title: Putamen in monkey P, replicate 2

city: PITTSBURGH

first: William

middle: R.

last: Stauffer

state: PA

address: 3501 Fifth Ave

department: Neurobiology

institute: University of Pittsburgh

description:
mRNA for single nuclei
WS_6N_STA706A12_S6

data_processing:
Basecalls performed using RTA3
10x cellranger count was used to align reads to a custom reference genome
Data were filtered, normalized, integrated, clutered and visualized using a Seurat v3 pipline
Supplementary_files_format_and_content: rds files containing filtered counting matrix or raw counting matrix
Supplementary_files_format_and_content: rds files containing clustering information for major cell classes
Supplementary_files_format_and_content: rds files containing clustering information for MSN types

organism: Macaca mulatta

source_name: Putamen in monkey P

extract_protocol:
We isolated nuclei using a loose glass dounce homogenizer followed by a tight glass homogenizer in EZ PREP buffer (Millipore Sigma, Cat# NUC-101).
Single nuclei RNA libraries were prepared for sequencing using standard 10x Chromium Single Cell 3’ Reagent kits v3 Chemistry (10x Genomics, Cat# PN-1000075).
10x Chromium Single Cell 3' v3 chemistry.

value: 5 years

value: wild type

value: Putamen


title: A764

status: Public on Nov 01 2021

type: RNA

city: Dallas

first: Yuqing

last: Zhang

state: TX

address: 6000 Harry Hines Blvd

department: Surgery

country: USA

institute: UTSouthwestern Medical Center

hyb_protocol: Total RNA from each sample was hybridized to the CodeSet nCounter PanCancer Immune Profiling Panel, Mouse.

scan_protocol: The scanning was processed on the NanoString Technologies nCounter Sprint Profiler.

data_processing:
We used the nSolver Analysis Software 4.0 (NanoString Technologies).
Samples were normalized based on the geometric means of the supplied positive controls and the panel of housekeeping genes.

label: NanoString nCounter probes

molecule: total RNA

organism: Mus musculus

source_name: KPfC pancreatic tumor

growth_protocol: 0.5 × 10^6 KPfC BMF-A3 cells were implanted orthotopically into WT C57BL/6 mice. Ultrasound was done on a cohort of animals to confirm tumor burden before therapy was initiated.

extract_protocol: KPfC tumor tissues from orthotopic endpoint experiment were lysed in RLT lysis buffer and purified according to the manufacturer’s instructions (QIAGEN). Quality control was performed with Agilent Bioanalyser.

treatment_protocol: For KPfC endpoint study, therapy was initiated at day 10 post tumor cell injection. Treatments consist of 8 groups: vehicle; TP-0903, 25 mg/kg, daily, oral gavage; gemcitabine, 25 mg/kg, ip, 3x/week; anti-PD1 antibody (clone: RMP14-1), 5 mg/kg, ip, twice per week; TP-0903+gemcitabine; TP-0903+anti-PD1; TP-0903+gemcitabine+anti-PD1; gemcitabine+anti-PD1. All mice were sacrificed on Day 35.

tag: tissue

value: KPfC orthotopic pancreatic tumor

tag: treatment

value: Vehicle


title: A8_IFNB1KO_ICP0_rep1

type: SRA

city: Berkeley

first: Nir

last: Yosef

state: CA

address: 629 Soda Hall

institute: University of California, Berkeley

description:
MG_A8_S8_L004
Replicate 1 for RNA-seq 5 days of trans-differentiation

library_source: transcriptomic

data_processing:
Sequencing quality of fastq files was evaluated with FASTQC
RNA-seq reads were aligned to the reference genome (GRCh38.83) using Bowtie2
Transcript and gene counts were quantified using RSEM with the parameter ‘strandedness’ set to ‘reverse’.
Genome_build: GRCh38.83
Supplementary_files_format_and_content: abundances_tpm, counts

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: BLaER1 cells were cultured in RPMI Medium 1640 supplemented with L-glutamine, sodium pyruvate, 100U/ml penicillin-streptomycin (Thermo Fisher) and 10% (v/v) FCS (Omega Scientific).

extract_protocol:
RNA from 2.8 million trans-differentiated BLaER1 monocytes was isolated using TRIzol™ Reagent (Thermo Fisher). DNA was removed with RQ1 RNase-free DNase (Promega) in the presence of RNasin plus Ribonuclease Inhibitor (Promega) and RNA isolated with Agencourt AMPure XP beads (Beckman Coulter).
mRNA-seq libraries were prepared from poly-A-enriched mRNA using a KAPA mRNA HyperPrep Kit (Roche) and sequenced on an Illumina Novaseq S4 150PE.

treatment_protocol: 1.4 million BLaER1 cells per well of a 6-well plate were trans-differentiated into monocytes for 5 days in medium containing 10 ng/ml of hrIL-3, 10 ng/ml hr-CSF-1 (M-CSF) (both PeproTech) and 100 nM β-Estradiol (Sigma-Aldrich) and  stimulated with 1µg/ml doxycycline hyclate (Sigma-Aldrich) for 24h.

tag: cell line

tag: genotype


title: Motor neurons - Unaffected parent clone 3

city: Cleveland

first: Ashleigh

last: Schaffer

state: OH

address: 2109 Adelbert Road

department: Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics

institute: Case Western Reserve University

description:
TotalRNAseq_U3
Mature d28 motor neurons differentiated from Unaffected parent, iPSC clone 3

data_processing:
Raw reads were aligned with STAR version 2.5.4b with settings "--outFilterMultimapNmax 1" to keep only unique alignments and "--sjdbOverhang 149" to maintain a readLength - 1 recommendation for splice junction overhangs during alignment.
Count files were generated with featureCounts version 1.6.1 using output BAM files above and gene annotations from Ensembl release 95. Stranded (reverse) and paired-end settings were used.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited genewise count files using Ensembl genome annotations release 95
Supplementary_files_format_and_content: Comma seaparated value genewise count matrix

source_name: iPSC-derived motor neurons

growth_protocol: Primary fibroblast cell lines were established from skin biopsies of affected children and an unaffected parent according to standard methods. Reprogramming of patient fibroblasts into induced pluripotent stem cells (iPSCs) was performed using the Epi5 Episomal iPSC Reprogramming Kit (ThermoFisher) with the following modifications. Electroporated fibroblasts were plated on Matrigel membrane matrix (Fisher). Reprogramming vectors were prepared in house and the medium was changed to StemFlex (ThermoFisher) at day 15. iPSC clones were selected for expansion and plated on vitronectin-coated plates. Motor neurons were differentiated from patient-derived iPSCs using a previously published protocol (Markmiller et a., Cell, 2018)

extract_protocol:
TRIzol
150bp paired-end sequencing was performed by Novogene with 2 ug of total RNA as starting material. Total RNA-seq utilized the dUTP protocol (Parkhomchuk et al., Nucleic Acids Res., 2009) after rRNA depletion with the RiboZero Gold kit.

tag: pch10 disease status

value: Unaffected


title: 3P_CGGCAGTTGCG

city: Rensselaer

first: Nathan

middle: C

last: Boles

state: NY

address: One Discovery Dr

institute: Neural Stem Cell Institute

data_processing:
After de-multiplexing fastq files were mapped with STAR aligner (version 2.7.0a)
A raw counts matrix was generated in R with the GenomicAlignments package.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-seperated file of raw counts with samples by column

source_name: meninges

extract_protocol:
Meninges were dissected from the anterior and posterior of the cortex of  C57BL/6 mice and a single cell suspension was generated. Cells were dispensed using the ICELL8 single cell system as single cells followed by reverse transcription and barcoding according to the manufacturer's protocol
RNA libraries were prepared for sequencing the 150 cycle Nextera DNA library preperation kit from Illumina.

value: Posterior meninges

tag: age

value: 3 months


title: Nacc in monkey P, replicate 2

description:
mRNA for single nuclei
WS_5N_STA706A11_S5

source_name: Nacc in monkey P

value: Nacc


title: A7_IFNB1KO_mCherry_rep1

description:
MG_A7_S7_L004
Replicate 1 for RNA-seq 5 days of trans-differentiation


title: 3P_CCTTAAGCATA


title: 3P_CGAACCGTACG


title: HBV100_S95

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: Illimuna next-generation sequencing (2x100bp, paired-end)

data_processing:
RNA-Seq data analysis was performed using a standard HISAT-StringTie-Ballgown pipeline. Briefly, raw RNA-Seq sequence reads (FASTQ format) were aligned to the reference human genome assembly (Dec. 2013, GRCh38) using HISAT2 (hierarchical indexing for spliced alignment of transcripts) software. Gene- and transcript-level expression were then comprehensively quantified with the StringTie program, which performed 1) genome-guided transcript assembly, 2) identification of splice variants, 3) quantification of expression as FPKM (fragments per kilobase of transcript per million mapped reads) values, and 4) normalization. This analysis yielded FPKM expression estimations for a total of 143,502 known transcripts that included annotated protein-coding genes and isoforms, noncoding RNAs, and unannotated transcripts.
Processed data is a data matrix generated from the output of StringTie and Ballgown and contains the Gene Symbol and FPKM values for each sample.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Data matrix in tab-delimited text format. The file contains the Gene Symbol and gene-level FPKM expression values for each sample.

source_name: Whole blood

extract_protocol:
Blood was drawn into PAXgene Blood RNA vacutainer tubes (BD Biosciences) and total RNA isolated using the PAXgene Blood RNA Kit (Qiagen).
Indexed, directional RNA-Seq libraries were prepared from total RNA (1.0 ug) using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Globin depletion (Illumina, San Diego, CA) according to the manufacturer’s protocol.

tag: biosource

value: Peripheral blood

tag: ethnicity

value: Chinese

tag: gender

value: Male

tag: hbv status

value: Active

tag: viral load

tag: viral load group

value: Treatment-naive


title: A6_IFNAR1KO_IFNAR2KO_E4ORF3_rep1

description:
MG_A6_S6_L004
Replicate 1 for RNA-seq 5 days of trans-differentiation

value: IFNAR1-/- IFNAR2-/-


title: HBV099_S94

value: Laotian

value: Female


title: A5_IFNAR1KO_IFNAR2KO_ICP0_rep1

description:
MG_A5_S5_L004
Replicate 1 for RNA-seq 5 days of trans-differentiation


title: Nacc in monkey P, replicate 1

description:
mRNA for single nuclei
WS_2N_STA706A8_S2

value: 5 years


title: Caudate in monkey P, replicate 2

description:
mRNA for single nuclei
WS_4N_STA706A10_S4

source_name: Caudate in monkey P

value: wild type

value: Caudate


title: 3P_CCGCAACTAGG


title: A4_IFNAR1KO_IFNAR2KO_mCherry_rep1

description:
MG_A4_S4_L004
Replicate 1 for RNA-seq 5 days of trans-differentiation


title: Putamen in monkey P, replicate 1

description:
mRNA for single nuclei
WS_3N_STA706A9_S3

value: Putamen


title: Putamen in monkey F

description:
mRNA for single nuclei
8N-Putamen_BYR85A21_S4

source_name: Putamen in monkey F

value: 12 years


title: Caudate in monkey P, replicate 1

description:
mRNA for single nuclei
WS_1N_STA706A7_S1


title: 3P_CCAGCATTCGC


title: Nacc in monkey F

description:
mRNA for single nuclei
7N-Nac_BYR85A20_S3

source_name: Nacc in monkey F


title: A3_WT_E4ORF3_rep1

description:
MG_A3_S3_L004
Replicate 1 for RNA-seq 5 days of trans-differentiation

value: WT


title: 3P_CCAATGCTGGT

value: Posterior meninges


title: HBV095_S91


title: 3P_CCTGATGCTAT

value: 3 months


title: A2_WT_ICP0_rep1

description:
MG_A2_S2_L004
Replicate 1 for RNA-seq 5 days of trans-differentiation


title: Caudate in monkey F

description:
mRNA for single nuclei
6N-Caudate_BYR85A19_S2

source_name: Caudate in monkey F


title: A1_WT_mCherry_rep1

description:
MG_A1_S1_L004
Replicate 1 for RNA-seq 5 days of trans-differentiation


title: 3P_ATTGGCTCTAT


title: Motor neurons - Unaffected parent clone 2

description:
TotalRNAseq_U2
Mature d28 motor neurons differentiated from Unaffected parent, iPSC clone 2

value: Unaffected


title: Control_hippocampus2

city: Mumbai

first: Shubha

last: Tole

state: Maharashtra

address: B304 TIFR Homi Bhabha road

department: Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

data_processing:
HISAT2
SAM tools
Feature Counts
DESEQ2
Genome_build: mm10
Supplementary_files_format_and_content: Normalised counts using feature counts

source_name: Control Hippocampus

growth_protocol: Preganant dams were harvested for embryos 14 days post vaginal plug

extract_protocol: Trizol

value: Hippocampus

value: Control


title: HBV094_S90

value: Peripheral blood

value: Hmong

value: Inactive


title: MG8_MORC3KO_MREKO_rep2

description:
Replicate 2 for RNA-seq 5 days of trans-differentiation
Raw files are merged from two independent sequencing runs of the same RNA-seq library.

