title: Male adult, Abx Morphine 2

description:
Library name: AbxD2
Sample names in column (minus "ReadsPerGene.out")

value: Male

value: adult

value: Abx morphine


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 455, 33530

status: Public on Aug 01 2025

type: SRA

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

country: USA

institute: University of Minnesota

description: Library name: G463_O07_ABL3_33530_D455

library_source: transcriptomic

data_processing:
Trimgalorev0.6.4 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.4.2
Aligned reads with STARv2.710b
Assembly: Rhesus macaques version10 Ensembl annoation v111
Supplementary files format and content: text file of counts for each sample

molecule: total RNA

organism: Macaca mulatta

source_name: Whole blood

extract_protocol:
Isolation of RNA from Whole Blood Using the RNAdvance Blood Kit – for NHP samples
mRNA Library Prep for RNA from Whole Blood using KAPA HyperPrep Reagents

treatment_protocol: A prime and boost of one of the 3 modified RhCMV/SIV vectors were given to female rhesus macaques

tag: tissue

value: Whole blood

tag: treatment

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

tag: time

value: day 455

tag: animal id

tag: Sex

value: female

tag: treatment outcome

value: Protected


title: Control 1b [RNA-seq]

city: Evanston

first: Stephenie

last: Droll

state: IL

address: Hogan 2-100 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

description:
control_1b
library_7
H2AZ1_knockdown.csv

data_processing:
Read quality control by FastQC
Adaptor trimming by Trimgalore
Alignment to hg38 with STAR
Gene expression quantification with Salmon
Differential expression calculated by DESeq2
Assembly: hg38
Supplementary files format and content: .csv file with gene expression data, log2fold-change, and statistics for all genes

molecule: polyA RNA

organism: Homo sapiens

source_name: foreskin epidermis

growth_protocol: Human primary epidermal keratinocytes pooled from a minimum of six donors were maintained at 37 degrees Celsius in a 1:1 mixture of Keratinocyte-SFM and Medium 154 at a confluency between 10-50%.

extract_protocol:
Quick-RNA MiniPrep Kit by Zymo Research with Dnase I digestion according to manufacturer's instructions
NEBNext Poly(A) mRNA Magnetic Isolation Module followed by NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Keratinocytes were centrifuged for one hour at 1250 RMP at 32 degrees Celsius with control- or shRNA- lentivirus. For double knockdown, transductions were performed serially on the same day. Cells were selected for 24 hours with puromycin. RNA was extracted ~72 hours post-transduction.

value: foreskin epidermis

tag: cell type

value: primary keratinocyte

tag: genotype

value: control for H2AZ1 knockdown


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 455, 32624

description: Library name: G467_O07_ABL3_32624_D455


title: SRCAP shRNA5 [RNA-seq]

description:
SRCAP_sh5
library_6
SRCAP_knockdown.csv

value: SRCAP knockdown


title: Male adult, Abx Saline 5

city: Winston-Salem

first: Rebecca

last: Hofford

state: NC

address: 115 S Chestnut St

department: Translational Neuroscience

institute: Wake Forest School of Medicine

description:
Library name: AbxC5
Sample names in column (minus "ReadsPerGene.out")

data_processing:
Reads were removed if they contained adaptor contamination, when nucleotides were uncertain for 10% or more of the read, or the base quality was less than 5 for 50% of the reads.
Aligned using STAR v2.7.10a
Normalized using DESeq2
Differential expression of genes using ExpressAnalyst
Assembly: mm10
Supplementary files format and content: HoffordZeroMale.csv (Read counts for all male samples)

organism: Mus musculus

source_name: Brain

extract_protocol:
Rneasy Mini Kit (Qiagen)
Fast RNA-seq Library Prep Kit V2 (abclonal Technology)

value: Brain

value: All

value: wild type

tag: developmental stage

value: Abx saline


title: YDBS_177

city: Zhengzhou

first: Yilin

last: Zhang

address: Zhengdong New District

country: China

institute: The First Affiliated Hospital of Henan University of Chinese Medicine

description: Library name: Sample 76

data_processing:
Preliminary quantification was performed using Qubit 2.0 Fluorometer. After dilution, insert size was detected by Agilent 2100 bioanalyzer, and the effective library concentration (>2 nM) was accurately quantified by qRT-PCR to ensure the library quality.
Libraries were pooled according to the effective concentration and target downstream data volume, then sequenced on Illumina NovaSeq 6000 to generate 150 bp paired-end reads to obtain the sequence information of the fragments to be tested.
Image data of sequencing fragments were obtained from high-throughput sequencer and converted to sequence data (reads) by CASAVA base recognition. After filtering, reads with undetermined base information, reads with splice, and reads with Qphred≤20 bases accounting for ≥50% of the whole read length were removed. Q20, Q30 and GC contents of cleaned data were calculated to obtain high-quality dataset.
Reference genome and gene annotation files were downloaded from genome website. HISAT2 v2.0.5 was used to build genome index and align the paired-end clean reads with the reference genome.
Quantification of gene expression levels: Feature Counts (1.5.0-p3) was used to calculate the reads mapped to each gene. FPKM (fragments per kilobase of transcript per million mapped reads) was calculated based on gene length to estimate gene expression levels.
The number of genes in the samples was normalized using DESeq2 software (1.20.0) , and the fold change (FC) was calculated. The P-values were adjusted to control the false discovery rate using the method of Benjamini and Hochberg.
Assembly: hg38
Supplementary files format and content: Txt files include FPKM values for each Sample

source_name: whole blood

extract_protocol:
Total RNA was extracted using PAXgene Blood miRNA Kit.
Library construction: Using total RNA as starting material, polyA-tailed mRNA was enriched by Oligo(dT) magnetic beads. The enriched mRNA was randomly fragmented by divalent cations in Fragmentation Buffer. In the M-MuLV reverse transcriptase system, random oligonucleotides were used as primers to synthesize the first-strand cDNA with fragmented mRNA as template, and the RNA strand was degraded using RNaseH. Subsequently, the second cDNA strand was synthesized using dNTPs as raw materials in DNA polymerase I system. About 370~420 bp of purified double-stranded cDNA was screened by using AMPure XP beads after end repair, A-tail addition and sequencing junction ligation steps, and further amplified by PCR, and then the PCR product was purified again by using AMPure XP beads, and the library was finally obtained.

value: whole blood


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 455, 32574

description: Library name: G461_O07_ABL3_32574_D455

value: Nonprotected


title: YDBS_170

description: Library name: Sample 75


title: Male adult, Abx Saline 4

description:
Library name: AbxC4
Sample names in column (minus "ReadsPerGene.out")

value: Male

value: adult


title: SRCAP shRNA3 [RNA-seq]

description:
SRCAP_sh3
library_4
SRCAP_knockdown.csv


title: YDBS_168

description: Library name: Sample 74


title: Male adult, Abx Morphine 4

description:
Library name: AbxD4
Sample names in column (minus "ReadsPerGene.out")

value: Abx morphine


title: SRCAP shRNA4 [RNA-seq]

description:
SRCAP_sh4
library_5
SRCAP_knockdown.csv


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 455, 32569

description: Library name: G460_O07_ABL3_32569_D455

value: Whole blood

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol


title: SRCAP shRNA1 [RNA-seq]

description:
SRCAP_sh1
library_3
SRCAP_knockdown.csv


title: YDBS_164

description: Library name: Sample 73


title: Male adult, Abx Saline 3

description:
Library name: AbxC3
Sample names in column (minus "ReadsPerGene.out")


title: YDBS_146

description: Library name: Sample 72


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 455, 32543

description: Library name: G459_O07_ABL3_32543_D455

value: day 455

value: female


title: Male adult, Abx Saline 1

description:
Library name: AbxC1
Sample names in column (minus "ReadsPerGene.out")


title: Control 2 [RNA-seq]

description:
control_2
library_2
SRCAP_knockdown.csv

value: foreskin epidermis

value: control for SRCAP knockdown


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 455, 32240

description: Library name: G457_O07_ABL3_32240_D455


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 455, 32290

description: Library name: G458_O07_ABL3_32290_D455


title: YDBS_141

description: Library name: Sample 71


title: YDBS_139

description: Library name: Sample 70


title: Male adolescent, Abx Morphine 5

description:
Library name: AbxB5
Sample names in column (minus "ReadsPerGene.out")

value: adolescent


title: Male adult, Abx Morphine 1

description:
Library name: AbxD1
Sample names in column (minus "ReadsPerGene.out")


title: Control 1 [RNA-seq]

description:
control_1
library_1
SRCAP_knockdown.csv

value: primary keratinocyte


title: Af109

city: beijing

first: Guangjian

last: Jiang

address: Beijing University of Traditional Chinese Medicine, No. 11 North Third Ring East Road, Beijing City

institute: Beijing University of Chinese Medicine, Beijing

data_processing:
Agilent 2100 Bioanalyzer was used to verify library concentration and fragment size 400-600 bp, and then qPCR was used to quantify the library.
Assembly: We denatured the mixed sequencing library of different samples with 0.1M NaOH in order to generate single-stranded DNA, which was diluted in situ and amplified using TruSeq SR Cluster Kit v3-cBot-Hs. Sequencing was performed using Illumina HiSeq4000 on the resulting fragments.
Supplementary files format and content: FPKM or CPM columns are expression matrices of genes.
Supplementary files format and content: DE Statistic includes FC and P values.

source_name: blood

extract_protocol:
The total RNA was extracted from venous blood collected from people with T2DM using Trizol (Invitrogen, USA).  To further control quality, agarose gel electrophoresis was used to test samples' integrity and NanoDrop-1000 was used to quantify them.
To construct each library, 1-2 g of total RNA were selected. Total RNA was first subjected to mRNA enrichment with NEB Next@ Poly A (or rRNA removal using RiboZero Magnetic Gold Kit). In this study, stranded RNA-seq libraries were prepared with KAPA Stranded RNA-Seq Library Prep kit. The KAPA kit uses a dUTP-based method for the construction of chain-specific libraries, which included the following steps: 1) Fragmentation of mRNA enrichment products, 2) reverse transcription of the first strand of cRNA, 3) dUTP synthesis of double-stranded cDNA, 4) Rt-PCR amplification was used to repair double-stranded cDNA ends to create RNA sequencing libraries.

