title: RFPSHApC4

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the remote area of hearts of Ki67TagRFP mice 14 days post-sham surgery, replicate 1 [C4]


title: RFPSHApC3

status: Public on Dec 05 2018

type: SRA

city: Würzburg

first: Kai

last: Kretzschmar

address: Josef-Schneider-Str. 2

country: Germany

institute: University Hospital Würzburg

description:
Murine hearts 14 days after sham surgery
barcode file: CEL-Seq_UMI_barcodes.csv.gz

library_source: transcriptomic

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: coutb files contain UMI barcode normalised abundance counts

molecule: total RNA

organism: Mus musculus

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the remote area of hearts of Ki67TagRFP mice 14 days post-sham surgery, replicate 1 [C3]

extract_protocol:
Live single cells were sorted in 384- well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: strain background

tag: genotype/variation

tag: time point

value: 14 days after sham surgery

tag: tissue

value: Heart

tag: heart region

value: remote area


title: 51156_D0_uns

type: RNA

city: Oxford

first: Julius

last: Muller

state: Oxfordshire

address: ORCRB, Roosevelt Drive

department: Nuffield Department of Medicine

country: United Kingdom

institute: The Jenner Institute, University of Oxford

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Probes were background corrected using negative control probes followed by quantile normalization using the neqc method of Shi et al. (2010) [PMID:20929874].

label: biotin

organism: Homo sapiens

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared with the Ambion Total Prep RNA amplification kit

growth_protocol: Rested PBMC (1 x 106 ) were resuspended in single wells of 200ul RPMI supplemented with 10% FBS and L-glutamine.

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions with the following modification; in the first step an equal volume of 80% ethanol was added to cells lysed in RLT buffer, mixed and total volume transferred to an RNeasy column.  RNA was quantified by Nanodrop and stored at -80°C until use.

treatment_protocol: Cells were stimulated for 12 hours at 37°C in single wells containing BCG SSI from pooled vaccine vials (~2 × 105  CFU/ml) or media only.  After 12 hours of stimulation cells were pelleted and lysed in RNA lysis buffer (RLT, Qiagen).

value: PBMC

tag: subject

tag: day

tag: stimulus

value: unstimulated

tag: risk for tb

value: Case

tag: cmv status

value: CMVn

tag: vaccine

value: Candin


title: 50015_D0_BCG

value: BCG

value: Control


title: 51914_D28_BCG

value: CMVp


title: 50153_D0_uns


title: 53416_D0_BCG


title: 52901_D0_BCG


title: 51035_D0_BCG


title: 50826_D0_BCG


title: 51156_D28_uns


title: RFPMIInfB4

description:
Murine hearts 14 days after myocardial infarction
barcode file: CEL-Seq_UMI_barcodes.csv.gz

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the infarcted area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 1 [B4]

value: 14 days post-MI

value: infarcted area


title: RFPSHApC2

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the remote area of hearts of Ki67TagRFP mice 14 days post-sham surgery, replicate 1 [C2]


title: RFPSHApC1

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the remote area of hearts of Ki67TagRFP mice 14 days post-sham surgery, replicate 1 [C1]


title: RFPMIInfB3

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the infarcted area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 1 [B3]


title: 51768_D0_uns


title: RFPMIInfB1

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the infarcted area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 1 [B1]


title: RFPMIInfB2

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the infarcted area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 1 [B2]


title: RFPMIRemA4

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the remote area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 1 [A4]


title: 51710_D0_BCG


title: 50153_D28_uns


title: 51124_D0_uns


title: 53416_D28_BCG


title: 50015_D28_BCG


title: WTadultJ4

description:
Adult murine hearts
barcode file: CEL-Seq_UMI_barcodes.csv.gz

source_name: Extracted RNA from living cells of the ventricles of hearts of adult wildtype mice, replicate 1 [J4]

value: wildtype

value: adult

value: ventricles


title: 51498_D28_uns


title: 51351_D0_BCG


title: 51108_D0_uns


title: RFPMIRemA3

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the remote area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 1 [A3]


title: Post-wounding day (PWD) 12 single cells

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

country: USA

institute: University of California, Irvine

description: RNA from single cells

data_processing:
Transcripts were mapped to the mm10 reference genome (GRCm38.91) using Cell Ranger Version 2.1.0 with the following standard parameters: cellranger mkgtf Mus_musculus.GRCm38.91.gtf mm10-filtered-ensembl.gtf --attribute=gene_biotype:protein_coding; cellranger –genome=mm10 –fasta=mm10.fa –genes=mm10-filtered-ensembl.gtf; cell ranger count – id=[ID] \ --transcriptome=[LOCATION] \ --fastqs=[LOCATION]; --sample=[NAME] \.
Genome_build: mm10

source_name: Skin wound tissue cells

extract_protocol:
Dermal wound compartment was microdissected, and single cell suspension was created by incubating tissues in Dispase/Collagenase/Liberase. Dead cells were removed using Dead Cell Removal Kit, counted using Countess, and loaded into the Chromium platform (10X Genomics).
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v2 chemistry. Library metrics were as follow: 550.19 pg/µl with an avg. size ~454 bps. Libraries were sequenced on an Illumina HiSeq 4000 platform (Illumina). Cell counting, capture, library preparation, quality control, and sequencing was performed at the Genomics High Throughput Sequencing facility at the University of California, Irvine.
Single Cell 3’ v2 chemistry - 10X Genomics

treatment_protocol: 3-8 week old mice were wounded as previously described. Briefly, 1.5 x 1.5 cm squared excisional wounds were inflicted on the dorsum of adult mice and were collected at PWD 12.

tag: strain

value: Mixed background

value: Skin wound tissue

tag: time

value: Post wounding day 12


title: 51067_D28_uns


title: 53747_D0_BCG


title: 52219_D0_BCG


title: RFPMIRemA2

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the remote area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 1 [A2]

value: Heart

value: remote area


title: RFPMIRemA1

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the remote area of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 1 [A1]


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_41

description:
Sm22-Cre;tdTomato
Plikus_C1_PWD21_v2_Mv13_Matrix.txt

data_processing:
RSEM was used for alignment, mapping and quantification of single cell transcripts.
Reads were not trimmed for adaptor sequence. Sequenced reads were aligned, mapped and quantified to the mouse genome (mm10/gencode.Mv13) using Bowtie (version 1.0.0) with the following standard parameters: rsem-prepare-reference --bowtie --gtf and quantified using the RNA-seq by Expectation-Maximization algorithm (RSEM) (version 1.2.31) with the following standard parameters: rsem-calculate-expression -p $CORES --paired-end. (B. Li, C. N. Dewey. BMC bioinformatics 12, 323 (2011).
FPKM values were used. FPKM values were added pseudo-count of 1. Gene expression values for each cell were scaled by the total number of transcripts and multiplied by 10,000. This scaled expression data were then natural-log transformed before further downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited (txt) text files include unprocessed FPKM values.

source_name: Skin wound cells

extract_protocol:
Skin wound tissues were harvested and dissegragated into single cell suspensions with collagenase. Cells were FACS sorted as viable tdTomatoHi. Pre-sorted, viable tdTomatohi single cells were re-suspended at appropriate concentrations in DMEM supplemented with 10% FBS, antibiotics and antifungals, diluted with suspension reagent for attribution of optimal buoyancy, and loaded onto a large 17-25μm 96-well microfluidic IFC (Fluidigm) for single cell capture in the automated C1 system for single-cell genomics (Fluidigm). Lysis, RT and cDNA pre-amplification were performed in loco (protocol 1.773x) with ultra-low input RNA reagents as suggested per manufacturer (Clonetech). RNA spike-in controls were omitted.
cDNA concentrations were estimated using Qubit 2.0 (Thermo) and cDNAs with concentration ≥ 1.0 ng/μl were used for downstream library preparation. Libraries were amplified using the Nextera XT v2 Index Kit (Illumina). Quality control on multiplexed libraries was performed using the Agilent Bioanalyzer and quantification was performed using KAPA for Illumina Sequencing Platforms (Illumina). Multiplexed libraries were sequenced as paired-end on an Illumina Next-Seq500 platform (Illumina).
SMART-seq2 - Fluidigm.

treatment_protocol: 3-8 week old mice were wounded as previously described. Briefly, 1.5 x 1.5 cm squared excisional wounds were inflicted on the dorsum of adult mice. Skin wound tissues (n=2-3/time point) were collected from Sm22-Cre;tdTomato mice on PWD 12, 15 and 21.

tag: cell type

value: Skin wound cells

tag: treatment

value: Post wounding day 21


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_42


title: Remitting sarcoidosis sample 14 [sarcexp]

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado - Anschutz Medical Campus

description: PolyA-selected total RNA extracted from BAL fluid

hyb_protocol: Agilent low input quick amp labeling protocol

scan_protocol: NimbleGen MS200

data_processing: Agilent Feature Extraction, followed by quantile normalization and log2 transformation

source_name: BALF

growth_protocol: NA, primary cells used

extract_protocol: Standard Qiagen AllPrep protocol

treatment_protocol: NA, cells were not treated prior to extraction

tag: group

value: Remit Sarc

tag: Sex

value: Male

tag: race

value: W

tag: ethnicity

value: non-hispanic

tag: smoking status

value: Former

tag: scadding

tag: total lung capacity, percent predicted

tag: forced vital capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

tag: diffusing capacity of the lung for carbon monoxide, percent predicted

tag: age

value: untreated


title: 51035_D0_uns

tag: tissue

value: PBMC

tag: subject

tag: day

tag: stimulus

value: unstimulated

tag: risk for tb

value: Case

tag: cmv status

value: CMVn

value: Candin


title: 53120_D28_BCG

value: BCG

value: Control

tag: vaccine


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_40

tag: strain

value: Mixed background

tag: cell type

tag: treatment


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_39


title: 52512_D28_uns


title: Remitting sarcoidosis sample 15 [sarcexp]

label_protocol: Agilent low input quick amp labeling protocol

tag: group

tag: Sex

tag: race

tag: ethnicity

tag: smoking status

value: Untreated


title: 51077_D0_uns


title: 53109_D28_BCG


title: 50830_D28_uns


title: Progressive sarcoidosis sample 6 [sarcexp]

value: Prog Sarc

value: female

tag: scadding

tag: forced vital capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

tag: diffusing capacity of the lung for carbon monoxide, percent predicted

value: Treated

value: Steroid


title: Progressive sarcoidosis sample 9 [sarcexp]

value: W

value: hispanic

tag: total lung capacity, percent predicted

tag: age

value: MTX


title: Progressive sarcoidosis sample 8 [sarcexp]

value: Male

value: non-hispanic

value: Never


title: Progressive sarcoidosis sample 7 [sarcexp]

