title: 8c_ERC_SVB

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

description: Library name: 8c_ERC_SVB

data_processing:
Sequenced chromium data was processed with 10x Genomics Cell Ranger
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, and fastq.gz files

source_name: entorhinal cortex (ERC)

extract_protocol:
Entorhinal cortex was dissected from fresh frozen postmortem human tissue, 100 micron sections were obtained via cryo sectioning. Frozen cryosections were homogenized in chilled Nuclei EZ Lysis Buffer, then filtered and centrifuged to isolate nuclei. Pellets were washed in PBS containing 1% BSA and RNase Inhibitor, stained with propidium iodide, and passed through 35 μm strainers. Fluorescence-activated nuclear sorting (FANS) was performed on a MoFlo Legacy Cell Sorter to select whole, singlet, G0/G1 nuclei.
Library preparation for Chromium Next Gem Single Cell 3' v3.1 was completed according to the manufacturer’s protocol.

value: entorhinal cortex (ERC)


title: 6c_ERC_SVB

status: Public on Nov 14 2025

type: SRA

country: USA

description: Library name: 6c_ERC_SVB

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: batch


title: 7c_ERC_SVB

description: Library name: 7c_ERC_SVB


title: 9c_ERC_SVB

description: Library name: 9c_ERC_SVB


title: h2263_PDX_Lineage_switch_VTP_1580_repeat_r6

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

description: Library name: L12

library_source: transcriptomic

data_processing:
Star aligner and kallisto to get alignment file and TPM per transcript
DEseq2 as the tool to identify over/under expressed genes at FDR less than 0.05
Assembly: HG38
Supplementary files format and content: tab separated TPM per sample

molecule: total RNA

source_name: bone marrow

growth_protocol: 6-8 week old NSG (NOD-scid IL2Rgnull) mice were obtained from Jackson laboratories® and maintained under specific pathogen free conditions. 24-48 hours prior to transplantation, mice were conditioned with 25 mg/kg busulfan i.p. Previously banked patient leukemia samples were thawed, resuspended in PBS and injected into the tail vein.

extract_protocol:
RNA was extracted using the RNeasy mini kit from QIAGEN
RNA-Seq libraries were prepared from PolyA selected mRNA (eukaryotic) using the NEBNext Ultra II RNA Library Prep Kit for Illumina 24. Multiplexed sequencing was conducted on a NovaSeq 6000  using the NovaSeq 6000 SP Reagent Kit v1.5, paird end to a read depth of 20-30 million per sample.

treatment_protocol: Mice underwent monitoring for leukemia development using weekly serial bleeds. Treatment with VTP-50469 0.1% chow was started once peripheral blood engraftment in the range of 1-5% was seen (day 14 for sample 5.1, and day 7 for sample 5.2). After three weeks of treatment, mice were sacrificed and leukemia cells were isolated by and sorted on live (FSC vs SSC and DAPI negative), human CD45+, mouse CD45-.

value: bone marrow

tag: cell line

value: patient derived xenograft

tag: cell type

value: leukemia

tag: genotype

value: Sample # 5.2 (late)

tag: treatment


title: 4c_ERC_SVB

description: Library name: 4c_ERC_SVB


title: 3c_ERC_SVB

description: Library name: 3c_ERC_SVB


title: 31c_ERC_SVB

description: Library name: 31c_ERC_SVB


title: 2c_ERC_SVB

description: Library name: 2c_ERC_SVB


title: 29c_ERC_SVB

description: Library name: 29c_ERC_SVB


title: 28c_ERC_SVB

description: Library name: 28c_ERC_SVB


title: 26c_ERC_SVB

description: Library name: 26c_ERC_SVB


title: 30c_ERC_SVB

description: Library name: 30c_ERC_SVB


title: h2263_PDX_Lineage_switch_Con_1540_r4

description: Library name: L4

value: control chow


title: 23c_ERC_SVB

description: Library name: 23c_ERC_SVB


title: 24c_ERC_SVB

description: Library name: 24c_ERC_SVB


title: 21c_ERC_SVB

description: Library name: 21c_ERC_SVB


title: corresponding adjacent tissues of patient 2

city: Changchun

first: Xiaosong

last: Wang

state: Jilin

address: No.519 Dongminmin Street Changchun 130021, China

country: China

institute: Department of Translational Medicine, the First Hospital of Jilin University

description: Library name: ATN02

data_processing:
The BD Resolve analysis pipeline was used to process sequencing data (fastq files). Raw data (raw reads) of fastq format were first processed to obtain clean data (clean reads). All the downstream analyses were based on the clean data with high quality. The p values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR). Gene with an adjusted p value < 0.05 was assigned as differentially expressed. Using Seurat 3.0(R package) analyses included identification of highly variable genes, data dimension reduction (PCA, T-SNE), cell clustering, identification of differentially expressed genes and markers.  Functional analysis including GO enrichment, KEGG enrichment, Reactome enrichment and Disease enrichment (human only) was performed on the genes with top20 differences in each Cluster. Protein-protein interaction was obtained from STRING database with combine_score >=700. Transcription Factors were predicted within 2000 bp upstream and 500 bp downstream of TSS for top 20 marker genes of each cluster using TFBSTools and JASPAR database. GSEA was performed by using GSEA software version 2.2.2.4, which uses predefined gene sets from the Molecular Signatures Database (MSigDB v6.2). Single-cell trajectories were built with Monocle (R package).
Assembly: GRCh38
Supplementary files format and content: Tap-separated values files and matrix files

source_name: corresponding adjacent tissues

extract_protocol:
cervical squamous cell carcinoma tissues and corresponding adjacent tissues were taken by pathologists from normal and tumor regions. Tissues were washed by PBS and put into a gentle Tube full of MACS Tissue Storage solution
The cell suspension was loaded onto the Rhapsody™ Cartridge (BD) to generate single-cell magnetic beads in the microwells according to the manufacturer’s protocol. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual microwells.     The cDNA was generated and then amplified, the quality assessed using an Agilent 4200 (performed by CapitalBio Technology, Beijing). Whole transcriptome libraries were prepared using the BD Resolve single cell whole transcriptome amplification workflow. The libraries were sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 50,000 reads per cell with pair-end 150 bp (PE150) reading strategy

value: corresponding adjacent tissues

value: tissue

value: corresponding adjacent tissue cell


title: 20c_ERC_SVB

description: Library name: 20c_ERC_SVB


title: 22c_ERC_SVB

description: Library name: 22c_ERC_SVB


title: 19c_ERC_SVB

description: Library name: 19c_ERC_SVB


title: 1c_ERC_SVB

description: Library name: 1c_ERC_SVB


title: 18c_ERC_SVB

description: Library name: 18c_ERC_SVB


title: 17c_ERC_SVB

description: Library name: 17c_ERC_SVB


title: cervical squamous cell carcinoma tissues of patient 2

description: Library name: CC02

value: cervical squamous cell carcinoma cell


title: 16c_ERC_SVB

description: Library name: 16c_ERC_SVB


title: 15c_ERC_SVB

description: Library name: 15c_ERC_SVB


title: 12c_ERC_SVB

description: Library name: 12c_ERC_SVB


title: 5c_ERC_SVB

description: Library name: 5c_ERC_SVB


title: 13c_ERC_SVB

description: Library name: 13c_ERC_SVB


title: 14c_ERC_SVB

description: Library name: 14c_ERC_SVB


title: 27c_ERC_SVB

description: Library name: 27c_ERC_SVB


title: 10c_ERC_SVB

description: Library name: 10c_ERC_SVB


title: 25c_ERC_SVB

description: Library name: 25c_ERC_SVB


title: V13Y24-344_C1

description: Library name: V13Y24-344_C1

data_processing:
Raw seqencing data and images were processed with 10x genomics Space Ranger pipeling, generating FASTQ files
Assembly: GRCh38
Supplementary files format and content: aligned_fiducials.jpg, barcodes.tsv.gz, detected_tissue_image.jpg, features.tsv.gz, matrix.mtx.gz, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png, tissue_positions.csv files
Library strategy: Spatial Transcriptomics

extract_protocol:
Entorhinal cortex was dissected from fresh frozen postmortem human tissue, 10 micron sections were obtained via cryosectioning. Tissue sections were mounted on Visium gene Expression slides.
Spatial transcriptomics sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Reagent Kit and protocol.


title: V13Y24-344_B1

description: Library name: V13Y24-344_B1


title: V13Y24-344_A1

description: Library name: V13Y24-344_A1


title: V13Y24-342_C1

description: Library name: V13Y24-342_C1


title: V13Y24-343_C1

description: Library name: V13Y24-343_C1


title: V13Y24-343_D1

description: Library name: V13Y24-343_D1


title: V13Y24-343_A1

description: Library name: V13Y24-343_A1


title: V13Y24-342_D1

description: Library name: V13Y24-342_D1


title: V13Y24-342_B1

description: Library name: V13Y24-342_B1


title: V13Y24-343_B1

description: Library name: V13Y24-343_B1


title: V13Y24-340_D1

description: Library name: V13Y24-340_D1


title: V13Y24-340_C1

description: Library name: V13Y24-340_C1


title: V13B23-366_D1

description: Library name: V13B23-366_D1


title: V13Y24-342_A1

description: Library name: V13Y24-342_A1


title: V13Y24-340_A1

description: Library name: V13Y24-340_A1


title: V13B23-366_C1

description: Library name: V13B23-366_C1


title: V13B23-366_B1

description: Library name: V13B23-366_B1


title: 11c_ERC_SVB

description: Library name: 11c_ERC_SVB


title: V13B23-365_D1

description: Library name: V13B23-365_D1


title: V13B23-365_B1

description: Library name: V13B23-365_B1


title: V13B23-364_C1

description: Library name: V13B23-364_C1


title: V13B23-364_B1

description: Library name: V13B23-364_B1


title: V13B23-364_D1

description: Library name: V13B23-364_D1


title: V13B23-365_A1

description: Library name: V13B23-365_A1


title: V13Y24-344_D1

description: Library name: V13Y24-344_D1


title: V13B23-363_D1

description: Library name: V13B23-363_D1


title: V13B23-363_C1

description: Library name: V13B23-363_C1


title: nuclear RNA from AC16 cells expressing dox-inducible shRPL3 and RPL3L D308N variant, replcate 2

city: New York

first: Xuebing

last: Wu

state: NY

address: 630 West 168th Street, P&S 10-401

institute: Columbia University

description: Library name: D308N-shRPL3-nuclear-rep2

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format
PolyA RNA: We perform a pseudoalignment to a kallisto index created by adding shRNA and RPL3L sequences to human transcriptome reference (GENCODE v41): kallisto quant -t 32 -i $genome -o $sample-kallisto-output --rf-stranded $files. Nuclear RNA: reads were mapped to 45S rRNA using bowtie (bowtie $index -1 $f1 -2 $f2 -S -p 100 --no-unal --best --strata --all) and coverage in each region calculated using bedtools multicov (bedtools multicov -bams ${bamfiles} -bed /home/xw2629/genomes/sequences/human_45S_rRNA.bed).
For polyA RNA: TPM counts for genes were aggregated from transcripts and output to a single table
Assembly: PolyA RNA: GENCODE v41 human transcriptome supplemented with shRNA and RPL3L sequences. Nuclear RNA: human 45S rRNA
Supplementary files format and content: polyA RNA samples: a gene expression table
Supplementary files format and content: nuclear RNA: read coverage in each region of 45S rRNA

molecule: nuclear RNA

growth_protocol: AC16 cells were cultured at 37oC, 5% CO2 in low-glucose DMEM (Fisher; 11-885-084) supplemented with 10% FBS. HEK293T cells were cultured in DMEM with 10% FBS. For immunofluorescence assays, 2 x 105 cells were plated in 6 well plates and incubated for 24 hours. For stable cell generation, EZ-Tet-RPL3-shRNA was co-transfected with CMV-dR8.91 and MD2.G plasmids for 72 hours in HEK293T cells to produce virus. The media was centrifuged for 5 minutes at RT, filtered using 0.45µm Syringe Filter Unit (Fisher), and 200µl viral media was added to 2 x 105 AC16 cells for 48 hours prior to selection using 200µg/ml Hygromycin B until control cells (non-transduced) were dead. For stable generation of pLenti-RPL3L, procedure was followed as above except transduction was carried out on EZ-Tet-RPL3-shRNA/AC16 cells and selection was carried out by sorting for BV421-positive cells.