treatment_protocol: 1.4 million BLaER1 cells per well of a 6-well plate were trans-differentiated into monocytes for 5 days in medium containing 10 ng/ml of hrIL-3, 10 ng/ml hr-CSF-1 (M-CSF) (both PeproTech) and 100 nM β-Estradiol (Sigma-Aldrich).

value: Cas9 STAT1-/- STAT2-/- MORC3-/- MRE{delta}/{delta}


title: HBV093_S89

value: Vietnamese

value: Male

value: Active

value: Treatment-naive


title: 3P_ATGGACTACCA


title: HBV091_S88


title: MG7_MREKO_rep2

value: Cas9 STAT1-/- STAT2-/- MRE{delta}/{delta}


title: 3P_AGTTACGGCAA


title: HBV096_S92

value: Chinese

value: Female


title: GOF_hippocampus2

source_name: Wnt Gain of function Hippocampus

value: Lmx1acre;Beta-catenin GOF


title: HBV090_S87


title: HBV088_S85


title: seventh day

city: shanghai

first: Renkai

last: Wang

address: 168 Changhai Road,

country: China

institute: changhai hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: fracture tissues

extract_protocol:
To obtain bone and bone marrow cells for scRNA-seq, mice were sacrificed via CO2 asphyxia. Bone fracture tissues (including bones and bone marrow 0.5cm from the fracture end) were dissected from mice and placed in DMEM/F12(Gibco), and cut bone fracture tissues into small fragments and digested them with 0.1mg/ml collagenase II (Invitrogen) for 2h at 37℃. After digestion, the obtained cells were filtered through a 70μm filter and collect it into a collection tube, and erythrocytes lysed in ACK-lysis buffer.
RNA libraries were generated by BD Rhapsody singel cell RNA-seq and prepared for sequencing using standard Illumina protocols

treatment_protocol: By constructing mouse fracture model, and extracting bone fracture end tissue at different time ( 0day, 3days, 7days, 14days),and extracting single cells by digestion

tag: strain

value: bone fracture tissues( bone and bone marrow)

tag: time point

value: 7 days


title: HBV098_S93


title: third day

description: zuoer

value: 3 days


title: MG5_WT_rep2

value: Cas9 STAT1-/- STAT2-/-


title: 3P_ACGAGACCTGG

value: Posterior meninges

value: 3 months


title: GOF_CP2

source_name: Wnt Gain of function Chorid plexus

value: Choroid plexus


title: 3P_ACGAACTGACG


title: MG6_MORC3KO_rep2

value: Cas9 STAT1-/- STAT2-/- MORC3-/-


title: MG4_MORC3KO_MREKO_rep1

description:
Replicate 1 for RNA-seq 5 days of trans-differentiation
Raw files are merged from two independent sequencing runs of the same RNA-seq library.

value: Cas9 STAT1-/- STAT2-/- MORC3-/- MRE{delta}/{delta}


title: SP CD8 Prmt5-CKO_72

city: Shanghai

first: zheyi

last: chen

address: 1665 Kong Jiang Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
For RNA-Seq, before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to the mouse genome (GRCm38) using Hisat2. HTseq was used to obtain gene counts, and the RPKM method was used to determine gene expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: For RNA-Seq, Matrix table with raw gene counts for every gene and every sample.

source_name: Spleen

extract_protocol:
Single-cell suspensions were harvested from fresh tissues according to standard procedures and surface-stained in FACS buffer with monoclonal antibodies. Related T cell subsets from mice spleen or thymus were sorted with FACS Aria II Cell Sorter.  For bulk RNA-seq, total RNA was extracted from tissue by Trizol reagent.
For bulk RNA-seq, complementary DNA (cDNA) libraries were prepared using the NEBNextTM Ultra Directional RNA Library Prep Kit, NEBNext Poly (A) mRNA Magnetic Isolation Module, and NEBNext Multiplex Oligos according to the manufacturer’s instructions. The products were purified and enriched by PCR to create the final cDNA libraries.

tag: cell type

value: T cells

value: CD4-Cre+ PRMT5fl/fl


title: Control_CP2

source_name: Control Choroid plexus

value: Control


title: 3P_AGAATCAACTA


title: 14th day

description: WRK

value: 14 days


title: MG1_WT_rep1


title: HBV085_S82

description: Illimuna next-generation sequencing (2x100bp, paired-end)

value: Peripheral blood

value: Active

value: Treatment-naive


title: HBV084_S81

value: Vietnamese

value: Male

value: Inactive


title: MG2_MORC3KO_rep1


title: SP CD8 Prmt5-CKO_68


title: HBV089_S86

value: Chinese


title: 3P_ACTTGGTCGCA


title: 3P_AGAAGACCTCT


title: 3P_AAGAGATGACC


title: MORC3KO_rep3  [RVMG021_F_ATAC-seq]

description: Replicate 3 for ATAC-seq 5 days of trans-differentiation

library_source: genomic

data_processing:
FASTQC version 0.11.5 was used to assess quality of ATAC-seq reads.
Adaptor sequences were removed using Cutadapt version 2.10 using a default error rate of 0.1. Reads shorter than 5 were discarded.
Reads were aligned to the hg19 reference genome using bowtie 2 version 2.3.2 and discordant alignments were removed. Reads with mapping quality less than 30 were removed using SAMtools version 1.3.1 and duplicates were removed using Picard Tools version 2.5.0.
Regions overlapping black list regions, identified from the ENCODE consortium, were removed. Blacklist regions were downloaded from ENCODE (accession ENCFF000KJP).
ATAC-seq reads aligned to the positive strand were shifted +4bp and reads aligned to the negative strand were shifted -5bp to adjust read start sites to represent the center of the transposase binding event. Peaks were called on shifted reads using MACS2 version 2.2.7.1, setting the FDR to 0.05 and the default human genome size.
Peaks from all samples were combined by taking the union of all peaks. Counts representing peak strength for all samples were obtained by counting the number of cut sites that overlapped each peak for each sample.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: Tn5_cut_sites.tsv

molecule: genomic DNA

extract_protocol:
50,000 BLaER1 monocytes were washed with PBS and lysed in 50 µL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Nuclei were harvested by centrifugation and resuspended in 50 µl TD Buffer (Illumina, FC-121-1030) with 2.5 µL Tn5 Transposase (Illumina, FC-121-1030). The reaction was incubated for 30 min at 37°C and DNA was isolated with a MinElute Kit (Qiagen).
Transposed DNA fragments were amplified to reach 30% of maximal amplification and sequenced on an Illumina Nova-Seq SP 50PE.

treatment_protocol: 1.4 million BLaER1 cells per well of a 6-well plate were trans-differentiated into monocytes for 5 days in medium containing 10 ng/ml of hrIL-3, 10 ng/ml hr-CSF-1 (M-CSF) (both PeproTech).

value: IFNAR1-/- IFNAR2-/- MORC3-/-

tag: molecule subtype

value: Tn5 transposed DNA


title: HBV086_S83

value: Hmong


title: 3P_AAGACCTCGCT

value: Posterior meninges

value: 3 months


title: HBV087_S84


title: HBV083_S80

value: Female


title: SP CD8 Prmt5-CKO_65

value: T cells


title: 3P_AACCTTGCCGT


title: control group

description: youer

value: bone fracture tissues( bone and bone marrow)

value: 0 day


title: WT_rep3  [RVMG021_E_ATAC-seq]

value: IFNAR1-/- IFNAR2-/-


title: MG3_MREKO_rep1

value: Cas9 STAT1-/- STAT2-/- MRE{delta}/{delta}


title: HBV082_S79

value: Peripheral blood


title: 3A_TTCAAGAGGTT

value: Anterior meninges


title: MORC3KO_rep1  [RVMG021_B_ATAC-seq]

description: Replicate 1 for ATAC-seq 5 days of trans-differentiation


title: SP CD8 WT_71

value: wild type


title: HBV077_S74

value: Male

value: Active

value: Treatment-naive


title: SP CD4 Prmt5-CKO_72

value: CD4-Cre+ PRMT5fl/fl


title: WT_rep2  [RVMG021_C_ATAC-seq]

description: Replicate 2 for ATAC-seq 5 days of trans-differentiation

value: Tn5 transposed DNA


title: SP CD8 WT_70


title: 3P_AACCTGAGGCA


title: HBV080_S77

value: Chinese


title: 3A_TTGGTCTAATT


title: 3A_TGGCCTGCCTT


title: SP CD4 Prmt5-CKO_68


title: SP CD4 Prmt5-CKO_65


title: HBV079_S76

value: Vietnamese


title: WT_rep1  [RVMG021_A_ATAC-seq]


title: HBV078_S75

value: Hmong


title: MORC3KO_rep2  [RVMG021_D_ATAC-seq]

value: IFNAR1-/- IFNAR2-/- MORC3-/-


title: 3A_TGGCGATTGCA

value: 3 months


title: Donor RPE/choroid 3

city: Melbourne

first: Raymond

middle: Ching-Bong

last: Wong

state: VIC

address: Level 7 Smorgan Family Wing, 32 Gisborne St

country: Australia

institute: Centre for Eye Research Australia Ltd/ University of Melbourne

description: Bilateral intraocular lens, exophthalmos

data_processing:
Transcript level quantification was performed using Salmon v1.0 to obtain gene-level counts (Patro R et al. 2017 Nat. Methods 14, 417–419), using the --gcBias flag to estimates a correction factor for systematic biases and --validateMappings flag for selective alignment.
Genome_build: GRCh38

source_name: pigment epithelial cells/choroid layers

extract_protocol:
The retinal pigment epithelial cells/choroid layers were dissected from donor retinas and processed for RNA extraction using the Rneasy kit with Dnase I (Qiagen). RNA quality was checked using bioanalyzer and transcriptome libraries were prepared using the TruSeq Stranded mRNA kit (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: retina


title: Donor RPE/choroid 2

description: Healthy ocular history


title: SP CD8 WT_67

value: T cells


title: HBV076_S73

value: Female


title: Thy CD8 Prmt5-CKO_3

source_name: Thymus


title: Donor RPE/choroid 1

description: Healthy ocular history


title: HBV072_S69

value: Inactive


title: 3A_TGGCCGAGCTG


title: 3A_TCGGTCTGAAC


title: Gastric Adenocarcinoma cells - MKN45 - Clofarabine-treated-rep1

city: miami

first: RIMPI

last: KHURANA

state: FL

address: Room 6112B, Rosenstiel Medical Science Building (RMSB),1600 NW 10th Avenue

institute: University of miami

data_processing:
Illumina Novaseq 6000 sequencer
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR
n RNA-seq experiments, gene expression level is estimated by the abundance of transcripts (count of sequencing) that mapped to genome or exon. Read counts is proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments
Genome_build: Homo sapiens grch38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Gastric Adenocarcinoma cells

growth_protocol: AGS cells were purchased from American Type Culture Collection (ATCC, Manassas, VA). MKN45 cells were obtained from the Riken Cell Bank (Tsukuba, Japan).  AGS cells were cultured in F12 media (GIBCO, Carlsbad, CA) supplemented with 5% fetal bovine serum (FBS, Invitrogen Life Technologies, Carlsbad, CA) and 1% penicillin/streptomycin (P/S) (GIBCO). MKN45  cells were cultured in RPMI medium (GIBCO) supplemented with 10% FBS and 1% P/S. EPC2 cells were cultured in Keratinocyte serum-free medium supplemented with recombinant epidermal growth factor and bovine pituitary extract (GIBCO). All cell lines were ascertained to conform to the original in vitro morphological characteristics and were authenticated using short tandem repeat (STR) profiling (Genetica DNA Laboratories, Burlington, NC). All cell lines reported here have been tested and had shown to be free of mycoplasma (R&D Systems, Minneapolis, MN).

