rep3

value: hepatocytes

tag: genotype

value: 14 days


title: RRBS_ApcMin_Rep2_Colon_control

value: Colon


title: RRBS_ApcMin_Rep1_Jejunem_tumor5

value: tumor


title: Arabidopsis, gcn5-7,nrp1-1,nrp2-2_H2A.Z, 12DAG, Rep2

description: Library name: gcn5-7,nrp1-1,nrp2-2_H2A.Z_Rep2,ChIP

value: Anti-H2A.Z antibody was raised in rabbits and further affinity-purified by ABClonal (China) using the peptudes:SGKGAKGLIMGKPSGSDKDKDKKKPIT-C/AGKGGKGLVAAKTMAANKDKDKDKKKPIS-C


title: RRBS_ApcMin_Rep1_Jejunem_tumor4


title: ATAC-seq-HBO1 KO, Dox 14 days rep2

value: Col:YAP/+, R26:sr/Cas9


title: Arabidopsis, gcn5-7_H3K27ac, 12DAG, Rep2

description: Library name: gcn5-7_H3K27ac_Rep2,ChIP


title: Arabidopsis, gcn5-7,nrp1-1,nrp2-2_H2A.Z, 12DAG, Rep1

description: Library name: gcn5-7,nrp1-1,nrp2-2_H2A.Z_Rep1,ChIP


title: CD69_hi_1_C1

source_name: MCC CD69-hi,1 hour

value: 5C.C7 TCR transgenic; B10.A-Rag2tm1FwaH2-T18aTg (Tcra5CC7,Tcrb5CC7)lwep

value: Lymph Node

value: MCC CD69-hi


title: ATAC-seq-HBO1 KO, Dox 14 days rep1

value: Dox


title: RRBS_ApcMin_Rep1_Jejunem_tumor3

value: Jejunem


title: NP_1_A1

source_name: No peptide (NP),1 hour


title: Arabidopsis, nrp1-1,nrp2-2_H2A.Z, 12DAG, Rep2

description: Library name: nrp1-1,nrp2-2_H2A.Z_Rep2,ChIP

value: 12DAG seedling


title: RRBS_ApcMin_Rep1_Ileum_tumor2

source_name: Ileum

value: Ileum

value: Apc(Min/+)


title: ATAC-seq-HBO1 KO, Dox 5 days rep3

value: 5 days


title: ATAC-seq-HBO1 KO, Dox 5 days rep2


title: ATAC-seq-HBO1 KO, Dox 28 days rep1

value: 28 days


title: RRBS_ApcMin_Rep1_Ileum_tumor1


title: Arabidopsis, gcn5-7_H2A.Z, 12DAG, Rep2

description: Library name: gcn5-7_H2A.Z_Rep2,ChIP


title: RRBS_ApcMin_Rep1_Duodenum_control

value: Duodenum

value: control


title: ATAC-seq-HBO1 KO, Dox 5 days rep1

value: hepatocytes


title: Arabidopsis, gcn5-7_H2A.Z, 12DAG, Rep1

description: Library name: gcn5-7_H2A.Z_Rep1,ChIP


title: RRBS_ApcMin_Rep1_Ileum_control


title: ATAC-seq-HBO1 KO, Dox 0 day rep3

value: 0 day


title: Arabidopsis, Columbia_H2A.Z, 12DAG, Rep2

description: Library name: Columbia_H2A.Z_Rep2,ChIP


title: RRBS_ApcMin_Rep1_Cecum_control

value: Cecum


title: ATAC-seq-HBO1 KO, Dox 0 day rep2


title: RRBS_ApcMin_Rep1_Colon_control

source_name: Colon

value: Colon


title: ATAC-seq-HBO1 KO, Dox 0 day rep1

value: Col:YAP/+, R26:sr/Cas9


title: Arabidopsis, Columbia_H2A.Z, 12DAG, Rep1

description: Library name: Columbia_H2A.Z_Rep1,ChIP

value: Anti-H2A.Z antibody was raised in rabbits and further affinity-purified by ABClonal (China) using the peptudes:SGKGAKGLIMGKPSGSDKDKDKKKPIT-C/AGKGGKGLVAAKTMAANKDKDKDKKKPIS-C


title: Day 21 Diseased, Lung, scRNAseq

status: Public on May 19 2025

city: Ann Arbor

first: Ian

last: Schrack

state: MI

address: 1600 Huron Parkway

department: Biomedical Engineering

institute: University of Michigan

description:
Library name: Sample 15
Drop-Seq

data_processing:
The Drop-Seq pipeline (v1.2) was used to map raw Illumina reads to the mouse genome (mm10), determine cell barcodes and gene counts, and create the digital gene expression (DGE) file.
DGE files were inputted into Seurat v2 designed by the Satija research group for cell type identification and analysis [27, 28]. Sequencing data from the healthy controls from each time point were combined to establish a single healthy control (day 0).
Cells were classified as having 200 to 5000 RNA fragments and less than 25% percent mitochondrial genes.
Assembly: mm10
Supplementary files format and content: Tab-separated text files.

source_name: Lung

extract_protocol:
Female Balb/c mice (7–8 weeks old) were orthotopically inoculated with 2,000,000 4T1-tdTomato-luc2 cells into the fourth right mammary fat pad. Healthy control mice did not receive tumor cell inoculation. At 7, 14, or 21 days post-inoculation, both tumor-bearing and control mice were euthanized via CO₂, and their lungs, spleens, and biomaterial scaffolds were surgically explanted for analysis.
Single-cell suspensions prepared from the isolated tissues were processed using a Drop-Seq device (FlowJEM; Toronto, CA), following the protocol described by Macosko et al., 2015. The device was run for 10 minutes, after which the resulting cell-bead pairs (STAMPs) were collected and the oil phase was removed. Approximately 1,000 STAMPs were subjected to reverse transcription, Exonuclease I treatment, and universal PCR amplification. cDNA concentration and quality were assessed using a Bioanalyzer with a DNA High Sensitivity chip (Agilent Technologies; Santa Clara, CA). cDNA tagmentation was performed using Tn5 transposase, as described by Picelli et al., 2014.

value: Lung

value: BALB/cJ

tag: tumor stage

value: 21 Day 4T1 Tumor

tag: age

value: 11 Weeks


title: PDAC cancer associated fibroblasts treated with isorhamnetin, biological rep3

type: RNA

city: Tsukuba

first: Munkhzul

last: Ganbold

state: Ibaraki Prefecture

address: 1 Chome-1-1 Tennodai

country: Japan

institute: AIST-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL)

description:
ISO-3
Gene expression data from human PDAC-derived CAFs treated with 20 µM Isorhamnetin for 96 h

hyb_protocol: After fragmentation and labelling, 2.3 µg of ss-cDNA were hybridized at 60 rpm for 16 h at 45C on GeneChip Hybridization Oven 645. Cartridge arrays were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: Cartridge arrays were scanned using the GeneChip Scanner 3000 7G system.

data_processing: The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out by Transcriptome Analysis Console (TAC) v4.0 (Affymetrix, Japan).

label: biotin

source_name: CAFs treated with Isorhamnetin

label_protocol: Single-stranded cDNA were fragmented and labelled according to the GeneChip WT PLUS protocol from 15 µg of cRNA (GeneChip WT PLUS Reagent kit user guide, MAN0018137, Applied Biosystems).

