title: Setd2_KO_rep2

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

data_processing:
Sequence reads were trimmed using trimmomatic
Sequence reads were mapped to mm10 reference genome using star
Sequence reads were count using htseq-count as gencode VM25.gtf model.
Differential gene expression analysis was detected using Bioconductor DESeq2 package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample ...

source_name: Germinal Center B cells

extract_protocol:
Splenic germinal center B cells were FACS sorted, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: spleen

value: Germinal Center B cells


title: Setd2_KO_rep1

status: Public on Sep 14 2024

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: cell type


title: CD8+T cells, Young, TRM condition

city: Shanghai

first: Siyu

last: Pei

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

data_processing:
Transcriptomic reads from the RNA-Seq experiments were mapped to a reference genome (GRCm38/mm10) using Bowtie.
Assembly: mm10
Supplementary files format and content: Processed data were csv format and all gene FPKM/TPM of each sample were contained in the file called gene_expression.

source_name: spleen and lymph node

growth_protocol: The 6-weeks-old young and 18-months-old aged mice were sacrificed, and primary CD8+T cells isolated from the spleen and lymph nodes were cultured under TCR condition (α-CD3/28: 1μg/ml) or TRM condition (α-CD3/28: 1μg/ml, IL-15: 20ng/ml, TGFβ: 5ng/ml) for 3 days.

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: spleen and lymph node

value: CD8+T cells

value: Young WT

tag: treatment

value: TRM


title: Setd2_WT_rep2


title: CD8+T cells, Young, TCR condition

value: TCR


title: T0_1

status: Public on Sep 15 2024

city: BRONX

first: Fabien

last: Delahaye

state: NY

address: 1300 Morris Park Avenue

department: Genetics

country: USA

institute: AECOM

data_processing:
RNAseq reads were aligned to human genome Hg38 using STAR
Normalization and Comparative analysis were performed with DESeq2 (v 1.10.1)
Genome_build: Hg38
Supplementary_files_format_and_content: count files

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: HeLa cells were grown in monolayer culture at 37°C and 5% CO2 in Dulbecco’s modified Eagle’s (DMEM) GlutaMAX™, high glucose, pyruvate medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin

extract_protocol:
Total RNA of HeLa cells was extracted using the NucleoSpin® RNA extraction (Macherey-Nagel, Hoerdt, France)
TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: HeLa cells were treated with DMSO, 20nM carfilzomib (CFZ), 15µM of compound 1a (CPD 1a) or the combination of these two compounds for 0h, 8h or 24h

value: Cervix

tag: cell line

value: HeLa

tag: passage

tag: time (hours)

value: untreated


title: UVB-Sal-B

first: Sun

middle: Jia

last: Ming

address: No. 639, Zhi Zao Ju Road,

department: Department of Plastic & Reconstructive Surgery

institute: Shanghai Ninth People’s Hospital

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Assembly: GRCm38
Supplementary files format and content: FPKM

source_name: HDF(Human dermal fibroblast)

extract_protocol:
fresh frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module (or rRNA removal by RiboZero Magnetic Gold Kit) to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina HiSeq 4000 Sequencer.
RNA libraries were prepared for sequencing using standard Illumina Hiseq protocols.

value: HDF(Human dermal fibroblast)

value: UVB-Sal-B


title: UVB

value: UVB


title: Setd2_WT_rep1


title: BEAS-2B_pl1_RP11-221_2_C, BEAS-2B, RP11221

city: Ghent

first: Jasper

last: Anckaert

address: Corneel Heymanslaan 10

country: Belgium

institute: OncoRNAlab

data_processing:
high performance computing 3'-RNAseq analysis pipeline (Quantseq)
QC via FASTQC 0.11.9
Quality related trimming via bbduk (BBMap v38.87, k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20)
read mapping via STAR 2.7.6a
bam file indexing via SAMtools 1.15
count tables generated via HTSeq 0.11.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw count tables

growth_protocol: BEAS-2B cells were cultured in RPMI medium (Gibco) supplemented with 10% fetal calf serum, 100U/ml penicillin, 100 µg/ml streptomycin and 2mM glutamine (Gibco). HEK-293T cells were cultured in DMEM medium (Gibco) supplemented with 10% fetal calf serum, 100 U/ml penicillin, 100 µg/ml streptomycin (Gibco) and 2mM L-glutamine (Gibco). Cell lines were grown in a 37°C humidified incubator under 5% CO2.

extract_protocol:
miRNEasy kit (Qiagen) with on-column Dnase treatment (Qiagen)
Library preparation for 3’-end shallow sequencing was performed using the Quantseq 3’ mRNA-seq library prep kit from Lexogen and following the manufacturer’s instructions
Library preparation for total RNA sequencing was done using the SMARTer® Stranded Total RNA-Seq Kit v3 kit from Takara following the manufacturer’s instructions

treatment_protocol:
DEP was dissolved in saline at a concentration of 1000 µg/ml. LPS(Sigma Aldrich) and TNF-α (Thermo Fisher) were dissolved in PBS at respectively 1000 µg/ml and 0.05 µg/µl. Total volume per well was always 200 µl. Exposures were done 24 hours after seeding or 48 hours after selection. Supernatans was collected and cells were lysed 24 hours after exposure.
dCas9-KARB-MeCP2 was introduced into the BEAS-2B cells by transfecting PiggyBac transposase (from System Biosciences) and dCas9-KRAB-MeCP2 plasmid (#110821 from addgene) simultaneously using CRISPRmax (from ThermoFisher). 24 hours after transfection cells were selected with 6 µg/ml blasticidin. dCas9-KRAB-MeCP2 presence was confirmed using immunoblotting and qPCR.


title: Ctrl

value: Ctrl


title: BEAS-2B_pl1_RP11-221_2_B, BEAS-2B, RP11221


title: SAM24425296

city: South San Francisco

first: Mitchell

last: Rezzonico

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Reads were aligned to the genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package.
Assembly: GRCh38
Supplementary files format and content: Each sample has a TSV data file with counts, gene exonic size (width) and RPKM as provided by HTSeqGenie

extract_protocol:
RNA was extracted using the RNeasy Lipid Tissue extraction kit with on-column DNase digestion (Qiagen). Quality and quantity of total RNA samples were determined using ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent), respectively.
For sequencing library generation, the Truseq Stranded mRNA kit (Illumina) was used with an input of 100-1000 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies)

tag: day


title: SAM24425292


title: SAM24425291


title: SAM24425295


title: SAM24425294


title: SAM24425290


title: SAM24425293


title: BEAS-2B_pl1_RP11-221_2_A, BEAS-2B, RP11221


title: SAM24425288


title: SAM24425289


title: SAM24425287


title: SAM24425285


title: Mild,23

city: Padang

first: Ika

middle: Kurnia

last: Febrianti

state: West  Sumatra

address: Perinstis Kemerdekaan No.94, Jati

department: Doctoral Programme of Biomedical

country: Indonesia

institute: Universitas Andalas

data_processing:
Raw sequencing data were processed using the CLC Genomics workbench 21 pipeline to generate FASTQ files
Sequences Were aligned to hg38 genome to gene expression count using CLC Genomics Workbench 21 default settings
Gene expression level of Refseq Coding Genes were Quantified using CLC Genomics Workbench 21 default settings
Assembly: hg38
Supplementary files format and content: features.csv.tar.gz: list of gene IDS
Supplementary files format and content: raw_counts.csv.tar.gz: gene expresion count data

source_name: Whole Blood

extract_protocol:
RNA was extracted from whole blood using the QIAamp RNA blot mini kit
Transcriptome sequencing libraries were prepare with Ilumina stranded mRNA prep, Ligation

value: Whole Blood

tag: group

value: Mild


title: Mild,24


title: Mild,25


title: Mild,22


title: SAM24425284


title: Moderate-Severe,25

value: Moderate-Severe


title: SAM24433834

tag: condition

value: Astrocytes conditioned


title: SAM24433833

value: Home brew media


title: SAM24425283


title: SAM24425282


title: Mild,20


title: Mild,21


title: SAM24433832


title: Mild,18


title: Mild,19


title: SAM24433830


title: Mild,16


title: Mild,17


title: SAM24433831


title: SAM24433828


title: Moderate-Severe,24


title: SAM24425286


title: SAM24433829


title: SAM24433826

value: Astrocytes co-culture


title: Mild,14


title: Moderate-Severe,23


title: SAM24433827


title: Mild,13


title: HA-progerin HEK293cells gSTXBP5_rep1

city: Tianjin

first: Jinchao

last: Liu

address: Tongyan Road

institute: Nankai University

data_processing:
Illumina RTA software were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed by Cutadapt.
the trimmed reads were mapped to the Ensembl human GRCh38 reference genome
Reads counts were calculated with featureCounts
Assembly: Ensembl human GRCh38 reference genome
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text file include raw count values for each Sample.

growth_protocol: HEK293 cells lines were cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum, 2mM L-glu-tamine and 1% penicillin-streptomycin at 37 °C in cell incubator containing 5% CO2,

extract_protocol:
For RNA-seq, total RNA was extracted by RNAiso Plus (Takara)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human embryonic kidney

value: STXBP5 knockdown


title: HA-progerin HEK293cells gSTXBP5_rep2


title: Moderate-Severe,22


title: HA-progerin HEK293cells gAAVS1_rep2

value: Control


title: Moderate-Severe,21


title: HA-progerin HEK293cells gAAVS1_rep1


title: Mild,10

value: MIld


title: Mild,12


title: Moderate-Severe,20


title: HA-progerin HEK293cells STXBP5_rep2

value: STXBP5 over-expressed


title: Mild,15


title: Mild,11


title: HA-progerin HEK293cells Control-OE_rep2


title: Mild,9


title: Moderate-Severe, 19


title: HA-progerin HEK293cells Control-OE_rep1


title: Mild,8


title: Normal1 [45368GYXZHX]

city: Zhengzhou

first: Xingyu

last: Fang

address: 1st Jianshe West street

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Sequencing was performed using an Illumina HiSeq2500 Analyzer (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.
Data filtering and analysis was controlled by Illumina's Data Collection software.
Reads were mapping with Spliced Mapping algorithm Hisat2 (Version :2.0.4) for sequence alignment on GRCh38 (hg38) reference.
Assembly: GRCh38 (hg38)
Supplementary files format and content: _FPKM
Supplementary files format and content: _counts

source_name: human testicular tissue

extract_protocol:
RNA was extracted using mir VanaTM miRNA Isolation kit (Cat# AM1561, Ambion) following the manufacturer’s instructions.Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
The library fragments were measured by Qubit® 2.0 Fluorometer and Agilent2100 was used to assess library quality.

value: human testicular tissue

tag: disease state

value: Normal


title: Moderate-Severe,17


title: NOA3 [46297XLWL]

value: Non-obstructive azoospermia (NOA)


title: Moderate-Severe,16


title: Moderate-Severe,15


title: SAM24433825


title: NOA1 [46837WJFL]


title: Moderate-Severe,13


title: Moderate-Severe,14


title: NOA2 [45455CCCC]


title: FgPH-1, in vitro MS-sucrose, 3dpi, biol rep 2

city: VILLENAVE D ORNON

first: Nadia

last: PONTS

state: Select State

address: 71 avenue E. Bourlaux

country: France

institute: INRAE

library_source: genomic

data_processing:
Sequenced reads were processed with BWA-MEM2 and FAN-C v0.9.26b2 to map read mates independently
Mate reads pairing using FAN-C v0.9.b2 pair
Generation of fragment-size hic contact maps with FAN-C v0.9.26b2
Assembly: reference genome for FgPH-1 obtained from FungiDB v58
Supplementary files format and content: sparse raw fragment-level matrices in tab-separated ext files

molecule: genomic DNA

organism: Fusarium graminearum

source_name: mycelium

growth_protocol: Fusarium graminearum PH-1 was grown for three days in modified liquid MS (glucose was substituted with sucrose).