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA).
mRNA sequencing was performed by Novogene corporation (Sacramento, CA). RNA purity was assessed using the NanoPhotometer spectrophotometer (IMPLEN, CA).RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA). A total of 1 µg RNA per sample was used as input material for the RNA sample preparations. The clustering of the index-coded samples was performed on an Illumina Novaseq 6000 sequencer (Illumina Inc, CA, USA) according to the manufacturer’s instructions

treatment_protocol: Cells were treated with clofarabine (200 nmol/L) for 48 hours

value: Gastric Adenocarcinoma cells

value: treated with Clofarabine 48 hours


title: HBV075_S72

value: Peripheral blood


title: SP CD4 WT_70

value: wild type


title: 3A_GGTTACTCCTT

value: Anterior meninges


title: Gastric Adenocarcinoma cells - MKN45 - Clofarabine-treated-rep3


title: HBV074_S71

value: Male

value: Active

value: Treatment-naive


title: SP CD4 WT_71


title: HBV081_S78

value: Chinese


title: 3P_AAGAATAAGTC

value: Posterior meninges


title: HBV071_S68

value: Hmong


title: Gastric Adenocarcinoma cells - MKN45 - Clofarabine-treated-rep2


title: 3A_GTTGATCTTCT


title: HBV073_S70


title: 3A_TCAGATAGTCC


title: SP CD4 WT_67


title: 3A_GCGGTTATATA


title: Gastric Adenocarcinoma cells - MKN45-rep3

value: untreated


title: Thy CD8 Prmt5-CKO_1

value: CD4-Cre+ PRMT5fl/fl


title: Gastric Adenocarcinoma cells - MKN45-rep2


title: HBV070_S67


title: Gastric Adenocarcinoma cells - MKN45-rep1


title: 3A_GCAATCCAAGA

value: 3 months


title: Thy CD8 WT_3

value: T cells


title: HBV068_S65

value: Female


title: Thy CD8 Prmt5-CKO_2


title: Gastric Adenocarcinoma cells - AGS - Clofarabine-treated-rep3


title: HBV069_S66

value: Inactive


title: 3A_GAAGACGAGTT


title: 3A_CTTATGAGACC


title: Gastric Adenocarcinoma cells - AGS - Clofarabine-treated-rep2

value: Gastric Adenocarcinoma cells


title: HBV067_S64

value: Vietnamese


title: Gastric Adenocarcinoma cells - AGS-rep3


title: HBV066_S63

value: Peripheral blood


title: Thy CD8 WT_1

value: wild type


title: Gastric Adenocarcinoma cells - AGS-rep2


title: Thy CD4 Prmt5-CKO_14

description:
HTSeq.counts_thy_DP_CD4.txt
ThyCD4_CRE14


title: HBV064_S61


title: Thy CD4 Prmt5-CKO_17

description:
HTSeq.counts_thy_DP_CD4.txt
ThyCD4_CRE17


title: HBV065_S62


title: Thy CD4 WT_24

description:
HTSeq.counts_thy_DP_CD4.txt
ThyCD4_WT24


title: Gastric Adenocarcinoma cells - AGS-rep1


title: 3A_CGGATGCCGTT

value: Anterior meninges


title: 3A_CGAAGAGCCTA


title: 3A_CTCCGAACGTA


title: G50: Foot skin of Healthy non-diabetic subject

city: Atlanta

first: Debasree

last: Sarkar

state: GA

address: 615 Michael Street

department: Pediatrics

institute: Emory University

data_processing: Raw scRNA-Seq data was demultiplexed, aligned to the reference human genome (Hg38) and processed for single cell gene counting using the Cell Ranger Software from 10X Genomics Inc

source_name: Foot skin

extract_protocol:
Skin biopsies were kept in sterile PBS on ice until processing, normally within a few hours post-surgery. The skin was cleaned by sequentially immersing in 10% Betadine, 70% ethanol and PBS for 1 minute at a time. Then it was incubated in 5 mg/ml Dispase II (Thermo Fisher) in HBSS (STEMCELL) overnight at 4°C. The next day, the epidermis was peeled off using forceps and the tissue was finely minced with a No. 10 disposable scalpel. The skin pieces were then placed in an enzyme cocktail consisting of 3.3 mg/ml Collagenase-P (Roche), 3.3 mg/ml Dispase II and 1.5 mg/ml DNase I in 0.25% Trypsin-EDTA, and incubated for 90 minutes at 37°C with constant shaking, using glass pipettes for trituration every 20 min. Enzymes were then inactivated with addition of complete DMEM (+10%FBS, +1% Pen/Strep). The single cell suspension was passed through 70 um and 40 um cell strainers and centrifuged 10min, 500g at 4°C. For RBC lysis ACK buffer (Lonza) was added.
Library preparation was performed using the Chromium 3’V2 and 3 reagent kits (10X genomics). Gel bead-in-emulsions (GEMs) were generated, and bar coded by loading single cell suspensions in Single cell chip B along with gel beads and reverse transcription (RT) master mix and running on the 10X genomics chromium controller. Following RT, the cDNA was amplified and used to generate 3’ libraries. The libraries were quantified using Qubit 3.0 fluorometer, and quality was assessed using HS DNA chips with 2100 Bioanalyzer (Agilent technologies). Sequencing was performed using massively parallel sequencing on the Novaseq S4 instrument (Illumina).

value: Foot skin

tag: disease

value: Non-diabetic


title: 3A_CCTACGTCATG

source_name: meninges

tag: tissue


title: Thy CD4 WT_18

description:
HTSeq.counts_thy_DP_CD4.txt
ThyCD4_WT18


title: Thy CD8 WT_2


title: Gastric Adenocarcinoma cells - AGS - Clofarabine-treated-rep1

tag: treatment

value: treated with Clofarabine 48 hours


title: G49: Foot skin of subject with healing DFU

value: DFU-healer


title: HBV062_S59

value: Male

value: Treatment-naive


title: G48: Forearm skin of Diabetic subject without DFU

source_name: Forearm skin

value: Forearm skin

value: Non-DFU Diabetic


title: 3A_CCGCAGGTAAG

value: 3 months


title: HBV061_S58

source_name: Whole blood

value: Hmong

value: Active


title: Thy CD4 WT_15

description:
HTSeq.counts_thy_DP_CD4.txt
ThyCD4_WT15

value: T cells


title: Thy DP Prmt5-CKO_23

description:
HTSeq.counts_thy_DP_CD4.txt
ThyCD4CD8_CRE23

value: CD4-Cre+ PRMT5fl/fl


title: HBV060_S57

value: Chinese


title: 3A_CCAAGACTTCT


title: G47: PBMCs of Diabetic subject without DFU

source_name: PBMCs

value: PBMCs


title: 3A_CAACCGACGCG


title: 3A_CCTCCTTAACG


title: Thy CD4 Prmt5-CKO_23

description:
HTSeq.counts_thy_DP_CD4.txt
ThyCD4_CRE23


title: HBV059_S56

value: Peripheral blood

value: Inactive


title: HBV058_S55


title: HBV063_S60

value: Female


title: Thy DP Prmt5-CKO_14

description:
HTSeq.counts_thy_DP_CD4.txt
ThyCD4CD8_CRE14


title: G46: Foot skin of Diabetic subject without DFU

value: Foot skin


title: G45: Foot skin of subject with healing DFU


title: 3A_ACGCGCTGGAG

value: Anterior meninges


title: Thy DP Prmt5-CKO_17

description:
HTSeq.counts_thy_DP_CD4.txt
ThyCD4CD8_CRE17


title: 3A_ACGGACCAAGA


title: Thy DP WT_24

description:
HTSeq.counts_thy_DP_CD4.txt
ThyCD4CD8_WT24

value: wild type


title: G44: Foot skin of Healthy non-diabetic subject

value: Non-diabetic


title: 3A_ACGACCTTGAA


title: HBV057_S54

value: Treatment-naive


title: Thy DP WT_18

description:
HTSeq.counts_thy_DP_CD4.txt
ThyCD4CD8_WT18


title: HBV056_S53

value: Male


title: G43: Foot skin of Healthy non-diabetic subject


title: 3A_AAGAATAACGA


title: HBV055_S52


title: G41: Foot skin of Diabetic subject without DFU

value: Non-DFU Diabetic


title: HBV054_S51


title: SP CD3 Control scRNA-seq (WT)

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Genome_build: mm10
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

extract_protocol:
Single-cell suspensions were harvested from fresh tissues according to standard procedures and surface-stained in FACS buffer with monoclonal antibodies. Related T cell subsets from mice spleen or thymus were sorted with FACS Aria II Cell Sorter.
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols


title: HBV053_S50

value: Vietnamese


title: 18P_TTGGTTATGGT

value: Posterior meninges

value: 18 months


title: SP CD3 Prmt5-CKO scRNA-seq (CRE)

value: T cells


title: Treg_PHD2_Hif1a_KO_2

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Adapters were removed with Trimmomatic-0.36 with the following parameters: Truseq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:4
Reads were then mapped to the reference genome mm10 by using STAR_2.5.3 software with default parameters
Reads from the alignment were sorted and indexed according to chromosomes
Read counts in the alignment BAM-files that overlap with the gene features were obtained using HTSeq-0.9.1 with “--nonunique all” option
Raw read counts were normalized and a differential expression analysis was performed with DESeq2 by applying an adjusted p-value <0.05 and an absolute log2-ratio larger than 1
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing read counts for each sample and gene

source_name: Splenic Treg cells

extract_protocol:
Total RNA was prepared from purified splenic Treg cells using the TRIzol method (Invitrogen).
200 ng of total RNA was subsequently used to prepare RNA-Seq library by using TruSeq RNA sample prep kit (Illumina) according to manufacturer’s instructions.

value: spleen

value: Treg


title: 3A_AACCTATTCAT

value: 3 months


title: HBV052_S49

value: Peripheral blood


title: G40: Foot skin of Healthy non-diabetic subject


title: 18P_TTATTCGTTAT


title: 18P_TTGCCGCATAT


title: HBV050_S47

value: Chinese

value: Inactive


title: Treg_PHD2_Hif1a_KO_1


title: G39: Foot skin of subject with non-healing DFU

value: Foot skin

value: DFU-nonhealer


title: 18P_TTATATAGATG


title: G38: Foot skin of Diabetic subject without DFU


title: HBV051_S48


title: G37: PBMCs of subject with non-healing DFU

value: PBMCs


title: HBV049_S46

value: Female


title: 18P_TGGACCAGCCA


title: 18P_TGGAAGGTTGG


title: Treg_PHD2_Hif1a_Hif2a_KO_1


title: Treg_PHD2_Hif2a_KO_3


title: G42: Foot skin of subject with healing DFU

value: DFU-healer


title: Treg_PHD2_Hif1a_Hif2a_KO_2


title: Thy DP WT_15

description:
HTSeq.counts_thy_DP_CD4.txt
ThyCD4CD8_WT15

value: wild type


title: HBV047_S44

value: Hmong

value: Treatment-naive


title: G36: Forearm skin of Healthy non-diabetic subject

value: Forearm skin

value: Non-diabetic


title: G34: Foot skin of subject with non-healing DFU


title: Treg_PHD2_Hif2a_KO_2


title: HBV048_S45

value: Active


title: 18P_TCATCAGTTGG

value: Posterior meninges

value: 18 months


title: 18P_TGACGTTCAGG


title: Treg_PHD2_Hif2a_KO_1

value: spleen

value: Treg


title: G33: Foot skin of subject with non-healing DFU


title: HBV046_S43

value: Peripheral blood

value: Vietnamese


title: Treg_PHD2_KO_3


title: G35: Forearm skin of subject with non-healing DFU


title: G32: Foot skin of Healthy non-diabetic subject

value: Foot skin


title: HBV045_S42

value: Inactive


title: 18P_GTTGAAGTTCG


title: HBV044_S41

value: Chinese

value: Male


title: G31: Foot skin of Healthy non-diabetic subject


title: 18P_GTTCATCGGAG


title: 18P_GTTCTCGTAGT


title: HBV043_S40


title: G30: PBMCs of Healthy non-diabetic subject

value: PBMCs


title: Treg_PHD2_KO_2


title: 18P_GTCTGCGATGA


title: Treg_WT_2

value: WT


title: 18P_GTCGTTCCTCC


title: G29: Forearm skin of Healthy non-diabetic subject


title: Treg_WT_1


title: HBV042_S39


title: HBV041_S38

value: Female


title: G28: Foot skin of Healthy non-diabetic subject


title: 18P_GGTTGAGCATC


title: G27: PBMCs of subject with healing DFU

value: DFU-healer


title: HBV039_S36

value: Treatment-naive


title: HBV040_S37


title: LLC1_CpG_day_21_4

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

country: Japan

institute: Kindai University Faculty of Medicine

data_processing:
Sequence reads were mapped to mm10 using STAR(version 2.7.0f).
Mapped reads were counted by FeatureCounts (version 1.6.4 ).
Genome_build: mm10
Supplementary_files_format_and_content: raw count

source_name: tumor tissue

extract_protocol:
Total RNA was isolated from tumor tissues using TRIzol (Thermo Fisher Scientific, Waltham, Massachusetts, USA) and RNeasy spin columns (Qiagen, Venlo, The Netherlands) according to the manufacturer's protocols.
Libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep kit (Sample 1-20) or  NEBNext Ultra II RNA Library Prep Kit for Illumina (Sample 21-32) according to the manufacturer's protocols.