growth_protocol: CAFs were maintained in DMEM medium supplemented with 5% FBS and 1% penicilin and streptomycin

extract_protocol: Total RNA was extracted by RNeasy Plus Mini kit (74134, QIAGEN) following the manufacturer's protocol

treatment_protocol: CAFs were treated or not with 20 µM isorhamnetin for 96 h

value: immortalized cells

tag: treatment

value: 20 µM Isorhamnetin for 96 h


title: Arabidopsis, nrp1-1,nrp2-2_H2A.Z, 12DAG, Rep1

description: Library name: nrp1-1,nrp2-2_H2A.Z_Rep1,ChIP

source_name: 12DAG seedling

value: 12DAG seedling


title: Day 21 Healthy Control, Spleen, scRNAseq

description:
Library name: Sample 18
Drop-Seq

source_name: Spleen

value: Spleen

value: 21 Day No Tumor


title: PDAC cancer associated fibroblasts treated with isorhamnetin, biological rep2

description:
ISO-2
Gene expression data from human PDAC-derived CAFs treated with 20 µM Isorhamnetin for 96 h


title: Day 21 Diseased, Spleen, scRNAseq

description:
Library name: Sample 17
Drop-Seq


title: PDAC cancer associated fibroblasts, biological rep3

description:
CTL-3
Gene expression data from human PDAC-derived CAFs

source_name: CAFs


title: PDAC cancer associated fibroblasts treated with isorhamnetin, biological rep1

description:
ISO-1
Gene expression data from human PDAC-derived CAFs treated with 20 µM Isorhamnetin for 96 h


title: Day 21 Healthy Control, Scaffold, scRNAseq

description:
Library name: Sample 14
Drop-Seq

source_name: Scaffold

value: Scaffold


title: PDAC cancer associated fibroblasts, biological rep2

description:
CTL-2
Gene expression data from human PDAC-derived CAFs


title: Day 21 Diseased, Scaffold, scRNAseq

description:
Library name: Sample 13
Drop-Seq


title: PDAC cancer associated fibroblasts, biological rep1

description:
CTL-1
Gene expression data from human PDAC-derived CAFs


title: Day 14 Healthy Control, Lung, scRNAseq

description:
Library name: Sample 11
Drop-Seq

value: 14 Day No Tumor

value: 10 Weeks


title: Day 14 Healthy Control, Scaffold, scRNAseq

description:
Library name: Sample 10
Drop-Seq


title: Day 14 Diseased, Spleen, scRNAseq

description:
Library name: Sample 9
Drop-Seq

value: 14 Day 4T1 Tumor


title: Day 14 Diseased, Scaffold, scRNAseq

description:
Library name: Sample 7
Drop-Seq


title: Day 14 Diseased, Lung, scRNAseq

description:
Library name: Sample 8
Drop-Seq


title: Day 14 Healthy Control, Spleen, scRNAseq

description:
Library name: Sample 12
Drop-Seq


title: Day 7 Healthy Control, Scaffold, scRNAseq

description:
Library name: Sample 6
Drop-Seq

value: 7 Day No Tumor

value: 9 Weeks


title: Day 7 Healthy Control, Lung, scRNAseq

description:
Library name: Sample 4
Drop-Seq


title: Day 7 Diseased, Spleen, scRNAseq

description:
Library name: Sample 3
Drop-Seq

value: 7 Day 4T1 Tumor


title: Day 7 Healthy Control, Spleen, scRNAseq

description:
Library name: Sample 5
Drop-Seq


title: Day 7 Diseased, Scaffold, scRNAseq

description:
Library name: Sample 2
Drop-Seq


title: L55R lens-induced myopia retina 6 days

city: New York

first: Andrei

middle: V.

last: Tkatchenko

state: NY

department: Edward S. Harkness Eye Institute

institute: Columbia University

data_processing:
The FASTQ raw data files generated by the Illumina sequencing system were imported into Partek Flow software package (Partek), libraries were separated based on their barcodes, adapters were trimmed and remaining sequences were subjected to pre-alignment quality control using the Partek Flow pre-alignment QA/QC module
After the assessment of various quality metrics, bases with the quality score < 34 were removed (≤ 5 bases) from each end.
Sequencing reads were then mapped to the chicken reference genome Gallus gallus GRCg6a using the STAR aligner resulting in 98.18 ± 0.18% mapped reads per library, which covered 41 ± 2% of the genome.
Aligned reads were quantified to transcriptome using the Partek E/M annotation model and the NCBI’s RefSeq annotation file to determine read counts per gene/genomic region.
The generated read counts were normalized by the total read count and subjected to the Gene Specific Analysis (GSA) to detect differentially expressed genes
Assembly: GRCg6a
Supplementary files format and content: Tab-delimited text file including matrix table with normalized gene counts for every gene and every sample

organism: Gallus gallus

source_name: Retina

extract_protocol:
The retinae were washed in RNAlater (Thermo Fisher Scientific) for 5 min., frozen in liquid nitrogen, and stored at -80°C. To isolate RNA, tissue samples were homogenized at 4°C in a lysis buffer using Bead Ruptor 24 tissue homogenizer (Omni). Total RNA was extracted from each tissue sample using miRNAeasy mini kit (QIAGEN) following the manufacturer’s protocol.
Illumina sequencing libraries were constructed from 1 μg of total RNA using the TruSeq Stranded Total RNA LT kit with the Ribo-Zero Gold ribosomal RNA depletion module (Illumina).

treatment_protocol: Three-day old chickens were fitted with a-10D lens in front of their eyes mounted on Velcro rings and glued to the feathers around the eyes. Lenses were cleaned twice every day. Lenses were removed and ocular tissues were collected for analysis after 1, 3, and 6 days of treatment.

value: White Leghorn

value: postnatal day 3-9

value: wild type


title: L54L lens-induced myopia retina 6 days


title: L53R lens-induced myopia retina 6 days


title: Day 21 Healthy Control, Lung, scRNAseq

description:
Library name: Sample 16
Drop-Seq

value: Lung

value: BALB/cJ


title: L48L lens-induced myopia retina 6 days


title: L47R lens-induced myopia retina 6 days


title: L46L lens-induced myopia retina 6 days


title: L39L lens-induced myopia retina 3 days


title: L38R lens-induced myopia retina 3 days


title: L29L lens-induced myopia retina 3 days


title: L25R lens-induced myopia retina 3 days


title: L36R lens-induced myopia retina 3 days


title: L27R lens-induced myopia retina 3 days


title: L26L lens-induced myopia retina 3 days


title: L13L lens-induced myopia retina 1 day


title: L14R lens-induced myopia retina 1 day


title: L3R lens-induced myopia retina 1 day


title: L4L lens-induced myopia retina 1 day


title: Day 7 Diseased, Lung, scRNAseq

description:
Library name: Sample 1
Drop-Seq


title: C64L control retina 6 days

treatment_protocol: Three groups of control chickens were raise under standard light regiment and ocular tissues were collected for analysis at postnatal day 4, 6, and 9

