title: FFC_3

value: FFC

value: Diet-induced NASH


title: F12-1001000357-TPO_AB-1

status: Public on Feb 01 2021

type: SRA

city: Stanford

first: Gerlinde

last: Wernig

state: CA

address: 265 Campus Drive

department: Pathology

country: USA

institute: Institute for Regenerative Medicine and Stem Cell Research, Stanford University School of Medicine

description: Single cell from HSC

library_source: transcriptomic

data_processing:
Sequencing reads were trimmed, adapter sequences removed and the reads aligned using STAR with default parameters.
Duplicate reads were removed using picard. Transcript counts were obtained using HT-Seq and hg19 UCSC exon/transcript annotations.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: CD34+ CD38- CD90+ CD45RA- HSC

growth_protocol: Human bone marrows were obtained from Stanford Medical Center with informed consent, according to Institutional Review Board (IRB)-approved protocols (Stanford IRB 39881). CD34+ progenitors from each sample were isolated by Ficoll separation and CD34+ progenitors were isolated by a positive selection using an immunomagnetic cell sorting system (AutoMacs; Miltenyi Biotec,Bergisch Gladbach, Germany). 56,000 cells were incubated in IMDM media supplemented with 10% BSA, 1% L-glutamine, 450 µM MTG, 1% ITG, liposomes (composition and concentration???), 1% penicillin/streptomycin, in the presence SCF 20 ng/ml and different diabodies at 100 nM for 12 days, with change medium every other day, and addition of new cytokines 3 times per day. After 12 days, cells were pelleted and resuspended in PBS 2% FCS. Fc block was performed for 20 min and the mononuclear cells were stained with directly conjugated anti-mouse CD34, CD38, CD45RA, CD90 and HSC were isolated as DAPI-CD34+CD38-CD45RA-CD90+ cells on a BD FACS ARIA sorter.

extract_protocol:
Single-cells were collected  in lysis buffer in 96-well plates, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analyzed on an automated Fragment Analyzer (Advanced Analytical).
Each cells cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (FC-131-1024; Illumina) according to the manufacturers instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq instrument.

treatment_protocol: CD34+ Bone Marrow derived cells were culture in IMDM media supplemented with 10% BSA, 1% L-glutamine, 450 µM MTG, 1% ITG, liposomes (composition and concentration???), 1% penicillin/streptomycin for 12 days. In all conditions 20 ng/ml SCF was added. Additional conditions receive 100 nM of TPO or different agonist or antagonist, with or without 14 µg/ml of TPO blocking antibody. Media was changed every other day and cytokines were added 3 times per day.

tag: cell type

value: HSC

tag: treatment

tag: days in culture

tag: date sequencing


title: FFC_2

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat (https://ccb.jhu.edu/software/tophat/index.shtml)
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes Raw counts and FPKM values for each gene per sample

organism: Mus musculus

source_name: mouse liver RNA

extract_protocol:
Liver total RNA was extracted using RNeasy-Mini kit (Qiagen) according to manufacturer's instruction.
RNA libraries were prepared using 200 ng of total RNA according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina).
The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip and Qubit fluorometry.

treatment_protocol: Eight-week-old C57BL/6J mice were fed either chow or a diet rich in fat, fructose, and cholesterol (FFC) for 30 weeks. Liver was harvested for RNA extraction.

tag: strain

tag: tissue

value: liver

tag: treatment group

tag: disease state


title: MOO2450A35: Rat 89

city: London

first: Lawrence

middle: DF

last: Moon

address: 16 - 18 Newcomen Street

department: Wolfson Centre for Age-Related Diseases

country: United Kingdom

institute: King's College London

data_processing:
Basecalling was performed with Illumina's bcl2fastq v1.8.4
Read quality and potential sequencing biases were assessed using custom scripts for quality control of the raw sequencing data
The 50bp paired-end reads were aligned to the reference genome (Rattus Norvegicus rn6) using TopHat2 with default parameters (except for setting mate-inner-dist=100 and mate-std-dev=50
Duplicate reads were identified using Picard tools MarkDuplicates and the highest quality read at each position was retained
Reads mapping to each gene feature were counted using htseq-count to create a raw gene count table (RefSeq annotations)
Genome_build: Rnor_6.0 for mRNA
Supplementary_files_format_and_content: counts per million for each sample; dedup.gene_counts files involve data where duplicate reads (those mapping to identical positions) were removed.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: C6-8 dorsal root ganglia

extract_protocol:
Total RNA for RNA sequencing was extracted from C6-C8 DRGs on the affected side for each rat. Tissue was homogenized in QIAZOL (Qiagen, 79306) and nucleic acids were separated in Phase Locked Gel columns (5Prime, 230 2830). 1.5 volume of 100% ethanol was added to the aqueous phase and transferred to filtered spin columns from the RNA extraction kit (miRNeasy kit, Qiagen, 217004) and we proceeded according to manufacturer's instructions. Samples were also DNase I treated with double volume of the recommended amount (Qiagen, 79254). We estimated the total RNA quality and quantity by spectrophotometry (NanoDrop, ND-1000) and measured the RIN scores (Agilent RNA 6000 Nano Reagents Part I and Agilent 2100 Bioanalyzer). The integrity number for each sample was greater than 7.6, with an average of 8.
The samples were subjected to poly-A enrichment with oligo-dT beads (Illumina) and the library was prepared using the TruSeq Stranded prep kit (Illumina)

value: Lister Hooded rats

value: C6-8 dorsal root ganglia

tag: week

tag: group

value: E


title: MOO2450A34: Rat 85

value: B


title: kidney_diabets_rep2 [E9; re-analysis]

type: RNA

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

country: China

institute: Peking Union Medical College Hospital

description: gene expression data from kidney of diabetic rat

hyb_protocol: The sample preparation and hybridation of each cDNAs on Affymetrix GeneChip® Mouse Gene 2.0 ST arrays based on manufacturer's instruction.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 Affymetrix)

data_processing: All arrays were uploaded into Genespring v12.5 (Agilent Tchnologies, USA) for data normalization, quality control and first-pass analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for differentially regulated genes was a fold change>1.5 and a P value<0.05.

label: biotin

source_name: diabetic, 17 weeks

label_protocol: biotin

extract_protocol: Total tissue RNA was extracted using total RNA Isolation Kit (mirVanaTM, ABI).

tag: strain background

value: Sprague Dawley

tag: age

value: 17 week

value: kidney


title: kidney_diabets_rep3 [H9; re-analysis]


title: MOO2450A33: Rat 83


title: E11-1001000355-AK113-1

description: Single cell from HSC


title: FFC_1


title: C11-1001000357-TPO_AB-1

description: Single cell from HSC


title: kidney_Qishen Yiqi Dripping Pill-treated_rep2 [F9]

description: gene expression data from kidney of Qishen Yiqi Dripping Pill-treated rat

source_name: Qishen Yiqi Dripping Pill-treated rats, 17week

value: Qishen Yiqi Dripping Pill-treated


title: LSECs, FFC_4 (ATAC-seq)

description: Sample 8

library_source: genomic

data_processing:
ATAC-seq data were analyzed using the HiChIP pipeline developed by the Mayo Bioinformatics Core
Paired-end reads were mapped to the mm10 genome reference using Burrows-Wheeler Alignment tool (BWA) (27). Pairs of reads with one or both reads uniquely mapped were retained and duplicates removed using Picard MarkDuplicates command (http://broadinstitute.github.io/picard/).
Peaks were identified using the Model-based Analysis of ChIP-Seq (MACS2) software package at FDR <=1%
For data visualization, BEDTools in combination with in-house scripts were used to generate normalized tag density profiles at a window size of 200 bp and step size of 20 bp.
Raw read counts were normalized using the trimmed mean of M values (TMM) method.
Sample 1 was omitted from the analysis because of the low signal captured.
Genome_build: mm10
Supplementary_files_format_and_content: Peaks identified in bed format

molecule: genomic DNA

source_name: Liver sinusodial endothelial cells

growth_protocol: Cell suspension of collagenase-perfused mouse liver was centrifuged at 50g for 2 minutes to remove hepatocytes. The supernatant which includes non-parenchymal cells was subjected to LSEC isolation using CD146 MicroBeads (Miltenyi Biotec) .

extract_protocol:
About 50,000 cells were preserved in 100 μl anti-freezing buffer (10% DMSO, 10% FCS in RPMI-1640) and subjected to Omni-ATAC following the published protocol (PMID:  28846090).
The size of library DNA was determined from amplified and purified libraries by Fragment Analyzer 25 (Advanced Analytical Technologies; AATI; Ankeny, IA), and the enrichment of accessible region was determined by the fold difference between positive and  negative genomic loci using real-time PCR.
The libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq 4000 instrument.

treatment_protocol: Eight-week-old C57BL/6J mice were fed with either chow or FFC diet for 24 weeks to induce NASH.

value: Primary mouse liver sinusodial endothelial cells

value: FFC-fed mouse

value: NASH


title: MOO2450A32: Rat 82

value: A

value: Vehicle


title: kidney_diabets_rep1 [C9; re-analysis]


title: kidney_Qishen Yiqi Dripping Pill-treated_rep1 [D9]


title: MOO2450A31: Rat 81

value: F

value: Sham


title: B11-1001000357-TPO_AB-1

description: Single cell from HSC

value: HSC


title: MOO2450A28: Rat 69


title: MOO2450A29: Rat 71


title: LSECs, FFC_3 (ATAC-seq)

description: Sample 7


title: kidney_Qishen Yiqi Dripping Pill-treated_rep3 [D10]


title: MOO2450A30: Rat 74

value: C


title: MOO2450A26: Rat 63

value: Lister Hooded rats


title: LSECs, FFC_2 (ATAC-seq)

description: Sample 6


title: F3-1001000355-AK113-1

description: Single cell from HSC


title: E12-1001000357-TPO_AB-1

description: Single cell from HSC


title: LSECs, FFC_1 (ATAC-seq)

description: Sample 5


title: MOO2450A24: Rat 61

value: C6-8 dorsal root ganglia


title: MOO2450A25: Rat 62


title: H9-1001000356-TPO-1

description: Single cell from HSC

value: TPO


title: LSECs, Chow_4 (ATAC-seq)

description: Sample 4

value: Chow-fed mouse

value: control


title: G3-1001000355-AK113-1

description: Single cell from HSC


title: LSECs, Chow_3 (ATAC-seq)

description: Sample 3


title: C3-1001000355-AK113-1

description: Single cell from HSC


title: MOO2450A20: Rat 54


title: MOO2450A19: Rat 51


title: LSECs, Chow_2 (ATAC-seq)

description: Sample 2


title: MOO2450A17: Rat 42


title: D3-1001000355-AK113-1

description: Single cell from HSC


title: MOO2450A16: Rat 36

value: E


title: E3-1001000355-AK113-1

description: Single cell from HSC


title: B3-1001000355-AK113-1

description: Single cell from HSC


title: MOO2450A15: Rat 33

value: D


title: MOO2450A18: Rat 50


title: LSECs, FFC_4 (RNA-seq)

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR-2.6.1 aligner
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes Raw counts and RPKM values for each gene per sample

growth_protocol: Mouse livers were mechanically and enzymatically dissociated using Liver Dissociation Kit (Miltenyi Biotec). After a red blood cell lysis and a debris removal using kits supplied by Miltenyi Biotec, LSEC were isolated using CD146 MicroBeads (Miltenyi Biotec). Freshly isolated LSEC were immediately used for RNA extraction.

extract_protocol:
Liver total RNA was extracted using RNeasy-Mini kit (Qiagen) according to manufacturer's instruction.
RNA libraries were prepared using 200 ng of total RNA according to the manufacturer’s instruction for the TruSeq RNA Sample Prep Kit v2 (Illumina).
Libraries were sequenced at 53 million to 90 million reads per sample following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cells were sequenced as 100 × 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit and HCS v3.3.20 collection software.