value: CpG

tag: agent


title: 18P_GGTTGGCTTGG


title: G26: PBMCs of Healthy non-diabetic subject

value: Non-diabetic


title: 18P_GGTTATAAGCT

value: Posterior meninges


title: G25: PBMCs of subject with healing DFU


title: 18P_GGTTAACGAGG

value: 18 months


title: HBV037_S35

value: Hmong

value: Active


title: LLC1_CpG_day_21_1


title: LLC1_CpG_day_21_2


title: G24: Foot skin of Healthy non-diabetic subject


title: 18P_GGTCGGACTGC


title: Treg_WT_3

value: spleen

value: Treg

tag: genotype


title: 18P_GGATTGAGTCT


title: G23: Foot skin of subject with healing DFU

value: Foot skin


title: LLC1_CpG_day_14_3


title: HBV034_S32

value: Peripheral blood

value: Vietnamese


title: HBV035_S33

value: Male

value: Inactive


title: LLC1_CpG_day_14_2


title: HBV033_S31


title: LLC1_CpG_day_21_3


title: 18P_GGATGCCTCGA


title: G21: PBMCs of subject with non-healing DFU

value: PBMCs

value: DFU-nonhealer


title: G22: PBMCs of subject with healing DFU

value: DFU-healer


title: LLC1_CpG_day_14_1


title: 18P_GCTCATGACGC


title: HBV032_S30

value: Chinese

value: Treatment-naive


title: HBV036_S34


title: G19: PBMCs of Diabetic subject without DFU

value: Non-DFU Diabetic


title: LLC1_CpG_day_7_4

value: CpG


title: HBV030_S29


title: 18P_GAAGCGTCCTG

value: Posterior meninges

value: 18 months


title: 18P_GCATGGATTGG


title: LLC1_CpG_day_14_4


title: HBV027_S27

value: Hmong

value: Female

value: Active


title: LLC1_CpG_day_7_3


title: HBV028_S28


title: LLC1_CpG_day_7_2


title: G17: Forearm skin of subject with healing DFU

value: Forearm skin


title: G18: Forearm skin of Healthy non-diabetic subject

value: Non-diabetic


title: G16: Foot skin of Healthy non-diabetic subject

value: Foot skin


title: 18P_GAACTAATTCG


title: G15: Foot skin of subject with healing DFU


title: G20: PBMCs of Healthy non-diabetic subject


title: 18P_CTGGCATGATA


title: HBV024_S24

value: Peripheral blood

value: Vietnamese


title: G14: Foot skin of Healthy non-diabetic subject


title: F127_2_LPS

city: Hangzhou

first: Yuxian

last: Guo

address: Department of Basic Medical Sciences,   School of Medicine, Zhejiang University,  388 Yuhangtang Rd

institute: Zhejiang University School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: gene_count.txt
Supplementary_files_format_and_content: gene_fpkm.txt
Supplementary_files_format_and_content: all_compare.txt

source_name: Bone marrow-derived macrophage

extract_protocol:
Harvest cells by using GenElute Single Cell RNA Purification Kit (Sigma, RNB300) and perform RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: One replicate was LPS treated for 24 hours.

value: Bone marrow-derived macrophages

tag: overexpression

value: FABP5 C127S

value: LPS for 24 hours


title: 18P_CGTATTCGAGA

tag: age


title: 18P_CGTAGAGGTAC


title: G13: Forearm skin of subject with healing DFU

value: DFU-healer


title: F127_1_LPS


title: HBV022_S22

tag: biosource

value: Male

value: Treatment-naive


title: LLC1_CpG_day_7_1

value: CpG


title: HBV021_S21

tag: ethnicity

value: Chinese

value: Inactive


title: HBV026_S26

tag: gender


title: F_2_LPS


title: F_1_LPS


title: 18P_CTTGAGGATGC

value: Posterior meninges

value: 18 months


title: 18P_CGGTTGCGTTG


title: F127_3_LPS


title: G10: Foot skin of Healthy non-diabetic subject


title: G11: Forearm skin of subject with non-healing DFU

value: DFU-nonhealer


title: 18P_CGCTGGCGTCG


title: 18P_CGCCAAGAGGT


title: HBV023_S23

tag: hbv status

value: Active


title: F127_3

value: untreated


title: HBV025_S25

value: Female

tag: viral load


title: G12: Forearm skin of subject with healing DFU

value: Forearm skin


title: HBV019_S19

value: Peripheral blood

tag: viral load group


title: HBV020_S20

value: Hmong


title: G9: Foot skin of subject with non-healing DFU

value: Foot skin


title: 18P_CGAATCGCGGC


title: HBV018_S18


title: F127_2

tag: strain

value: Bone marrow-derived macrophages

value: FABP5 C127S


title: F_3_LPS

value: LPS for 24 hours


title: 18P_GGAGGTCTTGC


title: F127_1


title: G7: Foot skin of subject with healing DFU

value: DFU-healer


title: F_3


title: F_2


title: 18P_CCGGATTACTA


title: 18P_CCGCGTCGGCG


title: G4A: Forearm skin of Diabetic subject without DFU

value: Non-DFU Diabetic


title: 18P_CCATCAATCGT


title: 18P_CCAATAGTTAT


title: G6: Foot skin of subject with non-healing DFU


title: F_1


title: HBV014_S14

value: Chinese

value: Treatment-naive


title: HBV017_S17

value: Inactive


title: G4: Foot skin of subject with healing DFU


title: 18P_CAACCGCCAGC

value: Posterior meninges

value: 18 months


title: HBV013_S13


title: HBV015_S15

value: Active


title: HBV012_S12

value: Vietnamese

value: Male


title: G3A: Foot skin of Diabetic subject without DFU


title: C2C12 cell line - siCOX7A2L_rep3

city: Beijing

first: Haining

address: Jia 3 Datun Road

institute: Institute of Zoology, Chinese Academy of Science

description: rRNA depletion

data_processing:
Basecalls performed using NGS Real-Time Analysis v3.4.4
Raw sequences were processed by first removing 3’ illumina universal adaptor sequence using Trim Galore v0.6.4 with parameters --stringency 5 --length 20 --paired --gzip.
Clean reads were aligned to the mouse transcript reference sequence (mm39) downloaded from GENCODE and quantified reads count and transcript per million (TPM) using Salmon v0.13.1 with parameters -l A -p 4 -g --validateMappings.
Differential expression analysis using R package DESeq2 v1.30.1 and the batch effect was removed by using R package v3.38.0.
Genome_build: mm39
Supplementary_files_format_and_content: tab-delimited text file with raw counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text file with TPM for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text file with results of DESeq2

source_name: C2C12 cell line

growth_protocol: C2C12  cells were maintained in 1% penicillin-streptomycin (#15140122, Gibco), Dulbecco’s Minimal Essential Medium (DMEM, #C11995500BT, Gibco) supplemented with 10% fetal bovine serum (FBS, #10099-141, Gibco) and 5% CO2, 95% air atmosphere at 37 ℃.

extract_protocol:
The total RNA of C2C12 cells treated with siRNA, plasmid and virus was extracted with Trizol reagent (#15596018, Invitrogen).
For cDNA library preparation, total RNA was isolated using Trizol from C2C12 cells treated with Control (n=3) or Cox7a2l (n=3) siRNA. RNA quality was determined with agarose gel and optical density. Only samples with a 260 nm/280 nm ratio within 1.8-2.1 and the intensity of a 28S/18S ratio between 1.5-2 were further processed. The cDNA library was prepared as previously described (Zhang et al., 2012). Briefly, total RNA sample (2 ug) were performed rRNA depletion and RNA fragmentation. Then the RNA was reversetranscribed into double-stranded cDNA with random primer. cDNA samples were end-repaired and polyadenylated before ligation of Y-shaped adapter containing the index for multiplexing, then performed the dUTP strand degradation. Fragments containing Y-shaped adapter on both ends were  enriched by PCR. The quantity of the cDNA library was validated using Qubit dsDNA HS Assay Kit (#Q32851, Invitrogen). The purity of the libraries was analyzed by fragment analyzer automated CE system (Advanced Analytical) and the sequencing was further performed only when the libraries had a size of 150 bp to 300 bp and no adaptor dimer contanmination. Sequencing was performed on the illumina novaseq 6000.

treatment_protocol: siRNA transfection procedure was processed according to manufacturer’s instructions of RNAiMAX (#13778-150, Invitrogen).

value: Muscle

tag: cell line


title: C2C12 cell line - siCOX7A2L_rep2

description: rRNA depletion


title: 18P_ATGCGGTACTA


title: HBV011_S11

value: Peripheral blood


title: 18P_CCGGTTCTGCC


title: 18P_AGAAGACGGTT


title: C2C12 cell line - siCOX7A2L_rep1

description: rRNA depletion


title: G3: Foot skin of Diabetic subject without DFU


title: HBV016_S16

value: Female


title: G5: Foot skin of Diabetic subject without DFU

value: Foot skin


title: C2C12 cell line - siCTRL_rep3

description: rRNA depletion

value: siCTRL


title: G2A: Foot skin of Diabetic subject without DFU


title: C2C12 cell line - siCTRL_rep2

description: rRNA depletion


title: HBV009_S9

value: Laotian


title: 18P_ACGTCGTTATA


title: C2C12 cell line - siCTRL_rep1

description: rRNA depletion


title: 18P_ACCTCTCGAGT


title: G2: Foot skin of subject with healing DFU


title: HBV008_S8


title: G1A: Foot skin of Diabetic subject without DFU


title: Meninges_mouse

first: Heping

last: Xu

state: Zhejiang

address: 18 Shilongshan Road

institute: Westlake University

description:
scRNA-seq
3'-end gene expression
Hashtag antibodies labeling

data_processing:
scRNA-seq data: the 10x Genomics Cell Ranger Single Cell Software Suite 3.1.0 was used to perform sample demultiplexing and single cell UMI counting
Genome_build: For mouse: mm10
Genome_build: For monkey: Mmul 10
Supplementary_files_format_and_content: For scRNA-seq data: tsv, a gene by cell count matrix in the tsv format

source_name: Meninges

growth_protocol: primary immune cells

extract_protocol:
RNA were extracted from cells using RNAClean XP beads (Backman)
10x 3'-end single cell RNA-seq; Feature barcode libraries were generated for murine B cells

tag: Sex

value: male


title: G1: Forearm skin of Healthy non-diabetic subject

value: Forearm skin

value: Non-diabetic


title: HBV007_S7

value: Hmong


title: 18P_AAGATAACGAC


title: 18P_AAGAGATATAG


title: HBV006_S6

value: Treatment-naive


title: HBV005_S5

value: Inactive


title: 18P_AAGACTACGAG

value: Posterior meninges


title: CD8+ venetoclax_rep4

city: Chicago

first: James

last: LaBelle

state: IL

address: 900 East 57th Street, KCBD 5122

institute: University of Chicago

description:
mRNA
CD8_combined_results_EdgeR.txt

data_processing:
RNA-seq reads were aligned to mm10 with HISAT2 using default parameters. Reads were counted using Rsubread and analyzed with EdgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_combined_results_EdgeR.txt: Tab-delimited text files include CPM values.

