title: GTEX-1H3O1-0626-SM-GW1RV

description:
sample name:
GTEX-1H3O1-0626-SM-GW1RV


title: GLAST122 pD [scNOMe-seq]

status: Public on Sep 16 2022

type: SRA

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

description: single-cell NOMe-seq

library_source: genomic

data_processing:
read trimming and adapter removal
Bisulfite-aware read mapping
quantification of CpG and GpC methylation
Assembly: GRCm38 (mm10)
Supplementary files format and content: .csv.gz files: cell x region methylation matrices in gzip-compressed csv (comma-separated values) format. acc: chromatin accessibility (=GpC methylation). meth: DNA (=CpG) methylation. VMR: variably methylated regions identified with the ‘scbs’ software. mfrac: fraction of methylated sites. shrunkResid: shrunken mean of residuals quantified with ‘scbs’.
Supplementary files format and content: .cov.gz files: gzip-compressed tab-separated files produced by Bismark with the following columns: chromosome, start position, end position, methylation percentage, number of methylated cytosines, number of unmethylated cytosines.
Library strategy: Single-cell NOMe-seq

molecule: genomic DNA

organism: Mus musculus

source_name: ventricular-subventricular zone

extract_protocol:
For the ischemia experiment, the vSVZ and striatum were isolated. For the naïve experiments, vSVZ, striatum, and olfactory bulb were isolated. Depending on the plate, individual or pooled mice were used to sort cells on plate. Tissues were processed and sorted in a BD FACSAria II at the DKFZ Flow Cytometry Facility. Cells were stained with the following antibodies (all conditions and tissues together): O4-APC and O4-APC-Vio770 (Miltenyi; diluted 1:50), Ter119-APC-Cy7 (Biolegend; 1:100), CD45-APC-Cy7 (BD; 1:200), GLAST (ACSA-1)-PE (Miltenyi: 1:20), PSA-NCAM-PE-Vio770 (Miltenyi; 1:75), Prominin1-A488 (eBioscience; 1:75), and Sytox Blue (Life Technologies, 1:1000), CD9-eFluo450 (eBioscience, 1:300).
For profiling the transcriptome and epigenome of single cells we developed and implemented a miniaturized and higher throughput version of the scNMT-seq protocol (Clark et al., 2018). On this new version, the Smart-seq3 (Hagemann-Jensen et al., 2020) method and specific normalization steps were implemented. A detailed version of the protocol is described in Cerrizuela et al., (2022). The samples listed here represent the epigenomic portion of this multi-omic data set, i.e. DNA methylation and chromatin accessibility assessed with single-cell NOMe-seq.

treatment_protocol: Two months old TiCY mice were intraperitoneally injected with tamoxifen. In these mice, tamoxifen-induced Cre recombination takes place in neural stem cells in the vSVZ, which express Tlx (Nr2e1) and will stably activate the production of enhanced YFP, labeling NSCs and their progeny. Two weeks after injection, an injury by bilateral carotid artery occlusion (BCCAO) was performed as described (Llorens-Bobadilla et al., 2015). The animals were sacrificed for single cell sorting either 48 h or 3 weeks after ischemia. WT mice were not subjected to tamoxifen or ischemia.

tag: tissue

value: ventricular-subventricular zone

tag: cell type

value: TAP

tag: genotype

value: WT

tag: treatment

value: naive


title: GTEX-SNOS-1526-SM-GW24A

type: genomic

city: Chicago

first: Meritxell

last: Oliva

state: Illinois

address: 5841 S. Maryland Ave

department: Public Health Sciences

country: USA

institute: University of Chicago

description:
sample name:
GTEX-SNOS-1526-SM-GW24A

hyb_protocol: All samples were  prepared and analyzed in accordance with the manufacturer guidelines and protocol for the Illumina Infinium HumanMethylationEPIC array (Illumina, San Diego, CA, USA). That is, bisulphite converted DNA was amplified, fragmented and hybridised to IIllumina Infinium HumanMethylationEPIC BeadChip using standard Illumina protocol

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

data_processing:
Raw DNAm data was processed with ChAMP software. For sample quality control (QC), we excluded (1) 3 samples with undetectable or missing methylation values (detection P > 0.01) in ≥ 5% of CpGs and (2) 6 samples with mismatched sex. For CpG QC, we excluded (1) CpGs that had detection P > 0.01 in ≥ 1 samples (N = 44,135) and that had a beadcount < 3 in ≥ 5% samples (N = 660), (2) cross-reactive CpGs (N = 40,812), (3) variant-overlapping CpGs or within a single base pair extension (N = 7,708) and (4) CpGs mapping to sex chromosomes. For filters (2) and (3), we selected CpG probes overlapping variants defined at MAF > 5% in 1000G. A total of 754,054 CpGs passed QC, could be mapped and lifted over from GRCh37 to GRCh38 human genome build and were retained for further analysis. Raw DNAm values were background-adjusted using the single sample normal-exponential out-of-band (ssnoob) method with dye bias correction. DNAm β values were normalized using the beta mixture quantile (BMIQ) method, adjusting for type I/II probe bias; output β values for each CpG were used in downstream analysis. After normalization, we removed one additional sample with array-derived genotype profile not matching the WGS-derived one. Principal component analysis (PCA) was conducted on DNAm β values within each tissue type, and 3 samples were removed for being outliers with respect to the top 5 principal components (PCs) of the corresponding tissue. A total of 987 samples passed final QC and were retained for further analysis.
Processed data file contains: Normalized Average Beta

label: Cy5 and Cy3

organism: Homo sapiens

source_name: Muscle - Skeletal

label_protocol: Standard Illumina Protocol

extract_protocol: DNA samples were extracted from GTEx tissue samples using Qiagen Gentra Puregene method at GTEx Laboratory Data, Analysis and Coordinating Center (LDACC), and sent to the Institute for Population and Precision Health Laboratory on 96-well plates. Tissue types were not batched by plate. Bisulfite conversion was applied to 500 ng of DNA using EZ-96 DNA methylation kit (Zymo Research, Irvine, CA, USA).

value: PT-SNOS

value: GTEX-SNOS

tag: Sex

value: Muscle - Skeletal

tag: age

value: Never


title: GTEX-T6MO-1826-SM-GW1Y2

description:
sample name:
GTEX-T6MO-1826-SM-GW1Y2


title: GTEX-1IKOE-0326-SM-GW1E1

description:
sample name:
GTEX-1IKOE-0326-SM-GW1E1

value: Former


title: GLAST117 pD [scNOMe-seq]

description: single-cell NOMe-seq


title: OB99 pF

description: single-cell RNA-seq

library_source: transcriptomic single cell

data_processing:
mapping with STAR via zUMIs
transcript quantification with featureCounts via zUMIs
Assembly: GRCm38 (mm10)
Supplementary files format and content: Single-cell RNA-seq count matrix in gzip-compressed csv (comma-separated values) format. Values are not normalized, decimals are due to distribution of multimapping reads.

molecule: total RNA

source_name: olfactory bulb & late RMS

extract_protocol:
For the ischemia experiment, the vSVZ and striatum were isolated. For the naïve experiments, vSVZ, striatum, and olfactory bulb were isolated. Depending on the plate, individual or pooled mice were used to sort cells on plate. Tissues were processed and sorted in a BD FACSAria II at the DKFZ Flow Cytometry Facility. Cells were stained with the following antibodies (all conditions and tissues together): O4-APC and O4-APC-Vio770 (Miltenyi; diluted 1:50), Ter119-APC-Cy7 (Biolegend; 1:100), CD45-APC-Cy7 (BD; 1:200), GLAST (ACSA-1)-PE (Miltenyi: 1:20), PSA-NCAM-PE-Vio770 (Miltenyi; 1:75), Prominin1-A488 (eBioscience; 1:75), and Sytox Blue (Life Technologies, 1:1000), CD9-eFluo450 (eBioscience, 1:300).
For profiling the transcriptome and epigenome of single cells we developed and implemented a miniaturized and higher throughput version of the scNMT-seq protocol (Clark et al., 2018). On this new version, the Smart-seq3 (Hagemann-Jensen et al., 2020) method and specific normalization steps were implemented. A detailed version of the protocol is described in Cerrizuela et al., (2022). The samples listed here represent the transcriptomic portion of this multi-omic data set.
Single-cell RNA-seq (Smart-seq3)

value: olfactory bulb & late RMS

value: neuroblast/neuron (OB)


title: GTEX-1H3NZ-0326-SM-GW1D6

description:
sample name:
GTEX-1H3NZ-0326-SM-GW1D6

value: Mild

value: Current


title: GTEX-1H1ZS-0626-SM-GW1DG

description:
sample name:
GTEX-1H1ZS-0626-SM-GW1DG


title: OB78 pF

description: single-cell RNA-seq


title: GLAST115 pD [scNOMe-seq]

description: single-cell NOMe-seq


title: GTEX-1F88E-1826-SM-GW1QK

description:
sample name:
GTEX-1F88E-1826-SM-GW1QK


title: OB77 pF

description: single-cell RNA-seq


title: GTEX-1F75B-0526-SM-GW1CD

description:
sample name:
GTEX-1F75B-0526-SM-GW1CD


title: GTEX-1GPI6-0326-SM-GW1QV

description:
sample name:
GTEX-1GPI6-0326-SM-GW1QV


title: OB74 pF

description: single-cell RNA-seq


title: GTEX-1J8QM-2226-SM-GW1GN

description:
sample name:
GTEX-1J8QM-2226-SM-GW1GN


title: GTEX-XV7Q-2926-SM-GW1TR

description:
sample name:
GTEX-XV7Q-2926-SM-GW1TR


title: GLAST118 pD [scNOMe-seq]

description: single-cell NOMe-seq


title: GLAST109 pD [scNOMe-seq]

description: single-cell NOMe-seq

value: neuroblast


title: GLAST114 pD [scNOMe-seq]

description: single-cell NOMe-seq


title: GLAST113 pD [scNOMe-seq]

description: single-cell NOMe-seq


title: OB720 pF

description: single-cell RNA-seq


title: GLAST110 pD [scNOMe-seq]

description: single-cell NOMe-seq

value: aNSC


title: OB668 pF

description: single-cell RNA-seq


title: OB691 pF

description: single-cell RNA-seq


title: OB65 pF

description: single-cell RNA-seq


title: OB667 pF

description: single-cell RNA-seq


title: OB66 pF

description: single-cell RNA-seq


title: OB648 pF

description: single-cell RNA-seq


title: OB646 pF

description: single-cell RNA-seq


title: GTEX-15DCD-0626-SM-GW1R4

description:
sample name:
GTEX-15DCD-0626-SM-GW1R4


title: GTEX-1F6IF-0226-SM-GW1QW

description:
sample name:
GTEX-1F6IF-0226-SM-GW1QW


title: GTEX-15SHU-0626-SM-GW1RF

description:
sample name:
GTEX-15SHU-0626-SM-GW1RF


title: GLAST107 pD [scNOMe-seq]

description: single-cell NOMe-seq


title: GLAST104 pD [scNOMe-seq]

description: single-cell NOMe-seq


title: GLAST102 pD [scNOMe-seq]

description: single-cell NOMe-seq


title: GLAST105 pD [scNOMe-seq]

description: single-cell NOMe-seq


title: GLAST106 pD [scNOMe-seq]

description: single-cell NOMe-seq


title: GLAST101 pD [scNOMe-seq]

description: single-cell NOMe-seq


title: GTEX-148VJ-0326-SM-GW1GP

description:
sample name:
GTEX-148VJ-0326-SM-GW1GP


title: GTEX-15D1Q-0926-SM-GW1S6

description:
sample name:
GTEX-15D1Q-0926-SM-GW1S6


title: GTEX-14B4R-1726-SM-GW1AZ

description:
sample name:
GTEX-14B4R-1726-SM-GW1AZ


title: GTEX-147GR-0126-SM-GW1T2

description:
sample name:
GTEX-147GR-0126-SM-GW1T2


title: GTEX-14753-0526-SM-GW1QL

description:
sample name:
GTEX-14753-0526-SM-GW1QL


title: GTEX-14A5H-0326-SM-GW1T1

description:
sample name:
GTEX-14A5H-0326-SM-GW1T1


title: GTEX-13X6K-0326-SM-GW1AG

description:
sample name:
GTEX-13X6K-0326-SM-GW1AG


title: GLAST108 pD [scNOMe-seq]

description: single-cell NOMe-seq


title: OB93 pF

description: single-cell RNA-seq


title: OB64 pF

description: single-cell RNA-seq


title: OB645 pF

description: single-cell RNA-seq


title: OB623 pF

description: single-cell RNA-seq


title: OB624 pF

description: single-cell RNA-seq


title: GTEX-13X6I-0526-SM-GW1GF

description:
sample name:
GTEX-13X6I-0526-SM-GW1GF


title: GTEX-ZDTS-1026-SM-GW23S

description:
sample name:
GTEX-ZDTS-1026-SM-GW23S

source_name: Lung

value: PT-ZDTS

value: GTEX-ZDTS

value: Moderate

value: Lung


title: GTEX-ZYFG-0226-SM-GW1G9

description:
sample name:
GTEX-ZYFG-0226-SM-GW1G9

value: PT-ZYFG

value: GTEX-ZYFG


title: GTEX-12WSF-0926-SM-GW2AE

description:
sample name:
GTEX-12WSF-0926-SM-GW2AE


title: GTEX-12584-0526-SM-GW1W4

description:
sample name:
GTEX-12584-0526-SM-GW1W4


title: GTEX-13RTJ-2726-SM-GW22R

description:
sample name:
GTEX-13RTJ-2726-SM-GW22R


title: GTEX-13SLX-0326-SM-GW1V9

description:
sample name:
GTEX-13SLX-0326-SM-GW1V9


title: GTEX-ZYY3-0926-SM-GW1XT

description:
sample name:
GTEX-ZYY3-0926-SM-GW1XT


title: GTEX-11XUK-2226-SM-GW2AB

description:
sample name:
GTEX-11XUK-2226-SM-GW2AB


title: GTEX-YEC3-0226-SM-GW17H

description:
sample name:
GTEX-YEC3-0226-SM-GW17H


title: GTEX-XYKS-0526-SM-GW18H

description:
sample name:
GTEX-XYKS-0526-SM-GW18H

value: PT-XYKS

value: GTEX-XYKS


title: GTEX-Z93S-0626-SM-GW18C

description:
sample name:
GTEX-Z93S-0626-SM-GW18C


title: GTEX-XV7Q-0426-SM-GW1TT

description:
sample name:
GTEX-XV7Q-0426-SM-GW1TT


title: GTEX-YFCO-0426-SM-GW1FK

description:
sample name:
GTEX-YFCO-0426-SM-GW1FK

value: PT-YFCO

value: GTEX-YFCO


title: GTEX-ZAB4-0626-SM-GW1G5

description:
sample name:
GTEX-ZAB4-0626-SM-GW1G5

value: Severe


title: GTEX-YJ89-0826-SM-GW1FD

description:
sample name:
GTEX-YJ89-0826-SM-GW1FD

value: Never


title: GTEX-XUJ4-1426-SM-GW22Z

description:
sample name:
GTEX-XUJ4-1426-SM-GW22Z


title: GTEX-YB5E-0726-SM-GW2CQ

description:
sample name:
GTEX-YB5E-0726-SM-GW2CQ


title: GTEX-YFC4-1126-SM-GW2BS

description:
sample name:
GTEX-YFC4-1126-SM-GW2BS


title: OB58 pF

description: single-cell RNA-seq

value: olfactory bulb & late RMS

value: neuroblast/neuron (OB)