title: MOO2450A13: Rat 25

value: B


title: MOO2450A12: Rat 17


title: A3-1001000355-AK113-1

description: Single cell from HSC


title: MOO2450A23: Rat 60


title: LSECs, FFC_2 (RNA-seq)

value: Primary mouse liver sinusodial endothelial cells


title: MOO2450A11: Rat 14


title: MOO2450A14: Rat 27


title: MOO2450A10: Rat 11


title: LSECs, Chow_1 (ATAC-seq)

description: Sample 1


title: MOO2450A22: Rat 57


title: MOO2450A21: Rat 56


title: F8-1001000356-TPO-1

description: Single cell from HSC


title: LSECs, FFC_1 (RNA-seq)

value: FFC-fed mouse


title: MOO2450A8: Rat 8


title: MOO2450A7: Rat 1


title: LSECs, Chow_4 (RNA-seq)


title: D5-1001000356-TPO-1

description: Single cell from HSC


title: LSECs, FFC_3 (RNA-seq)

value: NASH


title: LSECs, Chow_3 (RNA-seq)


title: LSECs, Chow_2 (RNA-seq)


title: C5-1001000356-TPO-1

description: Single cell from HSC


title: Ossabaw_Chimp_Olig2

city: Atlanta

first: Soojin

middle: V

last: Yi

state: GA

address: 950 Atlantic Dr

department: Biological Sciences

institute: Georgia Institute of Technology

data_processing:
Quality and adapter trimming was performed using TrimGalore version 0.4.1 (Babraham Institute).
Reads were mapped to the human GRCh37 reference genome using Bismark version: v0.14.4 (Krueger and Andrews 2011) and Bowtie2
Methylation calling was performed after deduplication using Bismark
Bsseq and DSS bioconductor packages were used to process DNA methylation data
Genome_build: Human hg19, Chimpanzee PanTro5, Rhesus Macaque RheMac8
Supplementary_files_format_and_content: Methylated read count and coverage for CpGs (bismark cytosine report format)

organism: Pan troglodytes

source_name: brain

extract_protocol:
Genomic DNA was isolated from 1mg to 5mg of tissue sample, using the Qiagen DNeasy Blood and Tissue DNA extraction kit according to manufacturer’s instructions. The extracted DNA was suspended in TE buffer and quantified by Qubit (Thermo Fisher Scientific).
Libraries were made with In-House Illumina sequencer compatible protocol. The extracted DNA was fragmented by S-series focused ultrasonicator (Covaris) using the “200bp-target peak size protocol”. Fragmented DNA was then size selected (200bp-600bp) with Agencourt aMPure XP bead-based (Beckman Coulter Cat. No. A63880) size selection protocol (Mark. A. Urich et al. 2015). The DNA End repair step was performed with End-It DNA end repair kit (Epicentre, Cat. No. ER81050. After End repair step, A-tailing (NEB, cat. No. M0202) and Ligation steps are performed to ligate methylated adaptors. Bisulfite treatment of genomic DNA was performed using the MethylCode Bisulfite Conversion Kit (Life technologies). Purified genomic DNA was treated with CT conversion reagent in a thermocycler for 10 minutes at 980C, followed by 2.5 hours at 640C. Bisulfite-treated DNA fragments remain Single-stranded as they are no longer complementary. Low-cycle (4-8) PCR amplification was performed with Kapa HiFi Uracil Hotstart polymerase enzyme (KAPA Biosystems, cat. No. KK2801) which can tolerate Uracil residues. The final library fragments contain Thymines and Cytosines in place of the original unmethylated cytosine and methylated cytosines, respectively.

value: brain

tag: nuclei

tag: tissue preparation

value: Frozen Brain Tissue

tag: region

value: Brodmann Area 46

tag: gender

value: M

tag: pmi

tag: bisulfite conversion rate


title: Ossabaw_Chimp_NeuN

value: NeuN


title: B4-1001000356-TPO-1

description: Single cell from HSC

tag: cell type

value: HSC

tag: treatment


title: LSECs, Chow_1 (RNA-seq)


title: A11-1001000357-TPO_AB-1

description: Single cell from HSC

tag: days in culture

tag: date sequencing


title: Melissa_Chimp_Olig2

tag: tissue

value: F


title: Melissa_Chimp_NeuN


title: MOO2450A9: Rat 9

tag: strain

value: Lister Hooded rats

value: C6-8 dorsal root ganglia

value: A

value: Vehicle


title: A4-1001000356-TPO-1

description: Single cell from HSC

value: TPO


title: Iyk_Chimp_NeuN


title: H3-1001000355-AK113-1

description: Single cell from HSC


title: Iyk_Chimp_Olig2


title: Lulu_Chimp_NeuN


title: Duncan_Chimp_Olig2


title: E5-1001000356-TPO-1

description: Single cell from HSC


title: E8-1001000357-TPO_AB-1

description: Single cell from HSC


title: S15: Hypothalamus_Esr1cKO_Tamoxifen

city: Los Angeles

first: John

middle: Edward

last: van Veen

address: 610 Charles E young Dr

department: Integrative Biology and Physiology

institute: UCLA

data_processing:
Library strategy: scRNA-seq
Base calling: Illumina RTA2
genome alignment: Star 2.6
normalization: Seurat 3.6.1
integration: Seurat 3.6.1
clustering: Seurat 3.6.1
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are provided as demultiplexed read matrices with associated gene and barcode files

source_name: Hypothalamus

extract_protocol:
prepared single cell suspensions, EvaGreen droplet generation oil (BIO-RAD, Hercules, CA, USA), and ChemGenes barcoded microparticles (ChemGenes, Wilmington, MA, USA) containing unique molecular identifiers (UMIs) and cell barcodes were co-flowed through a FlowJEM aquapel-treated Drop-seq microfluidic device (FlowJEM, Toronto, Canada) at recommended flow speeds (oil: 15,000 μl/h, cells: 4000 μl/h, and beads 4000 μl/h). After breakage of the droplets, the beads were washed and suspended in reverse transcriptase solution.
Nextera DNA Library Preparation kit

value: CD-1;129P2 Esr1cKO

tag: injection

value: Tamoxifen

tag: Sex

value: Female

value: Hypothalamus


title: Roger_Chimp_Olig2


title: Duncan_Chimp_NeuN


title: S14: Hypothalamus_Esr1cKO_Oil

value: Oil


title: Roger_Chimp_NeuN

value: brain


title: Callie_Chimp_Olig2

value: Frozen Brain Tissue


title: D7-1001000357-TPO_AB-1

description: Single cell from HSC


title: Callie_Chimp_NeuN

value: Brodmann Area 46


title: S13: Hypothalamus_WT_Tamoxifen

value: CD-1;129P2 mixed (wild-type)


title: Bjorn_Chimp_Olig2

value: M


title: A6-1001000357-TPO_AB-1

description: Single cell from HSC

value: HSC


title: Lulu_Chimp_Olig2

value: F


title: Bjorn_Chimp_NeuN

value: NeuN


title: S12: Hypothalamus_Esr1cKO_Oil


title: S16: Hypothalamus_WT_Tamoxifen


title: C7-1001000357-TPO_AB-1

description: Single cell from HSC


title: Anja_Chimp_Olig2


title: Beleka_Chimp_Olig2


title: S11: Hypothalamus_Esr1cKO_Tamoxifen


title: G11-1001000355-AK113-1

description: Single cell from HSC


title: Anja_Chimp_NeuN


title: Abby_Chimp_Olig2


title: Beleka_Chimp_NeuN


title: S10: Hypothalamus_WT_Oil


title: Abby_Chimp_NeuN


title: F8-1001000357-TPO_AB-1

description: Single cell from HSC


title: S8: Hypothalamus_WT_Tamoxifen


title: S9: Hypothalamus_WT_Tamoxifen


title: C10-1001000357-TPO_AB-1

description: Single cell from HSC


title: S7: Hypothalamus_Esr1cKO_Oil


title: E11-1001000357-TPO_AB-1

description: Single cell from HSC


title: S6: Hypothalamus_Esr1cKO_Tamoxifen


title: B10-1001000357-TPO_AB-1

description: Single cell from HSC


title: D10-1001000357-TPO_AB-1

description: Single cell from HSC


title: A9-1001000357-TPO_AB-1

description: Single cell from HSC


title: S4: Hypothalamus_Esr1cKO_Oil


title: MOO2450A27: Rat 64

value: Lister Hooded rats

value: C6-8 dorsal root ganglia

tag: week

tag: group

value: C

value: Sham


title: S3: Hypothalamus_WT_Tamoxifen


title: S2: Hypothalamus_Esr1cKO_Tamoxifen

value: CD-1;129P2 Esr1cKO


title: F2-1001000355-AK113-1

description: Single cell from HSC


title: H8-1001000356-TPO-1

description: Single cell from HSC

value: TPO


title: S5: Hypothalamus_WT_Oil

value: Female


title: S1: Hypothalamus_WT_Oil

value: Hypothalamus


title: G2-1001000355-AK113-1

description: Single cell from HSC


title: C2-1001000355-AK113-1

description: Single cell from HSC


title: 4-Myc-cap-Oxali_aPDL1

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
generate feature-barcode matrice by cellranger v3.1.0
Genome_build: mm10-3.0.0

source_name: CD8+CD3+ tumor infiltrating cells

growth_protocol: 2-3 × 106 mouse cancer cells as indicated were s.c. injected into the right flank of male FVB mice. Tumors were measured every 2-3 days using a caliper.

extract_protocol:
Myc-CaP tumors were isolated, digested and tumor-infiltrating CD8+ T cells sorted for scRNA-seq using Chromium Single Cell 3’ Reagent Kit v3
Chromium Single Cell 3’ Reagent Kit v3

treatment_protocol: Oxaliplatin was diluted in 5% dextrose and i.p. injected weekly at 6 mg/kg as indicated. Anti-PD-L1 antibody was i.p. injected at 10 mg/kg weekly. Mice were treated for 3-4 weeks.

value: CD8+CD3+ tumor infiltrating cells

tag: xenograft

value: Myc-CaP

value: Oxaliplatin + aPDL1


title: B7-1001000357-TPO_AB-1

description: Single cell from HSC


title: 3-Myc-cap-Oxali

value: Oxaliplatin


title: D2-1001000355-AK113-1

description: Single cell from HSC


title: 2-Myc-cap-aPDL1


title: H3K4me2 LKO Input rep2

city: Irvine

first: QIN

last: YANG

address: 825 Health Science Rd.

department: Physiology and Biophysics

institute: University of California, Irvine

description: Liver from LSD1-LKO C57/BL6 mouse

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2.
Picardtools was used to remove PCR duplicates.
Peaks were called using MACS2
Biologically reproducible peaks are found using BEDtools v2.25.0 intersect.
Genome_build: mm10
Supplementary_files_format_and_content: Bed files, biologically reproducalbe peaks.

source_name: Liver

extract_protocol:
Liver tissue chromatin precipitation was performed using SimpleChip Plus Sonication Chromatin IP kit (Cell Signaling cat No. 56383) following manufacturer’s instructions.
Libraries were prepared from immunoprecipitated DNA according to Illumina's instraction and subjected to deep-sequencing using a HiSeq 2000 (Illumina).

treatment_protocol: Liver specific LSD1 knockout in adult mice.

value: Liver

tag: genotype/variation

tag: chip antibody


title: E2-1001000355-AK113-1

description: Single cell from HSC


title: H3K4me2 LKO ChIP rep2

description: Liver from LSD1-LKO C57/BL6 mouse

value: H3K4me2 (Abcam 7766)


title: H3K4me2 LKO Input rep1

description: Liver from LSD1-LKO C57/BL6 mouse


title: B2-1001000355-AK113-1

description: Single cell from HSC

value: HSC


title: 1-Myc-cap-ctrl

value: ctrl


title: KO_3_LPS_RNA_seq

city: Santa Cruz

first: Susan

last: Carpenter

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

data_processing:
All samples were sequenced together on an Illumina HiSeq system (paired-end 150bp), and sequencing reads were mapped to mm10 using STAR. For analysis of differential genes, STAR outputs were processed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: deseq output

source_name: bone marrow derived macrophages

growth_protocol: Mouse bone marrow-derived macrophages (BMDMs) were generated by culturing erythrocyte-depleted bone-marrow cells in DMEM medium supplemented with 10% FCS, 5 mL pen/strep (100X), 500μl ciprofloxacin (10mg/ml) and 10% L929 supernatant, with the replacement of culture medium every 2-3 days.

extract_protocol:
Total RNA was purified from BMDMs using Direct-zol RNA MiniPrep Kit (Zymo Research) and TRIzol reagent (Ambion) according to the manufacturer’s instructions.
Total RNA was used to generate libraries using a NEXTflex Rapid Directional RNA-Seq kit (Bioo Scientific, $5138-07) according to the manufacturer’s instructions. Samples were quality assessed using TapeStation (Agilent, Santa Clara, CA) and read on a High-Seq System (Illumina, San Diego, CA.