extract_protocol:
Cells were washed with ice-cold PBS, scraped into 1.7ml tubes, and pelleted at 500 g for 5 minutes at 4°C. Total RNA was isolated using NucleoSpin RNA Plus kit (Macharey-Nagel) including use of gDNA removal column. Cytoplasmic RNA was extracted by lysing cells in Cytoplasmic Lysis Buffer (40 mM HEPES-NaOH pH 7.5, 160 mM KCl, 10 mM MgCl₂, 0.5% NP-40, 0.5% glycerol, and SuperaseIn) for 30 minutes at 4°C with rotation, followed by centrifugation at 2000 g for 2 minutes to separate the cytoplasmic supernatant. Nuclear pellets were washed in Cytoplasmic Lysis Buffer (without detergent), centrifuged at 500 g for 5 minutes, and subjected to a wash with Nuclear Lysis Buffer (10 mM Tris-HCl pH 8.0, 1.5 mM KCl, 2.5 mM MgCl₂, 5% glycerol, 0.5% Triton X-100, 0.5% deoxycholate, and 20U SuperaseIN) for 15 minutes at 4°C. Final washes were performed with Cytoplasmic Lysis Buffer (without detergent), and nuclei were pelleted at 2000 g for 2 minutes. Both cytoplasmic and nuclear RNA were extracted as above.
For polyA RNA, we use poly-A pull-down to enrich mRNAs from total RNA samples. Library construction using Illumina TruSeq chemistry. The final PCR step has been modified using the KAPA HiFi HotStart Ready Mix. For nuclear RNA, no polyA pulldown or rRNA depletion applied.

treatment_protocol: dox was added to cell media to a final concentration of 1ug/ml

value: cardiomyocyte-like

value: dox


title: nuclear RNA from AC16 cells expressing dox-inducible shRPL3 and RPL3L R161W variant, replcate 1

description: Library name: R161W-shRPL3-nuclear-rep1


title: nuclear RNA from AC16 cells expressing dox-inducible shRPL3 and RPL3L R161W variant, replcate 2

description: Library name: R161W-shRPL3-nuclear-rep2


title: V13Y24-340_B1

description: Library name: V13Y24-340_B1


title: nuclear RNA from AC16 cells expressing dox-inducible shRPL3 and RPL3L D308N variant, replcate 1

description: Library name: D308N-shRPL3-nuclear-rep1


title: V13B23-363_A1

description: Library name: V13B23-363_A1


title: nuclear RNA from AC16 cells expressing dox-inducible shRPL3 and RPL3L T189M variant, replcate 2

description: Library name: T189M-shRPL3-nuclear-rep2


title: nuclear RNA from AC16 cells expressing dox-inducible shRPL3 and RPL3L G27D variant, replcate 2

description: Library name: G27D-shRPL3-nuclear-rep2


title: V13B23-365_C1

description: Library name: V13B23-365_C1


title: nuclear RNA from AC16 cells expressing dox-inducible shRPL3, replcate 2

description: Library name: shRPL3-nuclear-2


title: nuclear RNA from AC16 cells expressing dox-inducible shRPL3 and RPL3L G27D variant, replcate 1

description: Library name: G27D-shRPL3-nuclear-rep1


title: nuclear RNA from AC16 cells expressing dox-inducible shRPL3 and RPL3L wild type, replcate 2

description: Library name: shRPL3-RPL3Lwt-nuclear-2


title: nuclear RNA from AC16 cells expressing dox-inducible shRPL3 and RPL3L wild type, replcate 1

description: Library name: shRPL3-RPL3Lwt-nuclear-1


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L R343W variant, replicate 2

description: Library name: R343W-shRPL3-rep2


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L R343W variant, replicate 3

description: Library name: R343W-shRPL3-rep3


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L R343W variant, replicate 1

description: Library name: R343W-shRPL3-rep1


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L D308V variant, replicate 2

description: Library name: D308V-shRPL3-rep2


title: nuclear RNA from AC16 cells expressing dox-inducible shRPL3, replcate 1

description: Library name: shRPL3-nuclear-1


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L D308V variant, replicate 3

description: Library name: D308V-shRPL3-rep3


title: V13B23-364_A1

description: Library name: V13B23-364_A1


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L D308V variant, replicate 1

description: Library name: D308V-shRPL3-rep1


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L D308N variant, replicate 3

description: Library name: D308N-shRPL3-rep3


title: nuclear RNA from AC16 cells expressing dox-inducible shRPL3 and RPL3L T189M variant, replcate 1

description: Library name: T189M-shRPL3-nuclear-rep1


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L T189M variant, replicate 3

description: Library name: T189M-shRPL3-rep3


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L D308N variant, replicate 1

description: Library name: D308N-shRPL3-rep1


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L T189M variant, replicate 1

description: Library name: T189M-shRPL3-rep1


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L D308N variant, replicate 2

description: Library name: D308N-shRPL3-rep2


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L T189M variant, replicate 2

description: Library name: T189M-shRPL3-rep2


title: V13B23-363_B1

description: Library name: V13B23-363_B1


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L R161W variant, replicate 3

description: Library name: R161W-shRPL3-rep3


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L R161W variant, replicate 1

description: Library name: R161W-shRPL3-rep1


title: AC16 cells expressing dox-inducible shRPL3 and dox-inducible  variant P291L, replicate 3

description: Library name: RPL3Lsnp-shRPL3-rep3


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L G27D variant, replicate 3

description: Library name: G27D-shRPL3-rep3


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L G27D variant, replicate 2

description: Library name: G27D-shRPL3-rep2


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L G27D variant, replicate 1

description: Library name: G27D-shRPL3-rep1


title: AC16 cells expressing dox-inducible shRPL3 and dox-inducible variant P291L, replicate 1

description: Library name: RPL3Lsnp-shRPL3-rep1


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L wild type, replicate 3

description: Library name: RPL3Lwt-shRPL3-rep3


title: AC16 cells expressing dox-inducible shRPL3 and dox-inducible  variant P291L, replicate 2

description: Library name: RPL3Lsnp-shRPL3-rep2


title: AC16 cells expressing dox-inducible scrambled shRNA, replicate 3

description: Library name: shScramble-rep3

value: shScramble


title: AC16 cells expressing dox-inducible shRPL3, replciate 3

description: Library name: shRPL3-rep3


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L wild type, replicate 1

description: Library name: RPL3Lwt-shRPL3-rep1


title: AC16 cells expressing dox-inducible scrambled shRNA, replicate 1

description: Library name: shScramble-rep1


title: AC16 cells expressing dox-inducible shRPL3, replciate 2

description: Library name: shRPL3-rep2


title: CHLA266_RG_1

first: Michael

last: Koldobskiy

state: MD

address: 1800 Orleans St., Bloomberg 11379

department: Oncology

institute: Johns Hopkins University

description:
Library name: CHLA266_RG_1
RG

data_processing:
We aligned reads to GRCh37 using STAR version 2.4.2a [8] with the following options --readFilesCommand zcat --outSAMtype BAM Unsorted SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts. We generated summarized experiment (se) objects using the gtf file Homo_sapiens.GRCh37.75.gtf and the following command from the Bioconductor package ‘GenomicAlignments’: summarizeOverlaps(features=exonsByGene, reads=bamfiles, mode="Union", singleEnd=FALSE, ignore.strand=FALSE, fragments=TRUE).
Assembly: hg38
Supplementary files format and content: CSV files of DESeq2 output

source_name: Homo sapiens

growth_protocol: Cell lines were cultured in DMEM/F12 human neurosphere proliferation medium (30% Hams F12 [Gibco 11765070], 70% DMEM [Gibco 11995073], 1% Antibiotic-Antimycotic [15240062], 2% B27 minus Vitamin A [12587001], 20 ng/ml EGF [Peprotech AF-100-15], 20 ng/ml FGF-2 [Peprotech 100-18B], and 5 ug/ml of heparin [Millipore Sigma H3149]. All cell lines were kept in 25 cm2 culture flasks at 37 °C and 5% CO2.

extract_protocol:
RNA extraction was carried out using the RNeasy Mini kit (Qiagen), including on-column DNase I digestion (Invitrogen). Integrity of genomic DNA was confirmed by gel electrophoresis. RNA was assessed on an Agilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano kit.
Strand specific mRNA libraries were generated by Novogene using the NEBNext Ultra II Directional RNA library prep Kit for Illumina (New England BioLabs #E7760), mRNA was isolated using Poly(A) mRNA magnetic isolation module (New England BioLabs #E7490). Stranded mRNA libraries were sequenced by Novogene on an Illumina NovaSeq6000 instrument,  using 150bp paired-end dual indexed reads.

treatment_protocol: Cells were treated with 100 nm DAC or DMSO for 5 days, with media and drug change every 24 hours. On day 5, 2.5 uM RG2833 or DMSO was added to the pre-treated cells. Treated cells were harvested at the 72 hour time point (day 8).

value: Homo sapiens

value: atypical teratoid rhabdoid tumor

value: mRNA


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L wild type, replicate 2

description: Library name: RPL3Lwt-shRPL3-rep2


title: AC16 cells expressing dox-inducible shRPL3, replciate 1

description: Library name: shRPL3-rep1


title: CHLA266_DMSO_3

description:
Library name: CHLA266_DMSO_3
DMSO


title: CHLA266_RG_2

description:
Library name: CHLA266_RG_2
RG


title: CHLA266_DMSO_2

description:
Library name: CHLA266_DMSO_2
DMSO


title: CHLA266_DAC_1

description:
Library name: CHLA266_DAC_1
DAC


title: CHLA266_COMB_3

description:
Library name: CHLA266_COMB_3
COMB


title: CHLA266_DAC_2

description:
Library name: CHLA266_DAC_2
DAC


title: CHLA266_COMB_1

description:
Library name: CHLA266_COMB_1
COMB


title: AC16 cells expressing dox-inducible shRPL3 and RPL3L R161W variant, replicate 2

