title: HepG2 48 hr FBS rep4

value: 10% FBS

value: 48 hr


title: HepG2 24 hr LPDS+statin rep4

status: Public on Dec 10 2024

type: SRA

city: Oakland

first: Marisa

last: Medina

state: CA

address: 5700 Martin Luther King Jr. Way

department: Pediatrics

country: USA

institute: UCSF

library_source: transcriptomic

data_processing:
Aligned using 2-pass alignment with STAR
Duplicate sequence fragments removed using Picard MarkDuplicates
Quantification of annotated genes using FeatureCounts
Library size adjustment, variance stabilization, and differential expression analysis in DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene counts; Library size adjusted and variance stabilized gene expression levels

molecule: polyA RNA

organism: Homo sapiens

source_name: HepG2 cells

growth_protocol: The HepG2 cell line was maintained under standard conditions and grown in Eagle’s minimum essential medium supplemented with 10% fetal bovine serum prior to experiment initiation.

extract_protocol:
RNA was extracted using the Qiagen RNAeasy mini-kit with QIAshredders.
Illumina polyA-selected, strand-specific (dUTP second strand marking protocol), paired-end library preparation

treatment_protocol: Some cell aliquots were maintained in FBS-containing media for 24 or 48 hours, while others were exposed to simvastatin in FBS or lipoprotein deficient serum (LPDS) containing media for 24 or 48 hours. Finally, after 24 hr statin+LPDS, LDL-cholesterol or 25-hydroxycholesterol was added to the media for an additional 24 hours.

tag: treatments

value: 10% LPDS + 2 µM simvastatin

tag: duration

value: 24 hr


title: control

city: Tianjin, China

first: Tang

last: Qiang

address: 22 Qixiangtai Road, Heping District 300070, Tianjin, China

country: China

institute: Tianjin medical university

library_source: transcriptomic single cell

data_processing:
Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific).
The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.
Reads were processed using the Cell Ranger 4.0 pipeline with default and recommended parameters.
Gene-Barcode matrices were generated for each sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts.
This output was then imported into the Seurat (v3.2.0) R toolkit for quality control and downstream analysis of our single-cell RNAseq data.
Assembly: GRCh38
Supplementary files format and content: raw-count

molecule: total RNA

organism: Mus musculus

source_name: mesenteric lymphatic node

extract_protocol:
All the remaining procedures of single cell including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: mesenteric lymphatic node

tag: cell line

value: immune cell

tag: strain

tag: treatment

value: PBS daily after 2 days of  DSS treatment


title: HepG2 LDL-C addback rep3

value: 10% LPDS + 2 µM simvastatin followed by 50 µg/ml LDL-cholesterol addback

value: 24 hr + 24 hr addback


title: tcr07

city: New Haven

first: Andrew

last: Martins

state: Connecticut

address: 100 College Street Rm 1155

department: Immunobiology

institute: Yale School of Medicine

description:
Mixed Pool of samples
T cell receptor amplicons from 10x 5' kit
VDJresults.tar.gz

library_source: other

data_processing:
*library strategy: CITE-seq
10x Genomics CellRanger
Data was analyzed using the Seurat R package. Please see manuscript for details and link to code.
Assembly: Hg19
Supplementary files format and content: R data objects: Seurat single cell objects; .csv files of demuxlet and VDJ results

molecule: other

source_name: Blood

extract_protocol:
10x Genomics Chromium single cell
10x Genomics 5'

value: Blood

tag: cell type

value: Peripheral blood mononuclear cells


title: HTH_1

city: 上海市

first: gui

last: liming

state: 上海市

address: 华山路1954号上海交通大学生物医学工程学院

institute: 上海交通大学

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to mouse genome (GRCm38,Ensembl100) using the Hisat2. [Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods. 2015. April;12(4):357–360. doi: 10.1038/nmeth.3317] HTseq [Anders S, Pyl P T, Huber W. HTSeq–A Python framework to work with high-throughput sequencing data[J]. Bioinformatics, 2014: btu638.] was used to get gene counts and RPKM method was used to determine the gene expression.
Assembly: The clean reads were then aligned to mouse genome (GRCm38,Ensembl100) using the Hisat2.
Supplementary files format and content: We applied DESeq2 algorithm [Love M I , Huber W , Anders S . Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2[J]. Genome Biology, 2014, 15(12):550.] to filter the differentially expressed genes, after the significant analysis, P-value and FDR analysis [Benjamini Y, et al. Controlling the false discovery rate in behavior genetics research. Behav Brain Res. 2001 Nov 1;125(1-2):279-84.] were subjected to the following criteria: i) Fold Change>1.5 or < 0.667; ii) ,P-value<0.05,FDR<0.05.

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Agilent 2200 and kept at −80°C. The RNA with RIN (RNA integrity number) > 7.0 is acceptable for cDNA library construction.
The cDNA libraries were constructed for each RNA sample using the TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc.) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: Poly-A containing mRNA was purified from 1ug total RNA using oligo(dT) magnetic beads and fragmented into 200-600 bp using divalent cations at 85℃ for 6 min. The cleaved RNA fragments were used for first- and second-strand complementary DNA (cDNA) synthesis . dUTP mix was used for second-strand cDNA synthesis, which allows for the removal of the second strand.
The cDNA fragments were end repaired, A-tailed and ligated with indexed adapters. The ligated cDNA products were purified and treated with uracil DNA glycosylase to remove the second-strand cDNA. Purified first-strand cDNA was enriched by PCR to create the cDNA libraries. The libraries were quality controlled with Agilent 2200 and sequenced by NovaSeq 6000 on a 150 bp paired-end run.


title: HepG2 24 hr FBS rep4


title: HTH_3

address: 华山路1954号上海交通大学生物医学工程学院


title: HepG2 48 hr FBS rep3


title: HepG2 24 hr LPDS+statin rep3


title: HepG2 24 hr FBS+statin rep3

value: 10% FBS + 2 µM simvastatin


title: tcr06


title: HTH_2

address: 华山路1954号上海交通大学生物医学工程学院


title: tcr05


title: Vehicle_2

address: 华山路1954号上海交通大学生物医学工程学院

value: vehicle


title: HepG2 48 hr LPDS+statin rep3


title: HepG2 LDL-C addback rep2


title: Vehicle_1

address: 华山路1954号上海交通大学生物医学工程学院


title: HepG2 48 hr LPDS+statin rep2


title: tcr01


title: tcr04


title: Vehicle_3

address: 华山路1954号上海交通大学生物医学工程学院


title: HepG2 48 hr FBS rep2


title: HepG2 24 hr FBS rep3


title: rna5p12

description:
Mixed Pool of samples
mRNA tags from 10x Genomics 5' kit
celltypeObjects.S.Rds

value: Peripheral blood mononuclear cells, FACS selected to enrich non-naive B and dendritic cells


title: tcr03


title: HepG2 24 hr FBS+statin rep2


title: tcr02


title: HepG2 25-HC addback rep2

value: 10% LPDS + 2 µM simvastatin followed by 1 µg/ml 25-hydroxycholesterol addback


title: rna5p11


title: HepG2 24 hr LPDS+statin rep2


title: 37C_2

city: Kunming

first: Jingming

last: Xie

state: Yunnan

address: 374# Dianmian Road

department: Orthopedics

institute: The Second Affiliated Hospital of Kunming Medical University

data_processing:
Quality control  Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome  Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Novel transcripts prediction The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: cell line

growth_protocol: ATDC5 cells inoculated in a medium consisting of 90% high sugar DMEM and 10% FBS, and incubated at 37°C in 95% air and 5% CO2.

extract_protocol:
Total RNA from ATDC5 cells treated with different temperatures (37°C, 40°C or 44°C) was extracted using the TRIzol™ Plus RNA Purification Kit.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: ATDC5 in the three groups was subjected to temperatures of 37C, 40C and 44C for 10 min, respectively.

value: cell line

value: Cartilage progenitor cells

tag: genotype

value: WT

value: Treatment at 37C for 10 min


title: rna5p10


title: HepG2 24 hr FBS+statin rep1


title: Control rep3

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.
RSEM was used to quantify gene abundances.R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include RAW counts for each sample.
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

source_name: C57BL/6J mouse immune cell

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Bone Marrow

value: Bone Marrow-Derived Dendritic Cells

value: PBS


title: HepG2 48 hr FBS rep1

value: 10% FBS

value: 48 hr


title: rna5p09


title: HepG2 25-HC addback rep1


title: HepG2 24 hr LPDS+statin rep1

value: 10% LPDS + 2 µM simvastatin

value: 24 hr


title: Control rep2


title: HepG2 24 hr FBS rep1


title: Lysine rep1

value: 18 mM lysine for 6 h


title: rna5p08

description:
Mixed Pool of samples
mRNA tags from 10x Genomics 5' kit
celltypeObjects.US.Rds

value: Blood

value: Peripheral blood mononuclear cells


title: HepG2 24 hr FBS rep2


title: Lysine H3K79me2

library_source: genomic

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <35 bp), and low-quality reads using Cutadapt v1.18 (non-default parameters: --max-n 0 --minimum-length 35) and Trimmomatic v0.38 (non-default parameters: SLIDINGWINDOW:4:15 LEADING:10 TRAILING:10 MINLEN:35).
Then FastQC (with default parameters) is used to ensure high reads quality. The clean reads were mapped to the mouse genome (assembly GRCm38) using the Bowtie2 v2.3.4.1 (with default parameters) software.
Duplicate reads were then removed using Picard MarkDuplicates.
Peak detection was performed using the MACS v2.1.2 (non-default parameters: -f BAMPE -g hs/mm -p 0.01) peak finding algorithm with 0.01 set as the p-value cutoff.
Annotation of peak sites to gene features was performed using the ChIPseeker R package.
Assembly: GRCm38
Supplementary files format and content: broadPeak; gappedPeak
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: BMDCs were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
BMDCs underwent crosslinking with 1% formaldehyde for 10 minutes at room temperature. The crosslinking reaction was then quenched by adding 125 mM glycine.
After reverse crosslinking, the ChIP and input DNA fragments were processed for end repair and A-tailing using the NEBNext End Repair/dA-Tailing Module (E7442, NEB). Subsequently, adaptor ligation was performed using the NEBNext Ultra Ligation Module (E7445, NEB). The DNA libraries were amplified through 15 cycles of PCR and sequenced using Illumina Hi-Seq with paired-end 2×150 sequencing mode.


title: embryonic RPC, day 35, rod induction, replicate 3

city: Toronto

first: Derek

last: van der Kooy

state: Ontario

address: 160 College Street

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: Library name: Sample 33

data_processing:
Sequencing analysis was done using a published open-source software package (Pertea et al., 2016). Briefly, HiSAT2 was used to align reads to GRCm38 with Ensembl GTF, transcripts were assembled using StringTie, raw read count assessed with HTseq, and differential expression analysis was done using Ballgown.
Assembly: GRCm38
Supplementary files format and content: csv files include raw counts for each sample.
Supplementary files format and content: csv files include raw counts for each sample.

source_name: embryonic day 14 retina

growth_protocol: Please see accompanying manuscript for detailed growth protocol.

extract_protocol:
RNA was extracted using the Takara pico input mammalian RNA extraction kit (634411) following manufacturer protocol.
Library prep was done with Takara low input RNA kit (634938) following manufacturer protocol.

value: embryonic day 14 retina

value: retinal progenitor cell (RPC)

value: rod induction with taurine + retinoic acid


title: Lysine rep2


title: Control rep1


title: rna5p07


title: Lysine input


title: Lysine rep3


title: rna5p06


title: HepG2 LDL-C addback rep1

value: 10% LPDS + 2 µM simvastatin followed by 50 µg/ml LDL-cholesterol addback

value: 24 hr + 24 hr addback


title: embryonic RPC, day 35, rod induction, replicate 2

description: Library name: Sample 32

treatment_protocol: Please see accompanying manuscript for detailed growth protocol.