treatment_protocol: Wild-type or GAPLINC-deficient BMDMs were left untreated or stimulated with LPS (200 ng/mL) for 6h.

value: bone marrow derived macrophages

tag: genotype

value: LPS


title: H3K4me2 Con Input rep2

description: Liver from GFP control C57/BL6 mouse

value: GFP control


title: H3K4me2 Con ChIP rep2

description: Liver from GFP control C57/BL6 mouse


title: G8-1001000356-TPO-1

description: Single cell from HSC


title: A2-1001000355-AK113-1

description: Single cell from HSC


title: H3K4me2 Con Input rep1

description: Liver from GFP control C57/BL6 mouse


title: KO_2_LPS_RNA_seq


title: H3K4me2 Con ChIP rep1

description: Liver from GFP control C57/BL6 mouse


title: KO_1_LPS_RNA_seq


title: WT_3_LPS_RNA_seq

value: WT


title: LSD1 ChIP rep2

description: Liver from wild type C57/BL6 mouse

value: wild type


title: LSD1 Input rep 1

description: Liver from wild type C57/BL6 mouse


title: F7-1001000356-TPO-1

description: Single cell from HSC


title: LSD1 ChIP rep1

description: Liver from wild type C57/BL6 mouse


title: WT_2_LPS_RNA_seq


title: SID4X_TIS_3

city: Lewiston

first: Andrew

middle: John

last: Kennedy

state: ME

address: 5 Andrews Rd, Dana 322

department: Chemistry

institute: Bates College

data_processing:
Reads were trimmed with trimmomatic using recommended settings for paired end libraries, and adaptor sequences matching TruSeq3_PE were trimmed
These high-quality reads were aligned to the mm10 genome with hisat. Stringtie was used to incorporate any novel transcripts from these sequencing libraries into the mm10 Refseq annotation of known transcripts, and featurecounts attributed reads to the resulting custom annotation
EdgeR was used for determining fold change and false discovery rates (FDR) for each gene with sufficient read depth. Statistics in EdgeR were determined with genewise negative binomial generalized linear models with quasi-likelihood tests (glmQLFit function)
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts text file for all genes tested with featureCounts
Supplementary_files_format_and_content: One tab-delimited text file includes percent CpG methylation values for each 25 CpG window

source_name: Cultured Hippocampal Neurons

extract_protocol:
2 µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 8.0), and was prepared for directional, PolyA+ RNA sequencing at Hudson Alpha using NEBNext reagents (New England Biolabs) according to manufacturer's recommendations with minor modifications (including the use of custom library adapters and indexes).
An AllPrep DNA/RNA Mini Kit was used for experiments requiring genomic DNA and total RNA from the sample.

value: Cultured Hippocampal Neurons

tag: age

tag: isoform


title: LSD1 Input rep 2

description: Liver from wild type C57/BL6 mouse


title: C4-1001000356-TPO-1

description: Single cell from HSC

value: TPO


title: E4-1001000356-TPO-1

description: Single cell from HSC


title: SID4X_TIS_2


title: WT_1_LPS_RNA_seq


title: H3K4me2 LKO ChIP rep1

description: Liver from LSD1-LKO C57/BL6 mouse


title: SID4X_TIS_1


title: VP64_TIS_2


title: VP64_TIS_3


title: B3-1001000356-TPO-1

description: Single cell from HSC


title: KO_3_RNA_seq

value: no treatment


title: NFD_TIS_3


title: KO_2_RNA_seq


title: OA_04_PBMC_match

type: genomic

city: La Jolla

first: Gary

middle: S

last: Firestein

state: California

address: 9500 Gilman Dr

institute: UCSD

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Kit chip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: R package

label: Cy3 and Cy5

source_name: OA PBMC CD3+ T cells

label_protocol: Standard Illumina Protocol

extract_protocol: Tissue was disaggregated using liberase TL digestion as previously described. T cells were isolated using anti-CD3 conjugated magnetic bead separation (Stemcell Technology EasySep CD3 Positive Selection Kit).

treatment_protocol: Synovial tissue was obtained at the time of joint replacement surgery and, when feasible, matched blood was also obtained.

value: Joint


title: RA_02_PBMC_match

source_name: RA PBMC CD3+ T cells


title: H2-1001000355-AK113-1

description: Single cell from HSC


title: NFD_TIS_2


title: G10-1001000357-TPO_AB-1

description: Single cell from HSC


title: OA_05_PBMC_match


title: D4-1001000356-TPO-1

description: Single cell from HSC


title: SID4X_TIL_3


title: SID4X_TIL_2


title: WT_3_RNA_seq


title: E10-1001000357-TPO_AB-1

description: Single cell from HSC


title: OA_04_synovium

source_name: OA synovium CD3+ T cells


title: OA_05_synovium


title: RA_06A_synovium

source_name: RA synovium CD3+ T cells


title: OA_03_PBMC_match


title: OA_02_PBMC_match


title: RA_01_synovium


title: WT_2_RNA_seq


title: RA_03_PBMC_match


title: VP64_TIL_3


title: OA_01_PBMC_match


title: RA_07_synovium


title: VP64_TIL_2


title: RA_08_PBMC


title: RA_02_synovium


title: D9-1001000357-TPO_AB-1

description: Single cell from HSC


title: OA_01_synovium


title: BMDMs_3_RNA_seq

growth_protocol: Mouse bone marrow-derived macrophages (BMDMs) were generated by culturing erythrocyte-depleted bone-marrow cells in DMEM medium supplemented with 10% FCS, 5 mL pen/strep (100X), 500μl ciprofloxacin (10mg/ml) and 10% L929 supernatant for 7-12 days, with the replacement of culture medium every 2-3 days.

extract_protocol:
Total RNA was purified from bone marrow cells or BMDMs using Direct-zol RNA MiniPrep Kit (Zymo Research) and TRIzol reagent (Ambion) according to the manufacturer’s instructions.
Total RNA was used to generate libraries using a NEXTflex Rapid Directional RNA-Seq kit (Bioo Scientific, $5138-07) according to the manufacturer’s instructions. Samples were quality assessed using TapeStation (Agilent, Santa Clara, CA) and read on a High-Seq System (Illumina, San Diego, CA.

treatment_protocol: Bone marrow erythrocyte-depleted cells from each mouse were split into two fractions, 1) to be immediately harvested in Trizol for RNA isolation (Day 0), and 2) to be differentiated into BMDMs upon addition of 10% L929 in culture media until harvest (Day 8).


title: NFD_TIL_2


title: WT_1_RNA_seq


title: KO_1_RNA_seq


title: NFD_TIL_3


title: C9-1001000357-TPO_AB-1

description: Single cell from HSC


title: OA_02_synovium


title: VP64_TIL_1


title: BMDMs_2_RNA_seq


title: A8-1001000357-TPO_AB-1

description: Single cell from HSC


title: NFD_TIL_1


title: BMDMs_1_RNA_seq


title: SID4X_TIL_1


title: RA_01_PBMC_match


title: RA_03_synovium


title: RNA-seq of test group IV of breast muscle rep 2

city: Zhengzhou

first: Donghua

last: Li

state: China

address: Wenhua Road 95, Zhengzhou City

institute: Henan Agricultural University

description: the experimental group IV was the basic diet + biological grass

data_processing:
Raw reads was stored in the FASTQC format. Raw reads were processed to remove adaptor sequences, low-quality reads and reads containing ploy-N from raw data by Seqtk (https://github.com/lh3/seqtk)
Genome mapping of clean reads using the spliced mapping algorithm of TopHat (version: 2.0.9), mapped to the reference genome based on the Ensemble (Galgal5)
Counting the number of Fragments per gene after Hisat2 alignment using Stringtie(version:1.3.0)
Genome_build: gallus gallus (Galgal5)
Supplementary_files_format_and_content: normalized by TMM (trimmed mean of M values)

organism: Gallus gallus

source_name: breast muscle

extract_protocol:
a total of 2-4g the breast meat were frozen immediately in liquid nitrogen and stored at −80°C until for RNA-seq
The sequencing process is controlled by data collection software provided by Illumina HiSeq X-ten platform.

value: breast muscle

tag: Stage

value: 48 weeks

value: Gushi chickens


title: RNA-seq of test group IV of breast muscle rep 1


title: RNA-seq of test group IV of breast muscle rep 3


title: RA_05_synovium


title: RA_06_synovium


title: B9-1001000357-TPO_AB-1

description: Single cell from HSC

source_name: CD34+ CD38- CD90+ CD45RA- HSC

tag: cell type


title: shZc_LPS_S15751

city: Milano

first: Viviana

last: Piccolo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

data_processing:
After quality filtering according to the Illumina pipeline and after checking reads quality using FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), strand specific single end reads (51 bp and 76 bp) were aligned to the mm9  reference genomes (Illumina iGenomes reference downloaded from UCSC, http://support.illumina.com/sequencing/sequencing_software/igenome.html) using TopHat v2.1.0 1 (PMID:23618408), allowing up to two mismatches and using the option --b2-very- sensitive --library-type fr-firststrand.
Indels due to sequencing errors were identified using Bowtie2 v 2.2.6 (PMID: 19261174). Reads originating from the two strands were separated according to the XS:A:+/XS:A:-flag provided by TopHat2 (PMID:23618408).
SICER v2 (PMID: 24743992) was used to detect the extra-genic transcripts regulated in cells depleted of individual factors. The entire genome was partitioned into blocks of non-overlapping 500 bp windows with a gap size <1000 nt. An effective genome fraction of 1, a fragment size of 0 and a False Discovery Rate (FDR) cut-off <0.01 were used.
*.bigWig files were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975) (-bs 1 --normalizeUsing RPKM --outFileFormat bigwig -filterRNAstrand forward or --filterRNAstrand reverse)
Genome_build: mm10 (GENCODE) https://www.gencodegenes.org/mouse/release_M24.html
Supplementary_files_format_and_content: .bigWig strand specific tracks

source_name: 4sU-RNAseq, shZc3h4_2, LPS 45 min, BMDMs

growth_protocol: Primary bone marrow cells were cultured in DMEM containing 10% North American FBS,  1% L-Glutamax solution, 1% Pen/Strep solution, and 30 % conditioned medium from L929 cells, 0,5% sodium pyruvate and 0,1% b-mercaptoethanol, to allow for differentiation into macrophages for 7 days. Cells under differentiation, from the day after plating, were infected twice per day for two consecutive days with retrovirus produced in Phoenix-ECO cells, containing plasmids expressing either scrambled shRNA or shRNA specific for the mRNA to be depleted. At the end of the second day of infections, puromycin-selection (3,5 ug/ml) were started, and the cells were kept under selection until harvesting at day 7 after plating.

extract_protocol:
Total RNA was extracted using Trizol whereafter nascent 4sU-labelled RNA was extracted as described in Austenaa et al. 2015 .
Library preparation was performed using the TruSeq Stranded Total RNA sample preparation kit (Illumina RS-122-9007) starting from ca. 100-300 ng of nascent 4sU-labelled RNA, without ribosomal depletion.

treatment_protocol: Cells were untreated or treated for 45 min with LPS (10 ng/ml) before harvesting. 4-thio-uridine was added to the medium to a final concentration of 150 uM for 45 min before harvesting to allow for incorporation into newly synthesized RNA.

value: Primary bone marrow derived macrophages

value: FVB/Hsd


title: bone_marrow_3_RNA_seq

source_name: bone marrow cells

value: bone marrow cells

tag: treatment

value: untreated


title: scr_LPS_S15750

source_name: 4sU-RNAseq, shScrambled_2, LPS 45 min, BMDMs


title: H7-1001000356-TPO-1

description: Single cell from HSC

value: HSC

tag: days in culture


title: F10-1001000357-TPO_AB-1

description: Single cell from HSC

tag: date sequencing


title: OA_03_synovium

tag: tissue


title: bone_marrow_2_RNA_seq

tag: strain


title: RA_04_synovium


title: RNA-seq of control group Test II group of breast muscle rep 3

description: test group II is high energy low protein diet (ME2.78 MJ; CP 14.51%) + biological grass


title: shZc-UT_S15749

source_name: 4sU-RNAseq, shZc3h4_2, untreated BMDMs


title: F1-1001000355-AK113-1

description: Single cell from HSC


title: RNA-seq of control group Test II group of breast muscle rep 2


title: G1-1001000355-AK113-1

description: Single cell from HSC


title: bone_marrow_1_RNA_seq


title: scr-UT_S15748

source_name: 4sU-RNAseq, shScrambled_2, untreated BMDMs


title: RNA-seq of control group Test II group of breast muscle rep 1


title: shZc_LPS_S15429

source_name: 4sU-RNAseq, shZc3h4_1, LPS 45 min, BMDMs


title: ck05rz04v004i3h5z83qi8jed

city: South San Francisco

first: Adam

last: Freund

address: 1170 Veterans Blvd

institute: Calico Life Sciences LLC

data_processing:
Sequencing quality control was performed using FastQC (v0.11.5)
Transcript expression was then quantified using Salmon [1] (v0.9.1) in pseudo-alignment mode, without adapter trimming, producing per-gene count estimates, using the Ensembl mm10 transcriptome
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes counts for each gene for each sample, in long-format

source_name: myeloid

growth_protocol: Mice were maintained on a 12:12 hour light:dark cycle at 22℃ with environmental enrichment (e.g., nesting material and/or huts) with access to water and food ad libitum.