value: untreated


title: 51986_D28_uns

tag: tissue

value: PBMC

tag: subject

tag: day

tag: stimulus

value: unstimulated

tag: risk for tb

value: CMVn


title: 52600_D28_uns

value: Control

tag: cmv status

tag: vaccine


title: 51093_D0_BCG

value: BCG

value: Candin


title: 50544_D28_BCG


title: 52640_D28_uns


title: 50011_D28_BCG


title: 50544_D0_uns


title: 52512_D0_BCG


title: 50544_D28_uns


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_37

tag: strain

value: Mixed background

tag: cell type

value: Skin wound cells

tag: treatment

value: Post wounding day 21


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_36


title: 52259_D0_BCG


title: Progressive sarcoidosis sample 5 [sarcexp]

tag: group

value: Prog Sarc

tag: Sex

tag: race

tag: ethnicity

tag: smoking status


title: 51995_D0_BCG


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_35


title: Progressive sarcoidosis sample 4 [sarcexp]

value: AA

value: Current

tag: total lung capacity, percent predicted

tag: forced vital capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

tag: diffusing capacity of the lung for carbon monoxide, percent predicted


title: 53215_D28_uns

tag: tissue

tag: subject

tag: day


title: 50352_D28_BCG

tag: stimulus

tag: risk for tb

value: Case

tag: cmv status


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_34

tag: strain

tag: cell type


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_33

tag: treatment


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_32


title: 52764_D0_uns

tag: vaccine


title: 30044_D28_BCG


title: 52549_D0_uns

value: CMVp


title: Progressive sarcoidosis sample 3 [sarcexp]

tag: group

tag: Sex

value: Male

tag: race

value: W

value: non-hispanic

value: Former

tag: scadding

tag: age

value: Treated

value: Steroid


title: Remitting sarcoidosis sample 12 [sarcexp]

value: Remit Sarc

value: female

tag: ethnicity

tag: smoking status

tag: total lung capacity, percent predicted

tag: forced vital capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

value: untreated


title: 50551_D28_uns

tag: tissue

value: PBMC

tag: subject

tag: day

tag: stimulus

value: unstimulated

value: Control


title: Remitting sarcoidosis sample 11 [sarcexp]

value: Never

tag: diffusing capacity of the lung for carbon monoxide, percent predicted

value: Untreated


title: 50329_D0_uns

tag: risk for tb

tag: cmv status

value: CMVn

value: Candin


title: Remitting sarcoidosis sample 9 [sarcexp]

tag: group

tag: treatment

value: MTX


title: 51462_D28_BCG

value: BCG

tag: vaccine


title: Remitting sarcoidosis sample 8 [sarcexp]

tag: Sex

tag: race

value: W

tag: scadding


title: 53748_D28_uns

value: Case


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_31

tag: strain

value: Mixed background

tag: cell type

value: Skin wound cells

value: Post wounding day 21


title: 52607_D28_BCG


title: 51360_D28_BCG


title: 51995_D0_uns


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_29


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_30


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_28


title: Remitting sarcoidosis sample 13 [sarcexp]

value: Remit Sarc

value: Male

value: AA

tag: ethnicity

value: non-hispanic

tag: smoking status

value: Former

tag: forced vital capacity, percent predicted

tag: age


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_27


title: Progressive sarcoidosis sample 2 [sarcexp]

value: Prog Sarc

value: female

tag: total lung capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted


title: 51841_D0_uns

tag: tissue

value: PBMC

tag: subject

tag: day

tag: stimulus

value: unstimulated


title: 52600_D28_BCG

tag: risk for tb

value: Control

tag: cmv status

value: CMVn


title: 51351_D0_uns

tag: vaccine

value: Candin


title: 51616_D28_uns

value: CMVp


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_38

tag: treatment


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_25


title: 51616_D0_uns


title: 51128_D28_uns

value: Case


title: Remitting sarcoidosis sample 7 [sarcexp]

tag: group

tag: Sex

tag: race

value: W

value: Never

tag: scadding

value: untreated


title: Progressive sarcoidosis sample 1 [sarcexp]

tag: ethnicity

tag: smoking status

tag: diffusing capacity of the lung for carbon monoxide, percent predicted

value: Treated

value: Steroid


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_26

tag: strain

value: Mixed background

tag: cell type

value: Skin wound cells

value: Post wounding day 21


title: 52741_D28_BCG

tag: tissue

value: BCG


title: 52884_D28_BCG

tag: subject


title: 50887_D0_BCG

tag: day


title: 50878_D28_uns

tag: stimulus


title: 50055_D0_uns

tag: risk for tb


title: 50957_D0_BCG

tag: cmv status


title: 53314_D0_BCG

tag: vaccine


title: 53091_D28_BCG


title: 53202_D0_uns


title: Remitting sarcoidosis sample 5 [sarcexp]

value: Remit Sarc

value: Male

value: non-hispanic

tag: total lung capacity, percent predicted

tag: forced vital capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

tag: age

tag: treatment

value: MTX


title: Remitting sarcoidosis sample 6 [sarcexp]

tag: group

tag: Sex

tag: race

tag: ethnicity

tag: scadding


title: Remitting sarcoidosis sample 10 [sarcexp]

value: female

tag: smoking status

value: Former

tag: diffusing capacity of the lung for carbon monoxide, percent predicted

value: Untreated


title: 51708_D28_BCG

tag: tissue

value: PBMC

tag: subject

tag: day

value: Control

value: CMVn


title: 51140_D28_BCG

tag: stimulus

tag: risk for tb

value: Case

tag: cmv status


title: 51462_D0_BCG

tag: vaccine

value: Candin


title: 50832_D0_uns

value: unstimulated


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_20

tag: strain

value: Mixed background

tag: cell type


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_22

value: Skin wound cells

tag: treatment


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_21

value: Post wounding day 21


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_24


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_23


title: Remitting sarcoidosis sample 4 [sarcexp]

tag: group

value: W

value: Never

tag: forced vital capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

tag: age

value: untreated


title: Remitting sarcoidosis sample 2 [sarcexp]

value: Remit Sarc

tag: Sex

tag: race

tag: ethnicity

value: non-hispanic

tag: scadding

tag: total lung capacity, percent predicted


title: Remitting sarcoidosis sample 3 [sarcexp]

value: Male

tag: smoking status

tag: diffusing capacity of the lung for carbon monoxide, percent predicted

value: MTX


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_19


title: 50878_D0_uns

tag: tissue

tag: subject

tag: day

tag: stimulus

tag: risk for tb


title: 51777_D28_BCG

value: BCG

tag: cmv status

tag: vaccine


title: 51129_D0_BCG

value: PBMC


title: Remitting sarcoidosis sample 1 [sarcexp]

tag: group

tag: forced vital capacity, percent predicted

tag: treatment

value: Untreated


title: 53794_D0_uns

value: Control

value: CMVn


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_18

tag: strain

tag: cell type


title: 52259_D28_uns

value: Candin


title: Differentially expressed genes by knocking down of PLODs(300μM_72hr) in T24, 2

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: mock

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

tag: cell line

value: carcinoma

tag: transfection

value: no transfection

source_name: miR-145-3p transfected cell line

value: esophageal cancer

value: PLODs


title: 30044_D28_uns

source_name: PBMC

value: unstimulated

value: Case


title: Differentially expressed genes by knocking down of PLODs(300μM_72hr) in T24, 1

source_name: miR-145-5p transfected cell line


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_17

value: Mixed background

value: Skin wound cells

value: Post wounding day 21


title: 52693_D28_BCG


title: 51456_D0_uns


title: 53171_D28_BCG


title: Differentially expressed genes by knocking down of PLODs(300μM_24hr) in BOY, 2

value: BOY

value: lung cancer


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_15


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_13


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_16


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_12


title: Identification of miR143-3p target genes in A549, 2

value: bladder cancer

source_name: miR-223-5p transfected cell line


title: 51539_D0_uns

value: PBMC


title: Differentially expressed genes by knocking down of KIF2A_2 in SK-MES, 2

value: SK-MES

value: renal cancer

source_name: si-PMM2-2 transfected cell line


title: 52556_D28_uns

value: CMVn


title: 51083_D0_uns

value: Control


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_14


title: 52470_D28_uns

value: Candin


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_11


title: 52117_D28_uns


title: 51566_D28_uns


title: 53748_D0_uns


title: Differentially expressed genes by knocking down of PLODs(300μM_72hr) in BOY, 1

value: no transfection


title: 52470_D0_uns


title: 53307_D28_uns


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_10


title: 53747_D28_uns


title: 51705_D28_BCG

value: BCG


title: Identification of si-AQP9_2 target genes in A498

source_name: si-AQP9_2 transfected cell line


title: 52797_D28_BCG

value: CMVp


title: 53471_D28_BCG


title: Identification of miR143-5p target genes in A549, 1

source_name: miR-223-3p transfected cell line


title: 51134_D28_uns

value: unstimulated


title: Differentially expressed genes by knocking down of KIF2A_1 in SK-MES, 1

source_name: si-PMM2-1 transfected cell line


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_9


title: Identification of si-AQP9_1 target genes in A498

source_name: si-AQP9_1 transfected cell line


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_7


title: 52889_D0_BCG


title: Identification of si-DONSON_2 target genes in 786-O

source_name: si-DONSON_2 transfected cell line


title: 52864_D0_BCG


title: 50919_D28_BCG


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_6


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_5


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_8


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_4


title: 53471_D0_BCG


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_3


title: 51077_D0_BCG


title: Identification of si-DONSON_1 target genes in 786-O

source_name: si-DONSON_1 transfected cell line


title: iPS-microglia_2.0_H9_3

first: Mathew

last: Blurton-Jones

address: 845 Health Sciences Rd

description: CountsTableGEO.txt

data_processing:
RNA-sequencing read integrity was verified using FastQC
BBDuk was used to trim adapters and filter out poor quality reads
Reads were mapped to the hg19 reference genome using HISAT aligner
Complete clustering linkage was measured by pearson coefficient
Lowly expressed genes (expression count summed over all samples < 10) were removed before differential expression analysis
Differential Expression of TPM was calculated using DESeq2
Genome_build: hg19

source_name: Differentiated in vitro H9 ES line

growth_protocol: Growth protocols explicitly defined in Development and Validation of a Simplified Method to Generate Human Microglia from Pluripotent Stem Cells

extract_protocol:
Samples were lysed in RLT and isolated using Rneasy Mini Kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Differentiated in vitro H9 ES line