title: embryonic RPC, day 21, rod induction, replicate 3

description: Library name: Sample 30


title: PBS input


title: embryonic RPC, day 21, rod induction, replicate 1

description: Library name: Sample 28


title: rna5p03


title: rna5p05


title: EB-noTreat3-02

city: Jeonju-si

first: Donghyun

last: Shin

state: Jeollabuk-do

address: 567 Baekje-daero, Deokjin-gu

department: Agricultural Convergence Technology

country: South Korea

institute: Jeonbuk National University

description:
experiment04, In the case of sequence data without CHIP processing, there is no result file because it was created for comparison.
EB-noTreat3-input
Control

data_processing:
(RNA) STAR Aligner (version 2.7.10b) / Picard tools (version 3.0.0) / StringTie (version 2.2.1) / FeatureCounts (version2.0.6) & HTSeq (version 2.0.3) / DESeq2 (version 1.18.1).
(CHIP) Bowtie / picard-tools / EPIC / Diffbind (R package) / ChIPseeker (R package).
Assembly: GRCm38/mm10
Supplementary files format and content: (RNA) Read count
Supplementary files format and content: (CHIP) Bed file (peak)

source_name: embryonic stem cell

extract_protocol:
(RNA) All bulk RNA sequencing and the initial analysis for differential genes were performed with Amera Health, NJ, USA. Briefly, total RNA prepared by the Direct-zol RNA miniprep kit (Zymo Research, Irvine, CA, USA) was subjected to the quality analysis with Agilent Tapestation using RNA ScreenTape (Agilent Technologies Inc., CA, USA) and quantification with Qubit 2.0 RNA HS assay (Thermofisher Scientific, Waltham, MA).
(RNA) Subsequently, the quality and the quantity of the libraries were analyzed by TapeStation HSD1000 ScreenTape (Agilent Technologies Inc., CA, USA) and Qubit 2.0 (Thermofisher Scientific, Waltham, MA), respectively.
(CHIP) The H3K9me3 ChIP-seq experiment was performed with Diagenode (Denville, NJ). The chromatin was prepared by Diagenode ChIP-seq/ChIP-qPCR Profiling service (Diagenode, Denville, NJ) using the iDeal ChIPseq kit for Histones (Diagenode, Denville, NJ).
(CHIP) Library preparations were performed with the ChIP’d DNA and input DNA using MicroPlex Library Preparation Kit v3/96 rxns (Diagenode, Denville, NJ) with UDI for MicroPlex v3 - Set I and Set II (Diagenode, Denville, NJ).

value: embryonic stem cell

value: Control

tag: antibody


title: embryonic RPC, day 35, rod induction, replicate 1

description: Library name: Sample 31


title: embryonic RPC, day 21, rod induction, replicate 2

description: Library name: Sample 29


title: rna5p02


title: HepG2 48 hr LPDS+statin rep1


title: embryonic RPC, day 12, rod induction, replicate 3

description: Library name: Sample 27


title: EB-noTreat3-01

description:
experiment04
EB-noTreat3-H3K9me3
Control/CHIP

value: yes


title: embryonic RPC, day 12, rod induction, replicate 2

description: Library name: Sample 26


title: rna5p04


title: PBS H3K79me2

value: Bone Marrow

value: Bone Marrow-Derived Dendritic Cells


title: rna5p01


title: embryonic RPC, day 12, rod induction, replicate 1

description: Library name: Sample 25


title: embryonic RPC, day 35, cone induction, replicate 1

description: Library name: Sample 19

value: cone induction with COCO protein


title: embryonic RPC, day 5, rod induction, replicate 3

description: Library name: Sample 24


title: embryonic RPC, day 5, rod induction, replicate 2

description: Library name: Sample 23


title: embryonic RPC, day 35, cone induction, replicate 3

description: Library name: Sample 21


title: EB-noTreat2-01

description:
experiment04
EB-noTreat2-H3K9me3
Control/CHIP


title: embryonic RPC, day 35, cone induction, replicate 2

description: Library name: Sample 20


title: EB-noTreat2-02

description:
experiment04, In the case of sequence data without CHIP processing, there is no result file because it was created for comparison.
EB-noTreat2-input
Control


title: EB-noTreat1-02

description:
experiment04, In the case of sequence data without CHIP processing, there is no result file because it was created for comparison.
EB-noTreat1-input
Control


title: embryonic RPC, day 5, rod induction, replicate 1

description: Library name: Sample 22


title: csp10

description:
Mixed Pool of samples
Feature Barcode (Cell surface proteins) from 10x Genomics 5' kit
celltypeObjects.S.Rds

value: Peripheral blood mononuclear cells, FACS selected to enrich non-naive B and dendritic cells


title: embryonic RPC, day 21, cone induction, replicate 3

description: Library name: Sample 18


title: embryonic RPC, day 12, cone induction, replicate 1

description: Library name: Sample 13


title: embryonic RPC, day 21, cone induction, replicate 2

description: Library name: Sample 17


title: embryonic RPC, day 5, cone induction, replicate 2

description: Library name: Sample 11


title: embryonic RPC, day 21, cone induction, replicate 1

description: Library name: Sample 16


title: csp11


title: EB-noTreat1-01

description:
experiment04
EB-noTreat1-H3K9me3
Control/CHIP


title: embryonic RPC, day 12, cone induction, replicate 3

description: Library name: Sample 15


title: embryonic RPC, day 12, cone induction, replicate 2

description: Library name: Sample 14


title: csp07

description:
Mixed Pool of samples
Feature Barcode (Cell surface proteins) from 10x Genomics 5' kit
celltypeObjects.US.Rds


title: EB-Er71-Flag-DOX-D2-01

description:
experiment04
EB-Er71-Flag-DOX-D2-H3K9me3
DOX/CHIP

value: DOX


title: csp09


title: EB-Er71-Flag-DOX-D2-02

description:
experiment04, In the case of sequence data without CHIP processing, there is no result file because it was created for comparison.
EB-Er71-Flag-DOX-D2-input
DOX


title: csp12


title: csp08


title: embryonic RPC, day 5, cone induction, replicate 1

description: Library name: Sample 10


title: embryonic RPC, day 0, rod primed, replicate 3

description: Library name: Sample 9


title: EB-DOX-D3-01

description:
experiment04
EB-DOX-D3-H3K9me3
DOX/CHIP


title: embryonic RPC, day 0, cone primed, replicate 2

description: Library name: Sample 5


title: embryonic RPC, day 0, cone primed, replicate 1

description: Library name: Sample 4


title: embryonic RPC, day 0, rod primed, replicate 2

description: Library name: Sample 8


title: embryonic RPC, day 0, rod primed, replicate 1

description: Library name: Sample 7


title: EB-DOX-D2-02

description:
experiment04, In the case of sequence data without CHIP processing, there is no result file because it was created for comparison.
EB-DOX-D2-input
DOX


title: EB-DOX-D3-02

description:
experiment04, In the case of sequence data without CHIP processing, there is no result file because it was created for comparison.
EB-DOX-D3-input
DOX


title: csp04


title: EB-DOX-D2-01

description:
experiment04
EB-DOX-D2-H3K9me3
DOX/CHIP


title: embryonic RPC, day 0, untreated, replicate 2

description: Library name: Sample 2


title: csp06


title: embryonic RPC, day 0, cone primed, replicate 3

description: Library name: Sample 6


title: HA_NSC_CUTandTag

city: Beijing

first: Yuying

last: Shen

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

data_processing:
Raw FASTQ reads were trimmed using Trim Galore (v0.6.10, with parameters --paired --quality 20 --stringency 3 -j 4).
Trimmed reads were mapped to Drosophila reference genome (version: dm6) using Bowtie2 (v2.5.1) very-sensitive-local mode
Picard tools were used to remove duplicate reads. Reads with a low mapping quality score were further filtered using Samtool
Assembly: dm6
Supplementary files format and content: bigwig files were generated using bamCoverage (--binSize 50 --normalizeUsing RPKM --extendReads)
Library strategy: CUT&Tag

organism: Drosophila melanogaster

source_name: larval brain

growth_protocol: Flies were reared and crossed according to standard procedures.

extract_protocol:
For CUT&Tag carried out by using neural stem cells, the cells were arrested by ConA beads, and the HA tag fused factor of interest are combined by the specific primary antibody (HA), followed by secondary antibody and Tn5 transposase.
CUT&Tag libraries were prepared using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) complemented with TruePrep Index Kit V2 for Illumina (Vazyme). 1w-100w cells were used as starting materials. Libraries were amplified using 13-19 cycles on the thermocycler. Post-amplification libraries were size selected at 200-2000 bp in length using VAHTS DNA Clean Beads (Vazyme).

value: larval brain

value: type II neural stem cell

value: wild type


title: csp03

value: Blood

value: Peripheral blood mononuclear cells


title: embryonic RPC, day 5, cone induction, replicate 3

description: Library name: Sample 12

value: embryonic day 14 retina

value: retinal progenitor cell (RPC)


title: embryonic RPC, day 0, untreated, replicate 3

description: Library name: Sample 3


title: Group-H-03

description:
experiment03
21053R-02-06
KDM4A/4C DKO

value: KDM4A/4C DKO


title: Group-H-02

description:
experiment03
21053R-02-05
KDM4A/4C DKO


title: csp02


title: HATBPctrl_NSC_CUTandTag


title: csp01


title: ATAC_mit__dEP400IR_NSC rep2

data_processing:
Raw FASTQ reads were trimmed using Trim Galore (v0.6.10, with parameters --paired --quality 20 --stringency 3 -j 4)
Trimmed reads were aligned to Drosophila reference genome (version: dm6) using Bowtie2
Duplicate reads were removed using Picard tools.
Mitochondrial and low-quality reads were filterer out using Samtools
Assembly: dm6
Supplementary files format and content: bigwig files were generated using bamCoverage (--binSize 50 --normalizeUsing RPKM --extendReads)

extract_protocol:
For ATAC-seq carried out by using mitotic neural stem cells, the cells were fixed with 1% formaldehyde for 7min and quenched by Glycine. The cells were lysised and tagmented by using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme).
ATAC-seq libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) complemented with TruePrep Index Kit V2 for Illumina (Vazyme). About 5k cells were used as starting materials. Libraries were amplified using 12-15 cycles on the thermocycler. Post-amplification libraries were size selected at 50-1000 bp in length using VAHTS DNA Clean Beads (Vazyme).


title: RNAseq_H2A.Z loss of function_NSC rep2

data_processing:
Raw FASTQ reads were trimmed using Trim Galore (v0.6.10, with parameters --paired --quality 20 --stringency 3 -j 4).
Trimmed reads were aligned to Drosophila genome (Version: dm6) using HISAT2 (v2.2.1) and processed with Samtools (v1.6) to generate bam files.
FeatureCounts (v2.0.3) was used to generate raw count matrix for ncbiRefSeq genes.
Assembly: dm6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvest using Discover-sc WTA Kit V2 (Vazyme). 1-2k cells are used for the extraction of RNA used to construct sequencing libraries.
RNA libraries for RNA-seq were prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocols.