extract_protocol:
Cultures were amended with 1.8 % formaldehyde final for 15 min prior harvest under constant agitation, and mycelia were collected by filtratiion before flash freezing in liquid nitrogen. Frozen fixed mycelium was ground for 4x45s at 30 Hz using a TissueLyzer (Qiagen) and placed on ice with 600 µL of HiC buffer (Tris-HCl pH8 15 mM, KCl 5 mM, NaCl 15 mM, MgCl2 3 mM, Igepal CA-630 0.2 %, Roche® cOmplete Mini EDTA-free protease inhibitor cocktail 1X) in 1.5 mL Diagenode microtubes. After eight cycles of gentle sonication (mode “low” – 15s ON/30s OFF) on a Bioruptor Standard Waterbath Sonicator (Diagenode), samples were filtered on Sefar Nitex (100 µm) by centrifugating 10 min at 4,700g and 4°C. Pellets were then carefully resuspended in one mL of nuclei buffer (Tris-HCl pH8 15 mM, sucrose 250 mM, KCl 5 mM, MgCl2 1 mM, glycerol 40 %, PMSF 1 mM, Roche® cOmplete Mini EDTA-free protease inhibitor cocktail 1X) and centrifuged at 7,000g for 5 min and 4°C. After a final wash with 0.5 mL of nuclei buffer, nuclei pellets were collected and stored at -80°C until in situ HiC sample preparation with the Arima-HiC technology, following the manufacturers protocol.
Arima Library Preparation using Swift Biosciences® Accell-NGS® 2S Plus DNA Library Kit and the KAPA Library Amplification Kit with Primer Mix, following the manufacturer’s instructions

value: mycelium

value: WT

value: in vitro MS-sucrose, 3dpi


title: FgPH-1, in vitro MS-sucrose, 3dpi, biol rep 1


title: Moderate-Severe,12

value: Whole Blood


title: Moderate-Severe,11


title: HA-progerin HEK293cells STXBP5_rep1


title: Normal3 [WXW]


title: Moderate-Severe,9


title: WT_95

city: Oklahoma City

first: Willard

last: Freeman

address: 825 NE 13th St

institute: Oklahoma Medical Research Foundation

data_processing:
Reads were trimmed and aligned before differential expression statistics and correlation analyses in Strand NGS software package (v4.0; Strand Life Sciences).
Samples with reads were aligned against the full mm10 transcriptome RefSeq build (2013.04.01). Alignment and filtering criteria included the following: adapter trimming, fixed 5-bp trim from 5′ and 3′ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum 5% gap, and trimming of 3′ ends with Q < 30.
All duplicate reads were then removed. Normalization was performed with the DESeq2 algorithm. Transcripts with an average read count value ≥ 1 in at least 30% of the cells in at least one group were considered expressed at a level sufficient for quantitation.
For statistical analysis of differential expression, a t-test with Benjamini–Hochberg multiple testing correction (BHMTC) was performed with a False Discovery Rate cutoff of <0.1. For those transcripts meeting this statistical criterion, an absolute fold change > 1.25 cutoff was used to eliminate those genes that were statistically significant but unlikely to be biologically significant and orthogonally confirmable because of their very small magnitude of change.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing RPKM values for each sample.

source_name: Neuron

extract_protocol:
Patch-seq required slight modifications to recording parameters to minimize confounds in both electrophysiological recordings and sequencing. Patch-seq internal was a modification of whole-cell internal solution containing (in mM) 124 K gluconate, 10 HEPES, 5 KCl, 5 MgCl2, 0.1 EGTA, 0.075 CaCl2, 20 µg/mL glycogen, and 0.5 units/µL RNase inhibitor (M0314L, New England Biolabs). The voltage step protocol used to measure the tail current was unchanged. To minimize recording time before cell extraction, additional electrophysiological parameters were not recorded. After recording was complete, light negative pressure was applied to the pipette until the nucleus was visible at the tip of the pipette, or for approximately three minutes. Next, the recording pipette was slowly retracted along the Z-axis. Successful extractions included an obvious nucleated patch67. After the nucleus was visualized above the slice, the pipette was rapidly retracted from the bath, and the cellular contents within the pipette were deposited in a 0.2 mL PCR tube containing 0.5 µL of NEB Next lysis buffer and 0.25 µL NEB murine RNase inhibitor. Tube contents were then rapidly spun down and flash frozen on dry ice. Samples were stored at -80°C until RNAseq libraries were generated.
Directional libraries were constructed using NEBNext Single Cell/Low Input RNA Library Prep Kits from Illumina following manufacturer instructions. In brief, poly-adenylated mRNA was magnetically captured and then eluted from the oligo-dT beads. mRNA was then fragmented and reverse-transcribed, and the cDNA was purified using SPRISelect beads (#B23318, Beckman Coulter). Purified cDNA was eluted in 50 μL 0.1 × TE buffer. Adaptors were diluted and ligated to cDNA, and the cDNA was amplified by 28 cycles of PCR. SPRISelect beads were used to select for proper library size. Purified library quality was then assessed on a tapestation (#4200, Agilent Technologies) using HSD1000 screentapes (#5067–5584; Agilent Technologies). Due to the high number of amplification cycles, occasionally libraries required additional rounds of SPRISelect purification. Qubit 1 × dsDNA HS Assay kit (#Q33230, Thermo Fisher Scientific) was used to quantify libraries. Libraries were pooled and sequenced 2x 100 bases on an Illumina MiSeq. Fastq data will be made available on the gene expression omnibus (GEO) upon acceptance.

value: Neuron

tag: library prep_kit

value: NEBNext Single Cell/Low Input RNA Library Prep Kits for Illumina


title: Normal2 [41429XXY]


title: WT_9


title: WT_94


title: WT_8


title: WT_96


title: Moderate-Severe,7

value: Moderate-Severe


title: Moderate-Severe,18


title: Moderate-Severe,8


title: WT_7


title: Moderate-Severe,6


title: WT_73


title: Moderate-Severe,5


title: Mild,7

value: Mild


title: WT_74


title: WT_72


title: Mild,6


title: WT_71


title: Mild,5


title: Mild,4


title: WT_6


title: Moderate-Severe,10


title: WT_69


title: WT_68


title: Mild,3


title: Mild,2


title: Mild,1


title: WT_66


title: WT_67


title: Moderate-Severe,4


title: WT_65


title: Moderate-Severe,3


title: Moderate-Severe,1


title: WT_64


title: WT_60


title: Moderate-Severe,2


title: WT_63


title: myo_4 [ATAC]

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

description: genomic DNA from mouse kidneytubuloids, treated with myoglobin

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 3.0.0a7 with FDR < 0.0001 (Zhang et al., Model-based Analysis of ChIP-Seq).
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
Remaining peaks were unified to represent a common set of regions for all samples.
Counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the promoter (TSS +- 5000 nt) of the nearest gene based on Ensembl release 101.
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts

source_name: kidney

growth_protocol: The kidney cortex of mice was dissected, digested, and dissociated. Tubuloids were grown in Matrigel.

extract_protocol:
50,000 cells were centrifuged at 500 g for 5 min at 4°C and washed with PBS. The cell pellet was resuspended in 50 µl lysis/transposition reaction (12.5 µl THS-TD-Buffer, 2.5 µl Tn5, 5 µl 0.1% digitonin and 30 µl water) and incubated at 37°C for 30 min with occasional snap mixing. DNA fragments were purified by MinElute PCR Purification Kit (Qiagen).
Library fragments were amplified together with indexing primers (1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2).

treatment_protocol: Mouse kidney tubuloids were treated without or with myoglobin. After 12 hours, tubuloids were subjected to ATAC-seq.

value: kidney

value: primary tubuloids

value: renal tubular epithelial cells

value: wildtype

value: myoglobin


title: WT_5


title: Young_CD8, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
After obtaining all 4 expression sequencing datasets we first analyzed the data using CellRanger (version 6.0.0) software from 10X Genomics. The single-cell expression data were then imported into R and integrated with Seurat (version 3.2.3). To minimize information loss and filter out low-quality and duplicated cells at the same time, genes expressed in at least 2 cells were kept, and cells with more than 100 but less than 4000 genes were kept. In addition, violin plot was made by the percentage of mitochondrial genes, and cells that were discrete in the violin plot were filtered out. The filtered cells were then integrated, normalized, scaled and clustered with Seurat. Cell type annotation was then performed using classic immune cell markers.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Tumor tissues were collected and cut into small pieces (approximately 1-2 mm). Then, we digested the tumor tissues with a mouse tumor dissociation kit (Miltenyi/MACS, 130-096-730) following the standard procedure. After that, the cell suspension was filtered with a 30 μm MACS SmarterStrainer. Then, we performed either FACS analysis or FACS sorting (sorting for CD45+CD8+T cells).
The cell suspension samples we obtained with this procedure were used for single-cell library construction. We performed single-cell immune profiling following the standard procedure from 10X Genomics. .Briefly, CD8+T cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10X Barcode.The pooled barcodeed cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for the subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: CD8+T cells

value: Tumor

tag: age

value: 8-10 weeks old


title: Aged_CD8, scRNAseq

description: 10x Genomics


title: IT_InterstitialMacrophages_gex_rep1

first: Sandra

last: Melo

institute: Genentech, Inc.

data_processing:
Alignment with STARSolo as implemented in Cumulus version 2.4.1. Settings “tenX_5p” to indicate 10X 5’ assay, and “Gene Velocyto” to obtain spliced/unspliced matrices
Alignment of barcodes with Cumulus (version 2.4.1)
Demultiplexing was performed with DemuxEM as implemented in Cumulus version 2.4.1
Assembly: mm10
Supplementary files format and content: h5ad format. They have the gex raw and normalized counts, the normalized cite-seq counts, the hto assignments, the cluster assignments, and the latent spaces and umaps.

molecule: polyA RNA

extract_protocol:
Lung lobes were collected making sure to separate them from the trachea and lymph nodes. Lungs were minced and then digested in 1-5ml of complete RPMI containing 25ug/ml of liberase (Roche) and 0.1mg/ml of DNAseI (Roche) in incubator at 37C for 30 minutes with gentle shaking. Samples were then mashed through 70um filters, centrifuged and red blood cells were lysed using ACK buffer (Gibco). Cell numbers were counted using Vicell cell counter, and aliquots from each sample were stained with fluorescent and citeSeq/hashtag antibodies before flow sorting.
DNA from antibody-derived tags (ADTs) was separated from cDNA based on size selection using SPRIselect beads (Beckman Coulter, cat. B23318) and cDNA was used to generate Gene expression libraries. ADT/HTO libraries were generated using 5' Feature Barcode Kit, (10Xgenomics PN-1000256). Gene expression and ADT/HTO libraries were then profiled using the Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, cat. 5067-4626) and quantified with Kapa Library Quantification Kit (Roche, cat. 07960255001). Illumina HiSeq and NovaSeq (Illumina) were used to sequence the libraries.