tag: hpc isolation method

value: Manual pipetting non-adherent cells

tag: replacement of tgfb

value: No


title: Identification of miR-143-3p target genes in TE8

value: esophagus cancer

source_name: miR-143-3p transfected cell line


title: iPS-microglia_2.0_H9_2

description: CountsTableGEO.txt


title: Identification of miR-143-3p target genes in TE1


title: iPS-microglia_2.0_H9_1

description: CountsTableGEO.txt


title: 52218_D0_uns


title: 51035_D28_BCG

value: Case


title: Identification ofmiR-143-5p target genes in TE8

source_name: miR-143-5p transfected cell line


title: 53153_D0_uns


title: 51134_D0_uns


title: 52569_D0_BCG


title: 50329_D0_BCG


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_2

source_name: Skin wound cells

value: Mixed background

value: Skin wound cells

value: Post wounding day 21


title: 50830_D28_BCG

value: PBMC


title: 52259_D28_BCG


title: 51374_D0_BCG


title: 50011_D0_uns


title: iPS-microglia_2.0_ADRC77_3

description: CountsTableGEO.txt

source_name: Differentiated in vitro ADRC77 iPS line

value: Differentiated in vitro ADRC77 iPS line


title: 51324_D0_uns

value: CMVn


title: Sample 2_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_1


title: iPS-microglia_2.0_ADRC77_2

description: CountsTableGEO.txt


title: iPS-microglia_2.0_ADRC77_1

description: CountsTableGEO.txt


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_48

description:
Sm22-Cre;tdTomato
Plikus_C1_PWD21_v1_Mv13_Matrix.txt


title: iPS-microglia_2.0_ADRC76_3

description: CountsTableGEO.txt

source_name: Differentiated in vitro ADRC76 iPS line

value: Differentiated in vitro ADRC76 iPS line


title: iPS-microglia_2.0_ADRC76_2

description: CountsTableGEO.txt


title: 51124_D28_BCG

value: Candin


title: 52512_D28_BCG

value: Control


title: 53169_D0_uns


title: 50424_D0_uns


title: 52219_D28_uns


title: 51108_D0_BCG

value: BCG


title: 51067_D28_BCG

value: CMVp


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_45


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_49


title: iPS-microglia_2.0_ADRC75_3

description: CountsTableGEO.txt

source_name: Differentiated in vitro ADRC75 iPS line

value: Differentiated in vitro ADRC75 iPS line


title: 51986_D28_BCG

source_name: PBMC


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_44


title: 50787_D0_uns

value: unstimulated


title: 53109_D0_uns


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_43


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_47


title: 50307_D0_BCG


title: 51196_D0_BCG


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_46


title: iPS-microglia_2.0_ADRC76_1

description: CountsTableGEO.txt

value: Manual pipetting non-adherent cells


title: iPS-microglia_2.0_ADRC75_1

description: CountsTableGEO.txt

value: No


title: IPS-HPC2.0_ADRC5_3

description: CountsTableGEO.txt

source_name: Differentiated in vitro ADRC5 iPS line

value: Differentiated in vitro ADRC5 iPS line


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_42


title: iPS-microglia_2.0_ADRC75_2

description: CountsTableGEO.txt


title: 50689_D0_uns

value: Case


title: 51324_D28_uns


title: 51360_D28_uns


title: 51991_D0_BCG


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_41

value: Mixed background


title: 51898_D28_uns


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_40

value: Skin wound cells


title: IPS-HPC2.0_ADRC5_1

description: CountsTableGEO.txt


title: 50329_D28_BCG


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_39

value: Post wounding day 21


title: IPS-HPC2.0_ADRC5_2

description: CountsTableGEO.txt


title: IPS-HPC2.0_EGFP_2

description: CountsTableGEO.txt

source_name: Differentiated in vitro EGFP iPS line

value: Differentiated in vitro EGFP iPS line


title: IPS-HPC2.0_EGFP_1

description: CountsTableGEO.txt


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_37


title: 53307_D28_BCG

value: PBMC


title: 51374_D28_BCG

value: CMVn


title: 53142_D28_BCG


title: 51089_D28_uns


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_36


title: 52884_D0_BCG


title: 52219_D0_uns


title: 51995_D28_BCG


title: 53747_D0_uns


title: IPS-HPC2.0_7028_3

description: CountsTableGEO.txt

source_name: Differentiated in vitro 7028 iPS line

value: Differentiated in vitro 7028 iPS line


title: 50421_D28_uns

value: Candin


title: 51067_D0_BCG

value: Control


title: 50551_D28_BCG

value: BCG


title: 51128_D0_uns

value: CMVp


title: 52741_D0_BCG


title: 50246_D28_BCG


title: IPS-HPC2.0_EGFP_3

description: CountsTableGEO.txt


title: IPS-HPC2.0_7028_1

description: CountsTableGEO.txt


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_34


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_33


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_38


title: iPS-microglia2.0 (IDE-1 5 uM) 5

source_name: Differentiated in vitro 10318 iPS line

value: Differentiated in vitro 10318 iPS line

value: 5 uM IDE-1


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_35


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_32


title: iPS-microglia2.0 (IDE-1 5 uM) 4

value: Manual pipetting non-adherent cells


title: IPS-HPC2.0_7028_2

description: CountsTableGEO.txt

value: No


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_31


title: 51089_D0_uns

value: unstimulated


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_30


title: iPS-microglia2.0 (IDE-1 5 uM) 3


title: 52549_D28_BCG


title: 51777_D0_BCG


title: 51595_D28_uns


title: 53314_D0_uns


title: 51710_D28_BCG


title: 50584_D0_uns


title: 51462_D28_uns


title: iPS-microglia2.0 (IDE-1 5 uM) 2


title: 52901_D0_uns


title: 51184_D0_BCG


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_29


title: 50178_D28_BCG

value: Case


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_28

value: Mixed background


title: iPS-microglia2.0 (IDE-1 5 uM) 1


title: iPS-microglia2.0 (IDE-1 50 uM) 5

value: 50 uM IDE-1


title: iPS-microglia2.0 (IDE-1 50 uM) 4


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_26

value: Skin wound cells

value: Post wounding day 21


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_27


title: 51270_D0_uns

value: PBMC


title: 53042_D0_uns

value: CMVn


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_25


title: 50842_D0_BCG


title: iPS-microglia2.0 (IDE-1 50 uM) 3


title: iPS-microglia2.0 (IDE-1 50 uM) 2


title: Identification ofmiR-143-5p target genes in TE1

source_name: mock

value: esophagus cancer

value: no transfection


title: 51566_D28_BCG

value: Control

value: Candin


title: 51539_D0_BCG

value: BCG


title: 51893_D28_uns


title: 52456_D28_uns


title: 52901_D28_uns


title: iPS-microglia2.0 (IDE-1 500 uM) 3

value: Differentiated in vitro 10318 iPS line

value: 500 uM IDE-1


title: 51841_D28_uns


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_23


title: iPS-microglia2.0 (IDE-1 500 uM) 2

value: Manual pipetting non-adherent cells


title: 51776_D0_BCG


title: 52456_D0_uns


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_24


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_21


title: 50689_D28_BCG


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_20


title: iPS-microglia2.0 (IDE-1 500 uM) 1


title: iPS-microglia2.0 (TGFB1) 4

value: No


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_19


title: 50887_D28_BCG


title: iPS-microglia2.0 (TGFB1) 3


title: 50689_D0_BCG


title: iPS-microglia2.0 (TGFB1) 2


title: 51035_D28_uns

value: unstimulated


title: 53153_D28_BCG

value: Case


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_17

value: Mixed background


title: 52736_D28_uns


title: 50821_D28_uns


title: 51270_D0_BCG


title: 52890_D28_uns


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_18


title: 50957_D28_BCG


title: 51077_D28_uns


title: iPS-microglia2.0 (TGFB1) 1


title: 52569_D0_uns


title: 50643_D0_BCG


title: 52687_D28_BCG


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_16


title: iPS-microglia2.0 MACS 2

value: Differentiated in vitro EGFP iPS line

value: MACS


title: iPS-microglia2.0 (IDE-1 50 uM) 1

value: 50 uM IDE-1


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_15

value: Skin wound cells

value: Post wounding day 21


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_14


title: iPS-microglia2.0 FACS 2

value: FACS


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_13


title: iPS-microglia2.0 FACS 1


title: 52569_D28_uns

value: PBMC

value: CMVn


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_12


title: iPS-microglia2.0 no sorting 3


title: 50617_D0_BCG

value: Control


title: iPS-microglia2.0 no sorting 2


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_11


title: iPS-microglia2.0 MACS 1


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_10


title: 50011_D0_BCG

value: BCG


title: 51708_D28_uns


title: 51093_D28_BCG

value: Candin


title: 51351_D28_BCG


title: 52378_D0_uns


title: 52219_D28_BCG

value: CMVp


title: 52600_D0_uns


title: 50352_D0_uns


title: 53257_D28_BCG


title: 52693_D0_uns


title: 51083_D28_BCG


title: iPS-microglia2.0 no sorting 1

value: Manual pipetting non-adherent cells


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_8


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_9


title: iPS-microglia 2

value: No


title: iPS-microglia 3

value: Differentiated in vitro 10318 iPS line


title: 50643_D28_BCG


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_7


title: iPS-microglia 1


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_6


title: 51270_D28_BCG

value: Case


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_5

value: Mixed background


title: 51863_D28_BCG


title: 50878_D28_BCG


title: 52890_D0_uns

value: unstimulated


title: 50263_D0_BCG


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_4


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_3


title: 50055_D0_BCG


title: 51595_D28_BCG


title: 53308_D28_BCG


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_2


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_1


title: 51140_D28_uns


title: 53202_D28_BCG


title: 53202_D0_BCG


title: 52850_D0_uns


title: Sarcoidosis sample 8 [cbdexp]

description: polyA selected RNA extracted from BALF

hyb_protocol: Affymetrix manufacturer instructions

scan_protocol: GCOS

data_processing: Partek Genomics Suite used for QC and analysis, data was quantile normalized and log transformed

source_name: BAL fluid

label_protocol: Ambion Message Amp II Kit

growth_protocol: NA, primary patient cells were used

extract_protocol: Qiagen AllPrep

treatment_protocol: NA, cells did not undergo treatment prior to extraction

tag: dx

value: Sarcoidosis

tag: Sex

value: Male

tag: race

value: W

tag: ethnicity

value: non-hispanic

tag: smoking status

value: Never

tag: total lung capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

tag: diffusing capacity of the lung for carbon monoxide, percent predicted

tag: age

value: Treated

value: Steroids


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_33

description:
Sm22-Cre;tdTomato
Plikus_C1_PWD15_v2_Mv13_Matrix.txt

value: Skin wound cells

value: Post wounding day 15


title: BeS sample 8 [cbdexp]

description: polyA selected RNA extracted from BALF

value: BeS

tag: forced vital capacity, percent predicted

value: Untreated


title: 51129_D28_uns

tag: tissue

value: PBMC

tag: subject

tag: day

tag: stimulus

tag: risk for tb

value: Control

tag: cmv status

value: CMVn

tag: vaccine


title: 50878_D0_BCG

value: BCG

value: Candin


title: 52549_D28_uns

value: unstimulated

value: CMVp


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_32

tag: strain

value: Mixed background

tag: cell type

tag: treatment


title: BeS sample 6 [cbdexp]

description: polyA selected RNA extracted from BALF

tag: dx

tag: Sex

value: female

tag: race

value: W

tag: ethnicity


title: 52850_D28_uns

value: Case


title: 51116_D28_BCG


title: 50687_D0_BCG


title: 51789_D0_uns


title: CBD sample 8 [cbdexp]