value: blood

value: after Baduanjin exercise intervention


title: YDBS_138

description: Library name: Sample 69


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 455, 33514

description: Library name: G462_O07_ABL3_33514_D455


title: Male adolescent, Abx Morphine 4

description:
Library name: AbxB4
Sample names in column (minus "ReadsPerGene.out")

value: Brain

value: All

value: wild type


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 455, 31893

description: Library name: G456_O07_ABL3_31893_D455

value: Protected


title: Af215


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 455, 31654

description: Library name: G455_O07_ABL3_31654_D455

value: Nonprotected


title: YDBS_121

description: Library name: Sample 68

value: whole blood


title: Af204


title: Male adolescent, Abx Morphine 3

description:
Library name: AbxB3
Sample names in column (minus "ReadsPerGene.out")

value: Male

value: Abx morphine


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 455, 31644

description: Library name: G454_O07_ABL3_31644_D455

value: Whole blood


title: Af202


title: Male adolescent, Abx Morphine 2

description:
Library name: AbxB2
Sample names in column (minus "ReadsPerGene.out")


title: Male adult, Abx Saline 2

description:
Library name: AbxC2
Sample names in column (minus "ReadsPerGene.out")

value: adult

value: Abx saline


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 455, 27769

description: Library name: G453_O07_ABL3_27769_D455

value: day 455

value: female


title: YDBS_11

description: Library name: Sample 67


title: Male adolescent, Abx Morphine 1

description:
Library name: AbxB1
Sample names in column (minus "ReadsPerGene.out")

value: adolescent


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 455, 26712

description: Library name: G452_O07_ABL3_26712_D455


title: QDBS_9

description: Library name: Sample 66


title: Af302


title: Be109

value: before Baduanjin exercise intervention


title: QDBS_91

description: Library name: Sample 64


title: Male adolescent, Abx Saline 5

description:
Library name: AbxA5
Sample names in column (minus "ReadsPerGene.out")


title: Male adolescent, Abx Saline 3

description:
Library name: AbxA3
Sample names in column (minus "ReadsPerGene.out")


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 455, 30438

description: Library name: G450_O07_ABL3_30438_D455

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol


title: QDBS_8

description: Library name: Sample 63


title: Male adolescent, Abx Saline 2

description:
Library name: AbxA2
Sample names in column (minus "ReadsPerGene.out")


title: Be215

value: blood


title: Be204


title: QDBS_88

description: Library name: Sample 62


title: Male adolescent, Abx Saline 1

description:
Library name: AbxA1
Sample names in column (minus "ReadsPerGene.out")

value: Brain


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 455, 30386

description: Library name: G449_O07_ABL3_30386_D455


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 455, 30310

description: Library name: G448_O07_ABL3_30310_D455


title: QDBS_7

description: Library name: Sample 61


title: Be202


title: Be302


title: Male adult, H2O Morphine 5

description:
Library name: H2OD5
Sample names in column (minus "ReadsPerGene.out")

value: All

value: H2O morphine


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 455, 30306

description: Library name: G447_O07_ABL3_30306_D455

value: Protected


title: QDBS_40

description: Library name: Sample 60


title: Male adult, H2O Morphine 3

description:
Library name: H2OD3
Sample names in column (minus "ReadsPerGene.out")

value: wild type


title: QDBS_337

description: Library name: Sample 59

value: whole blood


title: Male adult, H2O Morphine 4

description:
Library name: H2OD4
Sample names in column (minus "ReadsPerGene.out")

value: Male


title: QDBS_95

description: Library name: Sample 65


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 455, 30277

description: Library name: G446_O07_ABL3_30277_D455

value: Nonprotected


title: HEVs_rIGLL5_3

city: Guangzhou

first: Mingjie

last: An

address: Yanjiang Road

institute: Sun-Yat Sen university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome (version:hg38) using HISAT2 (version:2.0.4).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: High endothelial venules cells

extract_protocol:
The indicated HEVs were harvested and subjected into extracting the total RNA by TRIZOL (Invitrogen, Carlsbad, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: High endothelial venules cells


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 455, 31374

description: Library name: G451_O07_ABL3_31374_D455

value: Whole blood


title: HEVs_rIGLL5_2


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 455, 28299

description: Library name: G445_O07_ABL3_28299_D455


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 133, 35896

description: Library name: G444_O07_ABL3_35896_D133

value: RhCMV 68-1 Gag/RTN/Pol

value: day 133


title: HEVs_rIGLL5_1


title: QDBS_336

description: Library name: Sample 58


title: QDBS_232

description: Library name: Sample 57


title: Male adult, H2O Morphine 2

description:
Library name: H2OD2
Sample names in column (minus "ReadsPerGene.out")

value: adult


title: Male adult, H2O Morphine 1

description:
Library name: H2OD1
Sample names in column (minus "ReadsPerGene.out")


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 133, 35895

description: Library name: G443_O07_ABL3_35895_D133

value: female


title: HEVs_Mock_3


title: Male adult, H2O Saline 5

description:
Library name: H2OC5
Sample names in column (minus "ReadsPerGene.out")

value: H2O saline


title: QDBS_228

description: Library name: Sample 56


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 133, 35887

description: Library name: G442_O07_ABL3_35887_D133

value: Uninfected


title: HEVs_Mock_2


title: Male adult, H2O Saline 3

description:
Library name: H2OC3
Sample names in column (minus "ReadsPerGene.out")


title: HEVs_Mock_1


title: QDBS_21

description: Library name: Sample 54


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 133, 32607

description: Library name: G441_O07_ABL3_32607_D133


title: Male adult, H2O Saline 1

description:
Library name: H2OC1
Sample names in column (minus "ReadsPerGene.out")


title: QDBS_218

description: Library name: Sample 53


title: QDBS_212

description: Library name: Sample 52


title: 08 MAC infaction 7day

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

country: Japan

institute: Graduate School of Medical Sciences, Kumamoto University

data_processing:
illumina Local Run Manager v2.4.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim galore! v0.6.6
Trimmed sequence reads were mapped to UCSC hg19 using STAR v2.7.3a
Read count extraction and normalization were performed using RSEM v1.3.3
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: blood

value: macrophage

tag: time point

value: Cocultured with Micobacterium Avium


title: Male adolescent, H2O Morphine 4

description:
Library name: H2OB4
Sample names in column (minus "ReadsPerGene.out")

value: Brain

value: All

value: adolescent

value: H2O morphine


title: QDBS_20

description: Library name: Sample 51

value: whole blood


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 133, 31450

description: Library name: G431_O07_ABL3_31450_D133

value: Protected


title: 06 Control3

value: Control


title: Male adolescent, H2O Morphine 3

description:
Library name: H2OB3
Sample names in column (minus "ReadsPerGene.out")

value: wild type

value: Male


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 133, 31670

description: Library name: G433_O07_ABL3_31670_D133

value: Whole blood

value: RhCMV 68-1 Gag/RTN/Pol

value: day 133


title: D13_2

city: Chongqing

first: Huang

last: Wu

state: Chongqing

address: 10 Changjiang Access Road

department: Department of Blood Transfusion

institute: Daping Hospital, Army Medical University

data_processing:
Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned.
CircRNAs were detected and identified by using find_circ and CIRI2 programs with default parameters.
The raw counts were first normalized using TPM.
Differential expression analysis was performed using the DEGseq (2010) R package.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: umbilical cord blood CD34+ cells

growth_protocol: CD34+ cells cultured in StemSpan™ SFEM II Medium with antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNAs were extracted using Trizol Reagent. Ribosomal RNA was removed by Epicentre Ribozero™ rRNA Removal Kit or linear RNA was digested by RNaseR(Epicentre).
RNA-Seq libraries preparation with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®  according to the manufacturer's instructions.

treatment_protocol: megakaryocyte differentiation was induced by treatment  25 ng/ml stem cell factor (SCF) and 20 ng/ml thrombopoietin (TPO). Media was changed on days 3, 6 and 9; days 6 and 9 had no SCF and TPO was increased to 50 ng/mL.

tag: cell line

value: umbilical cord blood CD34+ cells

value: hematopoietic stem cell

value: WT

value: megakaryocyte differentiation

value: Day 13

tag: molecule subtype

value: RiboMinus RNA


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 133, 31432

description: Library name: G430_O07_ABL3_31432_D133

value: female

value: Nonprotected


title: QDBS_203

description: Library name: Sample 50


title: 07 MAC infaction 3day

value: blood

value: macrophage

value: Cocultured with Micobacterium Avium


title: Male adolescent, H2O Morphine 2

description:
Library name: H2OB2
Sample names in column (minus "ReadsPerGene.out")

value: Brain

value: All

value: adolescent

value: H2O morphine


title: QDBS_200

description: Library name: Sample 49

value: whole blood


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 133, 30653

description: Library name: G429_O07_ABL3_30653_D133

value: Whole blood

value: RhCMV 68-1 Gag/RTN/Pol

value: day 133

value: Protected


title: Male adolescent, H2O Morphine 1

description:
Library name: H2OB1
Sample names in column (minus "ReadsPerGene.out")

value: wild type

value: Male


title: D13_1

value: umbilical cord blood CD34+ cells

value: hematopoietic stem cell

value: WT

value: megakaryocyte differentiation

value: Day 13

value: RiboMinus RNA


title: D9_2

value: Day 9


title: QDBS_1

description: Library name: Sample 48


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 129, 35896

description: Library name: G422_O07_ABL3_35896_D129

value: day 129

value: female


title: QDBS_226

description: Library name: Sample 55


title: Male adolescent, H2O Saline 5

description:
Library name: H2OA5
Sample names in column (minus "ReadsPerGene.out")

value: Brain

value: All

value: adolescent

value: H2O saline


title: D9_1


title: QDBS_197

description: Library name: Sample 47

value: whole blood


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 133, 31687

description: Library name: G440_O07_ABL3_31687_D133

value: Whole blood

value: RhCMV 68-1 Gag/RTN/Pol

value: day 133

value: Protected


title: Male adolescent, H2O Morphine 5

description:
Library name: H2OB5
Sample names in column (minus "ReadsPerGene.out")

value: wild type

value: Male

value: H2O morphine


title: Male adolescent, H2O Saline 4

description:
Library name: H2OA4
Sample names in column (minus "ReadsPerGene.out")


title: D6_2

value: umbilical cord blood CD34+ cells

value: hematopoietic stem cell

value: WT

value: megakaryocyte differentiation

value: Day 6


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 129, 35887

description: Library name: G420_O07_ABL3_35887_D129

value: day 129

value: female

value: Uninfected


title: QDBS_187

description: Library name: Sample 46


title: Male adolescent, H2O Saline 3

description:
Library name: H2OA3
Sample names in column (minus "ReadsPerGene.out")

value: Brain

value: All

value: adolescent

value: H2O saline


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 129, 32607

description: Library name: G419_O07_ABL3_32607_D129

value: Whole blood

value: RhCMV 68-1 Gag/RTN/Pol


title: QDBS_183

description: Library name: Sample 45

value: whole blood


title: Male adolescent, H2O Saline 2

description:
Library name: H2OA2
Sample names in column (minus "ReadsPerGene.out")

value: wild type

value: Male


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 129, 31687

description: Library name: G418_O07_ABL3_31687_D129

value: Protected


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 129, 31670

description: Library name: G411_O07_ABL3_31670_D129


title: D6_1

value: umbilical cord blood CD34+ cells

value: hematopoietic stem cell

value: RiboMinus RNA


title: QDBS_181

description: Library name: Sample 43


title: shcircFUT8_2

data_processing:
Basecalls performed using CASAVA(version 1.8).
RNA-seq reads were  processed using FastP (version 0.20.0) and mapped to hg38 using HISAT2 (version 2.0.5).
FPKM (fragments per kilobase of transcript per million mapped reads)  were used for estimating gene expression levels.
Differential expression analysis was performed using the DESeq2 R package (1.16.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: hematopoietic stem cell

extract_protocol:
Total RNAs were extracted using Trizol Reagent. PolyA RNA was isolated with oligo dT magnetic beads and fragmented with divalent cations.
RNA-Seq libraries preparation with NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB #E7770) according to the manufacturer's instructions.

