title: hTERT-BJ-5ta cells, ALMS1 Knockout (KO) 3

city: Vigo

first: Brais

last: Bea Mascato

state: Pontevedra

address: Campus de Vigo As LagoasCtra. de Marcosende, 36310 Vigo, Pontevedra

country: Spain

institute: University of Vigo

data_processing:
Initially, the quality of the samples was analysed using the fastqc programme.
The fastq files were filtered and aligned using the STAR programme with the default parameters
After alignment, the bead matrix was generated with the HT-seq programme using the default parameters.
Finally, normalisation and differential expression analysis was performed with the DESeq2 R package.
Assembly: GRCh38
Supplementary files format and content: CountMatrixMerged: tab-delimited text files include the count matrix generated after joining the different samples count matrices created with HT-seq .
Supplementary files format and content: NormalizedCountMatrix_DESeq2: tab-delimited text files include the DESeq2 normalized count matrix generated with HT-seq
Supplementary files format and content: NormalizedCountMatrix_rlog: tab-delimited text files include the DESeq2 normalized count matrix generated with HT-seq after regularized log transformation
Supplementary files format and content: RNA-seq_results_DESeq2.txt: tab-delimited text files include The results for the differentially expressed genes detected with DESeq2

source_name: hTERT BJ-5TA

growth_protocol: hTERT BJ-5ta fibroblast cells were maintained in DMEM:199 (4:1, v/v) supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using NYZ total RNA isolation kit (NYZtech). 1.2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ion Total RNA-Seq Kit v2 following manufacturer's protocols.

treatment_protocol: The cells were incubated without FBS for 24 hours. After the first 24 hours, rhTGF-B1 ligand (R&D Systems, 240-B) was added at a final concentration of 2ng/mL and the cells were incubated again for another 24 hours.

tag: cell line

value: hTERT BJ-5TA

value: fibroblasts

value: ALMS1 KO

value: TGF-beta1 ligand


title: hTERT-BJ-5ta cells, ALMS1 Knockout (KO) 2

status: Public on Oct 31 2023

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: genotype

tag: treatment


title: A3

city: Raleigh

first: Terri

middle: A

last: Long

state: NC

department: Plant & Microbial Biology

country: USA

institute: North Carolina State University

data_processing:
sequenced using an Illumina HiSeq 2500 sequencing machine .
125bp single end reads
Adapters and low quality reads were filtered out using fastQC and fastq-mcf.
Assembly: Clean reads were mapped against the TAIR 10 reference genome using the tophat2
Supplementary files format and content: RPKM were acquired using RSubread, followed by edgeR to identify differentially expressed genes (DEGs), using a maximum false discovery rate (FDR) of 0.05 and minimum log fold change threshold of 0.75.

organism: Arabidopsis thaliana

source_name: Protoplast of root epidermal cells (GFP-positive)

growth_protocol: Plants grown vertically on top of mesh placed on MS

extract_protocol:
Roots were roots were harvested from both +Fe and -Fe conditions for protoplast collection, followed by fluorescence-activated cell sorting in triplicates. RNA was extracted from FACS epidermal protoplast using RNAeasy Plant RNA Purification Kit (Qiagen).
RNA libraries were prepared for sequencing by performing cDNA synthesis and amplification using the NEBNext® Poly(A) mRNA Magnetic Isolation Module followed by the NEBNext® Ultra™ II Directional RNA Library Prep and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1)

treatment_protocol: Iron-sufficient (+Fe) media is standard Murashige and Skoog media with 0.05% MES, 1% sucrose, 1% agar, and 0.1 mM FeEDTA. Iron deficient (−Fe) media is as mention above minus the 0.1mM FeEDTA, with the addition of 300 μM ferrozine, an iron chelator

tag: tissue

value: Root Cells

value: Plus Iron

tag: age

value: 7 day old

tag: gfp localization

value: Epidermis

tag: condition

value: Zero time point


title: hTERT-BJ-5ta cells, Wild type (WT) 2

value: WT


title: hTERT-BJ-5ta cells, Wild type (WT) 3


title: hTERT-BJ-5ta cells, Wild type (WT) 1


title: M1_donor3_neun (Multiome Gene Expression)

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: UCSD

description:
NeuN+ sorted nuclei
M1_donor3_neun_barcodes.tsv.gz
M1_donor3_neun_features.tsv.gz
M1_donor3_neun_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
Raw sequencing was processed using cellranger-arc (10x Genomics), generating snRNA-seq UMI count matrices for intronic and exonic reads mapping in the sense direction of a gene.
Cells were filtered for low quality nuclei by requiring ≥1000 ATAC fragments and ≥500 genes detected per nuclei.
Genes were annotated with hg38 Gencode v33 for human, mm10 Gencode vM22 for mouse, ensembl release 104 (and Refseq GCF_003339765.1 for 10x multiome) for macaque, and GCA_009663435.2 for marmoset. To maximize the number of orthologous protein-coding quantified in macaque 10x multiome RNA data, we supplemented any missing protein coding genes in GCF_003339765.1 gtf with annotations present in Ensembl release 104.
Assembly: hg38 GRCh38
Assembly: mm10 GRCm38
Assembly: Mmul_10 (rheMac10)
Assembly: cj1700_1.1 (calJac4)
Supplementary files format and content: "barcode.tsv.gz" contains cell barcode information. "features.tsv.gz" consists of rows containing features (genes and peaks) and columns containing cell-associated barcodes. "matrix.mtx.gz" contains sparse feature-barcode matrix.   Files provided in tar archives.

source_name: primary motor cortex

extract_protocol:
[nuclei preparation protocol]  Brain tissue was pulverized using a mortar and pestle on dry ice and pre-chilled with liquid nitrogen. Pulverized brain tissue was resuspended in 1mL of chilled NIM-DP-L buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH 7.5, 1mM DTT, 1X Protease Inhibitor (Pierce), 1U/μL Recombinant RNase inhibitor (Promega, PAN2515), and 0.1% Triton X-100). Tissue was Dounce homogenized with a loose pestle (5-10 strokes) followed by a tight pestle (15-25 strokes) or until solution was uniform. Nuclei were filtered using a 30μm CellTrics filter (Sysmex, 04-0042-2316) into a LoBind tube (Eppendorf, 22431021) and pelleted (1000 rcf, 10 min at 4˚C) (Eppendorf, 5920 R). Pellet was resuspended in 1 mL NIM-DP buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH 7.5, 1mM DTT, 1x Protease Inhibitor, 1U/μL Recombinant RNase inhibitor) and pelleted (1000 rcf, 10 min at 4˚C). Pelleted nuclei were resuspended in 400uL 2μM 7-AAD (Invitrogen, A1310) in Sort Buffer (1mM EDTA, 1U/μL Recombinant RNase inhibitor, 1X Protease Inhibitor, 1% fatty acid-free BSA in PBS).
120,000 nuclei were sorted (Sony, SH800S) into a LoBind tube containing Collection Buffer (5U/uL Recombinant RNase inhibitor, 1X Protease Inhibitor, 5% fatty acid-free BSA in PBS). 5X Permeabilization Buffer (50mM Tris-HCl pH 7.4, 50mM NaCl, 15mM MgCl2, 0.05% Tween-20, 0.05% IGEPAL, 0.005% Digitonin, 5% fatty acid-free BSA in PBS, 5mM DTT, 1U/μL Recombinant RNase inhibitor, 5X Protease Inhibitor) was added for a final concentration of 1X. Nuclei were incubated on ice for 1 minute, then centrifuged (500 rcf, 5min at 4C). Supernatant was discarded and 650uL of Wash Buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1%.Tween-20, 1% fatty acid-free BSA in PBS, 1mM DTT, 1U/μL Recombinant RNase inhibitor, 1X Protease Inhibitor) was added without disturbing the pellet followed by centrifuging (500 rcf, 5 min at 4˚C). Supernatant was removed, and the pellet was resuspended in 7uL of 1X Nuclei Buffer (Nuclei Buffer (10x Genomics), 1mM DTT, 1 U/μL Recombinant RNase inhibitor). 1 μL of nuclei was diluted in 1X Nuclei Buffer, stained with Trypan Blue (Invitrogen, T10282) and counted. 16-20k nuclei were used for tagmentation reaction and controller loading and libraries were generated following manufacturer’s recommended protocol (https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression).
10x multiome ATAC-seq and RNA-seq libraries were paired-end sequenced on NextSeq 500 and NovaSeq 6000 to a depth of ~50,000 reads per cell for each modality.

value: primary motor cortex

tag: species

value: Human

tag: donor id

tag: Sex

value: M

tag: library type

value: 10x Genomics Multiome Gene Expression


title: B - 2

value: Minus Iron

value: 7 day old plus 6 hours

value: 6hrs = 7d +Fe/ 6hrs -Fe


title: A1


title: hTERT-BJ-5ta cells, ALMS1 Knockout (KO) 1

value: hTERT BJ-5TA


title: B + 2

value: 6hrs = 7d +Fe/ 6hrs + Fe


title: M1_donor3_neun (Multiome ATAC)

library_source: genomic single cell

molecule: genomic DNA

value: 10x Genomics Multiome ATAC


title: M1_donor2_neun (Multiome Gene Expression)

description:
NeuN+ sorted nuclei
M1_donor2_neun_barcodes.tsv.gz
M1_donor2_neun_features.tsv.gz
M1_donor2_neun_matrix.mtx.gz


title: M1_donor2_neun (Multiome ATAC)


title: M1_donor1_neun (Multiome ATAC)

description:
NeuN+ sorted nuclei
M1_donor1_neun_barcodes.tsv.gz
M1_donor1_neun_features.tsv.gz
M1_donor1_neun_matrix.mtx.gz


title: M1_donor1_neun (Multiome Gene Expression)


title: M1_donor2 (Multiome Gene Expression)

description:
M1_donor2_barcodes.tsv.gz
M1_donor2_features.tsv.gz
M1_donor2_matrix.mtx.gz


title: M1_donor2 (Multiome ATAC)


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-E18

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: Mmul_10 (rheMac10), annotation: Ensembl release 104
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

organism: Macaca mulatta

extract_protocol:
Motor cortex of brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

treatment_protocol: For all snm3C-seq samples, in-situ 3C treatment was done during the nuclei preparation that allows capturing the chromatin conformation modality as described previously22. These steps were carried out using the Arima-3C BETA Kit (Arima Genomics). The nuclei were isolated and sorted into 384-well plates using previous methods21. Briefly, single-nuclei were stained with AlexaFluor488-conjugated anti-NeuN antibody (MAB377X, Millipore) and Hoechst 33342 (62249, ThermoFisher) followed by FANS using a BD Influx sorter with single-cell (1 drop single) mode.