extract_protocol:
RNA was extracted from unsorted bone marrow or sorted populations using the Qiagen RNeasy 96 Universal Tissue Kit (Qiagen, 74881) and was digested with DNAseI before preparation for RNA-seq
Lib Prep method: NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. PCR 100-13 cycles. Sequenced on Hiseq 4000

treatment_protocol: 8 week old male C57BL/6 mice were treated with control or anti-PAPP-A antibody for 4 weeks, then animals were sacrificed and bone marrow was collected and osrted

value: myeloid

value: male

value: aPAPPA

tag: batch

value: C


title: ck05rz04v004j3h5zt4xeh7yf

source_name: mesenchymal stromal cell (MSC)

value: mesenchymal stromal cell (MSC)

tag: Sex

value: control


title: E1-1001000355-AK113-1

description: Single cell from HSC

extract_protocol:
Single-cells were collected  in lysis buffer in 96-well plates, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analyzed on an automated Fragment Analyzer (Advanced Analytical).
Each cells cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (FC-131-1024; Illumina) according to the manufacturers instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq instrument.


title: scr_LPS_S15428

source_name: 4sU-RNAseq, shScrambled_1, LPS 45 min, BMDMs

value: wild type


title: B1-1001000355-AK113-1

description: Single cell from HSC


title: shZc-UT_S15427

source_name: 4sU-RNAseq, shZc3h4_1, untreated BMDMs


title: ck05rz04v004k3h5zztto3l2o


title: B2-1001000356-TPO-1

description: Single cell from HSC

value: TPO


title: scr-UT_S15426

source_name: 4sU-RNAseq, shScrambled_1, untreated BMDMs


title: ck05rz04v004h3h5zud1p9vii


title: ck05rz04u004e3h5zu8vtkzox


title: G7-1001000356-TPO-1

description: Single cell from HSC


title: shNudt21-LPS_S13391

source_name: 4sU-RNAseq, shCFI25m_2, LPS 45 min, BMDMs


title: A1-1001000355-AK113-1

description: Single cell from HSC


title: ck05rz04u004d3h5zj01lm7x6


title: TOF heart tissue_3

city: Shanghai

first: Xinrui

last: Wang

address: 197 Ruijin Rd II

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

description: TOF heart tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: default Agilent protocol

source_name: right ventricle outflow tract

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA of the aortic samples were isolated using Trizol Reagent (Invitrogen, Carlsbad, CA, USA). NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA) was utilized to assess the quality and quantification of the total RNA.

treatment_protocol: The fetal hearts were dissected (≈120 days gestation) by 1 of the surgeons who also performed many of the reconstructions of the conotruncal defects (J.E.O.), to ensure the heart tissue samples analyzed was from a similar location[16]. Samples were immediately stored in RNALater (Ambion) at −80 °C for subsequent processing.

value: heart

value: TOF


title: shInt11-LPS_S13390

source_name: 4sU-RNAseq, shInts11_2, LPS 45 min, BMDMs


title: TOF heart tissue_1

description: TOF heart tissue


title: D3-1001000356-TPO-1

description: Single cell from HSC

data_processing:
Sequencing reads were trimmed, adapter sequences removed and the reads aligned using STAR with default parameters.
Duplicate reads were removed using picard. Transcript counts were obtained using HT-Seq and hg19 UCSC exon/transcript annotations.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample


title: TOF heart tissue_2

description: TOF heart tissue


title: health control heart tissue_3

description: health control heart tissue


title: ck05rz04u004c3h5zse0fdnet


title: shArs2-LPS_S13389

source_name: 4sU-RNAseq, shArs2_2, LPS 45 min, BMDMs


title: health control heart tissue_2

description: health control heart tissue


title: D1-1001000355-AK113-1

description: Single cell from HSC


title: shExosc3-LPS_S13388

source_name: 4sU-RNAseq, shExosc3_2, LPS 45 min, BMDMs


title: ck05rz04u00483h5zgrjyxhnu


title: C3-1001000356-TPO-1

description: Single cell from HSC

source_name: CD34+ CD38- CD90+ CD45RA- HSC


title: health control heart tissue_1

description: health control heart tissue


title: ck05rz04u00473h5z1q30kuyn


title: sh830-LPS_S13387

source_name: 4sU-RNAseq, shWdr82_2, LPS 45 min, BMDMs


title: F6-1001000356-TPO-1

description: Single cell from HSC


title: ck05rz04u00463h5z8po2w30w


title: E3-1001000356-TPO-1

description: Single cell from HSC


title: scr-LPS_S13386


title: C1-1001000355-AK113-1

description: Single cell from HSC


title: VP64_TIS_1

source_name: Cultured Hippocampal Neurons

value: Cultured Hippocampal Neurons


title: shNudt21-UT_S13385

source_name: 4sU-RNAseq, shCFI25m_2, untreated BMDMs


title: induced_B

city: Armilla

first: Antonio

middle: M

last: Estevez

state: Granada

address: Avda. del Conocimiento 17

department: Lopez-Neyra

country: Spain

institute: CSIC

data_processing:
Truseq RNA Single Indexes (set A&B)
The resulting 76-nt paired end sequences were checked for quality using FastQC, and
mapped to the T. brucei 11 megabase chromosomes using the ‘align’ program of the Subread package with the options nTrim5=1, nTrim3=1 y tieBreakQS=TRUE
Reads assignment to mRNAs and counting were carried out using the ‘featureCounts’ program of the Subread package
Only fragments that had both ends successfully aligned were considered for summarization, and those mRNAs with ≤ 1 fragments per kilobase and million (FPKMs) were filtered out
Replicates were compared using the edgeR package
Genome_build: TriTrypDB-34 version
Supplementary_files_format_and_content: edgeR output, tab-delimited text file including gene product descriptions

organism: Trypanosoma brucei brucei

source_name: PuREBP1-depleted trypanosomes

growth_protocol: Grown in SDM-79 medium at 27ºC ± 1 µg/ml tetracycline for RNAi induction

extract_protocol:
Cells were centrifuged and RNA was extracted using peqGOLD TriFast Reagent (Trizol-like)
Standard Illumina protocols
TruSeq Stranded mRNA® Illumina

value: 449 strain (Biebinger et al)

value: procyclic stage

value: trasfected with pGR335 (RNAi plasmid)

value: induced


title: ck05rz04u00453h5zem0vce3e


title: induced_A


title: shInt11-UT_S13384

source_name: 4sU-RNAseq, shInts11_2, untreated BMDMs

value: Primary bone marrow derived macrophages

value: FVB/Hsd


title: shArs2-UT_S13383

source_name: 4sU-RNAseq, shArs2_2, untreated BMDMs


title: ck05rz04t00433h5z1uqh0vvw

source_name: whole bone marrow (WBM)

value: whole bone marrow (WBM)


title: H6-1001000356-TPO-1

description: Single cell from HSC

value: HSC


title: uninduced_B

source_name: non-induced (control) trypanosomes

value: uninduced


title: cjyhnzjsm000j3h62gpsyexof

source_name: myeloid

value: myeloid

value: male

value: aPAPPA

value: B


title: shExosc3-UT_S13382

source_name: 4sU-RNAseq, shExosc3_2, untreated BMDMs

value: wild type


title: ck05rz04u004b3h5zx9re3u7b

value: control

value: C


title: F12-1001000355-AK113-1

description: Single cell from HSC


title: uninduced_A


title: cjyhnzjsm000g3h62comwv1ay


title: A12-1001000355-AK113-1

description: Single cell from HSC


title: TAP_351_B

description:
NGS015-19-L11_S11
processed data file: TAP_PuREBP1_curated.txt

source_name: TAP_351_cultured trypanosomes

extract_protocol:
Input RNA was isolated using peqGOLD Tri-fast. Affinity purified RNA was isolated after TEV cleavage, phenol:chloroform extraction and ethanol precipitation
Standard Illumina protocols
TruSeq Stranded mRNA® Illumina

tag: molecule subtype

value: TAP affinity purified RNA


title: sh830-UT_S13381

source_name: 4sU-RNAseq, shWdr82_2, untreated BMDMs


title: scr-UT_S13380

source_name: 4sU-RNAseq, shScrambled_2, untreated BMDMs


title: TAP_351_A

description:
NGS015-19-L10_S10
processed data file: TAP_PuREBP1_curated.txt

value: 449 strain (Biebinger et al)


title: B1-1001000356-TPO-1

description: Single cell from HSC

value: TPO


title: cjyhnzjsm000d3h624s2th0v8


title: cjyhnzjsm00073h62dt4rr3sm


title: C2-1001000356-TPO-1

description: Single cell from HSC


title: input_351_B

description:
NGS015-19-L5_S5
processed data file: TAP_PuREBP1_curated.txt

source_name: input_351_cultured trypanosomes

value: procyclic stage


title: F4-1001000356-TPO-1

description: Single cell from HSC


title: input_351_A

description:
NGS015-19-L4_S4
processed data file: TAP_PuREBP1_curated.txt


title: NFD_TIS_1

value: Cultured Hippocampal Neurons


title: F9-1001000357-TPO_AB-1

description: Single cell from HSC


title: shArs2-LPS_S13127

source_name: 4sU-RNAseq, shArs2_1, LPS 45 min, BMDMs

value: Primary bone marrow derived macrophages


title: cjyhnzjsl00043h6252nzl8et


title: cjyhnzjsm000a3h62rrlf43u0


title: G9-1001000357-TPO_AB-1

description: Single cell from HSC


title: shExosc3-LPS_S13126

source_name: 4sU-RNAseq, shExosc3_1, LPS 45 min, BMDMs

value: FVB/Hsd


title: cjvfiz2zw001a3h62ntgp1fdd

source_name: mesenchymal stromal cell (MSC)

value: mesenchymal stromal cell (MSC)

value: A


title: H1-1001000355-AK113-1

description: Single cell from HSC

source_name: CD34+ CD38- CD90+ CD45RA- HSC

value: HSC


title: TAP_mock_A

description:
NGS015-19-L7_S7
processed data file: TAP_mock_curated.txt

source_name: TAP_mock_cultured trypanosomes


title: cjvfiz2zv00193h62lcczl5qj

source_name: megakaryocyte erythrocyte progenitor (MEP)


title: TAP_mock_B

description:
NGS015-19-L9_S9
processed data file: TAP_mock_curated.txt


title: sh1137-LPS_S13125

source_name: 4sU-RNAseq, shWdr82_1, LPS 45 min, BMDMs


title: E9-1001000357-TPO_AB-1

description: Single cell from HSC


title: input_mock_B

description:
NGS015-19-L3_S3
processed data file: TAP_mock_curated.txt

source_name: input_mock_cultured trypanosomes


title: cjvfiz2zv00183h625zfh49ks

source_name: granulocyte macrophage progenitor (GMP)

value: granulocyte macrophage progenitor (GMP)


title: scr-LPS_S13124

source_name: 4sU-RNAseq, shScrambled_1, LPS 45 min, BMDMs


title: A2-1001000356-TPO-1

description: Single cell from HSC


title: input_mock_A

description:
NGS015-19-L1_S1
processed data file: TAP_mock_curated.txt


title: D2-1001000356-TPO-1

description: Single cell from HSC


title: shNudt21-UT_S13123

source_name: 4sU-RNAseq, shCFI25m_1, untreated BMDMs


title: cjvfiz2zv00173h629e23i556

source_name: common lymphoid progenitor (CLP)

value: common lymphoid progenitor (CLP)