value: megakaryocyte differentiation

value: Day 13


title: CorticalSurfaceAssociated_scRNAseq_1

city: Vancouver

first: Freda

last: Miller

state: BC

address: 2185 East Mall

country: Canada

institute: University of British Columbia

description:
Library name: CorticalSurfaceAssociated_1
10X Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ reads were processed and aligned to the wild-type mouse genome (mm10) using Cell Ranger v3 software (cellranger count function) with settings as recommended by the manufacturer (10X Genomics).
The data packages contain the filtered digital gene expression for each sample obtained from the Cell Ranger Single Cell Pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
For single cell isolation the entire dorsal and lateral V-SVZ were microdissected out. Tissues were finely chopped and incubated in Hibernate A minus calcium medium (Brain Bits) supplemented with 2% B27, 20 units/mL papain, and 0.005% DNaseI for 30 minutes at 37°C in the dark. This enzymatic incubation solution also contained DRAQ5, a membrane permeable dye to stain for live cells (at 5 μM or 3000- fold dilution, Thermo Fisher). After enzymatic treatment, the tissue suspension was centrifuged at 300 x g for 5 minutes and resuspended in HBSS/0.025% BSA. A cell suspension was produced via manual trituration using blunt needles of sequentially decreasing diameter. The resultant cell suspension was filtered through a 40 μm strainer and labeled with 1 μg/mL propidium iodide (PI, Abcam). Viable cells were collected using flow cytometry sorting for propidium iodide-negative and DRAQ5-positive cells.
Libraries were prepared according to the manufacturer's instructions (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit.


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 129, 35895

description: Library name: G421_O07_ABL3_35895_D129

value: day 129

value: female


title: QDBS_182

description: Library name: Sample 44


title: QDBS_179

description: Library name: Sample 42


title: A10_cKO_S2_rep2

city: Miami

first: Roberta

last: Brambilla

state: FL

department: Neurological Surgery

institute: University of Miami Miller School of Medicine

description: Library name: A10_cKO_S2

data_processing:
Raw sequencing reads (FASTQ files) were quality-checked (e.g., using FastQC), trimmed for adapters/low-quality bases if necessary, and aligned to the Mus musculus reference genome. Gene counts or transcript abundance estimates were obtained using STAR/featureCounts. Differential expression analysis was performed in R using DESeq2 with a significance threshold of adjusted p-value (padj) ≤ 0.05. Normalized gene expression levels were calculated as fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: mm10 (GRCm38)
Supplementary files format and content: The processed data are provided as CSV files containing normalized FPKM values for each gene (rows) across each sample (columns)

source_name: Hippocampus

extract_protocol:
Hippocampal astrocytes were FACS-sorted from adult male GfapcreERT2:Tnfrsf1b^fl/fl and Tnfrsf1b^fl/fl mice. Cells were sorted based on ACSA-2 labeling using a BD FACSAria instrument. RNA was extracted from the sorted astrocytes using the SMART-Seq V4 Ultra Low Input RNA Kit (Clontech) following the manufacturer’s protocol.
cDNA was synthesized from the isolated RNA. Libraries were prepared (SMART-Seq V4 kit) and sequenced on an Illumina HiSeq 2500 platform to generate 125 bp paired-end reads.

value: Hippocampus

value: Astrocytes


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 129, 31432

description: Library name: G408_O07_ABL3_31432_D129

value: Nonprotected


title: shcircFUT8_1


title: QDBS_178

description: Library name: Sample 41


title: MK_D13_R2

value: WT

value: RiboMinus/RNaseR-treated RNA


title: A10_cKO_S1_rep1

description: Library name: A10_cKO_S1


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 129, 31450

description: Library name: G409_O07_ABL3_31450_D129

value: Whole blood

value: RhCMV 68-1 Gag/RTN/Pol


title: QDBS_176

description: Library name: Sample 40

value: whole blood


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 129, 30653

description: Library name: G407_O07_ABL3_30653_D129


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 126, 35895

description: Library name: G400_O07_ABL3_35896_D126

value: day 126


title: A9_cKO_S2_rep2

description: Library name: A9_cKO_S2


title: NC2

value: Negative control


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 126, 35896

description: Library name: G399_O07_ABL3_35895_D126

value: Protected


title: A9_cKO_S1_rep1

description: Library name: A9_cKO_S1


title: QDBS_173

description: Library name: Sample 39


title: Male adolescent, H2O Saline 1

description:
Library name: H2OA1
Sample names in column (minus "ReadsPerGene.out")

value: Brain

value: All

value: wild type

value: Male

value: adolescent

value: H2O saline


title: MK_D13_R1

value: umbilical cord blood CD34+ cells

value: hematopoietic stem cell

value: megakaryocyte differentiation

value: Day 13


title: QDBS_16

description: Library name: Sample 38


title: NC1


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 126, 35887

description: Library name: G398_O07_ABL3_35887_D126

value: female

value: Uninfected


title: A8_Ctrl_S2_rep2

description: Library name: A8_Ctrl_S2

value: Hippocampus

value: Astrocytes


title: QDBS_165

description: Library name: Sample 37

value: whole blood


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 126, 32607

description: Library name: G397_O07_ABL3_32607_D126

value: Whole blood

value: RhCMV 68-1 Gag/RTN/Pol

value: day 126


title: A8_Ctrl_S1_rep1

description: Library name: A8_Ctrl_S1


title: QDBS_163

description: Library name: Sample 36


title: QDBS_161

description: Library name: Sample 35


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 126, 31687

description: Library name: G396_O07_ABL3_31687_D126

value: Protected


title: A4_cKO_S1_rep1

description: Library name: A4_cKO_S1


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 126, 31670

description: Library name: G389_O07_ABL3_31670_D126


title: A2_Ctrl_S2_rep2

description: Library name: A2_Ctrl_S2


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 126, 31450

description: Library name: G387_O07_ABL3_31450_D126


title: A2_Ctrl_S1_rep1

description: Library name: A2_Ctrl_S1


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 126, 31432

description: Library name: G386_O07_ABL3_31432_D126

value: Nonprotected


title: Y1003FHGF_17571_1_1

type: RNA

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: T47D cells expressing MET Y1003F, stimulated by HGF.

hyb_protocol: Agilent-072363 Whole Human Genome Microarray 8x60 v3.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).
Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

label_protocol: Manufacturer's instructions.

growth_protocol: MEM, 10% FBS and 1% Zell-Shield, 37°C, 5% CO2.

extract_protocol: Total RNA extracted using manufacturer's instructions.

treatment_protocol: T47D cells were starved (0% FBS) during 2 hours and next stimulated 24 hours by HGF (20 ng/ml).

tag: genotype/variation

value: Expressing MET Y1003F

value: Stimulated by HGF


title: Y1003FHGF_28341_2_3


title: QDBS_154

description: Library name: Sample 34


title: QDBS_151

description: Library name: Sample 32


title: A1_Ctrl_S2_rep2

description: Library name: A1_Ctrl_S2


title: Y1003FHGF_17589_2_3


title: QDBS_148

description: Library name: Sample 31


title: Y1003F_17570_1_4

description: T47D cells expressing MET Y1003F, unstimulated.

value: Unstimulated


title: Y1003F_17571_2_2


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 126, 30653

description: Library name: G385_O07_ABL3_30653_D126


title: A4_cKO_S2_rep2

description: Library name: A4_cKO_S2


title: G3_3-b2_CD04_A

first: Jubao

last: Duan

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

description: Library name: CD04-G3-3-b2

data_processing:
Raw fastq files (pair-end) were aligned to human GRCh38.p13 genome using STAR 2.7.11 with GENCODE 35 annotations.
Counts were collected from the output of each STAR run and merged into one count matrix
Assembly: hunan GRCh38.p14 (hg38)
Supplementary files format and content: FASTQ
Supplementary files format and content: tab-delimited text included raw counts per sample

source_name: iPS-derived microglia

growth_protocol: iMG was generated from hiPSC lines as we described using the Brownjohn’s method. hiPSC were cultured in mTeSR plus media (100-0276, StemCell) with 2 ml daily media changes. At least 2 days after passaging, when hiPSC reached confluency ~80% they were dissociated with Accutase (07920, StemCell) and plated at 10,000 cells per well in 96-well round bottom ultra-low attachment plates (7007, Corning) in 100 µL EB media, and plates were centrifuged at 300 g for 3 min.