tag: brain region

value: Motor cortex

tag: gender


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-D18


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-E5


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-F17


title: CS13_Dorsal_Inner_Rep1 (DI_1)

city: Seattle

first: Edie

middle: I

last: Crosse

state: Washington

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description:
Dorsal inner layer of the dorsal aorta including endothelium and some adjacent mesenchyme
CS13_gene_counts.csv

data_processing:
Adaptor trimming with flexbar/2.5
Alignment with STAR/2.5.1b
Feature counts with BEDTools/2.27.1 multicov function
Assembly: Homo_sapiens.GRCh38.86
Supplementary files format and content: CS13_gene_counts.csv = raw read counts for all CS13 samples
Supplementary files format and content: CS14_gene_counts.csv = raw read counts for all CS14 samples

molecule: polyA RNA

source_name: CS13 embryo

extract_protocol: The previously published LCM-Seq protocol (Nichterwitz, et al. 2016) was used for RNA-Seq library preparation from LCM material in lysis buffer. LCM caps were vortexed for 15 s and spun in a tabletop centrifuge (8000 g) for 5 min. 5 μL lysate was added to 2 μL 10mM dNTP mix (Thermo Fisher) and 1 μL 10 μM oligodT (5′-AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN-3′, (IDT)). This was vortexed briefly and spun in a microcentrifuge for 30 s (700 g) then incubated at 72°C for 3 min and immediately snap cooled on ice. To each reaction, 2 μl SSRTIV 5 × buffer, 0.5 μl 100 mM DTT, 0.5 μl 200 U μl−1 SSRTIV (all Thermo Fisher), 2 μl 5 M betaine (Sigma-Aldrich), 0.1 μl 1 M MgCl2 (Sigma-Aldrich), 0.25 μl 40 U μl−1 RNase inhibitor (Takara) and 0.1 μl 100 μM TSO-LNA-oligo 5′- AAGCAGTGGTATCAACGCAGAGTACATrGrG+G −3′, Exiqon) was added. The reverse transcription reaction was performed in a thermal heat cycler with the following conditions; 90min 42°C, 10 cycles of (2 min 50°C, 2 min 42°C) and 15 s 70°C. For the amplification reaction 12.5 μl 2X KAPA HiFI Hotstart Mix (KAPA Biosystems), 0.2 μl 10 μM ISPCR primers (IDT, 5′ - AAG CAG TGG TAT CAA CGC AGA GT – 3′) and 2.3 μl nuclease-free H2O (Invitrogen) was added to each reaction. This was heat cycled as follows: 3 min 98°C, 18 cycles of (20 s 98°C, 15 s 67°C, 6 min 72°C) and 5 min 72°C. After bead purification using AMPure XP beads (Beckman Coulter), the concentration of the cDNA library was measured with an Agilent 2200 TapeStation using the High Sensitvity DNA 5000 kit (Agilent). 1 ng of cDNA from this reaction was amplified and barcoded using the Nextera XT DNA sample preparation kit and Nextera XT index kit (Illumina) following the manufacturer’s protocol. The libraries were purified again using AMPure XP beads, analyzed on the Tapestation 2200 using High Sensitivity DNA 100 Kit and quantified using the Qubit fluorometer and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).

tag: tissue region

value: CS13 embryo


title: CS13_Ventral_Inner_Rep1 (VI_1)

description:
Ventral inner layer of the dorsal aorta including endothelium and some adjacent mesenchyme
CS13_gene_counts.csv


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-F18


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-E6


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-D6


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-D5


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-E17


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-D17


title: M1_donor1 (Multiome Gene Expression)

description:
M1_donor1_barcodes.tsv.gz
M1_donor1_features.tsv.gz
M1_donor1_matrix.mtx.gz


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-C6


title: M1_donor1 (Multiome ATAC)


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-C18


title: Modle3

city: Hangzhou

first: Jiaxi

last: Fang

state: zhejiang

address: 浙江省杭州市钱塘区下沙街道中科院基础医学与肿瘤研究所

country: China

institute: Zhejiang Provincial People's Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: gene_count.xls contains readcount, FPKM of each gene in the sample and FPKM of each gene in the group

organism: Mus musculus

source_name: kidney

extract_protocol:
Total RNA was extracted from samples using RNA Isolater Total RNA Extraction Reagent (Vazyme, Nanjing, China). The RNA integrity and DNA contamination of the samples were analyzed by agarose gel electrophoresis, and the RNA purity (OD260/280 and OD260/230 ratio) and RNA integrity were determined using a NanoPhotometer spectrophotometer and Agilent 2100 bioanalyzer. The initial RNA for library construction was total RNA with a total amount ≥ 1 μg.
NEB common library construction: The first cDNA strand was synthesized in M-MuLV reverse transcriptase system using fragmented mRNA as template and random oligonucleotides as primer, then the RNA strand was degraded by RNaseH, and the second cDNA strand was synthesized using dNTPs as raw material in DNA polymerase I system. The purified double-stranded cDNA was end-repaired, A-tail was added, and sequencing joints were connected. cDNA of about 250-300bp was screened by AMPure XP beads for PCR amplification, and PCR products were purified by AMPure XP beads again, and finally A library was obtained. The NEBNext® Ultra™ RNA Library Prep Kit was used for Illumina®.

value: kidney

value: cisplatin


title: LCA2

address: 浙江省杭州市钱塘区下沙街道中科院基础医学与肿瘤研究所

value: cisplatin+CPS-A


title: Shame3

address: 浙江省杭州市钱塘区下沙街道中科院基础医学与肿瘤研究所


title: Modle2

address: 浙江省杭州市钱塘区下沙街道中科院基础医学与肿瘤研究所


title: LCA4

address: 浙江省杭州市钱塘区下沙街道中科院基础医学与肿瘤研究所


title: Modle1

address: 浙江省杭州市钱塘区下沙街道中科院基础医学与肿瘤研究所


title: LCA1

address: 浙江省杭州市钱塘区下沙街道中科院基础医学与肿瘤研究所


title: LCA3

address: 浙江省杭州市钱塘区下沙街道中科院基础医学与肿瘤研究所


title: Shame2

address: 浙江省杭州市钱塘区下沙街道中科院基础医学与肿瘤研究所


title: M1_donor3_rep2 (Multiome Gene Expression)

description:
replication of donor 3 sample
M1_donor3_rep2_barcodes.tsv.gz
M1_donor3_rep2_features.tsv.gz
M1_donor3_rep2_matrix.mtx.gz


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-C17


title: Shame1

address: 浙江省杭州市钱塘区下沙街道中科院基础医学与肿瘤研究所


title: Spinal cord tissue, SCI, rep1

city: Harbin

first: Zaixing

last: Jiang

state: Heilongjiang

address: 157 Health-care Road, Harbin City, Heilongjiang Province, China

institute: Harbin Medical university

description:
Normal1.readcount
miRNA_Readcount_TPM.txt

data_processing:
Novofinder for sRNA
clean datas(clean reads) were obtained by  removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads  from raw data.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Read count extraction and normalization were performed using Novofinder for sRNA
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and TPM values for each Sample

source_name: spinal cord tissue

extract_protocol:
RNA was harvested using TRlzol kit (B511311, Sangon, China). A total amount of 3 μg total RNA per sample was used as input material for the  small RNA library.
RNA libraries for RNA-seq were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following  manufacturer’s protocols.

value: spinal cord tissue

value: spinal cord hitter platform after laminectomy at the T10 level

value: mouse model of SCI


title: Spinal cord tissue, SCI, rep2

description:
Normal2.readcount
miRNA_Readcount_TPM.txt


title: Spinal cord tissue, Control, rep3

description:
Control5.readcount
miRNA_Readcount_TPM.txt

value: laminectomy

value: control


title: Spinal cord tissue, SCI, rep3

description:
Normal3.readcount
miRNA_Readcount_TPM.txt


title: M1_donor3_rep2 (Multiome ATAC)

value: primary motor cortex

value: Human

value: M


title: CD8_TRAPPC1_FRESH_1

city: Beijing

first: Zhaoqi

last: Zhang

state: Beijing

address: Beijing China Institute of Zoology，Chinese Academy of Sciences

institute: University of Chinese Academy of Sciences

data_processing:
Using Hisat String-Tie to mapped and analyzed data
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include Coverage, FPKM, TPM values for each Sample

source_name: mLNs and spleens

extract_protocol:
Naive CD4+ T cells and naive CD8+ T cells were sorted by CD4+/CD8+CD62L+CD44low from the mLNs and spleens of 4 weeks old WT and CD4-cre Trappc1 cKO mice. The total RNA of the sorted naive CD4+ T cells and naive CD8+ T cells were extracted using TRIzol reagent (Thermo Fisher, 15596018), and sequencing were done by the Annoroad Gene Technology Co., Ltd (Beijing). Differential expressed genes were carried out by DEseq2 software38. KEGG pathway enrichment was performed by KOBAS 3.0.28 (http://kobas.cbi.pku.edu.cn/)37,59. Protein and protein interaction network were analyzed by String (https://string-db.org/) and visualized by Cytoscape60.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: mLNs and spleens

value: TRAPPC1 KO


title: CD4_TRAPPC1_FRESH_2


title: CD8_TRAPPC1_FRESH_2


title: CD4_WT_FRESH_1

value: WT


title: CD4_WT_FRESH_2


title: CD8_WT_FRESH_1


title: CD4_TRAPPC1_FRESH_1


title: CD8_WT_FRESH_2


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-C5


title: Spinal cord tissue, Control, rep1

description:
Control2.readcount
miRNA_Readcount_TPM.txt


title: Spinal cord tissue, Control, rep2

description:
Control3.readcount
miRNA_Readcount_TPM.txt


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-B6


title: LV tissue, Sham3

city: Shanghai

first: YUE

last: CUI

state: Shanghai

address: 1678 Dongfang Road

institute: Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Seqtk.
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2 (version: 2.0.4).
Read count extraction was performed using Stringtie (version:1.3.0).
TMM (trimmed mean of M values) was used to normalization.
The FPKM values were then calculated.
Assembly: mm10
Supplementary files format and content: gene_expression_anno.xls and lncRNA_expression_anno.xls including FPKM values for each Sample

source_name: left ventricle

growth_protocol: Male C57BL/6 mice (8 weeks old) were housed under a 12h light/dark cycle under pathogen-free conditions and with free access to standard mouse chow and tap water.

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies). Qualified total RNA was further purified by RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set (Qiagen).
RNA libraries for RNA-seq were prepared using VAHTS Total RNA-Seq（H/M/R) Library PrepKit for Illumina following manufacturer's protocols.

treatment_protocol: Transverse aortic constriction (TAC) operation was performed and the sham-operated mice underwent the similar procedure except for without ligation. After 6 weeks, LV tissues were isolated from mice.

value: left ventricle

value: male

value: 8 week

value: Sham

tag: time

value: Week 6


title: LV tissue, Sham2


title: RNA_cortex_WT_rep14

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

data_processing:
Reads were aligned using Hisat2 (version 2.0.4) to the human genome (GRCh38/hg38), and the FPKM value was calculated using the Cufflinks program (version2.1.1)
Assembly: M. musculus, UCSC mm10 or H.sapiens hg38
Supplementary files format and content: fpkm_tracking: frgaments per kilobase of exon per million reads mapped.
Supplementary files format and content: GSE225162

source_name: cortex

extract_protocol:
1 × 106 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
Total RNA from culture cells was extracted using Trizol reagents (Life Technologies) following the manufacturer’s instructions. Total mRNA was prepared from 1 mg total RNA using poly(A) mRNA magnetic isolation reagents (NEB) and fragmented at 94 °C for 15 min. RNA was then reverse-transcribed into cDNA with random primers. After end repairing and A-tailing, cDNA was ligated with adapters and amplified by PCR with Illumina sequencing primers.

value: cortex

value: cortex-neuron

value: neuron

value: wildtype


title: LV tissue, TAC2

value: TAC


title: HL60_mut_Day4

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

description: RNAseq of A>T GATA enhancer mutant HL-60 at day4

data_processing:
Samples were trimmed with Trimmomatic 0.38
Trimmed reads were mapped to the reference genome with the HISAT2 2.1.0 splice-aware aligner
Transcripts were assembled using StringTie 1.3.4d
The read count per gene and transcript was normalized to fragments per kilobase of transcript per million mapped reads (FPKM)
Assembly: GRCh37
Supplementary files format and content: Processed data files represent counts for transcripts. This file is a plain-text, tab-separated file with with the following information: transcript, locus, transcript length, and count.