tag: protocol

value: WT mice were treated with a blocking anti-Notch2-antibody or control (both 15 mg/mkg, passive intratracheal inhalation) at days -14 and -7 before take down.

value: lung

value: Interstitial Macrophages

value: mixed (ctrl, aNotch2)

tag: library type

value: mRNA


title: WT_59

value: Neuron

value: WT


title: myo_3 [ATAC]


title: IT_Monocytes_gex_rep1

value: Monocytes


title: IT_AlveolarMacrophages_gex_rep1

value: Alveolar Macrophages


title: myo_2 [ATAC]

value: kidney


title: IT_AlveolarMacrophages_adt_rep1

description:
Hash 1-5: ctrl antibody IT; Hash 6-10: antiNotch2 antibody IT
IT.h5ad

library_source: other

data_processing:
Alignment with STARSolo as implemented in Cumulus version 2.4.1. Settings “tenX_5p” to indicate 10X 5’ assay, and “Gene Velocyto” to obtain spliced/unspliced matrices
Alignment of barcodes with Cumulus (version 2.4.1)
Demultiplexing was performed with DemuxEM as implemented in Cumulus version 2.4.1
Assembly: mm10
Supplementary files format and content: h5ad format. They have the gex raw and normalized counts, the normalized cite-seq counts, the hto assignments, the cluster assignments, and the latent spaces and umaps.
Library strategy: CITE-seq

molecule: protein

value: ADT

tag: adt

value: TotalSeq™-C0987 anti-Allophycocyanin (APC) Antibody

tag: hto

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody, up until, TotalSeq™-C0310 anti-mouse Hashtag 10 Antibody


title: WT_58

value: NEBNext Single Cell/Low Input RNA Library Prep Kits for Illumina


title: IP_Bleo_InterstitialMacrophages_hto_rep1

description:
Hash 1: Saline mice, ctrl antibody; Hash 3: saline mice, aNotch2 antibody; Hash2, 4, 5, 6: Bleo mice, ctrl Antibody; Hash 7-10: Bleo mice, aNotch2 antibody
IP_Bleo.h5ad

value: Adult mice (older than 12 weeks) were randomized based on their weights before the study to minimize variance between experimental and control groups. Mice were treated with a blocking anti-Notch2-antibody or control (both 20 mg/mkg, ip) at days -14 and -7. and bleomycin was administered via Oropharyngeal intratracheal (IT) dosing on days 0, 2, and 4 at 0.24 U/kg (DNC 0703-3155-01; TEVA). Mice were taked down on day 9.

tag: tissue

value: HTO


title: IT_Monocytes_adt_rep1

tag: genotype


title: myo_1 [ATAC]

value: primary tubuloids

tag: cell type

value: renal tubular epithelial cells

value: wildtype

value: myoglobin


title: veh_4 [ATAC]

description: genomic DNA from mouse kidneytubuloids, vehicle-treated

tag: treatment

value: vehicle


title: IP_Bleo_InterstitialMacrophages_hto_rep2

value: Interstitial Macrophages

value: mixed (ctrl, aNotch2)


title: veh_3 [ATAC]

tag: cell line


title: WT_2

value: Neuron

value: WT


title: veh_2 [ATAC]


title: WT_22


title: WT_21


title: Pre-GMP-1_2_3

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

description: UDiTaS

data_processing:
Analysis was performed by https://github.com/editasmedicine/uditas.
The UDTIAS experiments are genome-wide profiling. However, a primer was used to linearly amplify sequences around cas9 cut positions. There are only a few SV events.
Assembly: hg38
Supplementary files format and content: SV_frequency.csv is the result out from the UDITAS analysis.
Supplementary files format and content: sample_info.csv files provides the sample information, such as gRNA locations, for the UDITAS analysis.
Library strategy: UDiTaS

source_name: Human peripheral blood

extract_protocol:
CD34+ HSPCs edited with Cas9-3xNLS targeting HBG promoter, cultured in X-VIVO media with cytokines, and harvested cells at days 5 and 14 after electroporation (pre-GMP engineering runs, n=3). Genomic DNA extracted from control and edited cells using Agencourt DNAdvance according to manufacturer’s protocol.
A custom Tn5-transposome with the full-length Illumina forward (i5) adapter, a sample barcode, and unique molecule identifier was used for the genomic DNA tagmentation reaction. After genomic DNA tagmentation, two rounds of PCRs were performed. The first PCR was performed using the target-specific HBG promoter anchor primer, and the second round of PCR added with the reverse (i7) Illumina adapter and an additional sample barcode. Two primers targeting HBG1 and HBG2 gene promoters were used in parallel for the first PCR. For positive control, gene-specific primers designed for both BCL11A and HBG promoter complete libraries were then size selected for 400–850 bp using PippinHT, quantified by qPCR, and sequenced on Illumina MiSeq with paired-end 301-8-18-301 cycles.

value: Human peripheral blood

value: Human HSPCs


title: IP_Bleo_AlveolarMacrophages_hto_rep1

value: Alveolar Macrophages


title: g34_bcl11a

description: UDiTaS


title: WT_20


title: IP_Bleo_Monocytes_hto_rep2

value: Monocytes


title: IP_Bleo_Monocytes_hto_rep1

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody, up until, TotalSeq™-C0310 anti-mouse Hashtag 10 Antibody


title: veh_1 [ATAC]

value: kidney


title: myo-dex_4

description: total RNA from mouse kidneytubuloids, treated with myoglobin and dexamethasone

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.27.4 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.3 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

extract_protocol:
Total RNA was isolated from tubuloids using the miRNeasy Micro Kit (Qiagen, cat. no. 217084) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen, cat. no. 79254) to avoid contamination by genomic DNA.
Total RNA (1 µg) was used as input for VAHTS Stranded mRNA-seq V6 Library preparation following the manufacturer’s protocol (Vazyme).

treatment_protocol: Mouse kidney tubuloids were treated without or with myoglobin and dexamethasone. After 12 hours, total RNA was extracted from tubuloids and subjected to RNA-seq.

value: dexamethasone + myoglobin


title: WT_1

value: NEBNext Single Cell/Low Input RNA Library Prep Kits for Illumina


title: myo-dex_3

value: primary tubuloids


title: Phf19_KO

data_processing:
Sequence reads were trimmed using trimmomatic
Sequence reads were mapped to mm10 reference genome using star
Sequence reads were count using htseq-count as gencode VM25.gtf model.
Differential gene expression analysis was detected using Bioconductor DESeq2 package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample ...

tag: strain

value: spleen

value: Germinal Center B cells


title: Phf19_WT


title: IP_Monocytes_gex_rep2

value: WT mice were treated with a blocking anti-Notch2-antibody or control (both 20 mg/mkg, ip) at days -14 and -7 before take down.

value: lung

value: mRNA


title: WT_57


title: myo-dex_2

value: renal tubular epithelial cells

value: wildtype


title: IT_InterstitialMacrophages_adt_rep1

value: WT mice were treated with a blocking anti-Notch2-antibody or control (both 15 mg/mkg, passive intratracheal inhalation) at days -14 and -7 before take down.

value: Interstitial Macrophages

value: mixed (ctrl, aNotch2)

value: ADT

value: TotalSeq™-C0987 anti-Allophycocyanin (APC) Antibody


title: 22Rv-1 cells,lv-shARv7 3

city: Changchun

first: Chen

last: Shao

state: Jilin

address: 126 Xinmin ST

institute: Jilin University

data_processing:
RNA-sequencing reads were first trimmed to remove poly(A) and unqualified reads with Cutadapt(v2.7).
Assembly: hg18
Supplementary files format and content: txt,expression matrix

growth_protocol: C4-2, and 22RV1 cells were cultured in RPMI 1640 medium (Gibco Life Technologies, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum, 100 U/ ml penicillin, and 100 U/ml streptomycin in 5% CO2 at 37°C

extract_protocol:
Cells were plated in 10-cm dishes at a density of 1.5 × 106 cells/dish in triplicate and incubated overnight for attachment. They were lysed with TRIzol Reagent according to the manufacturers' instructions. The lysates were sent to Personalbio (Shanghai, China) for cDNA library construction and sequencing by Illumina NovaSeq 6000
The lysates were sent to Personalbio (Shanghai, China) for cDNA library construction and sequencing by Illumina NovaSeq 6000. RNA-sequencing reads were first trimmed to remove poly(A) and unqualified reads with Cutadapt(v2.7).

value: prostate cancer cells

value: ARv7 depletion

value: infected with lentivirus


title: WT_18

value: Neuron

value: WT

value: NEBNext Single Cell/Low Input RNA Library Prep Kits for Illumina


title: IP_AlveolarMacrophages_gex_rep1

value: Alveolar Macrophages


title: WT_17


title: myo-dex_1

value: kidney

value: primary tubuloids

value: dexamethasone + myoglobin


title: IP_AlveolarMacrophages_gex_rep2

value: WT mice were treated with a blocking anti-Notch2-antibody or control (both 20 mg/mkg, ip) at days -14 and -7 before take down.

value: lung

value: mRNA


title: 22Rv-1 cells,lv-shARv7 2


title: IP_Bleo_AlveolarMacrophages_hto_rep2

value: Adult mice (older than 12 weeks) were randomized based on their weights before the study to minimize variance between experimental and control groups. Mice were treated with a blocking anti-Notch2-antibody or control (both 20 mg/mkg, ip) at days -14 and -7. and bleomycin was administered via Oropharyngeal intratracheal (IT) dosing on days 0, 2, and 4 at 0.24 U/kg (DNC 0703-3155-01; TEVA). Mice were taked down on day 9.

value: HTO

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody, up until, TotalSeq™-C0310 anti-mouse Hashtag 10 Antibody


title: 22Rv-1 cells,lv-shARv7 1


title: WT_16


title: myo_4

description: total RNA from mouse kidneytubuloids, treated with myoglobin

value: renal tubular epithelial cells

value: wildtype

value: myoglobin


title: IP_Monocytes_gex_rep1

value: Monocytes

value: mixed (ctrl, aNotch2)


title: 22Rv-1 cells,lv-shcontrol 3

value: prostate cancer cells

value: vector control

value: infected with lentivirus


title: 22Rv-1 cells,lv-shcontrol 2


title: IP_InterstitialMacrophages_gex_rep2

value: Interstitial Macrophages


title: myo_3

value: kidney

value: primary tubuloids


title: WT_15

value: Neuron

value: WT

value: NEBNext Single Cell/Low Input RNA Library Prep Kits for Illumina


title: WT_14


title: Setd2_KO_INPUT_H3K36me3

data_processing:
Data were filtered using the Trimgalore with default model
CUT&TAG and ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 with  end to end ,very sensitive , no mixed, no discordant, -I 10 ,-X 700 model
Replication reads were discarded using picard with default model
bigwig files were product using deeptools using ignoreDuplicates model
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

extract_protocol:
For cuttag lysates were clarified using HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech Co., Ltd)  TD901-TD902 and histone-DNA complexes were isolated with antibody. For H3K27me3 chipseq,  the chromatin was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against H3K27me3. For H3K36me3 chipseq, the chromatin was prepared and followed by ChIP-Seq analysis by Shanghai Jiayin Biotechnology Co., Ltd, using the antibody against H3K36me3.
For cuttag libraries were prepared according to TruePrep® Index Kit V2 for Illumina®. For H3K27me3 and H3K36me3 Chipseq, libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: Germinal Center B cells

value: setd2 KO

tag: chip antibody

value: none (input)


title: WT_11


title: myo_1

value: renal tubular epithelial cells

value: wildtype


title: Setd2_WT_INPUT_H3K36me3

value: setd2 WT


title: C4-2 cells,lv-ARv7 3

value: ARv7 overexpression


title: 22Rv-1 cells,lv-shcontrol 1

value: prostate cancer cells


title: veh_4

description: total RNA from mouse kidneytubuloids, vehicle-treated

value: vehicle


title: Setd2_KO_H3K36me3


title: 3xTg_92


title: veh_3


title: C4-2 cells,lv-ARv7 2

value: infected with lentivirus


title: 3xTg_91


title: C4-2 cells,lv-ARv7 1


title: veh_2


title: IP_InterstitialMacrophages_gex_rep1

value: WT mice were treated with a blocking anti-Notch2-antibody or control (both 20 mg/mkg, ip) at days -14 and -7 before take down.