value: male


title: shNudt21-LPS_S13129

source_name: 4sU-RNAseq, shCFI25m_1, LPS 45 min, BMDMs


title: shInt11-LPS_S13128

source_name: 4sU-RNAseq, shInts11_1, LPS 45 min, BMDMs


title: cjvfiz2zv00163h62brw3pcx0

source_name: hematopoietic stem cells (HSC)

value: hematopoietic stem cells (HSC)

value: aPAPPA


title: E12-1001000355-AK113-1

description: Single cell from HSC


title: cjvfiz2zv00143h627n8m47qq

value: control


title: D12-1001000355-AK113-1

description: Single cell from HSC


title: shInt11-UT_S13122

source_name: 4sU-RNAseq, shInts11_1, untreated BMDMs

value: wild type


title: shArs2-UT_S13121

source_name: 4sU-RNAseq, shArs2_1, untreated BMDMs


title: WT rep3 in MM medium

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11. Only sequences at least 25 nt length were considered for further analysis.
Bowtie version 0.12.7 with default parameters, was used for alignment on the reference genome
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene -g locus_tag -s 1)
Count data were analyzed using R version 3.4.1 and the Bioconductor package DESeq2 version 1.16. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between the intracellular persisters and control conditions. Raw P values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p value lower than 0.05 were considered differentially expressed.
Genome_build: Aspergillus fumigatus A1163 from NCBI
Supplementary_files_format_and_content: Matrix count from DESeq2

organism: Aspergillus fumigatus

growth_protocol: Conidia (1,25 10^7) were inoculated  in 5 plates of 35 mL of Minimal Medium or  GPA  in non agitated platic plate at 37°C in triplicate to obtain 30-50% of germlings.. a.11 hours of germination in MM: Minimal Medium D-glucose 10g/L, ammonium tartrate dibasic 0.92 g/L, KH2PO4 1.52 g/L, MgSO4 0.52 g/L, KCL 0.52 g/L, Trace Element solution (Na2B4O7, CuSO4, MnSO4, Na2MoO4, ZnSO4(MM).   b. 30h of germination in GPA (glucose 10g/L  + KH2PO4 1.52 g/L + ammonium tartrate dibasic 0.92 g/L))   MOPS (34.5 g/l) was added to the medium with pH adjusted to 7 with NaOH.

extract_protocol:
RNA was isolated with phenol chloroformNucleic acid was extracted with phenol-chloroform, precipitation with Ethanol-Na acetate and cleaning of the RNA with the DNAase Ambion TURBO kit.
Total RNA from three independent replicates were checked on the Bioanalyser system (Agilent) for its quality and integrity. Ribosomal RNA depletion was performed using the Bacteria RiboZero kit (Illumina). From rRNA-depleted RNA, directional libraries were prepared using the TruSeq Stranded mRNA Sample preparation kit following the manufacturer’s instructions (Illumina). Libraries were checked for quality on Bioanalyser DNA chips Bioanalyser (Agilent). Quantification was performed with the fluorescent-based quantitation Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). Sequencing was performed as an SRM run (SR: Single Read, PE: Paired-end Reads, M: multiplexed samples) for 65 bp sequences on HiSeq 2500 Illumina sequencer (65 cycles). The multiplexing level was 6 samples per lane.

treatment_protocol: Conidia germinated  in Minimal Medium or GPA were collected in phenol. Germinated conidia  were disrupted in Fast prep 3x1min speed 4.0 with 0.5 mm diameter glass beads in a volume of 500 µl and then RNA was isolated with phenol chloroform

tag: medium

value: Minimal Medium


title: WT rep2 in MM medium


title: B12-1001000355-AK113-1

city: Stanford

first: Gerlinde

last: Wernig

address: 265 Campus Drive

institute: Institute for Regenerative Medicine and Stem Cell Research, Stanford University School of Medicine

description: Single cell from HSC


title: sh1137-UT_S13119

source_name: 4sU-RNAseq, shWdr82_1, untreated BMDMs


title: WT rep1 in MM medium


title: D8-1001000357-TPO_AB-1

description: Single cell from HSC


title: cjvfiz2zv00123h622gn8ncdc


title: A1-1001000356-TPO-1

description: Single cell from HSC


title: cjvfiz2zv00103h625rbx42wb


title: WT rep3 in GPA medium

value: GPA medium (glucose 10g/L  + KH2PO4 1.52 g/L + ammonium tartrate dibasic 0.92 g/L)


title: shScramble POL II LPS 45min

description:
Chromatin IP against  RNA pol II
GSM1634808

data_processing:
Pol II raw data were downloaded from GEO (GSM1634808) and re-analysed
Reads were mapped using Bowtie2 v 2.2.6 (PMID: 19261174). We used default parameters with the options --very-sensitive, --no-unal and with the pre-built bowtie2 index. Only uniquely mapping reads were retained.
Peak calling was performed using SICER v2 (PMID: 24743992). We identified significantly enriched clusters using a redundancy threshold of 1, a window size of 200 bp, a gap size of 600 bp  and a False Discovery Rate (FDR) cut-off <0.01 were used. Fragment size was set to 150nt and the effective genome fraction to 0.80. The ChIP was compared to input DNA from primary bone marrow-derived macrophages. Regions that overlapped with the blacklists of the ENCODE and modENCODE consortia (http://www.broadinstitute.org/~anshul/projects/mouse/blacklist/mm9-blacklist.bed.gz) were filtered out.
Tracks (*.bigWig files) were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975)
Genome_build: mm10 (GENCODE) https://www.gencodegenes.org/mouse/release_M24.html
Supplementary_files_format_and_content: Tracks (*.bigWig files)

source_name: Marcophages

growth_protocol: Primary bone marrow cells were cultured in DMEM containing 10% North American FBS,  1% L-Glutamax solution, 1% Pen/Strep solution, and 30 % conditioned medium from L929 cells to allow for differentiation into macrophages for 7 days before the experiments were performed.

extract_protocol:
Ca. 100-150 mill. cells were fixed with 1% formaldehyde for 10 min. Nuclear lysates were prepared, sonicated to reach an average fragment length of 300 bp, whereafter protein-DNA complexes were immunoprecipitated with specific antibodies.
DNA libraries of immunoprecipiated DNA were prepared for sequencing on the Illumina NextSeq as previously described (Ostuni, 2013).

treatment_protocol: Cells were treated for 45 min with LPS (10 ng/ml) before harvesting.

value: Bone marrow derived macrophages

value: anti-total RNA pol II, Santa Cruz sc-899


title: C8-1001000357-TPO_AB-1

description: Single cell from HSC


title: cjvfiz2zv000z3h62moeyyjgw

source_name: whole bone marrow (WBM)

value: whole bone marrow (WBM)


title: G12-1001000355-AK113-1

description: Single cell from HSC

source_name: CD34+ CD38- CD90+ CD45RA- HSC


title: WT rep2 in GPA medium


title: cjvfiz2zv000x3h6299hahn9b

value: megakaryocyte erythrocyte progenitor (MEP)


title: C12-1001000355-AK113-1

description: Single cell from HSC


title: WT rep1 in GPA medium

value: GPA medium


title: cjvfiz2zv00133h622yg2i20u


title: B8-1001000357-TPO_AB-1

description: Single cell from HSC


title: shExosc3-UT_S13120

source_name: 4sU-RNAseq, shExosc3_1, untreated BMDMs

value: Primary bone marrow derived macrophages

value: FVB/Hsd


title: A7-1001000357-TPO_AB-1

description: Single cell from HSC

value: HSC


title: cjvfiz2zv00113h62ioiuun36

value: A


title: cjvfiz2zv000w3h62ku9o2b16

value: granulocyte macrophage progenitor (GMP)


title: cjvfiz2zv000v3h62wt2jbz9p

value: common lymphoid progenitor (CLP)

value: male


title: scr-UT_S13118

source_name: 4sU-RNAseq, shScrambled_1, untreated BMDMs


title: cjvfiz2zv000u3h62dmvnccbn

value: hematopoietic stem cells (HSC)

value: aPAPPA


title: cjvfiz2zv000s3h629u3eczp2

source_name: mesenchymal stromal cell (MSC)

value: mesenchymal stromal cell (MSC)

value: control


title: E2-1001000356-TPO-1

description: Single cell from HSC

value: TPO


title: G6-1001000356-TPO-1

description: Single cell from HSC


title: cjvfiz2zv000r3h627e0bwp8u

source_name: megakaryocyte erythrocyte progenitor (MEP)


title: D9-1001000356-TPO-1

description: Single cell from HSC


title: MCF7 CtBP siRNA hypoxia, biological rep2

city: Southampton

first: Jeremy

middle: Paul

last: Blaydes

state: Hampshire

address: Southampton General Hospital, Tremona Road

department: Faculty of Medicine

institute: University of Southampton

hyb_protocol: RNA labeling, hybridisation and scanning were performed by the University College London Genomics Facility, UCL Cancer Institute and Wolfson Institute for Biomedical Research, UK

data_processing: The data were analyzed with GenePattern Expression File Creator module, using RMA with quantile normalisation and background correction.

source_name: MCF7 CtBP si. Hypoxia

growth_protocol: Cells were cultured in standard DMEM media containing 25 mM glucose

extract_protocol: Qiagen RNAeasy with on column DNAse digestion

treatment_protocol: mRNA was prepared from cells at circa 70% confluency.

tag: sirna knockdown

value: CtBP siRNA

value: hypoxia

tag: cell line

value: breast cancer


title: cjvfiz2zv000q3h628355hqa0

source_name: granulocyte macrophage progenitor (GMP)


title: MCF7 CtBP siRNA hypoxia, biological rep3

scan_protocol: RNA labeling, hybridisation and scanning were performed by the University College London Genomics Facility, UCL Cancer Institute and Wolfson Institute for Biomedical Research, UK


title: MCF7 CtBP siRNA normoxia, biological rep2

source_name: MCF7 CtBP si. Normoxia

label_protocol: RNA labeling, hybridisation and scanning were performed by the University College London Genomics Facility, UCL Cancer Institute and Wolfson Institute for Biomedical Research, UK

value: normoxia


title: Chilling_mature zone of leaf4_biolgical rep 3

city: Kocaeli

first: Fatma

last: Aydinoglu

state: Turkey

address: GTU Mol. Bio. Gen.

department: Molecular Biology and Genetics

country: Turkey

institute: GTU

description: Gene expression data from mature zone of leaf4 of maize under chilling stress

hyb_protocol: The labeled samples were hybridized to Affymetrix GeneChip miRNA 4.0 Microarrays at 48°C and 60 RPM for 16-18 hours in an oven (Affymetrix Hybridization Oven 645).

scan_protocol: Samples and array barcode information were recorded by Affymetrix GeneChip Command Console (AGCC). The hybridized samples were washed and stained in an Affymetrix Fluidics Station 450 (FS450_002), following the manufacturer’s manual.

data_processing: The cell extension files, produced after scanning, were analysed using Expression Console and Transcription Console software  (TAC) 3.1 (Affymetrix). Background signal correction and data normalization were applied according to data from spike-in control probes.

organism: Zea mays

source_name: Chilling_mature zone of leaf4

label_protocol: 10 µg total RNA from each sample was labeled using the FlashTag Biotin HSR kit (Affymetrix) following the manufacturer’s protocol. Briefly, this procedure includes poly (A) tailing and FlashTag Biotin HSR Ligation.

growth_protocol: Control seedlings were grown under a 16h day/8h night photoperiod, 25°C/20°C day/night temperature, 15000 lux light intensity and 70% relative humidity.

extract_protocol: Totatl RNA was isolated by Trizol method

treatment_protocol: For chilling stress treatment, night temperature was lowered to +4°C while other conditions were unchanged.


title: MCF7 CtBP siRNA normoxia, biological rep1


title: cjvfiz2zv000p3h62io8mt2a0

source_name: common lymphoid progenitor (CLP)


title: cjvfiz2zu000n3h627xm3hqa2

value: whole bone marrow (WBM)


title: B5t-CTRL_I-Ab-KO_2_HTO (3MF1)

city: Bethesda

first: Michael

middle: C

last: Kelly

state: MD

address: 41 Center Drive

department: Center for Cancer Research

institute: NCI

description: Multiplexed_3MF1_GEX_filtered_feature_bc_matrix.h5

data_processing:
Fastq demultiplexing with cellranger v3.1.0
Read alignment and single cell data parsing with cellranger v3.1.0
Sample multiplexing feature barcode reads aligned to custome reference containing TotalSeq C hashtag barcode sequences
Genome_build: mm10 (refdata-cellranger-mm10-3.0.0)
Supplementary_files_format_and_content: 10x Genomics filtered h5 files contain the gene expression and cell hashing feature barcode data for each of the multiplexed samples.