growth_protocol: HL60 cells were cultured in IMDM media (ThermoFisher Scientific, Waltham, MA) supplemented with 20% fetal calf serum (FCS) and 1% Penicillin-Streptomycin 10000 IU/mL (MP Biomedicals, Irvine, CA).

extract_protocol:
Total RNA was isolated from 1 X 10^7 cultured cells using the BD PAXgene Blood RNA Tube system
RNA-seq libraries were made with the Illumina TruSeq stranded mRNA LT sample pre kit and sequenced on the NovaSeq6000 S4 (150bp PE) by Psomagen (Rockville, MD).

value: HL-60 promyelocytic leukemia cell line

value: mutant


title: LV tissue, Sham1


title: LV tissue, TAC1


title: HL60_mut_Day2

description: RNAseq of A>T GATA enhancer mutant HL-60 at day2


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-B5

value: Motor cortex


title: LV tissue, TAC3


title: RNA_HS51bL_to_HS20_del_rep4

data_processing:
Reads were aligned using Hisat2 (version 2.0.4) to the human genome (GRCh38/hg38), and the FPKM value was calculated using the Cufflinks program (version2.1.1)
Assembly: M. musculus, UCSC mm10 or H.sapiens hg38
Supplementary files format and content: fpkm_tracking: frgaments per kilobase of exon per million reads mapped.

value: HS51bL_to_HS20_del -/-


title: M1_donor3 (Multiome ATAC)

description:
M1_donor3_barcodes.tsv.gz
M1_donor3_features.tsv.gz
M1_donor3_matrix.mtx.gz

value: primary motor cortex

value: Human

value: M

value: 10x Genomics Multiome ATAC


title: M1_donor3 (Multiome Gene Expression)

value: 10x Genomics Multiome Gene Expression


title: RNA_HS51bL_to_HS20_del_rep3


title: HL60_mut_Day1

description: RNAseq of A>T GATA enhancer mutant HL-60 at day1


title: RNA_HS51bL_to_HS20_del_rep2


title: RNA_HS51bL_to_HS20_del_rep1


title: HL60_mut_Day0

description: RNAseq of A>T GATA enhancer mutant HL-60 at day0


title: RNA_HS51bL_to_HS18_del_rep4

value: HS51bL_to_HS18_del -/-


title: RNA_cortex_WT_rep13


title: HL60_wt_Day4

description: RNAseq of wild-type HL-60 at day4

value: WT


title: RNA_HS51bL_to_HS18_del_rep3


title: HL60_mut_Day3

description: RNAseq of A>T GATA enhancer mutant HL-60 at day3


title: HL60_wt_Day3

description: RNAseq of wild-type HL-60 at day3


title: RNA_HS51bL_del_rep3

value: HS51bL_del -/-


title: RNA_HS51bL_del_rep4

value: cortex


title: RNA_HS51bL_to_HS18_del_rep1

value: cortex-neuron


title: HL60_wt_Day2

description: RNAseq of wild-type HL-60 at day2


title: RNA_HS51bL_to_HS18_del_rep2

value: neuron


title: RNA_HS51bL_del_rep1


title: HL60_wt_Day1

description: RNAseq of wild-type HL-60 at day1


title: RNA_HS51bL_del_rep2


title: RNA_HS19_to_20_del_rep4


title: HL60_wt_Day0

description: RNAseq of wild-type HL-60 at day0


title: 4C_HoxD13_del_sample3_rep2 [QHR4C-seq]

data_processing:
library strategy: QHR4C-seq
Duplicated paired-end reads were removed by FastUniq (version 1.1) program, and only the unique reads were used for analyses using the Bowtie and r3Cseq program.
Paired-end reads were aligned to the mouse genome (M. musculus, UCSC mm9) or the human genome (H. sapiens, UCSC hg19) using Bowtie (version 1.2.3).
The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3)
Assembly: M. musculus, UCSC mm9 or H. sapiens UCSC hg19
Supplementary files format and content: zipped bedGraph files include RPM values for each Sample

source_name: HEK 293T cell line

extract_protocol:
1 × 10^6 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase. Collagenase was quenched with 2-fold volumes of 10%FBS in NeuroBasal Medium and the suspended cells were used for library construction.
The neuron suspension or cultured cell were cross-linked using 2% formaldehyde in 10% FBS/PBS for 10 min at room temperature followed by washing twice with PBS solution containing proteinase inhibitors (Roche). Cells were then resuspended and lysed twice with 1ml prechilled lysis buffer containing proteinase inhibitors (Roche) for 10 min with slow rotations. The cells were then digested overnight at 37 °C with DpnII while shaking at 900 rpm. After inactivation of DpnII at 65 °C for 20 min, proximity ligation was carried out for 24 hr at 16 °C with T4 DNA ligase in 0.1 ml 1 × T4 ligation buffer. The ligated product was then reverse cross-linked and DNA was extracted using phenol-chloroform. Glycogen was added to facilitate DNA precipitation. The precipitated DNA was then dissolved in 50 ml water, and sonicated using the Biorupter system (with low energy setting at a train of 30-second sonication with 30 second intervals for 12 cycles) to obtain DNA fragments ranging from 200 to 600 bp.The captured fragments were linear-amplified using a 5’ biotin-tagged primer complementary to the viewpoint fragment in 100ul of PCR system for a total of 60 cycles. This primer should be neither too close to the DpnII site to facilitate the nested PCR at the final amplification step, nor too far away from the DpnII site to maximize the product amount. The amplification products were denatured by incubating at 95 °C for 5 min, and immediately chilled on ice to obtain ssDNA. The ssDNA was then enriched and purified with Streptavidin Magnetic Beads (Invitrogen) according to the manufacturer’s instructions. The ssDNA on-beads was then ligated in 15 µl with 0.1 µM of adapters (Supplementary Table 1) at 16 °C for 24 hr. The adapters were generated by annealing two complementary primers matching Illumina P7 sequences. After ligation, free adapters were removed by washing the beads twice with the B/W Buffer (5 mM Tris-HCl, 1 M NaCl, 0.5 mM EDTA, pH 7.5). Finally, the QHR-4C libraries were generated by one-step PCR amplification (94 °C, 2 min; 94 °C, 10 sec, 60 °C, 15 sec, 72 °C, 1 min for 19 cycles; and a final extension at 72 °C, 5 min) with captured ssDNA on beads as the template and a pair of PCR primers. The forward primer matches the Illumina P5 and the viewpoint sequence adjacent to the viewpoint DpnII site with barcodes, and the reverse primer matches Illumina P7 with indexes. The PCR products were purified with a PCR purification kit (Qiagen).

value: HEK 293T cell line

value: human embryonic kidney 293T cell

value: CBS3&5 del -/-


title: RNA_HS19_to_20_del_rep3


title: RNA_HS19_to_20_del_rep1


title: RNA_HS19_to_20_del_rep2


title: 4C_HoxD13_del_sample3_rep1 [QHR4C-seq]


title: 4C_HoxD13_del_sample2_rep2 [QHR4C-seq]


title: RNA_HS18_to_20_del_rep2


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-P3


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-O4


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-P4


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-O3


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-P15


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-A18


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-A5


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-A6


title: RNA_HS18_to_20_del_rep1


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-P16


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-A17


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-B17


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-O16


title: RNA_a_mut_rep4

value: CBSa mut -/-


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-B18

value: Motor cortex


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-N4


title: 4C_HoxD13_del_sample2_rep1 [QHR4C-seq]


title: RNA_a_mut_rep1


title: 4C_HoxD13_del_sample1_rep2 [QHR4C-seq]


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-O15


title: RNA_a_mut_rep3


title: floxed out, Basophil rep2

city: Daejeon

first: Jiyeon

last: Park

address: Daehak-ro 291

country: South Korea

institute: KAIST

data_processing:
HISAT2 aligned the trimmed reads to reference mouse genome
StringTie measured the gene expression in FPKM and TPM
Assembly: mm10

source_name: Bone marrow

extract_protocol:
RNA extraction were dealt with TRIZol LS and Direct-zol RNA kits from Zymo research.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: strain

value: Bone marrow

tag: cell population

value: Lineage- CD34- ckit- CD200R3+ MAR1INT


title: floxed out, Basophil rep1


title: ctrl, Basophil rep1

value: wild type


title: ctrl, pre-Baso rep2

value: Lineage- CD34- ckit- CD200R3+ MAR1HI


title: floxed out, pre-Baso rep1


title: floxed out, pre-Baso rep2


title: ctrl, pre-Baso rep1


title: RNA_a_mut_rep2

tag: cell line

tag: cell type


title: GFP+, replicate 1, scRNAseq

city: Toon

first: Daisuke

last: Shiokawa

state: Ehime

address: 454 Shitsukawa

department: Translational Research Center

country: Japan

institute: Ehime University Hospital

description:
10x Genomics
ST1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: A gene expression matrix file and a metadata file in csv format.

source_name: Stomach

extract_protocol:
Stomach tissues, obtained from Dox-treated or untreated mice, were minced with razor blades and incubated for 45 min at 37°C in HBSS (Gibco, #14025-092) supplemented with 3 mg/ml collagenase P (Roche, #11213865001), 1 mg/ml Dispase II (Roche, #04942078001), and 1 µg/ml DNase I (Roche, #10104159001). The dissociated cells were washed twice with FACS buffer [D-PBS(−) containing 0.5% BSA and 0.5 mM EDTA], and incubated with Accumax reagent (Innovative Cell Technologies, AM-105) for 15 min at 37°C. Subsequently, the cells were subjected to gentle pipetting and filtration with 100 µm filter and used for the following FACS experiments.  The enzymatically digested samples were subjected to antibody staining for 30 min on ice. Anti-mouse Cd31 antibody conjugated with APC (1:300; Biolegend, #102410), anti-mouse Cd45 antibody conjugated with APC (1:300; Biolegend, #103112), and anti-mouse Epcam antibody conjugated with PE (1:300; eBioscience, #12-5791-82) were used to stain the cells. After the immunostaining, the cells were subjected to Calcein Blue AM viability dye staining at 37°C for 15 min according to the manufacturer’s protocol (Invitrogen, #65-0855-39). The resulting cells were collected by centrifugation, re-suspended with FACS buffer, added with TO-PRO3 Ready Flow reagent (Invitrogen, R37170), and subjected to sorting by FACS AriaIIIu cell sorter (Becton Dickinson). Briefly, the cells were subjected to sequential sorting with forward scatter (FSC-H vs. FSC-W), side scatter (SSC-H vs. SSC-W) to select single-cells. Subsequently, cells with poor membrane integrities, hematopoietic and endothelial cells were removed by negative selection against TO-PRO3, Cd45 and Cd31 signals, respectively. After selecting Calcein blue-positive viable cells, Epcam-positive cells (Ep+) and Epcam/GFP-positive cells (GFP+) were selected and analyzed for GFP+ ratio or sorted for single-cell RNA-seq.
Libraries were constructed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, Ep+ and GFP+ single cells were prepared from the stomach of female H2B-GFP mice (n=2) at 6 weeks of post Dox treatment and FACS-sorted as described above. The cells were then loaded onto Chromium next GEM chip G (PN-2000177, 10x Genomics) and captured into Gel Beads-in-emulsion (GEMs) droplets using Chromium Controller (10x Genomics). cDNA synthesis and sample-indexed library construction were performed using Chromium next GEM single cell 3’ reagent kit (PN-1000121, 10x Genomics) according to the manufacturer’s protocol.