description: Library name: R161W-shRPL3-rep2


title: CHLA06_RG_3

description:
Library name: CHLA06_RG_3
RG


title: CHLA266_COMB_2

description:
Library name: CHLA266_COMB_2
COMB


title: CHLA06_RG_2

description:
Library name: CHLA06_RG_2
RG


title: CHLA06_DMSO_2

description:
Library name: CHLA06_DMSO_2
DMSO


title: CHLA06_DMSO_3

description:
Library name: CHLA06_DMSO_3
DMSO


title: CHLA06_DAC_3

description:
Library name: CHLA06_DAC_3
DAC


title: CHLA06_RG_1

description:
Library name: CHLA06_RG_1
RG


title: CHLA266_RG_3

description:
Library name: CHLA266_RG_3
RG


title: AC16 cells expressing dox-inducible scrambled shRNA, replicate 2

description: Library name: shScramble-rep2


title: CHLA06_DAC_1

description:
Library name: CHLA06_DAC_1
DAC


title: CHLA06_DAC_2

description:
Library name: CHLA06_DAC_2
DAC


title: CHLA06_COMB_2

description:
Library name: CHLA06_COMB_2
COMB


title: CHLA06_COMB_1

description:
Library name: CHLA06_COMB_1
COMB


title: CHLA05_RG_3

description:
Library name: CHLA05_RG_3
RG


title: CHLA05_DMSO_3

description:
Library name: CHLA05_DMSO_3
DMSO


title: CHLA05_RG_1

description:
Library name: CHLA05_RG_1
RG


title: CHLA266_DAC_3

description:
Library name: CHLA266_DAC_3
DAC


title: CHLA05_DMSO_2

description:
Library name: CHLA05_DMSO_2
DMSO


title: CHLA266_DMSO_1

description:
Library name: CHLA266_DMSO_1
DMSO


title: CHLA05_DAC_3

description:
Library name: CHLA05_DAC_3
DAC


title: CHLA05_DMSO_1

description:
Library name: CHLA05_DMSO_1
DMSO


title: CHLA05_DAC_2

description:
Library name: CHLA05_DAC_2
DAC


title: CHLA05_COMB_3

description:
Library name: CHLA05_COMB_3
COMB


title: CHLA05_DAC_1

description:
Library name: CHLA05_DAC_1
DAC


title: CHLA05_COMB_1

description:
Library name: CHLA05_COMB_1
COMB


title: CHLA05_COMB_2

description:
Library name: CHLA05_COMB_2
COMB


title: CHLA02_RG_1

description:
Library name: CHLA02_RG_1
RG


title: CHLA02_RG_2

description:
Library name: CHLA02_RG_2
RG


title: CHLA06_DMSO_1

description:
Library name: CHLA06_DMSO_1
DMSO


title: CHLA02_DMSO_3

description:
Library name: CHLA02_DMSO_3
DMSO


title: CHLA02_DMSO_2

description:
Library name: CHLA02_DMSO_2
DMSO


title: CHLA02_DAC_2

description:
Library name: CHLA02_DAC_2
DAC


title: CHLA02_DAC_3

description:
Library name: CHLA02_DAC_3
DAC


title: CHLA06_COMB_3

description:
Library name: CHLA06_COMB_3
COMB


title: CHLA02_DAC_1

description:
Library name: CHLA02_DAC_1
DAC


title: CHLA02_COMB_3

description:
Library name: CHLA02_COMB_3
COMB


title: CHLA05_RG_2

description:
Library name: CHLA05_RG_2
RG


title: Gaq_dBET6_DCZ_n2

city: Montreal

first: Jason

last: Tanny

address: 3655 Prom Sir William Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

description: Library name: Gaq_dBET6_DCZ_n2

data_processing:
FASTQ files were subjected to adaptor trimming and FASTP (v0.23.4) was used to filter the low quality and duplicate reads. The sequences were then aligned to the Homo sapiens genome (GRCh38, NCBI # GCF_000001405.26) using STAR (v2.7.11b). Pearson correlations and principal component analysis plots to compare biological replicates were generated using DESeq2  Gene-level read count matrices were obtained using FeatureCounts (v2.0.1). Differential expression analysis was performed with DESeq2 (v1.42.1).
Assembly: GRCh38, NCBI # GCF_000001405.26
Supplementary files format and content: csv file (output from FeatureCounts)

source_name: HEK 293 (PL)

growth_protocol: HEK293 (PL) cells were transfected with DREADD plasmids and seeded at 350,000 cells per well in 6-well plates, followed by recovery for 24 hours.

extract_protocol:
Cells were washed twice with cold PBS, and total RNA was extracted using the Qiashredder Homogenization kit and the RNeasy Mini kit (Qiagen) as per the manufacturer’s instructions. RNA concentrations were measured with a Nanodrop 2000 spectrophotometer, and RNA quality was assessed on an Agilent 2100 Bioanalyzer
Libraries were generated from 100 ng of total RNA as following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with NEBNext UltraExpress RNA Library Prep Kit (New England BioLabs) as per the manufacturer's recommendations. Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the KAPA Library Quanitification Kits - Complete kit (Universal) (Kapa Biosystems). Average fragment size was determined using a Fragment Analyzer 5300 (Agilent) instrument. The libraries were normalized and pooled and then denatured in 0.02N NaOH and neutralized using pre-load buffer. The pool was loaded at 140pM on a Illumina NovaSeq X Plus 25B lane following the manufacturer’s recommendations. The run was performed for 2x100 cycles (paired-end mode) (150 base pair reads at a depth of ~25 million reads per sample for 24 samples). A phiX library was used as a control and mixed with libraries at 1% level. Program BCL Convert 4.2.4 was then used to demultiplex samples and generate FASTQ files.

treatment_protocol: Cells were treated with 100 nM dBET6, 1 mM JQ1, or vehicle for 3 hours. During the last hour of inhibitor treatment, DCZ (1 mM) or vehicle was added.

value: HEK 293 (PL)


title: CHLA02_COMB_1

description:
Library name: CHLA02_COMB_1
COMB


title: CHLA02_COMB_2

description:
Library name: CHLA02_COMB_2
COMB


title: Gaq_dBET6_DCZ_n1

description: Library name: Gaq_dBET6_DCZ_n1


title: Gaq_JQ1_DCZ_n1

description: Library name: Gaq_JQ1_DCZ_n1


title: Gaq_DCZ_n1

description: Library name: Gaq_DCZ_n1

value: DCZ


title: Gaq_dBET6_n1

description: Library name: Gaq_dBET6_n1


title: Gaq_dBET6_n2

description: Library name: Gaq_dBET6_n2


title: Gaq_DCZ_n2

description: Library name: Gaq_DCZ_n2


title: Gas_JQ1_DCZ_n2

description: Library name: Gas_JQ1_DCZ_n2


title: CHLA02_RG_3

description:
Library name: CHLA02_RG_3
RG


title: Gas_JQ1_DCZ_n1

description: Library name: Gas_JQ1_DCZ_n1


title: Gaq_JQ1_n1

description: Library name: Gaq_JQ1_n1


title: Gas_dBET6_DCZ_n2

description: Library name: Gas_dBET6_DCZ_n2


title: Gas_dBET6_DCZ_n1

description: Library name: Gas_dBET6_DCZ_n1


title: Gas_DCZ_n2

description: Library name: Gas_DCZ_n2


title: CHLA02_DMSO_1

description:
Library name: CHLA02_DMSO_1
DMSO


title: Gas_DCZ_n1

description: Library name: Gas_DCZ_n1


title: Gaq_JQ1_DCZ_n2

description: Library name: Gaq_JQ1_DCZ_n2


title: Gas_JQ1_n2

description: Library name: Gas_JQ1_n2


title: Gas_JQ1_n1

description: Library name: Gas_JQ1_n1


title: Gas_DMSO_n2

description: Library name: Gas_DMSO_n2

value: control


title: Gas_dBET6_n1

description: Library name: Gas_dBET6_n1


title: OR6a Osimertinib-Resistant circRNA Profile

city: Taipei

first: Pinghsing

last: Tsai

state: Taiwan

address: Rm. 825, 7F., No.322, Sec. 2, Shipai Rd., Beitou D

country: Taiwan

institute: Taipei Veterans General Hospital

description:
Library name: OR6a_circRNA
circRNA sequencing of OR6a cells

data_processing:
Pseudo-alignment and quantification were performed using Kallisto with default parameters to generate transcript per million (TPM) values.
TPM values were normalized and differential expression analysis was performed to identify circRNAs. genome build/assembly hg19 processed data files format and content Excel files (summary_TPM.xlsx) include TPM values for each sample processed data files format and content
Assembly: hg19
Supplementary files format and content: excel files include TPM values for each Sample

growth_protocol: Osimertinib-resistant cell lines were generated from H1975 cell line as described in our previous study. All three single clones used in this study (OR3, OR4, and OR6) were selected from three separate wells of a 96-well plate (clones) and were maintained in the RPMI-1640 complete medium. The H1975, OR3, OR4 and OR6 cell lines were cultured in RPMI-1640 growth medium supplemented with 10% fetal bovine serum (FBS), 4mM L-glutamine and 1% penicillin-streptomycin (at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Plus Kit (Qiagen) following the manufacturer's instructions. RNA was treated with RNase R to enrich for circular RNAs
RNA libraries for circRNA sequencing were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina, with modifications to enrich for circRNAs following RNase R treatment. Libraries were constructed according to the manufacturer's protocols.

treatment_protocol: No specific treatment was applied prior to RNA extraction for circRNA sequencing. Osimertinib-resistant clones (OR3, OR4, OR6) were previously established by long-term osimertinib exposure, and HOsR was an independently derived osimertinib-resistant cell line.

value: Lung adenocarcinoma cells

value: EGFR L858R/T790M


title: OR6b Osimertinib-Resistant circRNA Profile

description:
Library name: OR6b_circRNA
circRNA sequencing of OR6b cells


title: OR4b Osimertinib-Resistant circRNA Profile

description:
Library name: OR4b_circRNA
circRNA sequencing of OR4b cells


title: H1975a Parental circRNA Profile

description:
Library name: PARa_circRNA
circRNA sequencing of parental H1975 cells


title: Gaq_DMSO_n1

description: Library name: Gaq_DMSO_n1


title: Gaq_JQ1_n2

description: Library name: Gaq_JQ1_n2


title: OR3a Osimertinib-Resistant circRNA Profile

description:
Library name: OR3a_circRNA
circRNA sequencing of OR3a cells


title: Gaq_DMSO_n2

description: Library name: Gaq_DMSO_n2


title: OR3b Osimertinib-Resistant circRNA Profile

description:
Library name: OR3b_circRNA
circRNA sequencing of OR3b cells


title: Hela cells, NC

city: 杭州市

first: 倩倩

last: 杨

state: 浙江省

address: 墩余路

institute: Westlake university

description:
Library name: sample 1
NC

data_processing:
Clean reads with adapter-deleted and quality control after processed by cutadapt 3.1(-m 20 –trim-n) were aligned to the human reference genome(T2T) using bowtie 1.2.3(-v 2 -m 10 –best –strata). Peaks were called using PARalyzer v1.5 with default and recommended parameters as described in the manual. Statistic computations and plots were implemented using the R software.
Assembly: T2T-CHM13v2.0
Supplementary files format and content: xlsx(reads count on each peaks, CPM value, fold change, p value)

source_name: human cervical carcinoma tissue

growth_protocol: Hela Cells were cultured at 37 °C with 5% CO2 in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Protein associated RNAs were released by proteinase K and were extracted by phenol/chloroform.
Following sample qualification, 1–10 ng of total RNA was utilized for library construction using the Clontech SMARTer Stranded Total RNA-Seq Kit V2 (Pico Input). Briefly, RNA was fragmented and combined with a 5’-end switching template to initiate reverse transcription for first-strand cDNA synthesis. Subsequently, index-containing adapters were ligated during the first-round PCR amplification. The ligation products were purified, and the optimal number of amplification cycles was selected based on the initial RNA quantity for library enrichment. Finally, the amplified libraries were purified using magnetic beads to generate strand-specific RNA-Seq libraries ready for sequencing.