value: lung

value: Interstitial Macrophages

value: mixed (ctrl, aNotch2)

value: mRNA


title: 3xTg_90

value: Neuron

value: NEBNext Single Cell/Low Input RNA Library Prep Kits for Illumina


title: Wildtype cornea from sample C8

city: Newark

first: Aarthi

last: Krishnan

state: DE

address: 18 Marvin Dr, Apt A2

department: Biology

institute: University of Delaware

data_processing:
Reads were trimmed for adaptor content, quality using "TrimGalore". The parameters used are-
Aligning was done usign Hisat2 with the following parameters-
Sorting of the aligned reads was done usign samtools sort by position
Quantification of the aligned reads was doen using Htseq-count with the followign parameters- -I gene_id -f bam -s reverse  -m union --type exon
EdgeR was used to analyze gene level counts
Genome_build: GRCm38, GTF File :Mouse Ensembl version 101
Supplementary_files_format_and_content: Htseq Count Tables - tab delimited text (files ending in _Count.txt), Tab Separated, Column 1: Ensembl Gene ID, Column 2: Count

source_name: PAX6 CORNEA

extract_protocol:
The cornea cells were harvested using Promega SV Total RNA Isolation System Catalog # Z3100
SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian v2 (Takara Bio USA, Inc.,  Mountain View, CA, USA).  Paired end 100 nucleotide reads

value: Cornea

value: 20 weeks

value: WT


title: C4-2 cells,lv-control 3

value: vector control


title: myo_2

value: kidney

value: primary tubuloids

value: renal tubular epithelial cells

value: wildtype

value: myoglobin


title: veh_1

value: vehicle


title: Wildtype cornea from sample C7


title: 3xTg_89


title: C4-2 cells,lv-control 2

value: prostate cancer cells

value: infected with lentivirus


title: Wildtype cornea from sample C


title: 3xTg_85


title: WT_10


title: IP_Bleo_InterstitialMacrophages_gex_rep2

value: Adult mice (older than 12 weeks) were randomized based on their weights before the study to minimize variance between experimental and control groups. Mice were treated with a blocking anti-Notch2-antibody or control (both 20 mg/mkg, ip) at days -14 and -7. and bleomycin was administered via Oropharyngeal intratracheal (IT) dosing on days 0, 2, and 4 at 0.24 U/kg (DNC 0703-3155-01; TEVA). Mice were taked down on day 9.

value: Interstitial Macrophages


title: IP_Bleo_InterstitialMacrophages_gex_rep1

value: mixed (ctrl, aNotch2)

value: mRNA


title: C4-2 cells,lv-control 1


title: 3xTg_84

value: Neuron

value: NEBNext Single Cell/Low Input RNA Library Prep Kits for Illumina


title: IP_Bleo_AlveolarMacrophages_gex_rep1

value: Alveolar Macrophages


title: Heterozygous mutant PAX6 cornea from sample 20

value: Cornea

value: 20 weeks

value: Heterozygous mutant PAX6


title: hMSCs,Ru-Cu/EDHJ+H2O2-3

city: Chengdu

first: Mingru

last: Bai

address: Renmin Road No.14

institute: Sichuan University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: bone

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: bone

value: mesenchymal stem cells


title: Setd2_WT_H3K36me3

first: Yuchao

last: Jing

institute: Nanjing Medical University

value: spleen

value: Germinal Center B cells

value: setd2 WT


title: 3xTg_82


title: hMSCs, Ru-Cu/EDHJ+H2O2-2


title: 3xTg_81


title: hMSCs, Ru-Cu/EDHJ+H2O2-1


title: IP_Bleo_Monocytes_gex_rep1

value: Monocytes


title: Heterozygous mutant PAX6 cornea from sample 19


title: 3xTg_79


title: IP_Bleo_AlveolarMacrophages_gex_rep2


title: CHP134 E2F1Cr cells, T1-44 treated, biological replicate 3

city: St. Petersburg

first: Alexander

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

country: Russia

institute: St Petersburg Universoty

data_processing: none provided

growth_protocol: CHP134 and GIMEN cells were maintained in DMEM supplemented with 10% FBS and penicillin/streptomycin antibiotics in a humidified atmosphere with 5% CO2 at 37ºC

extract_protocol:
RNA was extracted using TRIzol.  1ug of RNA was used to construct sequencing libraries
oligo dT based mRNA enrichment was used prior to RNA fragmentation and reverse transcription with random N6 primer. Second strand synthesis was performed. End repair and addition of A and adaptor ligation proceeded PCR amplification.  Single strands were heat separated and circularised for DNA nanoball synthesis and sequencing on DNBseq platform

treatment_protocol: CHP134 and GIMEN cells were treated with 200nM PRMT5 inhibitor (T1-44) or DMSO control for 48h

value: neuroblastoma

value: E2F1 CRISPR


title: 3xTg_78


title: IP_BleoMonocytes_gex_rep2

value: Adult mice (older than 12 weeks) were randomized based on their weights before the study to minimize variance between experimental and control groups. Mice were treated with a blocking anti-Notch2-antibody or control (both 20 mg/mkg, ip) at days -14 and -7. and bleomycin was administered via Oropharyngeal intratracheal (IT) dosing on days 0, 2, and 4 at 0.24 U/kg (DNC 0703-3155-01; TEVA). Mice were taked down on day 9.


title: CHP134 E2F1Cr cells, T1-44 treated, biological replicate 2


title: hMSCs, CeO2+H2O2-3


title: Pre-GMP-3_edit_2

description:
CHANGE-seq
GM012

data_processing:
Data was analyzed using https://github.com/tsailabSJ/changeseq
092123.yaml is the input file for the program
Assembly: hg38
Supplementary files format and content: yaml and csv
Library strategy: CHANGE-seq

extract_protocol:
CD34+ HSPCs edited with Cas9-3xNLS targeting HBG promoter, cultured in X-VIVO media with cytokines, and harvested cells at day 5 after electroporation. Genomic DNA extracted from control and edited cells using Agencourt DNAdvance according to manufacturer’s protocol.
Genomic DNA from edited CD34+ normal cells or unedited control cells (Pre-GMP engineering runs, n = 3) used to perform CHANGE-seq. Pooled libraries were sequenced with 151 bp paired end reads on Illumina Novaseq 2000.

value: Human peripheral blood

value: Human HSPCs


title: hMSCs, CeO2+H2O2-2


title: Heterozygous mutant PAX6 cornea from sample 21


title: CHP134 E2F1Cr cells, T1-44 treated, biological replicate 1


title: Pre-GMP-3_edit_1

description:
CHANGE-seq
GM011


title: hMSCs, CeO2+H2O2-1


title: CHP134 WT cells, T1-44 treated, biological replicate 3

value: WT


title: 3xTg_77

value: Neuron

value: NEBNext Single Cell/Low Input RNA Library Prep Kits for Illumina


title: Pre-GMP-3_control_2

description:
CHANGE-seq
GM010


title: 3xTg_55


title: 3xTg_76


title: CHP134 WT cells, T1-44 treated, biological replicate 2


title: hMSCs, H2O2-2


title: Pre-GMP-3_control_1

description:
CHANGE-seq
GM009


title: CHP134 WT cells, T1-44 treated, biological replicate 1


title: hMSCs, H2O2-1


title: 3xTg_53


title: 3xTg_50


title: hMSCs, Ctrl-3

value: Ctrl


title: Pre-GMP-2_edit_2

description:
CHANGE-seq
GM008


title: CHP134 E2F1 Cr cells, DMSO treated, biological replicate 3

value: DMSO


title: CHP134 E2F1 Cr cells, DMSO treated, biological replicate 2


title: Pre-GMP-2_edit_1

description:
CHANGE-seq
GM007


title: 3xTg_49


title: Pre-GMP-2_control_2

description:
CHANGE-seq
GM006


title: hMSCs, Ctrl-2


title: hMSCs, Ctrl-1


title: 3xTg_48


title: CHP134 E2F1 Cr cells, DMSO treated, biological replicate 1


title: CHP134 WT cells, DMSO treated, biological replicate 3


title: 3xTg_45


title: hMSCs, H2O2-3


title: iP11N-d56-DM-Rep2

data_processing:
Data were processed using the Cell Ranger ARC analysis pipeline. Reads were aligned to the genome with cellranger-arc mkfastq with introns included. Counts were generated using cellranger-arc count. For the purpose of this study, we only utilized the RNA assay of this data.
Cell barcodes from empty droplets were filtered by requiring a minimum number of detected transcripts. Sample quality was further assessed based on the distribution of per-cell statistics, such as total number of reads, percentage of reads mapping uniquely to the reference genome, percentage of mapped reads overlapping exons, number of detected transcripts (UMIs), number of detected genes, and percentage of mitochondrial transcripts.
Assembly: GRCh38
Supplementary files format and content: Raw counts mtx files

extract_protocol: Dual assay libraries were generated with the 10X Chromium Single Cell Multiome ATAC + Gene Expression kit following manufacturer's user guide. cDNA amplification was done with 10 cycle PCR, and sample index PCR was done with 12 cycles. Libraries were sequenced by NovaSeq6000 or NextSeq2000 (Illumina) following 10X Genomics sequencing specification.

tag: day

tag: media


title: Pre-GMP-1_edit_2

description:
CHANGE-seq
GM004


title: 3xTg_43


title: iP11N-d56-DM-Rep1


title: CHP134 WT cells, DMSO treated, biological replicate 1


title: 3xTg_42


title: CHP134 WT cells, DMSO treated, biological replicate 2


title: Pre-GMP-2_control_1

description:
CHANGE-seq
GM005


title: Pre-GMP-1_control_2

description:
CHANGE-seq
GM002


title: GIMEN cells, T1-44 treated, biological replicate 3

source_name: GIMEN

value: GIMEN


title: 3xTg_40


title: 3xTg_41


title: GIMEN cells, T1-44 treated, biological replicate 2


title: G12-d28-DM-Rep2


title: G12-d28-DM-Rep1


title: 3xTg_39


title: Pre-GMP-1_control_1

description:
CHANGE-seq
GM001


title: iP11N-d28-DM-Rep2


title: GIMEN cells, T1-44 treated, biological replicate 1


title: iP11N-d28-DM-Rep1


title: 3xTg_38


title: CHP134 cells, T1-44 treated, biological replicate 3


title: IP_Monocytes_adt_rep1

description:
Hash 1-4: cells from control treated lungs; Hash 5+6: cells from aNotch2 treated mice
IP.h5ad

value: WT mice were treated with a blocking anti-Notch2-antibody or control (both 20 mg/mkg, ip) at days -14 and -7 before take down.