value: postnatal day 3

value: 6 day


title: L12R lens-induced myopia retina 1 day


title: L2L lens-induced myopia retina 1 day


title: C63R control retina 6 days


title: L1R lens-induced myopia retina 1 day


title: C57L control retina 6 days


title: C65L control retina 6 days


title: C58R control retina 6 days


title: C59L control retina 6 days


title: L51L lens-induced myopia retina 6 days


title: C43R control retina 3 days

value: 3 day


title: C62L control retina 6 days


title: C44R control retina 3 days


title: C41R control retina 3 days


title: C42L control retina 3 days


title: C34L control retina 3 days


title: C33R control retina 3 days


title: C23R control retina 1 day

value: 1 day


title: C31L control retina 3 days


title: C22L control retina 1 day


title: C19L control retina 1 day


title: C18R control retina 1 day


title: C17L control retina 1 day


title: C10R control retina 1 day


title: C21R control retina 1 day


title: L51L lens-induced myopia retina

treatment_protocol: Three-day old chickens were fitted with a-10D lens in front of their eyes mounted on Velcro rings and glued to the feathers around the eyes. Lenses were cleaned twice every day. After 6 days of treatment, lenses were removed and ocular tissues were collected for analysis.

value: lens-induced myopia retina


title: L54L lens-induced myopia retina


title: L55R lens-induced myopia retina


title: L48L lens-induced myopia retina


title: L47R lens-induced myopia retina


title: C63R control retina

value: control retina


title: L53R lens-induced myopia retina


title: L46L lens-induced myopia retina


title: C64L control retina


title: C57L control retina


title: L39L lens-induced myopia retina

treatment_protocol: Three-day old chickens were fitted with a-10D lens in front of their eyes mounted on Velcro rings and glued to the feathers around the eyes. Lenses were cleaned twice every day. After 3 days of treatment, lenses were removed and ocular tissues were collected for analysis.


title: C62L control retina


title: C65L control retina


title: C59L control retina


title: L38R lens-induced myopia retina


title: L36R lens-induced myopia retina


title: L27R lens-induced myopia retina


title: C58R control retina


title: L29L lens-induced myopia retina


title: L26L lens-induced myopia retina


title: C44R control retina


title: C43R control retina


title: C42L control retina


title: C41R control retina


title: C33R control retina


title: C34L control retina


title: L14R lens-induced myopia

treatment_protocol: Three-day old chickens were fitted with a-10D lens in front of their eyes mounted on Velcro rings and glued to the feathers around the eyes. Lenses were cleaned twice every day. After 1 day of treatment, lenses were removed and ocular tissues were collected for analysis.

value: lens-induced myopia


title: C31L control retina


title: L13L lens-induced myopia


title: L12R lens-induced myopia


title: L3R lens-induced myopia


title: L2L lens-induced myopia


title: L1R lens-induced myopia


title: C23R control retina

value: control


title: C21R control retina


title: C19L control retina


title: C22L control retina


title: C10R control retina


title: C17L control retina


title: LVCP, postnatal day 60, n=2

city: Stockholm

first: Mónica

middle: da Silva

last: Fernandes

address: Nobels väg 6

country: Sweden

institute: Karolinska Institutet

description: Library name: P60_n2

data_processing:
bulk RNA-seq samples were preprocessed for adapter/quality trimming and then aligned to the transcriptome using STAR (Dobin et al., 2013) version 2.7 –quantMode –sjdbOverhang 99 with EnsEMBLv75 gtf annotations. Only uniquely mapped reads were retained for downstream analysis using SAMtools.
Assembly: Rnor_5.0
Supplementary files format and content: .txt file with count matrix, one per sample

organism: Rattus norvegicus

source_name: 60 days postnatal healthy rat

extract_protocol:
Bulk RNA-seq comprised 5 main timepoints: postnatal day (P) P1, P4, P7, P10 and P60. Rat males were anesthetized, transcardially perfused with sterile RNase free cold saline. Brains were removed and choroid plexuses (CP) from the lateral ventricles were isolated under a stereo microscope and stored at -80ºC. Total RNA extraction was performed using SPLIT RNA Extraction Kit (Lexogen, Viena, Austria). Briefly, the CPs were homogenized in an isolation buffer highly chaotropic. Samples, were then transferred to a phase lock gel column, which contains a gel matrix that, based on the density differences, acts as a barrier between the organic and aqueous phase. Acidic phenol and acidic buffer were added to create a monophasic solution, which allows the separation of genomic DNA into the organic phase. Chloroform was added and the phases were separated by centrifugation for 2min at 12.000xg at 18°C. The RNA, contained in the aqueous phase, was decanted into a new micro tube. The RNA was then precipitated onto a silica column by addition of 1.75x volume of isopropanol. The RNA was further purified by washing the column.
Library construction for QuantSeq 3' mRNA

value: Choroid plexus

value: Postnatal day 60 (P60)

value: Wistar Han


title: LVCP, postnatal day 10, n=3

description: Library name: P10_n3

source_name: 10 days postnatal healthy rat

value: Postnatal day 10 (P10)


title: LVCP, postnatal day 60, n=1

description: Library name: P60_n1


title: LVCP, postnatal day 10, n=1

description: Library name: P10_n1


title: LVCP, postnatal day 10, n=2

description: Library name: P10_n2


title: L25R lens-induced myopia retina

value: White Leghorn


title: LVCP, postnatal day 7, n=2

description: Library name: P7_n2

source_name: 7 days postnatal healthy rat

value: Postnatal day 7 (P7)


title: LVCP, postnatal day 7, n=1

description: Library name: P7_n1


title: LVCP, postnatal day 7, n=3

description: Library name: P7_n3


title: LVCP, postnatal day4, n=3

description: Library name: P4_n3

source_name: 4 days postnatal healthy rat

value: Postnatal day 4 (P4)


title: LVCP, postnatal day4, n=2

description: Library name: P4_n2


title: LVCP, postnatal day1, n=3

description: Library name: P1_n3

source_name: 1 day postnatal healthy rat

value: Postnatal day 1 (P1)


title: L4L lens-induced myopia

value: wild type


title: LVCP, postnatal day1, n=2

description: Library name: P1_n2


title: Stormal reversal surgery neonates tissue from Normal 2

city: Seoul

first: Murim

last: Choi

address: 103 Daehakro, Jongrogu

country: South Korea

institute: Seoul National University

description: Library name: T19-NE3

data_processing:
Read count extraction and normalization were performed using HTSeq
Assembly: RNA reads were aligned to the GRCh38 using STAR
Supplementary files format and content: Normalized count matrix (csv)

source_name: Intestine

extract_protocol:
The tissue samples were obtained as full-thickness sections from specimens collected during surgery, and immediately after collection, the samples were washed with PBS to remove any foreign substances such as feces. The tissue samples were immediately prepared for RNA extraction.
libraries were prepared and sequenced following TruSeq RNA library prep kit protocols

value: Intestine

tag: subject status

value: non-NEC patients

tag: molecular subtype

value: Normal

value: Female


title: Stormal reversal surgery neonates tissue from Normal 1

description: Library name: T19-NE1


title: Stormal reversal surgery neonates tissue from Normal 3

description: Library name: T19-NE5

value: Male


title: C18R control retina

value: postnatal day 3


title: DNMT3Awt_176

city: Taipei

first: Sao-Chih

last: Ni

address: Heping E. Rd

country: Taiwan

institute: National Taiwan University Hospital

description: Library name: Sample256

data_processing:
Trimming of adaptor sequences and removal of reads of low quality were performed using cutadapt (v2.3).
Quantified reads were aligned to the human genome (GRCh38.p12) by STAR (v2.6.1 a)(24) and then gene-level read counts were generated based on the annotations of Gencode (v28).
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: bone marrow

extract_protocol:
Total RNA were extracted using RNeasy kit (Qiagen) and reverse trasncribed using Superscript II RT (Invitrogen).
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer's recommendations.