value: WT

value: naive


title: OB57 pF

description: single-cell RNA-seq


title: OB61 pF

description: single-cell RNA-seq


title: OB56 pF

description: single-cell RNA-seq


title: OB52 pF

description: single-cell RNA-seq


title: OB552 pF

description: single-cell RNA-seq


title: OB550 pF

description: single-cell RNA-seq


title: OB548 pF

description: single-cell RNA-seq


title: GTEX-ZDXO-1326-SM-GW21U

description:
sample name:
GTEX-ZDXO-1326-SM-GW21U

value: PT-ZDXO

value: GTEX-ZDXO

value: Former


title: OB34 pF

description: single-cell RNA-seq


title: OB48 pF

description: single-cell RNA-seq


title: GTEX-XMD1-1026-SM-GW1VA

description:
sample name:
GTEX-XMD1-1026-SM-GW1VA

value: Current


title: GTEX-XBEC-1026-SM-GW18I

description:
sample name:
GTEX-XBEC-1026-SM-GW18I

value: PT-XBEC

value: GTEX-XBEC

value: Moderate

value: Lung


title: GTEX-XQ3S-0926-SM-GW1CL

description:
sample name:
GTEX-XQ3S-0926-SM-GW1CL


title: GTEX-XBED-0826-SM-GW17W

description:
sample name:
GTEX-XBED-0826-SM-GW17W

value: PT-XBED

value: GTEX-XBED

value: Mild


title: GTEX-XPT6-1226-SM-GW2AZ

description:
sample name:
GTEX-XPT6-1226-SM-GW2AZ


title: GTEX-XPVG-1026-SM-GW1B6

description:
sample name:
GTEX-XPVG-1026-SM-GW1B6

value: PT-XPVG

value: GTEX-XPVG


title: GTEX-X5EB-0426-SM-GW18S

description:
sample name:
GTEX-X5EB-0426-SM-GW18S


title: GTEX-WYBS-1126-SM-GW1Z1

description:
sample name:
GTEX-WYBS-1126-SM-GW1Z1

value: PT-WYBS

value: GTEX-WYBS

value: Severe


title: GTEX-X4EP-0526-SM-GW18O

description:
sample name:
GTEX-X4EP-0526-SM-GW18O

value: Never


title: GTEX-WZTO-0426-SM-GW1TS

description:
sample name:
GTEX-WZTO-0426-SM-GW1TS

value: PT-WZTO

value: GTEX-WZTO


title: GTEX-X62O-0726-SM-GW1ER

description:
sample name:
GTEX-X62O-0726-SM-GW1ER

value: Former


title: GTEX-X4XY-1026-SM-GW18J

description:
sample name:
GTEX-X4XY-1026-SM-GW18J


title: GTEX-X8HC-0926-SM-GW183

description:
sample name:
GTEX-X8HC-0926-SM-GW183

value: Current


title: GTEX-X4EO-0926-SM-GW1Z5

description:
sample name:
GTEX-X4EO-0926-SM-GW1Z5


title: GTEX-X261-1026-SM-GW18Q

description:
sample name:
GTEX-X261-1026-SM-GW18Q


title: GTEX-WVLH-0826-SM-GW182

description:
sample name:
GTEX-WVLH-0826-SM-GW182

value: PT-WVLH

value: GTEX-WVLH


title: GTEX-WY7C-0426-SM-GW1VR

description:
sample name:
GTEX-WY7C-0426-SM-GW1VR


title: GTEX-WXYG-0726-SM-GW18D

description:
sample name:
GTEX-WXYG-0726-SM-GW18D

value: PT-WXYG

value: GTEX-WXYG


title: GTEX-WWYW-0926-SM-GW186

description:
sample name:
GTEX-WWYW-0926-SM-GW186

value: PT-WWYW

value: GTEX-WWYW

value: Lung


title: GTEX-WRHU-0226-SM-GW18F

description:
sample name:
GTEX-WRHU-0226-SM-GW18F

value: PT-WRHU

value: GTEX-WRHU

value: Mild


title: GTEX-WQUQ-1126-SM-GW184

description:
sample name:
GTEX-WQUQ-1126-SM-GW184

value: PT-WQUQ

value: GTEX-WQUQ


title: GTEX-WK11-0526-SM-GW18G

description:
sample name:
GTEX-WK11-0526-SM-GW18G

value: Moderate


title: OB225 pF

description: single-cell RNA-seq

value: olfactory bulb & late RMS

value: neuroblast/neuron (OB)

value: WT

value: naive


title: OB27 pF

description: single-cell RNA-seq


title: GTEX-WOFL-1126-SM-GW29K

description:
sample name:
GTEX-WOFL-1126-SM-GW29K

value: PT-WOFL

value: GTEX-WOFL

value: Former


title: GTEX-WHWD-0626-SM-GW1B4

description:
sample name:
GTEX-WHWD-0626-SM-GW1B4

value: PT-WHWD

value: GTEX-WHWD

value: Never


title: OB29 pF

description: single-cell RNA-seq


title: AF8358

city: Madrid

first: Jose Maria

middle: Moreno

last: Navarrete

state: (None)

address: Calle de Monforte de Lemos nº 5

country: Spain

institute: CIBER

library_source: transcriptomic

data_processing:
RNA-seq reads mapped with STAR software v2.5.3a with ENCODE parameters.
Annotated genes quantified with RSEM v1.3.0
Assembly: GRCh38
Supplementary files format and content: Matrix with samples as columns and raw gene counts as rows

source_name: Small intestine - Jejunum

extract_protocol:
RNA purification was performed using RNeasy Lipid Tissue Mini Kit (QIAgen, Izasa SA, Barcelona, Spain)
RNA libraries were prepared using TruSeq Stranded total RNA kit (Ribozero)

value: Small intestine - Jejunum

tag: condition

value: morbidly obese


title: OB30 pF

description: single-cell RNA-seq


title: MTO d8 A

type: RNA

city: Barcelona

first: Adria

last: Caballe

address: C/ Baldiri Reixac 10

department: biostatistics

institute: IRB

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneChip scanner GSC3000 (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method as implemented in oligo Bioconductor R package

label: biotin

source_name: tumor organoids

label_protocol: 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: MTOs were cultured in Advanced DMEM containing HEPES, Glutamax, B27 and EGF

extract_protocol: RNA was isolated using magnetic beads from 5000 cells. Library preparation and amplification were performed using 4 ng of Total RNA as described by Gonzalez et al., 2010. Amplification was performed for 19 cycles.

treatment_protocol: No treatment was used in this study

tag: scanning batch

tag: population

value: MTO d8


title: GTEX-WFG8-0926-SM-GW18N

description:
sample name:
GTEX-WFG8-0926-SM-GW18N

value: Mild

value: Lung


title: GTEX-W5X1-0526-SM-GW241

description:
sample name:
GTEX-W5X1-0526-SM-GW241

value: Current


title: mix D

value: mix


title: Mouse 2 Emp1-tdTomato high

source_name: primary tumor

growth_protocol: AKTP MTO93 Emp1-iCasp9-tdTomato was injected in the caecum of b6 mice. After 4 weeks, primary tumors were dissociated, stained with Epcam and CD45 and Tom-high and -low cells were sorted

extract_protocol: RNA was isolated using magnetic beads from 2000 cels. Library preparation and amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 22 cycles.

tag: biological replicate

value: EMP1 high

value: CRC primary tumor


title: GTEX-UPK5-1126-SM-GW2BY

description:
sample name:
GTEX-UPK5-1126-SM-GW2BY


title: AF8357


title: AF8356


title: mix A


title: mix B


title: OB201 pF

description: single-cell RNA-seq

value: olfactory bulb & late RMS

value: neuroblast/neuron (OB)

value: WT


title: AF8355


title: GTEX-UJHI-0726-SM-GW1W5

description:
sample name:
GTEX-UJHI-0726-SM-GW1W5

value: PT-UJHI

value: GTEX-UJHI


title: OB204 pF

description: single-cell RNA-seq

value: naive


title: OB214 pF

description: single-cell RNA-seq


title: GTEX-WH7G-0726-SM-GW18W

description:
sample name:
GTEX-WH7G-0726-SM-GW18W


title: OB193 pF

description: single-cell RNA-seq


title: GTEX-U8XE-1426-SM-GW1VC

description:
sample name:
GTEX-U8XE-1426-SM-GW1VC

value: Former


title: Mouse 4 Emp1-tdTomato low

value: EMP1 low


title: GTEX-UPJH-0826-SM-GW19D

description:
sample name:
GTEX-UPJH-0826-SM-GW19D

value: PT-UPJH

value: GTEX-UPJH

value: Moderate

value: Never


title: Mouse 1 Emp1-tdTomato high


title: MTO d8 B

value: MTO d8


title: AF8354

value: Small intestine - Jejunum

value: morbidly obese


title: Mouse 3 Emp1-tdTomato low


title: Mouse 2 Emp1-tdTomato low


title: Mouse 4 Emp1-tdTomato high

value: EMP1 high


title: mix C

value: mix


title: GTEX-U3ZM-0426-SM-GW2BF

description:
sample name:
GTEX-U3ZM-0426-SM-GW2BF

value: Mild

value: Lung


title: Mouse 3 Emp1-tdTomato high

value: CRC primary tumor


title: GTEX-U8T8-2226-SM-GW17X

description:
sample name:
GTEX-U8T8-2226-SM-GW17X


title: GTEX-U3ZH-0526-SM-GW19I

description:
sample name:
GTEX-U3ZH-0526-SM-GW19I


title: AF8353


title: GTEX-TSE9-0726-SM-GW1WE

description:
sample name:
GTEX-TSE9-0726-SM-GW1WE


title: Mouse 1 Emp1-tdTomato low


title: OB185 pF

description: single-cell RNA-seq

value: olfactory bulb & late RMS

value: neuroblast/neuron (OB)

value: WT


title: MTO d8 C


title: MTO d8 D


title: AF8351


title: GTEX-T6MO-0426-SM-GW1GH

description:
sample name:
GTEX-T6MO-0426-SM-GW1GH


title: OB180 pF

description: single-cell RNA-seq

value: naive


title: GTEX-SNOS-0426-SM-GW1SU

description:
sample name:
GTEX-SNOS-0426-SM-GW1SU

value: PT-SNOS

value: GTEX-SNOS


title: OB174 pF

description: single-cell RNA-seq


title: GTEX-SN8G-0926-SM-GW23D

description:
sample name:
GTEX-SN8G-0926-SM-GW23D

value: Current


title: AF8350


title: GTEX-SIU8-0926-SM-GW2A7

description:
sample name:
GTEX-SIU8-0926-SM-GW2A7

value: Moderate


title: OB173 pF

description: single-cell RNA-seq


title: OB192 pF

description: single-cell RNA-seq


title: AF8352


title: AF8349


title: AF8348


title: OB163 pF

description: single-cell RNA-seq


title: GTEX-T2YK-0826-SM-GW1A9

description:
sample name:
GTEX-T2YK-0826-SM-GW1A9


title: GTEX-S7SE-0926-SM-GW181

description:
sample name:
GTEX-S7SE-0926-SM-GW181


title: OB161 pF

description: single-cell RNA-seq


title: GTEX-T8EM-0326-SM-GW1ZN

description:
sample name:
GTEX-T8EM-0326-SM-GW1ZN

value: Never


title: GTEX-RVPU-0526-SM-GW19H

description:
sample name:
GTEX-RVPU-0526-SM-GW19H

value: PT-RVPU

value: GTEX-RVPU


title: AF8346

value: Small intestine - Jejunum

value: morbidly obese


title: OB153 pF

description: single-cell RNA-seq


title: AF8347


title: GTEX-1RAZR-0726-SM-GW1VY

description:
sample name:
GTEX-1RAZR-0726-SM-GW1VY


title: GTEX-S341-0326-SM-GW23W

description:
sample name:
GTEX-S341-0326-SM-GW23W


title: OB148 pF

description: single-cell RNA-seq


title: GTEX-S33H-0626-SM-GW1ZK

description:
sample name:
GTEX-S33H-0626-SM-GW1ZK

value: Former


title: GTEX-1R46S-1226-SM-GW2CU

description:
sample name:
GTEX-1R46S-1226-SM-GW2CU

value: Mild


title: OB145 pF

description: single-cell RNA-seq


title: GTEX-S4Z8-0426-SM-GW2DD

description:
sample name:
GTEX-S4Z8-0426-SM-GW2DD

value: Lung


title: AF8344


title: GTEX-1QMI2-0926-SM-GW178

description:
sample name:
GTEX-1QMI2-0926-SM-GW178


title: GTEX-1QCLY-1026-SM-GW2CF

description:
sample name:
GTEX-1QCLY-1026-SM-GW2CF


title: GTEX-1OZHM-0826-SM-GW18Y

description:
sample name:
GTEX-1OZHM-0826-SM-GW18Y


title: AF8343


title: GTEX-1PBJJ-1326-SM-GW1VU

description:
sample name:
GTEX-1PBJJ-1326-SM-GW1VU


title: GTEX-RVPV-1726-SM-GW1XI

description:
sample name:
GTEX-RVPV-1726-SM-GW1XI

value: PT-RVPV

value: GTEX-RVPV


title: GTEX-1OJC3-0726-SM-GW1W7

description:
sample name:
GTEX-1OJC3-0726-SM-GW1W7


title: GTEX-1OFPY-0226-SM-GW2CZ

description:
sample name:
GTEX-1OFPY-0226-SM-GW2CZ


title: OB130 pF

description: single-cell RNA-seq

value: olfactory bulb & late RMS

value: neuroblast/neuron (OB)


title: GTEX-1O97I-1526-SM-GW2CY

description:
sample name:
GTEX-1O97I-1526-SM-GW2CY


title: AF8341


title: AF8345


title: AF8340


title: OB128 pF

description: single-cell RNA-seq

value: WT

value: naive


title: OB118 pF

description: single-cell RNA-seq


title: OB131 pF

description: single-cell RNA-seq


title: GTEX-1NHNU-0426-SM-GW1ZY

description:
sample name:
GTEX-1NHNU-0426-SM-GW1ZY


title: GTEX-1MJK2-1126-SM-GW179

description:
sample name:
GTEX-1MJK2-1126-SM-GW179


title: GTEX-1N5O9-1226-SM-GW17M

description:
sample name:
GTEX-1N5O9-1226-SM-GW17M


title: GTEX-1MGNQ-0826-SM-GW2D3

description:
sample name:
GTEX-1MGNQ-0826-SM-GW2D3


title: GTEX-1NUQO-1026-SM-GW2CK

description:
sample name:
GTEX-1NUQO-1026-SM-GW2CK


title: GTEX-1N2EE-1626-SM-GW17A

description:
sample name:
GTEX-1N2EE-1626-SM-GW17A


title: mAscl1_MyoD1, replicate 2

city: Planegg-Martinsried

first: Bob

last: Hersbach

address: Großhaderner Str. 9

department: Institute of Stem Cell Research

institute: Helmholtz Zentrum Munich

data_processing:
The CUT&RUN data was processed using the Nextflow based ChIP-seq workflow from nf-core (version 1.2.2)
For the different samples, a single pseudo antibody was defined and the samples of the same conditions sequenced in multiple experiments were defined as replicates
The computational pipeline was run in 2 independent executions to align against the yest genome (R64-1-1) and against the mouse genome (GRCm38)
The aligned reads from the yeast alignment were used for normalization as per the manufacturer’s instructions.
Assembly: GRCm38
Supplementary files format and content: Raw peak data in .bigWig format
Supplementary files format and content: Normalized peak data in .BroadPeak format (except for Input sample)
Supplementary files format and content: CUT&RUN library size summary from picard deduplication in .tsv format
Supplementary files format and content: Read counts on consensus peaks across all samples in .txt format
Library strategy: CUT&RUN