value: lung

value: mixed (ctrl, aNotch2)

value: ADT

value: TotalSeq™-C0431 anti-mouse CD170 (Siglec-F) Antibody, TotalSeq™-C0987 anti-Allophycocyanin (APC) Antibody, TotalSeq™-C0117 anti-mouse I-A/I-E Antibody, TotalSeqC CD206 Antibody (TCAACTCGGTGTTGC), custom TotalSeqC LYVE-1 (ALY7) antibody (ATCTGCGAGTCAGTC), TotalSeq™-C0090 Mouse IgG1, κ isotype Ctrl Antibody, TotalSeq™-C0095 Rat IgG2b, κ Isotype Ctrl Antibody, https://www.biolegend.com/en-us/products/totalseq-c0238-rat-igg2a-k-isotype-ctrl-19263, https://www.biolegend.com/en-us/products/totalseq-c0236-rat-igg1-kappa-isotype-ctrl-antibody-19603

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody, up until, TotalSeq™-C0306 anti-mouse Hashtag 6 Antibody


title: IP_Monocytes_adt_rep2

value: Monocytes

value: TotalSeq™-C0431 anti-mouse CD170 (Siglec-F) Antibody, TotalSeq™-C0987 anti-Allophycocyanin (APC) Antibody, TotalSeq™-C0117 anti-mouse I-A/I-E Antibody, TotalSeqC CD206 Antibody (TCAACTCGGTGTTGC), custom TotalSeqC LYVE-1 (ALY7) antibody (ATCTGCGAGTCAGTC), TotalSeq™-C0090 Mouse IgG1, κ isotype Ctrl Antibody, TotalSeq™-C0095 Rat IgG2b, κ Isotype Ctrl Antibody, https://www.biolegend.com/en-us/products/totalseq-c0238-rat-igg2a-k-isotype-ctrl-19263, https://www.biolegend.com/en-us/products/totalseq-c0236-rat-igg1-kappa-isotype-ctrl-antibody-19602


title: CHP134 cells, T1-44 treated, biological replicate 2

value: neuroblastoma


title: 786-O, DEK KO, rep2 RNA

city: Shenzhen

first: Wei

last: Chen

state: Guangdong

address: No. 1088 Xueyuan Avenue, Nanshan District

department: School of Life Sciences

institute: Southern University of Science and Technology

data_processing:
First, adapters were removed by cutadapt v 1.18 with parameters -m 20 -q 20,20.
Then, the clean reads were aligned by STAR v 2.7.8a against the human hg38 genome using GENCODE v37 annotations with parameters --runMode alignReads --alignEndsType Local --outFilterMultimapNmax 1.
unique-mapped read counts among genes were calculated using featureCounts(v 2.0.1) with parameters -t exon -g gene_name -s 2.
To obtain differential expressed genes(DEGs), DESeq2(v1.36.0) was applied to fit the raw counts by negative binomial model and perform the statistical test.
The bigWig files were generated from BAM files by home-made script and visualized by Integrative Genomics Viewer (IGV, https://software.broadinstitute.org/software/igv/).
Assembly: hg38
Supplementary files format and content: bigWig, comma-separated values (CSV) file include TPM values for each sample.

growth_protocol: 786-O cells were cultured in the 1640 media with 10% FBS (Gibco, #10270106) and 1% P/S (Gibco, #15070063) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted by TRIzol® Reagent (Ambion).
mRNA sequencing libraries were prepared according to the standard protocol provided by Hieff NGS® Ultima Dual-mode RNA Library Prep Kit (YEASEN, #12309ES96) with starting material of 1ug total RNA.

treatment_protocol: The Cas9-expressing cell clone was established by using LentiCas9-Blast virus. To generate KO cell clones, Cas9-expressing cells were infected with LentiGuide-Puro virus expressing DEK gRNAs and and single cell sorting.

value: human renal carcinoma

value: DEK KO


title: Pre-GMP-1_edit_1

description:
CHANGE-seq
GM003

value: Human peripheral blood

value: Human HSPCs


title: 3xTg_37

value: Neuron

value: NEBNext Single Cell/Low Input RNA Library Prep Kits for Illumina


title: 786-O, DEK KO, rep1 RNA


title: 3xTg_36


title: iP11N-d42-DM-Rep2


title: CHP134 cells, T1-44 treated, biological replicate 1

value: WT


title: 786-O, negative control, rep2 RNA


title: IP_InterstitialMacrophages_adt_rep1

value: Interstitial Macrophages

value: TotalSeq™-C0431 anti-mouse CD170 (Siglec-F) Antibody, TotalSeq™-C0987 anti-Allophycocyanin (APC) Antibody, TotalSeq™-C0117 anti-mouse I-A/I-E Antibody, TotalSeqC CD206 Antibody (TCAACTCGGTGTTGC), custom TotalSeqC LYVE-1 (ALY7) antibody (ATCTGCGAGTCAGTC), TotalSeq™-C0090 Mouse IgG1, κ isotype Ctrl Antibody, TotalSeq™-C0095 Rat IgG2b, κ Isotype Ctrl Antibody, https://www.biolegend.com/en-us/products/totalseq-c0238-rat-igg2a-k-isotype-ctrl-19263, https://www.biolegend.com/en-us/products/totalseq-c0236-rat-igg1-kappa-isotype-ctrl-antibody-19599


title: GIMEN cells, DMSO treated, biological replicate 3

value: GIMEN

value: DMSO


title: GIMEN cells, DMSO treated, biological replicate 2


title: IP_AlveolarMacrophages_adt_rep2

value: WT mice were treated with a blocking anti-Notch2-antibody or control (both 20 mg/mkg, ip) at days -14 and -7 before take down.

value: lung

value: Alveolar Macrophages

value: mixed (ctrl, aNotch2)

value: ADT

value: TotalSeq™-C0431 anti-mouse CD170 (Siglec-F) Antibody, TotalSeq™-C0987 anti-Allophycocyanin (APC) Antibody, TotalSeq™-C0117 anti-mouse I-A/I-E Antibody, TotalSeqC CD206 Antibody (TCAACTCGGTGTTGC), custom TotalSeqC LYVE-1 (ALY7) antibody (ATCTGCGAGTCAGTC), TotalSeq™-C0090 Mouse IgG1, κ isotype Ctrl Antibody, TotalSeq™-C0095 Rat IgG2b, κ Isotype Ctrl Antibody, https://www.biolegend.com/en-us/products/totalseq-c0238-rat-igg2a-k-isotype-ctrl-19263, https://www.biolegend.com/en-us/products/totalseq-c0236-rat-igg1-kappa-isotype-ctrl-antibody-19600


title: 3xTg_35


title: 3xTg_32


title: IP_InterstitialMacrophages_adt_rep2

value: TotalSeq™-C0431 anti-mouse CD170 (Siglec-F) Antibody, TotalSeq™-C0987 anti-Allophycocyanin (APC) Antibody, TotalSeq™-C0117 anti-mouse I-A/I-E Antibody, TotalSeqC CD206 Antibody (TCAACTCGGTGTTGC), custom TotalSeqC LYVE-1 (ALY7) antibody (ATCTGCGAGTCAGTC), TotalSeq™-C0090 Mouse IgG1, κ isotype Ctrl Antibody, TotalSeq™-C0095 Rat IgG2b, κ Isotype Ctrl Antibody, https://www.biolegend.com/en-us/products/totalseq-c0238-rat-igg2a-k-isotype-ctrl-19263, https://www.biolegend.com/en-us/products/totalseq-c0236-rat-igg1-kappa-isotype-ctrl-antibody-19598

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody, up until, TotalSeq™-C0306 anti-mouse Hashtag 6 Antibody


title: GIMEN cells, DMSO treated, biological replicate 1

value: neuroblastoma


title: 3xTg_31


title: 786-O, negative control, rep1 ChIP

data_processing:
First, adapters were removed by cutadapt v 1.18 with parameters -m 20 -q 20,20.
The clean fragments were aligned to GRCh38/hg38 genome by Bowtie2(v 2.2.5) with parameters --very-sensitive -X 2000.
MACS2(v 2.2.7.1) was used to call peaks with parameters ‘callpeak -f BAMPE -g hs’.
R package Diffbind (v3.6.5) was used to analyze differential binding between biological groups with default pipelines. ChIPseeker(v1.32.1) was used to annotate peaks compared with the gene model(downloaded from GENCODE version 37, basic annotation).
Bigwig files were generated by bamCoverage from deepTools (v 3.5.1) package with parameters ‘--binSize 10 --normalizeUsing RPGC’.
Assembly: hg38
Supplementary files format and content: narrowPeak: peaks from MACS2; bigWig

extract_protocol:
The ChIP assay was performed according to the standard protocol provided by SimpleChIP Plus Sonication Chromatin IP Kit (CST)
Libraries were prepared using standard protocol provided by VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (Vazyme)

tag: antibody

value: DEK

value: human renal carcinoma


title: KO_CD8, scRNAseq

first: Siyu

last: Pei

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

description: 10x Genomics

data_processing:
We first analyzed the data using CellRanger (version 6.0.0) software from 10X Genomics. The single-cell expression data were then imported into R and integrated with Seurat (version 3.2.3). To minimize information loss and filter out low-quality and duplicated cells at the same time, genes expressed in at least 2 cells were kept, and cells with more than 100 but less than 4000 genes were kept. In addition, violin plot was made by the percentage of mitochondrial genes, and cells that were discrete in the violin plot were filtered out. The filtered cells were then integrated, normalized, scaled and clustered with Seurat.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Tumor tissues were collected and cut into small pieces (approximately 1-2 mm). Then, we digested the tumor tissues with a mouse tumor dissociation kit (Miltenyi/MACS, 130-096-730) following the standard procedure. After that, the cell suspension was filtered with a 30 μm MACS SmarterStrainer. Then, we performed either FACS analysis or FACS sorting (sorting for CD45+CD8+T cells).
Library was performed according to the manufacter's instructions (single cell 3' v2 protocal, 10X Genomics).Briefly, CD8+T cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10X Barcode.The pooled barcodeed cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for the subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: CD8+T cells

value: Tumor

value: 10-12 weeks old


title: CHP134 cells, DMSO treated, biological replicate 3

value: WT


title: 3xTg_29

data_processing:
Reads were trimmed and aligned before differential expression statistics and correlation analyses in Strand NGS software package (v4.0; Strand Life Sciences).
Samples with reads were aligned against the full mm10 transcriptome RefSeq build (2013.04.01). Alignment and filtering criteria included the following: adapter trimming, fixed 5-bp trim from 5′ and 3′ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum 5% gap, and trimming of 3′ ends with Q < 30.
All duplicate reads were then removed. Normalization was performed with the DESeq2 algorithm. Transcripts with an average read count value ≥ 1 in at least 30% of the cells in at least one group were considered expressed at a level sufficient for quantitation.
For statistical analysis of differential expression, a t-test with Benjamini–Hochberg multiple testing correction (BHMTC) was performed with a False Discovery Rate cutoff of <0.1. For those transcripts meeting this statistical criterion, an absolute fold change > 1.25 cutoff was used to eliminate those genes that were statistically significant but unlikely to be biologically significant and orthogonally confirmable because of their very small magnitude of change.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing RPKM values for each sample.