value: bone marrow

tag: cell type

value: bone marrow mononuclear cells

value: pretreatment diagnostic


title: DNMT3Awt_184

description: Library name: Sample264


title: DNMT3Awt_181

description: Library name: Sample261


title: DNMT3Awt_183

description: Library name: Sample263


title: DNMT3Awt_175

description: Library name: Sample255


title: DNMT3Awt_179

description: Library name: Sample259


title: DNMT3Awt_177

description: Library name: Sample257


title: DNMT3Awt_173

description: Library name: Sample253


title: DNMT3Awt_172

description: Library name: Sample252


title: DNMT3Awt_171

description: Library name: Sample251


title: DNMT3Awt_169

description: Library name: Sample249


title: DNMT3Awt_182

description: Library name: Sample262


title: DNMT3Awt_167

description: Library name: Sample247


title: DNMT3Awt_178

description: Library name: Sample258


title: DNMT3Awt_165

description: Library name: Sample245


title: DNMT3Awt_166

description: Library name: Sample246


title: LVCP, postnatal day 1, n=1

description: Library name: P1_n1

value: Choroid plexus


title: DNMT3Awt_174

description: Library name: Sample254


title: LVCP, postnatal day4, n=1

description: Library name: P4_n1

value: Wistar Han


title: DNMT3Awt_164

description: Library name: Sample244


title: DNMT3Awt_159

description: Library name: Sample239


title: DNMT3Awt_163

description: Library name: Sample243


title: DNMT3Awt_161

description: Library name: Sample241


title: DNMT3Awt_160

description: Library name: Sample240


title: DNMT3Awt_162

description: Library name: Sample242


title: DNMT3Awt_180

description: Library name: Sample260


title: DNMT3Awt_158

description: Library name: Sample238


title: DNMT3Awt_157

description: Library name: Sample237


title: DNMT3Awt_168

description: Library name: Sample248


title: DNMT3Awt_150

description: Library name: Sample230


title: DNMT3Awt_149

description: Library name: Sample229


title: DNMT3Awt_170

description: Library name: Sample250


title: DNMT3Awt_154

description: Library name: Sample234


title: DNMT3Awt_146

description: Library name: Sample226


title: DNMT3Awt_155

description: Library name: Sample235


title: DNMT3Awt_148

description: Library name: Sample228


title: DNMT3Awt_152

description: Library name: Sample232


title: DNMT3Awt_145

description: Library name: Sample225


title: DNMT3Awt_153

description: Library name: Sample233


title: DNMT3Awt_151

description: Library name: Sample231


title: DNMT3Awt_143

description: Library name: Sample223


title: DNMT3Awt_142

description: Library name: Sample222


title: DNMT3Awt_140

description: Library name: Sample220


title: DNMT3Awt_141

description: Library name: Sample221


title: DNMT3Awt_147

description: Library name: Sample227


title: DNMT3Awt_139

description: Library name: Sample219


title: DNMT3Awt_144

description: Library name: Sample224


title: DNMT3Awt_138

description: Library name: Sample218


title: DNMT3Awt_136

description: Library name: Sample216


title: DNMT3Awt_135

description: Library name: Sample215


title: DNMT3Awt_137

description: Library name: Sample217


title: DNMT3Awt_132

description: Library name: Sample212


title: DNMT3Awt_131

description: Library name: Sample211


title: DNMT3Awt_134

description: Library name: Sample214


title: DNMT3Awt_130

description: Library name: Sample210


title: DNMT3Awt_129

description: Library name: Sample209


title: DNMT3Awt_156

description: Library name: Sample236


title: DNMT3Awt_126

description: Library name: Sample206


title: DNMT3Awt_123

description: Library name: Sample203


title: DNMT3Awt_128

description: Library name: Sample208


title: DNMT3Awt_122

description: Library name: Sample202


title: DNMT3Awt_127

description: Library name: Sample207


title: DNMT3Awt_125

description: Library name: Sample205


title: DNMT3Awt_120

description: Library name: Sample200


title: DNMT3Awt_121

description: Library name: Sample201


title: DNMT3Awt_119

description: Library name: Sample199


title: DNMT3Awt_116

description: Library name: Sample196


title: DNMT3Awt_118

description: Library name: Sample198


title: DNMT3Awt_114

description: Library name: Sample194


title: DNMT3Awt_113

description: Library name: Sample193


title: DNMT3Awt_112

description: Library name: Sample192


title: DNMT3Awt_111

description: Library name: Sample191


title: DNMT3Awt_115

description: Library name: Sample195


title: DNMT3Awt_109

description: Library name: Sample189


title: DNMT3Awt_110

description: Library name: Sample190


title: DNMT3Awt_117

description: Library name: Sample197


title: DNMT3Awt_133

description: Library name: Sample213


title: DNMT3Awt_107

description: Library name: Sample187


title: DNMT3Awt_106

description: Library name: Sample186


title: DNMT3Awt_103

description: Library name: Sample183


title: DNMT3Awt_105

description: Library name: Sample185


title: DNMT3Awt_104

description: Library name: Sample184


title: DNMT3Awt_101

description: Library name: Sample181


title: DNMT3Awt_102

description: Library name: Sample182


title: DNMT3Awt_100

description: Library name: Sample180


title: DNMT3Awt_124

description: Library name: Sample204


title: DNMT3Awt_99

description: Library name: Sample179


title: DNMT3Awt_97

description: Library name: Sample177


title: DNMT3Awt_98

description: Library name: Sample178


title: DNMT3Awt_88

description: Library name: Sample168


title: DNMT3Awt_91

description: Library name: Sample171


title: DNMT3Awt_90

description: Library name: Sample170


title: DNMT3Awt_92

description: Library name: Sample172


title: DNMT3Awt_108

description: Library name: Sample188


title: DNMT3Awt_93

description: Library name: Sample173


title: DNMT3Awt_94

description: Library name: Sample174


title: DNMT3Awt_87

description: Library name: Sample167


title: DNMT3Awt_95

description: Library name: Sample175


title: DNMT3Awt_86

description: Library name: Sample166


title: DNMT3Awt_85

description: Library name: Sample165


title: High DIPs, 6days, rep2

city: Changchun

first: Weiheng

last: Su

address: Qianjin Street, 2699

institute: Jilin University

description: Library name: High_DIP_6d_2

data_processing:
Data files were processed using HISAT2 (v2.2.1) against the mm10 mouse genome reference with default settings.
Assembly: mm10
Supplementary files format and content: Tab-delimited tex files include RPKM values for each sample

source_name: Turbinate

extract_protocol:
The turbinate and adjacent mucosal tissues were isolated at multiple timepoints. The RNA were extracted using the TRNzol Universal Reagent (TIANGEN).
The library preparation was conducted using the Fast RNA-seq Lib Prep Kit V2 (ABclonal) according to the manufacturer’s instructions. And the library was sequenced using the Illumina NovaSeq X Plus platform.