source_name: T cell

extract_protocol:
RNA was isolated using Trizol.
Barcoded RNA-seq libraries were generated using the standard Illumina TruSEQ v2 kit.

treatment_protocol: Animals underwent myeloablative transplantation with T cell depleted bone marrow harvested from congenic animals. Naïve (CD44lowCD62Lhigh) CD8+ and CD4+ T cells were sorted from bone marrow transplanted animals immediately following 28 days of in vivo treatment with venetoclax.

tag: cell type

value: Naive CD8+ T cells

value: B6.Cg-Foxp3tm2Tch/J (FOXP3-IRES-GFP)

value: Venetoclax


title: CD8+ venetoclax_rep3

description:
mRNA
CD8_combined_results_EdgeR.txt


title: HBV004_S4

value: Active


title: 18P_AAGACCAGGTC

value: 18 months


title: CD8+ venetoclax_rep2

description:
mRNA
CD8_combined_results_EdgeR.txt


title: HBV010_S10

value: Peripheral blood

value: Chinese


title: CD8+ venetoclax_rep1

description:
mRNA
CD8_combined_results_EdgeR.txt


title: EB Control rep 2

city: New York

first: Nadeera

middle: M

last: Wickramasinghe

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: Sample 104

data_processing:
FASTQ files were aligned with kallisto to a reference transcriptome model generated from the human genome hg38 using default parameters. Transcript-level counts were added to generate a collapsed gene-level count matrix. DESeq2 was used to normalize read counts and determine differentially expressed genes with p<0.05.
Genome_build: hg38
Supplementary_files_format_and_content: csv file containing gene-level counts for each RNA-Seq sample.

source_name: cardiomyocyte

growth_protocol: Standard EB-differentiation protocols were used to generate PSC-derived cardiomyocytes, which were either cultured as Ebs, dissociated and plated as monolayers or dissociated and constructed into EHTs. A subset of cells were also subjected to lactate selection.

extract_protocol:
PSC-derived cardiomyocytes were dissociated using Collagenase Type II and FACS-isolated through SIRPA+ CD90- gating.
RNA libraries were prepared for sequencing using RiboZero Gold library prep and standard Illumina protocols

treatment_protocol: PSC-derived cardiomyocytes were treated with either GW0742 (5µM), WY14643(5µM), Rosiglitazone (5µM), GSK0660 (2.5µM) or AICAR (2.5µM), and with or without LCFAs (12.5µM; palmitic acid, oleic acid, linoleic acid).

value: PSC-derived cardiomyocyte

value: Control

tag: treatment duration

value: 28 days


title: CD8+ control_rep4

description:
mRNA
CD8_combined_results_EdgeR.txt

value: Vehicle


title: HBV002_S2

value: Male


title: EB Control rep 1

description: Sample 103


title: 18P_ACCAACCGCGG

data_processing:
After de-multiplexing fastq files were mapped with STAR aligner (version 2.7.0a)
A raw counts matrix was generated in R with the GenomicAlignments package.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-seperated file of raw counts with samples by column

extract_protocol:
Meninges were dissected from the anterior and posterior of the cortex of  C57BL/6 mice and a single cell suspension was generated. Cells were dispensed using the ICELL8 single cell system as single cells followed by reverse transcription and barcoding according to the manufacturer's protocol
RNA libraries were prepared for sequencing the 150 cycle Nextera DNA library preperation kit from Illumina.

tag: tissue


title: G8: Foot skin of subject with healing DFU

value: Foot skin

tag: disease

value: DFU-healer


title: EHT GSK0660 rep 3

description: Sample 102

tag: treatment


title: HBV001_S1

data_processing:
RNA-Seq data analysis was performed using a standard HISAT-StringTie-Ballgown pipeline. Briefly, raw RNA-Seq sequence reads (FASTQ format) were aligned to the reference human genome assembly (Dec. 2013, GRCh38) using HISAT2 (hierarchical indexing for spliced alignment of transcripts) software. Gene- and transcript-level expression were then comprehensively quantified with the StringTie program, which performed 1) genome-guided transcript assembly, 2) identification of splice variants, 3) quantification of expression as FPKM (fragments per kilobase of transcript per million mapped reads) values, and 4) normalization. This analysis yielded FPKM expression estimations for a total of 143,502 known transcripts that included annotated protein-coding genes and isoforms, noncoding RNAs, and unannotated transcripts.
Processed data is a data matrix generated from the output of StringTie and Ballgown and contains the Gene Symbol and FPKM values for each sample.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Data matrix in tab-delimited text format. The file contains the Gene Symbol and gene-level FPKM expression values for each sample.

extract_protocol:
Blood was drawn into PAXgene Blood RNA vacutainer tubes (BD Biosciences) and total RNA isolated using the PAXgene Blood RNA Kit (Qiagen).
Indexed, directional RNA-Seq libraries were prepared from total RNA (1.0 ug) using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Globin depletion (Illumina, San Diego, CA) according to the manufacturer’s protocol.

value: Hmong

value: Treatment-naive


title: 18P_AACCTCTATAC

value: Posterior meninges


title: 18P_AACGCAAGAAT


title: CD8+ control_rep1

description:
mRNA
CD8_combined_results_EdgeR.txt

value: Naive CD8+ T cells


title: AHLM_3

city: San Francisco

first: Tien

last: Peng

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

data_processing:
FASTQC for  quality control, Cuadapt and Sickle for triming adaptors
reads were aligned and mapped using STAR
DESeq was use to call differential gene expression, in Rstudio
Genome_build: UCSC human GRCh37/hg19
Supplementary_files_format_and_content: raw_counts.xlsx

source_name: AHLM

growth_protocol: Cells were grown in DMEM/F12 with 10% FBS at 37°C, 5% CO2 in a humidified incubator

extract_protocol: The RNA was extracted by QIAGEN RNeasy Mini Kits from the cultured cells, and the amount and quality of extracted RNA was measured by RNA 6000 Pico Kit (Agilent). The Bulk RNA-seq was done in GENEWIZ.

tag: developmental stage

value: Adult

value: adult human lung mesenchyme (AHLM)


title: AHLM_2


title: CD4+ venetoclax_rep4

description:
mRNA
CD4_combined_results_EdgeR.txt

value: Naive CD4+ T cells

value: B6.Cg-Foxp3tm2Tch/J (FOXP3-IRES-GFP)

value: Venetoclax


title: EHT LCFA + GW0742 rep 3

description: Sample 99

value: LCFA + GW0742


title: AHLM_1


title: EB Control rep 3

description: Sample 105

value: PSC-derived cardiomyocyte


title: EHT LCFA + GW0742 rep 2

description: Sample 98


title: MRC5_3

value: Fetal

value: fetal human lung fibroblast cell line MRC5


title: Mouse mTEChi control - replicate 3

city: Parkville

first: Waruni

last: Abeysekera

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread version 1.30.8
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: Tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: mTEChi

extract_protocol:
RNA from FACS-purified cortical thymic epithelial cells (CD45neg TER-119neg CD31neg EpCAMpos MHC ClassIIpos Ly51pos UEA1neg) and MHC classIIhi medullary thymic epithelial cells (CD45neg TER-119neg CD31neg EpCAMpos MHC ClassIIhi Ly51neg UEA1pos) was isolated using the microRNeasy Micro Kit (Qiagen) with on column DNase digestion according to manufacturer’s instructions. First strand cDNA synthesis and cDNA amplification were performed using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech Laboratories) according to manufacturer’s instructions.
Complementary DNA libraries were prepared and indexed separately using the Nextera® XT DNA Library Preparation Kit (Illumina) following manufacturer’s instructions. Each indexed sample library was quantified using the Agilent Tapestation and the Qubit™ DNA BR assay kit for Qubit 3.0® Fluorometer (Life technologies).
RNA-seq. The indexed sample libraries were pooled and diluted to 1.5pM for 75 base paired-end sequencing on a NextSeq 500 instrument using the v2 150 cycle High Output kit (illumina) as per manufacturer’s instructions. Between 13 and 35 million read pairs were generated for each sample

tag: genotype

value: Wild type


title: CD4+ venetoclax_rep3

description:
mRNA
CD4_combined_results_EdgeR.txt


title: CD8+ control_rep3

description:
mRNA
CD8_combined_results_EdgeR.txt

value: Vehicle


title: CD8+ control_rep2

description:
mRNA
CD8_combined_results_EdgeR.txt


title: EHT GSK0660 rep 2

description: Sample 101

value: 28 days


title: 18P_AACGCCATATG

first: Nathan

address: One Discovery Dr

institute: Neural Stem Cell Institute

tag: age

value: 18 months


title: EHT LCFA rep 3

description: Sample 96

value: LCFA


title: Mouse mTEChi control - replicate 2

value: Male


title: CD4+ venetoclax_rep2

description:
mRNA
CD4_combined_results_EdgeR.txt


title: CD4+ control_rep3

description:
mRNA
CD4_combined_results_EdgeR.txt


title: EHT LCFA rep 2

description: Sample 95


title: MRC5_2


title: EHT LCFA rep 1

description: Sample 94


title: Mouse mTEChi lacking HOIL - replicate 2

value: HOIL knok-out


title: HBV003_S3

first: Clifford

address: 4645 2nd Avenue, Room 2300A

institute: UC Davis School of Medicine

tag: biosource

value: Peripheral blood

value: Hmong

value: Female

value: Inactive

value: Treatment-naive


title: CD4+ venetoclax_rep1

description:
mRNA
CD4_combined_results_EdgeR.txt

value: Naive CD4+ T cells

value: B6.Cg-Foxp3tm2Tch/J (FOXP3-IRES-GFP)

value: Venetoclax


title: Mouse mTEChi control - replicate 1


title: EHT GW0742 rep 3

description: Sample 93

value: PSC-derived cardiomyocyte


title: Mouse cTEC control - replicate 3

source_name: cTEC


title: EHT LCFA + GW0742 rep 1

description: Sample 97

value: LCFA + GW0742


title: MRC5_1

value: Fetal

value: fetal human lung fibroblast cell line MRC5


title: CD4+ control_rep1

description:
mRNA
CD4_combined_results_EdgeR.txt

value: Vehicle


title: Mouse mTEChi lacking HOIL - replicate 3


title: CD4+ control_rep4

description:
mRNA
CD4_combined_results_EdgeR.txt


title: EHT GSK0660 rep 1

description: Sample 100

value: 28 days


title: 18P_AACCAACTCCG

value: Posterior meninges

value: 18 months


title: Mouse mTEChi lacking HOIL - replicate 1

value: HOIL knok-out

value: Male


title: Single-cell transcriptomes of macrophages isolated from atherosclerotic lesions of nt-LNA-treated mice

city: Nashville

first: Ryan

last: Allen

state: TN

address: 2220 Pierce Ave

department: Medicine

institute: Vanderbilt University Medical Center

data_processing:
RTA (version 2.4.11; Illumina) was used for base calling and analysis was completed using 10X Genomics Cell Ranger software v2.1.1.
scRNABatchQC software package was used for assessment of scSEQ data quality control,
Clustering analysis was generated by Seurat
Initial cell type classification (i.e. myeloid/macrophage, B cells, T cells, NK cells) of complete datasets was based on cell activity database (PanglaoDB).
Genome_build: mm9
Supplementary_files_format_and_content: Mouse_aortas_4187_2nd_ur.html:  output from scRNABatchQC
Supplementary_files_format_and_content: Mouse_aortas_4187_2nd.cluster.summary.csv:  # of cells from each treatment/cluster
Supplementary_files_format_and_content: Mouse_aortas_4187_2nd.cluster.csv: barcoding of individual cells and assignment to cluster by gene activity database
Supplementary_files_format_and_content: Mouse_aortas_4187_2nd.cluster.count.csv: raw gene expression in each cluster
Supplementary_files_format_and_content: Mouse_aortas_4187_2nd.cluster.normByUpQuantile.csv: normalized gene expression in each cluster

source_name: nt-LNA-treated CD45+/CD3- Cells

extract_protocol:
10X Chromium system.
3' RNA Seq, P/N 1000006, 1000080, 1000020.
NovaSeq6000, 150 bp paired-end.