extract_protocol:
Total RNA was extracted using Qiagen RNEasy mini spin columns and the concentrations verified by NanoDrop
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Sequencing was performed on NovaX with 2x150 bp paired read

treatment_protocol: (MG)EB media was prepared by adding to the complete mTeSR media 50 ng/ml BMP-4 (120-05, PeproTech), 20 ng/ml SCF (300-07, PeproTech), 50 ng/ml VEGF-121 (100-20A, PeproTech), and ROCK inhibitor (1254/1, R&D Systems). Cells were cultured for 4 days, with half media change after 2 days. On day 4, 16 EBs were plated on a 6-well plate and cultured in 3 ml hematopoietic media with 2 ml media exchanges every 5 days. Hematopoietic media was prepared by adding to the X-VIVO 15 (BE08-879H, Lonza), 1% GlutaMax (35050061, Thermofisher), 1% Pen/strep (10378016, Thermofisher), 55 µM β-mercaptoethanol (21985023, Thermofisher), 100 ng/ml M-CSF (300-25, PeproTech), and 25 ng/ml IL-3 (200-03, PeproTech). After 5 days culturing EBs in hematopoietic media, PMPs started to appear in the suspension and were produced continuously in suspension for 34 days. After 10 days of culturing EBs, PMPs could be harvested from suspension and plated in RPMI 1640 media (21870076, Thermofisher) at 180,000 cells/cm2 in 6- or 12-well plates. After 1 hr, PMPs adhered to surface and media was changed to complete iMG media. Full media changes were done every 2 days. Complete iMG media was prepared with RPMI 1640 by adding 10% FBS (S11150H, R&D Systems), 1% Pen/strep, 1% GlutaMax, 100 ng/ml IL-24 (200-34, PeptroTech), and 10 ng/ml GM-CSF (300-03, PeproTech). Final differentiation of PMPs into iMG occurred over 25 days and cells could be kept for at least 1 month in this format; (iAst) NPCs were differentiated to astrocytes by seeding dissociated single cells at 15,000 cells/cm2 density on matrigel-coated plates in Astrocyte medium (1801, ScienCell: astrocyte medium, 2% FBS (0010), astrocyte growth supplement (1852) and 10U/ml Pen/Strep solution (0503)). Initial NPC seeding density and single cell dissociation are critical, particularly during the first 30 days of differentiation, in order to efficiently generate a homogenous population of astrocytes. At day -1, after 5-10 min incubation with accutase at 37˚C, NPCs were pipetted with a p1000 pipette 3-5 times, in order to yield a single cell suspension but limit cell death. Additional NPC medium was added and cells were transferred to a 15ml tube, spun at 250g for 5min, and plated on a matrigel-coated plate in Neural Expansion Medium medium. At day 0, NPC medium was switched to Astrocyte medium. From day 2, cells were fed every 48 hr for 20-30 days. When the cells reached 90- 95% confluency (approximately every 6-7 days), they were split to the initial seeding density (15,000 cells/cm2) as single cells in Astrocyte medium, and cultured on matrigel, following 5-10 min incubation with accutase, pipetting, and washing with DMEM (35050061, Thermofisher). After 30 days of differentiation, astrocytes could be split 1:3 every week with accutase and expanded up to 120 days (15-17 passages) in Astrocyte medium. Final differentiation of iAstoccurred over 30 days.

value: iPS-derived microglia

value: microglia


title: G3_1-b2_CD04_A

description: Library name: CD04-G3-1-b2


title: QDBS_152

description: Library name: Sample 33


title: V1001AHGF_17570_2_4

description: T47D cells expressing MET V1001A, stimulated by HGF.

value: Expressing MET V1001A


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 133, 32931

description: Library name: G304_O07_ABL3_32931_D133

value: day 133


title: QDBS_133

description: Library name: Sample 29


title: Y1003F_28341_1_1


title: QDBS_130

description: Library name: Sample 28


title: V1001AHGF_17589_1_2


title: V1001A_28341_2_2

description: T47D cells expressing MET V1001A, unstimulated.


title: A5_3-b2_CD04_G

description: Library name: CD04-A5-3-b2


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 133, 32886

description: Library name: G303_O07_ABL3_32886_D133

value: female


title: A1_Ctrl_S1_rep1

description: Library name: A1_Ctrl_S1


title: QDBS_127

description: Library name: Sample 26


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 133, 33705

description: Library name: G306_O07_ABL3_33705_D133


title: A5_1-b2_CD04_G

description: Library name: CD04-A5-1-b2


title: A3_2_b2_CD09_G

description: Library name: CD09-A3-2-b2


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 133, 32751

description: Library name: G302_O07_ABL3_32751_D133


title: QDBS_135

description: Library name: Sample 30


title: V1001AHGF_17571_1_4


title: QDBS_12

description: Library name: Sample 27


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 133, 32624

description: Library name: G301_O07_ABL3_32624_D133


title: A3_3_b2_CD09_G

description: Library name: CD09-A3-3-b2


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 133, 32319

description: Library name: G300_O07_ABL3_32319_D133


title: V1001A_17570_1_2


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 133, 33495

description: Library name: G305_O07_ABL3_33495_D133


title: V1001A_17589_2_4


title: QDBS_104

description: Library name: Sample 23


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 133, 35908

description: Library name: G299_O07_ABL3_35908_D133

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol


title: QDBS_114

description: Library name: Sample 24


title: A1_3_b2_CD09_A

description: Library name: CD09-A1-3-b2


title: A3_1_b2_CD09_G

description: Library name: CD09-A3-1-b2


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 133, 35907

description: Library name: G298_O07_ABL3_35907_D133


title: S985A_17589_1_3

description: T47D cells expressing MET S985A, unstimulated.

value: Expressing MET S985A


title: S985AHGF_17571_1_2

description: T47D cells expressing MET S985A, stimulated by HGF.


title: S985AHGF_17589_2_1


title: S985A_28341_2_4


title: A1_2_b2_CD09_A

description: Library name: CD09-A1-2-b2


title: A1_1_b2_CD09_A

description: Library name: CD09-A1-1-b2


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 133, 33514

description: Library name: G296_O07_ABL3_33514_D133


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 133, 33530

description: Library name: G297_O07_ABL3_33530_D133


title: HP_84

description: Library name: Sample 22


title: HP_80

description: Library name: Sample 20


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 133, 32574

description: Library name: G295_O07_ABL3_32574_D133


title: HP_79

description: Library name: Sample 19


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 133, 32569

description: Library name: G294_O07_ABL3_32569_D133


title: HP_77

description: Library name: Sample 17


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 133, 32543

description: Library name: G293_O07_ABL3_32543_D133


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B2_32

city: Boston

first: Mehmed

last: Dinc

state: MA

address: One Boston Medical Center Pl

institute: Boston Medical Center

description: Library name: dcSSc_TM_EF_B2_32

data_processing:
Raw sequencing reads were assessed for quality using FastQC v0.11.9
Adapter sequences and low-quality bases were trimmed using Trimmomatic v0.39
Trimmed reads were aligned to the human reference genome (hg38/GRCh38) using STAR v2.7.9a
Gene-level read counts were quantified using featureCounts from the Subread package v2.0.1
Differential expression analysis was performed using DESeq2 v1.32.0 with age as a covariate
Assembly: hg38/GRCh38
Supplementary files format and content: Tab-delimited text file containing raw gene counts for all samples. Rows represent genes (Ensembl gene IDs) and columns represent samples. First column contains gene IDs and gene symbols.

source_name: peripheral blood

extract_protocol:
Total RNA was extracted from CD14+ monocytes using the RNeasy Mini Kit (Qiagen) according to manufacturer's instructions. RNA quality and quantity were assessed using a NanoDrop spectrophotometer and Agilent Bioanalyzer. Only samples with RIN values ‚â• 7.0 were used for library preparation.
RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacturer's instructions.

value: peripheral blood


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B2_31

description: Library name: lcSSc_TM_EF_B2_31


title: HP_78

description: Library name: Sample 18

value: whole blood


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 133, 32290

description: Library name: G292_O07_ABL3_32290_D133

value: Whole blood


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B2_30

description: Library name: lcSSc_TM_EF_B2_30


title: D14HGF_17570_1_1

description: T47D cells expressing MET Exon14, stimulated by HGF.

value: Expressing MET Exon14


title: QDBS_115

description: Library name: Sample 25


title: CD14+ monocytes, healthy control, TM_EF_B2_29

description: Library name: HC_TM_EF_B2_29


title: S985A_17571_2_4


title: HP_82

description: Library name: Sample 21


title: D14HGF_17571_2_3


title: CD14+ monocytes, healthy control, TM_EF_B2_28

description: Library name: HC_TM_EF_B2_28


title: HP_76

description: Library name: Sample 16


title: D14_17570_2_3

description: T47D cells expressing MET Exon14, unstimulated.


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 133, 31893

description: Library name: G290_O07_ABL3_31893_D133


title: HP_75

description: Library name: Sample 15


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 133, 32240

description: Library name: G291_O07_ABL3_32240_D133


title: HP_74

description: Library name: Sample 14


title: D14_17589_1_1


title: CD14+ monocytes, healthy control, TM_EF_B2_27

description: Library name: HC_TM_EF_B2_27


title: CD14+ monocytes, healthy control, TM_EF_B2_26

description: Library name: HC_TM_EF_B2_26


title: HP_73

description: Library name: Sample 13


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B2_24

description: Library name: lcSSc_TM_EF_B2_24


title: d16_28341_1_3


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 133, 27769

description: Library name: G287_O07_ABL3_27769_D133


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B2_23

description: Library name: lcSSc_TM_EF_B2_23


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 133, 31654

description: Library name: G289_O07_ABL3_31654_D133


title: HP_59

description: Library name: Sample 12


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 133, 31644

description: Library name: G288_O07_ABL3_31644_D133


title: wtHGF_17570_1_3

description: T47D cells expressing MET WT, stimulated by HGF.

value: Expressing MET WT


title: HP_54

description: Library name: Sample 11


title: wtHGF_28341_1_2


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B2_22

description: Library name: dcSSc_TM_EF_B2_22


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B2_25

description: Library name: lcSSc_TM_EF_B2_25


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 133, 31374

description: Library name: G285_O07_ABL3_31374_D133

value: Protected


title: wtHGF_17589_1_4


title: CUT&Tag H3K18LA IP sample from rat pancreas with acute pancreatitis

city: 安徽省合肥市新站区

first: 诗亚

last: 马

address: 安徽省合肥市瑶海区银领时代

institute: Anhui Medical University

description: Library name: AP_H3K18LA_IP

library_source: genomic

data_processing:
Quality control of raw sequencing reads using FastQC
Adapter trimming and removal of low-quality reads using Trim Galore or Cutadapt
Alignment of cleaned reads to the Rattus norvegicus reference genome rn6 using Bowtie2 with parameters optimized for specificity
Removal of PCR duplicates using Picard MarkDuplicates
Generation of coverage tracks (bigWig files) and peak calling using MACS2 to identify H3K18LA-enriched promoter regions
Assembly: Rattus norvegicus rn6
Supplementary files format and content: Generation of coverage tracks (bigWig files) and peak calling using MACS2 to identify H3K18LA-enriched promoter regions
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Rattus norvegicus

source_name: IP sample using H3K18LA antibody for CUT&Tag in AP rat pancreas tissue

growth_protocol: Male Sprague-Dawley (SD) rats, weighing approximately 200-250 g, were maintained under standard laboratory conditions with controlled temperature and humidity, a 12-hour light/dark cycle, and ad libitum access to food and water.

extract_protocol:
Pancreatic tissues were rapidly harvested and flash-frozen. Samples were then pulverized, and nuclei were extracted using standard CUT&Tag nuclear extraction buffers to ensure nuclear integrity for subsequent assays.
CUT&Tag libraries were prepared using a transposase-mediated method. A transposase mix containing transposase and two equimolar adapters (Adapter 1 and Adapter 2) was added to the sample and incubated at 37°C for 30 minutes. This process simultaneously fragments DNA and attaches sequencing adapters. Libraries were then PCR-amplified, size-selected, and purified to generate the final sequencing-ready libraries.