molecule: other

source_name: Thymus

extract_protocol:
Thymocytes were stained for the expression of CD4, CD8-alpha, TCR-beta, CD69, and CCR7, and were sorted on FACS Aria II (BD Biosciences). Sorted cells were labeled with TotalSeqC hashtag oligos (BioLegend) before being combined for multiplexed loading on the 10x Genomics Chromium instrument using 5’ v1.1 chemistry (PN-1000165)
Libraries were constructed according to 10x Genomics User Guide (Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 User Guide with Feature Barcode technology for Cell Surface Protein - Revision F)

value: Thymus

value: T cells


title: G8-1001000357-TPO_AB-1

description: Single cell from HSC

value: HSC


title: F11-1001000355-AK113-1

description: Single cell from HSC


title: MCF7 CtBP siRNA normoxia, biological rep3


title: MCF7 CtBP siRNA hypoxia, biological rep1


title: Chilling_elongation zone of leaf4_biolgical rep 3

description: Gene expression data from elongation zone of leaf4 of maize under chilling stress

source_name: Chilling_elongation zone of leaf4


title: Chilling_meristem of leaf4_biolgical rep 3

description: Gene expression data from meristem of leaf4 of maize under chilling stress

source_name: Chilling_meristem of leaf4


title: B5t-KO_I-Ab-KO_2_HTO (3MF2)

description: Multiplexed_3MF2_GEX_filtered_feature_bc_matrix.h5


title: cjvfiz2zv000o3h62kult0xyk

source_name: hematopoietic stem cells (HSC)

value: A


title: cjvfiz2zu000l3h6202m5d6ki

value: megakaryocyte erythrocyte progenitor (MEP)


title: MCF7 control siRNA hypoxia, biological rep2

source_name: MCF7 control si. Hypoxia


title: MCF7 control siRNA hypoxia, biological rep3


title: B5t-KO_I-Ab-KO_1_HTO (1MF2)

description: Multiplexed_1MF2_GEX_filtered_feature_bc_matrix.h5


title: cjvfiz2zu000k3h62jl69xbo7

value: granulocyte macrophage progenitor (GMP)


title: MCF7 control siRNA hypoxia, biological rep1


title: Chilling_mature zone of leaf4_biolgical rep 1


title: Chilling_meristem of leaf4_biolgical rep 2


title: Chilling_meristem of leaf4_biolgical rep 1


title: MCF7 control siRNA normoxia, biological rep2

source_name: MCF7 control si. Normoxia


title: Chilling_elongation zone of leaf4_biolgical rep 2


title: Chilling_elongation zone of leaf4_biolgical rep 1


title: cjvfiz2zu000j3h62jjkmf6bf

value: common lymphoid progenitor (CLP)

value: male


title: cjvfiz2zu000i3h626esdg4so

value: hematopoietic stem cells (HSC)

value: aPAPPA


title: cjvfiz2zu000g3h62lxwf9csd

value: mesenchymal stromal cell (MSC)

value: control


title: B5t-CTRL_I-Ab-KO_2_GEX (3MF1)


title: B5t-KO_I-Ab-KO_2_GEX (3MF2)


title: Chilling_mature zone of leaf4_biolgical rep 2


title: Control_mature zone of leaf4_biolgical rep 3

description: Gene expression data from mature zone of leaf4 of maize under control

source_name: Control_mature zone of leaf4


title: MCF7 control siRNA normoxia, biological rep3


title: cjvfiz2zu000f3h62o0uor0uc


title: B5t-CTRL_I-Ab-KO_1_HTO (1MF1)

description: Multiplexed_1MF1_GEX_filtered_feature_bc_matrix.h5


title: MCF7 control siRNA normoxia, biological rep1


title: B5t-CTRL_I-Ab-KO_1_GEX (1MF1)


title: cjvfiz2zu000e3h62b0opaj72


title: Control_mature zone of leaf4_biolgical rep 2


title: Control_elongation zone of leaf4_biolgical rep 3

description: Gene expression data from elongation zone of leaf4 of maize under control

source_name: Control_elongation zone of leaf4


title: cjvfiz2zu000d3h62ev6go2zq


title: cjvfiz2zu000c3h6257hq732z


title: cjvfiz2zu000a3h629ttfcd9k


title: B5t-KO_I-Ab-KO_1_GEX (1MF2)


title: p20136-s018_Day4Pool_Group2_BAL2_GEX

city: Atlanta

first: Arun

last: Boddapati

address: 954 Gatewood Road, NE

department: Genomics Core

institute: Yerkes National Primate research center

data_processing:
Novo-seq 1000 lanes used for sequencing the samples
Sequence reads for both scRNA-seq and CITE-seq were demultiplexed and converted to counts matrix using Cellranger v3.1 & CITE-Seq tool resp.
Downstream analysis was carried out on Seurat v3.0
Genome_build: mmul10
Supplementary_files_format_and_content: tar.gz files containing barcodes, matrix and genes for each pooled sample
Supplementary_files_format_and_content: tsv files for cite-seq counts

organism: Macaca mulatta

source_name: Bronchoalveolar lavage (BAL), Day 4 Post SARS-CoV-2 challenge

extract_protocol:
Physiological saline, up to 50 ml was delivered through trachea to the lungs of anesthetized animals using a camera enabled fiberoptic bronchoscope. The flushed saline was re-aspirated 5 times before pulling out the bronchoscope. This collection was filtered through 70μm cell strainer and centrifuged at 2200 rpm for 5 minutes. Pelleted cells were suspended in 1ml R10 medium (RPMI(1X) and counted.
BAL samples from 5 monkeys in each group were pooled together and two technical replicate 10X captures were performed. One replicate capture failed for the control group. The libraries were run on Nova Seq 6000 lanes and the resultant bcl files were converted to count matrices using Cell Ranger v3.1
CITE-seq-Count and scRNA-seq

treatment_protocol: Single cell suspensions from BAL at Day 4 after SARS-CoV-2 infection were collected from MVA/S vaccinated (n=4), and MVA/Wt control (n=5) macaques and were subjected to single cell RNA sequencing. These analyses were performed only once since the macaque study was done only once.

value: vaccine


title: KDKD3

city: Boston

first: Eriene-Heidi

last: Sidhom

state: MA

address: 4 Blackfan Circle HIM 536

institute: Harvard Medical School

data_processing:
Cellranger toolkit (v2.1.1) used to perform de-multiplexing using the “cellranger mkfastq” command, and the “cellranger count” command for alignment to the mouse pre-mRNA transcriptome, cell barcode partitioning, collapsing unique molecular identifier (UMI) to transcripts, and gene-level quantification.
Genome_build: mm10, pre-mRNA
Supplementary_files_format_and_content: genes.tsv: This file contains all annotated genes; barcodes.tsv: This file contains the filtered barcodes (barcodes that were filtered as cells) represented in the mtx file; matrix.mtx: UMI counts per gene and barcode combination

molecule: nuclear RNA

source_name: kidney

growth_protocol: Mice were housed and bred according to the international standard conditions, with a 12-hour light/12-hour dark cycle and free access to food and water.

extract_protocol:
Nuclei isolation as described in corresponding publication.
Single nuclei were processed through the 10X Chromium 3' Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol.

treatment_protocol: Animals were euthanized by rapid carbon dioxide narcosis followed by cervical dislocation after disease onset (5 months). Kidneys were quickly removed. One kidney was frozen in the liquid phase of isopentane, pre-cooled toward its freezing point (-80°C) with dry ice and the second kidney was fixed in neutral buffered formalin. Experiments were performed in 3 mice for each group.

value: kidney

value: five months

value: female


title: KDKD1


title: KDKD2


title: Control_meristem of leaf4_biolgical rep 3

description: Gene expression data from meristem of leaf4 of maize under control

source_name: Control_meristem of leaf4


title: MDA-MB-231 in 10 mM fructose, biological rep3

description: gene expression data

hyb_protocol: RNA labeling, hybridisation and scanning were performed by the Molecular Biology Core Facility, Cancer Research UK Manchester Institute, UK

source_name: non-glycolytic MDA-MB-231

growth_protocol: Cells were cultured in DMEM media containing either 25 mM glucose or 10 mM fructose for 25 days, with regular passage and media changes

treatment_protocol: mRNA was prepared from cells at circa 70% confluency, circa 24 hours after replenishment of media

tag: growth media

value: 10 mM fructose


title: MDA-MB-231 in 25 mM glucose, biological rep3

description: gene expression data

scan_protocol: RNA labeling, hybridisation and scanning were performed by the Molecular Biology Core Facility, Cancer Research UK Manchester Institute, UK

source_name: glycolytic MDA-MB-231

value: 25 mM glucose


title: MDA-MB-231 in 10 mM fructose, biological rep2

description: gene expression data

label_protocol: RNA labeling, hybridisation and scanning were performed by the Molecular Biology Core Facility, Cancer Research UK Manchester Institute, UK


title: MDA-MB-231 in 10 mM fructose, biological rep1

description: gene expression data


title: Control_mature zone of leaf4_biolgical rep 1


title: Control_meristem of leaf4_biolgical rep 2


title: MDA-MB-231 in 25 mM glucose, biological rep2

description: gene expression data


title: p20136-s018_Day4Pool_Group2_BAL2_CITE

growth_protocol: Bronchoalveolar lavage (BAL), Day 4 Post SARS-CoV-2 challenge


title: cjvfiz2zu00093h62nrwigykf

source_name: granulocyte macrophage progenitor (GMP)


title: Control_elongation zone of leaf4_biolgical rep 1


title: p20136-s017_Day4Pool_Group2_BAL1_GEX


title: MDA-MB-231 in 25 mM glucose, biological rep1

description: gene expression data


title: cjvfiz2zu00083h62r84wk17s


title: MCF7 in 10 mM fructose, biological rep2

description: gene expression data

source_name: non-glycolytic MCF7

value: cell line MCF7 breast cancer


title: Control_elongation zone of leaf4_biolgical rep 2


title: Control_meristem of leaf4_biolgical rep 1


title: CTRL2

tag: genotype


title: CTRL1

tag: age


title: MCF7 in 10 mM fructose, biological rep1

description: gene expression data


title: MCF7 in 10 mM fructose, biological rep3

description: gene expression data


title: MCF7 in 25 mM glucose, biological rep3

description: gene expression data

source_name: glycolytic MCF7


title: cjvfiz2zu00073h621h6f82xh


title: CTRL3


title: cjvfiz2zt00053h62ei7kup34

source_name: megakaryocyte erythrocyte progenitor (MEP)


title: cjvfiz2zt00043h628grpwhbv


title: Adrenal gland P5 plate 1

city: Utrecht

first: Tito

last: Candelli

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

data_processing:
Cell barcodes and UMI were extracted from read 1 using the Sharq pipeline Version 1.0
Mapping was performed using STAR version 2.6.1
Count tables were generated using the Sharq pipeline Version 1.0
Genome_build: Genome Reference Consortium Mouse Build 38
Supplementary_files_format_and_content: Raw count matrix for all genes and all cells of each plate.