value: Epithelial cells

tag: cell type (sorted)

value: GFP+

value: Stomach

value: 14 weeks old


title: ctrl, Basophil rep2

tag: tissue

tag: genotype


title: Control_CTCF

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

institute: Graduate School of Medicine, The University of Osaka

data_processing:
The adapter sequences were removed from the FASTQs using Trimmomatic (0.39).
The cleaned FASTQs were aligned using Bowtie2 (2.4.4) to the mouse reference genome mm10.
The duplicated reads were removed using picard (2.26.2) MarkDuplicates.
The bigWig files were generated using bamCoverage (3.5.1).
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Lineage- cKit+ bone marrow cells in femora and tibiae

extract_protocol:
Cells were fixed with 2mM DSG (Thermo Fisher Scientific, 20593) for 30 min at room temperature and replaced with fixing buffer (50 mM HEPES-NaOH (pH 7.5), 100 mM NaCl, 1 mM EDTA) containing 1% paraformaldehyde (Electron Microscopy Sciences, 15714) and crosslinked for 10 min at 37°C.Crosslinking was quenched by adding glycine to a final concentration of 0.125 M. The nuclear fraction was extracted by first resuspending the pellet in 1 ml of lysis buffer (50 mM HEPES-NaOH (pH 8.0), 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4°C. Cells were pelleted, and washed in 1 ml of wash buffer (10 mM Tris-HCL (pH 8.0), 200 mM NaCl, 1 mM EDTA) for 10 min at 4°C. Cells were then pelleted and resuspended in 1 ml of shearing buffer (10 mM Tris-HCl (pH 8), 1 mM EDTA, 0.1% SDS) and sonicated.Lysate was centrifuged for 5 min at 14,000 rpm to purify the debris. Then 100 ml of 10% Triton X-100 and 30 ml of 5M NaCl were added. The sample was then incubated with 20 ml of Dynabeads Protein G (LifeTechnologies,10003D) for 1 h at 4°C. Primary antibodies were added to each tube and immunoprecipitation (IP) was conducted overnight in the cold room. Cross-linked complexes were precipitated with Dynabeads Protein G for 2 hr at 4°C. The beads were then washed in low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS) for 5 min at 4°C, high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4°C and LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4°C. DNA was eluted in elution buffer (100 mM sodium bicarbonate and 1% SDS). Cross-links were reversed overnight at 65°C. RNA and protein were digested with 0.2 mg/ml RNase A for 30 min at 37C followed by 0.2 mg/ml Proteinase K for 1 h at 55°C. DNA was purified with phenol-chloroform extraction and isopropanol precipitation.
ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from 1 ng of purified ChIP DNA or input DNA according to the manufacturer’s protocol.

treatment_protocol: Four weeks after BMT, the recipient mice received 20 mg/kg pIpC injection every other day for a total of 3 doses.

tag: donor genotype

value: CD45.2(+) Brd9fl/fl

tag: recipient genotype

tag: timing of preparation

value: 5 months after pIpC injection

tag: chip antibody

value: anti-CTCF (Millipore, 07-729)


title: Control_DSG_PFA_Input


title: Control_Brg1

value: anti-BRG1 (Abcam, ab110641)


title: Control_Brd9

value: anti-BRD9 (Bethyl, A700-153)


title: 4C_CBS4_del_sample2_rep1 [QHR4C-seq]

value: HEK 293T cell line

value: human embryonic kidney 293T cell


title: 4C_HoxD13_293T_WT_rep1 [QHR4C-seq]

value: wildtype


title: 4C_CBS4_del_sample2_rep2 [QHR4C-seq]

value: CBS3&5 del -/-


title: 4C_HoxD13_del_sample1_rep1 [QHR4C-seq]


title: 4C_CBS4_del_sample3_rep2 [QHR4C-seq]


title: 4C_HoxD13_293T_WT_rep2 [QHR4C-seq]


title: 4C_CBS4_del_sample1_rep2 [QHR4C-seq]


title: GFP+, replicate 2, scRNAseq

description:
10x Genomics
ST3

tag: age


title: Ep+, replicate 1, scRNAseq

description:
10x Genomics
ST2

value: Ep+


title: Ep+, replicate 2, scRNAseq

description:
10x Genomics
ST4


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-N3

value: Motor cortex

value: M


title: 4C_CBS4_del_sample3_rep1 [QHR4C-seq]


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-M4


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-N15


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-N16


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-M3


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-L4


title: Brd9KO_CTCF

value: CD45.2(+) Mx1-Cre Brd9fl/fl


title: Control_Brd4

value: anti-BRD4 (Bethyl, A301-985A100)


title: Brd9KO_DSG_PFA_Input


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-L3


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-M16


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-M15


title: Brd9KO_Brd9


title: Brd9KO_Brg1


title: 4C_CBS4_293T_WT_rep2 [QHR4C-seq]


title: 4C_CBS4_del_sample1_rep1 [QHR4C-seq]


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-L16


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-K4


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-K3


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-L15


title: 4C_CBS2_del_sample2_rep2 [QHR4C-seq]


title: 4C_CBS4_293T_WT_rep1 [QHR4C-seq]


title: 4C_CBS2_del_sample3_rep2 [QHR4C-seq]


title: 4C_CBS2_del_sample3_rep1 [QHR4C-seq]


title: Brd9_WT

extract_protocol: Cells harvest was followed by a transposition reaction and purification followed the manual of ATAC-seq kit from Active motif (#13150)

treatment_protocol: Four weeks after birth, the recipient mice received 20 mg/kg pIpC injection every other day for a total of 3 doses.

value: Five months after pIpC injection


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-K15


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-K16


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-J4


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-J3


title: Brd9KO_Brd4


title: Brd9_KO


title: 4C_CBS2_293T_WT_rep1 [QHR4C-seq]


title: RNA_del_sample3_rep2


title: RNA_del_sample3_rep1


title: LG3-EC_bRNA

city: Guangzhou

first: Yage

last: Nie

address: No.74 Zhongshan Rd.2, Guangzhou

institute: Sun Yat-sen University

data_processing:
Ror RNAseq data, alignment to the Ensembl reference genome mm9 was performed using the Tophat and bowtie2. Alignment files were sorted using SAMtools v.1.10.2. Count tables were generated using HTSeq-0.6.1.
ATAC-seq data were aligned using Bowtie2 and removed PCR duplicates using Picard. We called Peaks using MACS2. Peaks from the biological replicates were merged using Samtools and Bedtools.
For scRNAseq, the Cell Ranger Software (version 1.2.0) was used to perform the first preprocessing step. ‘cellranger count’ was used to performing read filtering, alignment, and count matrix generation from fastq files per sample. The reads were aligned to the mm10 (refdata-gex-mm10-2020-A) reference genome provided by 10xGenomics. The gene-barcode matrix was generated using only confidently mapped reads with valid barcodes and unique molecular identifiers
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: txt file include count and peak signal for each sample;txt file  include  barcode and gene count.

source_name: Endothelial cells

extract_protocol:
Mice were deeply anaesthetized and perfused transcardially with 20 ml of ice-cold phosphate buffered saline (PBS). After perfusion, whole brain, lung and liver were immersed in ice-cold PBS, which were minced with a razor blade and disaggregated in Type IV collagenase (400 U/ml, Worthington,Lakewood, NJ), Dispase (1.2 U/ml, Worthington, Lakewood, NJ) and DNase I (32 U/ml, Worthington, Lakewood, NJ) in 6 mL 1× PBS with Ca2+ and Mg2+ (GIBCO) at 37 °C for 60 min, with gentle trituration every 10 min. After adequate disaggregation, 1 ml of FBS was added to the disaggregation reaction then the disaggregated cells were washed with 1× ice-cold PBS and filtered through a 40-μm mesh. After centrifugation at 400g for 5 min, cell pellets were resuspended in 10 ml 20% BSA and centrifuged at 1,000 g at 4 °C for 25 min to remove the myelin (only for brain).   The pellets were then resuspended in 1× PBS/3% FBS/0.1% NaN3/2 mM EDTA and blocked with rat anti-mouse CD16/32 (Mouse BD Fc Block, BD Pharmingen) for 10 min on ice. Endothelial cells were labeled with PE-Cyanine7 rat anti-mouse CD31 (cat. # 25-0311-82, eBiosciences, CA), and pericytes were labeled with APC rat anti-mouse PDGFRβ (cat. #17-1402-82, eBiosciences, CA). PE rat anti-mouse CD45 (cat. #516087, BD Pharmingen, CA) and 7-AAD (Invitrogen) were added to exclude hematopoietic lineage cells and dead cells. Staining was done for 1 h at 4 °C. Cells were washed and PE-cyanine7-CD31+/APC-PDGFRβ−/PE-CD45−/7-AAD− cells were sorted into EGM-2/MV medium (cat. #CC3202, Clontech, Mountain View, CA) with an Aria III sorter (BD). ECs were centrifuged at 2,000 g at 4 °C for 10 min and resuspended in Trizol (Life Technologies) or extraction buffer for RNA , DNA, protein extraction.
RNAseq:RNA-seq was performed as we previously reported (PMID:28288111). The RNA-seq data were generated from EC cells after FACS purification. Each RNA-seq analysis was conducted on three biological replicates. ECs total RNA was extracted using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems). In brief, mRNA was first enriched from total RNA by poly-A. Oligo-dT-directed reverse transcription generated complementary DNAs corresponding to the 3′end of poly-A transcripts; the complementary DNA was amplified by PCR using the Ovation 3′-DGE System kit (NuGen Technologies, San Carlos, CA). Amplified cDNA was sheared using a Covaris ultrasonicator and then libraries were prepared using the Ovation SP + Ultralow DR Multiplex System (NuGen Technologies, San Carlos, CA). Deep sequencing was then performed on the Illumina Hiseq-2500 platform (Illumina, Hayward, CA) in single-end 50 bp format.  ATAC-seq:Briefly, ECs were lysed in cold lysis buffer (10 mM Tris-HCl, Ph7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal) and tagmentation performed using Illumina Nextera DNA kit (FC-121-1030) for 30 min at 37 °C on a shaking thermomixer. Tagmented DNA was purified using Qiagen MinElute kit (Cat no. 28004) and amplified using NEB Next High-Fidelity 2X PCR Mast Mix (Cat no. M0543S) for 11 cycles as follows: 72 °C, 5 min; 98 °C, 30 s; 98 °C, 10 s; 63 °C, 30 s; 72 °C, 1 min. Library preparation was complete after further clean up using Qiagen PCR MinElute kit (Cat no. 28004) and Beckman Coulter XP AMPpure beads (A63880). Tagmentation size was assessed using Agilent 2100 Bioanalyser. Libraries were quantified with Qubit 2.0 (Life Technologies) and sequenced using paired-end 150 bp reads on the Illumina HiSeq4000 platform at XX. Three biological replicates were used for analysis.scRNAseq:Single-cell RNA-seq libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kit 3.1(10X Genomics, US). Briefly, Brain ECs (1~2 x105) were isolated by FCAS from young, middle and aged mice (n=2 each group). Single-cell suspension at a density of 500-1000 cells/µL in FACS buffer was added to 10X Genomics GefmCode Single-cell instrument that generateed single-cell Gel Bead-In-EMlusion (GEMs). RNA transcripts from single cells were uniquely barcoded (16 nt) and reverse-transcribed within droplets. Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction. All libraries were quantified by using High Sensitivity DNA assay Kit (Agilent, US). All single-cell libraries were sequenced on a Novaseq 6000 system (Illumina, US).