treatment_protocol: Female 6–8-week-old BALB/c mice were intranasally immunized with 30 μL of low DIPs LAIV (5.25×10^6 EID50, 1.46×10^7 total particles) or high DIPs LAIV (same STV, 5.25×106 EID50, 1.05×10^9 total particles). The turbinate and adjacent mucosal tissues were isolated at 8 hpi, 2 dpi, 4 dpi, and 6 dpi, respectively for bulk RNA-Seq.

value: Turbinate

value: BALB/c

value: female

value: 6 days

value: immunized with High DIPs LAIV


title: DNMT3Awt_83

description: Library name: Sample163


title: High DIPs, 6days, rep3

description: Library name: High_DIP_6d_3


title: DNMT3Awt_81

description: Library name: Sample161


title: DNMT3Awt_79

description: Library name: Sample159


title: High DIPs, 6days, rep1

description: Library name: High_DIP_6d_1


title: DNMT3Awt_80

description: Library name: Sample160


title: Low DIPs, 6days, rep3

description: Library name: Low_DIP_6d_3

value: immunized with low DIPs LAIV


title: Low DIPs, 6days, rep2

description: Library name: Low_DIP_6d_2


title: DNMT3Awt_78

description: Library name: Sample158


title: DNMT3Awt_77

description: Library name: Sample157


title: DNMT3Awt_96

description: Library name: Sample176


title: Low DIPs, 6days, rep1

description: Library name: Low_DIP_6d_1


title: DNMT3Awt_89

description: Library name: Sample169


title: DNMT3Awt_76

description: Library name: Sample156


title: High DIPs, 4days, rep3

description: Library name: High_DIP_4d_3

value: 4 days


title: DNMT3Awt_75

description: Library name: Sample155


title: DNMT3Awt_84

description: Library name: Sample164


title: DNMT3Awt_74

description: Library name: Sample154


title: DNMT3Awt_73

description: Library name: Sample153


title: Low DIPs, 4days, rep3

description: Library name: Low_DIP_4d_3


title: High DIPs, 4days, rep1

description: Library name: High_DIP_4d_1


title: DNMT3Awt_70

description: Library name: Sample150


title: Low DIPs, 4days, rep2

description: Library name: Low_DIP_4d_2


title: High DIPs, 2days, rep2

description: Library name: High_DIP_2d_2

value: 2 days


title: High DIPs, 2days, rep1

description: Library name: High_DIP_2d_1


title: DNMT3Awt_68

description: Library name: Sample148


title: DNMT3Awt_72

description: Library name: Sample152


title: DNMT3Awt_82

description: Library name: Sample162


title: High DIPs, 4days, rep2

description: Library name: High_DIP_4d_2


title: Low DIPs, 2days, rep2

description: Library name: Low_DIP_2d_2


title: DNMT3Awt_66

description: Library name: Sample146


title: High DIPs, 8hours, rep3

description: Library name: High_DIP_8h_3

value: 8 hours


title: DNMT3Awt_67

description: Library name: Sample147


title: Low DIPs, 4days, rep1

description: Library name: Low_DIP_4d_1


title: DNMT3Awt_64

description: Library name: Sample144


title: High DIPs, 8hours, rep2

description: Library name: High_DIP_8h_2


title: High DIPs, 8hours, rep1

description: Library name: High_DIP_8h_1


title: DNMT3Awt_63

description: Library name: Sample143


title: Low DIPs, 8hours, rep3

description: Library name: Low_DIP_8h_3


title: DNMT3Awt_61

description: Library name: Sample141


title: Low DIPs, 8hours, rep2

description: Library name: Low_DIP_8h_2


title: Low DIPs, 8hours, rep1

description: Library name: Low_DIP_8h_1


title: DNMT3Awt_71

description: Library name: Sample151


title: DNMT3Awt_69

description: Library name: Sample149


title: DNMT3Awt_60

description: Library name: Sample140


title: DNMT3Awt_59

description: Library name: Sample139


title: DNMT3Awt_58

description: Library name: Sample138


title: TNFR2_WT_10

city: Durham

first: Aditya

middle: Anand

last: Mohan

state: NC

address: 126 Constitution Drive

institute: Duke University

description: Library name: Sample 18

data_processing:
Raw fastq files were assessed for quality with FastQC and mapped to the GRCm39 (GENCODE v33/Ensembl 110) mouse reference genome using STAR-2.7.11a alignment. featureCounts was used to quantify mapped reads and generate counts matrices for downstream analysis.
Assembly: GRCm39 (GENCODE v33/Ensembl 110)
Supplementary files format and content: CSV file contains FPKM values for each group

source_name: T Cell

extract_protocol:
Cells were lysed using the TRI reagent (Zymo, cat # R2050-1-50) and RNA was isolated using the Direct-Zol MinPrep kit from Zymo (Cat # R2050), including the optional DNaseI treatment step. RNA was eluted in 25µL RNase- and DNase-free water.
mRNA was purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, cat # E7490). Samples were processed using the NEBNext Ultra-II RNA library prep kit from New England Biolabs (cat # E7775S) and the NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer pairs) (NEB, cat # E6440S) according to manufacturer’s protocol.