source_name: Adrenal glands

extract_protocol:
Adrenal glands were collected in PBS containing 1 mg/mL collagenase/dispase and sheared using a 1 mL pipette on ice until single cell suspension was observed. Enzymatic digestion was stopped by the addition of basic medium and the suspension was centrifuged at 250xg and resuspended in pbs. single cells were stained using 1 uM DAPI and viable cells were sorted into 384-well plates containing 10 uL mineral oil and 50 nL RT primers.
Libraries were prepared using the Sort-seq method

tag: developmental stage

value: Adrenal glands


title: p20136-s003_Group1_BAL_Day4-capture1_GEX


title: p20136-s003_Group1_BAL_Day4-capture1_CITE


title: Adrenal gland P1 plate 2


title: SHAM_input

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Pre-processing to remove adpater sequences and low quality reads: Trimmomatic; version: 0.33; parameters:ILLUMINACLIP:/TruSeq3-SE.fa:2:30:10 AVGQUAL:20 TRAILING:20 MINLEN:33
Data were mapped to the mm10 reference genome with hisat2 v2.0.4 with Ensembl release 95 derived splice sites (--known-splicesite-infile) and strandedness 'R'
mapped read were stired as position sorted bam files by diretly piping hisat output through samtools (| samtools view -bu - | samtools sort -@ 4 -o out.bam )
read counting was performed with featurecounts (-a Ensemb85.gtf -s 2 -T 6 --primary *.bam)
Differential expressed genes were obtained with DESeq2 with standard analysis settings
Genome_build: mm10
Supplementary_files_format_and_content: processed files are a count matrix containg the counts output from featurecounts for all samples

source_name: liver

extract_protocol:
50mg of tissue was homogenized in PBS and then crosslinked with 2% formaldehyde in PBS for 20 min at RT while rotating. This reaction was stopped by adding 125mM glycine for 10min at RT. Tissue was then collected in ice-cold PBS and subsequently lysed in lysis buffer (0.1% SDS, 1% Triton X-100, 0.15M NaCl, 1mM EDTA and 20mM Tris pH8, supplemented with protease inhibitors). Lysates were sonicated at 4°C to yield 200-800bp DNA fragments. IP was performed on 100µl lysates diluted 1:3 in incubation buffer (0.15% SDS, 1% Triton X-100, 0.15M NaCl, 1mM EDTA and 20mM HEPES) with 5µg of rabbit anti-GR antibody (H300, sc-8992; Santa Cruz)   fter two hours BSA blocked nProtein sepharose beads (GE Healthcare) were added to the lysates. The following day, beads were washed in WBI, WBII, LiCl buffer and twice in EDTA/HEPES buffer (0.5M EDTA and 1M HEPES). Chromatin was eluted in 200µl elution buffer (0,1M NaHCO3 and 10% SDS) supplemented with proteinase K. Next, proteins were decrosslinked by raising the incubation temperature to 65°C for 16h and DNA purified using the PCR purification kit (Qiagen), and eluting in 50µl of Qiagen Elution Buffer
TruSeq ChIP Library Preparation Kit

treatment_protocol: mice were either given a CLP or SHAM surgery. After 06h both groups were divided in 2 and one subgroup was injected with PBS, the other with 10 mg/kg DEX. 2H after injection liver was isolated for GR ChIP-seq

value: C57BL/6J mice

value: pooled input DNA (no IP) for SHAM samples


title: cjvfiz2zt00033h62uqd6njfg

source_name: common lymphoid progenitor (CLP)

value: A


title: Adrenal gland P1 plate 1


title: CLP_input

value: pooled input DNA (no IP) for CLP samples


title: MCF7 in 25 mM glucose, biological rep1

description: gene expression data


title: p20136-s017_Day4Pool_Group2_BAL1_CITE


title: Adrenal gland E18.5 plate 2


title: MCF7 in 25 mM glucose, biological rep2

description: gene expression data


title: Adrenal gland E18.5 plate 1


title: cjn4wgc34001y3h60me4sp258

source_name: Bone marrow

extract_protocol:
RNA was extracted from whole tissues using the Qiagen RNeasy 96 Universal Tissue Kit (Qiagen, 74881) and was digested with DNAseI before preparation for RNA-seq
Lib Prep method: TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat, Input Total Conc: 100ng in 10ul. PCR 12 cycles. Sequencing  - 3nM on Hiseq 4000

treatment_protocol: Mice were treated with control or anti-PAPP-A antibody for 17 weeks, then sacrificied and nine tissues were harvested and processed for RNA-seq:  lung, liver, kidney, heart, spleen, bone marrow, gonadal fat, subscapular (subcutaneous) fat, skin

value: Bone marrow

value: male


title: cjn4wgc34001x3h609yny24me


title: SHAM_PBS-2

description: peaks.tar.gz

value: SHAM operation followed after 06h by injection of PBS (IP) with organ isolation 2h later

tag: chip antibody

value: Anti-GR (H300, sc-8992; Santa Cruz)


title: Adrenal gland P5 plate 2


title: Adrenal gland E17.5 plate 2


title: cjn4wgc34001w3h60bqnmdnhr

value: control


title: SHAM_PBS-1

description: peaks.tar.gz

value: SHAM operation followed after 06h by injection PBS (IP) with organ isolation 2h later


title: Adrenal gland E17.5 plate 1


title: SHAM_DEX-3

description: peaks.tar.gz

value: SHAM operation followed after 06h by injection of 10 mg/kg DEX (IP) with organ isolation 2h later


title: Adrenal gland E14.5 plate 2


title: cjn4wgc34001u3h60jo4z3v2y


title: SHAM_DEX-2

description: peaks.tar.gz


title: SHAM_PBS-3

description: peaks.tar.gz


title: pasage number 20 LBC technical replicate 3

city: Munich

first: Anastasia

last: Georgiadi

state: Germany

address: Ingolstädter Landstraße 1

department: Departement of Diabetic Complications

country: Germany

institute: Helmholtz Centre Munich

description: Gene expression data of LBC which have been sored and passage for 20 times.

hyb_protocol: 5ug of ss DNA target was hybridized to Mouse Gene 1.0 ST arrays in a GeneChip Hybridization Oven 645 (16h-18h at 45C). The arrays were washed and stained in the Gene Chip Fluidics Station 450.

scan_protocol: Arrays were scanned in an Affymetrix Gene Chip Scanner 3000 7G.

data_processing:
CEL files from scanning were analyzer in Affymetrix Expression Console using Plier normalization and Global Median normalization.
affymetrix-algorithm-name = plier-gene-default
affymetrix-algorithm-version = 2.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: sorted cells showing high levels of FcsFNDC4 binding (High binding cells -HBC)

label_protocol: 200ng of total RNA was used to generate amplified sense strand DNA targets with Ambion WT Expression Kit followed by fragmentation and biotinylation with Affymetrix GeneChip WT Terminal Labeling Kit Hybridization protocol.

growth_protocol: HBC and LBC which had been sorted for the 20th time were expanded in DMEM F12, high glucose , GlutaMax, 10% FBS , 1% P/S media+ normocin media

extract_protocol: RNA was isolated based on the Trizol RNA extraction protocol. In addition, RNA was cleaned using miniRNAcleanup columns from Qiagen.

treatment_protocol: Cells were washed twice with PBS and lysed in Trizol.

tag: cell type

value: SVF immportalized cells derived from the inguinal white fat of male 129SVE mice

tag: cell phenotype

value: low levels of FcsFNDC4 binding (low binding cells -LBC)


title: pasage number 20 HBC technical replicate 3

description: Gene expression data of HBC which have been sored and passage for 20 times.

value: high levels of FcsFNDC4 binding (High binding cells -HBC)


title: cjn4wgc34001t3h605ppvypx3

tag: treatment


title: Adrenal gland E13.5 plate 2


title: cjvfiz2zt00013h62orl2xlfx

source_name: whole bone marrow (WBM)

value: whole bone marrow (WBM)


title: pasage number 20 HBC technical replicate 2


title: pasage number 20 LBC technical replicate 2


title: pasage number 20 HBC technical replicate 1


title: cjn4wgc34001s3h602l52us3e

value: aPAPPA


title: CLP_PBS-3

description: peaks.tar.gz

value: CLP operation followed after 06h by injection of PBS (IP) with organ isolation 2h later


title: SHAM_DEX-1

description: peaks.tar.gz

value: C57BL/6J mice


title: Adrenal gland E13.5 Plate 1

value: Adrenal glands


title: pasage number 20 LBC technical replicate 1

source_name: sorted cells showing low levels of FcsFNDC4 binding (low binding cells -LBC)


title: CLP_PBS-2

description: peaks.tar.gz


title: cjn4wgc34001v3h602bxnfyu7


title: cjn4wgc34001r3h60u43nxs49


title: SHAM 24h + 2h of PBS 3

data_processing:
Pre-processing to remove adpater sequences and low quality reads: Trimmomatic; version: 0.33; parameters:ILLUMINACLIP:/TruSeq3-SE.fa:2:30:10 AVGQUAL:20 TRAILING:20 MINLEN:33
Data were mapped to the mm10 reference genome with hisat2 v2.0.4 with Ensembl release 95 derived splice sites (--known-splicesite-infile) and strandedness 'R'
mapped read were stired as position sorted bam files by diretly piping hisat output through samtools (| samtools view -bu - | samtools sort -@ 4 -o out.bam )
read counting was performed with featurecounts (-a Ensemb85.gtf -s 2 -T 6 --primary *.bam)
Differential expressed genes were obtained with DESeq2 with standard analysis settings
Genome_build: mm10
Supplementary_files_format_and_content: count matrix containg the counts output from featurecounts for all samples

source_name: SHAM 24h + 2h of PBS

extract_protocol:
RNA was isolated using the Aurum total RNA mini kit (Biorad) according to the manufacturer’s instructions
Illumina truseq RNA stranded library protocol (for single end sequencing)

treatment_protocol: mice were either given a CLP or SHAM surgery. After 24h both groups were divided in 2 and one subgroup was injected with PBS, the other with 10 mg/kg DEX. 2H after injection liver was isolated for RNA extraction

value: SHAM operation followed after 24h by injection of PBS (IP) with organ isolation 2h later

value: liver


title: CLP_PBS-1

description: peaks.tar.gz

value: CLP operation followed after 06h by injection PBS (IP) with organ isolation 2h later


title: Adrenal gland E14.5 plate 1


title: CLP_DEX-3

description: peaks.tar.gz

value: CLP operation followed after 06h by injection of 10 mg/kg DEX (IP) with organ isolation 2h later


title: cjn4wgc34001p3h60nkmfmfmy

value: Bone marrow

value: male


title: CLP_DEX-2

description: peaks.tar.gz

value: Anti-GR (H300, sc-8992; Santa Cruz)


title: cjn4wgc34001o3h602i5w8n9e


title: SHAM 24h + 2h of PBS 1

value: SHAM operation followed after 24h by injection PBS (IP) with organ isolation 2h later


title: SHAM 24h + 2h of DEX 3

source_name: SHAM 24h + 2h of DEX

value: SHAM operation followed after 24h by injection of 10 mg/kg DEX (IP) with organ isolation 2h later


title: shZc3h4_1_LPS_r3

source_name: Macrophages

growth_protocol: Primary bone marrow cells were cultured in DMEM containing 10% North American origin, low endotoxin Foetal Bovine Serum,  1% L-Glutamax solution, 1% Penicillin/Streptomycin solution, and 30 % conditioned medium from L929 cells and allowed to differentiate for 7 days.

extract_protocol:
Total RNA was extracted using Trizol (Thermofisher, cat 15596026) and nascent 4sU-labelled RNA was then extracted as described in Austenaa et al. 2015 (PMID 26593720).
Library preparation was performed using the TruSeq Stranded Total RNA sample preparation kit (Illumina RS-122-9007) starting from ca. 100-300 ng of nascent 4sU-labelled RNA, without ribosomal depletion.