value: H2A.Z loss of function


title: ATAC_mit__dEP400IR_NSC rep1


title: csp05


title: RNAseq_H2A.Z loss of function_NSC rep1


title: RNAseq_TBPIR_NSC rep2

value: TBP RNAi


title: RNAseq_control_NSC rep2


title: bcr11

description:
Mixed Pool of samples
B cell receptor amplicons from 10x 5' kit
VDJresults.tar.gz


title: Group-H-01

description:
experiment03
21053R-02-04
KDM4A/4C DKO

value: embryonic stem cell


title: RNAseq_control_NSC rep3


title: Group-G-01

description:
experiment03
21053R-02-01
Control

value: Control


title: HATBPSA_NSC_CUTandTag


title: Group-G-03

description:
experiment03
21053R-02-03
Control


title: Group-G-02

description:
experiment03
21053R-02-02
Control


title: embryonic RPC, day 0, untreated, replicate 1

description: Library name: Sample 1


title: KO/OEhiPSC-CM, 4 week after I/R, Pig 3

city: Birmingham

first: Thanh

middle: Minh

last: Nguyen

state: AL

address: 1670 University Blvd, Volker Hall G094

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

data_processing:
Sample demultiplexing, barcode processing, and gene counting were performed with the Cell Ranger v.6 toolkit
Assembly: Sscrofa11.1
Supplementary files format and content: 10X Genomics format; R object
Supplementary files format and content: Raw expression matrix (sparse matrix, 10XGenomics); Integrated-sample, normalized expression (via Seurat)

organism: Sus scrofa

source_name: Heart, left ventricle

extract_protocol:
Fresh tissues (100-200 mg) were cut into small pieces in cold UW solution or lysis buffer (10 mM Tris-HCl 8.0, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 0.5 mM EGTA, 2 mM EDTA, 1 mM PMSF, 1 mM DTT and 50 U/mL RNase inhibitor in 0.32 M sucrose buffer); then, the tissue samples were homogenized for 18 seconds in 10 mL of lysis buffer, placed on ice for 10 minutes, and filtered with 100-μm and 70-μm strainers. The lysate was centrifuged for 10 minutes at 700 g and 4 °C, resuspended in 5 mL nuclei wash and resuspension buffer (1.0% BSA supplemented with 80 U/mL RNase inhibitor), and filtered with a 40-μm strainer. Nuclei were collected by centrifuging for 10 minutes at 700 g at 4 °C and then resuspending the pellet in 400 μL of 1.0% BSA containing 200 U/mL RNase inhibitor. Nuclei were stained with propidium iodide for 5 minutes, selected by flow cytometry, and processed via the 10X Genomics Single-Cell Protocol
Library was prepared according to the manufacturer's instruction (10X Genomics, https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/sample-prep/isolation-of-nuclei-for-single-cell-rna-sequencing-and-tissues-for-single-cell-rna-sequencing)
single-nuclei RNA sequencing

value: Heart, left ventricle

value: All cell types

value: KO/OEhiPSC-CM injection


title: RNAseq_TBPIR_NSC rep1


title: RNAseq_control_NSC rep1


title: KO/OEhiPSC-CM, 4 week after I/R, Pig 2


title: bcr10

value: Peripheral blood mononuclear cells, FACS selected to enrich non-naive B and dendritic cells


title: bcr09


title: bcr07


title: DH-Dox-01

description:
experiment02
21053R-03-16
iETV2-KDM4A (H188A), DOX

value: iETV2-KDM4A (H188A)

value: DOX


title: WThiPSC-CM, 4 week after I/R, Pig 3

value: WThiPSC-CM injection


title: DH-Dox-03

description:
experiment02
21053R-03-18
iETV2-KDM4A (H188A), DOX


title: DH-Dox-02

description:
experiment02
21053R-03-17
iETV2-KDM4A (H188A), DOX


title: TBP_mitosis_NSC_CUTandTag rep2

data_processing:
Raw FASTQ reads were trimmed using Trim Galore (v0.6.10, with parameters --paired --quality 20 --stringency 3 -j 4).
Trimmed reads were mapped to Drosophila reference genome (version: dm6) using Bowtie2 (v2.5.1) very-sensitive-local mode
Picard tools were used to remove duplicate reads. Reads with a low mapping quality score were further filtered using Samtool
Assembly: dm6 or hg38
Supplementary files format and content: bigwig files were generated using bamCoverage (--binSize 50 --normalizeUsing RPKM --extendReads)

growth_protocol: Flies were reared and crossed according to standard procedures. HEK 293T cells were grown in DMEM containing 10% (v/v) fetal bovine serum, 1% non-essential amino acids at 37℃ with 5% CO2.

extract_protocol:
For CUT&Tag carried out by using interphase and mitosis neural stem cells or HEK 293T cells, the cells were fixed with 1% formaldehyde for 7min and quenched by Glycine. In other experiments, the cells are not fixed. The cells were arrested by ConA beads, and the factor of interest are combined by the specific primary antibody, followed by secondary antibody and Tn5 transposase.
CUT&Tag libraries were prepared using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) complemented with TruePrep Index Kit V2 for Illumina (Vazyme). 1w-100w cells were used as starting materials. Libraries were amplified using 13-19 cycles on the thermocycler. Post-amplification libraries were size selected at 200-2000 bp in length using VAHTS DNA Clean Beads (Vazyme).

value: larval brain

value: type II neural stem cell

value: wild type

value: sort out mitotic neural stem cells


title: bcr08

value: Blood

value: Peripheral blood mononuclear cells


title: bcr05


title: DH-No-03

description:
experiment02
21053R-03-15
iETV2-KDM4A (H188A), Control


title: KO/OEhiPSC-CM, 4 week after I/R, Pig 1


title: TBP_mitosis_NSC_CUTandTag rep1


title: DH-No-02

description:
experiment02
21053R-03-14
iETV2-KDM4A (H188A), Control


title: TBP_mitosis_NSC_CUTandTag rep3


title: bcr12


title: bcr04


title: bcr06


title: IgG_mitosis_NSC_CUTandTag


title: IgG_interphase_NSC_CUTandTag

value: sort out interphase neural stem cells


title: TBP_interphase_NSC_CUTandTag rep3


title: bcr03


title: TBP_interphase_NSC_CUTandTag rep2


title: MCS-Dox-03

description:
experiment01
21053R-03-06
iETV2, DOX


title: basal medium, 4 week after I/R, Pig 2

value: basal medium injection


title: MCS-Dox-02

description:
experiment01
21053R-03-05
iETV2, DOX

value: embryonic stem cell


title: bcr02


title: DH-No-01

description:
experiment02
21053R-03-13
iETV2-KDM4A (H188A), Control

value: Control


title: basal medium, 4 week after I/R, Pig 3

value: Heart, left ventricle


title: Placental tissue, Preeclampsia 7

city: Malatya

first: Berat

last: Dogan

address: Faculty of Eng.

department: Biomedical Eng.

country: Turkey

institute: Inonu University

data_processing:
Quality control was performed using the fastqc software.
TrimGalore, was utilized to remove adapters and trim low-quality reads.
The reads were then aligned to the human genome (GRCh38 version) using the STAR.
Following the alignment, the featureCounts  was used to obtain a count matrix.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Placental tissue

extract_protocol:
Total placental RNA was extracted from ~25 mg of tissue using the RNeasy Mini Kit (Qiagen)
RNA-seq libraries were prepared from the extracted RNA using the QIAseq Stranded mRNA Select Kit (180775) (Qiagen) following the manufacturer’s protocols.

value: Placental tissue

tag: condition

value: Preeclampsia


title: H2A.Z_NSC_CUTandTag rep3


title: WThiPSC-CM, 4 week after I/R, Pig 1

value: All cell types


title: MCS-No-02

description:
experiment01
21053R-03-02
iETV2, Control


title: Placental tissue, Preeclampsia 5


title: basal medium, 4 week after I/R, Pig 1


title: TBP_interphase_NSC_CUTandTag rep1


title: Placental tissue, Preeclampsia 6


title: MCS-Dox-01

description:
experiment01
21053R-03-04
iETV2, DOX


title: MCS-No-03

description:
experiment01
21053R-03-03
iETV2, Control


title: bcr01


title: H2A.Z_NSC_CUTandTag rep2


title: TBP_dEP400IR control_NSC_CUTandTag

value: dEP400 RNAi control


title: H2A.Z_NSC_CUTandTag rep1


title: WThiPSC-CM, 4 week after I/R, Pig 2


title: KO/OEhiPSC-CM, 1 week after I/R, Pig 1

value: KO/OEhiPSC-CM injection


title: KO/OEhiPSC-CM, 1 week after I/R, Pig 3


title: MycdEP400_TBPIR control_NSC_CUTandTag rep2

value: TBP RNAi control


title: WT, aortic root and ascending aorta, sc-RNA seq

first: Jiaqi

last: Huang

address: Xueyuan Road 38

description: 10× Genomics

data_processing:
The R package Seurat (version 3.2.2) was used for analyzing scRNA-seq data. Briefly, gene features expressed in at least three cells and cells with at least 100 detected genes were retained; then, cells displaying fewer than 200 gene features or having more than 5% mitochondrial counts were filtered. After passing the quality control metrics, 3888 cells in WT group and 6409 cells in Fbn1C1041G/+ group were further analyzed. Then, gene expression was normalized by “LogNormalize.”. Integrative analysis of the two groups was performed using canonical correlation analysis to remove batch effects. A standard integrated analysis was performed with default parameters. The top 2000 highly variable genes were selected and scaled by “ScaleData.”. Principal components analysis was then performed, and the first 15 principle components with a resolution of 0.2 were used for unbiased clustering. Clusters were visualized with tSNE. The markers for every cluster compared to all remaining cells were identified by “FindAllMarkers” (min.pct = 0.25, logfc.threshold = 0.25, only.pos = TRUE) and were used as DEGs in the following analyses. Reported Padjusted values were calculated using Benjamini-Hochberg correction. Heatmaps of scRNA-seq data were plotted with R package ggplot2.
Assembly: GRCm39
Supplementary files format and content: csv

source_name: aortic

extract_protocol:
The mice were sacrificed by sodium pentobarbital, followed by perfusion with cold PBS. The aortic root and ascending aortas were collected in a tube with 1 ml Kreb’s buffer on ice. Perivascular adipose were carefully removed. After collecting all arteries，the arteries were washed with PBS for three times and cutted into 1-2 mm2 in tube and digested with aortic dissociation enzyme solution (Collagenase I, 450 U/ml; Hyaluronidase type I-S, 60 U/ml; DNase I, 60 U/ml; Collagenase XI, 125 U/ml) . The digestion was performed at 37℃ shaker for 1-2 h, and the tube was gently invert every 15 mins21. Detached cells were collected until the tissue dissolved completely. After sufficient digestion, single cell suspension was strained through a 70-µm strainer. And the collected cells were centrifuged 10 min at 700 g speed at 4 ℃. For scRNA-seq, single cell suspensions from 3 mice were pooled as one sample.
Single cell suspensions of aortic root and ascending aortas from WT and Fbn1C1041G/+ mice were stained with a LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit (1:1000) and Hoechst 33342 (Invitrogen, H3570; 1:1000) for 20 min on ice. After being washed in PBS, cells were resuspended in PBS. Single live cells (Hoechst+/Dead Cell Stain−) were sorted into PBS with 0.04% BSA using a BD FACS Symphony S6 (BD Biosciences). A Chromium Single Cell 3’ Reagent Kit v3 was used, and Standard 10X Chromium Single Cell 3’ v3 (10X Genomics GemCode Technology) protocols were followed for scRNA-seq. Briefly, single cells with specific 10X barcodes and unique molecular identifiers were generated by partitioning the cells into Gel Bead-in-Emulsions. A cDNA library was generated and sequenced with a Novaseq (S4) 6000 instrument (PE150). Raw sequencing data were processed using Cell Ranger (version 3.1) to demultiplex raw data and generate FASTQ files, and the resulting data were aligned and counted with Cell Ranger pipelines.
The R package Seurat (version 3.2.2) was used for analyzing scRNA-seq data. Briefly, gene features expressed in at least three cells and cells with at least 100 detected genes were retained; then, cells displaying fewer than 200 gene features or having more than 5% mitochondrial counts were filtered. After passing the quality control metrics, 3888 cells in WT group and 6409 cells in Fbn1C1041G/+ group were further analyzed. Then, gene expression was normalized by “LogNormalize.”. Integrative analysis of the two groups was performed using canonical correlation analysis to remove batch effects. A standard integrated analysis was performed with default parameters. The top 2000 highly variable genes were selected and scaled by “ScaleData.”. Principal components analysis was then performed, and the first 15 principle components with a resolution of 0.2 were used for unbiased clustering. Clusters were visualized with tSNE. The markers for every cluster compared to all remaining cells were identified by “FindAllMarkers” (min.pct = 0.25, logfc.threshold = 0.25, only.pos = TRUE) and were used as DEGs in the following analyses. Reported Padjusted values were calculated using Benjamini-Hochberg correction. Heatmaps of scRNA-seq data were plotted with R package ggplot2.