source_name: Skin

growth_protocol: DMEM (High Glucose), 10% fetal bovine serum,1x Sodium Pyruvate, 1 mM HEPES, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol: CUT&RUN libraries were prepared using the SimpleChIP® DNA library prep kit for Illumina in combination with SimpleChIP® Multiplex Oligos for Illumina following  manufacturer’s instructions and adapting the protocol for CUT&RUN where needed  as instructed by the manufacturer. An equal amount of DNA was used for all samples. Input sample DNA was sheared using a 30 seconds on/30 seconds off protocol for a total of 10 cycles on a Bioruptor®Pico sonication device. Libraries were amplified according to manufacturers instructions and libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Skin

value: Mouse Embryonic fibroblasts

value: Doxycyline

tag: chip antibody

value: FLAG(Sigma, F1804)


title: GTEX-1LVAO-1226-SM-GW2D4

description:
sample name:
GTEX-1LVAO-1226-SM-GW2D4

value: Moderate


title: AF8342


title: GTEX-1LVA9-1126-SM-GW2D1

description:
sample name:
GTEX-1LVA9-1126-SM-GW2D1

value: Never


title: GTEX-1LSVX-0626-SM-GW2CX

description:
sample name:
GTEX-1LSVX-0626-SM-GW2CX


title: OB103 pF

description: single-cell RNA-seq


title: OB129 pF

description: single-cell RNA-seq


title: Ascl1_MyoD1, replicate 2


title: OB102 pF

description: single-cell RNA-seq


title: MyoD1, replicate 2


title: GLAST94 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: GTEX-1LSNL-1126-SM-GW2D6

description:
sample name:
GTEX-1LSNL-1126-SM-GW2D6

value: Current


title: Input, replicate 1


title: GTEX-1MCC2-0726-SM-GW2CC

description:
sample name:
GTEX-1MCC2-0726-SM-GW2CC


title: GTEX-1LG7Y-0826-SM-GW2D2

description:
sample name:
GTEX-1LG7Y-0826-SM-GW2D2


title: GTEX-1N7R6-0726-SM-GW1W9

description:
sample name:
GTEX-1N7R6-0726-SM-GW1W9


title: Input, replicate 2


title: GLAST88 pD

description: single-cell RNA-seq


title: AF8339

value: Small intestine - Jejunum

value: morbidly obese


title: GTEX-1LC47-1126-SM-GW2CJ

description:
sample name:
GTEX-1LC47-1126-SM-GW2CJ

value: Lung


title: OB116 pF

description: single-cell RNA-seq


title: GLAST87 pD

description: single-cell RNA-seq

value: aNSC


title: GTEX-1JMOU-0526-SM-GW2CI

description:
sample name:
GTEX-1JMOU-0526-SM-GW2CI

value: Mild


title: GLAST9 pD

description: single-cell RNA-seq


title: MyoD1, replicate 1,


title: mAscl1_MyoD1, replicate 1


title: GTEX-1JK1U-1126-SM-GW1VL

description:
sample name:
GTEX-1JK1U-1126-SM-GW1VL


title: GTEX-1JN76-0826-SM-GW1SB

description:
sample name:
GTEX-1JN76-0826-SM-GW1SB


title: GLAST86 pD

description: single-cell RNA-seq


title: GTEX-1J8Q3-0826-SM-GW1TO

description:
sample name:
GTEX-1J8Q3-0826-SM-GW1TO

value: Former


title: GTEX-1J8JJ-1126-SM-GW1Q2

description:
sample name:
GTEX-1J8JJ-1126-SM-GW1Q2


title: GTEX-1KXAM-0426-SM-GW2CW

description:
sample name:
GTEX-1KXAM-0426-SM-GW2CW


title: KO

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: CD31+CD45- cells isolated from bleomycin-treated Foxf1fl/fl mouse lungs

data_processing:
RNA from endothelial cells isolated from bleomycin-treated control and endFoxf1+/- mouse lungs were used for RNA-seq analysis.
RNeasy Mini kit (Qiagen) was used to isolate total RNA from total lung lysates or isolated endotheilal populations. mRNAs of specific genes were analyzed by qRT–PCR using the StepOnePlus Real-Time PCR system (Applied Biosystems)
Next-generation sequencing of equimolar pools of cDNA libraries was performed using a single read 75 rapid flow cell on a HiSeq 2500 sequencing platform (Illumina), generating greater than 20 million raw reads per sample.
The raw sequenced reads were aligned from FASTQ files to the mouse genome build GRCm38/mm10 and the UCSC reference transcriptome (http://ccb.jhu.edu/software/tophat/index.shtml) using “Cufflinks” .
Assembly: mm10
Supplementary files format and content: Excel sheet including Reads and TPM expression

molecule: polyA RNA

source_name: Bleomycin treated endFoxf1+/- Endothelial cell

growth_protocol: Mice were housed in barrier and all experiments were performed in accordance with approved IACUC protocols

extract_protocol:
Endothelial cells were sorted by FACS from lung  and RNA were extreacted.
Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina).

treatment_protocol: For bluk RNAseq, Pdgfb-iCreER/Foxf1fl/+ (abbreviated as endFoxf1+/-) as well as  Foxf1fl/+  adult mice in C57BL6 genetic background were given tamoxifen to induce deletion then treated with bleomycin.

tag: number

value: lung

tag: strain


title: GLAST85 pD

description: single-cell RNA-seq

value: WT


title: CON

description: CD31+CD45- cells isolated from bleomycin treated Control mice

source_name: Bleomcyin treated control Endothelial cell


title: GTEX-1L5NE-0726-SM-GW17C

description:
sample name:
GTEX-1L5NE-0726-SM-GW17C


title: GLAST84 pD

description: single-cell RNA-seq

value: naive


title: GTEX-1IKJJ-0926-SM-GW1DJ

description:
sample name:
GTEX-1IKJJ-0926-SM-GW1DJ


title: GTEX-1IL2U-0926-SM-GW1DV

description:
sample name:
GTEX-1IL2U-0926-SM-GW1DV


title: GTEX-1IKK5-1926-SM-GW1QN

description:
sample name:
GTEX-1IKK5-1926-SM-GW1QN


title: Ascl1_MyoD1, replicate 1

value: Skin


title: GTEX-1J1OQ-0926-SM-GW21Y

description:
sample name:
GTEX-1J1OQ-0926-SM-GW21Y


title: GTEX-1JMQJ-2126-SM-GW2D5

description:
sample name:
GTEX-1JMQJ-2126-SM-GW2D5


title: GTEX-1IDJU-0226-SM-GW1T6

description:
sample name:
GTEX-1IDJU-0226-SM-GW1T6


title: GLAST83 pD

description: single-cell RNA-seq


title: GTEX-1IGQW-0726-SM-GW1CE

description:
sample name:
GTEX-1IGQW-0726-SM-GW1CE


title: GTEX-1IDJI-0626-SM-GW1WO

description:
sample name:
GTEX-1IDJI-0626-SM-GW1WO


title: Crh-IRES-CRE IP3

city: New York

first: Ines

last: Ibanez-Tallon

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description: 5 males per sample

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using defaul settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Assembly: mm10
Supplementary files format and content: Text files of counts

source_name: Cortex, Prefrontal

growth_protocol: Not applicable

extract_protocol:
The prefrontal cortex was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: Control mice only. No treatment

tag: animal line

value: Crh-IRES-Cre mice (Jackson 012704)

tag: fraction

value: Immunopurified (IP)

value: male


title: Crh-IRES-CRE IP1

description: 5 males per sample


title: GTEX-1HCVE-0626-SM-GW1CF

description:
sample name:
GTEX-1HCVE-0626-SM-GW1CF


title: GLAST81 pD

description: single-cell RNA-seq

value: TAP


title: GTEX-1I6K6-0926-SM-GW2CT

description:
sample name:
GTEX-1I6K6-0926-SM-GW2CT


title: Crh-IRES-CRE IP2

description: 5 males per sample


title: GLAST80 pD

description: single-cell RNA-seq


title: GTEX-1HB9E-0726-SM-GW1XB

description:
sample name:
GTEX-1HB9E-0726-SM-GW1XB


title: GLAST8 pD

description: single-cell RNA-seq


title: Crh-IRES-CRE Input

description: 5 males per sample

value: Input


title: GTEX-1HR9M-0826-SM-GW18A

description:
sample name:
GTEX-1HR9M-0826-SM-GW18A

value: Moderate


title: MAB_Seq_Oligodendrocyte6

description: MAB-seq

data_processing:
read trimming and adapter removal
Bisulfite-aware read mapping
quantification of 5fC and 5caC
Assembly: GRCm38 (mm10)
Supplementary files format and content: gzip-compressed, tab-separated bedGraph files with the following 6 columns: chromosome, start, end, methylation percentage, number of alignments reporting methylated bases, number of alignments reporting unmethylated bases.

extract_protocol:
Cells were sorted as follows: NSCs/astrocytes: Glast+/CD9high, oligodendrocytes: O4+, neuroblasts (PSA-NCAM+). For every biological replicate, 12 mice were pooled. Between 10,000 and 20,000 cells were sorted and processed following the MAB-seq strategy described in Wu et al. (2014). Specifically, depending on the sample, 20 ng to 90 ng DNA were used for four successive M.SssI (NEB) treatments to ensure maximal methylation. DNA was purified using HighPrep beads (Biozym) added in a 1:1 ratio (v/v).
Four MAB-seq libraries per sample were generated and pooled according to the tagmentation-based whole genome bisulfite sequencing protocol for very low DNA input (PubMed ID: 30779037).

value: ventricular-subventricular zone

value: oligodendrocytes

tag: facs antibodies


title: GTEX-1J1R8-0226-SM-GW1C1

description:
sample name:
GTEX-1J1R8-0226-SM-GW1C1

value: Current


title: GTEX-1H3VY-1426-SM-GW2CN

description:
sample name:
GTEX-1H3VY-1426-SM-GW2CN

value: Lung


title: GTEX-1H3VE-1026-SM-GW2CS

description:
sample name:
GTEX-1H3VE-1026-SM-GW2CS


title: MAB_Seq_Oligodendrocyte5

description: MAB-seq


title: GTEX-RUSQ-0626-SM-GW19E

description:
sample name:
GTEX-RUSQ-0626-SM-GW19E

value: PT-RUSQ

value: GTEX-RUSQ

value: Never


title: MAB_Seq_Neuroblast2

description: MAB-seq

value: neuroblasts

value: PSA-NCAM+


title: GLAST98 pD

description: single-cell RNA-seq

value: aNSC

value: WT

value: naive


title: MAB_Seq_Neuroblast1

description: MAB-seq


title: GLAST75 pD

description: single-cell RNA-seq


title: GLAST78 pD

description: single-cell RNA-seq


title: GLAST74 pD

description: single-cell RNA-seq


title: MAB_Seq_n2_NSC_Astro

description: MAB-seq

value: Adult neural stem cells and astrocytes


title: GLAST76 pD

description: single-cell RNA-seq


title: GTEX-1H11D-0726-SM-GW1XA

description:
sample name:
GTEX-1H11D-0726-SM-GW1XA

value: Mild


title: GTEX-1H1DF-1226-SM-GW1D5

description:
sample name:
GTEX-1H1DF-1226-SM-GW1D5


title: GTEX-1GPI6-0726-SM-GW2D7

description:
sample name:
GTEX-1GPI6-0726-SM-GW2D7

value: Former


title: GTEX-1GTWX-0626-SM-GW1S8

description:
sample name:
GTEX-1GTWX-0626-SM-GW1S8


title: GTEX-1GZHY-0826-SM-GW1RD

description:
sample name:
GTEX-1GZHY-0826-SM-GW1RD


title: GTEX-1H23P-1026-SM-GW1WW

description:
sample name:
GTEX-1H23P-1026-SM-GW1WW


title: GTEX-1GN1W-1026-SM-GW17F

description:
sample name:
GTEX-1GN1W-1026-SM-GW17F


title: GLAST70 pD

description: single-cell RNA-seq


title: GLAST72 pD

description: single-cell RNA-seq

value: TAP


title: GLAST71 pD

description: single-cell RNA-seq


title: GLAST7 pD

description: single-cell RNA-seq

value: neuroblast


title: GTEX-1GMR2-0126-SM-GW1WR

description:
sample name:
GTEX-1GMR2-0126-SM-GW1WR


title: GLAST69 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: GLAST68 pD

description: single-cell RNA-seq


title: GLAST64 pD

description: single-cell RNA-seq


title: GTEX-1GMR3-0226-SM-GW1C2

description:
sample name:
GTEX-1GMR3-0226-SM-GW1C2


title: MAB_Seq_n1_NSC_Astro

description: MAB-seq


title: GLAST6 pD

description: single-cell RNA-seq


title: GLAST59 pD

description: single-cell RNA-seq


title: GTEX-1F5PK-0526-SM-GW189

description:
sample name:
GTEX-1F5PK-0526-SM-GW189


title: GTEX-1F88E-0226-SM-GW1TM

description:
sample name:
GTEX-1F88E-0226-SM-GW1TM


title: GTEX-1F6I4-1026-SM-GW1WX

description:
sample name:
GTEX-1F6I4-1026-SM-GW1WX


title: GTEX-1F75B-1026-SM-GW2D8

description:
sample name:
GTEX-1F75B-1026-SM-GW2D8


title: GTEX-1F75W-0626-SM-GW2D9

description:
sample name:
GTEX-1F75W-0626-SM-GW2D9

value: Moderate


title: GTEX-1F52S-0726-SM-GW1QO

description:
sample name:
GTEX-1F52S-0726-SM-GW1QO

value: Current


title: GTEX-1GL5R-0526-SM-GW1DT

description:
sample name:
GTEX-1GL5R-0526-SM-GW1DT

value: Lung


title: GTEX-1F6IF-1826-SM-GW1EE

description:
sample name:
GTEX-1F6IF-1826-SM-GW1EE


title: i35-ZnSO4-J4-exp-sample35_S1

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

data_processing:
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Assembly: Hg19
Supplementary files format and content: tab-delimited text files of read counts for each sample