treatment_protocol: For the pancreatitis group, rats were intraperitoneally injected with L-Arginine at a dose of 2.5 g/kg twice, with a 1-hour interval between injections, to induce pancreatitis. The total modeling time was 48 hours, after which pancreatic tissues were collected for downstream experiments.

value: Pancreas

value: WT

value: L-arginine 2×2.5g/kg, 1h interval, 48h

tag: batch


title: wt_17571_1_3

description: T47D cells expressing MET WT, unstimulated.

value: Unstimulated


title: wt_17589_2_2


title: CUT&Tag input sample from rat pancreas with acute pancreatitis

address: 安徽省合肥市瑶海区银领时代

description: Library name: AP_Input_Control

source_name: Input control sample for H3K18LA CUT&Tag from AP rat pancreas


title: HP_50

description: Library name: Sample 9


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 133, 30438

description: Library name: G284_O07_ABL3_30438_D133

value: Nonprotected


title: HP_37

description: Library name: Sample 8


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B2_20

description: Library name: lcSSc_TM_EF_B2_20


title: wt_17570_2_1


title: spinal cord,10-month-old,  LPC, C57/Bl6, 21 DPI

city: Edmonton

first: Jason

middle: R.

last: Plemel

state: Alberta

address: 5-64 Heritage Medical Research Centre

department: Department of Medicine

institute: University of Alberta

data_processing:
The samples were paired-end, single index sequenced at an average read depth of 50,000 reads per cell. The resulting BCL files were demultiplexed into FASTQ files and aligned to a custom Mus Musculus 10 (MM10) reference genome adjusted to include Clec7a, a polymorphic pseudogene. The Clec7a annotation was added to the 10x Genomics pre-built MM10 genome (2020-A) GTF file from the 10x Genomics parent GTF file (gencode.vM23.primary_assembly.annotation.gtf.gz). The custom genome was created by combining the MM10 genome (2020-A) FASTA file with the Clec7a modified GTF file using the cellranger mkref function in the 10x cell ranger pipeline (v3.0.0). Finally, the samples were aligned to a custom genome using the cellranger count function to generate barcoded and sparse matrices, both raw and filtered, along with BAM files for downstream analyses.
Assembly: MM10 genome (2020-A) modified to include the Clec7a gene.
Supplementary files format and content: Tab separated value files and matrix files.

source_name: Spinal cord

extract_protocol:
LPC-lesioned and naïve mice were injected with 0.4 mL 1% Neutral Red31 (Fisher Scientific, Cat. No. N129-25) in 0.1 M phosphate buffer (PB) two hours prior to euthanasia. Mice were euthanized with 0.1 mL Dorminal (Rafter Products, DIN 02333708) and transcardially perfused with 20 mL ice-cold Hanks’ Balanced Salt Solution (HBSS; Gibco, Cat. No. 14175-079). The spinal cords were dissected, and the lesions were isolated based visual identification through neutral red staining. Comparable segments of whole spinal cords were isolated as control tissue from naïve mice. Tissue from two mice was pooled per sample, finely micro-dissected on ice in ice-cold HBSS and then transferred to a tube with 1.5 mL Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Cat. No. 11960-044) for mechanical dissociation via five oscillations of a loose fitting dounce. The cells were sequentially filtered through 70 µm and 40 µm filters and washed with 7.5 mL DMEM after each filtration step. The cells were pelleted (300 G, 10 min, 4 °C) and resuspended in 6.2 mL HBSS and 1.8 mL Debris Removal Solution (Miltenyi Biotec, Cat. No. 130-109-398). The suspension was mixed by inverting the tube five times and 4 mL of HBSS was carefully overlayed. The suspension was centrifuged (3000 G, 10 min, 4 °C), the top two layers were aspirated and topped up to 15 mL with HBSS. The suspension was mixed by inverting the tube five times and pelleted (1000 G, 10 min, 4 °C).The spinal cords were labelled with Zombie AquaTM Fixable Viability Kit (BioLegend, Cat. No. 423102), DRAQ5TM Fluorescent probe solution (ThermoFisher Scientific, Cat. No. 62254) and FITC anti-mouse F4/80 antibody (Clone BM8; BioLegend, Cat. No. 123107) and sorted on the flow cytometry cell sorter (BD FACSAria III) at the University of Alberta Flow Cytometry Core. The Zombie Aqua-DRAQ5+F4/80+ cells were isolated and cell counts were manually confirmed using a hemocytometer.
The samples were processed on the 10x chromium controller following the 10x Genomics Next GEM Single Cell 3’ GEM, library, and Gel Bead kit v3.1

value: Spinal cord

value: Microglia

value: Lysolecithin (LPC)


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 133, 30386

description: Library name: G283_O07_ABL3_30386_D133

value: day 133

value: female


title: HP_32

description: Library name: Sample 7


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 133, 26712

description: Library name: G286_O07_ABL3_26712_D133


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B2_19

description: Library name: dcSSc_TM_EF_B2_19


title: HP_2

description: Library name: Sample 6


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 133, 30310

description: Library name: G282_O07_ABL3_30310_D133

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol


title: HP_51

description: Library name: Sample 10


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 133, 30306

description: Library name: G281_O07_ABL3_30306_D133


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B2_18

description: Library name: dcSSc_TM_EF_B2_18

value: peripheral blood


title: spinal cord,10-month-old,  LPC, C57/Bl6, 7 DPI


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B2_17

description: Library name: lcSSc_TM_EF_B2_17


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 133, 30277

description: Library name: G280_O07_ABL3_30277_D133


title: spinal cord, 2-month-old, LPC, C57/Bl6, 21 DPI, rep2


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B2_21

description: Library name: dcSSc_TM_EF_B2_21


title: HP_159

description: Library name: Sample 4

value: whole blood


title: CD14+ monocytes, healthy control, TM_EF_B2_16

description: Library name: HC_TM_EF_B2_16


title: spinal cord, 2-month-old, LPC, C57/Bl6, 7 DPI, rep2


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 133, 28299

description: Library name: G279_O07_ABL3_28299_D133

value: Whole blood


title: HP_158

description: Library name: Sample 3


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 129, 33705

description: Library name: G278_O07_ABL3_33705_D129

value: day 129


title: HP_157

description: Library name: Sample 2


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B2_14

description: Library name: dcSSc_TM_EF_B2_14


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B2_15

description: Library name: lcSSc_TM_EF_B2_15


title: spinal cord, 2-month-old, LPC, C57/Bl6, naïve, rep2


title: spinal cord,10-month-old, LPC, C57/Bl6, naïve


title: HP_132

description: Library name: Sample 1


title: spinal cord, 2-month-old, LPC, C57/Bl6, 14 DPI


title: hASC_TGFb_72h_3

first: Matthew

last: Layne

state: Massachusetts

address: 72 East Concord Street

institute: Boston University

description: Library name: T3_72

data_processing:
Raw reads were filtered by removing 1) reads with adapter sequences 2) reads with >10% undeterminable bases and 3) low quality reads containing  > 50% of  bases with a quality score ≤ 5
Filtered clean reads were mapped using HISAT2 software
Assembly: GRCh38/hg38
Supplementary files format and content: xls file includes raw counts for each sample

source_name: Omental white adipose tissue

growth_protocol: hASC were maintained in alpha-MEM with 10% Fetal Bovine Serum (FBS) and antibiotics in 5% CO2 at 37°C

extract_protocol:
Total RNA was collected using the GeneJET RNA purification kit (Thermo)
RNA-seq libraries were prepared by Novogene (Sacramento, CA) and included PolyA enrichment, cDNA synthesis, and Illumina adapter ligation

treatment_protocol: hASC were stimulated with 1 nM TGF-β1 (R&D) for 12 and 72 hours. Cells stimulated for 72 hours were re-stimulated at 48 hours to induce chronic TGF-β1 responses

value: Omental white adipose tissue

value: adipocyte stem cells

value: Primary

value: 72 hours


title: HP_29

description: Library name: Sample 5


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B2_13

description: Library name: dcSSc_TM_EF_B2_13


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 129, 32886

description: Library name: G275_O07_ABL3_32886_D129

data_processing:
Trimgalorev0.6.4 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.4.2
Aligned reads with STARv2.710b
Assembly: Rhesus macaques version10 Ensembl annoation v111
Supplementary files format and content: text file of counts for each sample

extract_protocol:
Isolation of RNA from Whole Blood Using the RNAdvance Blood Kit – for NHP samples
mRNA Library Prep for RNA from Whole Blood using KAPA HyperPrep Reagents

value: Protected


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 129, 32931

description: Library name: G276_O07_ABL3_32931_D129


title: spinal cord, 2-month-old, LPC, C57/Bl6, 21 DPI. rep1


title: spinal cord, 2-month-old, LPC, C57/Bl6, 7 DPI, rep1


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B2_11

description: Library name: lcSSc_TM_EF_B2_11


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 129, 32751

description: Library name: G274_O07_ABL3_32751_D129


title: hASC_TGFb_72h_1

description: Library name: T1_72


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B2_10

description: Library name: dcSSc_TM_EF_B2_10


title: spinal cord, 2-month-old, PBS, C57/Bl6, sham

value: Phosphate buffer saline (PBS)


title: spinal cord, 2-month-old, LPC, C57/Bl6, naïve, rep1


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 129, 32624

description: Library name: G273_O07_ABL3_32624_D129


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 129, 32319

description: Library name: G272_O07_ABL3_32319_D129


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 129, 33495

description: Library name: G277_O07_ABL3_33495_D129


title: spinal cord, 2-month-old, PBS, Cx3Cr1creER, sham


title: hASC_TGFb_12h_2

description: Library name: T2_12

value: 12 hours


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B2_8

description: Library name: lcSSc_TM_EF_B2_8


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 129, 35908

description: Library name: G271_O07_ABL3_35908_D129

value: Nonprotected


title: Infected RAW264.7, 40 uM KL1, rep3, run1

city: Chapel Hill

first: Kuan-Yi

last: Lu

address: 125 Mason Farm Road

institute: UNC Chapel Hill

data_processing:
Standard RNA analysis package by Azenta Life Sciences
Sequence quality check
Trim Reads
Mapping, differential gene expression, alternative splicing, and gene ontology analysis
Assembly: GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Supplementary files format and content: bam files: aligned data
Supplementary files format and content: raw_counts

growth_protocol: RAW 264.7 macrophages were seeded in Costar 24-well tissue culture-treated plates (Corning) (500 µL of 4x105 cells per well) in complete MEM (Minimum Essential Medium (Gibco) supplemented with 10% (vol/vol) heat-inactivated fetal bovine serum and 2 mM L-glutamine) at 37 °C and 5% CO2.