value: lung

value: Endothelial cells

value: 2-4 months


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-I4


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-J15


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-J16


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-I3


title: Squamous 9

city: Richmond

first: Michela

last: Saviana

state: Virginia

address: 1101 E Marshall St

department: Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine

institute: Virginia Commonwealth University

data_processing:
Raw fastq files were initially pre-processed by trimming Illumina adapter sequences via the Cutadapt tool and then qualitatively filtered by the Condetri tool (parameters: -pb=fq -lq=20 -hq=30 -minlen=15 -sc=33).
For each sample, all post-processed reads were mapped into the human genome (GRCh37) by using the miARma-Seq tool, which includes the Bowtie tool (v1) for aligning reads and the featureCounts tool to annotate them into microRNA space (miRBase v20). A minimum expression filtering is applied prior to normalization, retaining all those miRNA molecules with at least 10 reads in 50% of samples.
Filtered miRNAs were normalized by applying the TMM method (trimmed mean of M-values).
Assembly: hg19 (GRCh37)
Supplementary files format and content: Comma separated file that includes the RPM (Reads Per Million) values of miRNA molecules for all samples

source_name: plasma

extract_protocol:
200 µL of frozen plasma using the miRNeasy micro kit (QAIGEN, Germantown, MD)
Briefly, the method utilizes adapters containing four degenerate nucleotides at proper ends to enhance the adapter‐miRNA ligation and reduce ligation associated bias (3′ adapter sequence: /5rApp/(N:25252525)(N)(N)(N)TGGAATTCTCGGGTGCCAAGG/3ddC/; 5′ adapter sequence: rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrCr(N:25252525)r(N)r(N)r(N)).13 After adapter ligation and cDNA synthesis, the library was amplified for four cycles followed by an initial size‐selection of library inserts in the range between 127 bp and 156 bp on a Pippin HT automated size‐selection instrument (Sage Science, Beverly, MA). The purified fragments were then amplified for an additional 16 cycles, and then size selected again. This two‐step size selection significantly reduces the adapter dimer in the library.
Individual sRNAseq (small RNA sequencing)

tag: race

value: White

tag: Sex

value: Female

tag: Stage

value: IB

tag: group

value: Squamous

value: plasma


title: Squamous 8

value: IV


title: Squamous 10

value: Male


title: Squamous 7


title: LG1-EC_bRNA


title: LV1-EC_bRNA

value: liver


title: BR2-EC_bRNA

value: brain


title: BR3-EC_bRNA


title: MAR1HI rep2

data_processing:
Trimmomatic trimmed adapter sequence and low-quality(<3) bases.
HISAT2 aligned the trimmed reads to reference mouse genome
StringTie measured the gene expression in FPKM and TPM
Genome_build: mm10
Supplementary_files_format_and_content: anno.tab expression fpkm tpm store

extract_protocol:
RNA extraction were dealt with TRIZol LS
RNA-seq experiments were conducted using SureSelectXT RNA direct kit.

value: Bone marrow

value: Lineage - CD34 - ckit - CD200R3 + MAR1 HI


title: BaP rep2

source_name: Basophil Precursor

value: Lineage - CD34 + ckit - MAR1 +


title: MAR1HI rep1


title: MAR1INT rep2

value: Lineage - CD34 - ckit - CD200R3 + MAR1 INT


title: MAR1INT rep1


title: BaP rep1


title: BR1-EC_bRNA


title: LG2-EC_bRNA


title: Squamous 6

value: Black


title: LV3-EC_bRNA


title: LV2-EC_bRNA


title: 4C_CBS2_del_sample2_rep1 [QHR4C-seq]

value: HEK 293T cell line

value: human embryonic kidney 293T cell

value: CBS3&5 del -/-


title: 4C_CBS2_del_sample1_rep1 [QHR4C-seq]


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-I16

tag: brain region

value: Motor cortex

tag: gender

value: M


title: 4C_CBS2_293T_WT_rep2 [QHR4C-seq]

value: wildtype


title: 4C_CBS2_del_sample1_rep2 [QHR4C-seq]


title: Squamous 5

value: IIA

value: Squamous


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-I15


title: Squamous 4

value: White

value: Female

value: IB

value: plasma


title: Squamous 3

value: Male

value: IV


title: RNA_del_sample2_rep2


title: RNA_del_sample2_rep1


title: RNA_del_sample1_rep2


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-H4


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-H3


title: Squamous 2


title: SCLC 7

value: SCLC


title: SCLC 5

value: IVA


title: SCLC 8


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-H15


title: SCLC 6


title: SCLC 3


title: Squamous 1

value: IIIB


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-H16


title: RNA_293T_WT_rep4

value: HEK 293T cell line


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-G4


title: RNA_293T_WT_rep2

value: human embryonic kidney 293T cell


title: RNA_293T_WT_rep1


title: SCLC 4

value: Black

value: IIIA


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-G3

value: Motor cortex

value: M


title: RNA_del_sample1_rep1

value: CBS3&5 del -/-


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-G15


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-F4


title: RNA_293T_WT_rep3

value: wildtype


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-F3


title: SCLC 1

value: I


title: Adeno 6

value: Female

value: Adeno


title: Adeno 9

value: IA

value: plasma


title: SCLC 2

value: White


title: Adeno 7

value: IV


title: Adeno 10

value: Male

value: III


title: Adeno 8

value: IVA


title: Benign 6

value: Benign


title: Adeno 1

value: Black

value: IB


title: Adeno 4

value: IIIB


title: Adeno 2


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-G16

value: Motor cortex

value: M


title: Benign 8


title: Adeno 5


title: Screening [AML8004.1.TCR]

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Demultiplexing of raw reads using cellranger mkfastq
Alignment against GRCh38 and generation of count matrices using cellranger count
Assembly: GRCh38
Supplementary files format and content: count matrix, barcode list and feature list in csv file format

source_name: bone marrow

extract_protocol:
Ficoll-based extraction of bone marrow mononuclear cells and cryopreservation in FCS with 10% DMSO until analysis. Thawing in PBS supplemented with 10% FCS and 10% bovine DNase I, grade II. Bead-based dead cell removal with negative-selection strategy (Miltenyi). Resuspension in PBS with 0.04% ultra-pure BSA.
5' biased library construction according to manufacturer's specifications including T cell receptor sequencing and surface marker expression (CG000330, 10x Genomics).

value: bone marrow

tag: treatment


title: EOLN [AML8004.2.TCR]

value: decitabine


title: Benign 7


title: Adeno 3

value: Female


title: Screening [AML5003.1.TCR]


title: C1 [AML1005.3.TCR]

value: decitabine and ipilimumab


title: EOLN [AML5003.2.TCR]


title: Benign 5


title: C1 [AML5003.3.TCR]


title: EOLN [AML1005.2.TCR]


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-F15

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: Mmul_10 (rheMac10), annotation: Ensembl release 104
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

extract_protocol:
Motor cortex of brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: Benign 9


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-F16


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-E4


title: Benign 4


title: Screening [AML1005.1.TCR]


title: Benign 3


title: C4 [AML8007.4.TCR]


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-E3


title: Benign 2


title: Benign 1


title: hPSC-derived HCO Hematopoietic Floaters, Day 28, scRNA-seq

city: Cincinnati

first: Daniel

middle: O.

last: Kechele

state: OH

address: 3333 Burnet Ave Location R3.034

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

description: 10x Genomics

data_processing:
Standard 10x Genomics Cell Ranger (v3.0.2) pipeline to generate FASTQ and generate filtered matrices.
Assembly: hg19 for Day 28 and Day 37 HCO as well as HCO TXP
Assembly: hg38 for Day 22 HCO and Day 14 Monocyte/Macrophage
Supplementary files format and content: tab seperated value files and matrix files

source_name: hPSC-derived colonic organoids hematopoietic floaters

extract_protocol:
For Day 22 and Day 37 HCOs and Day 14 Macrophages: Organoid were washed with cold Cell Recovery solution and minced in HBSS with Mg2+ and Ca2+ 1% BSA. Original supernatants collected and spun down and readded into the sample. HCOs were mechanically and enzymatically digested enzymes from Neural Tissue Dissociation Kit as recommended by Manufacturer's instructions for 45-60 minutes at 37C. Samples were shaken and fluxed through a P1000 then P200 tip every 10 mins. Dissociated cells were washed and filtered through a BSA coated 70um follow 40um cell strainer, centrifuged at 300 RPM for 5 minutes, and resuspended in 2% FBS in HBSS with y-27632 and 1% BSA. Day 14 Macrophages were subjected to the same mechanical and enzymatic manipulations as the dissociated HCOs.
For Day 28 HCOs Hematopoietic Floaters: Supernatants of Day 28 HCOs was collected, spun down, and resuspended in HBSS with BSA and did not undergo enzymatic digestion.
For HCO TXP: Organoid was removed from mouse kidney capsule after 15 weeks in vivo growth. The organoid was separated from surrounding kidney capsule and outer most muscle layer, opened, and flushed the lumen of mucus. HCOs were shaken in 5mL TryPLe + 5uL y-27632 for 60 minutes at 4C. Cells were washed and filtered through a BSA coated 70um follow 40um cell strainer, centrifuged at 300 RPM for 5 minutes, and resuspended in 2% FBS in PBS without Mg++ or Ca++ with y-27632. Cells were stained with Sytox Blue viability dye and sorted on a FACS Aria cell sorter and 100,000 live cells were collected in 5mL PBS with 5% FBS, 0.5% BSA, 5uL y-27632.
Library was performed according to the manufacter’s instructions (single cell Chromium 3’ v3 GEM protocol, 10x Genomics) loading 12,800 cell for approximately 8,000 captured cells. Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: cell line

value: WA01 hESC

value: hematopoietic

value: 28 days post-hPSC


title: hPSC-derived HCO, Day 37, scRNA-seq

description: 10x Genomics

source_name: hPSC-derived colonic organoids

value: hPSC-derived colonic organoids

tag: cell type

value: epithelial, mesenchymal, hematopoietic

value: 37 days post hPSC


title: C1 [AML8007.3.TCR]


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-E15


title: 17MiaSOP1247N324h

city: London

first: Stephen

last: Neidle

address: Brunswick Square

department: School of Pharmacy

country: United Kingdom

institute: UCL

data_processing:
Illumina run data were demultiplexed and converted to fastq files using Illumina’s bcl2fastq Conversion Software (v2.19).
Fastq files were pre-processed to remove adapter contamination and poor quality sequences using the program Trimmomatic (v0.36)
Duplication levels were estimated using JE-Suite50
Reads per transcript were counted using the program FeatureCounts51 (v1.4.6p5)
Assembly: Mapped to a recent human genome build (UCSC hg38: https://genome.ucsc.edu/) using the RNA-seq alignment tool STAR (v2.5b: https://github.com/alexdobin/STAR)
Supplementary files format and content: Excel format, contains read counts and differential expression data for 6 h and 24 h SOP1247 exposure

source_name: pancreatic cancer

growth_protocol: MIA PaCa-2 cells were seeded in 100 mm plates (6 h = 2.5 × 10^6 cells/plate and 24 h = 1.0 × 10^6 cells/plate) and incubated overnight.

extract_protocol:
Total RNA was extracted from 2 - 4 x 10^6 cells using the RNeasy mini kit (Qiagen, cat no. 74104) and on-column DNase1 digestion (Qiagen, cat no. 79254)
RNA-seq libraries were generated using the KAPA mRNA Library HyperPrep Kit for Illumina Platforms.