value: aortic

value: WT


title: MCS-No-01

description:
experiment01
21053R-03-01
iETV2, Control


title: WThiPSC-CM, 1 week after I/R, Pig 3

value: WThiPSC-CM injection


title: Placental tissue, Preeclampsia 1


title: Placental tissue, Preeclampsia 4


title: C1.1, Input

city: Hong Kong

first: YIXIN

last: ZOU

state: State...

address: PB301, 3/F, Professorial Block, No.102, Pokfulam Road, Queen Mary Hospital

department: Department of Medicine

institute: the University of Hong Kong

data_processing:
Software from Illumina (bcl2fastq) was used for sequencing reads
Mapped reads were filtered to retain only unique reads that properly mapped and paired with a mapping quality > 30 (MQ >30).
Peak calling was done using MACS2 with default parameters (q-value < 0.05)
Peakcalls of MACS2 were further filtered with the ENCODE blacklist regions (Amemiya et al. 2019).
Assembly: Mouse Genome mm10
Supplementary files format and content: Binary Alignment/Map files (BAM), narrowPeak (except for Input sample)

growth_protocol: The murine tubular epithelial cell line (C1.1) was maintained in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F-12), GlutaMAX® medium, supplemented with 10% fetal bovine serum, 100 IU/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
Cells were cross-linked with 1% formaldehyde and cell pellet was digested by nuclease and sheared into small fragments by sonication. The digested chromatin sample was incubated with antibody followed by Protein G magnetic beads. The protein/Protein G-bound chromatin complex was immunoprecipitated and DNA was eluted and purified for further analysis.
All the libraries were prepared based on the protocols of KAPA Hyper Prep Kit. Illumina NovaSeq 6000 was used for sequencing. Input samples collected before immunoprecipitation were used as control for analysis.

treatment_protocol: C1.1 cells were transfected with Foxp2 CRISPR Activation Plasmid and stably selected according to the manufacturer’s instructions.

value: murine tubular epithelial cell


title: FBN1, aortic root and ascending aorta, sc-RNA seq

description: 10× Genomics


title: TBP_dEP400IR_NSC_CUTandTag

value: larval brain

value: type II neural stem cell

value: dEP400 RNAi


title: WThiPSC-CM, 1 week after I/R, Pig 2


title: Placental tissue, Control 4


title: MycdEP400_TBPIR_NSC_CUTandTag rep2

value: TBP RNAi


title: CUT&RUN, H3K4me3,Trp53_WT,Rep2

first: Sajid

middle: A

last: Marhon

state: ON

address: 101 College Street

institute: Princess Margaret Cancer Centre

data_processing:
library strategy: CUT&RUN-seq
Raw reads were trimmed using fastp tool to remove adapters and low quality bases. Trimmed reads were aligned to the mouse genome mm10 and yeast genome using bowtie2 tool. Peaks were called using MACS2 tool. Genome track coverage bigwig files were generated using the bamCoverage command from deepTools package.
Assembly: mm10
Supplementary files format and content: Bigwig files include genome coverage tracks.
Supplementary files format and content: Bed file include coordinates of called peaks.

source_name: ovarian surface epithelium

extract_protocol:
CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction.
DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer’s instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000.

value: ovarian surface epithelium

value: epithelial

value: immortilized, untreated


title: KO/OEhiPSC-CM, 1 week after I/R, Pig 2

value: Heart, left ventricle


title: Placental tissue, Preeclampsia 3

value: Placental tissue

value: Preeclampsia


title: WThiPSC-CM, 1 week after I/R, Pig 1

value: All cell types


title: Myc_control_NSC_CUTandTag rep1

value: wild type


title: Placental tissue, Preeclampsia 2


title: Control_Selective

city: Würzburg

first: Redmond

last: Smyth

state: Bayern

address: Josef-Schneider-Straße 2, D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description: Library name: Control_Selective

data_processing:
Basecalling and demultiplexing with dorado
Alignment with Last aligner
Mutations counted with rf-count
Data normalisation with rf-norm. Mutation rates of shared control are subtracted from corresponding cell samples
Assembly: Aligned against specific sequence; Non-selective CCCCCCCUAACGUUACUGGCCGAAGCCGCUUGGAAUAAGGCCGGUGUGCGUUUGUCUAUAUGUUAUUUUCCACCAUAUUGCCGUCUUUUGGCAAUGUGAGGGCCCGGAAACCUGGCCCUGUCUUCUUGACGAGCAUUCCUAGGGGUCUUUCCCCUCUCGCCAAAGGAAUGCAAGGUCUGUUGAAUGUCGUGAAGGAAGCAGUUCCUCUGGAAGCUUCUUGAAGACAAACAACGUCUGUAGCGACCCUUUGCAGGCAGCGGAACCCCCCACCUGGCGACAGGUGCCUCUGCGGCCAAAAGCCACGUGUAUAAGAUACACCUGCAAAGGCGGCACAACCCCAGUGCCACGUUGUGAGUUGGAUAGUUGUGGAAAGAGUCAAAUGGCUCUCCUCAAGCGUAUUCAACAAGGGGCUGAAGGAUGCCCAGAAGGUACCCCAUUGUAUGGGAUCUGAUCUGGGGCCUCGGUGCACAUGCUUUACAUGUGUUUAGUCGAGGUUAAAAAACGUCUAGGCCCCCCGAACCACGGGGACGUGGUUUUCCUUUGAAAAACACGAUGAUAAUAUGGCCACAACCAUGUCUAG; Selective CCCCCCCUAACGUUACUGGCCGAAGCCGCUUGGAAUAAGGCCGGUGUGCGUUUGUCUAUAUGUUAUUUUCCACCAUAUUGCCGUCUUUUGGCAAUGUGAGGGCCCGGAAACCUGGCCCUGUCUUCUUGACGAGCAUUCCUAGGGGUCUUUCCCCUCUCGCCAAAGGAAUGCAAGGUCUGUUGAAUGUCGUGAAGGAAGCAGUUCCUCUGGAAGCUUCUUGAAGACAAACAACGUCUGUAGCGACCCUUUGCAGGCAGCGGAACCCCCCACCUGGCGACAGGUGCCUCUGCGGCCAAAAGCCACGUGUAUAAGAUACACCUGCAAAGGCGGCACAACCCCAGUGCCACGUUGUGAGUUGGAUAGUUGUGGAAAGAGUCAAAUGGCUCUCCUCAAGCGUAUUCAACAAGGGGCUGAAGGAUGCCCAGAAGGUACCCCAUUGUAUGGGAUCUGAUCUGGGGCCUCGGUGCACAUGCUUUACAUGUGUUUAGUCGAGGUUAAAAAACGUCUAGGCCCCCCGAACCACGGGGACGUGGUUUUCCUUUGAAAAACACGAUGAUAAUAUGGCCACAACCAUGUCUAG
Supplementary files format and content: csv files containing DMS reactivities

organism: synthetic construct

extract_protocol:
Trizol extracts
Reverse transcribed with MarathonRT, amplified with gene specific primers. Sequencing libraries prepared using end-repiar dA-tailing, then ligation of nanopore barcodes and sequencing adaptors


title: MycdEP400_TBPIR_NSC_CUTandTag rep1


title: basal medium, 1 week after I/R, Pig 3

value: basal medium injection


title: ELL-Myc_NSC_CUTandTag rep2


title: C1.1, Foxp2,ChIP


title: ELL-Myc_NSC_CUTandTag rep1


title: MycdEP400_TBPIR control_NSC_CUTandTag rep1

value: TBP RNAi control


title: Placental tissue, Control 2

value: Control


title: CUT&RUN, H3K4me3,Trp53_KO,Rep2


title: basal medium, 1 week after I/R, Pig 1


title: Placental tissue, Control 3


title: Cell_Selective_2

description: Library name: Cell_Selective_2


title: TBP_TBPIR control_NSC_CUTandTag


title: Cell_Selective_1

description: Library name: Cell_Selective_1


title: Cell_Non-Selective_2

description: Library name: Cell_Non-Selective_2


title: CUT&RUN, H3K4me3,Trp53_KO,Rep1


title: IgG_mitosis_HEK_CUTandTag

source_name: HEK 293T

value: HEK 293T

value: sort out mitosis HEK 293T cells


title: Cell_Non-Selective_1

description: Library name: Cell_Non-Selective_1


title: CUT&RUN, H3K9me3,Trp53_WT,Rep2

data_processing:
Raw reads were trimmed using fastp tool to remove adapters and low quality bases. Trimmed reads were aligned to the mouse genome mm10 and yeast genome using bowtie2 tool. Peaks were called using MACS2 tool. Genome track coverage bigwig files were generated using the bamCoverage command from deepTools package.
Assembly: mm10
Supplementary files format and content: Bigwig files include genome coverage tracks.
Supplementary files format and content: Bed file include coordinates of called peaks.
Library strategy: CUT&RUN

growth_protocol: Asynchronous growth

value: immortalized, untreated

tag: time


title: IgG_NSC_CUTandTag

value: larval brain

value: type II neural stem cell


title: Placental tissue, Control 1


title: IgG_asy_HEK_CUTandTag


title: hTBP_mitosis_HEK_CUTandTag rep1


title: basal medium, 1 week after I/R, Pig 2


title: Control_Non-Selective

description: Library name: Control_Non-Selective


title: CUT&RUN, H3K9me3,Trp53_WT,Rep1


title: CUT&RUN, H3K4me3,Trp53_WT,Rep1


title: Myc_control_NSC_CUTandTag rep2


title: TBP_TBPIR_NSC_CUTandTag

value: TBP RNAi


title: CUT&RUN, H3K9me3,Trp53_KO,Rep2

value: ovarian surface epithelium


title: TBP_NSC_CUTandTag


title: SA-9h, scRNA-seq, High sequencing depth results (0609-7)

city: Wuhan

first: Xiaodan

last: Yan

state: Hubei Province

address: Donghu Road, No. 115, Wuchang District,

department: Medical Research Institute

institute: Wuhan University

description:
RiboD-PETRI
Detailed_Computational_Pipeline.txt
scripts.tar.gz

data_processing:
The demultiplexing, barcodes processing, gene counting and aggregation of scRNA-seq datas were made by scripts compiled in Python 2.7.15 as previously described with some modifications. [lattman, W. Jiang, P. Oikonomou, S. Tavazoie, Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing. Nature microbiology 5, 1192 (Oct, 2020).]. Downstream analysis of single cell data was performed using pipelines detailed in Seurat v4.3.0.
For corralation analysis of bulk RNA-Seq and scRNA-seq data, scRNA-seq data was combined with the UMI sums of all cells. Single-cell and bulk transcriptomes of E.coli were compared by computing the Pearson correlation of log2 transcripts reads of each gene between the two measurements.
For scRNA-seq data mRNA / total RNA ratio analysis, we removed the barcodes sequence contained in the front, and the interference of the last ten bases, and kept only 20 bases for mapping. Then we mapped the data from the different species to the corresponding reference genomes.
(Detailed codes were saved in "Detailed Computational Pipeline.docx" and "scripts" compressed package .)
Assembly: E.coli MG1655 K12
Supplementary files format and content: matrix files
Supplementary files format and content: xlsx file include raw counts for RNA-seq and UMI sums of scRNA-seq data
Supplementary files format and content: tab-delimited files includes raw counts for samples

organism: Staphylococcus aureus

source_name: bacterial cell

extract_protocol:
For RiboD-PETRI, all  cells were from pure culture in vitro. Cells were harvested by centrifuge;
For RiboD-PETRI, library was performed accarding to the Materials and Methods section;

value: bacterial cell

value: WT

value: stationary growth phase


title: hH2A.Z_HEK_CUTandTag rep2


title: hTBP_mitosis_HEK_CUTandTag rep2


title: hH2A.Z_HEK_CUTandTag rep1


title: CUT&RUN, H3K9me3,Trp53_KO,Rep1

value: epithelial


title: hTBP_asy_HEK_CUTandTag


title: CUT&RUN, H3K27me3,Trp53_WT,Rep2


title: ATAC_H2A.Z loss of function_NSC rep2

extract_protocol:
For ATAC-seq carried out by using mitotic neural stem cells, the cells were fixed with 1% formaldehyde for 7min and quenched by Glycine. In other experiments, the cells are not fixed. The cells were lysised and tagmented by using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme).
ATAC-seq libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) complemented with TruePrep Index Kit V2 for Illumina (Vazyme). About 1w cells were used as starting materials. Libraries were amplified using 12-15 cycles on the thermocycler. Post-amplification libraries were size selected at 50-1000 bp in length using VAHTS DNA Clean Beads (Vazyme).