value: T Cell

value: WT


title: Low DIPs, 2days, rep1

description: Library name: Low_DIP_2d_1


title: DNMT3Awt_57

description: Library name: Sample137


title: DNMT3Awt_55

description: Library name: Sample135


title: TNFR2_WT_9

description: Library name: Sample 17


title: DNMT3Awt_53

description: Library name: Sample133


title: DNMT3Awt_54

description: Library name: Sample134


title: DNMT3Awt_65

description: Library name: Sample145


title: DNMT3Awt_56

description: Library name: Sample136


title: TNFR2_WT_4

description: Library name: Sample 13


title: TNFR2_WT_3

description: Library name: Sample 12


title: TNFR2_WT_8

description: Library name: Sample 16


title: TNFR2_WT_7

description: Library name: Sample 15


title: DNMT3Awt_51

description: Library name: Sample131


title: TNFR2_WT_2

description: Library name: Sample 11


title: DNMT3Awt_62

description: Library name: Sample142


title: TNFR2_WT_1

description: Library name: Sample 10


title: DNMT3Awt_50

description: Library name: Sample130


title: TNFR2_MUT_9

description: Library name: Sample 9

value: TNFR2 KO


title: TNFR2_MUT_8

description: Library name: Sample 8


title: DNMT3Awt_49

description: Library name: Sample129

value: bone marrow


title: DNMT3Awt_48

description: Library name: Sample128

value: bone marrow mononuclear cells


title: TNFR2_MUT_7

description: Library name: Sample 7


title: TNFR2_WT_5

description: Library name: Sample 19


title: TNFR2_WT_6

description: Library name: Sample 20


title: DNMT3Awt_47

description: Library name: Sample127

value: pretreatment diagnostic


title: DNMT3Awt_46

description: Library name: Sample126


title: TNFR2_MUT_6

description: Library name: Sample 6


title: DNMT3Awt_45

description: Library name: Sample125


title: TNFR2_MUT_5

description: Library name: Sample 5


title: TNFR2_MUT_4

description: Library name: Sample 4


title: TNFR2_MUT_3

description: Library name: Sample 3


title: TNFR2_MUT_2

description: Library name: Sample 2


title: DNMT3Awt_52

description: Library name: Sample132


title: TNFR2_MUT_1

description: Library name: Sample 1


title: DNMT3Awt_42

description: Library name: Sample122


title: DNMT3Awt_43

description: Library name: Sample123


title: DNMT3Awt_39

description: Library name: Sample119


title: DNMT3Awt_40

description: Library name: Sample120


title: DNMT3Awt_37

description: Library name: Sample117


title: LVCP, postnatal day 60 RNA, n=2

description: Library name: P60_n2_RNA_P29810_1005

data_processing:
The demultiplexing, aligment, barcode processing, ATAC and GEX counting, barcode counting, and aggregation were made using the CellRanger ARC software (v1.0.0)
Assembly: mm10
Supplementary files format and content: h5, tsv.gz, tsv.gsz.tbi, rds

source_name: P60 healthy mouse

extract_protocol:
Single-cell RNA sequencing was performed on lateral ventricle choroid plexus (CP) samples from mice at postnatal days P2-3, P11, and young adults (10 weeks), while single-cell multiome included P11 and young adult mice. CPs were isolated from perfused mouse brains, pooled (3–4 CPs/sample from both sexes), and enzymatically and mechanically dissociated through a multi-step protocol with pronase (0.1 mg/ml)  for 15min, Enzyme P mix (adult brain dissociation kit, 130-107-677, Miltenyi Biotec) for 30 min, and trypsin (0.025%) for 15min, with mechanic digestion every 5min. Cells pellets were resuspended in PBS-2%BSA. The Chromium Next GEM Single Cell 3ʹ v3.1 kit (10x Genomics) was used for scRNA-seq, following the manufacturer’s guidelines. Single-cell multiome required additional steps of nuclei extraction using lysis buffer (IGEPAL (CA-630), 0.01% Tween-20, 0.001% Digitonin, 1% BSA, DTT 200mM, 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2 and RNAse inhibitor). After washing and centrifugation, an additional lysis step with Nuclei EZ buffer was performed (Sigma, #N3408). Nuclei were washed again and resuspended in diluted nuclei buffer (10x Genomics). A portion was used for viability counting, and the rest was prepared for tagmentation. The 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit was used, following the manufacturer’s protocol.
10x protocol to snMultiome

value: Choroid plexus

value: 60 days postnatal (P60)


title: LVCP, postnatal day 60 TTR eGFP ATAC, n=3

description: Library name: P60_n3_ATAC_P29809_1007

library_source: genomic single cell

source_name: P60 healthy mouse With ablation of TTR gene on epithelial cells and replaced with expresison of eGFP


title: DNMT3Awt_38

description: Library name: Sample118


title: LVCP, postnatal day 60 ATAC, n=2

description: Library name: P60_n2_ATAC_P29809_1005


title: DNMT3Awt_36

description: Library name: Sample116


title: LVCP, postnatal day 60 TTR eGFP RNA, n=3

description: Library name: P60_n3_RNA_P29810_1007


title: LVCP, postnatal day 11 RNA, n=3

description: Library name: P11_n3_RNA_P29810_1003

source_name: P11 healthy mouse

value: 11 days postnatal (P11)


title: DNMT3Awt_35

description: Library name: Sample115


title: LVCP, postnatal day 11 ATAC, n=3

description: Library name: P11_n3_ATAC_P29809_1003


title: LVCP, postnatal day 11 RNA, n=2

description: Library name: P11_n2_RNA_P29810_1002


title: DNMT3Awt_34

description: Library name: Sample114


title: DNMT3Awt_44

description: Library name: Sample124


title: LVCP, postnatal day 11 ATAC, n=2

description: Library name: P11_n2_ATAC_P29809_1002


title: DNMT3Awt_33

description: Library name: Sample113


title: DNMT3Awt_32

description: Library name: Sample112


title: DNMT3Awt_41

description: Library name: Sample121


title: DNMT3Awt_31

description: Library name: Sample111


title: DNMT3Awt_30

description: Library name: Sample110


title: LVCP, postnatal day 11 RNA, n=1

description: Library name: P11_n1_RNA_P29810_1001


title: LVCP, postnatal day 60 RNA, n=1

description: Library name: P60_n1_RNA_P25306_1006


title: DNMT3Awt_28

description: Library name: Sample108


title: DNMT3Awt_29

description: Library name: Sample109


title: CARLIN allele, injection at E7.5 and E8.5, collection at P4, otocyst cells, scRNA sequencing

city: Houston

first: Joel

last: Nelson

email: Joel.Nelson@bcm.edu, joeln@bcm.edu

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Library name: CARLIN_early_sc

data_processing:
Cell Ranger
Assembly: Mouse mm10
Supplementary files format and content: Processed data includes matrix (.mtx), barcodes, and features (.tsv) for single-cell experiment, and an analysis file (.mat) for the bulk experiment

source_name: postnatal inner ear tissue

extract_protocol:
Post natal mice were harvested in cold, sterile 1X CMF (Calcium Magnesium Free) PBS for each tissue extraction process. Following dissection of the inner ear, the tissue was dissociated via a 35-40 minute incubation period in 0.22 µm papain/ DNase solution at 37 deg C. Tissue was homogenized following dissociation by adding a 1:1 ratio of cold 1X CMF PBS + 4% FBS solution and pipetting up and down 150x per sample. Samples were centrifuged at 470 RCF for 5 min (at 4 deg), then supernatant was removed and replaced with fresh 1X CMF PBS + 4% FBS solution, re-suspending the pellet by pipetting. This process was repeated for more viscous samples. Cells then underwent a incubation step with a Apc-conjugated EpCAM antibody for 20 minutes at 4 deg, on a nutator. Finally, samples were filtered through 40 µm pluriSelect mini strainers into sterile 5 ml conical tubes. Purified APC+ cells from FACS were collected in 150 µl fresh 1X CMF PBS + 4% FBS solution per sample.
All libraries were prepared according to the 10X Genomics protocol (Chromium™ Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1). In summary, Gel Beads-in-emulsion (GEMS) were produced via mixing Single Cell 3' v3.1 Gel Beads with the cell solution master mix for each sample and Partitioning Oil, then loading these into the Chromium Chip G. The gel beads were lysed and combined with primers containing a Illumina TruSeq R1 primer, a 12 nt unique molecular identifier (UMI), 16 nt 10X Barcode, and 30 nt poly(dT) sequence for each GEM, as well as a reverse transcription Master Mix of reagents. Following production of pooled, barcoded full-length cDNA from the poly-adenylated mRNA of each cell, the cDNA was purified from this mixture using silane magnetic beads, then amplified by PCR. Appropriately sized fragments were selected for the library, and paired end P5 and P7 primers, the TruSeq R2 primer sequence, and a sample index were added in the later stages of library construction. The library and cDNA were then used to generate the single-cell and bulk RNAseq samples respectively.