treatment_protocol: Apoe-/- mice were treated with saline or nt-LNA (30 mg/kg) for 4 weeks in combination with a western diet. The aortic arch and thoracic aorta were removed and processed to yield a single cell suspension that was processed by FACS to yield a CD45+/CD3- population.

value: nt-LNA


title: CD4+ control_rep2

description:
mRNA
CD4_combined_results_EdgeR.txt


title: Single-cell transcriptomes of macrophages isolated from atherosclerotic lesions of saline-treated mice

source_name: Saline-treated CD45+/CD3- Cells

value: saline


title: EHT GW0742 rep 1

description: Sample 91


title: Mouse cTEC control - replicate 1

value: Wild type


title: EHT Control rep 3

description: Sample 90

value: Control


title: EHT GW0742 rep 2

description: Sample 92


title: Mouse cTEC lacking HOIL - replicate 3

value: Female


title: Mouse cTEC control - replicate 2


title: Mouse HSC-derived CAF from CMT93 liver metastasis model [RS033]

city: NEW YORK

first: Robert

last: Schwabe

address: 1130 St. Nicholas Ave

institute: COLUMBIA PRESBYTERIAN MED CTR

description:
RS033
scRNA-seq (10x) on fresh isolated cancer-associated-fibroblasts and tumor from mouse KRAS/P19-induced ICC.

data_processing:
Bulk RNA-seq:
20M paired-end 100bp sequencing was performed using the Illumina NovaSeq 6000.
RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
A pseudoalignment to a kallisto index was created from transcriptomes (GRCm38) using kallisto (0.44.0).
Differentially expressed genes were tested using DESeq2. Normalization was done internally using DESeq2's specialized algorithm and normalization to compare across samples, was performed using the TPM (transcripts per million) method.
scRNA-seq:
Illumina NovaSeq 6000.
10x Genomics' cellranger pipeline was used to process the data (v3).
BCL files were demultiplexed with 10x Cell Ranger's mkfastq command and analysis and alignment were performed using Cell Ranger's count command with Cell Ranger's reference mm10.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: [Bulk RNA-seq] tpm_values_genes_kallisto.txt: Tab-delimited text file includes TPM values for each Sample.
Supplementary_files_format_and_content: [scRNA-seq] *.mtx: Raw counts in MatrixMarket (mtx) format.
Supplementary_files_format_and_content: [scRNA-seq] *barcodes.tsv, *features.tsv

source_name: Liver

extract_protocol:
HSC,CAF and whole tumor specimens were obtained perfusing and digesting the liver, followed by FACS sorting.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ v3 Reagent Kit (10x Genomics) according to manufacturer’s instructions, 12 cycles of cDNA amplification and 12 cycles of library amplification were performed, and samples were sequenced on an Illumina HiSeq instrument (NovaSeq 6000 for AJ064) at the JP Sulzberger Columbia Genome Center.

treatment_protocol: Mice were injected through the intra-splenic route (hemi-spleen technique) with Pan02, CMT93, KPCYc2 to induce liver metastasis.

value: C57BL/6, LratCre+, TdTom+, Col1a1-GFP

tag: liver damage

value: Liver metastasis by intra-splenic injection

value: COL1A1+GFP+CAF, tumor cells and tumor microenvironment cells


title: PF28_M

city: Vancouver

first: Alexandre

middle: A

last: Lussier

state: British Columbia

department: Department of Medical Genetics

country: Canada

institute: University of British Columbia

data_processing:
Fastq files were aligned to the rat genome (Rn6, July 2014) using the Burrows-Wheeler Transform (BWA) tool to obtain .bam files (Li and Durbin, 2009).
Bam files were filtered using samtools to remove duplicate reads, unpaired reads, and reads with a minimum quality score below 10.
Following alignment and filtering, each the two runs for each sample were merged using samtools to obtain a single .bam file for each sample (Li et al., 2009).
Model-based analysis of ChIP-seq (MACS2; version 2.1.0.20140616) was used to identify enriched regions of DNA methylation across the genome (Zhang et al., 2008). The peak calling to identify peak regions (DNA methylation windows) was performed using the ‘callpeaks’ function on paired end bam files with no control input and the following options: –f BAMPE –m 5 50 –bw 300 –g 2.9e9 –q 0.05. Each sample was modeled individually, generating 60 total peaksets. These were imported into R using the DiffBind package (Stark and Brown, 2011). As all samples had slightly different predicted peaks, peaksets were combined into common regions using the dba.count function in DiffBind, which removed peaks found in less than 3 samples across the entire dataset and provided the total number of reads within each peak/sample. This created a final dataset of 469,162 peaks and 48 samples from the developmental profile of the hypothalamus, and a final dataset of 350,960 peaks and 24 samples in the P22 hypothalamus and WBC (tissue-concordant) peakset.
Genome_build: rn6
Supplementary_files_format_and_content: MACS2.1.4 peak file, one/animal/sex/group

organism: Rattus norvegicus

source_name: Prefrontal cortex, postnatal day 22, Pair-fed (PF)

growth_protocol: Details of the procedures for breeding and handling have been published previously (Bodnar et al., 2016). Briefly, outbred male and female Sprague-Dawley rats were obtained Charles River Laboratories (St. Constant, Quebec, Canada). Following a one-week habituation period, nulliparous females (n=39) were pair-housed with a male and vaginal lavage samples were collected daily for estrous cycle staging and to check for the presence of sperm, indicating gestation day (GD) 1. Pregnant dams were singly housed and assigned to one of three prenatal treatment groups: Prenatal alcohol exposure (PAE) - ad libitum access to liquid ethanol diet, 36% ethanol-derived calories, 6.37% v/v, n =13; Pair-fed (PF) - liquid-control diet, maltose-dextrin isocalorically substituted for ethanol, in the amount consumed by an PAE partner, g/kg body weight/GD, n =14; or Control (C) - pelleted version of the liquid control diet, ad libitum, n =12. All animals had ad libitum access to water. Experimental diets (Weinberg/Keiver Liquid Ethanol Diet #710324, Weinberg/Keiver Liquid Control Diet #710109, and Pelleted Control Diet #102698, Dyets Inc., Bethlehem, PA) were fed from gestation days 1-21, and then replaced with laboratory chow.

extract_protocol:
For each sample, 500 ng of DNA were diluted in a total volume of 60µL of EB buffer (Qiagen, Hilden, Germany). DNA was then transferred to a 96-well plate and sheared for 1 hour using the Covaris Focused-ultrasonicator. DNA was purified using Ampure XP in 20% polyethylene glycol (PEG) beads to obtain fragments sized from 200-500 basepairs (Beckman-Coulter, Brea, USA). Library preparation was performed on the Bravo Automated Liquid Handling Platform (Agilent, Santa Clara, USA) using the TruSeq DNA PCR-Free Sample Preparation Kit (Illumina, San Diego, USA). Following end-repair and A-tailing, adapters were ligated overnight at room temperature. PCR-free library preparation allowed for the conservation of methylated cytosines for subsequent methylated DNA immunoprecipitation. Finally, DNA was resuspended in 35µL of EB buffer (Qiagen, Hilden, Germany). DNA was quality controlled using Qubit Fluorometric Quantitation and the DNA 1000 Bioanalyzer 2100 kit (Agilent, Santa Clara, USA) to verify concentration and fragment size (250-550bp).
methylated DNA immunoprecipitation (meDIP): For each sample, 400ng of the sequencing library were diluted in a total volume of 50µL of IP Buffer (10mM sodium phosphate buffer, pH7.0, 140mM NaCl, 0.05% triton). DNA was denatured by incubation at 95˚C for 10 minutes, followed by the addition of 48µL ice-cold IP buffer and incubation on ice for 10 minutes. 2µL of anti-5-methylcytosine antibody (Eurogenetec, Liège, Belgium), diluted to 1/50 in IP buffer (1µL of antibody per 1µg of DNA ratio), was added to each sample. Immunoprecipitation reactions were incubated for 16 hours at 4˚C with overhead rotation. Following two 5 minute washes with 150uL of 0.1% BSA/PBS, 50µL of Dynabeads Protein G were incubated with 5µL of secondary antibody (rabbit anti-mouse IgG; Jackson Immunoresearch, West Grove, USA) in 45uL ice-cold IP buffer for 15 minutes at room temperature with overhead rotation. Beads were washed twice with IP buffer to remove unbound secondary antibody and resuspended in 50µL IP buffer. The antibody-bound beads were added to the immunoprecipitation reactions and incubated for 2 hours at 4˚C with overhead rotation. Beads were then washed 6 times with 150µL of ice-cold IP buffer and resuspended in 98.97µL of Proteinase K digestion buffer (TE with 0.5% SDS). Following the addition of 1.25µL Proteinase K (20mg/mL; Qiagen, Hilden, Germany), samples were incubated in a thermomixer for 2 hours at 55˚C with a rotation speed of 1250rpm. The reaction was then allowed to cool at room temperature for 15 minutes. Supernatant was collected and bead cleanup was performed using equal volume SeraMag beads with 30% PEG. DNA was resuspended in 35µL of EB buffer (Qiagen, Hilden, Germany). Two parallel rounds of the following PCR amplification cycle conditions were performed on each sample in order to reduce PCR amplification bias. The reaction mixes were as follows: 15µL DNA, 27µL H2O, 12µL 5X HF buffer, 1.5µL DMSO, 1.0µL paired-end primer (Illumina), 0.5µL Phusion High-Fidelity DNA polymerase (New England Biolabs), 2µL indexing primer (Illumina – specific to each sample). The amplification cycle was as follows: 98˚C for 1 minute, 12X (98˚C for 15 seconds, 65˚C for 30 seconds, 72˚C for 30 seconds), 72˚C for 5 minutes. Reactions from the same sample were pooled and bead cleanup was performed using SeraMag beads in 20% PEG (102µL of beads per 120µL of reaction). DNA was resuspended in a final volume of 35µL of EB buffer.
Indexed meDIP libraries were pooled as part of a larger set of 60 samples, which were combined into 5 pools of 12 samples each. Samples were distributed evenly by sex, prenatal treatment, and tissue type. Next-generation sequencing was performed on the pools by the Genome Sciences Centre in Vancouver, BC, Canada. Each sample pool was run on one HiSeq lanes, which produced approximately 600,000,000 paired-end reads of 125 bases per lane.

treatment_protocol: Total RNA and DNA were simultaneously extracted from the prefrontal cortex on postnatal day 22 (n=5/group/sex; Qiagen AllPrep DNA/RNA Mini kit, Hilden, Germany). Frozen tissue was thawed on ice, quickly weighed and placed in lysis buffer for 5 minutes. Homogenization was performed by 5 strokes of an 18G needle, 10 strokes of a 20G needle, and 10 strokes of a 23G needle. The resulting homogenate was centrifuged at 21,000g for 3 minutes and the supernatant was collected for DNA and RNA extraction. White blood cells were thawed on ice and then centrifuged at 10,000g for 10 minutes. RNAlater was carefully removed without disturbing the cell pellet and cells were resuspended in lysis buffer. The cells were then frozen at -80˚C to disrupt cell membranes and then thawed on ice. The resulting homogenate was then used for DNA and RNA extraction. DNA concentration was assessed using Qubit Fluorometric Quantitation (Life Technologies, Carlsbad, USA).

value: Pair-fed (PF)

tag: dam (i.e., litter)

value: postnatal day 22

value: Prefrontal cortex

value: Sprague-Dawley

value: TGACCA


title: Mouse cTEC lacking HOIL - replicate 2

tag: gender


title: Mouse HSC-derived CAF from Panc02 liver metastasis model [RS031]

description:
RS031
scRNA-seq (10x) on fresh isolated cancer-associated-fibroblasts from mouse YAP/AKT-induced ICC.

value: COL1A1-GFP+CAF-enriched cell fraction


title: Mouse HSC-derived CAF from CMT93 liver metastasis model [RSB64]

description:
RSB64
CAF from metastasis model CMT93.
tpm_values_genes_kallisto.txt

extract_protocol:
HSC,CAF and whole tumor specimens were obtained perfusing and digesting the liver, followed by FACS sorting.
Constructed libraries using Illumina TruSeq RNA Preparation Kit according to the manufacturer’s instructions.