treatment_protocol: Cells were cultured 14 h in DMEM medium supplemented with 100μM 4-SU

value: human cervical carcinoma tissue

value: Hela

value: Human cervical cancer cell

value: WT

value: PAR-Clip by streptavidin resin and Flag resin


title: Gas_DMSO_n1

description: Library name: Gas_DMSO_n1


title: H1975b Parental circRNA Profile

description:
Library name: PARb_circRNA
circRNA sequencing of parental H1975 cells


title: OR4a Osimertinib-Resistant circRNA Profile

description:
Library name: OR4a_circRNA
circRNA sequencing of OR4a cells


title: Hela cells, REIIBP

description:
Library name: sample 2
REIIBP

value: REIIBP overexpression


title: DSP-1001660020373-D-G12

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description:
Library name: DSP-1001660020373-D-G12
spatial transcriptomic sequencing

data_processing:
Digital count conversion (.dcc) files were produced from fastq files using the GeoMx NGS Pipeline 2.3.3.10 desktop application.  Briefly, reads are trimmed to remove adapter sequences followed by merging paired-end reads. Stitched reads are then aligned to RTS-ID barcodes in the reference assay. PCR duplicates are removed by sorting on UMIs. Supplemental file Hs_R_NGS_WTA_v1.0 contains RTS-ID mapping.
Assembly: GRCh38.p13. Reads are aligned to GeoMx RTS_ID barcodes as part of the GeoMx NGS Pipeline to generate .dcc files
Supplementary files format and content: deduplicated read counts
Library strategy: Spatial Transcriptomics

source_name: lung

extract_protocol:
Sample extraction from tissue slides was performed on the GeoMx Digital Spatial Profiler
Samples were amplified, pooled, purified, and checked for quality control according to the GeoMx NGS Readout NGS Library Preparation and Sequencing protocols

tag: slide name

value: lung

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: patient

tag: age

tag: condition

value: COPD GOLD 4

value: COPD

tag: former or_current_smoker

value: former

tag: pack years

tag: gender

value: male

tag: location

value: parenchyma

tag: roi

tag: scan name

value: paraffin


title: DSP-1001660020373-D-H02

description:
Library name: DSP-1001660020373-D-H02
spatial transcriptomic sequencing

tag: tissue

value: vessel


title: DSP-1001660020373-D-H01

description:
Library name: DSP-1001660020373-D-H01
spatial transcriptomic sequencing


title: DSP-1001660020373-D-H06

description:
Library name: DSP-1001660020373-D-H06
spatial transcriptomic sequencing


title: DSP-1001660020373-D-H04

description:
Library name: DSP-1001660020373-D-H04
spatial transcriptomic sequencing


title: DSP-1001660020373-D-H03

description:
Library name: DSP-1001660020373-D-H03
spatial transcriptomic sequencing


title: DSP-1001660020373-D-G10

description:
Library name: DSP-1001660020373-D-G10
spatial transcriptomic sequencing


title: DSP-1001660020373-D-H05

description:
Library name: DSP-1001660020373-D-H05
spatial transcriptomic sequencing


title: DSP-1001660020373-D-G09

description:
Library name: DSP-1001660020373-D-G09
spatial transcriptomic sequencing


title: Gas_dBET6_n2

description: Library name: Gas_dBET6_n2

value: HEK 293 (PL)


title: DSP-1001660020373-D-G08

description:
Library name: DSP-1001660020373-D-G08
spatial transcriptomic sequencing


title: DSP-1001660020373-D-G11

description:
Library name: DSP-1001660020373-D-G11
spatial transcriptomic sequencing


title: DSP-1001660020373-D-G07

description:
Library name: DSP-1001660020373-D-G07
spatial transcriptomic sequencing


title: DSP-1001660020373-D-G06

description:
Library name: DSP-1001660020373-D-G06
spatial transcriptomic sequencing


title: DSP-1001660020373-D-G05

description:
Library name: DSP-1001660020373-D-G05
spatial transcriptomic sequencing


title: DSP-1001660020373-D-G04

description:
Library name: DSP-1001660020373-D-G04
spatial transcriptomic sequencing


title: BL6-SOX2-Noco-1

city: Edinburgh

first: Charles

middle: A C

last: Williams

state: Midlothian

address: 5 Little France Dr, Bioquarter, Scottish Ctr For Regenerative Medicine, Scottish Ctr For Regenerative Medicine

department: Institute for Regeneration and Repair

country: United Kingdom

institute: University of Edinburgh

description: Library name: BL6-SOX2-Noco-1

library_source: genomic

data_processing:
We aligned paired-end reads (~150 bps and ~30 million reads per replicate, n=2) to the mm10 genome (GCA_000001635.2) using BWA (v0.7.17). All replicates contained >10 million total mapped reads. We removed multi-mapped and supplementary reads and reads overlapping the mm10 blacklisted regions (obtained from https://github.com/Boyle-Lab/Blacklist/tree/master/lists) using samtools (v1.9). We called peaks using macs2 (v2.1.1) with the settings q = 1e-5 for the SOX2 ChIP-seq samples and q=1e-2 for the BL6 ChIP-seq samples. We used Diffbind to analyse differentially bound peaks between the different SOX2 variants and cell cycle phases. To do this, we first merged the peaks from the same technical replicates. For additional control, we subtracted BL6 peaks (twice median width extended) from the SOX2 peaks. We ran Diffbind using the default settings, and annotated the differentially bound peaks using ChIPSeeker. Geneset enrichment was conducted by taking annotated peaks <=3kb from TSS and running GO Term analysis. Motif enrichment was conducted using Homer on differentially bound peak sets57. We generated coverage tracks using bamCoverage (deepTools v3.4.3).
Assembly: Genome_build: mm10
Supplementary files format and content: Merged bigwigs, Individual bigwigs per replicate

molecule: genomic DNA

organism: Mus musculus

source_name: BL6 mNSC

growth_protocol: NSCs were isolated from the young adult 6-8 weeks old SVZ and maintained in vitro in serum-free basal medium supplemented with N2 and B27 (Life Technologies), Laminin-1 (Sigma, 1 μg/ml) and growth factors EGF and FGF2 (Peprotech, 10 ng/ml each). All expoeriments were conducted in early passage cells after p8.

extract_protocol:
SOX2-ChIP analysis was performed as described previously with modifications. Briefly, 10 million cells were crosslinked with 2mM DSG in PBS for 50 min, followed by 1% formaldehyde for 10 min at room temperature, and quenched with 120mM Glycine for 10 min. The crosslinked cells were washed with ice-cold PBS, flash frozen, and stored at -80°C. For nuclear extraction, the cell pellet was thawed on ice, resuspended in lysis buffer (50mM HEPES-KOH [pH7.5], 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, Complete protease inhibitor cocktail) and lysed with a Dounce homogenizer. Nuclei were pelleted by centrifugation (1350g, 5min, 4°C), washed with wash buffer (10mM Tris-HCl [pH 8], 200mM NaCl, 1mM EDTA, 0.5mM EGTA, Complete protease inhibitor cocktail), and resuspended in sonication buffer (10mM Tris-HCl [pH 8], 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, Complete protease inhibitor cocktail). Nuclei were sonicated using a Covaris E220, and chromatin was centrifuged (20,000g, 10min, 4°C). Fragment size distribution and DNA content were assessed using a Nanodrop spectrophotometer and TapeStation. Chromatin and input samples were snap-frozen and stored at -80°C. For immunoprecipitation, 30μl Dyna Protein-G magnetic beads (Thermo Fisher Scientific) were washed with blocking solution (0.5% BSA in PBS-Tween-20), incubated with 10μg antibody (IgG or SOX2) and mixed with 40μg chromatin overnight at 4°C. Beads were washed with wash buffer (50mM HEPES-KOH pH7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and TE buffer (10mM Tris-HCl pH8, 1mM EDTA, 50mM NaCl). Bound chromatin was eluted with elution buffer (50mM Tris-HCl pH8, 10mM EDTA, 1% SDS) at 65°C for 30 min, and crosslinks were reversed by incubation at 65°C for 16 hr. RNA was digested with 0.2mg/ml RNase-A for 2 hr at 37°C, proteins with 0.2mg/ml Proteinase-K for 2 hr at 55°C. DNA was purified using Qiagen Qiaquick PCR cleanup columns, quantified by Qubit Fluorometric Quantitation, and sequenced on the Illumina Nextseq 2000 platform in paired-end mode with 150 bp per read.
NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1)

treatment_protocol: mNSCs were seeded onto 15cm dishes and cultured for 24hrs in NSC medium.Cells were stalled in mitosis using 50ng/ml Nocodazole where indicated

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: 50ng/ml Nocodazole (SML1665)

tag: replicate

tag: chip antibody


title: DSP-1001660020373-D-G03

description:
Library name: DSP-1001660020373-D-G03
spatial transcriptomic sequencing


title: BL6-pSOX2-Noco-2

description: Library name: BL6-pSOX2-Noco-2

tag: cell line

tag: cell type

value: phospho-SOX2 S253


title: DSP-1001660020373-D-G02

description:
Library name: DSP-1001660020373-D-G02
spatial transcriptomic sequencing


title: BL6-pSOX2-Noco-1

description: Library name: BL6-pSOX2-Noco-1

tag: treatment


title: BL6-Input-Noco-2

description: Library name: BL6-Input-Noco-2

value: Input


title: BL6-Input-Noco-1

description: Library name: BL6-Input-Noco-1


title: DSP-1001660020373-D-F05

description:
Library name: DSP-1001660020373-D-F05
spatial transcriptomic sequencing

tag: slide name

value: airway


title: DSP-1001660020373-D-F08

description:
Library name: DSP-1001660020373-D-F08
spatial transcriptomic sequencing

tag: panel


title: DSP-1001660020373-D-F07

description:
Library name: DSP-1001660020373-D-F07
spatial transcriptomic sequencing

tag: patient


title: DSP-1001660020373-D-F06

description:
Library name: DSP-1001660020373-D-F06
spatial transcriptomic sequencing

tag: age


title: BL6-IgG-Noco-1

description: Library name: BL6-IgG-Noco-1

value: IgG


title: BL6-IgG-Noco-2

description: Library name: BL6-IgG-Noco-2


title: DSP-1001660020373-D-F03

description:
Library name: DSP-1001660020373-D-F03
spatial transcriptomic sequencing

value: lung

tag: condition


title: BL6-SOX2-Control-2

description: Library name: BL6-SOX2-Control-2

value: DMSO


title: BL6-pSOX2-Control-2

description: Library name: BL6-pSOX2-Control-2


title: BL6-SOX2-Control-1

description: Library name: BL6-SOX2-Control-1


title: BL6-Input-Control-2

description: Library name: BL6-Input-Control-2


title: DSP-1001660020373-D-F01

description:
Library name: DSP-1001660020373-D-F01
spatial transcriptomic sequencing

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: SC

value: Smoker

tag: former or_current_smoker


title: DSP-1001660020373-D-E12

description:
Library name: DSP-1001660020373-D-E12
spatial transcriptomic sequencing

value: former

tag: pack years

value: male


title: BL6-pSOX2-Control-1

description: Library name: BL6-pSOX2-Control-1


title: DSP-1001660020373-D-F02

description:
Library name: DSP-1001660020373-D-F02
spatial transcriptomic sequencing

value: COPD GOLD 4

value: COPD

tag: gender

value: paraffin


title: BL6-SOX2-Noco-2

description: Library name: BL6-SOX2-Noco-2

value: BL6 mNSC


title: DSP-1001660020373-D-E11

description:
Library name: DSP-1001660020373-D-E11
spatial transcriptomic sequencing

tag: location

value: vessel


title: DSP-1001660020373-D-E10

description:
Library name: DSP-1001660020373-D-E10
spatial transcriptomic sequencing

tag: roi


title: BL6-Input-Control-1

description: Library name: BL6-Input-Control-1

value: Mouse Neural Stem Cell


title: BL6-IgG-Control-2

description: Library name: BL6-IgG-Control-2


title: DSP-1001660020373-D-F04

description:
Library name: DSP-1001660020373-D-F04
spatial transcriptomic sequencing

tag: scan name


title: BL6-IgG-Control-1

description: Library name: BL6-IgG-Control-1


title: DSP-1001660020373-D-E09

description:
Library name: DSP-1001660020373-D-E09
spatial transcriptomic sequencing

tag: tissue

value: parenchyma


title: DSP-1001660020373-D-E08

description:
Library name: DSP-1001660020373-D-E08
spatial transcriptomic sequencing


title: DSP-1001660020373-D-E07

description:
Library name: DSP-1001660020373-D-E07
spatial transcriptomic sequencing


title: WT multiplexed

first: Andrea

last: Caporali

state: Scotland

address: 47, Little France Crescent Edinburgh

data_processing:
The nf-core scRNA-Seq pipeline (10.5281/zenodo.3568187) v2.3.0 was run on the data using Salmon v1.10.0 paired with simpleaf v0.10.0.
Assembly: mm10_UCSC_20180903
Supplementary files format and content: matrix.mtx files are cell vs gene count matrices in matrix-market-exchange (mtx) format.
Supplementary files format and content: features.tsv files provide the row indices for the count tables.
Supplementary files format and content: barcodes.tsv files provide the column indices for the count tables.