treatment_protocol: Doxycycline injection via IP injection at E7.5 and E8.5 via retro-orbital injections with 25 ug/g of a 10 mg/mL solution.

value: postnatal inner ear tissue

tag: cell line

value: CARLIN x KH2/iGas9

value: P4 inner ear cells

value: Doxyclicline injection at E7.5 and E8.5


title: FFPE_ATAC_Mouse_brain_50um_S8_replicate_2

city: philadelphia

first: Pengfei

last: Guo

address: 422 Curie Boulevard, Stellar Chance Labs, 711-712 (lab), philadelphia

institute: University of Pennsylvania

description:
Library name: Sample 13
ATAC-seq

data_processing:
Linkers 1 and 2 are used for targeted filtering of read 2, aligning utilizing BWA followed by sorting and indexing via Samtools to facilitate efficient data handling and retrieval. This reformatting process assigned genome sequences to the first read and incorporated barcodes A and B into the second read. We aligned these fastq files against mouse (GRCm38) or human (GRCh38) reference genomes. The conversion produced tsv-like fragments files, enriched with spatial and genomic information through the integration of barcode pairs, facilitating comprehensive downstream analysis.
Assembly: GRCm38, GRCh38
Supplementary files format and content: TSV files for downstream analysis. The tsv file contains tissue location info (barcode A x barcode B) and fragments info on the genome.
Library strategy: Spatial ATAC-seq

source_name: Mouse brain

extract_protocol:
The workflow is summarized in Fig. 1a and Extended Data Fig. 1. Initially, FFPE tissues underwent antigen retrieval (AR) to break crosslinks, followed by in situ Tn5 transposition, where adapters were inserted into accessible genomic regions. Next, spatial barcodes (A1-50 and B1-50) were ligated onto the genomic DNA through two rounds of ligation, facilitated by microfluidic channels. Tissue slides were then imaged to link the spatial barcodes to tissue morphology. After tissue lysis, the barcoded DNA fragments were amplified for library preparation.
After antigen retrieval, tissue was washed twice with 1 ml of 1× DPBS and cleaned with ddH2O. The sequential order for spatial ATAC profiling is as follows: 1. ATAC-seq; 2. Ligation of barcode A; 3. Ligation of barcode B; 4. Reverse crosslink; 5. Library construction; 6. Library QC and sequencing.

value: Mouse brain


title: DNMT3Awt_27

description: Library name: Sample107


title: DNMT3Awt_26

description: Library name: Sample106


title: FFPE_ATAC_Mouse_brain_50um_S7_replicate_2

description:
Library name: Sample 11
ATAC-seq


title: LVCP, postnatal day 60 ATAC, n=1

description: Library name: P60_n1_ATAC_P25304_1006


title: DNMT3Awt_24

description: Library name: Sample104


title: FFPE_ATAC_Mouse_brain_50um_S7_replicate_1

description:
Library name: Sample 10
ATAC-seq


title: FFPE_ATAC_Mouse_brain_50um_S8_replicate_1

description:
Library name: Sample 12
ATAC-seq


title: DNMT3Awt_25

description: Library name: Sample105


title: FFPE_ATAC_Mouse_brain_50um_S6_replicate_2

description:
Library name: Sample 9
ATAC-seq


title: DNMT3Awt_23

description: Library name: Sample103


title: DNMT3Awt_22

description: Library name: Sample102


title: FFPE_ATAC_Mouse_brain_50um_S5_replicate_2

description:
Library name: Sample 7
ATAC-seq


title: FFPE_ATAC_Mouse_brain_50um_S6_replicate_1

description:
Library name: Sample 8
ATAC-seq


title: DNMT3Awt_21

description: Library name: Sample101


title: DNMT3Awt_20

description: Library name: Sample100


title: FFPE_ATAC_Mouse_brain_50um_S5_replicate_1

description:
Library name: Sample 6
ATAC-seq


title: LVCP, postnatal day 11 ATAC, n=1

description: Library name: P11_n1_ATAC_P29809_1001


title: DNMT3Awt_19

description: Library name: Sample99


title: DNMT3Awt_18

description: Library name: Sample98


title: FFPE_ATAC_Mouse_brain_50um_S4_replicate_2

description:
Library name: Sample 5
ATAC-seq


title: FFPE_ATAC_Mouse_brain_50um_S4_replicate_1

description:
Library name: Sample 4
ATAC-seq


title: FF_ATAC_Mouse_brain_50um_replicate _3

description:
Library name: Sample 3
ATAC-seq


title: DNMT3Awt_14

description: Library name: Sample94


title: FF_ATAC_Mouse_brain_50um_replicate _2

description:
Library name: Sample 2
ATAC-seq


title: Multimodal, T cells, D12.STAT5CA rep 1-3, ADT

city: ANN ARBOR

first: Adam

last: Courtney

address: 1150 W. Medical Center Dr., 2240 MSRB III

department: Pharmacology

description:
Library name: 11356-AC-3_ADT
ADT library: read1 file contrains cell barcode and UMI; read2 file contains Antibody Derived Tag reads for Total-Seq C kit

library_source: other

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files and the CellRanger Pipeline (v 8.0.1, 10x Genomics) was used to align reads, demultiplex samples using HTO tags, and generate count matrices.
Assembly: GRCm39
Supplementary files format and content: HDF5 format  of UMI counts associated with a feature (row) and barcode (column) filtered to cell-associated barcodes for each HTO tagged sample; includes features from both GEX and ADT libraries
Library strategy: CITE-seq

molecule: protein

source_name: B16-OVA derived solid tumor

extract_protocol:
Live CD8ab+ T cells were sorted and antibody labeled single cell suspensions were subjected to counting and viability checks before dilution to a concentration of 700-1000 cells/ml. For each treatment group, cells previously labelled with a unique HashTag antibody (N=3 per treatment group) were pooled.
Single cell Gene Expression and Total-Seq C libraries were generated using the 10x Genomics Chromium Controller with 5' Gene Expression reagents with Feature Barcoding following the manufacturer’s protocol (10x Genomics) before paired-end sequencing (Illumina NovaSeq X Plus).