growth_protocol: Cells were grown in 10% FCS RPMI

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®
RNA libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: Cells were treated with either DMSO control, GSK-J4 or ZnSO4 for 3, 6 or 24 hours

tag: time

tag: cell line


title: i37-ZnSO4-J4-exp-sample37_S25


title: i39-ZnSO4-J4-exp-sample39_S31


title: i36-ZnSO4-J4-exp-sample36_S26


title: i38-ZnSO4-J4-exp-sample38_S8


title: GTEX-1CAMQ-1026-SM-GW1QU

description:
sample name:
GTEX-1CAMQ-1026-SM-GW1QU

tag: tissue


title: GTEX-1E1VI-0926-SM-GW1DZ

description:
sample name:
GTEX-1E1VI-0926-SM-GW1DZ


title: GTEX-1B98T-1226-SM-GW1S5

description:
sample name:
GTEX-1B98T-1226-SM-GW1S5


title: GTEX-1C4CL-0826-SM-GW1D4

description:
sample name:
GTEX-1C4CL-0826-SM-GW1D4


title: GTEX-1BAJH-1326-SM-GW1FE

description:
sample name:
GTEX-1BAJH-1326-SM-GW1FE


title: GTEX-1C64N-1126-SM-GW1CB

description:
sample name:
GTEX-1C64N-1126-SM-GW1CB


title: GTEX-1EN7A-0826-SM-GW1R8

description:
sample name:
GTEX-1EN7A-0826-SM-GW1R8


title: GTEX-1CAV2-0626-SM-GW29Z

description:
sample name:
GTEX-1CAV2-0626-SM-GW29Z


title: GTEX-1C64O-1226-SM-GW1TA

description:
sample name:
GTEX-1C64O-1226-SM-GW1TA


title: i32-ZnSO4-J4-exp-sample32_S32

source_name: DMSO

value: DMSO


title: i34-ZnSO4-J4-exp-sample34_S21


title: i33-ZnSO4-J4-exp-sample33_S13


title: i31-ZnSO4-J4-exp-sample31_S33


title: GTEX-1AYD5-1226-SM-GW1EA

description:
sample name:
GTEX-1AYD5-1226-SM-GW1EA


title: i30-ZnSO4-J4-exp-sample30_S30


title: i28-ZnSO4-J4-exp-sample28_S3


title: GLAST58 pD

description: single-cell RNA-seq

tag: cell type

tag: genotype


title: i27-ZnSO4-J4-exp-sample27_S4

tag: treatment


title: i26-ZnSO4-J4-exp-sample26_S18


title: i25-ZnSO4-J4-exp-sample25_S27


title: i29-ZnSO4-J4-exp-sample29_S2


title: GLAST53 pD

description: single-cell RNA-seq


title: GLAST56 pD

description: single-cell RNA-seq


title: GLAST54 pD

description: single-cell RNA-seq


title: GLAST52 pD

description: single-cell RNA-seq


title: GLAST49 pD

description: single-cell RNA-seq


title: GLAST5 pD

description: single-cell RNA-seq


title: GLAST51 pD

description: single-cell RNA-seq


title: GLAST43 pD

description: single-cell RNA-seq


title: i22-ZnSO4-J4-exp-sample22_S16


title: i21-ZnSO4-J4-exp-sample21_S5


title: i23-ZnSO4-J4-exp-sample23_S36


title: i24-ZnSO4-J4-exp-sample24_S19


title: GTEX-15SZO-0926-SM-GW2DF

description:
sample name:
GTEX-15SZO-0926-SM-GW2DF

tag: Sex

tag: age


title: GTEX-17HG3-0326-SM-GW231

description:
sample name:
GTEX-17HG3-0326-SM-GW231


title: GTEX-1AX9I-0826-SM-GW1R7

description:
sample name:
GTEX-1AX9I-0826-SM-GW1R7


title: GTEX-18A66-0926-SM-GW29X

description:
sample name:
GTEX-18A66-0926-SM-GW29X


title: GTEX-15SHW-0926-SM-GW1RW

description:
sample name:
GTEX-15SHW-0926-SM-GW1RW


title: GTEX-1A3MX-0726-SM-GW1DP

description:
sample name:
GTEX-1A3MX-0726-SM-GW1DP


title: GTEX-15SKB-0826-SM-GW1S9

description:
sample name:
GTEX-15SKB-0826-SM-GW1S9


title: GTEX-19HZE-0526-SM-GW1RP

description:
sample name:
GTEX-19HZE-0526-SM-GW1RP


title: GTEX-17EVQ-1526-SM-GW1R3

description:
sample name:
GTEX-17EVQ-1526-SM-GW1R3


title: GTEX-18D9U-0526-SM-GW1XD

description:
sample name:
GTEX-18D9U-0526-SM-GW1XD


title: GTEX-16AAH-0426-SM-GW1DR

description:
sample name:
GTEX-16AAH-0426-SM-GW1DR


title: GTEX-16YQH-1626-SM-GW17E

description:
sample name:
GTEX-16YQH-1626-SM-GW17E


title: GTEX-18D9B-1026-SM-GW1QG

description:
sample name:
GTEX-18D9B-1026-SM-GW1QG


title: GTEX-16NPV-0726-SM-GW2DE

description:
sample name:
GTEX-16NPV-0726-SM-GW2DE


title: GTEX-15UKP-1926-SM-GW22M

description:
sample name:
GTEX-15UKP-1926-SM-GW22M


title: GTEX-1A3MV-0526-SM-GW2DB

description:
sample name:
GTEX-1A3MV-0526-SM-GW2DB


title: GTEX-15UF6-1226-SM-GW1WV

description:
sample name:
GTEX-15UF6-1226-SM-GW1WV


title: GTEX-18465-0626-SM-GW1C9

description:
sample name:
GTEX-18465-0626-SM-GW1C9


title: i20-ZnSO4-J4-exp-sample20_S9


title: i19-ZnSO4-J4-exp-sample19_S20


title: GLAST66 pD

description: single-cell RNA-seq


title: GTEX-15SDE-0226-SM-GW1S7

description:
sample name:
GTEX-15SDE-0226-SM-GW1S7


title: GTEX-15RJE-1026-SM-GW2CM

description:
sample name:
GTEX-15RJE-1026-SM-GW2CM


title: GTEX-15SHV-0326-SM-GW1QS

description:
sample name:
GTEX-15SHV-0326-SM-GW1QS


title: i17-ZnSO4-J4-exp-sample17_S23


title: GLAST40 pD

description: single-cell RNA-seq


title: GLAST4 pD

description: single-cell RNA-seq


title: i18-ZnSO4-J4-exp-sample18_S22


title: i16-ZnSO4-J4-exp-sample16_S14


title: i15-ZnSO4-J4-exp-sample15_S10


title: GLAST381 pD

description: single-cell RNA-seq


title: GTEX-15EU6-1226-SM-GW17S

description:
sample name:
GTEX-15EU6-1226-SM-GW17S


title: GTEX-15RIE-0326-SM-GW1GV

description:
sample name:
GTEX-15RIE-0326-SM-GW1GV


title: GTEX-15G1A-0426-SM-GW1BS

description:
sample name:
GTEX-15G1A-0426-SM-GW1BS


title: i14-ZnSO4-J4-exp-sample14_S11


title: GLAST379 pD

description: single-cell RNA-seq


title: GLAST380 pD

description: single-cell RNA-seq


title: GLAST38 pD

description: single-cell RNA-seq


title: GTEX-15D79-1026-SM-GW1CY

description:
sample name:
GTEX-15D79-1026-SM-GW1CY


title: GTEX-15CHR-0726-SM-GW1RR

description:
sample name:
GTEX-15CHR-0726-SM-GW1RR


title: GTEX-15D1Q-0526-SM-GW2DA

description:
sample name:
GTEX-15D1Q-0526-SM-GW2DA


title: GTEX-15DDE-0826-SM-GW21H

description:
sample name:
GTEX-15DDE-0826-SM-GW21H


title: GTEX-15EO6-0326-SM-GW1T5

description:
sample name:
GTEX-15EO6-0326-SM-GW1T5


title: GTEX-14PN3-0926-SM-GW1DX

description:
sample name:
GTEX-14PN3-0926-SM-GW1DX


title: GLAST378 pD

description: single-cell RNA-seq


title: GLAST39 pD

description: single-cell RNA-seq


title: GLAST377 pD

description: single-cell RNA-seq


title: GLAST57 pD

description: single-cell RNA-seq


title: GLAST375 pD

description: single-cell RNA-seq


title: GTEX-14PJ4-0626-SM-GW1QR

description:
sample name:
GTEX-14PJ4-0626-SM-GW1QR


title: GTEX-14LZ3-0726-SM-GW18U

description:
sample name:
GTEX-14LZ3-0726-SM-GW18U


title: GTEX-14PJM-0926-SM-GW2CR

description:
sample name:
GTEX-14PJM-0926-SM-GW2CR


title: GTEX-14JG1-0926-SM-GW1CZ

description:
sample name:
GTEX-14JG1-0926-SM-GW1CZ


title: GTEX-14PJO-0926-SM-GW1RZ

description:
sample name:
GTEX-14PJO-0926-SM-GW1RZ


title: GTEX-14PJ6-0426-SM-GW1C8

description:
sample name:
GTEX-14PJ6-0426-SM-GW1C8


title: GTEX-14JG6-0326-SM-GW1ED

description:
sample name:
GTEX-14JG6-0326-SM-GW1ED


title: GTEX-14JFF-1126-SM-GW1CX

description:
sample name:
GTEX-14JFF-1126-SM-GW1CX


title: GLAST374 pD

description: single-cell RNA-seq


title: GLAST376 pD

description: single-cell RNA-seq


title: GTEX-14E7W-1326-SM-GW217

description:
sample name:
GTEX-14E7W-1326-SM-GW217


title: GTEX-14PK6-0326-SM-GW1C7

description:
sample name:
GTEX-14PK6-0326-SM-GW1C7


title: GTEX-14AS3-0926-SM-GW1X7

description:
sample name:
GTEX-14AS3-0926-SM-GW1X7


title: GTEX-14DAR-0226-SM-GW1WU

description:
sample name:
GTEX-14DAR-0226-SM-GW1WU


title: GTEX-14A6H-0526-SM-GW1DA

description:
sample name:
GTEX-14A6H-0526-SM-GW1DA


title: GTEX-14E6C-1426-SM-GW1CP

description:
sample name:
GTEX-14E6C-1426-SM-GW1CP


title: GTEX-14A5I-0926-SM-GW2DC

description:
sample name:
GTEX-14A5I-0926-SM-GW2DC


title: GTEX-14BIN-0226-SM-GW188

description:
sample name:
GTEX-14BIN-0226-SM-GW188


title: GTEX-14BIM-0726-SM-GW18T

description:
sample name:
GTEX-14BIM-0726-SM-GW18T


title: GTEX-14BMV-0826-SM-GW1QQ

description:
sample name:
GTEX-14BMV-0826-SM-GW1QQ


title: GTEX-146FH-1226-SM-GW1RN

description:
sample name:
GTEX-146FH-1226-SM-GW1RN


title: GTEX-145MH-0626-SM-GW1ZB

description:
sample name:
GTEX-145MH-0626-SM-GW1ZB


title: GTEX-14753-0826-SM-GW1E7

description:
sample name:
GTEX-14753-0826-SM-GW1E7


title: GTEX-1477Z-0626-SM-GW1RM

description:
sample name:
GTEX-1477Z-0626-SM-GW1RM


title: GLAST373 pD

description: single-cell RNA-seq


title: GLAST371 pD

description: single-cell RNA-seq


title: GLAST370 pD

description: single-cell RNA-seq


title: GLAST367 pD

description: single-cell RNA-seq


title: GLAST369 pD

description: single-cell RNA-seq


title: GLAST368 pD

description: single-cell RNA-seq


title: GLAST366 pD

description: single-cell RNA-seq


title: i9-ZnSO4-J4-exp-sample9_S38


title: i10-ZnSO4-J4-exp-sample10_S28


title: i12-ZnSO4-J4-exp-sample12_S34


title: i6-ZnSO4-J4-exp-sample6_S29


title: i8-ZnSO4-J4-exp-sample8_S24


title: i11-ZnSO4-J4-exp-sample11_S37


title: i5-ZnSO4-J4-exp-sample5_S7


title: i7-ZnSO4-J4-exp-sample7_S39


title: i13-ZnSO4-J4-exp-sample13_S6


title: i4-ZnSO4-J4-exp-sample4_S17


title: i3-ZnSO4-J4-exp-sample3_S12


title: GLAST364 pD

description: single-cell RNA-seq


title: i2-ZnSO4-J4-exp-sample2_S35


title: GTEX-13QIC-0326-SM-GW1TX

description:
sample name:
GTEX-13QIC-0326-SM-GW1TX


title: GTEX-13O3P-1026-SM-GW1UY

description:
sample name:
GTEX-13O3P-1026-SM-GW1UY


title: GTEX-13W46-1426-SM-GW1AA

description:
sample name:
GTEX-13W46-1426-SM-GW1AA


title: GTEX-13OW8-1726-SM-GW1U6

description:
sample name:
GTEX-13OW8-1726-SM-GW1U6


title: GTEX-13OW5-0726-SM-GW1V7

description:
sample name:
GTEX-13OW5-0726-SM-GW1V7


title: GTEX-13OVK-0126-SM-GW1XG

description:
sample name:
GTEX-13OVK-0126-SM-GW1XG


title: GTEX-13RTJ-1126-SM-GW18K

description:
sample name:
GTEX-13RTJ-1126-SM-GW18K


title: i1-ZnSO4-J4-exp-sample1_S15


title: GTEX-13PL6-2426-SM-GW1UQ

description:
sample name:
GTEX-13PL6-2426-SM-GW1UQ


title: GLAST359 pD

description: single-cell RNA-seq


title: GTEX-13NZA-1426-SM-GW1VS

description:
sample name:
GTEX-13NZA-1426-SM-GW1VS


title: GTEX-13NYS-1626-SM-GW1VT

description:
sample name:
GTEX-13NYS-1626-SM-GW1VT


title: 6hr_J4_R2

tag: donor


title: GTEX-13IVO-1026-SM-GW1EL

description:
sample name:
GTEX-13IVO-1026-SM-GW1EL


title: 6hr_J4_R3


title: GTEX-139YR-0926-SM-GW1FL

description:
sample name:
GTEX-139YR-0926-SM-GW1FL


title: GLAST357 pD

description: single-cell RNA-seq


title: GLAST358 pD

description: single-cell RNA-seq


title: GTEX-13112-0826-SM-GW1ST

description:
sample name:
GTEX-13112-0826-SM-GW1ST


title: GTEX-139TT-0726-SM-GW1XV

description:
sample name:
GTEX-139TT-0726-SM-GW1XV


title: GLAST356 pD

description: single-cell RNA-seq


title: GLAST355 pD

description: single-cell RNA-seq


title: 6hr_J4_R1