value: H2A.Z loss of function


title: ATAC_H2A.Z loss of function_NSC rep1


title: Erythroblasts differentiated from human CD34+ cells edited at the HBG1/2 promoters C

city: Cambridge

first: KaiHsin

last: Chang

state: Massachusetts

address: 11 Hurley St

institute: Editas Medicine

description: Transcriptome analysis of erythroblast cells edited with HBG1_2-targeting RNP at 8µM, replicate C.

data_processing:
NovaSeq Control software, bcl2fastq 2.20 software, HiSat2 v2.2.1, Subread package v2.0.6, edgeR v3.42.4
Image analysis and base calling were conducted by the NovaSeq Control software. Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification
Reads were aligned to the human reference genome (hg38) using HiSat2 v2.2.1.
Reads aligned to exon regions of genes based on Ensembl-98 annotation were counted using featureCounts in Subread package v2.0.6 . Read counts were normalized by using edgeR v3.42.4 after filtering genes with low read counts (CPM<1 in more than 6 samples).
Assembly: hg38
Supplementary files format and content: Comma-separated CSV file contains raw counts for each sample.
Supplementary files format and content: Comma-separated CSV files contains normalized TMM counts for each sample.

source_name: Erythroblast Cells

growth_protocol: Mobilized human CD34+ cells, either electroporated without RNP (unedited control), or electroporated with 8 μM RNP targeting either BCL11A erythroid enhancer or HBG1/2 promoters were placed in erythroid culture conditions for 11 days.

extract_protocol:
Total RNA was extracted from frozen cell pellet samples using the RNeasy Plus Mini Kit (Qiagen) following manufacturer’s instructions.
RNA libraries for strand-specific sequencing were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, according to the manufacturer's instructions.

treatment_protocol:
CD34+ cells were electroporated without RNP (unedited control) or with 8 μM RNP targeting either the BCL11A erythroid enhancer or the HBG1 and HBG2 promoters.
Electroporation was carried out using a MaxCyte GT electroporation device per manufacturer’s instructions.

value: Erythroblast Cells

value: Edited HBG1_2 promoter

value: HBG1_2 8µM


title: SA-3h-ΔΔ-replicate 2, scRNA-seq (0612-2)

description:
RiboD-PETRI
SA rRNA and mRNA reads.txt
Detailed_Computational_Pipeline.txt
scripts.tar.gz

value: exponential growth phase


title: ATAC_H2A.Z loss of function control_NSC

value: H2A.Z loss of function control


title: CUT&RUN, H3K27me3,Trp53_WT,Rep1


title: SA-3h, replicate 2, scRNA-seq (0119-F)

description:
PETRI
SA rRNA and mRNA reads.txt
Detailed_Computational_Pipeline.txt
scripts.tar.gz


title: SA-3h-ΔΔ-replicate 1, scRNA-seq (0612-1)


title: CUT&RUN, H3K27me3,Trp53_KO,Rep2


title: ATAC_dEP400IR control_NSC

value: dEP400 RNAi control


title: CUT&RUN, H3K27me3,Trp53_KO,Rep1


title: SA-3h, replicate 1, scRNA-seq (0119-E)


title: Erythroblasts differentiated from human CD34+ cells edited at the HBG1/2 promoters A

description: Transcriptome analysis of erythroblast cells edited with HBG1_2-targeting RNP at 8µM, replicate A.


title: EC-3h-ΔΔ, scRNA-seq, High sequencing depth results (0427-3_HSD)

organism: Escherichia coli str. K-12 substr. MG1655


title: EC-3h, replicate 2, scRNA-seq (0615-2)

description:
PETRI
ECOLI rRNA and mRNA reads.txt
Result of correlation analysis between bulk and RiboD-PETRI.xlsx
Detailed_Computational_Pipeline.txt
scripts.tar.gz


title: CUT&RUN, H3K27ac,Trp53_KO,Rep2


title: ATAC_dEP400IR_NSC

value: dEP400 RNAi


title: Erythroblasts differentiated from human CD34+ cells edited at the BCL11A erythroid enhancer B

description: Transcriptome analysis of erythroblast cells edited with BCL11A-targeting RNP at 8µM, replicate B.

value: Edited BCL11A erythroid enhancer

value: BCL11A 8µM


title: CUT&RUN, H3K27ac,Trp53_WT,Rep1

value: immortalized, untreated


title: EC-3h-ΔΔ, replicate 2, scRNA-seq (0427-4)

description:
RiboD-PETRI
ECOLI rRNA and mRNA reads.txt
Detailed_Computational_Pipeline.txt
scripts.tar.gz


title: CUT&RUN, p53,Trp53_WT,Rep2

description:
Trp53_WT.Specific.p53.Peaks.bed
p53_WT.Pooled.bw
Mouse_Trp53_WT_p53_Peaks_mm10.tsv.gz
Mouse_Trp53_WT_Specific_p53_Peaks_Genomic_Annotation_mm10.tsv.gz
Mouse_Trp53_WT_Specific_p53_Peaks_mm10.tsv.gz
Mouse_Trp53_WT_Specific_p53_Peaks_Repeat_Annotation_mm10.tsv.gz


title: Erythroblasts differentiated from human CD34+ cells edited at the BCL11A erythroid enhancer C

description: Transcriptome analysis of erythroblast cells edited with BCL11A-targeting RNP at 8µM, replicate C.


title: EC-3h-ΔΔ, replicate 1, scRNA-seq (0427-3)

description:
RiboD-PETRI
ECOLI rRNA and mRNA reads.txt
Result of correlation analysis between PETRI and RiboD-PETRI.xlsx
Detailed_Computational_Pipeline.txt
scripts.tar.gz


title: ATAC_mitosis_NSC rep3

value: larval brain

value: type II neural stem cell

value: wild type

value: sort out mitotic neural stem cells


title: Erythroblasts differentiated from human CD34+ cells edited at the BCL11A erythroid enhancer A

description: Transcriptome analysis of erythroblast cells edited with BCL11A-targeting RNP at 8µM, replicate A.


title: Erythroblasts differentiated from unedited human CD34+ cells C

description: Transcriptome analysis of unedited erythroblast cells, replicate C.

value: Wild Type

value: MOCK 0µM


title: CUT&RUN, p53,Trp53_WT,Rep1

value: ovarian surface epithelium

value: epithelial


title: EC-3h, replicate 1, scRNA-seq (0615-1)

description:
PETRI
ECOLI rRNA and mRNA reads.txt
Result of correlation analysis between PETRI and RiboD-PETRI.xlsx
Detailed_Computational_Pipeline.txt
scripts.tar.gz

value: bacterial cell

value: WT


title: Erythroblasts differentiated from unedited human CD34+ cells B

description: Transcriptome analysis of unedited erythroblast cells, replicate B.

value: Erythroblast Cells


title: ATAC_asyn_NSC rep1


title: ATAC_mitosis_NSC rep2


title: CUT&RUN, H3K27ac,Trp53_KO,Rep1


title: Erythroblasts differentiated from human CD34+ cells edited at the HBG1/2 promoters B

description: Transcriptome analysis of erythroblast cells edited with HBG1_2-targeting RNP at 8µM, replicate B.

value: Edited HBG1_2 promoter

value: HBG1_2 8µM


title: EC-24h-static-ΔΔ, replicate 1, scRNA-seq, High sequencing depth results (1214-7)

value: 24 h static biofilm


title: CUT&RUN, IgG_CST

value: IgG


title: ATAC_mitosis_NSC rep1


title: whole blood, cow 13, PI

city: Knoxville

first: Sonia

middle: Josefina

last: Moisa

state: Knox

address: 2506 River Drive

department: Animal Science

institute: University of Tennessee

data_processing:
A total number of 2,986,548 read pairs were generated for the 36 libraries, with sequencing yields ranging from 8,015 to 221,822 per sample. The read quality was checked by FastQC v11.5.
Sequencing adapter sequences and low-quality bases were trimmed using Trimmomatic v0.3. The high-quality reads were mapped to the cattle reference genome (GenBank: GCA_002263795.2). Finally, Salmon 1.10.2 was used to quantify the expression of the transcripts.
The DESeq2 package in R was used to normalize read counts and detect differentially expressed genes (DEGs) at a False Discovery Rate (FDR) threshold of 0.05. The log2 fold change (LogFC) was determined for each gene.
Assembly: Raw sequence reads were aligned to the cow reference genome (Bos taurus ARS-UCD1.2) using STAR (Dodson et al., 2015), and counted using HtSeq.
Supplementary files format and content: Excel file determines raw count for each sample.

organism: Bos taurus

extract_protocol:
RNA was extracted from frozen PBMC pellets using TRIzol according to the manufacturer’s recommendations. RNA pellets were resuspended in 20 uL of 1:40 RNAse inhibitor/RNAse-free water mix and stored at -80°C. A NanoDrop C Spectrophotometer was used for RNA quantification measuring absorbance at 260 nm. Samples were assessed for quality based on AD 260/280 ratios of > 1.9 and OD 260/230 > 2.0.  Finally, quality of RNA samples was confirmed using a Tapestation 4200 (Agilent, Inc). RNA samples having a RIN > 7 were used for subsequent analysis.
A targeted RNA sequencing approach was used to quantify expression levels in PBMC from the coccygeal vein of previously diagnosed PI calves vs. controls. Primers were selected to produce amplicons that span exon-intron boundaries, using gene models extracted from Ensembl (www.ensembl.org) based on the cow genome assembly ARS-UCD1.2. The primer sets information is provided in Additional Table 2. After validating the primers set, cDNAs were amplified in triplicates and sequenced using the same multiplex approach. Targeted RNA-seq was performed by an optimized Hi-Plex approach by Floodlight Genomics (Knoxville, TN, USA) as part oftheir Educational and Research Outreach Program (EROP) and sequencing on an Illumina MiSeq device running a 2 × 150 configuration. The resulting sequences were mapped to the Bos Taurus genome assembly using CLC Genomics Workbench version 9.5.2 (Qiagen; Bethesda, MD) with default settings.  Multi-dimensional scaling (MDS) showed a separation in PI status compared to the control animals with the remove unwanted variation factor (RUV) set to 4.
Targeted RNAseq

value: Blood

value: PI

value: BVDV


title: CUT&RUN, H3K27ac,Trp53_WT,Rep2

value: immortalized, untreated


title: ATAC_asyn_NSC rep2

value: larval brain

value: type II neural stem cell

value: wild type


title: CUT&RUN, p53,Trp53_KO,Rep2

description:
p53_KO.Pooled.bw
Mouse_Trp53_KO_p53_Peaks_mm10.tsv.gz


title: EC-24h-static-ΔΔ, replicate 2, scRNA-seq, High sequencing depth results (1214-8)