value: B16-OVA derived solid tumor

value: CD45+ CD8a/b+ T cells

tag: timepoint

tag: library type

value: ADT

tag: adt

value: CD45.1, CD45.2, CD90.1, CD8a TotalSeq-C antibodies


title: FF_ATAC_Mouse_brain_50um_replicate _1

description:
Library name: Sample 1
ATAC-seq


title: DNMT3Awt_15

description: Library name: Sample95


title: DNMT3Awt_17

description: Library name: Sample97


title: Multimodal, T cells, D12.STAT5CA rep1-3, GEX

description:
Library name: 11356-AC-3_HTO
HTO library: read1 file contains cell barcode and UMI for 5' GEX kit; read2 file contains Hashtag Antibody Derived Tag reads

value: HTO

tag: hto

value: TotalSeq-C HashTag antibodies


title: DNMT3Awt_12

description: Library name: Sample92

value: bone marrow


title: DNMT3Awt_13

description: Library name: Sample93

value: bone marrow mononuclear cells


title: Multimodal, T cells, D12.aSTAT5 rep1-3, GEX

description:
Library name: 11356-AC-2_HTO
HTO library: read1 file contains cell barcode and UMI for 5' GEX kit; read2 file contains Hashtag Antibody Derived Tag reads


title: DNMT3Awt_10

description: Library name: Sample90

value: pretreatment diagnostic


title: Multimodal, T cells, D12.EmptyVec rep 1-3, ADT

description:
Library name: 11356-AC-1_ADT
ADT library: read1 file contrains cell barcode and UMI; read2 file contains Antibody Derived Tag reads for Total-Seq C kit


title: DNMT3Awt_11

description: Library name: Sample91


title: Multimodal, T cells, D12.aSTAT5 rep 1-3, ADT

description:
Library name: 11356-AC-2_ADT
ADT library: read1 file contrains cell barcode and UMI; read2 file contains Antibody Derived Tag reads for Total-Seq C kit


title: Multimodal, T cells, D12.EmptyVec rep1-3, GEX

description:
Library name: 11356-AC-1_HTO
HTO library: read1 file contains cell barcode and UMI for 5' GEX kit; read2 file contains Hashtag Antibody Derived Tag reads


title: Multimodal, T cells, D5.PepControl rep 1-3, ADT

description:
Library name: 11099-AC-4_ADT
ADT library: read1 file contrains cell barcode and UMI; read2 file contains Antibody Derived Tag reads for Total-Seq C kit


title: DNMT3Awt_08

description: Library name: Sample88


title: Multimodal, T cells, D5.STAT5CA rep 1-3, ADT

description:
Library name: 11099-AC-3_ADT
ADT library: read1 file contrains cell barcode and UMI; read2 file contains Antibody Derived Tag reads for Total-Seq C kit


title: Multimodal, T cells, D5.PepControl rep1-3, GEX

description:
Library name: 11099-AC-4_HTO
HTO library: read1 file contains cell barcode and UMI for 5' GEX kit; read2 file contains Hashtag Antibody Derived Tag reads


title: DNMT3Awt_09

description: Library name: Sample89


title: DNMT3Awt_05

description: Library name: Sample85


title: Multimodal, T cells, D5.STAT5CA rep1-3, GEX

description:
Library name: 11099-AC-3_HTO
HTO library: read1 file contains cell barcode and UMI for 5' GEX kit; read2 file contains Hashtag Antibody Derived Tag reads


title: DNMT3Awt_06

description: Library name: Sample86


title: Multimodal, T cells, D5. Empty Vec rep 1-3, ADT

description:
Library name: 11099-AC-2_ADT
ADT library: read1 file contrains cell barcode and UMI; read2 file contains Antibody Derived Tag reads for Total-Seq C kit


title: DNMT3Awt_16

description: Library name: Sample96


title: DNMT3Awt_03

description: Library name: Sample83


title: DNMT3Awt_04

description: Library name: Sample84


title: Multimodal, T cells, D5.EmptyVec rep1-3, GEX

description:
Library name: 11099-AC-2_HTO
HTO library: read1 file contains cell barcode and UMI for 5' GEX kit; read2 file contains Hashtag Antibody Derived Tag reads


title: Multimodal, T cells, D5.aSTAT5 rep 1-3, ADT

description:
Library name: 11099-AC-1_ADT
ADT library: read1 file contrains cell barcode and UMI; read2 file contains Antibody Derived Tag reads for Total-Seq C kit


title: DNMT3Awt_02

description: Library name: Sample82


title: Multimodal, T cells, D5.aSTAT5 rep1-3, GEX

description:
Library name: 11099-AC-1_HTO
HTO library: read1 file contains cell barcode and UMI for 5' GEX kit; read2 file contains Hashtag Antibody Derived Tag reads


title: DNMT3Amut_80

description: Library name: Sample80


title: Nipbl +/-; Isl1 +/- 9

city: Irvine

first: Anne

last: Calof

state: CA

address: Biological Sciences III, 519 Ring Rd

department: Developmental & Cell Biology

institute: University of California, Irvine

data_processing:
Reads were mapped onto the GRCm38 mm10 mouse reference genome using STAR. Reads that mapped to genes were counted using featureCounts to generate a raw read count matrices for every sample.
Assembly: mm10
Supplementary files format and content: raw-counts-all-samples.txt contains a raw read count matrix for all samples in comma delimited format.

source_name: Heart

extract_protocol:
Total RNA was extracted from mouse E10.5 hearts using New England Biolabs' Monarch Total RNA Miniprep Kit (Catalog #: T2010S).
RNA libraries were constructed using New England Biolabs' NEBNext Ultra II RNA Library Prep Kit for Illumina (Catalog #: E7765).

tag: developmental stage

value: Embryonic day E10.5

value: Heart

value: Nipbl +/-; Isl1 +/-


title: DNMT3Awt_01

description: Library name: Sample81


title: Nipbl +/-; Isl1 +/- 8


title: DNMT3Amut_78

description: Library name: Sample78


title: DNMT3Amut_77

description: Library name: Sample77


title: DNMT3Amut_76

description: Library name: Sample76


title: Nipbl +/-; Isl1 +/- 5


title: Nipbl +/-; Isl1 +/- 6


title: Nipbl +/-; Isl1 +/- 7


title: DNMT3Awt_07

description: Library name: Sample87


title: DNMT3Amut_75

description: Library name: Sample75


title: Nipbl +/-; Isl1 +/- 4


title: DNMT3Amut_79

description: Library name: Sample79


title: Nipbl +/-; Isl1 +/- 2


title: Nipbl +/-; Isl1 +/- 3


title: DNMT3Amut_74

description: Library name: Sample74


title: Nipbl +/- 9

value: Nipbl +/-


title: DNMT3Amut_72

description: Library name: Sample72


title: DNMT3Amut_71

description: Library name: Sample71


title: Nipbl +/- 8


title: DNMT3Amut_70

description: Library name: Sample70


title: DNMT3Amut_69

description: Library name: Sample69


title: Nipbl +/- 6


title: Nipbl +/- 7


title: Nipbl +/- 5


title: DNMT3Amut_67

description: Library name: Sample67


title: DNMT3Amut_68

description: Library name: Sample68


title: DNMT3Amut_66

description: Library name: Sample66


title: DNMT3Amut_65

description: Library name: Sample65


title: Nipbl +/- 3


title: Nipbl +/- 4


title: Nipbl +/- 1


title: Nipbl +/- 2


title: DNMT3Amut_64

description: Library name: Sample64


title: Isl1 +/- 9


title: DNMT3Amut_62

description: Library name: Sample62


title: DNMT3Amut_73

description: Library name: Sample73


title: DNMT3Amut_61

description: Library name: Sample61


title: Isl1 +/- 8


title: Isl1 +/- 6


title: DNMT3Amut_60

description: Library name: Sample60


title: DNMT3Amut_59

description: Library name: Sample59


title: DNMT3Amut_58

description: Library name: Sample58


title: Isl1 +/- 5


title: Isl1 +/- 4


title: DNMT3Amut_57

description: Library name: Sample57


title: Isl1 +/- 3


title: DNMT3Amut_56

description: Library name: Sample56


title: Isl1 +/- 2


title: Isl1 +/- 1