value: Neuron

value: NEBNext Single Cell/Low Input RNA Library Prep Kits for Illumina


title: IP_AlveolarMacrophages_adt_rep1

value: WT mice were treated with a blocking anti-Notch2-antibody or control (both 20 mg/mkg, ip) at days -14 and -7 before take down.

value: TotalSeq™-C0431 anti-mouse CD170 (Siglec-F) Antibody, TotalSeq™-C0987 anti-Allophycocyanin (APC) Antibody, TotalSeq™-C0117 anti-mouse I-A/I-E Antibody, TotalSeqC CD206 Antibody (TCAACTCGGTGTTGC), custom TotalSeqC LYVE-1 (ALY7) antibody (ATCTGCGAGTCAGTC), TotalSeq™-C0090 Mouse IgG1, κ isotype Ctrl Antibody, TotalSeq™-C0095 Rat IgG2b, κ Isotype Ctrl Antibody, https://www.biolegend.com/en-us/products/totalseq-c0238-rat-igg2a-k-isotype-ctrl-19263, https://www.biolegend.com/en-us/products/totalseq-c0236-rat-igg1-kappa-isotype-ctrl-antibody-19601


title: 786-O, DEK KO, rep1

data_processing:
First, adapters were removed by cutadapt v 1.18 with parameters -m 20 -q 20,20.
The clean fragments were aligned to GRCh38/hg38 genome by Bowtie2(v 2.2.5) with parameters --very-sensitive -X 2000.
Alignments with low mapping quality(MAPQ<30) or secondary alignments were removed by Samtools(v1.7). Fragments that aligned to the mitochondria chromosome were further filtered. PCR duplicates were removed by Picard(v 2.26.9) with default parameters.
Before peak calling, to rule out the technical influence generated by the Tn5 dimer, the filtered alignments in BAM format were shifted using alignmentSieve from deepTools(v 3.5.1) package with parameters ‘–ATACshift’
MACS2(v 2.2.7.1) was used to call peaks with parameters ‘callpeak -f BAMPE -g hs --keep-dup all --cutoff-analysis’. R package Diffbind (v3.6.5) was used to analyze differential accessibility between biological groups with default pipelines. ChIPseeker(v1.32.1)  was used to annotate peaks compared with the gene model(downloaded from GENCODE version 37, basic annotation).
Bigwig files were generated by bamCoverage from deepTools (v 3.5.1) package with parameters ‘--binSize 10 --normalizeUsing RPGC’.
Assembly: hg38
Supplementary files format and content: narrowPeak: peaks from MACS2; bigWig

extract_protocol:
Total RNA of cultured cells was isolated using RNA Isolator Total RNA Extraction Reagent (Vazyme) followed by isopropanol precipitation according to standard protocols.
Libraries were prepared using standard protocol provided by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme).

value: DEK KO


title: WT_CD8, scRNAseq

description: 10x Genomics


title: 3xTg_26

extract_protocol:
Patch-seq required slight modifications to recording parameters to minimize confounds in both electrophysiological recordings and sequencing. Patch-seq internal was a modification of whole-cell internal solution containing (in mM) 124 K gluconate, 10 HEPES, 5 KCl, 5 MgCl2, 0.1 EGTA, 0.075 CaCl2, 20 µg/mL glycogen, and 0.5 units/µL RNase inhibitor (M0314L, New England Biolabs). The voltage step protocol used to measure the tail current was unchanged. To minimize recording time before cell extraction, additional electrophysiological parameters were not recorded. After recording was complete, light negative pressure was applied to the pipette until the nucleus was visible at the tip of the pipette, or for approximately three minutes. Next, the recording pipette was slowly retracted along the Z-axis. Successful extractions included an obvious nucleated patch67. After the nucleus was visualized above the slice, the pipette was rapidly retracted from the bath, and the cellular contents within the pipette were deposited in a 0.2 mL PCR tube containing 0.5 µL of NEB Next lysis buffer and 0.25 µL NEB murine RNase inhibitor. Tube contents were then rapidly spun down and flash frozen on dry ice. Samples were stored at -80°C until RNAseq libraries were generated.
Directional libraries were constructed using NEBNext Single Cell/Low Input RNA Library Prep Kits from Illumina following manufacturer instructions. In brief, poly-adenylated mRNA was magnetically captured and then eluted from the oligo-dT beads. mRNA was then fragmented and reverse-transcribed, and the cDNA was purified using SPRISelect beads (#B23318, Beckman Coulter). Purified cDNA was eluted in 50 μL 0.1 × TE buffer. Adaptors were diluted and ligated to cDNA, and the cDNA was amplified by 28 cycles of PCR. SPRISelect beads were used to select for proper library size. Purified library quality was then assessed on a tapestation (#4200, Agilent Technologies) using HSD1000 screentapes (#5067–5584; Agilent Technologies). Due to the high number of amplification cycles, occasionally libraries required additional rounds of SPRISelect purification. Qubit 1 × dsDNA HS Assay kit (#Q33230, Thermo Fisher Scientific) was used to quantify libraries. Libraries were pooled and sequenced 2x 100 bases on an Illumina MiSeq. Fastq data will be made available on the gene expression omnibus (GEO) upon acceptance.


title: Setd2_INPUT_H3K27me3

city: Nanjing

address: 101 Longmian Ave Jiangning District

value: spleen

value: Germinal Center B cells

value: pooled setd2 WT and KO

value: none (input)


title: 786-O, negative control, rep2


title: Phf19_KO_H3K27me3

data_processing:
Library strategy: CUT&TAG
Data were filtered using the Trimgalore with default model
CUT&TAG and ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 with  end to end ,very sensitive , no mixed, no discordant, -I 10 ,-X 700 model
Replication reads were discarded using picard with default model
bigwig files were product using deeptools using ignoreDuplicates model
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

value: Phf19 KO


title: Setd2_KO_H3K27me3

value: setd2 KO


title: 786-O, negative control, rep1


title: 786-O, negative control, rep1 RNA


title: 3xTg_24


title: 786-O, negative control, rep2 ChIP

value: DEK


title: 860-2

status: Public on Sep 13 2024

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

data_processing:
FASTQC software (v0.11.8) was used to check the quality of the raw sequencing reads.
Sequencing indexing adapters were removed using Cutadapt (v2.6)
Input reads were then aligned to the bovine reference genome (ARS-UCD1.2) using the miRDeep2 package (version 2.00.8), the miRDeep2 quantifier module was used to quantify all expressed miRNAs in the sequence data, producing read counts for each individual sample.
The R (v3.4) Bioconductor package, EdgeR (v3.5), was applied to identify statistically significant differentially expressed genes.
A false discovery rate (FDR) of <0.1 was applied as a threshold to call genes with differential expression levels.
Assembly: ARS-UCD1.2
Supplementary files format and content: Tab delimited txt file of merged gene read counts

organism: Bos taurus

source_name: Skeletal muscle

growth_protocol: Charolais and Holstein-Friesian steers were fed two diets over consecutive test periods: 1: zero-grazed grass; 2: high concentrate

extract_protocol:
RNA was  precipitated and purified from skeletal muscle samples using the Qiagen RNeasy Plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
cDNA libraries were prepared from high quality RNA  using the Illumina TruSeq stranded RNA sample prep kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.

treatment_protocol: dietary intakes were recorded for 90 Charolais and 77 Holstein-Friesian steers over two consecutive contrasting dietary phases, each of which lasted 70 days, with a 14 day interim acclimatisation period in between. The diets consisted as follows: Diet 1: zero-grazed grass (ZG; steers were individually offered fresh herbage, harvested twice daily from Lolium perenne dominant swards, ad libitum); Diet 2: high-concentrate (HC; steers were offered the same concentrate ad libitum (86% rolled barley, 6% soya bean meal, 6% molasses, and 2% minerals and vitamins) with a restricted daily allowance of grass silage).

value: Skeletal muscle

tag: breed

value: Charolais

value: High-RFI

value: High concentrate diet


title: Dextrose_RNAseq

city: Durham

first: David

last: MacAlpine

state: NC

address: 308 Research Dr, Durham, NC 27710

department: Department of Pharmacology and Cancer Biology

institute: Duke University

data_processing:
FASTQ reads were aligned to sacCer3 (Saccharomyces cerevisiae) using bowtie v1.1.1 (Langmead 2010) using the single-end option with the following bowtie flags: -m1 -n 2 -l 20 --best --strata -S - y --phred 33 --nProc 32. Aligned files were processed and converted into BAM format using samtools v1.2 (Heng Li et al. 2009).
Read counts were generated for each gene using featureCounts.
Assembly: sacCer3, R64
Supplementary files format and content: Read counts per gene

organism: Saccharomyces cerevisiae

extract_protocol:
Total RNA was extracted using the hot phenol method.
RNA-seq libraries were prepared using TruSeq Stranded Total RNA-seq Kit (Illumina) and ribosomal RNA was removed with Ribo-Zero Gold Kit (Human-Mouse-Rat, Illumina)

value: yeast

value: wt

value: Dextrose 20 min.


title: GAL80_Mutant_RNAseq

value: YPD


title: 3xTg_30

value: Neuron

tag: library prep_kit

value: NEBNext Single Cell/Low Input RNA Library Prep Kits for Illumina


title: 871


title: Setd2_WT_H3K27me3

value: spleen

value: setd2 WT


title: 723

value: Holstein-Friesian

value: Low-RFI


title: 5617


title: 5632


title: 786-O, DEK KO, rep2

value: human renal carcinoma

value: DEK KO


title: 954


title: CHP134 cells, DMSO treated, biological replicate 1

value: neuroblastoma

value: WT

value: DMSO


title: 5609

value: Skeletal muscle

value: High-RFI


title: CHP134 cells, DMSO treated, biological replicate 2


title: 419

value: Charolais

value: High concentrate diet


title: 364


title: 546


title: 5588


title: 322


title: 509


title: 310-2


title: 443


title: 2722


title: 2266


title: 307-2


title: Phf19_WT_H3K27me3

value: Germinal Center B cells

value: Phf19 WT


title: 2220


title: 856


title: 2071


title: 5612


title: 1913


title: 1920


title: 1918


title: 1484-2


title: 1661


title: 1657


title: 1320


title: 1483


title: 1639-2


title: 1316


title: 860-1

value: zero-grazed grass diet


title: 789


title: 571


title: 5635


title: 846


title: 5616


title: 786


title: 5613


title: 545


title: 5605


title: 5633


title: 449


title: 437


title: 310-1


title: 357


title: 307-1


title: 2085


title: 2087


title: 1683


title: 1961


title: 1798


title: 2069


title: 1831


title: 2065


title: 2064


title: 1668


title: 1492


title: 1484-1


title: 1639-1


title: 1100


title: 427


title: IBC-11B, Luminal, high

city: Bangkok

first: Kitiporn

last: Plaimas

address: 254 Phayathai Rd., Wangmai, Patumwan

department: Department of Mathematics and Computer Science

country: Thailand

institute: Chulalongkorn University

data_processing:
The samples were sequenced using an Illumina HiSeq 2500 High Output v4 flowcell, and analysis by BCL2FASTQ software (Illumina, USA).
The FASTQ files were aligned to the Human Whole Transcriptome v2.0 panel using STAR.
Assembly: hWTv2
Supplementary files format and content: comma separated values file includes raw counts for each sample
Library strategy: TempO-Seq (BioClavis, Glasgow, UK)