description:
RiboD-PETRI
Detailed_Computational_Pipeline.txt
scripts.tar.gz


title: STIC,P10,Normal

description:
total RNA (rRNA-depleted)
All_Repeats_STIC_Lesion_vs_STIC_Normal_hg38.tsv.gz
Genes_STIC_Lesion_vs_STIC_Normal_statistics.tsv.gz
Human_STIC_RNASeq_Genes_Counts.tsv.gz
Upregulated_Repeats_STIC_Lesion_vs_STIC_Normal_hg38.tsv.gz

data_processing:
Raw reads were trimmed to remove adapters and low quality bases. Trimmed reads were aligned to the human genome hg38 using the STAR pipeline. Read counts were calculated for genes and repeat elements using featureCount tool. Differential analysis was performed using edgeR tool.
Assembly: hg38
Supplementary files format and content: Counts and FC

source_name: fallopian tube epithelium

extract_protocol:
RNA isolated from LCM-captured region from FFPE sections
Laser capture miscrodissection of pathologist-annotated lesion or adjacent normal tissue from FFPE sections. Dual RNA/DNA extraction from FFPE samples was performed by the OICR Diagnostic Development Program laboratory using the ThermoFisher KingFisher handler. The extraction protocol was specifically optimized for this work using excess LCM ‘waste’ material from the same clinical samples. Isolated RNA was quantified using a Qubit Fluorometer.
25ng of isolated RNA from FFPE tissue was subjected to rRNA depletion and library preparation using the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (Illumina, cat# 20040529) with 13 cycles of amplification used. Prepared libraries were assessed for quality and fragment size distribution using Agilent High Sensitivity DNA kit (Agilent, cat# o 5067-4627) on the Bioanalyzer 2100 system. Where relevant, dimers were removed using AMPure XP reagents (Beckman, cat# A63880). Libraries were then sequenced on an Illumina MiSeq to confirm sufficient unique alignment rates to hg38 as a validation of rRNA-depletion and sufficient library complexity. Libraries were subsequently sequenced on an Illumina NovaSeq6000 to obtain >80M reads per sample

value: fallopian tube epithelium

tag: tissue type

value: normal

tag: individual


title: Erythroblasts differentiated from unedited human CD34+ cells A

description: Transcriptome analysis of unedited erythroblast cells, replicate A.

value: Wild Type

value: MOCK 0µM


title: CUT&RUN, p53,Trp53_KO,Rep1

value: ovarian surface epithelium

value: epithelial


title: whole blood, steer 34, PI


title: whole blood, cow 2205, control

value: control


title: STIC,P11,Normal


title: STIC,P09,Normal


title: ARC_914005

first: Yaxin

last: Wang

address: No. 2, No. 1, Beichen West Road, Olympic Village Subdistrict

department: Institute of Genetics and Developmental Biology

institute: Chinese Academy of Sciences

data_processing:
Raw sequencing reads from DIPSEQ T-series sequencer were filtered and demultiplexed using PISA (v0.10) (https://github.com/shiquan/PISA). Reads were aligned to the modified GRCm38 mouse genome using STAR (v2.7.4a) (https://github.com/alexdobin/STAR) and sorted using Sambamba (v0.7.0) (1). A nucleus versus gene UMI count matrix was generated by PISA for downstream analysis.
Seurat R package (v4) was used for analysis.
Assembly: mm10
Supplementary files format and content: scdata_52022cells.rds are serialized R objects of the Bioconductor class ExpressionSet that contains the final data used to generate the results. It can be imported into R with `readRDS(“scdata_52022cells.rds”)`. It contains the gene counts, sample metadata, and feature metadata for single cells that passed quality control.

source_name: Brian

extract_protocol:
To isolate single nuclei from ARC of mice, we immersed the tissues in ice-cold homogenization buffer containing 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl, 0.1 mM DTT, 1% BSA, 0.1% NP-40, and ribonuclease inhibitor (0.4 U/μl). The tissues were then mechanically homogenized using a glass homogenizer for 10 cycles to obtain a single-nucleus suspension for snRNA-seq.
Single-nucleus RNA-seq libraries were prepared using DNBSEQ technology platforms (BGI Genomics, China) and the DNBelab C4 Single-Cell Library Prep Set (MGI Tech, #1000021082).

value: Brian


title: ARC_914008


title: whole blood, cow 43, PI


title: STIC,P11,Lesion

value: Lesion


title: whole blood, bull 16081, PI


title: Pp4, scRNAseq

city: Jinan

first: ling

middle: feng

last: lai

state: Shandong

address: Number 6699, Qingdao road

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

description: 10× Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cell Ranger software v7.1.0.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: pancreatic islet

extract_protocol:
Extracted islets from mice were pooled and dissociated into single cell suspension with 0.05 % trypsin (Cat# 25300062, Gibco) at 37 °C for 15 min, with shaking up and down once in every 2 min. And the digestion was stopped with RPMI1640 supplemented with 10 % FBS. Then cells were filtering with 30 μm cell strainers and centrifuged at 500 rpm for 5 min and resuspended with RPMI1640 (Cat# C11875500BT, Gibco) supplemented with 10 % FBS.
The prepared single cell suspension, 10× barcode gel magnetic bead and oil were loaded into 10× Genomics Chromium and sort into different cells of Chromium Chip (Cat# 1000120, 10× Genomics) to formed GEMs (Gel Bead-in-Emulsions), in which one droplet contain a gel magnetic bead with barcode and a cell. Chromium Next GEM Single Cell 3ʹ GEM Kit v3.1 (Cat# 1000123, 10× Genomics) were used for reverse transcription in the individual GEM and barcoded cDNA which purified by magnetic beads were amplified by PCR reaction. Also, Chromium Next GEM Single Cell 3ʹ Library Kit v3.1 (Cat# 1000157, 10× Genomics) were used for scRNA-seq library preparation according to the manufacturer’s protocols.

value: pancreatic islet

tag: time point


title: GD6_5, scRNAseq

description: 10× Genomics


title: ARC_914003


title: whole blood, heifer 9065, PI

value: Blood


title: ARC_914007


title: STIC,P08,Lesion


title: GD18_5, scRNAseq

description: 10× Genomics


title: ARC_914006


title: 3h, RNA-seq (1209-A)

data_processing:
RNA-Seq clean data was mapped to the MG1655 k12 genome using the BWA aligner software (version 0.7.17-r1188, https://github.com/lh3/bwa.git).
Then we converted the sam files to bam files using samtool.
The bam files were counted by featureCounts (v2.0.1, https://github.com/topics/featurecounts) to generate expression results. (Detailed codes were saved in "Detailed Computational Pipeline.docx".)
Assembly: E.coli MG1655 K12
Supplementary files format and content: tab-delimited file includes raw counts for RNA-seq sample
Supplementary files format and content: xlsx file include raw counts for RNA-seq and UMI sums of scRNA-seq data

extract_protocol:
RNA was harvested using Bacteria RNA Extraction Kit (Vazyme). 1μg of total RNA was used for construction of sequencing libraries;
RNA libraries for RNA-seq were prepared using Total RNA-seq (H/M/R) Library Prep Kit following manufacturer's protocols;

value: bacterial cell

value: WT

value: exponential growth phase


title: STIC,P08,Normal


title: GD14_5, scRNAseq

description: 10× Genomics


title: whole blood, cow 8022, control

value: BVDV


title: whole blood, cow 9014, control


title: whole blood, PI, bull 16064, PI

value: PI


title: GD10_5, scRNAseq

description: 10× Genomics


title: ARC_914004

value: wild type


title: STIC,P09,Lesion

value: fallopian tube epithelium


title: STIC,P10,Lesion


title: whole blood, cow 9550, control


title: ARC_914002


title: CC-3h, scRNA-seq, High sequencing depth results (0129-3)

organism: Caulobacter vibrioides NA1000


title: Virgin, scRNAseq

description: 10× Genomics

value: Virgin


title: ARC_914001


title: Stretch Follicle Cells, Well-fed, Rep3

city: Boston

first: Kimberly

last: McCall

address: 24 Cummington Mall

department: Biology

institute: Boston University

data_processing:
Base calling using Bcl2fastq v2.2 and adapter trimming using Cutadapt were performed by Boston University Microarray and Sequencing Core
Reads aligned to the Drosophila melanogaster reference genome BDGP6.32 release 104 using Salmon v1.1.0 in the quasi-mapping mode (parameters -  -l A,  gc-bias, –validatemappings)
Assembly: BDGP6.32 release 104
Supplementary files format and content: tab-delimited text file contains counts for each sample

source_name: Abdomen

growth_protocol: All flies were raised on standard molasses/yeast/agar/cornmeal food. Long term fly stocks were stored at 18 ̊C. Active stocks were raised at 25 ̊C. Crosses were performed at 25 ̊C

extract_protocol:
Whole fly thorax and abdomens were collected from approximately 100 flies for each sample. Ribosome immunoprecipitation was performed as per You S. et al 2021 PLOS Genetics
RNA libraries for RNA-seq were prepared using the Illumina TruSeq RNA Sample Preparation kit v2 by following the manufacturer's protocols

treatment_protocol: For the well-fed experimental condition, flies were aged 3 days at 25°C on standard cornmeal, molasses, and agar mixture, and then fed fresh yeast paste every 24 hours for 2 consecutive days before abdomens were dissected. For the protein starvation condition, flies were transferred for 16-20 hours to apple juice agar lacking yeast.

value: Abdomen

value: Stretch Follicle Cells

tag: group

value: Well-fed


title: STIC,P07,Normal

value: normal


title: Stretch Follicle Cells, Well-fed, Rep2


title: STIC,P04,Normal

description:
All_Repeats_STIC_Lesion_vs_STIC_Normal_hg38.tsv.gz
Genes_STIC_Lesion_vs_STIC_Normal_statistics.tsv.gz
Human_STIC_RNASeq_Genes_Counts.tsv.gz
Upregulated_Repeats_STIC_Lesion_vs_STIC_Normal_hg38.tsv.gz

value: Normal


title: CC-3h-ΔΔ-replicate 3, scRNA-seq (0225-6)

description:
RiboD-PETRI
CC rRNA and mRNA reads.txt
Detailed_Computational_Pipeline.txt
scripts.tar.gz


title: whole blood, cow 9520,  control

source_name: Blood

value: control


title: whole blood,steer 9303,  control


title: STIC,P07,Lesion

value: Lesion


title: STIC,P04,Lesion


title: STIC,P02,Normal


title: Stretch Follicle Cells, Well-fed, Rep1


title: chimeric_oligodendroglia_MET_3

city: Edinburgh

first: Nadine

last: Bestard-Cuche

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

description: 10X Genomics

data_processing:
The alignment to the reference genome, demultiplexing, barcoded processing, gene counting and cell calling were made using the Cell Ranger software (v5.0.0).
Assembly: GRCh38 2020-A, mm10, GRCh38-and-mm10-2020-A concatenation
Supplementary files format and content: CellRanger output (h5 format)
Supplementary files format and content: metadata in CSV files, with for each cell (on the rows) the following information (columns): nCount_originalexp nFeature_originalexp Barcode Project Treatment animalID Chemistry sum detected subsets_mt_sum subsets_mt_detected subsets_mt_percent total outlier subsets_mt_percent.1 sizeFactor scDblFinder.sample scDblFinder.class scDblFinder.score scDblFinder.weighted scDblFinder.cxds_score SampleID Sample chip S.Score G2M.Score Phase paper_annot