description: polyA selected RNA extracted from BALF

value: CBD

value: Male

value: non-hispanic

tag: smoking status

value: Never

tag: total lung capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

tag: diffusing capacity of the lung for carbon monoxide, percent predicted

value: Treated


title: Sample 1_PWD21_WoundDermis_SingleCells_Fluidigm_Cell_22

value: Skin wound cells

value: Post wounding day 21


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_30

value: Post wounding day 15


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_29


title: 51116_D0_BCG

tag: tissue

value: PBMC

tag: subject

value: CMVn


title: BeS sample 7 [cbdexp]

description: polyA selected RNA extracted from BALF

value: BeS

value: Former

tag: forced vital capacity, percent predicted

tag: age

value: Untreated


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_31

value: Mixed background


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_28


title: CBD sample 7 [cbdexp]

description: polyA selected RNA extracted from BALF


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_25


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_26


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_27


title: 51238_D0_uns

tag: day

tag: stimulus

value: unstimulated

tag: risk for tb

value: Control

tag: cmv status


title: Sarcoidosis sample 7 [cbdexp]

description: polyA selected RNA extracted from BALF

value: Sarcoidosis

value: female

value: W

tag: treatment


title: 51558_D0_BCG

value: BCG

tag: vaccine

value: Candin


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_24

tag: strain

tag: cell type


title: BeS sample 4 [cbdexp]

description: polyA selected RNA extracted from BALF

tag: dx

tag: Sex

value: Male

tag: race

tag: ethnicity

value: hispanic


title: Sarcoidosis sample 2 [cbdexp]

description: polyA selected RNA extracted from BALF

value: non-hispanic

tag: smoking status

value: Never

tag: total lung capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

tag: diffusing capacity of the lung for carbon monoxide, percent predicted


title: 51776_D0_uns

tag: tissue

value: PBMC

tag: subject


title: 50833_D0_BCG

tag: day

tag: stimulus

value: Case

value: CMVn


title: 52456_D0_BCG

tag: risk for tb

tag: cmv status


title: 50833_D28_BCG

value: CMVp

tag: vaccine


title: 50957_D28_uns


title: CBD sample 6 [cbdexp]

description: polyA selected RNA extracted from BALF

value: CBD

tag: forced vital capacity, percent predicted

tag: age

tag: treatment

value: Treated

value: Steroids


title: 51616_D0_BCG

value: Control


title: 51089_D0_BCG


title: 51616_D28_BCG


title: 51776_D28_uns

value: unstimulated


title: BeS sample 5 [cbdexp]

description: polyA selected RNA extracted from BALF

tag: dx

value: BeS

tag: Sex

value: Untreated


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_23

tag: strain

value: Mixed background

tag: cell type

value: Skin wound cells

value: Post wounding day 15


title: 52607_D0_uns


title: BeS sample 2 [cbdexp]

description: polyA selected RNA extracted from BALF

value: Male

tag: race

value: W

tag: ethnicity

tag: smoking status

tag: total lung capacity, percent predicted


title: 51128_D28_BCG

tag: tissue

tag: subject

value: BCG

value: Candin


title: 52884_D28_uns

value: PBMC

tag: day

tag: stimulus


title: 50887_D28_uns

tag: risk for tb

value: Case

tag: cmv status

value: CMVn


title: Sarcoidosis sample 3 [cbdexp]

description: polyA selected RNA extracted from BALF

value: Sarcoidosis

value: non-hispanic

value: Current

tag: forced vital capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

tag: diffusing capacity of the lung for carbon monoxide, percent predicted

value: MTX


title: 51558_D28_uns

value: unstimulated

value: Control

tag: vaccine


title: 51089_D28_BCG


title: BeS sample 3 [cbdexp]

description: polyA selected RNA extracted from BALF

tag: dx

value: BeS

tag: Sex

tag: age

tag: treatment

value: Untreated


title: Sarcoidosis sample 4 [cbdexp]

description: polyA selected RNA extracted from BALF

tag: race

tag: ethnicity

value: Never


title: 52741_D0_uns


title: 50246_D28_uns

value: CMVp


title: 53142_D28_uns


title: 50421_D0_BCG


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_22

tag: strain

value: Mixed background

tag: cell type

value: Skin wound cells

value: Post wounding day 15


title: 50826_D0_uns

tag: tissue

tag: subject


title: CBD sample 5 [cbdexp]

description: polyA selected RNA extracted from BALF

value: CBD

value: female

value: W

value: hispanic

tag: smoking status

tag: total lung capacity, percent predicted

value: Treated

value: Steroids


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_21


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_20


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_19


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_18


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_17


title: MixCellLines-HTO

city: Boston

first: Soumya

last: Badrinath

state: MA

address: One Jimmy Fund Way

institute: Dana-Farber Cancer Institute

description: polyA HTO

data_processing:
Read 1 includes cell barcode, UMI; read 2 includes cDNA read.
10x data were processed using Drop-seq tools v1.12 (Macosko et al., 2015), specifying 50,000 cell barcodes to return
ADT data were mapped to a 12 bases or a 10 bases reference ADT list separately
HTO data were mapped to a 12 bases reference HTO list
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file for 10x data; comma-delimited file for ADT and HTO mapping

molecule: polyA RNA

source_name: HEK, THP1, K562 and KG1 cells

extract_protocol:
For genotyping genomic DNA was purified using the All-prep kit (Qiagen, USA). For HTO and ADT we followed the protocol as described for CITE-seq (Stoeckius et al, 2017)
For genotyping the Infinium core exome 24 array (Illumina, USA) was used according to manufacturer instructions; ‘Stained’ and washed cells were loaded into 10x Genomics single cell 3’ system and processed according to manufacturer’s instructions, and the CITE-seq protocols (Stoeckius et al, 2017).

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from Allcells (USA). For HTO and ADT cells were ‘stained’ with hashtagging antibodies and CITE-seq antibodies as described for CITE-seq (Stoeckius et al, 2017)

tag: cell line

value: mixed sample (non-demultiplexed) comprising HEK, THP1, K562 and KG1 cells

tag: antibodies/tags

value: HEK_A, HEK_B, HEK_C, THP1_A

tag: library type

value: 10x Genomics single cell 3' v2


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_16


title: MixCellLines-RNA

description: polyA RNA


title: 51238_D28_BCG

value: PBMC

tag: day

tag: stimulus

value: BCG

tag: risk for tb

value: Control

tag: cmv status

value: CMVn


title: 50617_D28_uns

value: unstimulated

tag: vaccine


title: 50833_D28_uns

value: Case

value: CMVp


title: Sarcoidosis sample 1 [cbdexp]

description: polyA selected RNA extracted from BALF

tag: dx

value: Sarcoidosis

tag: Sex

value: Male

value: AA

value: non-hispanic

value: Former

tag: forced vital capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

tag: diffusing capacity of the lung for carbon monoxide, percent predicted

tag: age

tag: treatment

value: Untreated


title: CBD sample 4 [cbdexp]

description: polyA selected RNA extracted from BALF

value: CBD

tag: race

value: W

tag: ethnicity

tag: smoking status

value: Never

value: Treated

value: Steroids


title: BeS sample 1 [cbdexp]

description: polyA selected RNA extracted from BALF

value: BeS

tag: total lung capacity, percent predicted


title: CBD sample 1 [cbdexp]

description: polyA selected RNA extracted from BALF


title: 50617_D0_uns

tag: tissue

value: PBMC

tag: subject

value: Control


title: 51156_D0_BCG

tag: day

tag: stimulus

value: BCG

value: CMVn

value: Candin


title: 52687_D0_uns

value: unstimulated

tag: risk for tb

tag: cmv status


title: 1742: PRRX1b-infected hOPCs

city: Buffalo

first: Fraser

middle: James

last: Sim

state: NY

address: 3435 Main Street

department: Pharmacology

institute: University at Buffalo

data_processing:
tophat (2.1.1)
htseq-count (0.6.1)
Genome_build: hg19
Supplementary_files_format_and_content: htseq output file

source_name: human oligodendrocyte progenitor cells

extract_protocol:
Omega Total RNA Kit
Illumina TruSeq RNA sample preparation kit

tag: sample

value: c

value: Human oligodendrocyte progenitor cells (hOPCs)

tag: genotype/variation

value: PRRX1b over-expression


title: 50543_D28_BCG

value: Case

tag: vaccine


title: CBD sample 2 [cbdexp]

description: polyA selected RNA extracted from BALF

tag: dx

tag: Sex

value: Male

value: non-hispanic

value: Former

tag: forced vital capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

value: Untreated


title: 52850_D28_BCG


title: 20079_D0_uns


title: 52956_D0_uns


title: 53042_D0_BCG


title: CBD sample 3 [cbdexp]

description: polyA selected RNA extracted from BALF

value: CBD

tag: race

value: W

tag: diffusing capacity of the lung for carbon monoxide, percent predicted

tag: age

tag: treatment


title: 1741: PRRX1a-infected hOPCs

tag: tissue

value: PRRX1a over-expression


title: 51374_D0_uns

value: PBMC

tag: subject


title: 51768_D28_uns

tag: day


title: 50245_D0_BCG

tag: stimulus


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_15

tag: strain

value: Mixed background

tag: cell type

value: Skin wound cells

value: Post wounding day 15


title: 51083_D28_uns

tag: risk for tb

value: Control

tag: cmv status

value: CMVn


title: 53430_D28_uns

value: unstimulated

value: CMVp

tag: vaccine

value: Candin


title: 50066_D28_BCG

value: BCG


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_13


title: 50643_D28_uns


title: 1740: mCherry-infected hOPCs

tag: sample

value: c

value: Human oligodendrocyte progenitor cells (hOPCs)

tag: genotype/variation

value: mCherry control


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_12


title: 1714: PRRX1b-infected hOPCs

value: b

value: PRRX1b over-expression


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_11


title: 1713: PRRX1a-infected hOPCs


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_10


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_9


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_8


title: 1547: PRRX1a-infected hOPCs

value: a


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_7


title: 50643_D0_uns


title: 1546: mCherry-infected hOPCs


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_6


title: 1712: mCherry-infected hOPCs


title: 50821_D28_BCG


title: WF9_HE463_SMC12_8_3d

city: La Jolla

first: Kristin

last: Baldwin

address: 10550 North Torrey Pines Road

department: Department of Neuroscience

institute: The Scripps Research Institute

description: Day3,   genotype NRNR, patient2, WT, cell line wf9, experiment: D1, sequencing  batch: Set3

data_processing:
Illumina Casava1.8 software used for basecalling.
Adapters and low quality bases were removed using Trimmomatic (v0.32, ILLUMINACLIP: TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3), reads were then aligned using STAR and counts were generated using HTSeq.
Raw and vst-normalized count tables were generated using the R package, 'DESeq2'.
Genome_build: hg19
Supplementary_files_format_and_content: Raw and vst-normalized counts are supplied as tab-delimited text files for all bulk RNA-Seq samples.