source_name: Aorta

growth_protocol: The whole mouse aorta was harvested from 6-month-old wild-type and miR-26bKO mice. The aortae were dissected from surrounding tissue, and the perivascular fat was removed.

extract_protocol:
Isolated whole aortas were finely cut and incubated in enzyme digestion buffer (400 U/mL collagenase type I, 120 U/mL collagenase type XI, 60 U/mL hyaluronidase and 20mM HEPEs in DPBS containing calcium) for 50 minutes at 37oC. The cell suspension was strained through a 100μM filter and washed with FACS buffer for 10 minutes at 4oC. After centrifugation at 300 g, the cells were resuspended in 1mL FACS buffer for FACS sorting.  Cell suspensions were washed and re-suspended in PBS at 4 °C and analysed using a BD 5 L LSR Fortessa and BD FACSDiva software (BD Biosciences). To exclude dead cells, DAPI was added before flow cytometry analysis. Cells were sorted using a FACS Aria II instrument and BD FACSDiva software (BD Biosciences).
For single-cell RNA-seq experiments, cells were prepared using 10X Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 with Feature Barcode technology for cell multiplexing (CG000389) following manufacturer instructions. After resuspension and before incubation with antibodies for FACS sorting, cells were stained using 10X Genomics CellPlex CMO oligos to hash individual samples (Supplementary Table S2). After FACS sorting, samples were grouped in pools of 3. Each pool was resuspended in an appropriate volume of PBS+1%BSA, and a maximum of 60000 cells per pool were loaded on a 10X Genomics Chip G with V3.1 gel beads and partitioning oil. Cells were then encapsulated with gel beads using a 10X Genomics Chromium X instrument. After encapsulation and cDNA synthesis, each reaction was amplified by PCR, and both low- and high-MW fractions were separately purified. The high-MW fraction containing cDNA was fragmented, ligated with sequencing adapters and amplified to generate gene expression (GEX) libraries. The low-MW fraction was further amplified with sequencing adapters to generate multiplexing (MP) libraries. All libraries were pooled at a molar ratio of GEX:MP=10:1 and sequenced on an Illumina NextSeq 2000 P3 flow cell with 100 cycles configuration.

value: Aorta

tag: strain

tag: Sex

tag: genotype

value: wild type


title: DSP-1001660020373-D-E06

description:
Library name: DSP-1001660020373-D-E06
spatial transcriptomic sequencing


title: WT gene expression


title: DSP-1001660020373-D-E04

description:
Library name: DSP-1001660020373-D-E04
spatial transcriptomic sequencing


title: miR-26bKO multiplexed


title: miR-26bKO gene expression


title: DSP-1001660020373-D-E05

description:
Library name: DSP-1001660020373-D-E05
spatial transcriptomic sequencing


title: A30-CX-4

city: Melbourne

first: Paul

middle: J

last: Neeson

state: Victoria

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

description: Library name: Sample 60

data_processing:
The quality of the 3' end reads was assessed with FastQC 0.11.2.
Adapters were trimmed using Cutadapt v1.7
Reads were mapped to the human reference genome (hg19/GRCh37) using HISAT2 (v2.0.4)
Samtools 1.8 was used to sort and merge.
featureCounts (v2.0.3) was used to count the number of reads per gene with GRCh37 ENSEMBL 62
Assembly: hg19
Supplementary files format and content: text format, gene count

growth_protocol: OVCAR3, OVCAR4, OVCAR8, AOCS14 and AOCS30 cells were cultured in RPMI medium + 20 mM HEPES,10% fetal bovine serum (FBS), and 1% GlutaMAX L-alanyl-L-glutamine dipeptide at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted using the Bioline Isolate II RNA Mini Kit as per the manufacturer's instructions.
RNA libraries were prepared for sequencing according to standard protocols (QuantSeq 3’ mRNA-Seq FWD, Lexogen).

treatment_protocol: OVCAR3, OVCAR4, OVCAR8, AOCS14 and AOCS30 cells were treated with cisplatin, CX-5461, or vehicle controls for 48h, followed by drug washout and RNA-seq was performed using total RNA extracted from triplicate samples on Day 6 post-drug washout.

tag: cell line

tag: batch


title: DSP-1001660020373-D-E03

description:
Library name: DSP-1001660020373-D-E03
spatial transcriptomic sequencing

tag: slide name


title: DSP-1001660020373-D-E01

description:
Library name: DSP-1001660020373-D-E01
spatial transcriptomic sequencing

tag: panel


title: A30-CX-1

description: Library name: Sample 58

tag: treatment


title: A30-VCX-4

description: Library name: Sample 57


title: DSP-1001660020373-D-D12

description:
Library name: DSP-1001660020373-D-D12
spatial transcriptomic sequencing

tag: patient

tag: age


title: A30-CP-4

description: Library name: Sample 54

value: cisplatin


title: DSP-1001660020373-D-D07

description:
Library name: DSP-1001660020373-D-D07
spatial transcriptomic sequencing

value: lung

tag: condition

tag: former or_current_smoker


title: DSP-1001660020373-D-D05

description:
Library name: DSP-1001660020373-D-D05
spatial transcriptomic sequencing

tag: pack years

tag: gender


title: A30-VCX-3

description: Library name: Sample 56


title: DSP-1001660020373-D-D03

description:
Library name: DSP-1001660020373-D-D03
spatial transcriptomic sequencing

tag: location

tag: roi


title: DSP-1001660020373-D-D02

description:
Library name: DSP-1001660020373-D-D02
spatial transcriptomic sequencing

tag: tissue

tag: scan name


title: A30-CP-1

description: Library name: Sample 52


title: DSP-1001660020373-D-D04

description:
Library name: DSP-1001660020373-D-D04
spatial transcriptomic sequencing


title: DSP-1001660020373-D-D06

description:
Library name: DSP-1001660020373-D-D06
spatial transcriptomic sequencing


title: DSP-1001660020373-D-E02

description:
Library name: DSP-1001660020373-D-E02
spatial transcriptomic sequencing


title: A30-VCP-3

description: Library name: Sample 50

value: saline


title: A30-VCP-1

description: Library name: Sample 49


title: A30-VCP-4

description: Library name: Sample 51


title: A14-CX-4

description: Library name: Sample 48


title: A14-CX-1

description: Library name: Sample 46


title: A14-CX-3

description: Library name: Sample 47


title: DSP-1001660020373-D-C12

description:
Library name: DSP-1001660020373-D-C12
spatial transcriptomic sequencing

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: DSP-1001660020373-D-C11

description:
Library name: DSP-1001660020373-D-C11
spatial transcriptomic sequencing


title: DSP-1001660020373-D-C09

description:
Library name: DSP-1001660020373-D-C09
spatial transcriptomic sequencing


title: DSP-1001660020373-D-D01

description:
Library name: DSP-1001660020373-D-D01
spatial transcriptomic sequencing


title: A30-CP-3

description: Library name: Sample 53


title: A14-VCX-4

description: Library name: Sample 45


title: A30-CX-3

description: Library name: Sample 59


title: DSP-1001660020373-D-C10

description:
Library name: DSP-1001660020373-D-C10
spatial transcriptomic sequencing


title: A30-VCX-1

description: Library name: Sample 55


title: DSP-1001660020373-D-C08

description:
Library name: DSP-1001660020373-D-C08
spatial transcriptomic sequencing


title: DSP-1001660020373-D-C07

description:
Library name: DSP-1001660020373-D-C07
spatial transcriptomic sequencing


title: A14-VCX-1

description: Library name: Sample 43


title: DSP-1001660020373-D-C06

description:
Library name: DSP-1001660020373-D-C06
spatial transcriptomic sequencing


title: A14-CP-2

description: Library name: Sample 41


title: A14-CP-3

description: Library name: Sample 42


title: DSP-1001660020373-D-C02

description:
Library name: DSP-1001660020373-D-C02
spatial transcriptomic sequencing

value: airway


title: DSP-1001660020373-D-C01

description:
Library name: DSP-1001660020373-D-C01
spatial transcriptomic sequencing


title: A14-VCX-3

description: Library name: Sample 44


title: A14-CP-1

description: Library name: Sample 40


title: A14-VCP-3

description: Library name: Sample 39


title: DSP-1001660020373-D-B11

description:
Library name: DSP-1001660020373-D-B11
spatial transcriptomic sequencing


title: A14-VCP-2

description: Library name: Sample 38


title: DSP-1001660020373-D-B10

description:
Library name: DSP-1001660020373-D-B10
spatial transcriptomic sequencing


title: DSP-1001660020373-D-B12

description:
Library name: DSP-1001660020373-D-B12
spatial transcriptomic sequencing


title: A14-VCP-1

description: Library name: Sample 37


title: DSP-1001660020373-D-B08

description:
Library name: DSP-1001660020373-D-B08
spatial transcriptomic sequencing


title: DSP-1001660020373-D-B09

description:
Library name: DSP-1001660020373-D-B09
spatial transcriptomic sequencing


title: OV8-CX-3

description: Library name: Sample 35


title: OV8-CX-4

description: Library name: Sample 36


title: OV8-CX-1

description: Library name: Sample 34


title: OV8-VCX-4

description: Library name: Sample 33


title: OV8-VCX-3

description: Library name: Sample 32


title: DSP-1001660020373-D-B06

description:
Library name: DSP-1001660020373-D-B06
spatial transcriptomic sequencing


title: DSP-1001660020373-D-B07

description:
Library name: DSP-1001660020373-D-B07
spatial transcriptomic sequencing


title: OV8-VCX-1

description: Library name: Sample 31


title: DSP-1001660020373-D-B03

description:
Library name: DSP-1001660020373-D-B03
spatial transcriptomic sequencing


title: DSP-1001660020373-D-B05

description:
Library name: DSP-1001660020373-D-B05
spatial transcriptomic sequencing


title: DSP-1001660020373-D-B02

description:
Library name: DSP-1001660020373-D-B02
spatial transcriptomic sequencing


title: OV8-CP-3

description: Library name: Sample 29


title: DSP-1001660020373-D-A12

description:
Library name: DSP-1001660020373-D-A12
spatial transcriptomic sequencing


title: DSP-1001660020373-D-A05

description:
Library name: DSP-1001660020373-D-A05
spatial transcriptomic sequencing


title: OV8-CP-1

description: Library name: Sample 28


title: OV8-CP-4

description: Library name: Sample 30


title: DSP-1001660020373-D-B01

description:
Library name: DSP-1001660020373-D-B01
spatial transcriptomic sequencing


title: OV8-VCP-3

description: Library name: Sample 26


title: DSP-1001660020373-D-A04

description:
Library name: DSP-1001660020373-D-A04
spatial transcriptomic sequencing