organism:
Homo sapiens
Mus musculus

source_name: corpus callosum

extract_protocol:
To harvest cells for single-cell RNAseq the monolayer oligodendrocytes were incubated in accutase solution for 5min at 37°C. Cells were collected into centrifuges 400×g for 5 min. The pellet was resuspended in Oligo Base medium for counting. The cell suspension was placed on ice when possible. The cortical brain organoids were dissociated using the Worthington Papain dissociation system, with extended sphere incubation in papain/DNase to 45min. Ten organoids were pulled together per sample. Cells from chimeric animal tissue were collected as previously described in (Neumann et al., 2019), with noted variations. In brief, animals were perfused using ice-cold HBSS+/+ (14025092, Thermo Fisher Scientific) and a brain matrix was used to excise the cc into HBSS-/- (12549069, Thermo Fisher Scientific) supplemented with 0.4 Units of RNase inhibitors (N808011, Life Technologies), where the tissue was mechanically dissociated with a scalpel. From this point onwards, 0.2 Units of RNase inhibitors were used at each step. The tissue was washed twice with HBSS-/-, centrifuged for 5min at 1,500rpm, resuspended in 0.62 units Research Grade Liberase DH (LIBDH-RO, Roche) and incubated for 40min at 37°C with gentle rocking. 2ml of MEM (12492013, Thermo Fisher Scientific) containing 0.5% BSA, 500 Units bovine pancreas DNase (DN25, Sigma-Aldrich) & 0.5ml FBS were added, and the tissue was mechanically triturated with a P1000 pipette and strained through a 70μm mesh. Tubes containing tissue were filled to full volume with MEM containing 0.5% BSA, centrifuged for 10min at 1,500rpm and resuspended into 0.2% BSA. Two cc were pulled together per sample. Live cells were sorted with LSRFortessa analyser (BIO-RAD) at the FACS facility at the Centre for Regenerative Medicine by Fiona Rossi and mixed human and mouse cells were centrifuged and resuspended in 100μl of 0.2% BSA.
Cell suspensions were processed by the Chromium Controller (10X Genomics) and barcoded libraries constructed using the Chromium Next GEM Single Cell 3’ v3.1 kit (PN-1000121) following manufacturer’s instructions. Samples were sequenced with Illumina NovaSeq6000.

value: corpus callosum

value: Shi/Shi x Rag2-/-

value: metformin


title: CC-3h-ΔΔ-replicate 2, scRNA-seq (0225-5)

value: bacterial cell

value: WT


title: Main Body Follicle Cells, Starved, Rep2

value: Main Body Follicle Cells

value: Starved


title: Main Body Follicle Cells, Starved, Rep3


title: Main Body Follicle Cells, Well-fed, Rep3


title: chimeric_oligodendroglia_MET_1

description: 10X Genomics


title: chimeric_oligodendroglia_MET_2

description: 10X Genomics


title: CC-3h-ΔΔ-replicate 1, scRNA-seq (0225-4)

value: exponential growth phase


title: chimeric_oligodendroglia_CTRL_2

description: 10X Genomics

value: vehicle (ddH2O)


title: CC--3h, replicate 3, scRNA-seq (0225-3)

description:
PETRI
CC rRNA and mRNA reads.txt
Detailed_Computational_Pipeline.txt
scripts.tar.gz


title: Main Body Follicle Cells, Starved, Rep1


title: CC--3h, replicate 2, scRNA-seq (0225-2)


title: STIC,P01,Normal

value: fallopian tube epithelium


title: STIC,P02,Lesion


title: STIC,P01,Lesion


title: Main Body Follicle Cells, Well-fed, Rep1

value: Abdomen


title: Main Body Follicle Cells, Well-fed, Rep2


title: CC--3h, replicate 1, scRNA-seq (0225-1)


title: chimeric_oligodendroglia_CTRL_1

description: 10X Genomics


title: BM5_Burn_Isotype

status: Public on Dec 09 2024

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: University of Cincinnati, 160 Panzeca Way

institute: University of Cincinnati

data_processing:
Data were de-multiplexed, and appropriate quality control checks were performed before aligning the sequences to the mouse reference genome  using  TopHat2 aligner
Assembly: Mm10
Supplementary files format and content: Counts data in Excell spreadsheet format

source_name: Whole bone marrow cells

extract_protocol:
The RNA was extracted by using mirVana miRNA Isolation Kit (Thermo Fisher, Grand Island, NY) with total RNA extraction protocol. NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used for polyA RNA purification with a total of 50 ng to 1 µg good quality total RNA as input. The Core used Apollo 324 system (WaferGen, Fremont, CA) and run PrepX PolyA script for automated ployA RNA isolation.
NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA) was used for library preparation, which used dUTP in cDNA synthesis to maintain strand specificity. In short, the isolated polyA RNA or rRNA/globin depleted RNA was Mg2+/heat fragmented (~200 bp), reverse transcribed to 1st strand cDNA, followed by 2nd strand cDNA synthesis labelled with dUTP. The purified cDNA was end repaired and dA tailed, and then ligated to adapter with a stem-loop structure. The dUTP-labelled 2nd strand cDNA was removed by USER enzyme to maintain strand specificity. After indexing via PCR (~12 cycles) enrichment, the amplified library was cleaned up by AMPure XP beads for QC analysis.

tag: Sex

value: Female

tag: age

value: 8 weeks old

value: Whole bone marrow cells

tag: injury

value: Burn

value: Isotype Antibody


title: BM4_Sham_Isotype

value: Sham


title: BM3_Sham_Isotype


title: BM6_Burn_Isotype


title: 7013_Scc2G1Depleted_N1

city: London

first: Thomas

middle: M.

last: Guerin

address: nw1 1at, 1 Midland Road

institute: The Francis Crick Institute

description: Library name: 7013_Scc2G1Depleted_N1

data_processing:
*library strategy: micro-c
Micro-C datasets were processed through the Distiller pipeline (https://github.com/open2c/distiller-nf, commit 8aa86e)
Reads were aligned to W303 using bwa 0.17.7 and the resulting maps filtered to remove low-quality alignments (MAPQ<30) and cis alignment pairs within 150 bp
Replicates were analysed independently, and their quality assessed before aggregation into sample-level datasets.
Merged contact matrix are provided in mcool files
Assembly: w303
Supplementary files format and content: mcool files contain the contact probabilities of merged replicates

organism: Saccharomyces cerevisiae

extract_protocol:
Micro-C was performed following published protocols[Costantino, 2020 #1788][Slobadyanyuk, 2022 #1888] with minor modifications. Yeast cultures were crosslinked with 3% formaldehyde for 15 minutes at 30 °C. The reactions were quenched by the addition of 250 mM glycine at 30 °C for 5 minutes with agitation. Cells were pelleted by centrifugation at 4000 rpm at 4 °C for 5 minutes and washed twice with water. Cells were then resuspended in Buffer Z (50 mM Tris-HCl pH 7.5, 1M sorbitol, 10 mM β-mercaptoethanol) and spheroplasted by addition of 250 mg/ml Zymolyase (100T) in a 30 °C incubator at 200 rpm for 40 to 60 minutes. Spheroplasts were washed once by 4 °C PBS and then pelleted at 4000 rpm at 4 °C for 10 minutes. Chromatin was further crosslinked by suspending pellets in PBS supplemented with 3 mM disuccinimidyl glutarate (ThermoFisher) and incubated at 30 °C for 40 minutes with gentle shaking before quenching by addition of 400 mM glycine for 5 minutes at 30 °C. Cells were pelleted by centrifugation at 4000 rpm at 4 °C for 10 minutes, washed once with ice-cold PBS and stored at −80 °C. Pellets were then treated as described[Costantino, 2020 #1788] until the de-crosslinking step. The De-crosslinking solution was added with an equal volume of phenol-chloroform-isoamyl alcohol (25:24:1), vortexed intensively and centrifuged for 15 minutes at room temperature. The aqueous phase was purified on a ZymoClean column (Zymo Research) according to the manufacturer instructions. Dinucleosome-sized DNA fragments were purified and excised from a 3% NuSieve GTG agarose gel (Lonza) using the Zymoclean Gel DNA Recovery Kit (Zymo).
17 ul of recovered DNA were treated with an end polishing following End-It DNA End-Repair Kit (Lucigen) manufacturer instruction before being diluted in 125 μL of water and added with 150 μL of 2x BW buffer. Biotynilated DNAs were precipitated using 5 μL of Dynabeads™ MyOne™ Streptavidin C1 for 30 minutes at 25 °C on a nutator. Beads were washed twice in 1x TBW buffer at 55 °C and once in 10 mM Tris HCl pH 7.5. Beads were then treated following NEBNext® Ultra™ DNA Library Prep Kit for Illumina® procedure. Briefly, beads were resuspended in 30 μL of End prep master mix and incubated according to the manufacturer instruction, followed by a standard adaptator ligation and USER enzyme digestion protocol. Adaptors were then washed 2 times in 1x TBW at 55 °C followed by one wash in 10 mM Tris pH 7.5. Beads were resuspended in 20 μL of Zymo Elution Buffer and an on-bead PCR was performed (8 to 12 cycles). Two rounds of 0.85X AMPure cleanup were performed. DNA fragments size were assessed on a Tapestation. Library were sequenced using an Illumina NovaSeq 6000 sequencer (100 bp paired). (see Slobodyanyuk et al. 2022 https://doi.org/10.1007/978-1-0716-2497-5_4)

value: Mata rat1-1::LEU2 pADH1-OsTir1-9Myc::ADE2 SCC2-IAA17::KANMX6


title: BM2_Sham_Isotype


title: BM1_Sham_Isotype


title: 7013_Scc2G1Depleted_N2

description: Library name: 7013_Scc2G1Depleted_N2


title: BM11_Burn_AntiGCSF

value: Anti-G-CSF Antibody


title: BM7_Burn_Isotype


title: BM10_Burn_AntiGCSF


title: BM9_Burn_AntiGCSF


title: 7013_Scc2G2Depleted_25_N1

description: Library name: 7013_Scc2G2Depleted_25_N1


title: 7013_Scc2G2Depleted_35_N2

description: Library name: 7013_Scc2G2Depleted_35_N2


title: 7013_Scc2G2Depleted_35_N1

description: Library name: 7013_Scc2G2Depleted_35_N1


title: 7013_Scc2G2Depleted_25_N2

description: Library name: 7013_Scc2G2Depleted_25_N2


title: BM12_Burn_AntiGCSF


title: ctrl1_cxcr4

first: Oliver

last: Ziff

address: Institute of Neurology, Queen Square

institute: University College London

description: Library name: CLA5651A8

data_processing:
Reads were processed using the nfcore/rna-seq v3.6 pipeline.  Detailed quality control of aligned reads was assessed utilising FastQC, RSeQC, Qualimap, dupRadar, Preseq and MultiQC tools.
Raw reads underwent adaptor trimming with Trim Galore, removal of ribosomal RNA with SortMeRNA, alignment to Ensembl GRCh38.99 human reference genome using splice-aware aligner, STAR v2.7.1 and BAM-level quantification with Salmon.
Assembly: Ensembl GRCh38.99
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

growth_protocol: hiPSC derived microglia were maintained in Advanced DMEM/F12 (Invitrogen) with 100 ng/mL IL-34, 10 ng/mL GM-CSF, 1% N2 (Invitrogen), 2 mM Glutamax, penicillin/streptomycin and 0.055 mM β-mercaptoethanol for 14 days, with half media changes twice a week. Motor neurons and astrocytes were treated with microglia conditioned media at a ratio of 50:50 with fresh N2B27 (containing 0.1 μM compound E for motor neuron culture) for 72 hours.

extract_protocol:
The Promega Maxwell RSC simplyRNA cells kit including DNase treatment was used for RNA extractions using the Maxwell RSC instrument. A nanodrop was used to assess RNA concentration and the 260/280 ratio. RNA integrity was assessed using the Agilent TapeStation.
Poly(A)+ selected reverse stranded RNA sequencing libraries were prepared from 4 control and 3 VCP lines using the KAPA mRNA HyperPrep Library kit for Illumina®, with 50 ng of total RNA as input. Libraries were sequenced on the NovaSeq 6000

treatment_protocol: Microglia were transfected using RNAiMAX (Thermo Fisher) to deliver 8.3 nM siRNAs targeting GPNMB (Horizon, ON-TARGETplus; L-011741-01) or a scrambled control siRNA (Horizon, ON-TARGETplus; D-001810-10) in Optimem overnight followed by a media change and then harvested or assayed 48 hours later.