source_name: hiPSC

growth_protocol: Chemically defined media, see the paper for the details

extract_protocol:
Direct-zol RNA MiniPrep Kit (Zymo Rsearch)
Ovation RNA-Seq System V2, Agilent SureSelect XT2

value: mesenchymal progenitors

tag: day post-induction

tag: genotype

value: NRNR

value: WT

tag: cell line

tag: experiment

tag: sequencing  batch


title: 51863_D28_uns

value: PBMC


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_5

value: Mixed background

value: Skin wound cells

tag: treatment

value: Post wounding day 15


title: 51901_D0_uns

tag: tissue

value: unstimulated

value: Control

value: CMVn


title: 51239_D0_uns

tag: subject

value: Candin


title: 1548: PRRX1b-infected hOPCs


title: 52329_D28_uns

tag: day


title: WF5_HE463_SMC12_8_3d

description: Day3,   genotype NRNR, patient2, KO, cell line wf5, experiment: D1, sequencing  batch: Set3

value: KO


title: 53747_D28_BCG

tag: stimulus

value: BCG

value: Case


title: 51134_D28_BCG


title: 51456_D0_BCG


title: 51705_D28_uns


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_4

tag: strain


title: WF5_HE463_SMC12_8_17d

description: Day17,  genotype NRNR, patient2, KO, cell line wf5, experiment: D1, sequencing  batch: Set3

tag: cell type

value: vascular smooth muscle cells


title: 51710_D0_uns

tag: risk for tb


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_3


title: 50178_D28_uns

tag: cmv status


title: 52470_D0_BCG

tag: vaccine


title: 51024_D28_BCG


title: 52190_D0_BCG

value: CMVp


title: 53457_D28_BCG


title: WF36_HE463_SMC12_8_3d

description: Day3,   genotype NRNR, patient2, KO, cell line wf36, experiment: D1, sequencing  batch: Set3


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_1


title: 51184_D0_uns


title: 53298_D28_BCG


title: WF12_HE463_SMC12_8_3d

description: Day3,   genotype NRNR, patient2, WT, cell line wf12, experiment: D1, sequencing  batch: Set3


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_84

description:
Sm22-Cre;tdTomato
Plikus_C1_PWD15_v1_Mv13_Matrix.txt


title: WB46_C512_SMC12_8_3d

description: Day3,  genotype _R_R, patient1, KO, cell line wb46, experiment: D1, sequencing  batch: Set3


title: WB46_C512_SMC12_8_17d

description: Day17,  genotype _R_R, patient1, KO, cell line wb46, experiment: D1, sequencing  batch: Set3


title: WF36_HE463_SMC12_8_17d

description: Day17,  genotype NRNR, patient2, KO, cell line wf36, experiment: D1, sequencing  batch: Set3


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_2


title: 52889_D28_uns


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_82


title: WB46_C512_SMC12_18Day17

description: Day17,  genotype _R_R, patient1, KO, cell line wb46, experiment: D2, sequencing  batch: Set3


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_83


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_81


title: 52764_D28_uns


title: 51129_D0_uns


title: 51140_D0_uns


title: 52586_D28_uns


title: 53215_D28_BCG


title: 53298_D0_BCG


title: 50687_D28_BCG


title: 53202_D28_uns


title: 50055_D28_uns


title: 52607_D0_BCG


title: 51196_D0_uns


title: 50551_D0_uns


title: 51129_D28_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_79


title: TAL1_9_C512_SMC12_18Day17

description: Day3,  genotype _R_R, patient1, KO, cell line Tal1_9, experiment: D1, sequencing  batch: Set3


title: 50153_D28_BCG


title: 50015_D28_uns


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_80


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_78


title: TAL2_3C512_SMC12_8_3d

description: Day17,  genotype _R_R, patient1, WT, cell line Tal2_3, experiment: D1, sequencing  batch: Set3


title: TAL2_3C_512_SMC12_8_17

description: Day3,  genotype _R_R, patient1, WT, cell line Tal2_3, experiment: D1, sequencing  batch: Set3


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_77


title: TAL1_9C_512_SMC12_8_17d

description: Day17,  genotype _R_R, patient1, KO, cell line Tal1_9, experiment: D1, sequencing  batch: Set3


title: TAL1_9C512_SMC12_8_3d

description: Day17,  genotype _R_R, patient1, KO, cell line Tal1_9, experiment: D2, sequencing  batch: Set3


title: 52736_D28_BCG


title: Sample 2_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_14


title: TAL1_2C512_SMC12_8_3d

description: Day17,  genotype _R_R, patient1, WT, cell line Tal1_2, experiment: D1, sequencing  batch: Set3


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_76


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_75


title: 50352_D0_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_74


title: HE463_7SMC9_25E17_D17

description: Day17,  genotype NRNR, patient2, WT, cell line E17, experiment: C3, sequencing  batch: Set2


title: 52693_D0_BCG


title: HE463_7SMC9_25E14_D17

description: Day17,  genotype NRNR, patient2, WT, cell line E14, experiment: C3, sequencing  batch: Set2


title: 53314_D28_uns


title: 20079_D0_BCG


title: TAL1_2_C512_SMC12_8_17d

description: Day3,  genotype _R_R, patient1, WT, cell line Tal1_2, experiment: D1, sequencing  batch: Set3


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_72


title: HE463_7SMC9_18E17_D17

description: Day17,  genotype NRNR, patient2, WT, cell line E17, experiment: C2, sequencing  batch: Set2


title: 50153_D0_BCG


title: 52864_D0_uns


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_73


title: 50967_D28_uns


title: 50842_D0_uns


title: 53471_D28_uns


title: 51184_D28_BCG


title: 50919_D28_uns


title: 51239_D28_BCG


title: 52210_D0_uns


title: HE463_7SMC9_18E14_D17

description: Day17,  genotype NRNR, patient2, WT, cell line E14, experiment: C2, sequencing  batch: Set2


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_69


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_68


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_71


title: 53472_D28_uns


title: E56_HE463_SMC12_8_17d

description: Day17,  genotype NRNR, patient2, KO, cell line E56, experiment: D1, sequencing  batch: Set3


title: 50967_D28_BCG


title: 50617_D28_BCG


title: 53302_D0_uns


title: 50879_D28_uns


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_70

description:
Sm22-Cre;tdTomato
Plikus_C1_PWD15_v1_Mv13_Matrix.txt


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_67


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_66


title: 52970_D28_BCG


title: 52956_D0_BCG


title: E17_HE463_SMC12_8_3d

description: Day3,   genotype NRNR, patient2, WT, cell line E17, experiment: D1, sequencing  batch: Set3


title: 52207_D28_BCG


title: 51705_D0_uns


title: 50178_D0_uns


title: 50832_D28_uns


title: E14_HE463_SMC12_8_3d

description: Day3,   genotype NRNR, patient2, WT, cell line E14, experiment: D1, sequencing  batch: Set3


title: E14_HE463_SMC12_8_17d

description: Day17,  genotype NRNR, patient2, WT, cell line E14, experiment: D1, sequencing  batch: Set3


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_63


title: E50_HE463_SMC12_8_17d

description: Day17,  genotype NRNR, patient2, KO, cell line E50, experiment: D1, sequencing  batch: Set3


title: D3_SMC_patient2_NRNR2_WT_exp3_lineE17

description: Day3,   genotype NRNR, patient2, WT, cell line E17, experiment: B3, sequencing  batch: Set1


title: 52556_D28_BCG


title: 53794_D28_uns


title: E56_HE463_SMC12_8_3d

description: Day3,   genotype NRNR, patient2, KO, cell line E56, experiment: D1, sequencing  batch: Set3


title: 51024_D0_BCG


title: 53472_D28_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_65


title: 51768_D28_BCG


title: 50584_D0_BCG


title: 52470_D28_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_64


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_61


title: D3_SMC_patient2_NRNR2_WT_exp3_lineE14

description: Day3,   genotype NRNR, patient2, WT, cell line E14, experiment: B3, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_60


title: D3_SMC_patient2_NRNR2_WT_exp2_lineE17

description: Day3,   genotype NRNR, patient2, WT, cell line E17, experiment: B2, sequencing  batch: Set1


title: D3_SMC_patient2_NRNR2_WT_exp2_lineE14

description: Day3,   genotype NRNR, patient2, WT, cell line E14, experiment: B2, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_62


title: 53171_D28_uns


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_59


title: D3_SMC_patient2_NRNR2_KO_exp3_lineE56

description: Day3,   genotype NRNR, patient2, KO, cell line E56, experiment: B3, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_58


title: 51373_D0_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_57


title: D3_SMC_patient2_NRNR2_KO_exp3_line53

description: Day3,   genotype NRNR, patient2, KO, cell line E53, experiment: B3, sequencing  batch: Set1


title: 51901_D28_uns


title: 53308_D28_uns


title: D3_SMC_patient2_NRNR2_KO_exp3_lineE50

description: Day3,   genotype NRNR, patient2, KO, cell line E50, experiment: B3, sequencing  batch: Set1


title: 51140_D0_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_56


title: 53308_D0_BCG


title: 50821_D0_BCG


title: D3_SMC_patient2_NRNR2_KO_exp2_lineE56

description: Day3,   genotype NRNR, patient2, KO, cell line E56, experiment: B2, sequencing  batch: Set1


title: 53137_D28_BCG


title: D3_SMC_patient2_NRNR2_KO_exp2_lineE50

description: Day3,   genotype NRNR, patient2, KO, cell line E50, experiment: B2, sequencing  batch: Set1


title: 51239_D28_uns


title: 53308_D0_uns


title: 53430_D28_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_54


title: 51893_D28_BCG


title: D3_SMC_patient1_R_R_1_WT_exp5_line2_3

description: Day3,  genotype _R_R, patient1, WT, cell line Tal2_3, experiment: A5, sequencing  batch: Set1


title: 51789_D28_uns


title: 53091_D0_uns


title: 51841_D0_BCG


title: 52456_D28_BCG


title: 51201_D0_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_53


title: D3_SMC_patient1_R_R_1_WT_exp5_line1_5

description: Day3,  genotype _R_R, patient1, WT, cell line Tal1_5, experiment: A5, sequencing  batch: Set1


title: 50349_D28_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_52

description:
Sm22-Cre;tdTomato
Plikus_C1_PWD15_v1_Mv13_Matrix.txt


title: D3_SMC_patient1_R_R_1_WT_exp5_line1_2

description: Day3,  genotype _R_R, patient1, WT, cell line Tal1_2, experiment: A5, sequencing  batch: Set1


title: D3_SMC_patient1_R_R_1_WT_exp4_line2_3

description: Day3,  genotype _R_R, patient1, WT, cell line Tal2_3, experiment: A4, sequencing  batch: Set1