source_name: FFPE breast cancer tissues

extract_protocol:
The cancer cell area in the fifteen formalin-fixed paraffin-embedded (FFPE) sample was labeled by the pathologist and sent for transcriptomic analysis using Templated Oligo-Sequencing (TempO-Seq) analysis (BioClavis, Glasgow, UK). Briefly, FFPE tissues were deparaffinized and then digested. The tissue lysate was incubated with detector oligos annealing to the targeted RNA template. Amplification of the ligated oligos was performed using a unique primer set of each sample, introducing a sample-specific barcode and Illumina adaptors.
Tempo-Seq libraries were prepared following manufacturer's protocol

value: FFPE breast cancer tissues

tag: subtype

value: Luminal

tag: age (y)

tag: tumor size_(cm)

tag: os (y)

tag: dfs (y)

tag: tumor staging

value: III

tag: pathological differentiation

value: PD

tag: tb level

value: high


title: B165, HER2+, low

tag: tissue

value: low


title: 2094

value: Holstein-Friesian

tag: treatment

value: Low-RFI


title: ozt_S1

city: Tampa

first: Rays HY

last: Jiang

state: FL

address: 3720 Spectrum Blvd, Suite 304

department: Department of Global Health

institute: University of South Florida

description: 10x Genomics

data_processing:
Data processing, sample demultiplexing, and gene expression quantification were performed using the Cell Ranger Single-Cell software Suite (10x Genomics). Genes with more than one unique molecular identifier (UMI) count were considered for analysis. The top 1000 most variably expressed genes were used for clustering, and t-Distributed Stochastic Neighbor Embedding (t-SNE) analysis was employed to reduce data dimensionality. K-means clustering identified cell populations, with cell classification based on Spearman’s correlation of mean expression profiles.
Assembly: GRCh38
Supplementary files format and content: Tab seperated value files and matrix file

source_name: Liver

extract_protocol:
Single-cell RNA sequencing (scRNAseq) was conducted on primary human liver cell populations obtained from the healthy donor UBV. The mixture of hepatic cell populations were carefully washed in Dulbecco's phosphate-buffered saline (DPBS, 1X; Corning, Cat No. 21-031-CV) and resuspended at a concentration of 10^6 cells/mL to prevent cell aggregates.
The scRNAseq protocol utilized the 10x Genomics Chromium controller and the Chromium single-cell 3’ library and gel bead kit (10x Genomics, Cat No. PN-1000075) following the standard manufacturer's protocols. Briefly, gel beads-in-emulsion (GEMs) were generated by combining barcoded single-cell 3’ v3 gel beads, a master mix containing cells, and partitioning oil onto Chromium chip B. Cells were delivered at a limiting dilution to achieve single-cell resolution, with the majority (~ 90–99%) of generated GEMs containing no cells. Between 2,000–21,000 live cells were loaded onto the Chromium controller to recover between 1,500 − 15,000 cells for library preparation and sequencing. Following GEM generation, the gel beads were dissolved, primers were released, and any co-partitioned cells were lysed.   An Illumina TruSeq Read 1, 16 nt 10x barcode, 12 nt unique molecular identifier (UMI), and 30 nt poly(dT) sequence were mixed with the cell lysate and a master mix containing reverse transcription (RT) reagents. Incubation of the GEMs produced barcoded, full-length cDNAs from poly-adenylated mRNAs. Subsequently, GEMs were broken, and cDNA was amplified and quantified using an Agilent high sensitivity DNA screentape. SPRIselect magnetic beads were used to purify the first-strand cDNA, followed by PCR amplification to generate sufficient mass for library construction. Enzymatic fragmentation and size selection optimized the cDNA amplicon size, with TruSeq Read 1 added during GEM incubation. P5, P7, a sample index, and TruSeq Read 2 were added via end repair, A-tailing, adaptor ligation, and PCR. Library quality was assessed using an Agilent Bioanalyzer high sensitivity chip. Sequencing was performed on the Illumina HiSeq 2500 with a target of 150,000 reads/cell.

value: Liver

tag: cell type

value: Liver Homegenate


title: P09, TNBC, high

value: TNBC

value: IIA


title: PC-B-099, TNBC, high

value: IIIA


title: PC-B-130, TNBC, high

value: IIIC


title: siZEB1_3

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

data_processing:
Trimmomatic (version: v0.39) was used for filter reads, parameters: -ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Hisat2 (version: v2.0.4) was used to map clean reads to reference gene with the default parameter.
Samtools (version: v1.7) was used to build index to bam file.
FPKM method was used in calculated expression level with featureCounts (version: v2.0.1).
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include count values for each sample.

source_name: cell line

extract_protocol:
Total RNA was extracted from the SW480 cells using Trizol reagent (Invitrogen). RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using standard capitalbiotech protocols.

value: cell line

tag: cell line

value: colorectal cancer

tag: genotype

value: ZEB1 knockdown


title: siNC_3

value: WT

value: siNC


title: siNC_2


title: siNC_1


title: P06, TNBC, high

value: FFPE breast cancer tissues

value: MD


title: P04, TNBC, high

value: PD

value: high


title: G03, TNBC, high


title: G19, TNBC, high

value: IIIB


title: B041, TNBC, high


title: B031, TNBC, high


title: B168, TNBC, low

value: low


title: HCT116 cells, shikonin 3

city: Xi'an

first: wen

last: liu

address: New temple Road num 1

institute: Tangdu Hospital of Air Force Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cancer cell

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using chloroform, isopropanol and washed with ethanol
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: HCT116 cells were treated with 8μm shikonin for 24 hours,then collected cells and dissolved in trizol

value: cancer cell

value: colon cancer cells

value: shikonin


title: B166, TNBC, high

value: TNBC


title: siZEB1_1


title: siZEB1_2


title: HCT116 cells, shikonin 1


title: HCT116 cells, shikonin 2


title: HCT116 cells, Control 1


title: SpPat15_Unaffected, spatial RNA-seq

city: Philadelphia

first: Satish

last: Sati

state: Pennsylvania

address: 421 Curie Blvd, BRB 1039

department: Dermatology

institute: University of Pennsylvania

description: 10x Genomics Visium

data_processing:
The sequencing data was mapped to the GRCh38 reference genome using the spaceranger pipeline (version 1.3.0, 10X Genomics) to generate gene count and cell barcode matrices.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files and H&E image file
Library strategy: Spatial Transcriptomics

source_name: Skin

growth_protocol: Patients diagnosed with skin granulomatous diseases were recruited to the study at Perelman Center For Advanced Medicine, University of Pennsylvania. Written informed consent was obtained before participation in the study under a protocol approved by the IRB of the University of Pennsylvania School of Medicine. The diagnosis was confirmed by a team of dermatopathologists and clinicians based on histological assessment, patient history and clinical phenotype.

extract_protocol:
Spatial transcriptomics was performed on three patient samples using the Visium Spatial Gene Expression Slide & Reagent kit (10X Genomics). The tissue permeabilization conditions were optimized using Visium Spatial Tissue Optimization Slide & Reagent kit (10X Genomics).  Fresh skin punch biopsies were frozen in OCT blocks and stored at −80 °C until sectioning.
For each patient two sections for lesional tissue and one section from non lesional tissue were taken at 10 mm thickness. The sections were then mounted onto capture areas marked on Visium slides. All the steps including hematoxylin and eosin (H&E) staining of the slides, bright-field image capture, tissue permeabilization (30 minutes), cDNA amplification (16 cycles) and library generation were done following the manufacturer’s protocol. The Libraries were sequenced in house using the recommended 28-10-10-120 cycle read setup on the Illumina HiSeq2500 platform.
spatial RNA-seq (Visium)

tag: individual

tag: disease state

value: Sarcoidosis

value: Skin

tag: tissue condition

value: non-lesional


title: SpPat15_Affected1, spatial RNA-seq

description: 10x Genomics Visium

value: lesional


title: SpPat10_Unaffected, spatial RNA-seq

description: 10x Genomics Visium


title: Pixel Battipaglia 3

city: Portici

first: Daniela

last: D'Esposito

address: Via Università 100

department: Department of Agriculture

country: Italy

institute: University of Naples Federico II

data_processing:
Base calling was performed with CASAVA 1.8.2
Data filtering (trimming and clipping) was performed with Trimmomatic (minimum quality 25 and minimum length 35bp)
Read alignment was performed with TopHat2
Read count was performed usign HT-seq with default setting
Differential expression analysis was performed using the R package edgeR
Assembly: SL3.00
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

organism: Solanum lycopersicum

source_name: Fruit

extract_protocol:
Total RNA was extracted from frozen, homogenized, and powdered fruit tomato samples following the protocol previously described in D'Esposito et al., 2009, Unraveling the complexity of transcriptomic, metabolomic and quality environmental response of tomato fruit
The cDNA libraries were prepared with TruSeq Stranded mRNA Library Prep kit (Il-lumina Inc., San Diego, CA, USA)

value: Fruit

value: Pixel


title: SpPat10_Affected1, spatial RNA-seq

description: 10x Genomics Visium


title: SpPat09_Affected1, spatial RNA-seq

description: 10x Genomics Visium


title: SpPat09_Unaffected, spatial RNA-seq

description: 10x Genomics Visium


title: Pixel Battipaglia 1


title: SpPat15_Affected2, spatial RNA-seq

description: 10x Genomics Visium


title: SpPat10_Affected2, spatial RNA-seq

description: 10x Genomics Visium


title: G01, TNBC, high

value: IIIA


title: G06, TNBC, low

value: FFPE breast cancer tissues

value: IIA


title: SpPat09_Affected2, spatial RNA-seq

description: 10x Genomics Visium


title: Pixel Fondi 3


title: Pixel Battipaglia 2


title: HCT116 cells, Control 2

value: WT


title: TNBC_BC_106

city: Maribor

first: Mario

middle: Smode

last: Gorenjak

address: Taborska ulica 8

country: Slovenia

institute: Faculty of Medicine, University of Maribor

data_processing:
Raw .fastq files were first assessed for quality using FastQC software (0.11.9, Babraham Bioinformatics, Cambridge, UK) [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/]. Subsequently, trimming of technical sequences was done using the Trimmomatic tool (version 0.39, USADEL LAB, Aa-chen, Germany). Transcript specific RNA-seq analysis was performed using the Kallisto pseudoalignment program (Pachter Lab, Berkeley, CA, USA) with GRCh37 reference genome. Furthermore, the R 4.2.1 environment (R Core Team 2020, Vienna, Austria) and a pipeline described elsewhere (PMID: 33750834) were used for further processing of estimated counts and tpms. Statistically significant differential gene expression was identified using a false discovery rate (FDR) ≤ 0.1 and log2 count per million (logCPM) ≥ 1.
Assembly: GRCh37
Supplementary files format and content: abundance.tsv; transcript ids, counts, tpms

source_name: Peripheral venous blood

extract_protocol:
Peripheral venous blood was collected into K2EDTA tubes (Vacutainer BD, Franklin Lakes, NJ, USA). The PBMCs were isolated using density gradient centrifugation with Lympholyte H Cell Separation Medium (Cedarlane, Burlington, ON, Canada) and SepMate 50 centrifuge tubes (StemCells Technologies, Vancouver, BC, Canada). The remaining platelets and erythrocytes were removed using the low-speed centrifugation and red blood cell lysis, respectively. The isolated PBMCs were stored in liquid nitrogen at a density of 1-10E6 cells/mL. A combination of 10% dimethyl sulfoxide (Sigma-Aldrich, Bur-lington, MA, USA) and 40% heat-inactivated fetal bovine serum (Gibco, ThermoFisher Scientific, Waltham, MA, USA) was used as the cryopreservation medium. The cell concentration was determined using the CytoSmart automated cell counter (Corning Inc., Corning, NY, USA). To perform scRNA-seq the 10X Chromium System (10X Genomics, Pleasanton, CA, USA) was used. First, the cryopreserved PBMCs were thawed and washed in Dulbecco's Phosphate-Buffered Saline supplemented with 5% FBS to remove the cryopreservation medium. The quality of the cell samples was confirmed using the trypan blue exclusion and viability of all samples was >90%. 2E6 cells per sample were used for the library preparation.
RNA-seq was performed on 26 RNA samples extracted from PMBCs. Paired-end RNA-seq (oligo dT, stranded mRNA library, DNBseq platform, PE150, 20M reads/6Gb clean data) was performed at BGI (Hong Kong, China) using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and BGI kit.