title: OV8-VCP-1

description: Library name: Sample 25


title: OV8-VCP-4

description: Library name: Sample 27


title: DSP-1001660020373-D-A03

description:
Library name: DSP-1001660020373-D-A03
spatial transcriptomic sequencing


title: DSP-1001660020372-E-G12

description:
Library name: DSP-1001660020372-E-G12
spatial transcriptomic sequencing

value: SC

value: Smoker

value: female


title: OVCAR4-CX-1

description: Library name: Sample 22


title: DSP-1001660020372-E-G11

description:
Library name: DSP-1001660020372-E-G11
spatial transcriptomic sequencing

value: former


title: DSP-1001660020373-D-B04

description:
Library name: DSP-1001660020373-D-B04
spatial transcriptomic sequencing

value: COPD GOLD 4

value: COPD

value: male


title: OVCAR4-VCX-3

description: Library name: Sample 21


title: OVCAR4-VCX-2

description: Library name: Sample 20


title: DSP-1001660020372-E-G10

description:
Library name: DSP-1001660020372-E-G10
spatial transcriptomic sequencing

value: vessel

value: paraffin


title: DSP-1001660020372-E-G08

description:
Library name: DSP-1001660020372-E-G08
spatial transcriptomic sequencing

value: parenchyma


title: OVCAR4-VCX-1

description: Library name: Sample 19


title: OVCAR4-CP-3

description: Library name: Sample 18


title: OVCAR4-CP-2

description: Library name: Sample 17


title: OVCAR4-CP-1

description: Library name: Sample 16


title: DSP-1001660020372-E-G06

description:
Library name: DSP-1001660020372-E-G06
spatial transcriptomic sequencing


title: DSP-1001660020372-E-G05

description:
Library name: DSP-1001660020372-E-G05
spatial transcriptomic sequencing


title: OVCAR4-VCP-2

description: Library name: Sample 14


title: DSP-1001660020372-E-G04

description:
Library name: DSP-1001660020372-E-G04
spatial transcriptomic sequencing


title: OVCAR4-VCP-1

description: Library name: Sample 13


title: DSP-1001660020372-E-G02

description:
Library name: DSP-1001660020372-E-G02
spatial transcriptomic sequencing


title: OV3-CX-4

description: Library name: Sample 12


title: DSP-1001660020372-E-G03

description:
Library name: DSP-1001660020372-E-G03
spatial transcriptomic sequencing


title: OVCAR4-CX-3

description: Library name: Sample 24


title: DSP-1001660020372-E-F12

description:
Library name: DSP-1001660020372-E-F12
spatial transcriptomic sequencing


title: OV3-CX-2

description: Library name: Sample 11


title: DSP-1001660020373-D-A02

description:
Library name: DSP-1001660020373-D-A02
spatial transcriptomic sequencing


title: DSP-1001660020372-E-G01

description:
Library name: DSP-1001660020372-E-G01
spatial transcriptomic sequencing


title: OV3-VCX-4

description: Library name: Sample 9


title: OVCAR4-CX-2

description: Library name: Sample 23


title: OV3-VCX-2

description: Library name: Sample 8


title: DSP-1001660020372-E-E11

description:
Library name: DSP-1001660020372-E-E11
spatial transcriptomic sequencing


title: DSP-1001660020372-E-G07

description:
Library name: DSP-1001660020372-E-G07
spatial transcriptomic sequencing


title: DSP-1001660020372-E-G09

description:
Library name: DSP-1001660020372-E-G09
spatial transcriptomic sequencing


title: DSP-1001660020372-E-E10

description:
Library name: DSP-1001660020372-E-E10
spatial transcriptomic sequencing


title: DSP-1001660020372-E-F11

description:
Library name: DSP-1001660020372-E-F11
spatial transcriptomic sequencing


title: DSP-1001660020372-E-E12

description:
Library name: DSP-1001660020372-E-E12
spatial transcriptomic sequencing


title: OV3-CP-4

description: Library name: Sample 6


title: OV3-VCX-1

description: Library name: Sample 7


title: DSP-1001660020372-E-E08

description:
Library name: DSP-1001660020372-E-E08
spatial transcriptomic sequencing


title: OV3-CP-2

description: Library name: Sample 5


title: OVCAR4-VCP-3

description: Library name: Sample 15


title: OV3-CP-1

description: Library name: Sample 4


title: OV3-VCP-4

description: Library name: Sample 3


title: DSP-1001660020372-E-E07

description:
Library name: DSP-1001660020372-E-E07
spatial transcriptomic sequencing


title: OV3-CX-1

description: Library name: Sample 10


title: OV3-VCP-2

description: Library name: Sample 2


title: DSP-1001660020372-E-E06

description:
Library name: DSP-1001660020372-E-E06
spatial transcriptomic sequencing


title: DSP-1001660020372-E-E05

description:
Library name: DSP-1001660020372-E-E05
spatial transcriptomic sequencing


title: OV3-VCP-1

description: Library name: Sample 1


title: DSP-1001660020372-E-E04

description:
Library name: DSP-1001660020372-E-E04
spatial transcriptomic sequencing


title: Exp04 TCR T cells

city: Rochester

first: Abhinav

last: Jain

address: 200 1st ST SW

institute: Mayo Clinic

description: Library name: Exp04_TCR

data_processing:
The FASTQ files reads were assessed using FastQC v0.11.9. Following quality assessment, the raw reads were aligned to the GRCh38 human genome using Cell Ranger multi v7.1.0 (10x Genomics). The cellranger multi pipeline was employed to quantify libraries of antibody-derived tags (ADT) and identify hashtagged samples from pooled CITE-seq libraries. Seurat v4.2.1 was used for downstream analysis following data preprocessing. Quality control was conducted to exclude low-quality cells based on the following thresholds: cells with fewer than 200 or more than 4000 genes, UMIs > 10% mapping to mitochondrial-encoded transcript, or more than 20,000 ADT UMIs. DoubletFinder was applied to identify and remove cell doublets.
We have identified CD4+ and CD8+ T cells based on their CD4 and CD8 gene and protein expression and processed them separately. For RNA normalization, individual samples were processed using SCTransform PMID:31870423, regressing out mitochondrial gene expression, while ADT counts were normalized using centralized log-ratio (CLR) transformation.
Further samples across experiments were integrated using diagonalized Canonical Correlation Analysis (CCA) to identify mutual nearest neighbors that act as anchors employing the FindTransferAnchors and IntegrateData functions PMID:31178118.
The Integrated RNA and ADT matrices were scaled and PCA were calculated. A weighted nearest-neighbor (WNN) graph was subsequently constructed using the FindMultiModalNeighbors function to integrate the modalities effectively PMID:34062119. The WNN graph is utilized to generate the UMAP embeddings, facilitating the visualization for both the modalities. Clustering was performed based on WNN using a smart local moving algorithm, revealing populations enriched in gE-stimulated versus control cultures.
Assembly: GRCh38
Supplementary files format and content: CellRanger Output Files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: scTCR-Seq

source_name: Blood

extract_protocol:
Forty-two hours after peptide stimulation, cultures were pre-purified with EasySep Human T Cell Isolation Kit (using 20% of the recommended reagents, Stemcell Technologies, # 17951). T cells were stained with hashtag TotalSeq-B antibodies and subjected to FACS. Live, single CD3+ CD8+ or CD3+ CD4+ cells that were CD69hi and/or CD137+ were collected. After FACS, cells were counted and pooled into one sample across T cell subsets and donors at similar cell numbers, if possible. The pooled sample was stained with diluted TotalSeq-B cell surface marker antibodies (BioLegend) in PBS containing 2% FBS for 30 minutes at 4C. Cells were washed twice with PBS containing 2% FBS, and cell viability was determined with Trypan Blue which was consistently >90%.
Cells were subjected to high-throughput single cell capture via the Chromium controller (10x genomics), Chromium Next GEM Single Cell 3' Kit v3.1 (Single Index, 10x genomics, #PN-1000121) and gel beads (10x genomics, #1000376). About 20,000 cells per pooled samples were targeted for cell capture. 3’ gene expression as well as antibody-derived tags (ADT) for TotalSeq-B antibodies including hashtag antibodies and cell surface marker (3' Feature Barcode Library Kit, 10x genomics, #PN-1000079) collective known as CITE-seq, were generated from each captured sample.

treatment_protocol: Lymphoprep was used to purify PBMCs of vaccine recipients by density centrifugation according to the manufacturer’s instructions. Cells were used fresh in all experiments and cultured in RPMI 1640 medium supplemented with 5% filtered human AB serum (Sigma Aldrich, #H4522), 100 U/mL penicillin, and 100 U/mL streptomycin (Sigma Aldrich, #P0781) in an incubator with 5% CO2 and atmospheric O2. We employed activation-induced marker (AIM) assays to collect VZV gE-responsive T cells. Briefly, PBMCs were seeded at 20x10^6 per 12-well and stimulated with 1 ug/ml of a VZV glycoprotein E (gE) peptide pool diluted in 0.2% DMSO (15-mer peptides with 11 amino acids overlap, total of 153 peptides; # PM-VZV-gE, JPT Peptide Technologies). Ultra-LEAF anti-CD28 stimulation antibody was added at 1 ug/ml (clone 28.2, BioLegend, #302943) as well anti-CD40 blocking antibody at 1 ug/ml (clone HB14, Miltenyi, #130-094-133). Parallel control PBMC cultures of the same individuals, received 0.2% DMSO instead of the VZV gE peptide mix. PBMCs were spun in plates at 300×g for 3 min before culturing for 42 hours to allow activation of antigen-specific T cells before further sample processing.

value: Blood

tag: cell type

value: T cell

value: Activation through VZV gE peptide stimulation, or DMSO background stimulation

tag: t cell_subset

value: VZV gE-responsive CD4 and CD8 T cells, DMSO-reactive CD4 and CD8 T cells


title: Exp07 TCR T cells

description: Library name: Exp07_TCR


title: DSP-1001660020372-E-E09

description:
Library name: DSP-1001660020372-E-E09
spatial transcriptomic sequencing

value: lung


title: DSP-1001660020372-E-E01

description:
Library name: DSP-1001660020372-E-E01
spatial transcriptomic sequencing

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: DSP-1001660020372-E-E03

description:
Library name: DSP-1001660020372-E-E03
spatial transcriptomic sequencing


title: DSP-1001660020372-E-D12

description:
Library name: DSP-1001660020372-E-D12
spatial transcriptomic sequencing


title: Exp05 TCR T cells

description: Library name: Exp05_TCR


title: Exp03 TCR T cells

description: Library name: Exp03_TCR


title: DSP-1001660020372-E-D11

description:
Library name: DSP-1001660020372-E-D11
spatial transcriptomic sequencing


title: DSP-1001660020372-E-D09

description:
Library name: DSP-1001660020372-E-D09
spatial transcriptomic sequencing


title: DSP-1001660020372-E-D10

description:
Library name: DSP-1001660020372-E-D10
spatial transcriptomic sequencing


title: ND_oil_2

city: Daejeon

first: Tae-Su

last: Han

address: 125 Gwahak-ro

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description:
Library name: Sample 6
Column name in RNA-seq-Mouse-FPKM.txt: ND_oil_S16_FPKM

data_processing:
Sequence reads were assessed for quality using FastQC (v0.11.9)
Sequence reads were trimmed for adapter sequences and low-quality bases using cutadapt (v3.7)
Trimmed sequence reads were mapped to GRCm38 using HISAT2(v2.2.1)(default parameters)
Transcript assembly and expression quantification were performed using StringTie(v2.1.0) with the reference annotation.
Assembly: GRCm38(Genome Reference Consortium Mouse Build 38)
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

source_name: Liver

extract_protocol:
Total RNAs were extracted from liver tissues using NucleoZol reagent (Macherey-Nagel GmbH & Co. KG, Düren, Germany)
RNA libraries for RNA-Seq were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer's protocols.