value: HSC-CAF


title: Mouse cTEC lacking HOIL - replicate 1

value: HOIL knok-out


title: AICAR LCFA + GW0742 rep 2

description: Sample 86

value: PSC-derived cardiomyocyte

value: AICAR LCFA + GW0742

value: 28 days


title: AICAR LCFA + GW0742 rep 3

description: Sample 87


title: Mouse HSC-derived CAF from CMT93 liver metastasis model [RSB63]

description:
RSB63
CAF from metastasis model CMT93.
tpm_values_genes_kallisto.txt


title: EHT Control rep 2

description: Sample 89


title: PF24_M

value: Male

value: ACCGGC


title: PF27_M

value: ATAATT


title: AICAR LCFA + GW0742 rep 1

description: Sample 85


title: PF26_M

value: ATACGG


title: EHT Control rep 1

description: Sample 88

value: Control


title: NOS_negative_expressing_fibroblasts_1

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

description: Cells were transduced with the EOS C3+ Oct4 lentiviral vector and fluorescence-activated cell sorted based on GFP expression.

hyb_protocol: According to manufacturer's protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

scan_protocol: The microarray was scanned for fluorescence (GeneChip Scanner 3000 7G, Affymetrix) using the GeneChip Operating software 1.0 (GCOS, Affymetrix).

data_processing: Expression values were calculated using an invariant set normalization method using Dchip (https://sites.google.com/site/dchipsoft/).

label: Biotin

source_name: Adult dermal fibroblasts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from amplified total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using the Norgen Total RNA Purification Kit as per manufacturer's instructions (http://www.norgenbiotek.com/).

value: female

value: normal breast skin

value: Human fibroblasts lacking NOS-expression


title: NOS_positive_expression_fibroblasts_1

hyb_protocol: According to the manufacturer's protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from amplified total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using the Norgen Total RNA Purification Kit as per manufacturer's instructions (http://www.norgenbiotek.com).

value: NOS (Nanog, OCT4, Sox2)-expressing human fibroblasts


title: Total_human_fibroblasts

description: Bulk cultures from human dermal fibroblasts from breast.

data_processing: Expression values were calculated using an invariant set normalization method using Dchip (https://sites.google.com/site/dchipsoft).

value: Adult human dermal fibroblasts from breast


title: E9_M

source_name: Prefrontal cortex, postnatal day 22, Prenatal alcohol exposed (PAE)

value: Prenatal alcohol exposed (PAE)

value: postnatal day 22

value: Prefrontal cortex

value: Sprague-Dawley

value: TATAAT


title: NOS_positive_expression_fibroblasts_2


title: NOS_negative_expressing_fibroblasts_2


title: Mouse HSC-derived CAF from KPCY liver metastasis model [RSB61]

description:
RSB61
CAF from metastasis model KPCY.
tpm_values_genes_kallisto.txt

value: C57BL/6, LratCre+, TdTom+, Col1a1-GFP

value: Liver metastasis by intra-splenic injection

value: HSC-CAF


title: PF22_M

value: Pair-fed (PF)

value: Male

value: GCAAGG


title: NPCG_DMDR_INPUT

city: Dallas

first: Joseph

middle: S

last: Takahashi

address: 5323 Harry Hines Blvd., NA4.118

department: HHMI, Neuroscience

institute: University of Texas Southwestern Medical Center

description: genomic DNA

data_processing:
Illumina bcl2fastq version 2.17 for base calling and demultiplexing.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2
Uniquely mapped reads were selected by Samtools v1.5
Subsampled to the minimum uniquely mapped read number and duplicates were removed (the final BED file)
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were made from Uniquely mapped duplicate-removed bed files.

source_name: The mouse liver

extract_protocol:
Lysates were clarified from sonicated nuclei and Cry1-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions with regular barcodes.

value: 11 weeks of age

value: liver

tag: time

tag: chip antibody

value: none (input)


title: Mouse HSC-derived CAF from KPCY liver metastasis model [RSB60]

description:
RSB60
CAF from metastasis model KPCY.
tpm_values_genes_kallisto.txt

tag: strain


title: NPCG_DRB_04hr

description: CRY1-bound genomic DNA

value: 4 hr

value: Cry1 (lab made antibody, Koike et al., 2012, Science)


title: E3_M

value: AGCGCT


title: Mouse HSC-derived CAF from KPCY liver metastasis model [RSB62]

description:
RSB62
CAF from metastasis model KPCY.
tpm_values_genes_kallisto.txt


title: AICAR LCFA rep 2

description: Sample 83

value: PSC-derived cardiomyocyte

value: AICAR LCFA

value: 28 days

tag: cell line


title: Mouse HSC-derived CAF from Panc02 liver metastasis model [RSB59]

description:
RSB59
CAF from metastasis model Panc02.
tpm_values_genes_kallisto.txt


title: AICAR GW0742 rep 3

description: Sample 81

value: AICAR GW0742


title: 18P_AACTGGCCGTC

city: Rensselaer

last: Boles

source_name: meninges

value: Posterior meninges

value: 18 months


title: NPCG_DMSO_00hr

description: CRY1-bound genomic DNA

value: 0 hr


title: C46_M

source_name: Prefrontal cortex, postnatal day 22, Control

value: Control

value: postnatal day 22

value: Prefrontal cortex

value: Sprague-Dawley

tag: Sex

value: CAACTA


title: Mouse HSC-derived CAF from Panc02 liver metastasis model [RSB57]

description:
RSB57
CAF from metastasis model Panc02.
tpm_values_genes_kallisto.txt

value: C57BL/6, LratCre+, TdTom+, Col1a1-GFP

value: Liver metastasis by intra-splenic injection

tag: cell type

value: HSC-CAF


title: Quiescent mouse HSC [RSB12A]

description:
RSB12A
Ultra-pure HSC.
tpm_values_genes_kallisto.txt

value: C57BL/6, LratCre+, TdTom+

value: HSC


title: C45_M

value: Male

value: AAACAT


title: Tcf7 knock-out natural killer thymic cells replicate 2

first: Alexandra

last: Garnham

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the human genome by Rsubread version 1.22.2
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files wre written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

growth_protocol: Thymi were collected and single-cell suspensions were generated by forcing organs through 70 μm sieves. TCRbeta-CD3-CD8-CD1dtetramer-NK1.1+NKp46+ cells were sorted using a FACS Aria III machine from BD Biosciences.

extract_protocol:
Cells were lysed and RNA purified using a Qiagen Rneasy Micro Plus kit.
Total RNA were prepared and indexed separately for illumina sequencing using the SMART-Seq v4 Ultra Low Input RNA Kit as per manufacturer’s instructions. The indexed libraries were pooled and diluted to 1.5pM for paired end sequencing on a NextSeq instrument using the v2 150 cycle High Output kit (illumina) as per manufacturer’s instructions.

tag: strain background

tag: genotype/variation

value: Tcf7 knock-out

value: female

value: thymus

value: natural killer thymic cells


title: NPCG_DRB_02hr

description: CRY1-bound genomic DNA

value: 11 weeks of age

tag: tissue

value: liver

value: 2 hr

value: Cry1 (lab made antibody, Koike et al., 2012, Science)


title: AICAR LCFA rep 3

description: Sample 84

value: PSC-derived cardiomyocyte

tag: treatment

value: AICAR LCFA

tag: treatment duration

value: 28 days


title: C43_M

value: Control

value: postnatal day 22

value: Prefrontal cortex

value: Sprague-Dawley

value: TAATCG


title: NPCG_DRB_00hr

description: CRY1-bound genomic DNA

value: 0 hr


title: AICAR rep 2

description: Sample 77

value: AICAR


title: AICAR GW0742 rep 2

description: Sample 80

value: AICAR GW0742


title: E2_M

value: Prenatal alcohol exposed (PAE)

value: Male

value: GCCTTA


title: NPCG_DMSO_04hr

description: CRY1-bound genomic DNA

value: 11 weeks of age

value: liver

value: 4 hr


title: AICAR LCFA rep 1

description: Sample 82

value: PSC-derived cardiomyocyte


title: C41_M

value: CCGTCC


title: Mouse HSC-derived CAF from Panc02 liver metastasis model [RSB58]

description:
RSB58
CAF from metastasis model Panc02.
tpm_values_genes_kallisto.txt

value: C57BL/6, LratCre+, TdTom+, Col1a1-GFP

value: Liver metastasis by intra-splenic injection

value: HSC-CAF


title: E6_M

value: postnatal day 22

value: Prefrontal cortex

value: CGATGT


title: NPCG_DMSO_02hr

description: CRY1-bound genomic DNA

value: 2 hr

value: Cry1 (lab made antibody, Koike et al., 2012, Science)


title: E1_M

value: Sprague-Dawley

value: GGCTAC


title: AICAR GW0742 rep 1

description: Sample 79

value: AICAR GW0742

value: 28 days


title: Lactate LCFA + GW0742 rep 3

description: Sample 75

value: Lactate LCFA + GW0742


title: Tcf7 knock-out natural killer thymic cells replicate 1

value: Tcf7 knock-out

value: male

value: thymus

value: natural killer thymic cells


title: MLL-AF9-i139_DOX_clone_1

city: Rotterdam

first: Stefan

middle: J.

last: Erkeland

state: Zuid-Holland

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus University Medical Center

description:
RNA-seq of MLL-AF9-transformed HSPC-enriched bonemarrow cells transduced with inducible miR-139 vector
MLL_AF9_Clone3_DOX_GFP
The file str-ReadCount.tab includes samples from GSE160404.

data_processing:
After sequencing and demultiplexing, the quality of the reads was determined with fastQC(v 0.11.8).
Fastq files were mapped to the reference GRCm38 using STAR (v.2.5.3e).
The annotation was done with FeatureCounts (v1.6.0) using genecodevM15.annotation.gtf as a reference.
The quality of the data was assessed with MultiQC.
Noise reduction was applied to the count data by removing the rows with read counts lower than 10.
Next, rlog transformation was used for visualization and comparison purposes which include correlation and clustering analysis generating the heatmaps and PCA plots.
For differential expression analysis, DESeq2(v1.22.2) was used.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimeted text file containing raw RNA counts per gene

source_name: Bone marrow cells

growth_protocol: HSPCs were isolated from femur and tibiae from WT C57BL/6 mice (8 – 20 wks) using the BD Mouse Hematopoietic Progenitor (Stem) Cell  Enrichment Set (cat 558451, Becton Dickinson). Cells were expanded in StemPro-34 SFM (Thermo Fisher Scientific, 10639011) supplemented with Interleukin (IL)-3 (1:1000 supernatant), IL-6 (10 ng/mL; SRP3330 Sigma Aldrich), Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) (10 ng/mL; CYT-222, Prospec Ltd) and Stem Cell Factor (SCF) (20 ng/mL; 5223SF, Cell Signaling Technology) and Penicillin-Streptomycin (P/S) (100U/mL; 15140163, Thermo Fisher Scientific) overnight, followed by retroviral transduction with pMSCV-MLL-AF9-neo or pMSCV-MLL-AF9-puro (Wong et al., 2007) with RetroNectin (T100A, Takara) according to manufacturer’s  protocol. Transduced cells were selected on Neomycin (800µg/mL; 10131035, Thermo Fisher Scientific) or Puromycin. After at least two re-platings in MethoCult (M3231, Stem Cell Technologies), MLL-AF9 cells were further expanded in Iscove’s Modified Dulbecco’ Media (IMDM) (12440053, Thermo Fisher Scientific), supplemented with P/S (100 U/mL), FBS (10%) (S181G-500, Biowest), IL-3 (1:1000 supernatant), IL-6 (10 ng/mL), GM-CSF (10 ng/mL) and SCF (20 ng/mL). Subsequently, MLL-AF9 cells were retrovirally transduced with pBabe-tetR-KRAB-Hygro (Kumar et al., 2008) with RetroNectin according to manufacturer’s protocol and selected on Hygromicin B (0,8 mg/mL; 10687010, Thermo Fisher Scientific) for two weeks. Finally, selected cells were lentivirally transduced with pCW-miR-139 by spinfection and incubated for 24 hours in expansion medium and plated in MetchoCult with Puromycin (1 µg/mL; P8833, Sigma Aldrich). To generate MLL-AF9-i139 cells, colonies were picked and further expanded for experiments.