extract_protocol:
Infect RAW cells with JE2-Lux at MOI 20 in 4 mL fresh MEM in 6-well plates for 35 min. Replace with 4 mL MEM containing 100 ug/mL gentamicin and 40 uM KL1 or 0.1% DMSO for 24 h. Wash the cells with 4 mL PBS and harvest the cells by EDTA dissociation. Wash three times in 10 mL PBS to remove excessive EDTA at 4 C. Resuspend in 1 mL PBS, transfer to microcentrifuge tubes and pellet the cells. Remove the supernatans and store at -80 C. Submit samples to Azenta Life Sciences
RNA libraries for RNA-seq were prepared based on the standard protocol by Azenta Life Sciences

treatment_protocol: RAW264.7 cells were infected with S. aureus strain JE2-Lux at an MOI of 20 and treated with and without 40 uM KL1 for 24 h in triplicate and harvested for RNA-seq.

value: Macrophage

value: WT

value: 40 uM KL1


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B2_12

description: Library name: lcSSc_TM_EF_B2_12


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B2_7

description: Library name: lcSSc_TM_EF_B2_7


title: hASC_control_72h_3

description: Library name: C3_72

value: Control


title: hASC_TGFb_12h_1

description: Library name: T1_12


title: Infected RAW264.7, 0.1% DMSO, rep3, run1

value: 0.1% DMSO


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B2_5

description: Library name: lcSSc_TM_EF_B2_5

value: peripheral blood


title: hASC_control_72h_1

description: Library name: C1_72


title: hASC_control_72h_2

description: Library name: C2_72


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 129, 33514

first: Michael

last: Gale

institute: University of Minnesota

description: Library name: G268_O07_ABL3_33514_D129

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

value: female


title: hASC_TGFb_72h_2

description: Library name: T2_72


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 129, 33530

description: Library name: G269_O07_ABL3_33530_D129

value: Whole blood

value: day 129


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B2_6

description: Library name: lcSSc_TM_EF_B2_6


title: Infected RAW264.7, 40 uM KL1, rep2, run1


title: hASC_TGFb_12h_3

description: Library name: T3_12

value: Omental white adipose tissue

value: adipocyte stem cells


title: Infected RAW264.7, 0.1% DMSO, rep2, run1


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B2_9

description: Library name: dcSSc_TM_EF_B2_9


title: hASC_control_12h_3

description: Library name: C3_12

value: Primary


title: CD14+ monocytes, healthy control, TM_EF_B2_3

description: Library name: HC_TM_EF_B2_3


title: Infected RAW264.7, 40 uM KL1, rep1, run1


title: D14HGF_28341_2_1

value: Expressing MET Exon14

value: Stimulated by HGF


title: Infected RAW264.7, 0.1% DMSO, rep1, run1


title: hASC_control_12h_2

description: Library name: C2_12

value: 12 hours


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 129, 32569

description: Library name: G266_O07_ABL3_32569_D129

value: Protected


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B2_2

description: Library name: dcSSc_TM_EF_B2_2


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 129, 35907

description: Library name: G270_O07_ABL3_35907_D129

value: Nonprotected


title: hASC_control_12h_1

description: Library name: C1_12


title: High Fat Diet, Vitamin C, replicate 3

city: Houston

first: Yuhan

last: Yang

address: 2121 W. Holcombe Blvd.

institute: Texas A&M University

data_processing:
Read quality assessed with fastqc v 0.12.1, and reads trimmed with trim-galore v 0.6.10 and discarding reads with less than 30 bp
Trimmed Reads aligned to mm10 reference genome using bowtie2 v 2.2.8 in paired-end mode with all default parameters except with k=5 (up to 5 valid and distinct alignments for each read)
Peaks were called using Genrich v 0.6.1 with ATAC-seq mode, keeping unpaired alignments, removing pcr duplicates
bigWig files generated with bamCoverage from deepTools v 3.5.2 with reads are normalized by RPKM and reads are extended by 110 bp
Assembly: mm10
Supplementary files format and content: broadPeak, containing the called ATAC-seq peaks
Supplementary files format and content: bigWig, generated as described above for each sample

source_name: E15.5 Ventricle

growth_protocol: C57/BL6 WT pure female mice feeding with normal diet/high-fat diet 9 weeks before mating until E15.5

extract_protocol:
Actice Motif ATAC-seq kit is used for E15.5 embryonic ventricle nuclei extraction.
Actice Motif ATAC-seq kit is used for generating the library

treatment_protocol: ViC or PBS(solvent) i.p. injection 1g/kg every other day, 1 week before mating until E15.5

value: E15.5 Ventricle

value: High Fat Diet, Vitamin C

value: C57/BL6 WT


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 129, 32543

description: Library name: G265_O07_ABL3_32543_D129


title: CD14+ monocytes, healthy control, TM_EF_B2_1

description: Library name: HC_TM_EF_B2_1


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 129, 32290

description: Library name: G264_O07_ABL3_32290_D129


title: CD14+ monocytes, healthy control, TM_EF_B2_4

description: Library name: HC_TM_EF_B2_4


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 129, 32574

description: Library name: G267_O07_ABL3_32574_D129


title: High Fat Diet, Vitamin C, replicate 2


title: CD14+ monocytes, healthy control, TM_EF_B1_30

description: Library name: HC_TM_EF_B1_30


title: CD14+ monocytes, healthy control, TM_EF_B1_31

description: Library name: HC_TM_EF_B1_31


title: 10x Multiome with D0, D2, D4 and D7 of iPSC to HPC differentiation in one lane. ATAC

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 450 Serra Mall

department: Genetics

institute: Stanford University

description:
Library name: WTC11_HPC_multiome_ATAC
10x Genomics Multiome
Unique processed file id: 1

library_source: genomic single cell

data_processing:
FASTQs were analyzed with 10x cloud analysis web browser version using cellranger-arc-2.0.2
Assembly: human hg38
Supplementary files format and content: filtered feature bc matrix file (.tar.gz format) that is output directly from cellranger. Contains matrix, barcodes and features files for ATAC and GEX

growth_protocol: We seeded human iPS cells (WTC11) harboring dCas9-KRAB (Metzl-Raz et al., Stem Cell Res., 2022) in 6-well plates coated with 1:100 LDEV-Free Reduced Growth Factor Basement Membrane Matrix (Thermo Fisher Scientific). The culture medium used was StemFlex Medium supplemented with 10% StemFlex supplement (SF complete media, Thermo Fisher Scientific), 2   l of Normocin per ml of media (1:500 final, Invivogen), and 0.4   l of 10 mM Rock Inhibitor (Y-27632 Dihydrochloride, STEMCELL Technologies). After 24 hours of seeding, we continued to maintain the cells with SF complete media without Rock Inhibitor and passaged them with 1 ml of accutase (STEMCELL Technologies) as necessary, aiming to maintain below 80-90% confluence and prevent stacked cell growth.

extract_protocol:
hiPSC (WTC11) with the dCas9-KRAB was differentiated into hepatic progenitor cells over 7 days of differentiation. We seeded 550,000 cells per well in 6-well plates in StemFlex media, Normocin with Rock Inhibitor and 1   g/ml Doxycycline. Next day, we changed the media with fresh StemFlex, Normocin and Doxycycline. The following day, we collected the cells from some wells and froze them in CryoStor media (STEMCELL Technologies); these were denoted as Day 0 (D0) cells. For the remaining wells, we changed the media with fresh RPMI (Thermo), B27 supplement (Thermo), 4 uM CHIR99021 (Reprocell), Normocin and Doxycycline. Next day, we changed the media with fresh RPMI, B27, Normocin and Doxycycline. The following day, we collected the cells from some wells and froze them in CryoStor media; these were denoted as Day 2 (D2) cells. For the remaining wells, we changed the media with fresh Hepatic Differentiation Media consisting of Knockout DMEM (Thermo), 20% knockout serum replacement (Thermo), 2 mM GlutaMax (Thermo), 100 uM 2-Mercaptoethanol (Sigma), 1x MEM Non-essential amino acids (Thermo), 1% DMSO (Sigma), along with Normocin and Doxycycline. The cells were incubated for 2 days after which we collected the cells from some of the wells and froze them in CryoStor media; these were denoted as Day 4 (D4) cells. For the remaining wells, we changed the media with fresh Hepatic Differentiation Media with Normocin and Doxycycline. The cells were incubated for 2 days after which the media was again changed with fresh Hepatic Differentiation Media with Normocin and Doxycycline. The following day, we collected the cells from all the wells and froze them in CryoStor media; these were denoted as Day 7 (D7) cells.
For the multiome experiment, we thawed one vial each of D0, D2, D4 and D7 cells and centrifuged at 300 x g for 5 min, then resuspended in 1 ml of chilled PBS with 0.04% BSA. We washed the cells again in PBS with 0.04% BSA and proceeded with nuclei isolation from 0.5-1 million cells. We centrifuged the cells at 500 x g for 5 min at 4  C, removed the supernatant and resuspended in 100 ul of chilled 1x lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40, 0.01% Digitonin, 1% BSA, 1 mM DTT, 1U/ul Sigma Protector RNase Inhibitor). We incubated the cells for 4 mins on ice and then added 1 ml of chilled wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 1 mM DTT, 0.2U/ul Thermo RNaseOUT, 0.2U/ul Takara Recombinant RNase Inhibitor). We centrifuged the nuclei at 500 x g for 5 min at 4  C, removed the supernatant and resuspended in 1 ml of chilled wash buffer. After counting we combined nuclei for the D0-D7 samples, centrifuged at 500 x g for 5 min at 4  C, resuspended in diluted nuclei buffer (1x Nuclei buffer, 1U/ul Sigma Protector RNase Inhibitor, 1 mM DTT), and adjusted the concentration to ~7300 nuclei/ul. We proceeded with transposition and library preparation using the 10x Genomics Multiome kit (PN-1000284), loading the sample onto one well of the multiome chip for GEM generation. ATAC and gene expression (GEX) libraries were prepared according to the 10x Genomics protocol.