value: Peripheral venous blood

value: Breast Cancer

tag: patient id

value: PBMC

tag: phenotype

tag: library type

value: mRNA


title: TNBC_BC_091


title: Pixel Fondi 1


title: Pixel Fondi 2


title: TNBC_BC_084


title: Dardo Battipaglia 3

value: Dardo


title: HCT116 cells, Control 3

value: cancer cell

value: colon cancer cells


title: TNBC_BC_045

value: TNBC


title: Dardo Battipaglia 2


title: TNBC_BC_044


title: Dardo Battipaglia 1


title: TNBC_BC_040


title: Dardo Fondi 3


title: Dardo Fondi 2


title: LuminalA_BC_204

value: LuminalA


title: LuminalA_BC_191


title: LuminalA_BC_187


title: Dardo Fondi 1


title: TNBC_BC_033


title: S-8

city: Wuhan

first: haoran

last: lu

state: Hubei

address: Renmin Hospital of Wuhan University, 238 Jiefang Street

institute: wuhan university

description: SAH 7d-5

data_processing:
Basecalling is performed by Illumina RTA software in sequencer.
Raw data (raw reads) of FASTQ format were firstly processed through fastp to generate clean reads.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Differential expression analysis of two conditions/groups (five biological replicates per condition) was performed using the DESeq2 R package (1.16.1).Genes with an  P-value <0.05 found by DESeq2 were assigned as differentially expressed.
GO and KEGG enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package.
Assembly: mm9
Supplementary files format and content: Fragments Per Kilo bases per Million mapped Reads (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene
Supplementary files format and content: Excel spreadsheet of differentially expressed genes

organism: Rattus norvegicus

source_name: cerebral cortex

growth_protocol: Animals were housed in a specific pathogen-free laboratory with fixed 12-h light/dark cycles under controlled temperature and humidity conditions (22 ± 1°C; 45–55%)

extract_protocol:
At the set time points, fresh tissue samples from the bilateral cerebral cortex of mice were collected and rapidly frozen in liquid nitrogen, and then stored in a -80 ℃ refrigerator. After the tissues were homogenized, total RNA was extracted employing Trizol reagent (Invitrogen, CA, USA). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Total RNA samples were converted into cDNA libraries using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (Catalog E7530L, NEB, USA) following the manufacturer's recommendations

value: cerebral cortex

value: SAH

tag: time


title: LuminalA_BC_182


title: LuminalA_BC_185


title: S-3

description: SAH 7d-2


title: LuminalA_BC_179


title: S-6

description: SAH 7d-4


title: O-9

description: SAH 1d-6


title: LuminalA_BC_115


title: LuminalA_BC_057


title: S-5

description: SAH 7d-3


title: LuminalA_BC_056


title: S-2

description: SAH 7d-1


title: TNBC_BC_022


title: S-9

description: SAH 7d-6


title: LuminalA_BC_053


title: O-12

description: SAH 1d-3


title: LuminalA_BC_035


title: O-1

description: SAH 1d-1


title: O-11

description: SAH 1d-2


title: LuminalA_BC_034


title: sham-6

value: sham


title: sham-5


title: LuminalA_BC_060


title: TNBC_BC_137


title: TNBC_BC_111


title: TNBC_BC_005


title: sham-3


title: sham-4


title: Human_B-cell_aRP105, HTO-derived cDNA

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Hashtag-derived oligonucleotide (HTO)

data_processing:
Sequencing was performed on DNBSEQ-G400 platform in a 100+100 base paired-end mode.
The DNBSEQ-G400 control software operated base calling analysis software and delivered raw sequencing data.
Generated reads were input into the cellranger pipeline (Cell Ranger v.6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: genematrix.csv: comma-delimited text files including UMI counts for all cells detected
Supplementary files format and content: surface_protein.csv: comma-delimited text file including barcodes associated with each hashtag ID
Supplementary files format and content: Hashtag-condition.csv: comma-delimited text file including condition/treatment information for each hashtag

source_name: B-cell

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.

value: B-cell


title: TNBC_BC_152


title: Human_B-cell_aRP105, mRNA-derived cDNA

description: poly A RNA

value: Radioprotective 105 (RP105, CD180), a type I transmembrane protein belonging to the Toll-like receptor (TLR) family, possesses a short cytoplasmic tail lacking the Toll–interleukin-1 receptor domain. Agonistic anti-human RP105 monoclonal antibodies (clone name:MHR73) crosslink with mRP105, inducing robust proliferation and antibody production in mouse B-cells.


title: sham-2


title: NGN2 neuron high density rep2

city: South San Francisco

first: Ai

last: Zhang

state: California

address: 1 DNA way

department: Neuroscience

institute: Genentech

data_processing:
Bulk RNAseq FASTQ data were aligned to the human reference genome (GRCh38) using the GSNAP aligner and HTSeqGenie pipeline
Assembly: human reference genome (GRCh38)
Supplementary files format and content: csv file of raw counts

source_name: Brain

growth_protocol: NGN2 induction via doxycline for 5 days, followed by neuronal maturaion in a neuralbasal-B27 based media until day 28 of induction

extract_protocol:
RNA was extracted via the RNAeasy mini plus kit (Qiagen)
the Truseq Stranded mRNA kit (Illumina) was used with an input of 100-1000 nanograms of total RNA

value: Brain

value: Neuron

value: high density


title: NGN2 neuron low density rep3

value: WT

value: low density


title: Patient 15 PBMC scRNA-seq

description: 10x Genomics

data_processing:
The scRNA sequencing data was mapped to the GRCh38 reference genome to generate gene count and cell barcode matrices using the “cellranger count” function from cellranger pipeline (version 5.0.1, 10X Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
The skin punch biopsies were incubated in 200 μl of Dispase solution (2mg/mL) for 30 minutes at  37 C. Following the incubation, the epidermis was peeled from dermis with curved forceps, washed in PBS and successively minced into < 1 mm3 pieces, using scalpel in a serum free RPMI 1640 media with DNase I (0.2 mg/mL), 20 mM HEPES and 0.25 mg/ml Liberase TM, Roche. The suspension was incubated for 90 minutes at 37 C. The digestion was stopped by adding 100 μl FBS and 3 μl of 0.5 M EDTA and filtered through a 70-mm cell strainer. The cells were pelleted and washed twice with PBS containing 1% BSA. Finally the cells were resuspended in PBS containing 0.04% BSA and an aliquot was taken for counting.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Blood

value: PBMCs


title: Patient 14 PBMC scRNA-seq

description: 10x Genomics


title: O-5

description: SAH 1d-4


title: NGN2 neuron low density rep2


title: Patient 12 PBMC scRNA-seq

description: 10x Genomics


title: Patient 13 PBMC scRNA-seq

description: 10x Genomics


title: NGN2 neuron high density rep1


title: Patient 11 PBMC scRNA-seq

description: 10x Genomics


title: Patient 9 PBMC scRNA-seq

description: 10x Genomics


title: Patient 8 PBMC scRNA-seq

description: 10x Genomics


title: O-8

description: SAH 1d-5


title: NGN2 neuron low density rep1


title: 546_PC3_progeny_2

city: LOS ANGELES

first: Michaek

middle: James

last: Schmidt

address: 1002 Childs Way

department: Cancer Biology and Genomics

institute: University of Southern California

data_processing:
raw fastq files
Assembly: hg19
Supplementary files format and content: RDS file contains gene counts processed with htseq-count and aligned with hisat2
Supplementary files format and content: for RDS file: hisat2 & htseq-count

source_name: prostate

extract_protocol:
smart-seq2
Nextera-XT

treatment_protocol: treat with chemotherapy for 72 hours and then allowed to recover for 1 or 10 days in regular medium.

value: prostate

value: epithelial cell line


title: 545_PC3_progeny_2


title: sham-1


title: NGN2 neuron high density rep3


title: 543_PC3_progeny_2


title: Patient 26 unaffected skin scRNA-seq

description: 10x Genomics

value: Skin


title: Patient 25 unaffected skin scRNA-seq

description: 10x Genomics


title: 542_PC3_progeny_2


title: 544_PC3_progeny_2


title: Patient 27 unaffected skin scRNA-seq

description: 10x Genomics


title: Patient 22 unaffected skin scRNA-seq

description: 10x Genomics


title: Patient 21 unaffected skin scRNA-seq

description: 10x Genomics


title: 541_PC3_progeny_2


title: 538_PC3_progeny_2


title: Patient 20 unaffected skin scRNA-seq

description: 10x Genomics


title: Patient 23 unaffected skin scRNA-seq

description: 10x Genomics


title: Patient 18 unaffected skin scRNA-seq

description: 10x Genomics


title: 534_PC3_progeny_2


title: 537_PC3_progeny_2


title: 540_PC3_progeny_2


title: Patient 19 unaffected skin scRNA-seq

description: 10x Genomics


title: Patient 16 unaffected skin scRNA-seq

description: 10x Genomics


title: 531_PC3_progeny


title: Patient 14 unaffected skin scRNA-seq

description: 10x Genomics


title: 532_PC3_progeny


title: Patient 17 unaffected skin scRNA-seq

description: 10x Genomics


title: Patient 24 unaffected skin scRNA-seq

description: 10x Genomics


title: Patient 13 unaffected skin scRNA-seq

description: 10x Genomics


title: Patient 15 unaffected skin scRNA-seq

description: 10x Genomics


title: 530_PC3_progeny


title: 529_PC3_progeny


title: 533_PC3_progeny


title: Patient 11 unaffected skin scRNA-seq

description: 10x Genomics


title: Patient 12 unaffected skin scRNA-seq

description: 10x Genomics


title: 528_PC3_progeny


title: 536_PC3_progeny_2


title: Patient 10 unaffected skin scRNA-seq

description: 10x Genomics


title: 526_PC3_progeny


title: 539_PC3_progeny_2


title: 525_PC3_progeny


title: Patient 9 unaffected skin scRNA-seq

description: 10x Genomics


title: 535_PC3_progeny_2


title: Patient 8 unaffected skin scRNA-seq

description: 10x Genomics


title: 527_PC3_progeny


title: Patient 7 unaffected skin scRNA-seq

description: 10x Genomics


title: Patient 6 unaffected skin scRNA-seq

description: 10x Genomics


title: 523_PC3_progeny


title: 656_PC3_doc_DPT10


title: 522_PC3_progeny


title: 655_PC3_doc_DPT10


title: Patient 5 unaffected skin scRNA-seq

description: 10x Genomics