treatment_protocol: Male C57BL/6N mice (Orientbio, Seongnam, Korea) were fed a normal chow diet (ND; LabDiet, St. Louis, MO, USA, Rodent diet 20, #5053) and normal tap water, or western diet (WD) containing high-fat diet (Teklad diets, Indianapolis, IN, USA, TD. 120528) and high sugar solution consisting of 23.1 g/L d-fructose (Sigma-Aldrich, St. Louis, MO, USA, F0127) and 18.9 g/L d-glucose (Sigma-Aldrich). Carbon tetrachloride (CCl4; Sigma-Aldrich, 289116-1L) or corn oil, a control vehicle, was intraperitoneally injected once weekly.

value: Liver

tag: strain

tag: Sex

tag: genotype

value: WT

value: ND


title: WD_oil_2

description:
Library name: Sample 8
Column name in RNA-seq-Mouse-FPKM.txt: WD_oil_S17_FPKM

value: WD


title: DSP-1001660020372-E-D07

description:
Library name: DSP-1001660020372-E-D07
spatial transcriptomic sequencing

tag: slide name

tag: panel

value: former


title: WD_CCl4_1

description:
Library name: Sample 4
Column name in RNA-seq-Mouse-FPKM.txt: WD_CCl4_S19_FPKM

tag: treatment

value: WD with CCl4


title: DSP-1001660020372-E-D08

description:
Library name: DSP-1001660020372-E-D08
spatial transcriptomic sequencing

tag: patient

tag: age

value: COPD GOLD 4

value: COPD


title: DSP-1001660020372-E-D02

description:
Library name: DSP-1001660020372-E-D02
spatial transcriptomic sequencing

tag: condition

tag: former or_current_smoker

value: male

value: airway


title: DSP-1001660020372-E-D03

description:
Library name: DSP-1001660020372-E-D03
spatial transcriptomic sequencing

tag: pack years

tag: gender

value: paraffin


title: ND_oil_1

description:
Library name: Sample 3
Column name in RNA-seq-Mouse-FPKM.txt: ND_oil_S13_FPKM


title: Exp10 TCR T cells

description: Library name: Exp10_TCR

value: Blood

value: DMSO_V_Y_IMAG051F_Exp10 (21y) DMSO_V_Y_IMAG052F_Exp10 (20y) DMSO_V_Y_IMAG053M_Exp10 (21y) gE_V_Y_IMAG051F_Exp10 (21y) gE_V_Y_IMAG052F_Exp10 (20y) gE_V_Y_IMAG053M_Exp10 (21y)


title: WD_oil_1

description:
Library name: Sample 2
Column name in RNA-seq-Mouse-FPKM.txt: WD_oil_S14_FPKM


title: ND_CCl4_1

description:
Library name: Sample 1
Column name in RNA-seq-Mouse-FPKM.txt: ND_CCl4_S15_FPKM

value: ND with CCl4


title: DSP-1001660020372-E-D01

description:
Library name: DSP-1001660020372-E-D01
spatial transcriptomic sequencing

tag: location

tag: roi


title: DSP-1001660020372-E-C12

description:
Library name: DSP-1001660020372-E-C12
spatial transcriptomic sequencing

tag: tissue

tag: scan name


title: DSP-1001660020372-E-E02

description:
Library name: DSP-1001660020372-E-E02
spatial transcriptomic sequencing

value: parenchyma


title: Sample: H8-615 , Mother: 965 , Day: 48

city: Austin

first: Hans

middle: A

last: Hofmann

address: 2415 Speedway

department: Integrative Biology

institute: The University of Texas

description: Library name: H8-615

data_processing:
sequencing reads were trimmed for adapter sequences and filtered for quality
trimmed reads were aligned using the BWA-MEM algorithm to Flounder_ref_guided_V1.0 (GCF_001970005.1)
read counts were quantified and extracted with htseq-count
Assembly: GCF_001970005.1
Supplementary files format and content: tab delimited text files with raw counts

organism: Paralichthys lethostigma

source_name: Whole fish

extract_protocol:
RNA was extracted using the GeneJET RNA purification kit
The University of Texas Genomic Sequencing and Analysis Facility performed library preparation for 3’ tag-based RNA sequencing (tag-seq), based on prior protocol

value: Whole fish

tag: time

tag: pooled samples

tag: pigmentation

value: unknown

tag: batch


title: Sample: H9-643 , Mother: 94E , Day: 48

description: Library name: H9-643


title: ND_oil_3

description:
Library name: Sample 7
Column name in RNA-seq-Mouse-FPKM.txt: ND_oil_S20_FPKM

value: Liver

tag: strain

tag: Sex

tag: genotype


title: DSP-1001660020372-E-C10

description:
Library name: DSP-1001660020372-E-C10
spatial transcriptomic sequencing

tag: slide name

value: lung

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: patient

value: vessel


title: DSP-1001660020372-E-C09

description:
Library name: DSP-1001660020372-E-C09
spatial transcriptomic sequencing

tag: age

tag: condition

tag: former or_current_smoker

value: former


title: Sample: H7-233 , Mother: FD247 , Day: 55

description: Library name: H7-233

value: normal


title: Sample: H7-587 , Mother: FD247 , Day: 41

description: Library name: H7-587


title: DSP-1001660020372-E-C08

description:
Library name: DSP-1001660020372-E-C08
spatial transcriptomic sequencing

value: COPD GOLD 4

tag: pack years

tag: gender

tag: location


title: ND_CCl4_2

description:
Library name: Sample 5
Column name in RNA-seq-Mouse-FPKM.txt: ND_CCl4_S18_FPKM

tag: tissue

value: WT

tag: treatment


title: DSP-1001660020372-E-C07

description:
Library name: DSP-1001660020372-E-C07
spatial transcriptomic sequencing

value: COPD

value: male

tag: roi

tag: scan name


title: Sample: H6-579 , Mother: FD247 , Day: 41

description: Library name: H6-579

tag: time

tag: pooled samples

tag: pigmentation

tag: batch


title: Sample: H6-225 , Mother: FD247 , Day: 55

description: Library name: H6-225

value: pseudoalbino


title: Sample: H5-217 , Mother: 94E , Day: 55

description: Library name: H5-217


title: Sample: H5-571 , Mother: 94E , Day: 41

description: Library name: H5-571


title: DSP-1001660020372-E-C04

description:
Library name: DSP-1001660020372-E-C04
spatial transcriptomic sequencing

tag: slide name

value: paraffin


title: DSP-1001660020372-E-C06

description:
Library name: DSP-1001660020372-E-C06
spatial transcriptomic sequencing

tag: panel


title: Sample: H4-196 , Mother: 965 , Day: 55

description: Library name: H4-196


title: DSP-1001660020372-E-C05

description:
Library name: DSP-1001660020372-E-C05
spatial transcriptomic sequencing

tag: patient


title: DSP-1001660020372-E-C01

description:
Library name: DSP-1001660020372-E-C01
spatial transcriptomic sequencing

tag: age


title: DSP-1001660020372-E-C02

description:
Library name: DSP-1001660020372-E-C02
spatial transcriptomic sequencing

tag: condition


title: Sample: H4-543 , Mother: 965 , Day: 41

description: Library name: H4-543


title: DSP-1001660020372-E-C03

description:
Library name: DSP-1001660020372-E-C03
spatial transcriptomic sequencing

tag: former or_current_smoker


title: Sample: H3-333 , Mother: 94E , Day: 20

description: Library name: H3-333


title: Sample: H3-138 , Mother: FD247 , Day: 34

description: Library name: H3-138


title: DSP-1001660020372-E-B06

description:
Library name: DSP-1001660020372-E-B06
spatial transcriptomic sequencing

tag: pack years

value: airway


title: DSP-1001660020372-E-C11

description:
Library name: DSP-1001660020372-E-C11
spatial transcriptomic sequencing

tag: gender


title: Sample: H2-247 , Mother: FD247 , Day: 13

description: Library name: H2-247


title: DSP-1001660020372-E-B05

description:
Library name: DSP-1001660020372-E-B05
spatial transcriptomic sequencing

tag: location


title: Sample: H2-130 , Mother: 94E , Day: 34

description: Library name: H2-130

tag: tissue


title: DSP-1001660020372-E-B04

description:
Library name: DSP-1001660020372-E-B04
spatial transcriptomic sequencing

value: SC

value: Smoker


title: Sample: H12-70 , Mother: FD247 , Day: 27

description: Library name: H12-70

value: Whole fish


title: DSP-1001660020372-E-B03

description:
Library name: DSP-1001660020372-E-B03
spatial transcriptomic sequencing


title: Sample: H10-651 , Mother: FD247 , Day: 48

description: Library name: H10-651

value: unknown


title: DSP-1001660020372-E-B01

description:
Library name: DSP-1001660020372-E-B01
spatial transcriptomic sequencing

value: parenchyma


title: DSP-1001660020372-E-B02

description:
Library name: DSP-1001660020372-E-B02
spatial transcriptomic sequencing

value: lung


title: Sample: H11-59 , Mother: 965 , Day: 27

description: Library name: H11-59


title: DSP-1001660020372-E-A12

description:
Library name: DSP-1001660020372-E-A12
spatial transcriptomic sequencing

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: Sample: H1-155 , Mother: FD247 , Day: 6

description: Library name: H1-155


title: Sample: H1-122 , Mother: 94E , Day: 34

description: Library name: H1-122


title: DSP-1001660020372-E-A11

description:
Library name: DSP-1001660020372-E-A11
spatial transcriptomic sequencing


title: Sample: G9-642 , Mother: 94E , Day: 48

description: Library name: G9-642


title: Sample: G8-614 , Mother: 965 , Day: 48

description: Library name: G8-614


title: DSP-1001660020372-E-A09

description:
Library name: DSP-1001660020372-E-A09
spatial transcriptomic sequencing


title: Sample: G7-586 , Mother: FD247 , Day: 41

description: Library name: G7-586


title: Sample: G7-232 , Mother: FD247 , Day: 55

description: Library name: G7-232


title: DSP-1001660020372-E-A10

description:
Library name: DSP-1001660020372-E-A10
spatial transcriptomic sequencing


title: Sample: G6-224 , Mother: FD247 , Day: 55

description: Library name: G6-224


title: DSP-1001660020372-E-A07

description:
Library name: DSP-1001660020372-E-A07
spatial transcriptomic sequencing


title: DSP-1001660020372-E-A03

description:
Library name: DSP-1001660020372-E-A03
spatial transcriptomic sequencing


title: Sample: G5-216 , Mother: 94E , Day: 55

description: Library name: G5-216


title: DSP-1001660020372-E-A02

description:
Library name: DSP-1001660020372-E-A02
spatial transcriptomic sequencing


title: DSP-1001660020372-E-A04

description:
Library name: DSP-1001660020372-E-A04
spatial transcriptomic sequencing


title: Sample: G5-570 , Mother: 94E , Day: 41

description: Library name: G5-570


title: DSP-1001660020371-A-H12

description:
Library name: DSP-1001660020371-A-H12
spatial transcriptomic sequencing

value: female

value: vessel


title: Sample: G4-542 , Mother: 965 , Day: 41

description: Library name: G4-542


title: DSP-1001660020371-A-H11

description:
Library name: DSP-1001660020371-A-H11
spatial transcriptomic sequencing