title: 51991_D28_uns


title: 53091_D28_uns


title: 51238_D28_uns


title: 50830_D0_uns


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_50


title: D3_SMC_patient1_R_R_1_WT_exp4_line1_5

description: Day3,  genotype _R_R, patient1, WT, cell line Tal1_5, experiment: A4, sequencing  batch: Set1


title: D3_SMC_patient1_R_R_1_KO_exp5_line2_24

description: Day3,  genotype _R_R, patient1, KO, cell line Tal2_24, experiment: A5, sequencing  batch: Set1


title: 53109_D0_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_49


title: 51093_D28_uns


title: D3_SMC_patient1_R_R_1_KO_exp5_line1_9

description: Day3,  genotype _R_R, patient1, KO, cell line Tal1_9, experiment: A5, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_47


title: D3_SMC_patient1_R_R_1_KO_exp5_line1_15

description: Day3,  genotype _R_R, patient1, KO, cell line Tal1_15, experiment: A5, sequencing  batch: Set1


title: 50424_D28_BCG


title: 50329_D28_uns


title: D3_SMC_patient1_R_R_1_KO_exp4_line1_9

description: Day3,  genotype _R_R, patient1, KO, cell line Tal1_9, experiment: A4, sequencing  batch: Set1


title: 51498_D0_uns


title: 50544_D0_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_46


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_45


title: 51995_D28_uns


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_48


title: 51351_D28_uns


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_44


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_51


title: 51067_D0_uns


title: 50424_D0_BCG


title: 52797_D28_uns


title: E50_HE463_SMC12_8_3d

description: Day3,   genotype NRNR, patient2, KO, cell line E50, experiment: D1, sequencing  batch: Set3


title: 50879_D28_BCG


title: 51346_D28_BCG


title: 51134_D0_BCG


title: 51789_D0_BCG


title: 50879_D0_BCG


title: D17SMC_patient2_NRNR2_WT_exp4_lineE14

description: Day17,  genotype NRNR, patient2, WT, cell line E14, experiment: B4, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_43


title: D17SMC_patient2_NRNR2_WT_exp3_lineE17

description: Day17,  genotype NRNR, patient2, WT, cell line E17, experiment: B3, sequencing  batch: Set1


title: D17SMC_patient2_NRNR2_WT_exp4_lineE17

description: Day17,  genotype NRNR, patient2, WT, cell line E17, experiment: B4, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_41


title: D3_SMC_patient1_R_R_1_KO_exp4_line1_15

description: Day3,  genotype _R_R, patient1, KO, cell line Tal1_15, experiment: A4, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_42


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_40


title: D17SMC_patient2_NRNR2_WT_exp3_lineE14

description: Day17,  genotype NRNR, patient2, WT, cell line E14, experiment: B3, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_39


title: 53215_D0_BCG


title: D17SMC_patient2_NRNR2_WT_exp2_lineE17

description: Day17,  genotype NRNR, patient2, WT, cell line E17, experiment: B2, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_38


title: D17SMC_patient2_NRNR2_WT_exp2_lineE14

description: Day17,  genotype NRNR, patient2, WT, cell line E14, experiment: B2, sequencing  batch: Set1


title: 52207_D0_uns


title: 52207_D28_uns


title: 53314_D28_BCG


title: D17SMC_patient2_NRNR2_KO_exp4_lineE56

description: Day17,  genotype NRNR, patient2, KO, cell line E56, experiment: B4, sequencing  batch: Set1


title: 52190_D28_BCG


title: 52640_D0_BCG


title: 51710_D28_uns


title: 51184_D28_uns


title: 52970_D0_uns


title: 51566_D0_uns


title: 53207_D28_uns


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_37

description:
Sm22-Cre;tdTomato
Plikus_C1_PWD15_v1_Mv13_Matrix.txt


title: 52970_D28_uns


title: 50066_D28_uns


title: 52044_D28_uns


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_36


title: 50263_D0_uns


title: D17SMC_patient2_NRNR2_KO_exp4_lineE50

description: Day17,  genotype NRNR, patient2, KO, cell line E50, experiment: B4, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_35


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_34


title: 52329_D28_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_33


title: 51626_D0_uns


title: D17SMC_patient2_NRNR2_KO_exp3_lineE53

description: Day17,  genotype NRNR, patient2, KO, cell line E53, experiment: B3, sequencing  batch: Set1


title: D17SMC_patient2_NRNR2_KO_exp3_lineE50

description: Day17,  genotype NRNR, patient2, KO, cell line E50, experiment: B3, sequencing  batch: Set1


title: D17SMC_patient2_NRNR2_KO_exp3_lineE56

description: Day17,  genotype NRNR, patient2, KO, cell line E56, experiment: B3, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_55


title: D17SMC_patient2_NRNR2_KO_exp2_lineE56

description: Day17,  genotype NRNR, patient2, KO, cell line E56, experiment: B2, sequencing  batch: Set1


title: 52218_D28_uns


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_32


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_31


title: D17SMC_patient2_NRNR2_KO_exp4_lineE53

description: Day17,  genotype NRNR, patient2, KO, cell line E53, experiment: B4, sequencing  batch: Set1


title: 52207_D0_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_30


title: D17SMC_patient2_NRNR2_KO_exp2_lineE50

description: Day17,  genotype NRNR, patient2, KO, cell line E50, experiment: B2, sequencing  batch: Set1


title: 53153_D28_uns


title: 52890_D28_BCG


title: 52259_D0_uns


title: 53169_D28_uns


title: 50011_D28_uns


title: 52569_D28_BCG


title: 51077_D28_BCG


title: 50349_D28_uns


title: 52378_D0_BCG


title: 50307_D28_uns


title: 50424_D28_uns


title: 51108_D28_BCG


title: D17SMC_patient1_R_R_1_WT_exp4_line1_5

description: Day17,  genotype _R_R, patient1, WT, cell line Tal1_5, experiment: A4, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_28


title: 52891_D28_BCG


title: D17SMC_patient1_R_R_1_WT_exp3_line1_2

description: Day17,  genotype _R_R, patient1, WT, cell line Tal1_2, experiment: A3, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_27


title: D17SMC_patient1_R_R_1_WT_exp4_line2_3

description: Day17,  genotype _R_R, patient1, WT, cell line Tal2_3, experiment: A4, sequencing  batch: Set1


title: D17SMC_patient1_R_R_1_KO_exp4_line1_15

description: Day17,  genotype _R_R, patient1, KO, cell line Tal1_15, experiment: A4, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_29


title: D17SMC_patient1_R_R_1_KO_exp3_line2_24

description: Day17,  genotype _R_R, patient1, KO, cell line Tal2_24, experiment: A3, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_26


title: 50842_D28_uns


title: D0_iPS_patient2_NRNR2_WT_lineE17

description: Day0,  genotype NRNR, patient2, WT, cell line E17, experiment: exp1, sequencing  batch: Set1

value: hiPSC


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_23


title: 52797_D0_uns


title: 52864_D28_uns


title: 53305_D28_BCG


title: 52687_D28_uns


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_24


title: 52210_D0_BCG


title: D0_iPS_patient2_NRNR2_WT_lineE14

description: Day0,  genotype NRNR, patient2, WT, cell line E14, experiment: exp1, sequencing  batch: Set1


title: D0_iPS_patient2_NRNR2_KO_lineE56

description: Day0,  genotype NRNR, patient2, KO, cell line E56, experiment: exp1, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_22


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_25


title: 52546_D28_BCG


title: 52956_D28_uns


title: 50887_D0_uns


title: 50957_D0_uns


title: 52117_D28_BCG


title: 52890_D0_BCG


title: 51558_D0_uns


title: D0_iPS_patient2_NRNR2_KO_lineE53

description: Day0,  genotype NRNR, patient2, KO, cell line E53, experiment: exp1, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_20

description:
Sm22-Cre;tdTomato
Plikus_C1_PWD15_v1_Mv13_Matrix.txt


title: 51128_D0_BCG


title: D0_iPS_patient2_NRNR2_KO_lineE50

description: Day0,  genotype NRNR, patient2, KO, cell line E50, experiment: exp1, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_21


title: 50689_D28_uns


title: 52741_D28_uns


title: D0_iPS_patient1_R_R_1_WT_line2_4

description: Day0,  genotype _R_R, patient1, WT, cell line Tal2_4, experiment: exp1, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_19


title: D0_iPS_patient1_R_R_1_WT_line1_5

description: Day0,  genotype _R_R, patient1, WT, cell line Tal1_5, experiment: exp1, sequencing  batch: Set1


title: D0_iPS_patient1_R_R_1_WT_line1_2

description: Day0,  genotype _R_R, patient1, WT, cell line Tal1_2, experiment: exp1, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_16


title: 52901_D28_BCG


title: 50307_D28_BCG


title: 51196_D28_BCG


title: 51777_D28_uns


title: 52190_D28_uns


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_17


title: 53457_D28_uns


title: 50832_D28_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_15


title: 50830_D0_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_18


title: 51498_D28_BCG


title: 51991_D28_BCG


title: 53307_D0_uns


title: D0_iPS_patient1_R_R_1_KO_line1_9

description: Day0,  genotype _R_R, patient1, KO, cell line Tal1_9, experiment: exp1, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_13


title: D0_iPS_patient1_R_R_1_KO_line1_19

description: Day0,  genotype _R_R, patient1, KO, cell line Tal1_19, experiment: exp1, sequencing  batch: Set1


title: D0_iPS_patient1_R_R_1_WT_line2_3

description: Day0,  genotype _R_R, patient1, WT, cell line Tal2_3, experiment: exp1, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_14


title: 50178_D0_BCG


title: D0_iPS_patient1_R_R_1_KO_line1_15

description: Day0,  genotype _R_R, patient1, KO, cell line Tal1_15, experiment: exp1, sequencing  batch: Set1


title: C512_17SMC9_25TAL1_2_D17

description: Day17,  genotype _R_R, patient1, WT, cell line Tal1_2, experiment: C3, sequencing  batch: Set2


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_11


title: 52190_D0_uns


title: C512_17SMC9_18TAL2_3_D17

description: Day17,  genotype _R_R, patient1, WT, cell line Tal2_3, experiment: C2, sequencing  batch: Set2


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_9


title: 53794_D28_BCG


title: 51108_D28_uns


title: 53169_D28_BCG


title: C512_17SMC9_18TAL1_2_D17

description: Day17,  genotype _R_R, patient1, WT, cell line Tal1_2, experiment: C2, sequencing  batch: Set2


title: 51898_D28_BCG


title: 52891_D28_uns


title: C512_17SMC8_17WB46_D3

description: Day3,  genotype _R_R, patient1, KO, cell line wb46, experiment: C1, sequencing  batch: Set2

value: mesenchymal progenitors


title: 51024_D28_uns


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_12


title: 50352_D28_uns


title: 52764_D0_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_10


title: 52693_D28_uns


title: 51324_D0_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_7


title: 52600_D0_BCG


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_8


title: 53416_D28_uns


title: C512_17SMC8_17TAL2_3_D3

description: Day3,  genotype _R_R, patient1, WT, cell line Tal2_3, experiment: C1, sequencing  batch: Set2


title: 51124_D28_uns


title: D17SMC_patient1_R_R_1_KO_exp4_line1_9

description: Day17,  genotype _R_R, patient1, KO, cell line Tal1_9, experiment: A4, sequencing  batch: Set1