title: 6hr_DMSO_R2


title: GTEX-12ZZX-0926-SM-GW18L

description:
sample name:
GTEX-12ZZX-0926-SM-GW18L


title: GTEX-13CF2-0726-SM-GW1FT

description:
sample name:
GTEX-13CF2-0726-SM-GW1FT


title: GTEX-13111-0426-SM-GW1YH

description:
sample name:
GTEX-13111-0426-SM-GW1YH


title: GLAST352 pD

description: single-cell RNA-seq


title: GTEX-12WSE-0826-SM-GW22V

description:
sample name:
GTEX-12WSE-0826-SM-GW22V


title: GTEX-12584-1426-SM-GW1UR

description:
sample name:
GTEX-12584-1426-SM-GW1UR


title: GTEX-12WSA-1026-SM-GW18E

description:
sample name:
GTEX-12WSA-1026-SM-GW18E


title: GTEX-12WSD-0826-SM-GW21I

description:
sample name:
GTEX-12WSD-0826-SM-GW21I


title: GTEX-1212Z-1026-SM-GW1UX

description:
sample name:
GTEX-1212Z-1026-SM-GW1UX


title: 6hr_DMSO_R1


title: GTEX-13FXS-0826-SM-GW2AX

description:
sample name:
GTEX-13FXS-0826-SM-GW2AX


title: GLAST349 pD

description: single-cell RNA-seq

value: oligodendrocyte


title: GLAST351 pD

description: single-cell RNA-seq


title: 3hr_J4_R2


title: GTEX-11ZUS-0126-SM-GW2BW

description:
sample name:
GTEX-11ZUS-0126-SM-GW2BW

value: Never


title: GTEX-11ZTS-1226-SM-GW1A7

description:
sample name:
GTEX-11ZTS-1226-SM-GW1A7


title: GTEX-11XUK-0326-SM-GW19G

description:
sample name:
GTEX-11XUK-0326-SM-GW19G


title: GTEX-11TTK-0926-SM-GW19B

description:
sample name:
GTEX-11TTK-0926-SM-GW19B


title: GTEX-11WQK-1226-SM-GW2CV

description:
sample name:
GTEX-11WQK-1226-SM-GW2CV


title: 3hr_DMSO_R3


title: 3hr_J4_R1


title: GTEX-11I78-0126-SM-GW226

description:
sample name:
GTEX-11I78-0126-SM-GW226


title: GTEX-11GSP-0726-SM-GW2CL

description:
sample name:
GTEX-11GSP-0726-SM-GW2CL


title: GTEX-11NV4-1126-SM-GW17Z

description:
sample name:
GTEX-11NV4-1126-SM-GW17Z


title: 3hr_DMSO_R1


title: 3hr_DMSO_R2


title: GTEX-11DXZ-0726-SM-GW23R

description:
sample name:
GTEX-11DXZ-0726-SM-GW23R


title: 24hr_J4_R2


title: 24hr_J4_R3


title: GTEX-1192W-0626-SM-GW224

description:
sample name:
GTEX-1192W-0626-SM-GW224


title: 6hr_DMSO_R3


title: GTEX-1192X-1326-SM-GW191

description:
sample name:
GTEX-1192X-1326-SM-GW191

value: Severe


title: 24hr_DMSO_R3


title: GTEX-11DYG-0626-SM-GW1XU

description:
sample name:
GTEX-11DYG-0626-SM-GW1XU


title: 3hr_J4_R3


title: 24hr_J4_R1


title: 24hr_DMSO_R2


title: 24hr_DMSO_R1


title: NK cells

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description: The sample used to obtain RNA for sequencing was 97.6% pure NK cells.

data_processing:
Illumina BaseSpace FastQ v1.0.0 used for basecalling
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Homo sapiens reference genome assembly (hg38) using Star version 2.6. The STAR option –outFilterMultimapNmax was set to 1 to allow only uniquely mapped reads.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Gencode annotations (V39).
Assembly: hg38
Supplementary files format and content: Normalized expression tracks for the UCSC Genome Browser were created from Star alignment files for each cell type using UCSC file conversion utilities.

source_name: Peripheral Blood NK Cells

growth_protocol: Peripheral blood mononuclear cells (PBMC) were obtained from venous blood of a healthy male donor by density gradient separation using Lymphoprep Density Gradient Media and Sepmate PBMC Isolation Tubes Tubes (StemCell Technologies, 85450). The indicated cell types were then purified using negative magnetic selection via EasySep kits (Stemcell Technologies, CD4 T=17952, CD8 T=19053, NK=19055, Pan B=19554).

extract_protocol:
Two million (B cell) or three million (CD4 T, CD8 T, and NK cell) isolated cells were lysed, and total cellular RNA was extracted and purified using RNeasy Plus Mini Kit (Qiagen, 74134) following the manufacturer’s protocol. RNA was kept frozen until library preparation.
Libraries were prepared using the Universal Plus mRNA-Seq with NuQuant (NuGEN Cat# MO1485) and PolyA selection.

tag: donor sex

value: Male

tag: donor age

value: 57 years

value: Nk Cells


title: B cells

description: The sample used to obtain RNA for sequencing was 95.8% pure Pan B cells.

source_name: Peripheral Blood Pan B Cells

value: B Cells


title: CD8 T cells

description: The sample used to obtain RNA for sequencing was 91.7% pure CD8 T cells.

source_name: Peripheral Blood CD8 T Cell

value: Cd8 T Cells


title: GLAST348 pD

description: single-cell RNA-seq

value: WT

value: naive


title: GTEX-1117F-1026-SM-GW2CO

description:
sample name:
GTEX-1117F-1026-SM-GW2CO


title: GTEX-113JC-1326-SM-GW1F2

description:
sample name:
GTEX-113JC-1326-SM-GW1F2


title: GTEX-YFC4-1926-SM-GW244

description:
sample name:
GTEX-YFC4-1926-SM-GW244

source_name: Kidney - Cortex

value: Kidney - Cortex


title: CD4 T cells

description: The sample used to obtain RNA for sequencing was 98.2% pure CD4 T cells.

source_name: Peripheral Blood CD4 T Cell

value: CD4 T Cells


title: GLAST339 pD

description: single-cell RNA-seq

source_name: ventricular-subventricular zone

value: ventricular-subventricular zone

value: TAP


title: GLAST336 pD

description: single-cell RNA-seq

value: aNSC


title: GLAST335 pD

description: single-cell RNA-seq


title: GLAST337 pD

description: single-cell RNA-seq


title: GLAST341 pD

description: single-cell RNA-seq


title: GLAST343 pD

description: single-cell RNA-seq


title: GLAST34 pD

description: single-cell RNA-seq


title: GLAST333 pD

description: single-cell RNA-seq


title: GLAST345 pD

description: single-cell RNA-seq


title: GLAST334 pD

description: single-cell RNA-seq


title: GLAST331 pD

description: single-cell RNA-seq


title: GLAST342 pD

description: single-cell RNA-seq


title: GLAST347 pD

description: single-cell RNA-seq


title: GLAST344 pD

description: single-cell RNA-seq


title: Bronchial, Heated Tobacco Product, rep7

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

data_processing:
The “Demultiplex QIAseq UPX 3’ reads” tool of the CLC Genomics Workbench 21.0.4 was used to demultiplex the raw sequencing reads according to the sample indices.
The “Quantify QIAseq UPX 3’ workflow” was used to process the demultiplexed sequencing reads with default settings. In short, the reads are annotated with their UMI and are then trimmed for poly(A) and adapter sequences, minimum reads length (15 nucleotides), read quality, and ambiguous nucleotides (maximum of 2). They are then deduplicated using their UMI. Reads are grouped into UMI groups when they (1) start at the same position based on the end of the read to which the UMI is ligated (i.e., Read2 for paired data), (2) are from the same strand, and (3) have identical UMIs. Groups that contain only one read (singletons) are merged into non-singleton groups if the singleton’s UMI can be converted to a UMI of a non-singleton group by introducing an SNP (the biggest group is chosen). The reads were then mapped to the Human genome GRCh38
The ‘Empirical analysis of DGE’ algorithm of the CLC Genomics Workbench 21.0.4 was used for differential expression analysis with default settings. It is an implementation of the ‘Exact Test’ for two-group comparisons developed by Robinson and Smyth, 2008 (Small-sample estimation of negative binomial dispersion, with applications to SAGE data) and incorporated in the EdgeR Bioconductor package (Robinson et al., 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data).
Genome_build: Human genome GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized CPM values for each sample

source_name: Primary bronchial epithelial cells from donor_1

growth_protocol:
As described in the paper. Briefly, the bro-ALI model was developed using PBEC. The PBEC were harvested from healthy bronchial tissues obtained from donors in connection with lobectomy following written and informed consent, and approval by the Swedish Ethical Review Authority (Institutional ethic committee reference number 99-357, approved on 10th January 2000 ). The detailed protocol and details of cellular differentiation (club cells, goblet cells, basal cells, ciliated cells, etc.) of the bro-ALI model have been described previously (PMID: 28107509) and have been used in several studies (PMID: 28107509, PMID: 31462114, PMID: 31381966). All experiments and methods were carried out in accordance with relevant guidelines and regulations.
The alveolar model was developed using NCI-H441 (ATCC HTB-174) cell line, known to express constitutively the mRNA and protein of the major surfactant apo-protein. NCI-H441 cells were co-cultured with HULEC-5a (ATCC CRL-3244) representative of human lung microvascular endothelial cells for this purpose. Details of the development of alv-ALI model and its characteristics have been described recently (PMID: 33235237).

extract_protocol:
RNeasy Micro (QIAGEN)
UPX 3’ RNA sequencing technology using Qiagen Genomic Services, Germany
3’ RNAseq

treatment_protocol: The HTP-smoke was generated using IQOS 3 Duo HTP instrument and HEETS-Kelly Selection (intense menthol and citrus flavoured) HTP sticks. An ISO puffing regimen (puff volume: 35 mL, puff duration: 2s, puff frequency: one puff per minute) was mimicked. Each puffing session consisted of 10 puffs and in a one day 6 puffing sessions were mimicked with 1 hour (h) interval in between each session.  Therefore, each of bro-ALI and alv-ALI were exposed to 60 puffs in total.  HTP-smoke exposure experiments were carried out using the exposure system previously illustrated [PMID: 33235237]. An air-tight pre-heated glass syringe was used to repeatedly collect 35 mL of HTP-smoke and injected into a 3 L desiccator glass jar (37°C and 60% humidity). The bro-ALI and alv-ALI models were exposed to HTP-smoke or clean air (sham) for 15 minutes (min) under identical conditions. Thereafter, the lung models were transferred to a cell incubator (37°C, 60% humidity and 5% CO2) for 1 h until next exposure session. At the completion of repeated exposures (ie. 6 puffing sessions), the lung models were incubated for 24 h prior to collection of basal media and cell inserts.  All HTP-exposed samples were compared to their corresponding sham exposed samples (n= 6 - 7 independent experiments per exposure condition). The replicates were randomly distributed in the plates and experiments performed on different days were used for both bro-ALI (developed from one donor) and alv-ALI (developed from different cell vials) for the different assays.