extract_protocol:
Total RNA was isolated with TRIzol, according to the manufacturer’s protocol. The quality of the was analyzed with the Bioanalyzer RNA 6000 Nano Kit (5067-1511, Agilent).
Libraries were generated with 500ng of RNA using the KAPA RNA HyperPrep Kit with RiboErase (KK8560, Roche) according to manufacturer’s protocol. Quality control of the libraries was performed with the Bioanalyzer High Sensitivity DNA kit (5067-4626, Agilent Technologies). Library quantity was determined with NEBNext Library Quant Kit (E6730, New England Biolabs). Libraries were run on the NovaSeq (Illumina).

treatment_protocol: MLL-AF9 cells were retrovirally transduced with pBabe-tetR-KRAB-Hygro (Kumar et al., 2008) with RetroNectin according to manufacturer’s protocol and selected on Hygromicin B (0,8 mg/mL; 10687010, Thermo Fisher Scientific) for two weeks. Finally, selected cells were lentivirally transduced with pCW-miR-139 by spinfection and incubated for 24 hours in expansion medium and plated in MetchoCult with Puromycin (1 µg/mL; P8833, Sigma Aldrich). To generate MLL-AF9-i139 cells, colonies were picked and further expanded for experiments. MLL-AF9-i139-clone 1 and 2 were treated with 5µg/mL DOX for 48 hours, while clone 3 was treated with DOX for 72 hours. MLL-AF9-ieGFP was treated for 48 and 72 hours for comparison reasons.

tag: background strain

tag: dox status

value: with Dox


title: Lactate LCFA + GW0742 rep 2

description: Sample 74

value: PSC-derived cardiomyocyte


title: MLL-AF9-ieGFP_DOX_clone_1_72h

description:
RNA-seq of MLL-AF9-transformed HSPC-enriched bonemarrow cells transduced with inducible eGFP vector
MLL_AF9_Clone7_DOX_GFP2
The file str-ReadCount.tab includes samples from GSE160404.


title: AICAR rep 3

description: Sample 78

value: AICAR


title: C44_M

value: Control

tag: age

value: postnatal day 22

value: Male

value: GAGTGG


title: MLL-AF9-ieGFP_noDox_clone_1_72h

description:
RNA-seq of MLL-AF9-transformed HSPC-enriched bonemarrow cells transduced with inducible eGFP vector
MLL_AF9_Clone7_noDOX_GFP2
The file str-ReadCount.tab includes samples from GSE160404.

value: no Dox


title: Wild type natural killer thymic cells replicate 4

source_name: Wild type natural killer thymic cells

value: wild type

value: female


title: MLL-AF9-ieGFP_DOX_clone_1_48h

description:
RNA-seq of MLL-AF9-transformed HSPC-enriched bonemarrow cells transduced with inducible eGFP vector
MLL_AF9_Clone7_DOX_GFP1
The file str-ReadCount.tab includes samples from GSE160404.


title: MLL-AF9-i139_DOX_clone_3

description:
RNA-seq of MLL-AF9-transformed HSPC-enriched bonemarrow cells transduced with inducible miR-139 vector
MLL_AF9_Clone10_DOX_GFP
The file str-ReadCount.tab includes samples from GSE160404.


title: PF26_F

value: Pair-fed (PF)

value: Prefrontal cortex

value: Sprague-Dawley

value: Female

value: TAGCTT


title: MLL-AF9-i139_noDox_clone_3

description:
RNA-seq of MLL-AF9-transformed HSPC-enriched bonemarrow cells transduced with inducible miR-139 vector
MLL_AF9_Clone10_noDOX_GFP
The file str-ReadCount.tab includes samples from GSE160404.


title: PF22_F

value: TGCTGG


title: Lactate LCFA rep 2

description: Sample 71

value: Lactate LCFA

value: 28 days


title: MLL-AF9-i139_noDox_clone_2

description:
RNA-seq of MLL-AF9-transformed HSPC-enriched bonemarrow cells transduced with inducible miR-139 vector
MLL_AF9_Clone9_noDOX_GFP
The file str-ReadCount.tab includes samples from GSE160404.


title: Wild type natural killer spleen cells replicate 1

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the human genome by Rsubread version 1.16.1
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files wre written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: Wild type natural killer spleen cells

growth_protocol: Spleens were collected and single-cell suspensions were generated by forcing organs through 70 μm sieves. TCRbeta-NK1.1+NKp46+CD11b+KLRG1+ cells were sorted using a FACS Aria III machine from BD Biosciences.

extract_protocol:
Cells were lysed and RNA purified using a Qiagen Rneasy Micro Plus kit.
An input of 200ng of total RNA were prepared and indexed separately for illumina sequencing using the TruSeq RNA sample Prep Kit (illumina) as per manufacturer’s instruction.  Each library was quantified using the Agilent Tapestation and the Qubit™ DNA BR assay kit for Qubit 3.0® Fluorometer (Life technologies).  The indexed libraries were pooled and diluted to 1.5pM for paired end sequencing on a NextSeq instrument using the v2 150 cycle High Output kit (illumina) as per manufacturer’s instructions.

value: Spleen

value: natural killer spleen cells


title: AICAR rep 1

description: Sample 76

value: PSC-derived cardiomyocyte

value: AICAR


title: MLL-AF9-i139_DOX_clone_2

description:
RNA-seq of MLL-AF9-transformed HSPC-enriched bonemarrow cells transduced with inducible miR-139 vector
MLL_AF9_Clone9_DOX_GFP
The file str-ReadCount.tab includes samples from GSE160404.

value: with Dox


title: PF28_F

value: postnatal day 22

value: TACAGC


title: Wild type natural killer thymic cells replicate 2

value: wild type

value: thymus

value: natural killer thymic cells


title: Wild type natural killer thymic cells replicate 1

value: male


title: MLL-AF9-i139_noDox_clone_1

description:
RNA-seq of MLL-AF9-transformed HSPC-enriched bonemarrow cells transduced with inducible miR-139 vector
MLL_AF9_Clone3_noDOX_GFP
The file str-ReadCount.tab includes samples from GSE160404.

value: no Dox


title: Wild type natural killer thymic cells replicate 3


title: Tcf7 knock-out nature killer spleen cells replicate 2

value: Tcf7 knock-out


title: Tcf7 knock-out double negative 3 thymocytes replicate 1

growth_protocol: Thymi were collected and single-cell suspensions were generated by forcing organs through 70 μm sieves. TCRbeta-CD3-CD8-CD1dtetramer-NK1.1-CD44-CD25+ cells were sorted using a FACS Aria III machine from BD Biosciences.


title: MLL-AF9-ieGFP_noDox_clone_1_48h

description:
RNA-seq of MLL-AF9-transformed HSPC-enriched bonemarrow cells transduced with inducible eGFP vector
MLL_AF9_Clone7_noDOX_GFP1
The file str-ReadCount.tab includes samples from GSE160404.


title: PF27_F

value: Pair-fed (PF)

value: Prefrontal cortex

value: Sprague-Dawley

value: Female

value: ACAGTG


title: E6_F

value: Prenatal alcohol exposed (PAE)

value: CAAAAG


title: Lactate GW0742 rep 3

description: Sample 69

value: PSC-derived cardiomyocyte

value: Lactate GW0742

value: 28 days


title: Lactate LCFA + GW0742 rep 1

description: Sample 73

value: Lactate LCFA + GW0742


title: PF24_F

value: postnatal day 22

value: CTCAGA


title: MLL-AF9_6

description:
RNA-seq of MLL-AF9-transformed WT HSPC-enriched bone marrow cells
MLL_AF9_WT_PURO3
The file str-ReadCount.tab includes samples from GSE160405.

growth_protocol: HSPCs were isolated from femur and tibiae from WT or Mir139KO C57BL/6 mice (8 – 20 wks) using the BD Mouse Hematopoietic Progenitor (Stem) Cell  Enrichment Set (cat 558451, Becton Dickinson). Cells were immediately resuspended in TRIzol or HPSCs were expanded in StemPro-34 SFM (Thermo Fisher Scientific, 10639011) supplemented with Interleukin (IL)-3 (1:1000 supernatant), IL-6 (10 ng/mL; SRP3330 Sigma Aldrich), Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) (10 ng/mL; CYT-222, Prospec Ltd) and Stem Cell Factor (SCF) (20 ng/mL; 5223SF, Cell Signaling Technology) and Penicillin-Streptomycin (P/S) (100U/mL; 15140163, Thermo Fisher Scientific) overnight, followed by retroviral transduction with pMSCV-MLL-AF9-neo or pMSCV-MLL-AF9-puro (Wong et al., 2007) with RetroNectin (T100A, Takara) according to manufacturer’s  protocol. Transduced cells were selected on Neomycin (800µg/mL; 10131035, Thermo Fisher Scientific) or Puromycin. After at least two re-platings in MethoCult (M3231, Stem Cell Technologies), MLL-AF9 cells were resuspended in TRIzol.

treatment_protocol: WT HSPCs were cultured overnight, followed by retroviral transduction with pMSCV-MLL-AF9-neo or pMSCV-MLL-AF9-puro (Wong et al., 2007) with RetroNectin (T100A, Takara) according to manufacturer’s  protocol. Transduced cells were selected on Neomycin (800µg/mL; 10131035, Thermo Fisher Scientific) or Puromycin. After at least two re-platings in MethoCult (M3231, Stem Cell Technologies), MLL-AF9 cells were resuspended in TRIzol.

value: MLL-AF9-transformed HSPC-enriched bonemarrow cells

tag: genotype

value: WT

tag: retroviral transduction


title: Tcf7 knock-out nature killer spleen cells replicate 1

value: Spleen

value: natural killer spleen cells


title: Lactate LCFA rep 3

description: Sample 72

value: Lactate LCFA


title: Wild type natural killer spleen cells replicate 2

value: wild type


title: E2_F

tag: dam (i.e., litter)

value: Prefrontal cortex

value: Sprague-Dawley

value: AAGGAC


title: MLL-AF9_5

description:
RNA-seq of MLL-AF9-transformed WT HSPC-enriched bone marrow cells
MLL_AF9_WT_PURO2
The file str-ReadCount.tab includes samples from GSE160405.


title: Wild type double negative 3 thymocytes replicate 3

source_name: Wild type double negative 3 thymocytes

tag: gender

value: female

value: thymus


title: Lactate LCFA rep 1

description: Sample 70

source_name: cardiomyocyte

value: PSC-derived cardiomyocyte


title: Tcf7 knock-out double negative 3 thymocytes replicate 2

value: Tcf7 knock-out


title: Wild type double negative 3 thymocytes replicate 2


title: E9_F

value: Prenatal alcohol exposed (PAE)

value: Female

value: AAGACT


title: Wild type double negative 3 thymocytes replicate 1


title: E3_F

value: postnatal day 22

value: TCCCGA


title: MLL-AF9_2

description:
RNA-seq of MLL-AF9-transformed WT HSPC-enriched bone marrow cells
MLL_AF9_WT_NEO2
The file str-ReadCount.tab includes samples from GSE160405.

value: MLL-AF9-transformed HSPC-enriched bonemarrow cells

value: WT


title: C45_F

value: Control

value: CTGCTG


title: Lactate Control rep 1

description: Sample 64

value: Lactate Control

value: 28 days


title: Lactate GW0742 rep 1

description: Sample 67

value: Lactate GW0742


title: Wild type double negative 3 thymocytes replicate 4

value: wild type

value: male


title: high LCFA + GW0742 rep 3

description: Sample 63

value: high LCFA + GW0742


title: MLL-AF9_4

description:
RNA-seq of MLL-AF9-transformed WT HSPC-enriched bone marrow cells
MLL_AF9_WT_PURO1
The file str-ReadCount.tab includes samples from GSE160405.


title: Lactate GW0742 rep 2

description: Sample 68

value: PSC-derived cardiomyocyte


title: Lactate Control rep 3

description: Sample 66


title: C46_F

value: Prefrontal cortex

value: Sprague-Dawley

value: TGAATG


title: E1_F

value: Prenatal alcohol exposed (PAE)

value: Female

value: CCACGC


title: MLL-AF9_1

description:
RNA-seq of MLL-AF9-transformed WT HSPC-enriched bone marrow cells
MLL_AF9_WT_NEO1
The file str-ReadCount.tab includes samples from GSE160405.

value: MLL-AF9-transformed HSPC-enriched bonemarrow cells


title: Lactate Control rep 2

description: Sample 65