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_6


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_5


title: 50787_D0_BCG


title: C512_17SMC8_17TAL2_3_D17

description: Day17,  genotype _R_R, patient1, WT, cell line Tal2_3, experiment: C1, sequencing  batch: Set2


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_4


title: C512_17SMC8_17WB46_D17

description: Day17,  genotype _R_R, patient1, KO, cell line wb46, experiment: C1, sequencing  batch: Set2


title: C512_17SMC8_17TAL2_24_D3

description: Day3,  genotype _R_R, patient1, KO, cell line Tal2_24, experiment: C1, sequencing  batch: Set2


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_2

description:
Sm22-Cre;tdTomato
Plikus_C1_PWD15_v1_Mv13_Matrix.txt


title: C512_17SMC8_17TAL2_24_D17

description: Day17,  genotype _R_R, patient1, KO, cell line Tal2_24, experiment: C1, sequencing  batch: Set2


title: 50687_D28_uns


title: 52586_D0_BCG


title: 52607_D28_uns


title: C512_17SMC8_17TAL1_9_D3

description: Day3,  genotype _R_R, patient1, KO, cell line Tal1_9, experiment: C1, sequencing  batch: Set2


title: 51024_D0_uns


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_1


title: C512_17SMC8_17TAL1_9_D17

description: Day17,  genotype _R_R, patient1, KO, cell line Tal1_9, experiment: C1, sequencing  batch: Set2


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_40

description:
Sm22-Cre;tdTomato
Plikus_C1_PWD12_v2_Mv13_Matrix.txt

value: Post wounding day 12


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_39


title: 53137_D28_uns


title: C512_17SMC8_17TAL1_2_D3

description: Day3,  genotype _R_R, patient1, WT, cell line Tal1_2, experiment: C1, sequencing  batch: Set2

value: WT


title: Sample 1_PWD15_WoundDermis_SingleCells_Fluidigm_Cell_3


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_38


title: 50687_D0_uns

value: PBMC


title: 50055_D28_BCG


title: C512_17SMC8_17TAL1_2_D17

description: Day17,  genotype _R_R, patient1, WT, cell line Tal1_2, experiment: C1, sequencing  batch: Set2


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_37

value: Mixed background


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_35

value: Skin wound cells


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_36


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_34


title: D0_iPS_patient1_R_R_1_KO_line2_24

description: Day0,  genotype _R_R, patient1, KO, cell line Tal2_24, experiment: exp1, sequencing  batch: Set1


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_33


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_32


title: 51324_D28_BCG


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_31


title: 50263_D28_BCG


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_30


title: Normal BM sample 16

city: Tapei

first: Yi

middle: Tsung

address: No.7, Chung Shan S. Rd.（Zhongshan S. Rd.）, Zhongzheng Dist., Taipei City 10002, Taiwan (R.O.C.)

department: Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital

hyb_protocol: Samples were hybridized with Affymetrix Human Transcriptome 2.0 Array and scanned at the Microarray Core Lab of the National Health Research Institutes according to Affymetrix protocols.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
The data was analyzed with Affymetrix AGCC software, Affymetrix Expression Console software and Transcriptome Analysis Console (TAC) version 3.0 software with Affymetrix default settings.
affymetrix-algorithm-name = sst-rma-alt-splice : sst-dabg
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HTA-2_0
program-name = Expression Console
program-version = 1.4.1.46

source_name: Normal donor

label_protocol: Single-stranded cDNA was generated from the amplified cRNA then labeled with biotin according to the standard Affymatrix protocols

growth_protocol: Whole bone marrow mononuclear cells were collected and then stored at liquid nitrogen temperature at once with ptotected by RNase inhibitor

extract_protocol: RNA was isolated from bone marrow mononuclear cells according to the manufacturer’s instructions.

tag: subject status

value: Normal donor

tag: subject id

tag: gender

value: female

value: bone marrow


title: Normal BM sample 20


title: Normal BM sample 19

value: male


title: Normal BM sample 13


title: Normal BM sample 11


title: Normal BM sample 15


title: MDS BM sample 175

source_name: MDS patient

value: myelodysplastic syndrome (MDS) patient


title: Normal BM sample 7


title: Normal BM sample 10


title: Normal BM sample 2


title: Normal BM sample 8


title: Normal BM sample 4


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_27


title: Normal BM sample 18


title: MDS BM sample 173


title: Normal BM sample 3


title: MDS BM sample 176


title: Normal BM sample 14


title: MDS BM sample 174


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_25


title: MDS BM sample 172


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_26


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_29


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_28


title: Normal BM sample 17


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_24


title: Normal BM sample 5


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_23


title: Normal BM sample 6


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_22


title: MDS BM sample 171


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_21


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_20


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_19


title: MDS BM sample 169


title: Normal BM sample 12


title: Normal BM sample 9


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_18


title: MDS BM sample 167


title: Normal BM sample 1


title: MDS BM sample 168


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_16


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_17


title: MDS BM sample 161


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_15


title: MDS BM sample 162


title: MDS BM sample 147


title: MDS BM sample 154


title: MDS BM sample 159


title: MDS BM sample 170


title: MDS BM sample 155


title: MDS BM sample 148


title: MDS BM sample 164


title: MDS BM sample 160


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_13


title: MDS BM sample 152


title: MDS BM sample 165


title: MDS BM sample 149


title: MDS BM sample 157


title: MDS BM sample 163


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_12


title: MDS BM sample 145


title: MDS BM sample 153


title: MDS BM sample 150


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_14


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_11


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_10


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_9


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_8


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_7


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_6


title: MDS BM sample 156


title: MDS BM sample 158


title: MDS BM sample 151


title: MDS BM sample 143


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_5


title: MDS BM sample 144


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_4


title: MDS BM sample 142


title: MDS BM sample 141


title: MDS BM sample 139


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_3


title: MDS BM sample 146


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_2


title: MDS BM sample 140


title: MDS BM sample 138


title: Sample 3_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_1


title: MDS BM sample 136


title: MDS BM sample 124


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_65


title: MDS BM sample 132


title: MDS BM sample 131


title: MDS BM sample 166


title: MDS BM sample 137


title: MDS BM sample 126


title: MDS BM sample 120


title: MDS BM sample 125


title: MDS BM sample 121


title: MDS BM sample 133


title: MDS BM sample 129


title: MDS BM sample 135


title: MDS BM sample 134


title: MDS BM sample 127


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_62


title: MDS BM sample 128


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_64


title: MDS BM sample 119


title: MDS BM sample 130


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_63


title: MDS BM sample 122


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_60


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_61


title: MDS BM sample 123


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_59


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_57


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_58


title: MDS BM sample 117


title: MDS BM sample 118


title: MDS BM sample 116


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_56


title: MDS BM sample 115


title: MDS BM sample 114


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_55


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_54


title: MDS BM sample 112


title: MDS BM sample 111


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_53


title: MDS BM sample 113


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_52


title: MDS BM sample 109


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_51


title: MDS BM sample 108


title: MDS BM sample 110


title: MDS BM sample 103


title: MDS BM sample 100


title: MDS BM sample 106


title: MDS BM sample 99


title: MDS BM sample 95


title: MDS BM sample 102


title: MDS BM sample 91


title: MDS BM sample 90


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_49


title: MDS BM sample 93


title: MDS BM sample 89


title: MDS BM sample 94


title: MDS BM sample 96


title: MDS BM sample 97


title: MDS BM sample 92


title: MDS BM sample 88


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_50


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_47


title: MDS BM sample 98


title: MDS BM sample 101


title: MDS BM sample 104


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_48


title: MDS BM sample 85


title: MDS BM sample 83


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_45


title: MDS BM sample 86


title: MDS BM sample 105


title: MDS BM sample 87


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_43


title: MDS BM sample 107


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_42


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_46


title: MDS BM sample 84


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_41


title: MDS BM sample 81


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_39


title: MDS BM sample 82


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_40


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_37


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_36


title: MDS BM sample 80


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_38


title: DIP_MSL2_antiMSL2_3

city: Planegg-Martinsried

first: Christian

last: Albig

address: Großhaderner Strasse 9

department: Biomedical Center

institute: Ludwig-Maximilians-University Munich

library_source: genomic

data_processing:
For ChIP‑seq and DIP‑seq samples, sequence reads were aligned to the D. melanogaster release 6 reference genome using Bowtie (Langmead et al., 2009) version 1.1.2 (parameter –m 1). Aligned reads were extended to 200 bp fragments.
For ATAC-seq samples, sequence reads were aligned to the D. melanogaster release 6 reference genome using Bowtie2 (Langmead and Salzberg, 2012) version 2.2.9 (parameters --very-sensitive, --no-discordant, --no-mixed, -X 100) considering read‑pairs as non‑nucleosome if less than 100 bp according to (Buenrostro et al., 2013).
bigWig files were generated by counting overlapping fragments at each genomic position.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files with coverage

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: S2 cell genomic DNA

growth_protocol: Cells were cultured in Schneider’s Drosophila Medium (Thermo Fisher), supplemented with 10% heat-inactivated Fetal Bovine Serum (Sigma‑Aldrich), 100 units/mL penicillin and 0.1 mg/mL streptomycin (Sigma‑Aldrich).

extract_protocol:
For genomic DNA (gDNA) extraction, 5x10e7 S2 cells were harvested, washed in PBS and gDNA was extracted with NucleoSpin Tissue kit (Macherey‑Nagel). Remaining RNA contaminants in eluted gDNA were digested with 0.1 mg/mL RNaseA (Sigma‑Aldrich) for 1 h at 37°C. Subsequently, gDNA was sonicated with Covaris AFA S220 using microTUBEs at 175 W peak incident power, 10% duty factor and 200 cycles per burst for 430 s at 5°C to generate ~150‑200 bp fragments, as described in (Villa et al., 2016). Sheared gDNA was purified with MinElute kit (QIAGEN). DIP‑seq was performed accordingly to (Villa et al., 2016), with modifications for combined DIP of two proteins. Sheared gDNA was diluted to 4 mg/mL in Binding Buffer (2 mM Tris/HCl pH 7.5, 100 mM KCl, 2 mM MgCl2, 10% (v/v) Glycerol, 10 µM ZnCl2). Per reaction, 100 nM recombinant MSL2 and/or 50 nM recombinant CLAMP was added to 100 µL diluted gDNA and incubated for 30 min at 26°C. For immunoprecipitation, the reaction was added to 7.5 µL (15 µL 50% slurry) Protein G beads (GE Healthcare) pre‑coupled with antibodies and incubated for 15 min at RT. Beads were washed twice in 100 µL Binding Buffer and resuspended in 50 µL Binding Buffer. Protein was digested by adding Proteinase K at 0.5 mg/mL and incubated for 1 h at 56°C and DNA was purified with 1.8x AMPure XP beads (Beckmann Coulter).
Libraries were prepared with MicroPlex Library Preparation Kit v2 (Diagenode).