value: ctrl

tag: lps treatment

value: untx

tag: microglia media

tag: sirna treatment

tag: strandedness

value: auto

tag: library type

value: NEBNext Ultra II Directional NEBNext Ultra II Directional RNA + ribodepletion


title: glia_scramble

description: Library name: CLA5651A5

source_name: glia

tag: cell line

value: glia

tag: cell type

value: vcp

value: scramble


title: vcpf10_scramble

description: Library name: CLA5651A4

tag: genotype


title: ctrl5_scramble

description: Library name: CLA5651A3


title: glib_scramble

description: Library name: CLA5651A6

source_name: glib

value: glib


title: ctrl4_scramble

description: Library name: CLA5651A2


title: cb1e_gpnmb

description: Library name: CLA5651A19

value: gpnmb


title: glib_gpnmb

description: Library name: CLA5651A18


title: cb1e_scramble

description: Library name: CLA5651A7


title: glia_gpnmb

description: Library name: CLA5651A17


title: ctrl5_gpnmb

description: Library name: CLA5651A16


title: BM8_Burn_Isotype

tag: strain

value: Female

tag: treatment


title: ctrl4_cxcr4

description: Library name: CLA5651A9


title: cb1e_cxcr4

description: Library name: CLA5651A13


title: ctrl4_gpnmb

description: Library name: CLA5651A15


title: ctrl1_gpnmb

description: Library name: CLA5651A14


title: glib_cxcr4

description: Library name: CLA5651A12


title: ctrl2_vcp_untx

description: Library name: CLA5813A9

value: NEBNext Ultra II Directional PolyA mRNA


title: ctrl1_scramble

description: Library name: CLA5651A1


title: ctrl1_nil_lps

description: Library name: CLA5813A6

value: lps


title: ctrl2_nil_untx

description: Library name: CLA5813A7


title: ctrl1_vcp_lps

description: Library name: CLA5813A5


title: ctrl1_vcp_untx

description: Library name: CLA5813A3


title: ctrl2_ctrl_untx

description: Library name: CLA5813A8


title: ctrl6_vcp_lps

description: Library name: CLA5813A23


title: ctrl6_ctrl_untx

description: Library name: CLA5813A20


title: ctrl4_vcp_untx

description: Library name: CLA5813A15


title: ctrl6_ctrl_lps

description: Library name: CLA5813A22


title: ctrl1_ctrl_untx

description: Library name: CLA5813A2


title: ctrl4_nil_lps

description: Library name: CLA5813A18


title: ctrl4_nil_untx

description: Library name: CLA5813A13


title: ctrl2_nil_lps

description: Library name: CLA5813A12


title: ctrl6_vcp_untx

description: Library name: CLA5813A21


title: ctrl6_nil_untx

description: Library name: CLA5813A19


title: ctrl4_ctrl_lps

description: Library name: CLA5813A16


title: ctrl2_ctrl_lps

description: Library name: CLA5813A10


title: glia_cxcr4

description: Library name: CLA5651A11


title: ctrl4_ctrl_untx

description: Library name: CLA5813A14


title: vcpf10_cxcr4

description: Library name: CLA5651A10


title: ctrl2_vcp_lps

description: Library name: CLA5813A11


title: ctrl4_untx_ctrl

description: Library name: CLA5407A8

value: reverse


title: ctrl1_ctrl_lps

description: Library name: CLA5813A4


title: ctrl6_nil_lps

description: Library name: CLA5813A24


title: ctrl4_vcp_lps

description: Library name: CLA5813A17


title: ctrl4_untx_fresh

description: Library name: CLA5407A7


title: ctrl1_nil_untx

description: Library name: CLA5813A1


title: ctrl3_lps_ctrl

description: Library name: CLA5407A5


title: cb1e_untx_vcp

description: Library name: CLA5407A33


title: cb1e_lps_fresh

description: Library name: CLA5407A34


title: cb1e_untx_ctrl

description: Library name: CLA5407A32


title: ctrl3_lps_fresh

description: Library name: CLA5407A4


title: cb1e_lps_ctrl

description: Library name: CLA5407A35


title: cb1e_untx_fresh

description: Library name: CLA5407A31


title: ctrl3_untx_vcp

description: Library name: CLA5407A3


title: cb1d_lps_ctrl

description: Library name: CLA5407A29


title: cb1d_lps_vcp

description: Library name: CLA5407A30


title: ctrl4_untx_vcp

description: Library name: CLA5407A9


title: cb1d_untx_vcp

description: Library name: CLA5407A27


title: cb1d_untx_ctrl

description: Library name: CLA5407A26


title: cb1d_untx_fresh

description: Library name: CLA5407A25


title: glia_lps_vcp

description: Library name: CLA5407A24


title: cb1d_lps_fresh

description: Library name: CLA5407A28


title: glia_lps_ctrl

description: Library name: CLA5407A23


title: glia_lps_fresh

description: Library name: CLA5407A22


title: glia_untx_vcp

description: Library name: CLA5407A21


title: cb1e_lps_vcp

description: Library name: CLA5407A36


title: glia_untx_fresh

description: Library name: CLA5407A19


title: glia_untx_ctrl

description: Library name: CLA5407A20


title: ctrl5_lps_ctrl

description: Library name: CLA5407A17


title: ctrl5_lps_fresh

description: Library name: CLA5407A16


title: ctrl3_lps_vcp

description: Library name: CLA5407A6


title: ctrl3_untx_ctrl

description: Library name: CLA5407A2


title: ctrl5_lps_vcp

description: Library name: CLA5407A18


title: ctrl5_untx_vcp

description: Library name: CLA5407A15


title: ctrl4_lps_vcp

description: Library name: CLA5407A12


title: ctrl5_untx_fresh

description: Library name: CLA5407A13


title: lps_cb1d

description: Library name: CLA3553A34


title: lps_glib

description: Library name: CLA3553A33


title: lps_ctrl4

description: Library name: CLA3553A30


title: lps_ctrl3

description: Library name: CLA3553A29


title: untx_ncrme6

description: Library name: CLA3553A28


title: ctrl4_lps_ctrl

description: Library name: CLA5407A11


title: untx_glib

description: Library name: CLA3553A26


title: ctrl3_untx_fresh

description: Library name: CLA5407A1


title: ctrl4_lps_fresh

description: Library name: CLA5407A10


title: lps_ncrme6

description: Library name: CLA3553A35


title: untx_ctrl4

description: Library name: CLA3553A23


title: untx_ncrm1

description: Library name: CLA3553A24


title: untx_ctrl3

description: Library name: CLA3553A22


title: KYSE-150 cells,PAK5-OE3

city: Haikou

first: Yue

last: Zeng

address: Longhua District Yehai Avenue

institute: The Second Affiliated Hospital of Hainan Medical University

description: Library name: PAK5_3

data_processing:
The original image Data files Sequenced by high-throughput sequencing (such as illumina HiSeqTM2500 and other sequencing platforms) are converted into Sequenced Reads by Base Calling analysis, which are called Raw Data or Raw Reads. The results were stored in FASTQ (fq) file format, which contained sequence information of sequencing sequences (reads) and their corresponding sequencing quality information.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: The human esophageal carcinoma cell line KYSE-150 was cultured in RPMI-1640 medium with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin with 5% CO2 at 37℃.

extract_protocol:
After the sample is qualified, eukaryotic mRNA is enriched with magnetic beads with Oligo (dT) (in the case of prokaryotes, mRNA is enriched by removing rRNA by the kit). Then mRNA was fragmented into short fragments by fragmentation buffer. A cDNA strand was synthesized using the mRNA template with six-base random hexamers, and then a two-strand cDNA was synthesized by buffer solution, dNTPs and DNA polymerase I. AMPure XP beads were then used to purify double-stranded cDNA. The purified double-stranded cDNA was then end-repaired, A tail was added and sequencing joints were connected. Then AMPure XP beads were used for fragment size selection, and finally PCR enrichment was performed to obtain the final cDNA library.
After the completion of the library construction, Qubit2.0 was used for preliminary quantification, and the library was diluted to 1ng/ul. Then Agilent 2100 was used to detect the insert size of the library. After the insert size met the expectation, Q-PCR method was used to quantify the effective concentration of the library accurately (effective concentration of the library > 2nM) to ensure the quality of the library.

value: Human esophageal squamous cells

value: PAK5 overexpression


title: KYSE-150 cells,Control3

description: Library name: WT_3

value: WT


title: KYSE-150 cells,Control1

description: Library name: WT_1


title: lps_vcpf10

description: Library name: CLA3553A32


title: lps_ncrm1

description: Library name: CLA3553A31


title: Input DNA

city: Pittsburgh

first: Hisato

last: Yagi

state: PA

address: 530 45th street, Rangos Res Center 8162

institute: University of Pittsburgh

description: Library name: Input DNA

data_processing:
Reads were mapped to the mouse reference genome (GRCm38 from Illumina iGenomes website) using Bowtie1 (Version: 1.1.2) with the commandline options: bowtie -v 2 -t -k 2 -m 1 Peaks were called using MACS2 (Model-based Analysis for ChIP-Seq, version: MACS-2.1.0.20140616) with the command-line options: macs2 callpeak -t sap130File -c ctrlFile -f BOWTIE -g mm -B -q 0.01. (FDR cutoff of 0.01).
Assembly: GRCm38/mm10
Supplementary files format and content: CHiPseqResults; peaks found by comparing Sap130 to Input.

source_name: Brain

extract_protocol:
Chromatin immunoprecipitation of Sap130 was performed with rabbit anti-Sap130 antibody (A302-491A: Bethyl laboratories, 2ug) and iDeal ChIP-seq Kit for Transcription Factors (Diagenode) following the manufacturer’s protocol
ChIP-seq libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s protocol.

tag: tissue

value: Brain

value: B6 wildtype

tag: Stage


title: untx_cb1d

description: Library name: CLA3553A27

value: untx


title: Sample 177_Healthy control_38

city: Santiago de Compostela

first: Alberto

last: Gómez-Carballa

state: A coruña

address: Choupana sn

country: Spain

institute: GENVIP research group

data_processing:
Quality control of raw data was carried out using fastq.gzC.
Alignment and read counting were performed using STAR, alignment filtering was done with SAMtools and read counting was carried out using FeatureCounts.
Assembly: Ensembl GCh38 genome
Supplementary files format and content: Coma-delimited excell file with raw counts (Counts_raw_data.csv)
Supplementary files format and content: Coma-delimited excell file with normalized counts (Normalized_data.csv)

source_name: Whole blood

extract_protocol:
RNA was extracted using PAXgene Blood RNA Kit (IVD) and Tempus™ Spin RNA Isolation Kit
The Illumina’s TruSeq RNA Sample Preparation Kit was used for library preparation, and ribosomal and globin RNA depletion was performed using the Illumina® Ribo-Zero Gold kit

value: Whole blood

value: M

tag: etiology

value: C

tag: collection tube

value: tempus

tag: batch

value: B

tag: condition

value: Control


title: Sample 174_Healthy control_35

tag: Sex

value: F


title: untx_vcpf10

description: Library name: CLA3553A25

value: ctrl

tag: lps treatment


title: KYSE-150 cells,PAK5-si3

description: Library name: PAK5_shRNA_3

value: PAK5 knock down


title: KYSE-150 cells,PAK5-si1

description: Library name: PAK5_shRNA_1


title: Sample 167_Healthy control_28


title: KYSE-150 cells,PAK5-si2

description: Library name: PAK5_shRNA_2


title: KYSE-150 cells,PAK5-OE2

description: Library name: PAK5_2


title: KYSE-150 cells,PAK5-OE1

description: Library name: PAK5_1