treatment_protocol: Cells were treated with 400 nM SOP1247  for 6 h and 24 h

tag: source

value: ATCC cell line

value: pancreas ductal adenocarcinoma cell line


title: 11MiaSOP1247N224h


title: 5MiaSOP1247N124h


title: 2MiaSOP1247N16h


title: 8MiaSOP1247N26h


title: 14MiaSOP1247N36h


title: C2 [AML8002.3.TCR]

tag: tissue


title: Screening [AML8007.1.TCR]


title: EOLN [AML8007.2.TCR]


title: EOLN [AML8002.2.TCR]


title: Screening [AML8002.1.TCR]


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-D15


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-D16


title: Myocardial hypertrophy_input_6

city: Nanjing

first: Chuanxi

last: Yang

state: China

address: 300 Guangzhou Road, 210029, Nanjing, PR China

department: Department of Cardiology

institute: School of Medicine, Southeast University

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For acRIP-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
For acRIP-seq: The m6A peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”. Identified m6A peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 6 -rna”.
For Ribo-seq: The reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using bowtie2 software, remaining reads were used to align to reference genome and transcriptome (Ensembl Version 91) using hisat23 and bowtie2 software separately.
For Ribo-seq:ORF identification was performed using Price5 software.  Read counts were calculated using featureCounts6 software.  Raw counts were further normalized as RPKM values using fpkm function in DESeq27 package.
Assembly: mm10 and hg38
Supplementary files format and content: mRNA-seq_9 mouse_All.count.txt
Supplementary files format and content: Ribo-seq_9 mouse_All.count.txt
Supplementary files format and content: 12hsa_acRIP-seq_input.count.txt
Supplementary files format and content: 12mmu_acRIP-seq_input.count.txt

source_name: heart ventricular tissue

extract_protocol:
For acRIP-seq: Briefly, the concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852).   Total RNA was fragmented into 100-200 nt RNA fragments using ZnCl2.   Subsequently, the purified RNA was incubated with anti-ac4c polyclonal antibody  for 3 h at 4℃ and then with protein A/G magnetic beads (Thermo Fisher Scientific, 88802) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments.   The ac4c-enriched RNA was eluted from the beads in RLT buffer supplied in RNeasy Mini Kit (QIAGEN, 74106).   The RNA-seq library was prepared by NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, E7775).  For Ribo-seq:tissue were pulverized manually under liquid nitrogen and treated by ice-cold PBS containing 100 μg/mL cycloheximide.     Ribosome profiling was performed using Epi™ Ribosome Profiling Kit (Epibiotek, R1814).     Subsquently, RPFs (ribosome-protected RNA fragments) was extracted using RNA clean&ConcentratorTM-5 kit (ZYMO, R1016).     EpiTM RiboRNA Depletion Kit  (Epibiotek, R1805) was used for rRNA depletion.     Sequencing libraries were constructed using QIAseq miRNA Library kit (QIAGEN, 1103679).
RNA libraries were prepared for sequencing using standard Illumina protocols
acRIP-seq; Ribo-seq; RNA-seq

treatment_protocol: Silencing and inhibiting NAT10

value: heart ventricular tissue

tag: genotype

value: Myocardial hypertrophy


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-C4

first: Joseph

last: Ecker

institute: HHMI-Salk-Institute


title: hPSC-derived HCO, transplanted, Week 15, scRNA-seq

description: 10x Genomics

value: 15 weeks in vivo (19 weeks post hPSC)


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-D4

value: Motor cortex


title: Myocardial hypertrophy_input_5


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-C3

value: M


title: Non-myocardial hypertrophy_input_4

value: Non-myocardial hypertrophy


title: Non-myocardial hypertrophy_input_5


title: Myocardial hypertrophy_input_3


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-C16


title: Non-myocardial hypertrophy_input_6


title: Myocardial hypertrophy_input_2


title: Myocardial hypertrophy_input_1


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-C15


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-E16


title: C1 [AML3005.3.TCR]

value: bone marrow


title: Non-myocardial hypertrophy_input_3


title: Non-myocardial hypertrophy_input_2


title: Screening [AML3005.1.TCR]


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-D3


title: C7 [AML3003.4.TCR]


title: EOLN [AML3005.2.TCR]

value: decitabine


title: C2 [AML3003.3.TCR]

value: decitabine and ipilimumab


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-B4


title: Non-myocardial hypertrophy_input_1


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-B3


title: Myocardial hypertrophy_input_4


title: Myocardial hypertrophy_IP_6


title: Myocardial hypertrophy_IP_5


title: EOLN [AML3003.2.TCR]


title: Myocardial hypertrophy_IP_4


title: Screening [AML3003.1.TCR]


title: Non-myocardial hypertrophy_IP_6


title: Non-myocardial hypertrophy_IP_5


title: EOLN [AML3001.2.TCR]


title: EOT [AML1008.5.TCR]

value: end of treatment


title: C4 [AML3001.4.TCR]


title: BE2C-siJMJD6#45-2

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to human genome assembly (hg19) (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (v19) .
Genome_build: GRCh37(hg19)
Supplementary_files_format_and_content: gene-level FPKM txt files

source_name: cell line

growth_protocol: SKNAS,BE2C cells were cultured with RPMI 1640 media supplemented with 100 U/mlpenicillin/streptomycin and 10% fetal bovine serum. Cells were maintained at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
Total RNA from cells were performed using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

treatment_protocol: For siRNA knockdown treatment, SKNAS,BE2C cell were treated with siRNA control and siJMJD6 #43 and #45 for 72h.

value: siJMJD6 #45


title: BE2C-siJMJD6#45-1


title: BE2C-siJMJD6#43-2

value: siJMJD6 #43


title: Non-myocardial hypertrophy_IP_2


title: Myocardial hypertrophy_IP_3


title: Non-myocardial hypertrophy_IP_4


title: Non-myocardial hypertrophy_IP_3


title: Myocardial hypertrophy_IP_1


title: Myocardial hypertrophy_IP_2


title: Non-myocardial hypertrophy_IP_1


title: C4 [AML1008.4.TCR]


title: Screening [AML1008.1.TCR]


title: BE2C-siJMJD6#43-1


title: C1 [AML1008.3.TCR]


title: C4 [AML1002.4.TCR]


title: EOLN [AML1008.2.TCR]


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-A4

city: La Jolla

address: 10010 North Torrey Pines Road


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-A3


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-A15


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-B15


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-P13


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-A16


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-P2


title: CEMBA3C_MacaqueM1_R1_P1-2-B11-B16


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-P14


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-P1


title: BE2C-siCtrl-1

value: siCtrl


title: S2-013 cells, 6 hour acetate treatment, input

city: Oklahoma City

first: Pankaj

middle: K

last: Singh

state: OK

address: 940 Stanton L. Young Blvd., BMSB 332A

department: Oncology Science

institute: OUHSC

data_processing:
Resulting indexed libraries were sequenced by the UNMC Sequencing Core Facility using an Illumina NextSeq 500.
Adaptor sequences and low quality (Phred score < 20) ends were trimmed from sequences using Trim Galore software package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Resulting fastq files were aligned to the human genome (GRCh38/hg38) using the sequence aligner Bowtie2 (version 2.2.3)
The software package Picard routine MarkDuplicates (http://broadinstitute.github.io/picard/) was used to remove sequence duplications. Sequencing count of 49.7 million was acquired using samtools (http://samtools.sourceforge.net/) for each sample.
For peak calling, of ChIP enriched regions the MACS2 peak caller [2] software (version 2.1.1) of each ChIP to corresponding input DNA sample was used to determine binding regions based on a FDR adjusted p-value (q-value) <0.25.
Bigwig files were generated using the deeptools bamCoverage routine (https://deeptools.readthedocs.io/en/develop/). Alignment of significant peaks to gene specific regions was accomplished using the bedtools routine intersect (https://bedtools.readthedocs.io/en/latest/).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: peaks file

source_name: S2-013 6 hour treatment input

growth_protocol: The pancreatic cancer cell line was cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with  10% fetal bovine serum and 1:100 antibiotic-antimycotic (Gibco). The low pH of the media was adjusted  at 6.9~7.1 by adding 1g/L NaHCO3, and the control pH was set by using 3.7g/L NaHCO3.

extract_protocol:
8 ng of chromatin immunoprecipitation DNA was extracted using the specific antibody H3K27Ac (Active Motif, #39133) and the Zymo-Spin ChIP Kit according to manufactures instructions and recommendations.
The captured and purified DNA was prepared for high throughput sequencing using the New England Biolabs NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: The cells were treated for 6h in low pH condition.

value: pancreatic cancer cell line S2-013

value: Acetate


title: S2-013 cells, control treatment, input

source_name: S2-013 cell line input

value: Vehicle


title: S2-013 cells, 6 hour acetate treatment, ChIP-seq

source_name: S2-013 6 hour treatment

value: H3K27Ac (Active Motif, #39133)


title: S2-013 cells, control treatment, ChIP-seq

source_name: S2-013 cell line control


title: SKNAS-siJMJD6#45-2

value: SKNAS


title: SKNAS-siJMJD6#43-2


title: SKNAS-siJMJD6#43-1


title: BE2C-siCtrl-2


title: SKNAS-siJMJD6#45-1


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-O14


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-O2


title: SKNAS-siCtrl-2


title: SKNAS-siCtrl-1


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-O1


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-N2


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-O13


title: EOT [AML1026.4.TCR]


title: EOLN [AML1002.2.TCR]


title: Screening [AML1002.1.TCR]


title: Screening [AML1026.1.TCR]


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-N14


title: EOLN [AML1022.2.TCR]


title: Screening [AML1022.1.TCR]


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-N13


title: C1 [AML1026.3.TCR]


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-M2


title: C1 [AML1022.3.TCR]


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-N1


title: EOLN [AML1026.2.TCR]


title: C2 [AML1016.2.TCR]


title: NL1

first: Liu

last: Dan

address: 2699 Gaoke West Road, Pudong District

institute: Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University

description: mRNA expression of granulosa cells from the age and BMI matched normal control women

data_processing:
Raw data (raw reads) were processed using Trimmomatic to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks and the read counts of each gene were obtained by htseq count. DEGs were identified using the DESeq (2012) R package functions estimateSizeFactors and nbinomTest.
Pvalue < 0.05 and foldChange > 2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern.
GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Assembly: GRCh38.p12
Supplementary files format and content: *_counts.txt: Tab-delimited text files include raw count values for each gene.

source_name: granulosa cells

extract_protocol:
Total RNA from human granulosa cells was extracted using the RNeasy Micro Kit (Qiagen, Hilden, Germany ) following the manufacturer’s instruction.
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instruction. The Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) was used to evaluate the RNA integrity.

value: granulosa cells

value: Female

tag: condition

value: Control


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-M1

value: Motor cortex

value: M


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-M13


title: DL6

description: mRNA expression of granulosa cells from the bPOI patients

value: bPOI


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-L2


title: DL5


title: DL4


title: DL7


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-L14


title: DL3


title: DL2


title: P-5-D5

first: Shanshan

last: Wang

state: JiangSu

address: No. 53, Zhongshan North Road, Nanjing, Jiangsu 210028

institute: The Affiliated Drum Tower Hospital of Nanjing University Medical School

data_processing:
These RNAs were aligned with bowtie and then subjected to the BLAST search against Rfam v.10.1 and GenBank databases.
The known miRNAs were determined through aligning against miRBase v.21 database, and unannotated small RNAs were identified with mirdeep2 to predict novel miRNAs.
With DESeq, DEmiRNAs were determined with p-value < 0.05 and |log2FC|> 1.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: spent culture medium of pregnant groups at D5 blastocyst

extract_protocol:
According to the manufacturer’s protocol, total RNA was extracted respectively from 16 SCM using miRNeasy Serum/Plasma Kit
NEBNext Multiplex Small RNA Library Prep Set for Illumina was used to generate smRNA-seq libraries.