title: NMN-4

city: HangZhou

first: Yuyan

last: Xu

address: Yuhang Tang Road

institute: Zhejiang university

description: Library name: Sample 8

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: Homo sapiens GRCh38 release-109/GRCh38.106
Supplementary files format and content: Matrix table with FPKM for every gene and every sample

source_name: Mesenchymal stem cells

extract_protocol:
RNA-seq:Cells were dissociated with Trypsin for 5 min, stopped with serum containing media, total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer's instructions.Embryos (five embryos per sample) were collected in a 0.2-mL PCR tube, and 4 µL lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTP, and oligo-dT primers) was added. The samples were immediately incubated at 72 °C for 3 min, and cDNA was produced using SuperScript II reverse transcriptase.
The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Mesenchymal stem cells

value: LMNA

value: NMN

value: total RNA


title: High Fat Diet, Vitamin C, replicate 1


title: NMN-3

description: Library name: Sample 7


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 129, 31893

city: Minneapolis

address: 689 23rd Ave SE

description: Library name: G262_O07_ABL3_31893_D129

source_name: Whole blood

value: Whole blood

value: female


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 129, 32240

description: Library name: G263_O07_ABL3_32240_D129

value: day 129


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_29

description: Library name: lcSSc_TM_EF_B1_29

value: peripheral blood


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 129, 31654

description: Library name: G261_O07_ABL3_31654_D129


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B1_28

description: Library name: dcSSc_TM_EF_B1_28


title: NMN-2

description: Library name: Sample 6


title: High Fat Diet, No Vitamin C, replicate 3

value: High Fat Diet, No Vitamin C


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 129, 31644

description: Library name: G260_O07_ABL3_31644_D129


title: High Fat Diet, No Vitamin C, replicate 2


title: NMN-1

description: Library name: Sample 5


title: High Fat Diet, No Vitamin C, replicate 1


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B1_27

description: Library name: dcSSc_TM_EF_B1_27


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 129, 27769

description: Library name: G259_O07_ABL3_27769_D129


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_26

description: Library name: lcSSc_TM_EF_B1_26


title: Normal Diet, Vitamin C, replicate 3

value: Normal Diet, Vitamin C


title: Normal Diet, Vitamin C, replicate 2


title: Ctr-3

description: Library name: Sample 3


title: CD14+ monocytes, healthy control, TM_EF_B1_25

description: Library name: HC_TM_EF_B1_25


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 129, 26712

description: Library name: G258_O07_ABL3_26712_D129


title: Normal Diet, Vitamin C, replicate 1


title: Ctr-2

description: Library name: Sample 2


title: CD14+ monocytes, healthy control, TM_EF_B1_23

description: Library name: HC_TM_EF_B1_23


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 129, 30438

description: Library name: G256_O07_ABL3_30438_D129

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol


title: CD14+ monocytes, healthy control, TM_EF_B1_24

description: Library name: HC_TM_EF_B1_24


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 129, 30386

description: Library name: G255_O07_ABL3_30386_D129


title: Normal Diet, No Vitamin C, replicate 2

value: Normal Diet, No Vitamin C


title: Ctr-1

description: Library name: Sample 1


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 129, 30310

description: Library name: G254_O07_ABL3_30310_D129

value: Protected


title: Normal Diet, No Vitamin C, replicate 1


title: MCF7_TRIM24KOB_Input

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

description: Library name: U13

data_processing:
Reads were aligned to the human genome build Hg38/GRCh38 using BWA
Reads with a mapping quality (MAPQ) < 20 were removed from further analysis and duplicates were marked by PICARD/GATK markDuplicates
Enrichment over input control was determined using MACS2 (q < 0.001, narrowPeak mode). Only peaks not overlapping with the ENCODE hg38/GRCh38 blacklisted regions, were retained.
BigWigs have been generated using bamCoverage from Deeptools using reads extension, RPGC normalization and a average bin of 50bp.
Assembly: hg38/GRCh38
Supplementary files format and content: .bed, narrowPeaks
Supplementary files format and content: .bw, bigWigs

source_name: Breast cancer

growth_protocol: MCF7 cells have been cultured in DMEM + 10% FBS + 1% Pen/Strep, at 5% CO2 and 37°C.

extract_protocol:
Chromatin immunoprecipitation followed by sequencing (ChIP)-seq was performed as previously described (Schmidt, D. et al. Methods 48, 240–248 (2009). In brief, cells were fixed in 1% formaldehyde for 10 min and quenched with 0.125M glycine. Nuclear lysates were extracted as previously described and sonicated for 15 cycles (30 sec on/30 sec off) using the Bioruptor® Pico (B01060001, Diagenode). Per ChIP, 50 µL of magnetic Protein A beads (10008D, Thermo Fisher Scientific) were conjugated to 5µL of ERa, TRIM24, H3K23ac, H3K27ac, pSer2-RNApolII-CTD antibodies.
Illumina

treatment_protocol: None (full media condition)

value: Breast cancer

tag: chip antibody

value: Input

value: Full-media


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 129, 30306

description: Library name: G253_O07_ABL3_30306_D129


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B1_20

description: Library name: dcSSc_TM_EF_B1_20


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_22

description: Library name: lcSSc_TM_EF_B1_22


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_21

description: Library name: lcSSc_TM_EF_B1_21


title: MCF7_NT2_Phospho-Ser2POL2_rep3

description: Library name: U12

value: pSer2-RNApolII-CTD (abab5095)


title: MCF7_NT2_Input

description: Library name: U14


title: Normal Diet, Vitamin C, Replicate 4

data_processing:
Read quality assessed with fastqc v 0.12.1, and reads trimmed with trim-galore v 0.6.10 and discarding reads with less than 30 bp
Trimmed Reads aligned to mm10 reference genome using bowtie2 v 2.2.8 in paired-end mode with all default parameters except with k=5 (up to 5 valid and distinct alignments for each read)
Read counts were generated with the featureCounts program v 2.0.1 where reads are assigned to features based on the largest number of overlapping bases, where exon is the feature type and attribute type is gene_id
Read count normalization was performed using the DESeq2 package v 1.40.1
Assembly: mm10
Supplementary files format and content: text file with raw counts for each sample
Supplementary files format and content: excel file with normalized read counts  (normalized by the DESeq2 package)

extract_protocol:
NucleoSpin© RNA Plus kit is used for E15.5 embryonic ventricle total RNA extraction.
1ug total RNA and 10 PCR cycles are used generating library by NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina

value: E15.5 Ventricle

value: C57/BL6 WT


title: MCF7_NT2_Phospho-Ser2POL2_rep2

description: Library name: U11


title: Ctr-4

description: Library name: Sample 4

value: Mesenchymal stem cells

value: LMNA


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 129, 28299

description: Library name: G251_O07_ABL3_28299_D129

value: Whole blood

value: Nonprotected


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 129, 30277

description: Library name: G252_O07_ABL3_30277_D129

value: day 129

value: female


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_19

description: Library name: lcSSc_TM_EF_B1_19

value: peripheral blood


title: Normal Diet, Vitamin C, Replicate 3

value: Normal Diet, Vitamin C


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_18

description: Library name: lcSSc_TM_EF_B1_18


title: Normal Diet, No Vitamin C, replicate 3


title: Normal Diet, Vitamin C, Replicate 2


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 126, 33705

description: Library name: G250_O07_ABL3_33705_D126

value: day 126


title: Normal Diet, Vitamin C, Replicate 1


title: MCF7_TRIM24KOB_Phospho-Ser2POL2_rep3

description: Library name: U9


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 126, 33495

description: Library name: G249_O07_ABL3_33495_D126


title: Normal Diet, No Vitamin C, Replicate 4

value: Normal Diet, No Vitamin C


title: MCF7_TRIM24KOB_Phospho-Ser2POL2_rep2

description: Library name: U8


title: Normal Diet, No Vitamin C, Replicate 3


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 126, 32931

description: Library name: G248_O07_ABL3_32931_D126

value: Protected


title: MCF7_TRIM24KOB_Phospho-Ser2POL2_rep1

description: Library name: U7

value: Breast cancer


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 126, 32886

description: Library name: G247_O07_ABL3_32886_D126


title: Normal Diet, No Vitamin C, Replicate 1


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 126, 32751

description: Library name: G246_O07_ABL3_32751_D126


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_14

description: Library name: lcSSc_TM_EF_B1_14


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 129, 31374

description: Library name: G257_O07_ABL3_31374_D129

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol


title: MCF7_NT2_Phospho-Ser2POL2_rep1

description: Library name: U10

value: Full-media


title: MCF7_NT1_Phospho-Ser2POL2_rep3

description: Library name: U6

value: pSer2-RNApolII-CTD (abab5095)


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B1_15

description: Library name: dcSSc_TM_EF_B1_15


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B1_17

description: Library name: dcSSc_TM_EF_B1_17


title: Normal Diet, No Vitamin C, Replicate 2

value: E15.5 Ventricle


title: MCF7_NT1_Phospho-Ser2POL2_rep2

description: Library name: U5


title: MCF7_NT1_Phospho-Ser2POL2_rep1

description: Library name: U4


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 126, 32624

description: Library name: G245_O07_ABL3_32624_D126


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B1_12

description: Library name: dcSSc_TM_EF_B1_12


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 126, 32319

description: Library name: G244_O07_ABL3_32319_D126


title: High Fat Diet, Vitamin C, Replicate 3

value: C57/BL6 WT

value: High Fat Diet, Vitamin C


title: MCF7_TRIM24KOA_Phospho-Ser2POL2_rep3

description: Library name: U3


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 126, 35908

description: Library name: G243_O07_ABL3_35908_D126


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_10

description: Library name: lcSSc_TM_EF_B1_10


title: MCF7_TRIM24KOA_Phospho-Ser2POL2_rep2

description: Library name: U2


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_16

description: Library name: lcSSc_TM_EF_B1_16


title: High Fat Diet, Vitamin C, Replicate 2


title: High Fat Diet, Vitamin C, Replicate 1


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 126, 35907

description: Library name: G242_O07_ABL3_35907_D126


title: CD14+ monocytes, healthy control, TM_EF_B1_9

description: Library name: HC_TM_EF_B1_9


title: MCF7_TRIM24KOA_Phospho-Ser2POL2_rep1

description: Library name: U1


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 126, 33530

description: Library name: G241_O07_ABL3_33530_D126


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_13

description: Library name: lcSSc_TM_EF_B1_13


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B1_8

description: Library name: dcSSc_TM_EF_B1_8


title: High Fat Diet, No Vitamin C, Replicate 3

value: High Fat Diet, No Vitamin C


title: High Fat Diet, No Vitamin C, Replicate 4


title: Patient 8

city: Clemson

first: David

middle: Matthew

last: Feliciano

state: South Carolina

address: 132 Long Hall

department: Biological Sciences

institute: Clemson University

description: Library name: Patient 8

data_processing:
BCL files from the sequencer were demultiplexed and converted to FASTQ files using the mkfastq command and default parameters within the Cell Ranger 7.0.1 pipeline. FASTQ files were preprocessed for quality and length and aligned to the human reference genome GRCh38 using the counts command with -force-cells parameter set to 10,000 based on the nuclei isolation target density and prior data. The output from the counts command was exported into R for quality control, multi-sample integration, cell-type clustering, cell-type marker identification and differential expression within each cluster using the Seurat v4 single cell analysis platform91. Differential expression lists were curated by removing mitochondrial encoded transcripts. The bash and R code for Cell Ranger and Seurat pipeline, respectively can be found here: https://github.com/vshanka23/tsc_human_scrna_feliciano
Assembly: GRCh38
Supplementary files format and content: Fastq files are converted into barcodes, features, and matrix files.