treatment_protocol: RNAi against target genes in S2 and Kc cells was performed as previously described (Villa et al., 2016). In brief, double-stranded RNA fragments (dsRNA) were generated with MEGAscript kit (Thermo Fisher) from PCR products. Cells were incubated with 10 µg dsRNA per 1x10e6 cells at a concentration of 10 µg/mL in serum‑free medium (1x10e6 cells in 6‑well plate for ATAC‑seq) or 4.2 µg dsRNA at 6.3 µg/mL serum free medium per 1x10e6 cells (12x10e6 cells in 75 cm^2 flask for ChIP‑seq) for 1 hour. Two volumes of growth medium were added and cells were incubated for 5 days at 26°C. Then, 1x of initial volume (6‑well plate) or 0.75x of initial volume (75 cm2 flask) of growth medium was added and cells were incubated for further 2 days at 26°C.

value: untreated

tag: antibody

value: recombinant MSL2 protein with anti-MSL2


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_44

source_name: Skin wound cells


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_35


title: DIP_MSL2_antiMSL2_2

tag: cell line


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_34


title: DIP_MSL2_antiMSL2_1


title: DIP_MSL2.CLAMP_antiMSL2_3

value: recombinant MSL2 and CLAMP protein with anti-MSL2


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_33


title: MDS BM sample 79


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_32


title: DIP_MSL2.CLAMP_antiMSL2_2


title: MDS BM sample 78


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_31


title: DIP_MSL2.CLAMP_antiMSL2_1


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_30


title: MDS BM sample 66


title: MDS BM sample 74


title: MDS BM sample 71


title: MDS BM sample 68


title: DIP_MSL2.CLAMP_antiCLAMP_3

value: recombinant MSL2 and CLAMP protein with anti-CLAMP


title: MDS BM sample 75


title: MDS BM sample 72


title: MDS BM sample 73


title: MDS BM sample 60


title: MDS BM sample 77


title: MDS BM sample 76


title: MDS BM sample 62


title: MDS BM sample 63


title: MDS BM sample 57


title: MDS BM sample 70


title: DIP_MSL2.CLAMP_antiCLAMP_2


title: MDS BM sample 64


title: DIP_MSL2.CLAMP_antiCLAMP_1


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_26


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_27


title: DIP_Input_2

value: none (Input)


title: MDS BM sample 69


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_29


title: MDS BM sample 55


title: MDS BM sample 61


title: MDS BM sample 65


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_25


title: MDS BM sample 56


title: MDS BM sample 59


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_24


title: DIP_CLAMP_antiCLAMP_3

value: recombinant CLAMP protein with anti-CLAMP


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_23


title: MDS BM sample 67


title: DIP_CLAMP_antiCLAMP_2


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_28


title: DIP_CLAMP_antiCLAMP_1


title: MDS BM sample 53


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_21


title: DIP_Input_3


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_22


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_20


title: MDS BM sample 58


title: DIP_Input_1


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_19


title: ChIP_MSL2_trl_RNAi_1

source_name: S2 cells

extract_protocol:
ChIP‑seq was performed as previously described (Straub et al., 2013) with slight modification. S2 cells (~1x10e8 cells) after RNAi were harvested and chilled on ice. Cells were cross‑linked with 1% formaldehyde for 55 min on ice and the reaction was stopped by adding glycine. Isolated nuclei were resuspended in RIPA (10 mM Tris/HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% (v/v) Triton‑X 100, 0.1%(v/v) SDS, 0.1% (v/v) DOC) at 1x10e8 cells/mL in 1 mL for shearing with Covaris AFA S220 using 12x12 tubes at 100 W peak incident power, 20% duty factor and 200 cycles per burst for 25 min at 5°C to generate 150‑200 bp fragments. 100 µL soluble chromatin was pre‑cleared with 3 µL (6 µL 50% slurry) Protein A:Protein G (1:1) beads (GE Healthcare) and supernatant was directly used for immunoprecipitation by adding antibody to 200 µL chromatin adjusted to 500 µL with RIPA and incubated for 16 h at 4°C. 100 µL supernatant was added to 3 µL (6 µL 50% slurry) Protein A:Protein G beads (1:1) and icubated for 4 h at 4°C. Beads were washed five times with RIPA. For DNA recovery, beads were resuspended in 6.7 bed volumes TE Buffer (10 mM Tris/HCl pH 8.0, 1 mM EDTA), RNA was digested with 50 µg/mL RNaseA (Sigma‑Aldrich) for 30 min at 37°C, and protein was digested with 0.5 µg/mL Proteinase K (Sigma‑Aldrich) supplemented with 0.5% (v/v) SDS for 16 h at 65°C. DNA was purified with 1.8x AMPure XP beads (Beckmann Coulter).
Libraries were prepared with NEBNext ChIP‑Seq Library Perp Kit for Illumina (NEB).

value: trl RNAi


title: ChIP_MSL2_gst_RNAi_3

value: gst RNAi


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_18

value: Post wounding day 12


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_17


title: ChIP_MSL2_trl_RNAi_3


title: MDS BM sample 54


title: ChIP_MSL2_gst_RNAi_1


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_16


title: ChIP_MSL2_clamp2_RNAi_2

value: clamp RNAi


title: ChIP_MSL2_clamp2_RNAi_3


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_14

value: Mixed background


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_13

value: Skin wound cells


title: ChIP_MSL2_trl_RNAi_2


title: MDS BM sample 52


title: ChIP_MSL2_clamp1_RNAi_3


title: ChIP_MSL2_gst_RNAi_2


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_12


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_11


title: ChIP_Input_trl_RNAi_2


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_10


title: ChIP_MSL2_clamp1_RNAi_1


title: MDS BM sample 51


title: ChIP_Input_trl_RNAi_3


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_9


title: ChIP_Input_trl_RNAi_1


title: ChIP_Input_gst_RNAi_3


title: MDS BM sample 48


title: ChIP_Input_gst_RNAi_2


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_15


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_8


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_7


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_6


title: ChIP_Input_gst_RNAi_1


title: ChIP_Input_clamp2_RNAi_3


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_4


title: MDS BM sample 45


title: MDS BM sample 50


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_5


title: ChIP_Input_clamp1_RNAi_3


title: MDS BM sample 44


title: MDS BM sample 46


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_3


title: MDS BM sample 49


title: MDS BM sample 37


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_2


title: ChIP_Input_clamp2_RNAi_2


title: MDS BM sample 39


title: MDS BM sample 42


title: Sample 2_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_1


title: ChIP_CLAMP_trl_RNAi_3

value: CLAMP


title: ChIP_Input_clamp1_RNAi_1


title: MDS BM sample 47


title: MDS BM sample 38


title: MDS BM sample 43


title: MDS BM sample 40


title: MDS BM sample 35


title: ChIP_CLAMP_trl_RNAi_1


title: MDS BM sample 41


title: ChIP_CLAMP_gst_RNAi_3


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_51

description:
Sm22-Cre;tdTomato
Plikus_C1_PWD12_v1_Mv13_Matrix.txt


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_54


title: MDS BM sample 30


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_53


title: ChIP_CLAMP_gst_RNAi_2


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_50


title: ChIP_CLAMP_gst_RNAi_1


title: MDS BM sample 33


title: ChIP_CLAMP_trl_RNAi_2


title: MDS BM sample 31


title: MDS BM sample 28

value: female


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_48


title: ChIP_CLAMP_clamp2_RNAi_2


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_49


title: ChIP_CLAMP_clamp2_RNAi_3


title: MDS BM sample 34

value: bone marrow


title: MDS BM sample 36

value: male


title: MDS BM sample 32

value: myelodysplastic syndrome (MDS) patient


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_45


title: ATAC_S2_untreated_4

extract_protocol:
ATAC‑seq was performed as described earlier (Buenrostro et al., 2013; Buenrostro et al., 2015) with some modification for Drosophila cells. In brief, 50,000 S2 or Kc cells, also with prior RNAi, were used per reaction. Cells were washed in 100 µL PBS, resuspended in 100 µL Lysis Buffer (10 mM Tris/HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) IGEPAL CA‑630) with cOmplete, EDTA‑free Protease Inhibitor Cocktail (Sigma‑Aldrich) and incubated for 3 min on ice. Nuclei were spun down at 4°C for 10 min at 600 g, resuspended in 50 µL 1x TD buffer with 2.5 µL TD Enzyme (Illumina) and incubated with slight agitation for 30 min at 37°C. Tagmented DNA was purified with MinElute kit (QIAGEN).
Cycle number for library amplification was determined by qPCR. Cycle number at quarter maximal intensity was used for library amplification (typically 11‑13 cycles). ATAC libraries were purified with MinElute kit (QIAGEN).

value: untreated


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_52


title: MDS BM sample 29


title: MDS BM sample 27


title: ChIP_CLAMP_clamp1_RNAi_1


title: ChIP_CLAMP_clamp1_RNAi_3


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_47


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_46


title: ATAC_S2_untreated_3

extract_protocol:
ATAC‑seq was performed as described earlier (Buenrostro et al., 2013; Buenrostro et al., 2015) with some modification for Drosophila cells. In brief, 50,000 S2 or Kc cells, also with prior RNAi, were used per reaction. Cells were washed in 100 µL PBS, resuspended in 100 µL Lysis Buffer (10 mM Tris/HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) IGEPAL CA‑630) with cOmplete, EDTA‑free Protease Inhibitor Cocktail (Sigma‑Aldrich) and incubated for 3 min on ice. Nuclei were spun down at 4°C for 10 min at 600 g, resuspended in 50 µL 1x TD buffer with 2.5 µL TD Enzyme (Illumina) and incubated with slight agitation for 30 min at 37°C. Tagmented DNA was purified with MinElute kit (QIAGEN). Cycle number for library amplification was determined by qPCR. Cycle number at quarter maximal intensity was used for library amplification (typically 11‑13 cycles). ATAC libraries were purified with MinElute kit (QIAGEN).
Cycle number for library amplification was determined by qPCR. Cycle number at quarter maximal intensity was used for library amplification (typically 11‑13 cycles). ATAC libraries were purified with MinElute kit (QIAGEN).


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_43


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_44


title: ATAC_S2_untreated_2


title: ATAC_S2_untreated_1


title: ATAC_S2_msl2_RNAi_3

value: msl2 RNAi


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_42


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_40


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_39


title: MDS BM sample 26


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_38


title: ATAC_S2_msl2_RNAi_2


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_41


title: MDS BM sample 24


title: MDS BM sample 23


title: ATAC_S2_gst_RNAi_3


title: MDS BM sample 22


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_36


title: ATAC_S2_msl2_RNAi_1