value: female

tag: bmi


title: P-3-D5


title: P-4-D5


title: NL8


title: NL6


title: NL7


title: NL3


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-L1


title: C2 [AML1012.3.TCR]

value: bone marrow

value: decitabine and ipilimumab


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-L13


title: EOLN [AML1012.2.TCR]

value: decitabine


title: Screening [AML1016.1.TCR]


title: EOT [AML1012.4.TCR]

value: end of treatment


title: Screening [AML1012.1.TCR]


title: C10 [AML1010.5.TCR]


title: C4 [AML1010.4.TCR]


title: P-2-D5


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-K2


title: P-1-D5


title: C1 [AML1010.3.TCR]


title: P-5-D3

source_name: spent culture medium of pregnant groups at D3 cleavage


title: EOLN [AML1010.2.TCR]


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-K14


title: P-4-D3


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-K13


title: P-2-D3


title: Screening [AML1010.1.TCR]


title: P-3-D3


title: NP-3-D5

source_name: spent culture medium of non-pregnant groups at D5 blastocyst


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-J2


title: NP-2-D5


title: P-1-D3


title: EOLN [AML1006.2.TCR]


title: NP-1-D5


title: C2 [AML1019.5.TCR]


title: lung_hypoxic_3days_rep2

type: RNA

first: Olena

last: Rudyk

address: St Thomas Hospital, The Rayne, Lambeth Wing, Westminster Bridge Rd

department: School of Cardiovascular and Metabolic Medicine & Sciences

institute: King's College London

hyb_protocol: Hybridization cocktails prepared as recommended by NuGEN. Samples were hybridized to Mouse Gene 2.0 ST arrays using standard protocols as recommended by the manufacturer (Affymetrix).

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000.

data_processing: The data was processed using the RMA-sketch algorithm in Expression Console software (Affymetrix)

label: Biotin

label_protocol: ~5 μg of SPIA-amplified complementary DNA was fragmented and biotin-labelled using the Encore Biotin module (NuGEN)

growth_protocol: Mice were kept in pathogen-free conditions, had ad libitum access to standard chow and water and were kept in a 12-hour day/night cycle at 20-22°C, 60% humidity.

extract_protocol: mRNA extraction was performed using the RNeasy Plus Universal kit (Qiagen)

treatment_protocol: Hypoxic mice were housed in a normobaric hypoxia chamber for 3 days where they were given 10% oxygen. Normoxic mice were housed in the biological service unit.

value: lung

value: hypoxic

tag: strain


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-J14


title: NP-2-D3

source_name: spent culture medium of non-pregnant groups at D3 cleavage


title: Between C1 and C2 [AML1019.4.TCR]


title: lung_normoxic_3days_rep5

value: normoxic


title: lung_normoxic_3days_rep2


title: lung_hypoxic_3days_rep1


title: lung_hypoxic_3days_rep6


title: NP-1-D3


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-K1


title: lung_hypoxic_3days_rep5


title: lung_hypoxic_3days_rep3


title: lung_normoxic_3days_rep6


title: lung_normoxic_3days_rep3


title: lung_hypoxic_3days_rep4


title: C1 [AML1019.3.TCR]


title: EOLN [AML1019.2.TCR]


title: NP-3-D3


title: H3i, YPD, RNA-seq biol rep3

city: Pathumthani

first: Peerapat

last: Khamwachirapithak

address: Phahonyothin Road, Khlong Luang

country: Thailand

institute: Thammasat University

data_processing:
FastQC
Reads were align to Saccer3 genome using the Hisat2
Sorting and indexing using Samtools
Duplication was removed by Picard tools
Raw read counts were normalized by DEseq2
Assembly: Saccer3
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Saccharomyces cerevisiae

source_name: Cell pellet

growth_protocol: Cells were cultured in YPGal medium at 30°C and 230 rpm before H3-shutoff experiment. The H3 inducible shut-off strain (i.e., “DGS200.1” or  “H3i”) from the YEF473A strain by knocking out the HHT1 gene (encoding H3), and replacing the native promoter of the HHT2 gene (the other H3-encoding gene) with an inducible Gal1 promoter.

extract_protocol:
RNA was extracted by MagMax96 total RNA isolation kit (AM1830, Invitrogen) for the first and second replicates. Trizol reagent (15596026, Invitrogen) was used in extraction with glass beads for the third replicate.
Librarires of the first and second replicates were prepared using the Illumina TruSeq Stranded mRNA Library Prep. For the third replicate, the TruSeq Stranded mRNA LT sample prep kit was used for library construction.

treatment_protocol: Switching media from YPGal to YPD

value: Cell pellet

value: Yeast cell

value: YPD


title: H3i, YPGal, RNA-seq biol rep3

value: YPGal


title: WT, YPGal, RNA-seq biol rep3

value: WT


title: WT, YPD, RNA-seq biol rep3


title: lung_normoxic_3days_rep1


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-H2


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-I13


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-J13


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-I14


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-I2


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-J1


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-I1


title: EOT [AML1007.5.TCR]


title: C4 [AML1007.4.TCR]


title: EOLN [AML1007.2.TCR]


title: Attp_Glia_biolrep2

city: Salt Lake CIty

first: Katie

middle: G

last: Owings

state: UT

address: 15 North 2030 East EIHG 5200

department: Human Genetics

institute: University of Utah

data_processing:
Trim adapters withcutadapt
Align withSTAR
Collect alignment statistics withPicardand other tools
Generate count matrices withfeatureCountsandRSEM
Summarize alignments statistics and counts withmultiQC
Perform differential expression withDESeq2
Assembly: dm6, D_melanogaster_Aug_2014
Supplementary files format and content: results_piga_neuron.csv : Differentially expressed genes in the PIGA neuronal KD vs Attp neuronal control
Supplementary files format and content: results_piga_glia.csv : Differentially expressed genes in the PIGA glia KD vs Attp glia control

organism: Drosophila melanogaster

source_name: Whole Head

growth_protocol: Flies were maintained at 25°C on a standard diet based on the Bloomington Stock Center standard medium with malt and without soy flour. Flies were on a 12-hour light/dark cycle.  Strains were obtained from the Bloomington Drosophila Stock Center. Flies were 3-5 days old and had gone 48 hours without CO2 exposure.

extract_protocol:
Direct-zol RNA Miniprep (Zymo Research R2061) using TRIzol Reagent (ThermoFisher Cat # 15596026) and including the DNAse step
Illumina TruSeq Stranded mRNA Library Prep with UDI prepared and sequenced by the Huntsman Cancer Institute High-Throughput Genomics Core

treatment_protocol: No treatment was applied to the flies.

value: Whole Head

value: glia

value: REPO-GAL4 x AttP (BDSC 36304)


title: PIGA KD_Neuron_biolrep3

value: neuron

value: ELAV-GAL4 x RNAi (BDSC 62696)


title: Attp_Glia_biolrep1


title: Attp_Neuron_biolrep3

value: ELAV-GAL4 x AttP (BDSC 36304)


title: Attp_Glia_biolrep3


title: Attp_Neuron_biolrep2


title: PIGA KD_Neuron_biolrep1


title: PIGA KD_Glia_biolrep3

value: REPO-GAL4 x RNAi (BDSC 62696)


title: PIGA KD_Glia_biolrep2


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-M14

state: CA

value: Motor cortex

value: M


title: Screening [AML1019.1.TCR]

source_name: bone marrow

value: bone marrow


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-H14


title: Screening [AML1007.1.TCR]


title: PIGA KD_Glia_biolrep1


title: PIGA KD_Neuron_biolrep2


title: C1 [AML1007.3.TCR]

value: decitabine and ipilimumab


title: Attp_Neuron_biolrep1


title: EOLN [AML8004.2.GEX]

value: decitabine


title: C2 [AML8004.3.GEX]


title: 2 Weeks BCG-vaccinated, HTO

city: Ithaca

first: Davide

last: Pisu

state: NY

address: 930 Campus Road

department: Microbiology and Immunology

institute: Cornell University

description: HTO: Read 1 contains Cell Barcode and UMI, Read 2 contains Antibody tag

library_source: other

data_processing:
Sequencing data derived from each run underwent processing using distinct software tailored to the library type. mRNA libraries were processed using the CellRanger software (v. 6.0) from 10X Genomics and the mouse mm10 genome (GRCm38). The ADT and HTO libraries were processed using CITE-Seq-Count (v. 1.4.3), available at https://hoohm.github.io/CITE-seq-Count/. This processing yielded raw count matrices for both mRNA and proteins. Downstream data analysis was conducted in Seurat (v. 4.3), following methods outlined by Stuart et al. Cells with less than 200 unique genes or with over 30% of the total reads belonging to mitochondria were filtered out. The HTOs multiplexed samples were then demultiplexed using the MULTIseqDemux() function in Seurat. This step allowed for the removal of doublets and empty droplets and ensured the correct assignment of identities to each sample.
All scRNA-seq datasets from individual timepoints were preprocessed using Seurat's regularized negative binomial regression, where both the number of counts and the percentage of mitochondrial reads were regressed out, as per Hafemeister and Satija. For analysis of the macrophage populations in the uninfected naïve lungs we used the previously generated datasets from Pisu et al. Metadata columns, namely “Timepoint”, “Batch”, “Infection Status”, and “Vaccination Status”, were added to each dataset prior to subsequent steps.
Datasets were combined into a unified Seurat object. The raw counts contained in the RNA slot of the merged object were used as an input for Harmony integration. Raw counts underwent log-normalization, followed by the identification of the top 3,000 variable genes. These genes were scaled and centered. PCA was then performed on these values. Integration in Harmony incorporated “Batch”, “Infection Status”, “Timepoint”, and “Vaccination Status” as covariates.
Using the Harmony-aligned embeddings, graph-based cluster detection was achieved utilizing principal components (PCs) that had been marked statistically significant by the jackstraw method. For community detection, we employed the Louvain algorithm. Cell types for each identified cluster were annotated using both reference-based and canonical marker genes.
Assembly: mm10
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CiteSeq-count output files for ADT and HTO: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-Seq