value: Heated Tobacco Product

value: Primary bronchial epithelial cells

tag: model

value: bronchial lung mucosa model

tag: replicate type

value: Technical


title: GLAST33 pD

description: single-cell RNA-seq


title: Bronchial, Heated Tobacco Product, rep6


title: GTEX-1GTWX-1826-SM-GW2A3

description:
sample name:
GTEX-1GTWX-1826-SM-GW2A3

value: Mild

value: Former


title: GTEX-1F6IF-1626-SM-GW1TL

description:
sample name:
GTEX-1F6IF-1626-SM-GW1TL

value: Moderate

value: Never


title: GTEX-1B98T-2526-SM-GW1SX

description:
sample name:
GTEX-1B98T-2526-SM-GW1SX

value: Severe


title: GTEX-1H1ZS-2026-SM-GW22H

description:
sample name:
GTEX-1H1ZS-2026-SM-GW22H


title: GTEX-SIU8-1826-SM-GW1AO

description:
sample name:
GTEX-SIU8-1826-SM-GW1AO

value: Current


title: GTEX-S33H-1426-SM-GW22P

description:
sample name:
GTEX-S33H-1426-SM-GW22P


title: GTEX-X4XX-2326-SM-GW1CN

description:
sample name:
GTEX-X4XX-2326-SM-GW1CN


title: GTEX-X4EP-1926-SM-GW2AD

description:
sample name:
GTEX-X4EP-1926-SM-GW2AD


title: GTEX-UTHO-2326-SM-GW1FP

description:
sample name:
GTEX-UTHO-2326-SM-GW1FP

value: PT-UTHO

value: GTEX-UTHO


title: GTEX-WWYW-2226-SM-GW1YQ

description:
sample name:
GTEX-WWYW-2226-SM-GW1YQ

value: PT-WWYW

value: GTEX-WWYW

value: Kidney - Cortex


title: GTEX-WRHU-0526-SM-GW196

description:
sample name:
GTEX-WRHU-0526-SM-GW196

value: PT-WRHU

value: GTEX-WRHU


title: GTEX-X62O-1926-SM-GW19P

description:
sample name:
GTEX-X62O-1926-SM-GW19P


title: GLAST326 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: aNSC

value: WT

value: naive


title: GLAST329 pD

description: single-cell RNA-seq

value: TAP


title: GLAST328 pD

description: single-cell RNA-seq


title: GTEX-15SHU-2026-SM-GW22D

description:
sample name:
GTEX-15SHU-2026-SM-GW22D


title: GTEX-X585-2126-SM-GW23B

description:
sample name:
GTEX-X585-2126-SM-GW23B

value: Former


title: GTEX-X261-1126-SM-GW1YZ

description:
sample name:
GTEX-X261-1126-SM-GW1YZ


title: GTEX-WOFL-1826-SM-GW1ZV

description:
sample name:
GTEX-WOFL-1826-SM-GW1ZV

value: PT-WOFL

value: GTEX-WOFL

value: Moderate


title: GTEX-13W46-2326-SM-GW1ZG

description:
sample name:
GTEX-13W46-2326-SM-GW1ZG

value: Never


title: GTEX-148VJ-1926-SM-GW22I

description:
sample name:
GTEX-148VJ-1926-SM-GW22I


title: GTEX-13SLX-1526-SM-GW29U

description:
sample name:
GTEX-13SLX-1526-SM-GW29U

value: Current


title: GTEX-13OW5-2026-SM-GW23Y

description:
sample name:
GTEX-13OW5-2026-SM-GW23Y

value: Severe


title: GTEX-15DDE-2126-SM-GW1SW

description:
sample name:
GTEX-15DDE-2126-SM-GW1SW


title: GTEX-13QJC-1226-SM-GW1H7

description:
sample name:
GTEX-13QJC-1226-SM-GW1H7


title: GTEX-14C39-2126-SM-GW22J

description:
sample name:
GTEX-14C39-2126-SM-GW22J


title: GTEX-14A5H-2526-SM-GW22F

description:
sample name:
GTEX-14A5H-2526-SM-GW22F


title: GLAST325 pD

description: single-cell RNA-seq


title: GTEX-13O3P-1926-SM-GW2C3

description:
sample name:
GTEX-13O3P-1926-SM-GW2C3


title: GTEX-13NYS-1426-SM-GW195

description:
sample name:
GTEX-13NYS-1426-SM-GW195


title: GTEX-13N1W-2126-SM-GW1XQ

description:
sample name:
GTEX-13N1W-2126-SM-GW1XQ


title: GTEX-13112-2126-SM-GW2BK

description:
sample name:
GTEX-13112-2126-SM-GW2BK


title: Bronchial, Control, rep7

value: Control

value: Primary bronchial epithelial cells

value: bronchial lung mucosa model

value: Technical


title: GTEX-12ZZX-2226-SM-GW1BD

description:
sample name:
GTEX-12ZZX-2226-SM-GW1BD

value: Kidney - Cortex


title: Bronchial, Control, rep6


title: GTEX-12ZZW-2126-SM-GW23V

description:
sample name:
GTEX-12ZZW-2126-SM-GW23V


title: GTEX-12WSA-2126-SM-GW23P

description:
sample name:
GTEX-12WSA-2126-SM-GW23P


title: Bronchial, Heated Tobacco Product, rep1

value: Heated Tobacco Product


title: GLAST322 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: aNSC


title: GTEX-12WSF-2126-SM-GW2C8

description:
sample name:
GTEX-12WSF-2126-SM-GW2C8


title: GTEX-12WSI-1826-SM-GW1EH

description:
sample name:
GTEX-12WSI-1826-SM-GW1EH


title: GLAST323 pD

description: single-cell RNA-seq

value: WT

value: naive


title: GLAST321 pD

description: single-cell RNA-seq


title: Bronchial, Control, rep5


title: GLAST320 pD

description: single-cell RNA-seq

value: TAP


title: GLAST319 pD

description: single-cell RNA-seq


title: Bronchial, Control, rep3


title: GTEX-12KS4-1826-SM-GW19V

description:
sample name:
GTEX-12KS4-1826-SM-GW19V


title: GLAST324 pD

description: single-cell RNA-seq


title: Bronchial, Control, rep4


title: GTEX-12ZZZ-1026-SM-GW1F4

description:
sample name:
GTEX-12ZZZ-1026-SM-GW1F4


title: GTEX-12696-0926-SM-GW2AJ

description:
sample name:
GTEX-12696-0926-SM-GW2AJ

value: Mild


title: GLAST317 pD

description: single-cell RNA-seq


title: GTEX-12ZZY-2226-SM-GW1EI

description:
sample name:
GTEX-12ZZY-2226-SM-GW1EI


title: GTEX-12WSD-2226-SM-GW21W

description:
sample name:
GTEX-12WSD-2226-SM-GW21W


title: GTEX-1212Z-1626-SM-GW2AS

description:
sample name:
GTEX-1212Z-1626-SM-GW2AS


title: GTEX-11WQC-1426-SM-GW1EM

description:
sample name:
GTEX-11WQC-1426-SM-GW1EM


title: Bronchial, Control, rep2


title: GLAST310 pD

description: single-cell RNA-seq


title: GLAST311 pD

description: single-cell RNA-seq


title: GLAST316 pD

description: single-cell RNA-seq


title: Alveolar, Heated Tobacco Product, rep5

source_name: NCI-H441 (ATCC HTB-174) cell line

value: NCI-H441 (ATCC HTB-174)

value: representative type II pneumocytes

value: alveolar lung mucosa model

value: Biological


title: Bronchial, Control, rep1


title: GLAST307 pD

description: single-cell RNA-seq


title: Alveolar, Heated Tobacco Product, rep6


title: GTEX-11UD2-2126-SM-GW1YM

description:
sample name:
GTEX-11UD2-2126-SM-GW1YM

value: Moderate

value: Never


title: GTEX-11EMC-1326-SM-GW1UW

description:
sample name:
GTEX-11EMC-1326-SM-GW1UW

value: Severe

value: Current


title: GTEX-1192X-2026-SM-GW1GI

description:
sample name:
GTEX-1192X-2026-SM-GW1GI


title: GTEX-11NV4-1526-SM-GW1YO

description:
sample name:
GTEX-11NV4-1526-SM-GW1YO

value: Former


title: Alveolar, Heated Tobacco Product, rep4


title: GTEX-1192W-1326-SM-GW1BO

description:
sample name:
GTEX-1192W-1326-SM-GW1BO

value: Kidney - Cortex


title: GTEX-11WQK-1926-SM-GW29M

description:
sample name:
GTEX-11WQK-1926-SM-GW29M


title: GTEX-117YW-1226-SM-GW1UU

description:
sample name:
GTEX-117YW-1226-SM-GW1UU


title: GTEX-11ZU8-1826-SM-GW1BE

description:
sample name:
GTEX-11ZU8-1826-SM-GW1BE


title: GTEX-ZYY3-2026-SM-GW1GL

description:
sample name:
GTEX-ZYY3-2026-SM-GW1GL

source_name: Colon - Transverse

value: Colon - Transverse


title: Alveolar, Heated Tobacco Product, rep3

value: Heated Tobacco Product


title: GTEX-117XS-1326-SM-GW22U

description:
sample name:
GTEX-117XS-1326-SM-GW22U


title: GLAST306 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: GTEX-ZYFG-1926-SM-GW23Q

description:
sample name:
GTEX-ZYFG-1926-SM-GW23Q

value: PT-ZYFG

value: GTEX-ZYFG


title: GTEX-ZVZQ-2526-SM-GW1UV

description:
sample name:
GTEX-ZVZQ-2526-SM-GW1UV

value: PT-ZVZQ

value: GTEX-ZVZQ


title: GLAST303 pD

description: single-cell RNA-seq

value: WT

value: naive


title: Alveolar, Heated Tobacco Product, rep2

value: NCI-H441 (ATCC HTB-174)

value: representative type II pneumocytes

value: alveolar lung mucosa model


title: GTEX-ZVZP-1926-SM-GW1XM

description:
sample name:
GTEX-ZVZP-1926-SM-GW1XM

value: PT-ZVZP

value: GTEX-ZVZP

value: Mild


title: GTEX-ZDXO-1826-SM-GW229

description:
sample name:
GTEX-ZDXO-1826-SM-GW229

value: PT-ZDXO

value: GTEX-ZDXO

value: Severe

value: Former


title: GTEX-ZDTS-2526-SM-GW1GB

description:
sample name:
GTEX-ZDTS-2526-SM-GW1GB

value: PT-ZDTS

value: GTEX-ZDTS

value: Colon - Transverse

value: Never


title: GTEX-ZAB4-2226-SM-GW1GJ

description:
sample name:
GTEX-ZAB4-2226-SM-GW1GJ

value: Current


title: Alveolar, Control, rep5

value: Control

value: Biological


title: Alveolar, Control, rep6

value: NCI-H441 (ATCC HTB-174)


title: GLAST3 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: neuroblast

value: WT

value: naive


title: GLAST296 pD

description: single-cell RNA-seq

value: aNSC


title: GTEX-YFCO-1426-SM-GW1A4

description:
sample name:
GTEX-YFCO-1426-SM-GW1A4

value: PT-YFCO

value: GTEX-YFCO

value: Mild


title: GTEX-Z93S-2426-SM-GW1UT

description:
sample name:
GTEX-Z93S-2426-SM-GW1UT

value: Severe


title: GTEX-Y111-1426-SM-GW1YN

description:
sample name:
GTEX-Y111-1426-SM-GW1YN


title: Alveolar, Control, rep4

value: representative type II pneumocytes

value: alveolar lung mucosa model


title: GTEX-YB5E-1626-SM-GW1B9

description:
sample name:
GTEX-YB5E-1626-SM-GW1B9

value: Colon - Transverse


title: GTEX-XV7Q-2126-SM-GW1WA

description:
sample name:
GTEX-XV7Q-2126-SM-GW1WA

value: Moderate


title: GTEX-XYKS-2226-SM-GW1F7

description:
sample name:
GTEX-XYKS-2226-SM-GW1F7

value: PT-XYKS

value: GTEX-XYKS

value: Current


title: Alveolar, Heated Tobacco Product, rep1

value: Heated Tobacco Product

value: NCI-H441 (ATCC HTB-174)

value: Biological


title: GTEX-YJ89-2426-SM-GW1Y9

description:
sample name:
GTEX-YJ89-2426-SM-GW1Y9

value: Never


title: GTEX-XUJ4-2026-SM-GW1WN

description:
sample name:
GTEX-XUJ4-2026-SM-GW1WN


title: Alveolar, Control, rep2

value: Control


title: GTEX-XQ3S-2626-SM-GW1CK

description:
sample name:
GTEX-XQ3S-2626-SM-GW1CK


title: Alveolar, Control, rep3


title: GTEX-XPVG-1826-SM-GW2BB

description:
sample name:
GTEX-XPVG-1826-SM-GW2BB

value: PT-XPVG

value: GTEX-XPVG


title: Alveolar, Control, rep1


title: GTEX-XPT6-1126-SM-GW246

description:
sample name:
GTEX-XPT6-1126-SM-GW246


title: GTEX-XMK1-1726-SM-GW2AO

description:
sample name:
GTEX-XMK1-1726-SM-GW2AO


title: GTEX-XMD2-2526-SM-GW247

description:
sample name:
GTEX-XMD2-2526-SM-GW247


title: GTEX-XBED-1526-SM-GW1XS

description:
sample name:
GTEX-XBED-1526-SM-GW1XS

value: PT-XBED

value: GTEX-XBED


title: GLAST294 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: WT

value: naive


title: GLAST293 pD

description: single-cell RNA-seq


title: GLAST292 pD

description: single-cell RNA-seq

value: TAP


title: GLAST288 pD

description: single-cell RNA-seq


title: MTO54 parental Folfiri3

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

data_processing:
Reads were aligned to the musmusculus reference genome version mm10 using STAR (v2.5.2) with default parameters. SAM files were converted to BAM and sorted using Sambamba (v0.7.1)
Count matrices were generated using The Rsubread R package with the ENSEMBL Mus_musculus.GRCm38.97 custom annotation
Assembly: mm10
Supplementary files format and content: Raw count matrix in tab-delimited txt format

source_name: MTO

growth_protocol: Organoids were dissociated using TryplE Express (12604039, Thermo Fisher) and single cells were resuspended in BME (3533-010-02, Bio-Techne) in 6 well plates in comple stem cell medium.

extract_protocol:
Cell media was aspirated and 400 μl of RNA Lysis buffer supplemented with β-mercaptoethanol were added per well. RNA was purified using PureLink RNA mini kit (12183025, Thermo Fisher) following manufacturer´s instructions adding a Dnase step using PureLink DNase set (12185010, Thermo Fisher).
RNA libraries were prepared for sequencing using the kits NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# E7490) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (Cat#E7770), following manufacturer´s instructions and 8 cycles of library amplification

treatment_protocol: Two days after organoid seeding, the media was removed and fresh media containing Folfiri (5FU at 50 μg/μl (SIGMA, F6627) plus SN38 at 100 nM (MedChem, HY-13704)) or control (complete stem cell media) was added for two days.