source_name: Brain

extract_protocol:
Frozen tissue (0.5-2.0 cm) into 1.0 mL cold 292 mM NaCl 29.2, 2 mM CaCl2, 42 mM MgCl2, 20 mM Tris-HCl pH 8.0, 1% CHAPs, 2% BSA, in Ultrapure H2O (CST buffer) into one well of a 6-well plate. Tissue was minced in CST buffer with spring scissors for 10 minutes on ice until homogenized. The cell/tissue solution was through a 40 µm cell strainer. The well was washed with 1.0 ml CST and filtered. Samples were filtered into a 15 mL canonical tube using 5.0 ml CST lacking CHAPs and BSA (ST buffer). Filtered samples were centrifuged at 4oC for 5 min at 500×g. The supernatant was removed, and the pellet resuspended in 1% BSA with RNAsin Plus in phosphate buffered saline (Nuclei Suspension Buffer). The nuclei were suspended in up to 500 µl nuclei suspension buffer with approximately 1200 nuclei per µl. Nuclei were filtered again through a 35 µm cell strainer (FACS filter cap tube). Nuclei were counted using a hemocytometer. An aliquot was subsequently resuspend in a 1:1000 dilution of Hoescht and TOPRO-3 for visualization of nuclei integrity as we have previously described85. Nuclei were transported on ice until gel-bead-in-emulsion (GEM) generation.
Libraries were made after GEM generation in accordance with 10X Genomics Single Cell 3’ kit v3.1 (10x Genomics, #1000269) according to the manufacturer’s guidelines and Chromium Next GEM Single Cell 3’ v. 3.1 (Dual Index Kit TT Set A, 10X Genomics, #1000215) protocol. The libraries were quantified and qualified using Qubit 4 Fluorometer (Thermo Fisher Scientific, #Q33238, 1X dsDNA, high sensitivity, 500 rxns (Thermo Fisher Scientific, #Q33231) and TapeStation 4150 (Aglient, #G2992AA, High Sensitivity D5000 ScreenTape Aglient, #5067-5592, High Sensitivity D5000 Ladder Agilent, #5067-5594. Libraries were constructed using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs Inc., #E7770S) and the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs Inc., #E7490S). These libraries were dual-indexed using the NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (New England Biolabs Inc., E7600S). The libraries were quantified and qualified using Qubit (Thermo-Fischer, #Q32852) and TapeStation (Agilent, # 5067-5579). Pooled libraries were sequenced using 150 bp paired-end reads on a NovaSeq 6000 SP v1.5 (300 cycles) flow cell (Illumina, #20028400).

value: Brain

value: TSC


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 126, 32574

description: Library name: G239_O07_ABL3_32574_D126

value: Whole blood

value: Nonprotected


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_11

description: Library name: lcSSc_TM_EF_B1_11

value: peripheral blood


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_7

description: Library name: lcSSc_TM_EF_B1_7


title: High Fat Diet, Vitamin C, Replicate 4


title: Patient 6

description: Library name: Patient 6


title: Patient 5

description: Library name: Patient 5


title: Patient 7

description: Library name: Patient 7


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 126, 33514

description: Library name: G240_O07_ABL3_33514_D126

value: female


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_6

description: Library name: lcSSc_TM_EF_B1_6


title: High Fat Diet, No Vitamin C, Replicate 2


title: Patient 4

description: Library name: Patient 4

value: Control


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 126, 32569

description: Library name: G238_O07_ABL3_32569_D126

value: day 126


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_4

description: Library name: lcSSc_TM_EF_B1_4


title: High Fat Diet, No Vitamin C, Replicate 1


title: CD14+ monocytes, healthy control, TM_EF_B1_5

description: Library name: HC_TM_EF_B1_5


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 126, 32543

description: Library name: G237_O07_ABL3_32543_D126

value: Protected


title: BRCAP2-CM

city: Lausanne

first: Aspram

last: Minasyan

address: Bugnon 25A

country: Switzerland

institute: Ludwig Institute for Cancer Research / CHUV

description: CMO

data_processing:
Barcoded 3’GEX libraries and CML were pooled and sequenced on an on Illumina HiSeq 4000 or NovaSeq6000 system, following 10X Genomics recommendations. GEX libraries were sequenced to a median depth of 20,000 unique reads per cell and CMO libraries were sequenced to a median depth of 5’000 unique reads per cell.
Alignment, barcode and UMI counting were performed using mm10-2020-A reference genome and cellranger-6.1.1 multi from 10x Genomics and processed in Seurat R package. Barcodes that were not mapped to any of the CMO libraries, were pooled together for each corresponding group as a pseudo-mouse.
The cell populations and states were annotated as described in the methods section of the Ghisoni et al. manuscript.
Assembly: mm10-2020-A
Supplementary files format and content: RDS object

source_name: tumour (C57BL/6NHsd female mice)

extract_protocol:
Cells were counted on the ADAM automated cell counter and viability was estimated with the AccuStain solution kit (NanoEntek). Samples were labeled and multiplexed by group, allowing to be pooled in a single GEM for encapsulation. Cell labeling was performed according to the Cell multiplexing oligo labeling protocol from 10x Genomics (CG00391).
libraries were generated using the Chromium Next GEM Single Cell 3’ Library and Gel beads kit v3.1 according to the manufacturer’s instructions

value: tumour (C57BL/6NHsd female mice)

value: ID8 tumour cells


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_2

description: Library name: lcSSc_TM_EF_B1_2


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 126, 32290

description: Library name: G236_O07_ABL3_32290_D126


title: Patient 2

description: Library name: Patient 2


title: Patient 1

description: Library name: Patient 1


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 126, 32240

description: Library name: G235_O07_ABL3_32240_D126


title: Patient 3

description: Library name: Patient 3


title: BRCAP2-3G


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 126, 31654

description: Library name: G233_O07_ABL3_31654_D126


title: BRCAP1-3G


title: CD14+ monocytes, diffuse cutaneous systemic sclerosis, TM_EF_B1_1

description: Library name: dcSSc_TM_EF_B1_1


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 126, 31644

description: Library name: G232_O07_ABL3_31644_D126


title: BRCAB2-3G


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 126, 31893

description: Library name: G234_O07_ABL3_31893_D126


title: BRCAB2-CM

description: CMO


title: HCC1806 cells, Luc-3D, 3

first: Allison

last: Makovec

address: 425 E River Parkway

description: Library name: H_L_3_3D

data_processing:
Reads were trimmed for low quality and adaptors using Trimmomatic. Sequences were mapped to the human reference genome (GRCh38.110) using HISAT2 and sorted using SAMTools. Raw gene counts were generated with featureCounts and converted to normalized oounts and variance stabilizing transformed (VST) normalized counts using DESeq2. Genes with zero expression across all samples were filtered out and duplicate gene names were made unique.
Assembly: GRCh38.110
Supplementary files format and content: comma-separated value files includes DESeq2 normalized count values for each 2D sample
Supplementary files format and content: comma-separated value files includes DESeq2 VST normalized count values for each 2D sample
Supplementary files format and content: comma-separated value files includes DESeq2 normalized count values for each 3D sample
Supplementary files format and content: comma-separated value files includes DESeq2 VST normalized count values for each 3D sample

source_name: Breast tissue

growth_protocol: The human breast cancer cell lines MDA-MB-231 and HCC1806 were cultured in RPMI medium 1640, supplemented with 10% FBS , 0.2% GlutaMax, and 1% Penicillin Streptomycin grown at 37° C and 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA library preparation was completed by Novogene

value: Breast tissue

value: Triple-negative breast cancer

value: Luciferase overexpression


title: BRCAB1-CM

description: CMO


title: HCC1806 cells, Luc-3D, 2

description: Library name: H_L_2_3D


title: CD14+ monocytes, limited cutaneous systemic sclerosis, TM_EF_B1_3

description: Library name: lcSSc_TM_EF_B1_3


title: S2133_00182_R1_S42

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

description: Column 'S2133_00182' in counts.matrix

data_processing:
Adapter & low quality reads removal with cutadapt v2.0
Alignment with star v2.4.2a
quantification with featureCount (subread v1.5.0.post3)
Assembly: GRCh37
Supplementary files format and content: counts.matrix contains gene counts of each sample

source_name: SKIN

extract_protocol: RNA-Seq

value: SKIN

tag: disease

value: HC

tag: timepoint

tag: group

value: Normal


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 126, 27769

description: Library name: G231_O07_ABL3_27769_D126

tag: tissue

tag: treatment


title: BRCAB1-3G


title: S2133_00177_R1_S32

description: Column 'S2133_00177' in counts.matrix


title: S2133_00190_R1_S22

description: Column 'S2133_00190' in counts.matrix


title: BRCAP1-CM

description: CMO


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 126, 26712

description: Library name: G230_O07_ABL3_26712_D126

tag: time

tag: animal id


title: S2133_00188_R1_S9

description: Column 'S2133_00188' in counts.matrix


title: HCC1806 cells, C5-3D, 3

description: Library name: H_C5_3_3D

value: CREB5 overexpression


title: BRCA-DCM

description: CMO


title: HCC1806 cells, C5-3D, 2

description: Library name: H_C5_2_3D


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 126, 31374

description: Library name: G229_O07_ABL3_31374_D126

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

tag: Sex

tag: treatment outcome


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 126, 30438

description: Library name: G228_O07_ABL3_30438_D126

value: Whole blood


title: S2133_00175_R1_S47

description: Column 'S2133_00175' in counts.matrix


title: BRCA-D3G

tag: cell type


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 126, 30386

description: Library name: G227_O07_ABL3_30386_D126


title: BRCA-CCM

description: CMO


title: S2133_00197_R1_S16

description: Column 'S2133_00197' in counts.matrix


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 126, 30310

description: Library name: G226_O07_ABL3_30310_D126


title: HCC1806 cells, Luc-3D, 1

description: Library name: H_L_1_3D

tag: genotype


title: MDA-MB-231 cells, Luc-3D, 2

description: Library name: M_L_2_3D


title: BRCA-C3G


title: S2133_00179_R1_S43

description: Column 'S2133_00179' in counts.matrix


title: BRCA-BCM

description: CMO