molecule: protein

source_name: Lung

extract_protocol:
At 2, 4, and 6 weeks post-infection (w.p.i.), mice were euthanized. Lungs were aseptically removed and immersed in PBS containing 5% FBS and Collagenase IV (250U/mL). To preserve the gene expression profiles of both the host and bacteria, samples were immediately processed using a GentleMACS tissue dissociator (Miltenyi Biotec) and maintained on ice. The dissociated lung material was subsequently strained through a 70-µM mesh, and red blood cells were lysed using ammonium-chloride-potassium (ACK) lysis buffer (Lonza). Cells from infected mice (n = 5/timepoint) were washed in PBS containing 5% FBS, resuspended in sorting buffer (PBS, 1% FBS, 5 mM EDTA, and 25 mM Hepes), filtered through a 40-µM strainer, and sorted. Throughout the sorting, samples were kept at 4°C and directly collected into Cell Staining Buffer (BioLegend). Sorted cells were centrifuged at 500 g for 5 min and then resuspended in 50 µl of cell staining buffer containing 0.25 µg of TruStain FcX PLUS (BioLegend), followed by a 10 min incubation at 4°C. An ADT plus HTO antibody cocktail mix (50 µl) was then added to the samples, and the cells were further incubated for 30 min at 4°C. After two washes in cell staining buffer, differentially tagged samples (e.g., hspx′::GFPhigh/hspx′::GFPlow) were combined and resuspended in 1× Dulbecco’s PBS. The samples were then fixed by slowly adding ice-cold methanol to a final concentration of 90% (vol/vol) and stored at −20°C overnight.
Post-fixation, the samples were brought out of the BSL3 facility, equilibrated on ice for 15 min, and washed twice with rehydration buffer (1× Dulbecco’s PBS with 1.0% BSA [Thermo Fisher Scientific] and 0.5 U/µl RNase Inhibitor [Sigma-Aldrich]). The cell count was determined prior to loading onto the 10× chip. For mRNA library preparation, we adapted the 10× protocol (CG000206 Rev D), making a minor alteration in step 2.2. Specifically, we incorporated 1 μl of ADT and HTO additive primers (0.2 μM stock) following the method described by Stoeckius et al76. HTO and ADT libraries were prepared according to BioLegend's standard protocols.
The mRNA, HTO, and ADT libraries underwent quality control assessment using an Agilent Fragment Analyzer. Their concentrations were determined using the QX200 digital PCR system from Bio-Rad. Libraries were pooled in the same sequencing run at specific ratios: 90% mRNA, 5% ADT, and 5% HTO. Sequencing was performed on the Nextseq 2k (50bp kit) or NextSeq500 (Illumina) using the 75-bp NextSeq kit. The cycle distribution was: read 1 (28 cycles), i7 index (8 cycles), and read 2 (55 cycles for nextseq 500 and 52 cycles for nextseq 2k). Sequencing depth exceeded 50,000 reads/cell.

value: Lung

value: mCherry+

tag: timepoint

value: 2 Weeks

value: Vaccinated

tag: infection

tag: library type

value: HTO

tag: hto

value: TotalSeq Hashtag 1 murine (cat. # 155801), Hashtag 2 murine (cat. # 155803)


title: Screening [AML8004.1.GEX]


title: WT, YPGal, inputRap1, biol rep3

data_processing:
FastQC
ChIP-seq reads were aligned to Saccer3 genome using the Bowtie2
Sorting and indexing using Samtools
Samtools depth was used to estimate depth of each sample, and used for normalization
Normalized ChIP-seq coverages were calculated by Bedtools and pseudocount was added, before being converted to bigWig files using WigtoBigWig
Assembly: Saccer3
Supplementary files format and content: bigWig

extract_protocol:
Cell were fixed with 1% formaldehyde and quenched by Tris pH 8.  Genomic DNA was sonicated, and Rap1 binding DNA  was pulled down using anti-FLAG beads (Sigma, M8223)
ChIP libraries were prepared for sequencing using standard Illumina protocol

treatment_protocol: Switching media to from YPGal to YPD

value: Cell pellet

value: Yeast cell

value: WT

tag: chip antibody

value: YPGal


title: H3i, YPD, Rap1, biol rep3

value: anti-FLAG beads (Sigma, M8223)

value: YPD


title: C1 [AML5003.3.GEX]


title: EOLN [AML5003.2.GEX]


title: H3i, YPGal, Rap1, biol rep3


title: Screening [AML5003.1.GEX]


title: WT, YPD, Rap1, biol rep3


title: C4 [AML1005.4.GEX]


title: WT, YPGal, Rap1, biol rep3


title: 2 Weeks BCG-vaccinated, mRNA

description: GEX (3' mRNA) library: read 1 file contains cell barcode and UMI; read 2 file contains transcript

value: mRNA


title: C1 [AML1005.3.GEX]


title: H3i, YPD, input, biol rep2

data_processing:
FastQC
ChIP-seq reads were align to Saccer3 genome using the Bowtie2
Sorting and indexing using Samtools
Samtools depth was used to estimated depth of each sample, and used for spike-in normalization
Spike-in normalized ChIP-seq coverages were calculated by Bedtools and pseudocount was added, before being converted to bigWig files using WigtoBigWig
Assembly: Saccer3
Supplementary files format and content: bigWig

extract_protocol:
Cell were fixed with 1% formaldehyde and quenched by Tris pH 8.  Genomic DNA was fragmented by MNase enzyme, and H3-binding DNA pull down using anti-H3 antibody coupled with Dynabeads magnetic protein A beads
ChIP libraries were prepared for sequencing using standard Illumina protocol


title: sample DLT

city: beijing

first: xinyu

last: She

address: shuangqing road, haidian district

department: school of life sciences

institute: Tsinghua university

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v5.0.0.
Assembly: Ensemble release 98 Drosophila melanogaster genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: larval trachea

growth_protocol: Animals were raised in the 25 ℃ incubator all the time before the dissection

extract_protocol:
Trachea were manually dissected on the dissection dish with ice-cold Schneider’s medium described  Chen (2016).Then trachea was transferred into a new petri dish filled with ice-cold Schneider’s medium on ice after dissection. The dissection work was managed within 1 hour.
Single-cell gene expression libraries were generated with theChromium™ Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics, Pleasanton, California, USA) according to the manufacturers manual.

value: larval trachea

value: epithelial cells and the cells associated with trachea


title: H3i, YPD, inputRap1, biol rep3


title: WT, YPD, inputRap1, biol rep3


title: EOLN [AML1005.2.GEX]

value: bone marrow


title: H3i, YPGal, inputRap1, biol rep3


title: ChIP-Seq IGG_CLP

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
reads were quality checked with fastqc and preprocessed in order to remove adapters with trimmomatic (v0.39)
reads were aligned to the mm10 reference genome with the BWA aligner (bwa mem) and reads annotated as PCR duplicates with picard or mapping to the mitochondrial genome were excluded
ChIP-seq peaks were called with MACS2 (v2.1.0), using input/IGG conrol and c a minimal 4-fold local enrichment above the background and the control sample and q-value cut-off of 0.05
in addition, bigwig coverage files were generated using python deeptools
Assembly: mm10
Supplementary files format and content: narrowPeak
Supplementary files format and content: bigwig

source_name: liver

extract_protocol:
ChIP was performed on 200-400 mg of snapfrozen liver tissue. First, DynabeadsTM protein G (Thermo Fisher Scientific) were washed three times with BSA/PBS and coupled to a primary antibody against HNF4α (3 µg/IP sample; PP-H1415-00, R&D systems) or mouse IgG (3 µg/IP sample; sc-2025, SantaCruz), as an internal control, overnight at 4°C. Afterwards, the beads with coupled antibody were washed with BSA/PBS twice. Livers were homogenized and fixed in Farnham Lysis buffer with 1% formaldehyde, supplemented with protease inhibitor cocktail (Roche), for 10 min at RT. Released nuclei were isolated by centrifugation at 2000 rpm for 5 min and washed with PBS, supplemented with protease inhibitor cocktail (Roche). The nuclei were further lysed in RIPA buffer, supplemented with protease inhibitor cocktail (Roche), and sonicated (Bioruptor, Diagenode) at 4°C for 40 cycles (30s ON, 30s OFF) with high settings to yield 200-800 bp DNA fragments. Cell debris was removed by centrifugation at full speed for 20-30 min at 4°C. Sonication efficiency was checked (after reverse crosslinking with proteinase K for 1h at 65°C and DNA purification) on a 1.5% agarose gel. For immunoprecipitation (IP), antibody-coupled magnetic beads were added to the sonicated samples and incubated overnight at 4°C. Input samples containing sonicated lysate were used as a control during analysis. The day after, bead-antibody-DNA complexes were washed 5 times with LiCl wash buffer (100 mM Tris-HCl; pH 7.5, 500 mM LiCl, 1% IGEPAL, 1% sodium deoxycholate) at 4°C and 2 times with TE buffer (10 mM Tris-HCl; pH 7.5, 0.1 mM EDTA) at 4°C. Chromatin was eluted by incubating the IP samples with elution buffer (1% SDS, 0.1M NaHCO3) 1h at 65°C. Both IP and input samples were incubated with proteinase K for 4h at 65°C for reverse crosslinking and DNA was purified in 50 µL elution buffer according to the manufacturer’s protocol by using the Monarch PCR&DNA Cleanup kit (Biolabs). DNA concentration was measured with Qubit Fluorometer using the Qubit 1x dsDNA high sensitivity kit (Thermo Fisher Scientific)
15 ng of purified chromatin was used to generate a ChIP-Seq library according to the manufacturer’s protocol using NEBNext Ultra II DNA Library Prep kit (E7645L, NEB).

treatment_protocol: mice were subjected to SHAM or CLP surgery and livers are isolated 8h after the procedure and snap frozen in liquid nitrogen

value: liver

value: CLP


title: ChIP-Seq liver_input


title: H3i, YPGal, input, biol rep2


title: ChIP-Seq liver_CLP-4


title: ChIP-Seq IGG_SHAM

value: SHAM


title: ChIP-Seq liver_CLP-3


title: lung_normoxic_3days_rep4

value: lung

value: normoxic


title: ChIP-Seq liver_CLP-2


title: WT, YPD, input, biol rep2


title: C4 [AML8007.4.GEX]

data_processing:
Demultiplexing of raw reads using cellranger mkfastq
Alignment against GRCh38 and generation of count matrices using cellranger count
Assembly: GRCh38
Supplementary files format and content: count matrix, barcode list and feature list in csv file format

extract_protocol:
Ficoll-based extraction of bone marrow mononuclear cells and cryopreservation in FCS with 10% DMSO until analysis. Thawing in PBS supplemented with 10% FCS and 10% bovine DNase I, grade II. Bead-based dead cell removal with negative-selection strategy (Miltenyi). Resuspension in PBS with 0.04% ultra-pure BSA.
5' biased library construction according to manufacturer's specifications including T cell receptor sequencing and surface marker expression (CG000330, 10x Genomics).

value: decitabine and ipilimumab


title: Screening [AML1005.1.GEX]


title: C1 [AML8007.3.GEX]


title: H3i, YPD, H3, biol rep2

value: Anti-histone H3 (Abcam, ab1791)


title: EOLN [AML8007.2.GEX]

value: decitabine


title: H3i, YPGal, H3, biol rep2

value: Cell pellet

value: Yeast cell


title: Screening [AML8007.1.GEX]


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-E1

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: Mmul_10 (rheMac10), annotation: Ensembl release 104
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

extract_protocol:
Motor cortex of brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: Motor cortex

value: M


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-H1


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-H13


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-E2


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-G1


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-E14


title: ChIP-Seq liver_SHAM-2


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-G14


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-E13


title: ChIP-Seq liver_SHAM-4


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-F14


title: ChIP-Seq liver_CLP-1


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-F13


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-D2


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-G13


title: ChIP-Seq liver_SHAM-3


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-G2


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-F2


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-F1


title: ChIP-Seq liver_SHAM-1


title: C2 [AML8002.3.GEX]


title: CEMBA3C_MacaqueM1_R1_P1-1-B11-D14


title: WT, YPGal, input, biol rep2

value: WT

value: YPGal


title: EOLN [AML8002.2.GEX]


title: WT, YPD, H3, biol rep2

value: YPD


title: WT, YPGal, H3, biol rep2


title: Screening [AML8002.1.GEX]


title: C1 [AML3005.3.GEX]