value: AKP CRC organoid

value: Folfiri


title: MTO54 parental Folfiri1


title: MTO54 parental Folfiri2


title: MTO54 parental Ctr3

value: Ctrl


title: GTEX-XBEC-2426-SM-GW1EU

description:
sample name:
GTEX-XBEC-2426-SM-GW1EU

value: PT-XBEC

value: GTEX-XBEC

value: Severe

value: Colon - Transverse

value: Current


title: GTEX-X62O-2626-SM-GW2BO

description:
sample name:
GTEX-X62O-2626-SM-GW2BO

value: Former


title: GTEX-X8HC-2426-SM-GW1BF

description:
sample name:
GTEX-X8HC-2426-SM-GW1BF


title: GTEX-X585-2626-SM-GW23A

description:
sample name:
GTEX-X585-2626-SM-GW23A


title: GTEX-X4XY-2626-SM-GW23M

description:
sample name:
GTEX-X4XY-2626-SM-GW23M

value: Never


title: MTO54 parental Ctr2


title: MTO54 parental Ctr1


title: GTEX-X4EP-2726-SM-GW2AY

description:
sample name:
GTEX-X4EP-2726-SM-GW2AY


title: GTEX-X5EB-0926-SM-GW22S

description:
sample name:
GTEX-X5EB-0926-SM-GW22S

value: Mild


title: GTEX-X4EO-2526-SM-GW22T

description:
sample name:
GTEX-X4EO-2526-SM-GW22T


title: GTEX-X4XX-2526-SM-GW1CH

description:
sample name:
GTEX-X4XX-2526-SM-GW1CH


title: GTEX-X261-1826-SM-GW1ES

description:
sample name:
GTEX-X261-1826-SM-GW1ES


title: Bronchial, Heated Tobacco Product, rep3

value: Heated Tobacco Product

value: Primary bronchial epithelial cells

value: bronchial lung mucosa model

value: Technical


title: Bronchial, Heated Tobacco Product, rep5


title: Bronchial, Heated Tobacco Product, rep2


title: GLAST282 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: WT

value: naive


title: GLAST284 pD

description: single-cell RNA-seq


title: GLAST285 pD

description: single-cell RNA-seq


title: GLAST277 pD

description: single-cell RNA-seq

value: TAP


title: Bronchial, Heated Tobacco Product, rep4


title: GLAST278 pD

description: single-cell RNA-seq


title: GLAST283 pD

description: single-cell RNA-seq


title: GLAST280 pD

description: single-cell RNA-seq


title: GLAST275 pD

description: single-cell RNA-seq


title: GLAST279 pD

description: single-cell RNA-seq


title: GLAST281 pD

description: single-cell RNA-seq


title: GTEX-WYBS-2326-SM-GW2AI

description:
sample name:
GTEX-WYBS-2326-SM-GW2AI

value: PT-WYBS

value: GTEX-WYBS


title: GTEX-WXYG-1826-SM-GW1FQ

description:
sample name:
GTEX-WXYG-1826-SM-GW1FQ

value: PT-WXYG

value: GTEX-WXYG

value: Moderate


title: GTEX-WY7C-1626-SM-GW1WC

description:
sample name:
GTEX-WY7C-1626-SM-GW1WC

value: Colon - Transverse


title: GTEX-WWYW-2326-SM-GW1YR

description:
sample name:
GTEX-WWYW-2326-SM-GW1YR

value: PT-WWYW

value: GTEX-WWYW

value: Severe

value: Current


title: GLAST298 pD

description: single-cell RNA-seq

value: aNSC


title: GTEX-WQUQ-2526-SM-GW1YS

description:
sample name:
GTEX-WQUQ-2526-SM-GW1YS

value: PT-WQUQ

value: GTEX-WQUQ

value: Never


title: GTEX-WVLH-2426-SM-GW1ZT

description:
sample name:
GTEX-WVLH-2426-SM-GW1ZT

value: PT-WVLH

value: GTEX-WVLH

value: Former


title: GTEX-WRHU-2326-SM-GW1ZI

description:
sample name:
GTEX-WRHU-2326-SM-GW1ZI

value: PT-WRHU

value: GTEX-WRHU


title: GTEX-WH7G-1326-SM-GW1H6

description:
sample name:
GTEX-WH7G-1326-SM-GW1H6

value: Mild


title: GTEX-WK11-2326-SM-GW1BH

description:
sample name:
GTEX-WK11-2326-SM-GW1BH


title: GTEX-WOFL-2626-SM-GW1FR

description:
sample name:
GTEX-WOFL-2626-SM-GW1FR

value: PT-WOFL

value: GTEX-WOFL


title: GLAST272 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: WT

value: naive


title: GLAST273 pD

description: single-cell RNA-seq

value: TAP


title: GTEX-WFG8-1526-SM-GW2C7

description:
sample name:
GTEX-WFG8-1526-SM-GW2C7

value: Moderate

value: Colon - Transverse


title: GTEX-T2IS-2726-SM-GW1ZR

description:
sample name:
GTEX-T2IS-2726-SM-GW1ZR

value: Severe

value: Current


title: GTEX-SN8G-2726-SM-GW1YA

description:
sample name:
GTEX-SN8G-2726-SM-GW1YA


title: GTEX-U3ZH-1326-SM-GW1U2

description:
sample name:
GTEX-U3ZH-1326-SM-GW1U2


title: GTEX-U8T8-1326-SM-GW19F

description:
sample name:
GTEX-U8T8-1326-SM-GW19F


title: GTEX-UJHI-1126-SM-GW1B7

description:
sample name:
GTEX-UJHI-1126-SM-GW1B7

value: PT-UJHI

value: GTEX-UJHI


title: GTEX-UPJH-2026-SM-GW1ZF

description:
sample name:
GTEX-UPJH-2026-SM-GW1ZF

value: PT-UPJH

value: GTEX-UPJH

value: Never


title: GTEX-S341-1426-SM-GW1XN

description:
sample name:
GTEX-S341-1426-SM-GW1XN


title: GTEX-T2YK-2126-SM-GW193

description:
sample name:
GTEX-T2YK-2126-SM-GW193


title: GTEX-S7SE-2226-SM-GW19R

description:
sample name:
GTEX-S7SE-2226-SM-GW19R


title: GTEX-SJXC-2226-SM-GW23Z

description:
sample name:
GTEX-SJXC-2226-SM-GW23Z

value: PT-SJXC

value: GTEX-SJXC


title: GTEX-UPK5-2226-SM-GW2AP

description:
sample name:
GTEX-UPK5-2226-SM-GW2AP


title: GTEX-S4Z8-1526-SM-GW1US

description:
sample name:
GTEX-S4Z8-1526-SM-GW1US

value: Mild


title: GTEX-T8EM-1426-SM-GW19O

description:
sample name:
GTEX-T8EM-1426-SM-GW19O


title: GTEX-U3ZM-1126-SM-GW1YU

description:
sample name:
GTEX-U3ZM-1126-SM-GW1YU


title: GTEX-TSE9-1826-SM-GW245

description:
sample name:
GTEX-TSE9-1826-SM-GW245


title: GTEX-W5X1-1726-SM-GW1ZH

description:
sample name:
GTEX-W5X1-1726-SM-GW1ZH


title: GTEX-S33H-2126-SM-GW1AJ

description:
sample name:
GTEX-S33H-2126-SM-GW1AJ

value: Former


title: GTEX-SIU8-2426-SM-GW2BZ

description:
sample name:
GTEX-SIU8-2426-SM-GW2BZ


title: GTEX-UTHO-2526-SM-GW1B2

description:
sample name:
GTEX-UTHO-2526-SM-GW1B2

value: PT-UTHO

value: GTEX-UTHO


title: GLAST269 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: aNSC

value: WT

value: naive


title: GLAST259 pD

description: single-cell RNA-seq


title: GLAST271 pD

description: single-cell RNA-seq


title: GLAST268 pD

description: single-cell RNA-seq

value: TAP


title: GLAST264 pD

description: single-cell RNA-seq


title: GLAST257 pD

description: single-cell RNA-seq


title: GLAST270 pD

description: single-cell RNA-seq


title: GLAST256 pD

description: single-cell RNA-seq


title: GLAST258 pD

description: single-cell RNA-seq


title: GLAST260 pD

description: single-cell RNA-seq


title: GLAST255 pD

description: single-cell RNA-seq


title: GLAST254 pD

description: single-cell RNA-seq


title: GTEX-1IKJJ-2426-SM-GW1PX

description:
sample name:
GTEX-1IKJJ-2426-SM-GW1PX

value: Severe

value: Colon - Transverse


title: GTEX-RVPV-2226-SM-GW23T

description:
sample name:
GTEX-RVPV-2226-SM-GW23T

value: PT-RVPV

value: GTEX-RVPV


title: GTEX-1IDJI-2326-SM-GW1GZ

description:
sample name:
GTEX-1IDJI-2326-SM-GW1GZ

value: Moderate


title: GTEX-1IDJV-2726-SM-GW1WP

description:
sample name:
GTEX-1IDJV-2726-SM-GW1WP


title: GTEX-1IKK5-2726-SM-GW1C3

description:
sample name:
GTEX-1IKK5-2726-SM-GW1C3

value: Never


title: GTEX-1IY9M-2126-SM-GW1QM

description:
sample name:
GTEX-1IY9M-2126-SM-GW1QM


title: GTEX-1JN6P-1926-SM-GW1EO

description:
sample name:
GTEX-1JN6P-1926-SM-GW1EO

value: Current


title: GTEX-1IGQW-2326-SM-GW29Y

description:
sample name:
GTEX-1IGQW-2326-SM-GW29Y


title: GTEX-1IDJU-2026-SM-GW1GM

description:
sample name:
GTEX-1IDJU-2026-SM-GW1GM


title: GTEX-1J1R8-1126-SM-GW1T4

description:
sample name:
GTEX-1J1R8-1126-SM-GW1T4


title: GTEX-1JN1M-2626-SM-GW1VZ

description:
sample name:
GTEX-1JN1M-2626-SM-GW1VZ


title: GTEX-1JMOU-2426-SM-GW2CD

description:
sample name:
GTEX-1JMOU-2426-SM-GW2CD


title: GTEX-1JMQJ-2826-SM-GW1EP

description:
sample name:
GTEX-1JMQJ-2826-SM-GW1EP


title: GTEX-1JMPZ-2426-SM-GW177

description:
sample name:
GTEX-1JMPZ-2426-SM-GW177


title: GTEX-1J8Q3-2326-SM-GW1BV

description:
sample name:
GTEX-1J8Q3-2326-SM-GW1BV


title: GTEX-1JK1U-1526-SM-GW2CH

description:
sample name:
GTEX-1JK1U-1526-SM-GW2CH


title: GTEX-1J1OQ-2726-SM-GW1QH

description:
sample name:
GTEX-1J1OQ-2726-SM-GW1QH


title: GTEX-RVPU-1626-SM-GW1ZJ

description:
sample name:
GTEX-RVPU-1626-SM-GW1ZJ

value: PT-RVPU

value: GTEX-RVPU


title: GTEX-1J8Q2-2426-SM-GW219

description:
sample name:
GTEX-1J8Q2-2426-SM-GW219


title: GTEX-RUSQ-1226-SM-GW19J

description:
sample name:
GTEX-RUSQ-1226-SM-GW19J

value: PT-RUSQ

value: GTEX-RUSQ

value: Mild


title: GTEX-1JN76-1226-SM-GW211

description:
sample name:
GTEX-1JN76-1226-SM-GW211


title: GLAST225 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: GLAST252 pD

description: single-cell RNA-seq


title: GLAST253 pD

description: single-cell RNA-seq


title: GLAST248 pD

description: single-cell RNA-seq

value: aNSC


title: GLAST243 pD

description: single-cell RNA-seq

value: WT


title: GLAST245 pD

description: single-cell RNA-seq

value: naive


title: GLAST249 pD

description: single-cell RNA-seq


title: GLAST250 pD

description: single-cell RNA-seq


title: GLAST244 pD

description: single-cell RNA-seq


title: GTEX-1IDJH-2726-SM-GW1X1

description:
sample name:
GTEX-1IDJH-2726-SM-GW1X1


title: GTEX-1HCVE-2526-SM-GW1QI

description:
sample name:
GTEX-1HCVE-2526-SM-GW1QI

value: Former


title: GTEX-1H3VE-2426-SM-GW1WI

description:
sample name:
GTEX-1H3VE-2426-SM-GW1WI


title: GLAST216 pD

description: single-cell RNA-seq


title: GTEX-1HSKV-2226-SM-GW1BW

description:
sample name:
GTEX-1HSKV-2226-SM-GW1BW


title: GTEX-1I6K6-1826-SM-GW1PW

description:
sample name:
GTEX-1I6K6-1826-SM-GW1PW


title: GLAST214 pD

description: single-cell RNA-seq


title: GLAST215 pD

description: single-cell RNA-seq

value: TAP


title: GTEX-1HGF4-2126-SM-GW1GX

description:
sample name:
GTEX-1HGF4-2126-SM-GW1GX

value: Colon - Transverse


title: GTEX-1ICLY-2626-SM-GW1RB

description:
sample name:
GTEX-1ICLY-2626-SM-GW1RB

value: Severe


title: GTEX-1HB9E-2426-SM-GW1TC

description:
sample name:
GTEX-1HB9E-2426-SM-GW1TC


title: ATACseq adult alveolar macrophages Lip WT rep4 [ATACseq_AM_Lip8_S8]

city: Turku

first: alexander

last: mildner

address: Tykistökatu 6A

department: Biomedicine

country: Finland

institute: University of Turku / Medicity

description:
ATACseq_AM_Lip8_S8
processed data file: counts_matrix.xlsx

data_processing:
RNA-seq:
We used fastuniq to collapse PCR duplicates
STAR v2.6.1a was used to align unique reads to the mouse genome (GRCm38).
Gene expression was quantified using featureCounts v1.6.3 and the Gencode vM12 reference
ATAC-seq:
ATAC-seq reads were aligned to the mouse genome v. GRCm38 using the BWA-MEM algorithm implemented in the bwa program (Li, 2013), v. 0.7.17.
peaks were called with MACS2 v. 2.2.7.1
Peak calling was done with the R package DiffBind v. 2.14
Differential binding was done using the R package DESeq2 v. 1.26
Peaks were annotated using ChIPseeker v. 1.22.1
Genome_build: GRCm38
Supplementary_files_format_and_content: gene counts (featureCounts) as csv file
Supplementary_files_format_and_content: Annotation file peak_annotation.xlsx contains the PrimaryIDs and the output of ChIPseeker. Count matrix count_matrix.xlsx contains the counts collected from DiffBind.

growth_protocol: no growth protocol; ex vivo isolation

extract_protocol:
bronchoalveolar lavage with 5x 1ml PBS with 2mM EDTA and 1% FBS
Cells for RNA-Seq or ATAC-Seq were isolated by FACS. Cells for RNA-Seq (500-20,000 sorted cells) were lysed with 50-200µl of lysis/binding buffer (Life Technologies), frozen on dry ice and stored at -80°C until further use. The mRNA was purified using a Dynabeads mRNA DIRECT Purification Kit (Life Technologies) according to the manufacturer’s guidelines. Reverse transcription was performed with oligo(dT) primers (Thermo Scientific) or MARS-seq barcoded RT primers and the Affinity Script cDNA Synthesis Kit (Agilent) in a 10µl reaction volume.
mRNA was subjected to reverse transcription using an Affinity Script cDNA Synthesis Kit (Agilent) and MARS-seq barcoded RT primers. Samples were analyzed by qPCR and up to 8 samples with similar Ct values were combined. Pooled samples were then treated with Exonuclease I (New England BioLabs (NEB)) and incubated at 37°C for 30min and 80°C for 10min followed by a 1.2X AMPure XP beads (Beckman Coulter) cleanup. Second strand synthesis of the cDNA was performed using a second strand synthesis kit (NEB) at 16°C for 2h and samples were cleaned with 1.4X volumes of AMPure XP beads. Afterwards samples were subjected to in vitro transcription (IVT) with a HiScribe T7 RNA Polymerase kit (NEB) at 37°C for 13-16h. The DNA template was removed by Turbo DNase I (Life Technologies) treatment at 37°C for 15min and the samples were cleaned with 1.2X volumes of AMPure XP beads. Subsequently, the RNA was fragmented at 70°C using RNA fragmentation buffer (Invitrogen), after 3min the reaction was stopped with Stop buffer (Invitrogen) and samples were purified by 2X SPRI cleanup. Afterwards T4 RNA ligase (NEB) was used to ligate the fragmented RNA to the MARS-seq ligation adapter (22°C 2h) and samples were purified with a 1.5X AMPure XP beads cleanup. In a second reverse transcription reaction (reaction volume 20µl) using the MARS-seq RT2 primer and an Affinity Script cDNA Synthesis Kit (Agilent Technologies) the RNA was transcribed into cDNA followed by another 1.5X AMPure XP beads purification. As final step the library was amplified in a nested PCR with P5_Rd1 and P7_Rd2 primers and Kapa HiFi Hotstart ready mix (Kapa Biosystems) and purified with a 0.7X AMPure XP beads cleanup. The fragment size of the final libraries was measured using a TapeStation (Agilent Technologies) and library concentrations were quantified with a Qubit fluorometer (Life Technologies). The samples were sequenced using a NextSeq 500 system (Illumina).
For the preparation of ATAC-seq libraries 15,000-20,000 cells were used as described earlier (Lara-Astiaso et al., 2014; Buenrostro et al., 2013). Briefly, nuclei were isolated by lysis with cold lysis buffer (10mM Tris-HCl pH7.4, 10mM MgCl2, 0.1% Igepal CA-630) and centrifuged for 25min at 500xg and 4°C with low acceleration and brake using a swing-out rotor. The supernatant was carefully removed and nuclei were resuspended in 25μl reaction buffer containing 2μl of Tn5 transposase and 12.5μl of TD buffer (Nextera DNA library preparation kit; Illumina). The mix was incubated at 37°C for 1hr. Afterwards, the DNA was purified by adding 5μl of cleanup buffer (900mM NaCl, 30mM EDTA), 2μl of proteinase K (NEB) and 2μl of 5% SDS. After an incubation phase of 30min at 40°C, the tagmented DNA was enriched using AMPure XP beads (Beckman Coulter). The DNA was PCR-amplified with indexed primers and Kapa HiFi Hotstart ready mix (Kapa Biosystems). After the PCR, tagmented DNA fragments were selected for fragments smaller than 600bp and purified using AMPure XP beads. Libraries were subjected to a second PCR amplification with Kapa HiFi Hotstart ready mix (Kapa Biosystems), indexing primers and an appropriate number of reaction cycles depending on the library concentration. Library sizes were determined using a TapeStation (Agilent Technologies) and measurement of DNA concentration was performed with a Qubit fluorometer (Life Technologies). Libraries where sequenced with an average of 20 million reads per sample on a NextSeq500 system (Illumina).