value: Primary bone marrow derived macrophages

value: wild type

value: FVB/Hsd

value: shZc3h4_1, LPS 45 min, BMDMs


title: cjn4wgc34001m3h60z79mzxrh

value: female

value: control


title: cjn4wgc34001n3h60aj3ptgj4


title: SHAM 24h + 2h of DEX 2


title: CLP_DEX-1

description: peaks.tar.gz

value: C57BL/6J mice


title: P/S low 6

city: Groningen

first: vincent

last: bloks

department: Pediatrics

institute: UMCG

description: Low P/S Dieet

hyb_protocol: Hybridisation of 5.5ug labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual

scan_protocol: Washing and staining of the arrays was done on a Affymetrix 450 fluidics stations using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual. Arrays where then scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual

data_processing: The data where normalized using VSN normalisation strategies using the MADMAX analysis pipeline pmid:21778530

label: Biotin

source_name: Small Intestine

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 500ng of total RNA without rRNA reduction

extract_protocol: total RNA

treatment_protocol: Intestine were dissected from wildtype FVB mouse that were either fed an control HF diet of a diet low in Polyunsaturated /Saturated fatty acid ratio during 8wks

value: FVB

tag: gender

value: Males

tag: diet

value: Low P/S Diet

value: Small Intestine


title: sh830-LPS_r3

data_processing:
After quality filtering according to the Illumina pipeline and after checking reads quality using FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), strand specific single end reads (51 bp and 76 bp) were aligned to the mm9  reference genomes (Illumina iGenomes reference downloaded from UCSC, http://support.illumina.com/sequencing/sequencing_software/igenome.html) using TopHat v2.1.0 1 (PMID:23618408), allowing up to two mismatches and using the option --b2-very- sensitive --library-type fr-firststrand.
Indels due to sequencing errors were identified using Bowtie2 v 2.2.6 (PMID: 19261174). Reads originating from the two strands were separated according to the XS:A:+/XS:A:-flag provided by TopHat2 (PMID:23618408).
SICER v2 (PMID: 24743992) was used to detect the extra-genic transcripts regulated in cells depleted of individual factors. The entire genome was partitioned into blocks of non-overlapping 500 bp windows with a gap size <1000 nt. An effective genome fraction of 1, a fragment size of 0 and a False Discovery Rate (FDR) cut-off <0.01 were used.
*.bigWig files were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975) (-bs 1 --normalizeUsing RPKM --outFileFormat bigwig -filterRNAstrand forward or --filterRNAstrand reverse)
Genome_build: mm10 (GENCODE) https://www.gencodegenes.org/mouse/release_M24.html
Supplementary_files_format_and_content: .bigWig strand specific tracks

tag: strain

value: shWdr82_2, LPS 45 min, BMDMs


title: cjn4wgc34001q3h60dewdcp88

data_processing:
Sequencing quality control was performed using FastQC (v0.11.5)
Transcript expression was then quantified using Salmon [1] (v0.9.1) in pseudo-alignment mode, without adapter trimming, producing per-gene count estimates, using the Ensembl mm10 transcriptome
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes counts for each gene for each sample, in long-format

tag: tissue

value: Bone marrow

value: aPAPPA


title: P/S low 4

description: Low P/S Dieet


title: SHAM 24h + 2h of DEX 1

value: liver


title: SHAM 24h + 2h of PBS 2

value: SHAM operation followed after 24h by injection of PBS (IP) with organ isolation 2h later


title: P/S low 3

description: Low P/S Dieet


title: P/S low 5

description: Low P/S Dieet


title: P/S low 2

description: Low P/S Dieet


title: scr-LPS_r3

value: shScrambled_2, LPS 45 min, BMDMs


title: Control 6

description: Control HF Dieet

value: Control HF Diet


title: P/S low 1

description: Low P/S Dieet


title: cjn4wgc34001k3h60xagtbroc

tag: Sex


title: sh1137-LPS_r4

value: Primary bone marrow derived macrophages

value: wild type

value: shWdr82_1, LPS 45 min, BMDMs


title: cjn4wgc34001j3h606dkmwd30

value: female


title: scr-LPS_r4

source_name: Marcophages

value: FVB/Hsd

value: shScrambled_1, LPS 45 min, BMDMs


title: CLP 24h + 2h of PBS 2

source_name: CLP 24h + 2h of PBS

value: CLP operation followed after 24h by injection of PBS (IP) with organ isolation 2h later


title: LDE2

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: MI

address: 1500 E medical drive

institute: University of Michigan

data_processing:
RNA-seq libraries were mapped to GENCODE GRCm38 primary assembly using STAR (v2.7.3)
gene expression estimations were performed using RSEM (v1.2.29). DESeq2 (v1.22.2) was used for identifying differentially expressed genes with default parameters
Genome_build: GENCODE GRCm38
Supplementary_files_format_and_content: STAR (v2.7.3) bam files

source_name: PANCREAS TUMOR

extract_protocol:
TRIZOL reagent
RNA was assessed for quality using the TapeStation (Agilent, Santa Clara, CA). Samples were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (catalog number E7760L) Ribo depletion Module NEBNext rRNA Human/Mouse/Rat (catalog number E6310X) and NEBNext Multiplex Oligos for Illumina Unique dual (catalog number E6440L) (NEB, Ipswitch, MA). Where 5ng of total RNA was ribosomal depleted using rRNA Depletion module. The rRNA-depleted RNA is then fragmented 7 minutes determined by RIN (RNA Integrity Number) of input RNA as per protocol, and copied into first strand cDNA using reverse transcriptase and dUTP mix. Samples undergo end repair and dA-Tailing step followed by ligation of NEBNext adapters. The products are purified and enriched 16 cycles by PCR to create the final cDNA library. Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835) (Kapa Biosystems,Wilmington MA).

treatment_protocol: vehicle or LDE225 treated tumors, by oral gavage for 14 days, once tumors formed

value: LDE


title: CLP 24h + 2h of DEX 2

source_name: CLP 24h + 2h of DEX

value: CLP operation followed after 24h by injection of 10 mg/kg DEX (IP) with organ isolation 2h later


title: cjn4wgc34001l3h60s9gik7pl

value: control


title: cjn4wgc34001g3h60scknhfl5


title: cjn4wgc34001i3h60k94lutsi


title: Control 4

description: Control HF Dieet

value: FVB

value: Males

value: Small Intestine


title: LDE1


title: Control 2

description: Control HF Dieet


title: cjn4wgc34001h3h60cuuggao2

value: Bone marrow

value: aPAPPA


title: CLP 24h + 2h of DEX 1

value: liver


title: VEH3

value: VEH


title: Control 3

description: Control HF Dieet

value: Control HF Diet


title: Control 5

description: Control HF Dieet


title: cjn4wgc34001f3h600qhjlytx


title: Diabetic_24h_06

city: Leganes

first: carlos

last: leon

state: Madrid

address: Avenida Universidad 30

department: Bioengineering

hyb_protocol: 16h of hybridization at 45ºC,

scan_protocol: arrays were washed, stained with streptavidin phycoerythrin, and were then scanned with the GeneArray Scanner (Affymetrix) to generate an image file.

data_processing: PCA on samples detected two outliers (C0_04 and C0_06). Raw data from microarrays excluding outliers was normalized using the rma algorithm from the affy package (Bioconductor)

source_name: 6mm skin biopsy around wound edge

label_protocol: generate double-stranded cDNA using the protocol for one-cycle cDNA synthesis. Biotin-labeled cRNA was fragmented and hybridized overnight to Affymetrix HU133 2.0 GeneChip

growth_protocol: Human skin biopsies of healthy donors, isolated by biomechanical and enzimatic digestion and expanded in vitro

extract_protocol: RNA isolation was performed using Trizol (Invitrogen) extraction based methods, followed by purification in columns (Qiagen).

treatment_protocol: Experimental diabetes was induced by intraperitoneal injections of STZ, administered on five consecutive days. Wound healing experiments were performed using a biopsy punch (Pfm Medical Ag.,Cologne, Germany) in the stable human skin engrafted on immunodeficient mice exposed to sustained hyperglycaemia for 6 weeks. Specifically, 2mm-circular excisional wounds were created and the excised tissue was harvested and used as a reference for gene expression analysis

value: Human skin grafted in diabetic mice

tag: disease state

value: diabetic

tag: time

value: 24 hours


title: SHAM 6h + 2h of PBS 3

data_processing:
Pre-processing to remove adpater sequences and low quality reads: Trimmomatic; version: 0.33; parameters:ILLUMINACLIP:/TruSeq3-SE.fa:2:30:10 AVGQUAL:20 TRAILING:20 MINLEN:33
Data were mapped to the mm10 reference genome with hisat2 v2.0.4 with Ensembl release 85 derived splice sites (--known-splicesite-infile) and strandedness 'R'
mapped read were stired as position sorted bam files by diretly piping hisat output through samtools (| samtools view -bu - | samtools sort -@ 4 -o out.bam )
read counting was performed with featurecounts (-a Ensemb85.gtf -s 2 -T 6 --primary *.bam)
Differential expressed genes were obtained with DESeq2 with standard analysis settings
Genome_build: mm10
Supplementary_files_format_and_content: processed files are a count matrix containg the counts output from featurecounts for all samples

treatment_protocol: mice were either given a CLP or SHAM surgery. After 6h both groups were divided in 2 and one subgroup was injected with PBS, the other with 10 mg/kg DEX. 2H after injection liver was isolated for RNA extraction

value: SHAM operation followed after 6h by injection of PBS (IP) with organ isolation 2h later


title: cjn4wgc34001e3h608ai6qlu5

value: female


title: CLP 24h + 2h of PBS 1

value: CLP operation followed after 24h by injection PBS (IP) with organ isolation 2h later


title: Diabetic_24h_04


title: Diabetic_24h_03


title: Control 1

description: Control HF Dieet


title: VEH2


title: SHAM 6h + 2h of PBS 2


title: VEH1


title: Diabetic_24h_05


title: CLP 24h + 2h of DEX 3


title: cjn4wgc34001d3h60rj07bhfs


title: cjnw5krpc007g3h5vtqgv9uga

source_name: Subscapular fat

value: Subscapular fat


title: KPC

data_processing:
single cell RNA-seq libraries were mapped to mm10-3.0.0 using Cell Ranger
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: Cell ranger (version 3.1.0) aligned .5h processed file

growth_protocol: tumor developed in mouse, which was harvested at 19 weeks of age

extract_protocol:
RNA was assessed for quality using the TapeStation (Agilent, Santa Clara, CA). Samples were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (catalog number E7760L) Ribo depletion Module NEBNext rRNA Human/Mouse/Rat (catalog number E6310X) and NEBNext Multiplex Oligos for Illumina Unique dual (catalog number E6440L) (NEB, Ipswitch, MA). Where 5ng of total RNA was ribosomal depleted using rRNA Depletion module. The rRNA-depleted RNA is then fragmented 7 minutes determined by RIN (RNA Integrity Number) of input RNA as per protocol, and copied into first strand cDNA using reverse transcriptase and dUTP mix.
Samples undergo end repair and dA-Tailing step followed by ligation of NEBNext adapters. The products are purified and enriched 16 cycles by PCR to create the final cDNA library.
Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835) (Kapa Biosystems,Wilmington MA).

value: 19 weeks


title: SHAM 6h + 2h of PBS 1

value: SHAM operation followed after 6h by injection PBS (IP) with organ isolation 2h later


title: SHAM 6h + 2h of DEX 3

value: SHAM operation followed after 6h by injection of 10 mg/kg DEX (IP) with organ isolation 2h later


title: Diabetic_24h_01


title: cjnw5krpc007f3h5v31fi6trk

source_name: Gonadal fat

value: Gonadal fat


title: SHAM 6h + 2h of DEX 2

source_name: liver


title: SHAM 6h + 2h of DEX 1


title: cjnw5krpc007e3h5vjfio463e

source_name: Skin

value: Skin


title: CLP 6h + 2h of PBS 3

value: CLP operation followed after 6h by injection of PBS (IP) with organ isolation 2h later


title: cjnw5krpc007d3h5vbcpd4qp4

source_name: Lung

value: Lung

value: aPAPPA


title: cjnw5krpc007c3h5vo88am7cc

source_name: Liver

value: Liver


title: CLP 6h + 2h of PBS 2


title: CLP 6h + 2h of PBS 1


title: cjnw5krpc007b3h5va8zowh39

source_name: Heart

value: Heart


title: Sample 2_Adult Control

city: Urbana

first: Sushant

last: Bangru

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: University of Illinois, Urbana-Champaign

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Fastq files were mapped the mm10 genome assembly using Cellranger software from 10X Genomics
Downstream analysis was performed using Seurat V3.1
Genome_build: Mus Musculus mm10
Supplementary_files_format_and_content: Processed files are outputs from the Cellranger pipeline and are basically the matrixfiles with UMI values for genes in every cell

source_name: Adult Control

extract_protocol:
Cells isolated using 2 step perfusion protocol and then passed through Miltenyl Dead Cell removal kit to isolate only live cells
10X v3 kit was used to make the single cell libraries and then sequenced on Illumina Novaseq platform

treatment_protocol:
sample 1: For these study Normal Postnatal day 14 mice were taken from the C57Bl/6J strain
sample 2-5: 2/3rd partial hepatectomy performed on Adult 8Wk old mice

value: adult

value: liver cells


title: Sample 4_Adult PHx 48 hr

source_name: Adult PHx 48 hr

value: partial hepatectomy (PHx)


title: Sample 1_Postnatal Day 14

source_name: Postnatal Day 14

value: Postnatal Day 14


title: Sample 3_Adult PHx 24 hr

source_name: Adult PHx 24 hr


title: Sample 5_Adult PHx 96 hr

source_name: Adult PHx 96 hr


title: cjnw5krpc007a3h5ve96kcyio

city: South San Francisco

first: Adam

last: Freund

state: CA

source_name: Spleen

value: Spleen

value: female


title: CLP 6h + 2h of DEX 3

value: CLP operation followed after 6h by injection of 10 mg/kg DEX (IP) with organ isolation 2h later