treatment_protocol: no treatment

tag: strain

tag: background

value: mixed background

value: Lip +/+

value: adult

tag: sample/tissue type

value: bronchoalveolar lavage

value: alveolar macrophages


title: GTEX-1F75W-2226-SM-GW1BY

description:
sample name:
GTEX-1F75W-2226-SM-GW1BY

value: Current


title: GTEX-1GL5R-2426-SM-GW1TE

description:
sample name:
GTEX-1GL5R-2426-SM-GW1TE

value: Never


title: GTEX-1F88E-2226-SM-GW1RS

description:
sample name:
GTEX-1F88E-2226-SM-GW1RS


title: GTEX-1GZ4I-2426-SM-GW1GO

description:
sample name:
GTEX-1GZ4I-2426-SM-GW1GO

value: Moderate


title: GTEX-1GTWX-2326-SM-GW1E2

description:
sample name:
GTEX-1GTWX-2326-SM-GW1E2


title: GTEX-1H2FU-2726-SM-GW1TF

description:
sample name:
GTEX-1H2FU-2726-SM-GW1TF


title: GTEX-1H11D-2626-SM-GW1WM

description:
sample name:
GTEX-1H11D-2626-SM-GW1WM

value: Mild


title: GTEX-1H1ZS-2326-SM-GW22W

description:
sample name:
GTEX-1H1ZS-2326-SM-GW22W


title: GTEX-1GMR2-1726-SM-GW1DS

description:
sample name:
GTEX-1GMR2-1726-SM-GW1DS


title: GTEX-1H23P-2426-SM-GW1RE

description:
sample name:
GTEX-1H23P-2426-SM-GW1RE


title: GTEX-1GZHY-2626-SM-GW1WJ

description:
sample name:
GTEX-1GZHY-2626-SM-GW1WJ


title: GTEX-1GMR3-2826-SM-GW1RA

description:
sample name:
GTEX-1GMR3-2826-SM-GW1RA


title: GTEX-1H1DF-2526-SM-GW1PY

description:
sample name:
GTEX-1H1DF-2526-SM-GW1PY


title: GTEX-1H3VY-2426-SM-GW1DQ

description:
sample name:
GTEX-1H3VY-2426-SM-GW1DQ


title: GTEX-1F6IF-1226-SM-GW2A1

description:
sample name:
GTEX-1F6IF-1226-SM-GW2A1


title: GTEX-1F6RS-2526-SM-GW1E4

description:
sample name:
GTEX-1F6RS-2526-SM-GW1E4


title: GTEX-1F75A-2726-SM-GW1UL

description:
sample name:
GTEX-1F75A-2726-SM-GW1UL


title: GTEX-1F5PK-1926-SM-GW1AY

description:
sample name:
GTEX-1F5PK-1926-SM-GW1AY


title: GTEX-1F6I4-2626-SM-GW1WQ

description:
sample name:
GTEX-1F6I4-2626-SM-GW1WQ


title: GTEX-1F52S-2626-SM-GW1PV

description:
sample name:
GTEX-1F52S-2626-SM-GW1PV


title: GTEX-1F5PL-2126-SM-GW1TK

description:
sample name:
GTEX-1F5PL-2126-SM-GW1TK


title: GTEX-1EN7A-2626-SM-GW1S2

description:
sample name:
GTEX-1EN7A-2626-SM-GW1S2


title: GTEX-1E2YA-2626-SM-GW1QZ

description:
sample name:
GTEX-1E2YA-2626-SM-GW1QZ


title: GLAST20 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: GLAST200 pD

description: single-cell RNA-seq

value: aNSC


title: GLAST212 pD

description: single-cell RNA-seq

value: WT


title: GLAST206 pD

description: single-cell RNA-seq

value: naive


title: GLAST198 pD

description: single-cell RNA-seq


title: GLAST195 pD

description: single-cell RNA-seq


title: GLAST201 pD

description: single-cell RNA-seq


title: GLAST211 pD

description: single-cell RNA-seq


title: GLAST207 pD

description: single-cell RNA-seq


title: GLAST213 pD

description: single-cell RNA-seq


title: GLAST193 pD

description: single-cell RNA-seq


title: GLAST210 pD

description: single-cell RNA-seq


title: GLAST208 pD

description: single-cell RNA-seq


title: GLAST196 pD

description: single-cell RNA-seq


title: GTEX-1CB4H-2126-SM-GW1QJ

description:
sample name:
GTEX-1CB4H-2126-SM-GW1QJ


title: GTEX-1CAMQ-1926-SM-GW1WS

description:
sample name:
GTEX-1CAMQ-1926-SM-GW1WS

value: Former


title: GTEX-1CAV2-1826-SM-GW1EG

description:
sample name:
GTEX-1CAV2-1826-SM-GW1EG


title: ATACseq adult alveolar macrophages Lip rep1 [ATACseq_AM_Lip1_S1]

description:
ATACseq_AM_Lip1_S1
processed data file: counts_matrix.xlsx

source_name: ATACseq adult alveolar macrophages Lip

value: Lip Lip/Lip


title: ATACseq adult alveolar macrophages Lip WT rep2 [ATACseq_AM_Lip4_S4]

description:
ATACseq_AM_Lip4_S4
processed data file: counts_matrix.xlsx


title: ATACseq adult alveolar macrophages Lip WT rep3 [ATACseq_AM_Lip7_S7]

description:
ATACseq_AM_Lip7_S7
processed data file: counts_matrix.xlsx


title: ATACseq adult alveolar macrophages Lip rep3 [ATACseq_AM_Lip5_S5]

description:
ATACseq_AM_Lip5_S5
processed data file: counts_matrix.xlsx


title: ATACseq adult alveolar macrophages Lip rep4 [ATACseq_AM_Lip6_S6]

description:
ATACseq_AM_Lip6_S6
processed data file: counts_matrix.xlsx


title: ATACseq adult alveolar macrophages Lip WT rep1 [ATACseq_AM_Lip3_S3]

description:
ATACseq_AM_Lip3_S3
processed data file: counts_matrix.xlsx


title: ATACseq adult alveolar macrophages Lip rep2 [ATACseq_AM_Lip2_S2]

description:
ATACseq_AM_Lip2_S2
processed data file: counts_matrix.xlsx


title: ATACseq adult alveolar macrophages Cebpb KO rep3 [AL_DD_251_S6]

description:
AL_DD_251_S6
processed data file: counts_matrix.xlsx

value: C/EBPb tm1Pfj

value: Cebpb -/-


title: ATACseq adult alveolar macrophages Cebpb KO rep1 [AL_DD_249_S4]

description:
AL_DD_249_S4
processed data file: counts_matrix.xlsx

value: mixed background


title: ATACseq adult alveolar macrophages Cebpb WT rep1 [AL_DD_246_S1]

description:
AL_DD_246_S1
processed data file: counts_matrix.xlsx

value: Cebpb +/+


title: ATACseq adult alveolar macrophages Cebpb KO rep2 [AL_DD_250_S5]

description:
AL_DD_250_S5
processed data file: counts_matrix.xlsx

value: adult


title: ATACseq adult alveolar macrophages Cebpb WT rep2 [AL_DD_247_S2]

description:
AL_DD_247_S2
processed data file: counts_matrix.xlsx

value: bronchoalveolar lavage


title: ATACseq adult alveolar macrophages Cebpb WT rep3 [AL_DD_248_S3]

description:
AL_DD_248_S3
processed data file: counts_matrix.xlsx

value: alveolar macrophages


title: GLAST191 pD

description: single-cell RNA-seq


title: GLAST192 pD

description: single-cell RNA-seq


title: RNA-for-ATACseq adult alveolar macrophages Lip rep4 [RNA-for-ATAC_Lip_4]

description:
Lip6_S48
processed data file: RNA-for-ATAC_samples_gene_counts.csv


title: GTEX-1B8KE-1926-SM-GW1QT

description:
sample name:
GTEX-1B8KE-1926-SM-GW1QT

value: Colon - Transverse

value: Current


title: GTEX-1AX9I-2626-SM-GW1RQ

description:
sample name:
GTEX-1AX9I-2626-SM-GW1RQ

value: Moderate


title: GTEX-1AYD5-1726-SM-GW1UK

description:
sample name:
GTEX-1AYD5-1726-SM-GW1UK

value: Severe

value: Never


title: GTEX-1A3MV-1126-SM-GW1TJ

description:
sample name:
GTEX-1A3MV-1126-SM-GW1TJ

value: Mild


title: GTEX-19HZE-2626-SM-GW1BU

description:
sample name:
GTEX-19HZE-2626-SM-GW1BU


title: GTEX-1A3MX-2226-SM-GW1EF

description:
sample name:
GTEX-1A3MX-2226-SM-GW1EF


title: GTEX-18D9B-2526-SM-GW22E

description:
sample name:
GTEX-18D9B-2526-SM-GW22E


title: GTEX-1A32A-2426-SM-GW1GU

description:
sample name:
GTEX-1A32A-2426-SM-GW1GU


title: GTEX-18D9U-1926-SM-GW1D2

description:
sample name:
GTEX-18D9U-1926-SM-GW1D2


title: GTEX-17EVQ-1826-SM-GW1Q1

description:
sample name:
GTEX-17EVQ-1826-SM-GW1Q1


title: GTEX-16YQH-2526-SM-GW1DF

description:
sample name:
GTEX-16YQH-2526-SM-GW1DF


title: GTEX-18A7A-2226-SM-GW1RX

description:
sample name:
GTEX-18A7A-2226-SM-GW1RX


title: GTEX-16AAH-1326-SM-GW22B

description:
sample name:
GTEX-16AAH-1326-SM-GW22B


title: RNA-for-ATACseq adult alveolar macrophages Lip rep3 [RNA-for-ATAC_Lip_3]

description:
Lip5_S47
processed data file: RNA-for-ATAC_samples_gene_counts.csv


title: GTEX-17HGU-2426-SM-GW1GQ

description:
sample name:
GTEX-17HGU-2426-SM-GW1GQ


title: GTEX-16NPV-2626-SM-GW1R1

description:
sample name:
GTEX-16NPV-2626-SM-GW1R1


title: GTEX-1C64O-2326-SM-GW22L

description:
sample name:
GTEX-1C64O-2326-SM-GW22L


title: GTEX-1C64N-2326-SM-GW22X

description:
sample name:
GTEX-1C64N-2326-SM-GW22X


title: GTEX-1B98T-2826-SM-GW1UE

description:
sample name:
GTEX-1B98T-2826-SM-GW1UE


title: GTEX-1BAJH-2326-SM-GW1RI

description:
sample name:
GTEX-1BAJH-2326-SM-GW1RI


title: GTEX-1C4CL-2126-SM-GW21V

description:
sample name:
GTEX-1C4CL-2126-SM-GW21V


title: GTEX-1C6WA-2726-SM-GW1DK

description:
sample name:
GTEX-1C6WA-2726-SM-GW1DK


title: GTEX-15SZO-2626-SM-GW1CT

description:
sample name:
GTEX-15SZO-2626-SM-GW1CT


title: GTEX-15SHW-2526-SM-GW1QY

description:
sample name:
GTEX-15SHW-2526-SM-GW1QY


title: GTEX-15SKB-2626-SM-GW1DC

description:
sample name:
GTEX-15SKB-2626-SM-GW1DC


title: GTEX-15SHV-1326-SM-GW1DY

description:
sample name:
GTEX-15SHV-1326-SM-GW1DY


title: RNA-for-ATACseq adult alveolar macrophages Cebpb WT rep2 [RNA-for-ATAC_CebpbWT_2]

description:
AL_DD_155_S2
processed data file: RNA-for-ATAC_samples_gene_counts.csv


title: GTEX-15EU6-1926-SM-GW1D3

description:
sample name:
GTEX-15EU6-1926-SM-GW1D3


title: RNA-for-ATACseq adult alveolar macrophages Cebpb WT rep1 [RNA-for-ATAC_CebpbWT_1]

description:
AL_DD_154_S1
processed data file: RNA-for-ATAC_samples_gene_counts.csv


title: GTEX-15SHU-2526-SM-GW1EC

description:
sample name:
GTEX-15SHU-2526-SM-GW1EC


title: GTEX-15SDE-1026-SM-GW1E5

description:
sample name:
GTEX-15SDE-1026-SM-GW1E5


title: GTEX-15RIE-1826-SM-GW1EB

description:
sample name:
GTEX-15RIE-1826-SM-GW1EB


title: RNA-for-ATACseq adult alveolar macrophages Lip WT rep2 [RNA-for-ATAC_LipWT_2]

description:
Lip4_S46
processed data file: RNA-for-ATAC_samples_gene_counts.csv

value: Lip +/+


title: RNA-for-ATACseq adult alveolar macrophages Cebpb WT rep3 [RNA-for-ATAC_CebpbWT_3]

description:
AL_DD_156_S3
processed data file: RNA-for-ATAC_samples_gene_counts.csv


title: RNA-for-ATACseq adult alveolar macrophages Lip WT rep1 [RNA-for-ATAC_LipWT_1]

description:
Lip3_S45
processed data file: RNA-for-ATAC_samples_gene_counts.csv


title: RNA-for-ATACseq adult alveolar macrophages Cebpb KO rep1 [RNA-for-ATAC_CebpbKO_1]

description:
AL_DD_157_S4
processed data file: RNA-for-ATAC_samples_gene_counts.csv


title: RNA-for-ATACseq adult alveolar macrophages Lip WT rep4 [RNA-for-ATAC_LipWT_4]

description:
Lip8_S50
processed data file: RNA-for-ATAC_samples_gene_counts.csv


title: RNA-for-ATACseq adult alveolar macrophages Cebpb KO rep2 [RNA-for-ATAC_CebpbKO_2]

description:
AL_DD_158_S5
processed data file: RNA-for-ATAC_samples_gene_counts.csv


title: GTEX-15EO6-2126-SM-GW1DH

description:
sample name:
GTEX-15EO6-2126-SM-GW1DH


title: RNA-for-ATACseq adult alveolar macrophages Lip WT rep3 [RNA-for-ATAC_LipWT_3]

description:
Lip7_S49
processed data file: RNA-for-ATAC_samples_gene_counts.csv


title: RNA-for-ATACseq adult alveolar macrophages Cebpb KO rep3 [RNA-for-ATAC_CebpbKO_3]

description:
AL_DD_159_S6
processed data file: RNA-for-ATAC_samples_gene_counts.csv


title: RNA-for-ATACseq adult alveolar macrophages Lip rep1 [RNA-for-ATAC_Lip_1]

description:
Lip1_S43
processed data file: RNA-for-ATAC_samples_gene_counts.csv


title: RNA-for-ATAC seqadult alveolar macrophages Lip rep2 [RNA-for-ATAC_Lip_2]

description:
Lip2_S44
processed data file: RNA-for-ATAC_samples_gene_counts.csv


title: GLAST182 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: aNSC

value: WT

value: naive


title: GLAST184 pD

description: single-cell RNA-seq


title: GLAST188 pD

description: single-cell RNA-seq


title: GLAST186 pD

description: single-cell RNA-seq

value: TAP


title: GLAST189 pD

description: single-cell RNA-seq


title: GLAST187 pD

description: single-cell RNA-seq


title: GLAST183 pD

description: single-cell RNA-seq


title: GLAST179 pD

description: single-cell RNA-seq


title: GLAST178 pD

description: single-cell RNA-seq


title: GLAST190 pD

description: single-cell RNA-seq


title: GLAST180 pD

description: single-cell RNA-seq


title: GLAST185 pD

description: single-cell RNA-seq