value: former


title: Sample: G4-195 , Mother: 965 , Day: 55

description: Library name: G4-195


title: Sample: G3-332 , Mother: 94E , Day: 20

description: Library name: G3-332


title: Sample: G3-137 , Mother: FD247 , Day: 34

description: Library name: G3-137


title: DSP-1001660020371-A-H08

description:
Library name: DSP-1001660020371-A-H08
spatial transcriptomic sequencing

value: COPD GOLD 4


title: DSP-1001660020371-A-H10

description:
Library name: DSP-1001660020371-A-H10
spatial transcriptomic sequencing


title: Sample: G2-129 , Mother: 94E , Day: 34

description: Library name: G2-129


title: Sample: G12-69 , Mother: FD247 , Day: 27

description: Library name: G12-69


title: DSP-1001660020371-A-H07

description:
Library name: DSP-1001660020371-A-H07
spatial transcriptomic sequencing


title: DSP-1001660020372-E-A08

description:
Library name: DSP-1001660020372-E-A08
spatial transcriptomic sequencing


title: DSP-1001660020371-A-H06

description:
Library name: DSP-1001660020371-A-H06
spatial transcriptomic sequencing


title: DSP-1001660020372-E-A05

description:
Library name: DSP-1001660020372-E-A05
spatial transcriptomic sequencing


title: DSP-1001660020371-A-H05

description:
Library name: DSP-1001660020371-A-H05
spatial transcriptomic sequencing


title: Sample: G1-154 , Mother: FD247 , Day: 6

description: Library name: G1-154


title: Sample: G11-658 , Mother: FD247 , Day: 48

description: Library name: G11-658


title: Sample: G1-121 , Mother: 94E , Day: 34

description: Library name: G1-121


title: DSP-1001660020371-A-H03

description:
Library name: DSP-1001660020371-A-H03
spatial transcriptomic sequencing


title: DSP-1001660020371-A-H02

description:
Library name: DSP-1001660020371-A-H02
spatial transcriptomic sequencing


title: Sample: F9-641 , Mother: 94E , Day: 48

description: Library name: F9-641


title: DSP-1001660020371-A-G08

description:
Library name: DSP-1001660020371-A-G08
spatial transcriptomic sequencing


title: Sample: F8-613 , Mother: 965 , Day: 48

description: Library name: F8-613


title: Sample: F7-585 , Mother: FD247 , Day: 41

description: Library name: F7-585


title: Sample: G6-578 , Mother: 94E , Day: 41

description: Library name: G6-578


title: DSP-1001660020371-A-H04

description:
Library name: DSP-1001660020371-A-H04
spatial transcriptomic sequencing


title: Sample: F7-231 , Mother: FD247 , Day: 55

description: Library name: F7-231

value: normal


title: DSP-1001660020371-A-G05

description:
Library name: DSP-1001660020371-A-G05
spatial transcriptomic sequencing

value: COPD


title: DSP-1001660020371-A-G06

description:
Library name: DSP-1001660020371-A-G06
spatial transcriptomic sequencing


title: Sample: G2-246 , Mother: 94E , Day: 13

description: Library name: G2-246


title: DSP-1001660020371-A-H09

description:
Library name: DSP-1001660020371-A-H09
spatial transcriptomic sequencing


title: DSP-1001660020371-A-G07

description:
Library name: DSP-1001660020371-A-G07
spatial transcriptomic sequencing


title: DSP-1001660020371-A-G04

description:
Library name: DSP-1001660020371-A-G04
spatial transcriptomic sequencing


title: Sample: F6-223 , Mother: 94E , Day: 55

description: Library name: F6-223


title: DSP-1001660020371-A-G03

description:
Library name: DSP-1001660020371-A-G03
spatial transcriptomic sequencing


title: Sample: F5-215 , Mother: 94E , Day: 55

description: Library name: F5-215


title: DSP-1001660020371-A-G02

description:
Library name: DSP-1001660020371-A-G02
spatial transcriptomic sequencing


title: Sample: G10-650 , Mother: FD247 , Day: 48

description: Library name: G10-650


title: Sample: F4-541 , Mother: 965 , Day: 41

description: Library name: F4-541


title: Sample: F4-194 , Mother: 965 , Day: 55

description: Library name: F4-194


title: DSP-1001660020371-A-F12

description:
Library name: DSP-1001660020371-A-F12
spatial transcriptomic sequencing


title: DSP-1001660020371-A-F10

description:
Library name: DSP-1001660020371-A-F10
spatial transcriptomic sequencing


title: Sample: F3-136 , Mother: FD247 , Day: 34

description: Library name: F3-136


title: Sample: F12-68 , Mother: FD247 , Day: 27

description: Library name: F12-68


title: DSP-1001660020371-A-F08

description:
Library name: DSP-1001660020371-A-F08
spatial transcriptomic sequencing


title: DSP-1001660020371-A-F09

description:
Library name: DSP-1001660020371-A-F09
spatial transcriptomic sequencing


title: DSP-1001660020371-A-F06

description:
Library name: DSP-1001660020371-A-F06
spatial transcriptomic sequencing


title: Sample: F11-657 , Mother: FD247 , Day: 48

description: Library name: F11-657


title: DSP-1001660020371-A-F07

description:
Library name: DSP-1001660020371-A-F07
spatial transcriptomic sequencing


title: Sample: F2-245 , Mother: 94E , Day: 13

description: Library name: F2-245


title: DSP-1001660020371-A-F05

description:
Library name: DSP-1001660020371-A-F05
spatial transcriptomic sequencing


title: Sample: F6-577 , Mother: 94E , Day: 41

description: Library name: F6-577


title: Sample: F10-649 , Mother: FD247 , Day: 48

description: Library name: F10-649


title: Sample: F1-153 , Mother: 94E , Day: 6

description: Library name: F1-153


title: DSP-1001660020371-A-E11

description:
Library name: DSP-1001660020371-A-E11
spatial transcriptomic sequencing


title: DSP-1001660020371-A-E12

description:
Library name: DSP-1001660020371-A-E12
spatial transcriptomic sequencing


title: Sample: F5-569 , Mother: 94E , Day: 41

description: Library name: F5-569


title: Sample: E9-640 , Mother: 94E , Day: 48

description: Library name: E9-640


title: DSP-1001660020371-A-G01

description:
Library name: DSP-1001660020371-A-G01
spatial transcriptomic sequencing


title: Sample: F3-331 , Mother: 94E , Day: 20

description: Library name: F3-331


title: DSP-1001660020371-A-E08

description:
Library name: DSP-1001660020371-A-E08
spatial transcriptomic sequencing


title: Sample: E8-612 , Mother: 965 , Day: 48

description: Library name: E8-612


title: Sample: E7-230 , Mother: FD247 , Day: 55

description: Library name: E7-230


title: Sample: E7-584 , Mother: FD247 , Day: 41

description: Library name: E7-584


title: DSP-1001660020371-A-E09

description:
Library name: DSP-1001660020371-A-E09
spatial transcriptomic sequencing


title: DSP-1001660020371-A-F11

description:
Library name: DSP-1001660020371-A-F11
spatial transcriptomic sequencing


title: DSP-1001660020371-A-E07

description:
Library name: DSP-1001660020371-A-E07
spatial transcriptomic sequencing

value: COPD GOLD 2

value: current

value: male


title: DSP-1001660020371-A-E06

description:
Library name: DSP-1001660020371-A-E06
spatial transcriptomic sequencing

value: paraffin


title: Sample: F2-128 , Mother: 94E , Day: 34

description: Library name: F2-128


title: Sample: E5-548 , Mother: 965 , Day: 41

description: Library name: E5-548


title: Sample: E6-576 , Mother: 94E , Day: 41

description: Library name: E6-576


title: Sample: E5-214 , Mother: 94E , Day: 55

description: Library name: E5-214


title: DSP-1001660020371-A-E03

description:
Library name: DSP-1001660020371-A-E03
spatial transcriptomic sequencing


title: DSP-1001660020371-A-E04

description:
Library name: DSP-1001660020371-A-E04
spatial transcriptomic sequencing


title: DSP-1001660020371-A-E02

description:
Library name: DSP-1001660020371-A-E02
spatial transcriptomic sequencing


title: Sample: E6-222 , Mother: 94E , Day: 55

description: Library name: E6-222

value: pseudoalbino


title: DSP-1001660020371-A-E05

description:
Library name: DSP-1001660020371-A-E05
spatial transcriptomic sequencing


title: DSP-1001660020371-A-E10

description:
Library name: DSP-1001660020371-A-E10
spatial transcriptomic sequencing

value: airway


title: DSP-1001660020371-A-D11

description:
Library name: DSP-1001660020371-A-D11
spatial transcriptomic sequencing


title: Sample: F1-110 , Mother: 965 , Day: 34

description: Library name: F1-110

value: Whole fish


title: Sample: E4-540 , Mother: 965 , Day: 41

description: Library name: E4-540

value: unknown


title: Sample: E3-275 , Mother: 965 , Day: 20

description: Library name: E3-275


title: DSP-1001660020371-A-D12

description:
Library name: DSP-1001660020371-A-D12
spatial transcriptomic sequencing

value: parenchyma


title: Sample: E3-135 , Mother: FD247 , Day: 34

description: Library name: E3-135


title: Sample: E4-193 , Mother: 965 , Day: 55

description: Library name: E4-193


title: Sample: E2-244 , Mother: 94E , Day: 13

description: Library name: E2-244


title: DSP-1001660020371-A-D09

description:
Library name: DSP-1001660020371-A-D09
spatial transcriptomic sequencing

value: lung


title: DSP-1001660020371-A-D10

description:
Library name: DSP-1001660020371-A-D10
spatial transcriptomic sequencing

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: Sample: E2-127 , Mother: 94E , Day: 34

description: Library name: E2-127


title: Sample: E12-67 , Mother: 94E , Day: 27

description: Library name: E12-67


title: DSP-1001660020371-A-D07

description:
Library name: DSP-1001660020371-A-D07
spatial transcriptomic sequencing

value: female


title: DSP-1001660020371-A-D08

description:
Library name: DSP-1001660020371-A-D08
spatial transcriptomic sequencing


title: Sample: E11-656 , Mother: FD247 , Day: 48

description: Library name: E11-656


title: DSP-1001660020371-A-D06

description:
Library name: DSP-1001660020371-A-D06
spatial transcriptomic sequencing

value: vessel


title: Sample: E10-648 , Mother: 94E , Day: 48

description: Library name: E10-648


title: DSP-1001660020371-A-D05

description:
Library name: DSP-1001660020371-A-D05
spatial transcriptomic sequencing

value: former


title: Sample: E1-152 , Mother: 94E , Day: 6

description: Library name: E1-152


title: DSP-1001660020371-A-D04

description:
Library name: DSP-1001660020371-A-D04
spatial transcriptomic sequencing

value: COPD GOLD 4


title: DSP-1001660020371-A-E01

description:
Library name: DSP-1001660020371-A-E01
spatial transcriptomic sequencing


title: Sample: E1-106 , Mother: 965 , Day: 34

description: Library name: E1-106


title: Sample: D9-639 , Mother: 94E , Day: 48

description: Library name: D9-639


title: DSP-1001660020371-A-D03

description:
Library name: DSP-1001660020371-A-D03
spatial transcriptomic sequencing


title: Sample: D8-611 , Mother: 965 , Day: 48

description: Library name: D8-611


title: DSP-1001660020371-A-D02

description:
Library name: DSP-1001660020371-A-D02
spatial transcriptomic sequencing


title: Sample: D7-583 , Mother: FD247 , Day: 41

description: Library name: D7-583


title: DSP-1001660020371-A-D01

description:
Library name: DSP-1001660020371-A-D01
spatial transcriptomic sequencing


title: Sample: D7-229 , Mother: FD247 , Day: 55

description: Library name: D7-229

value: normal


title: DSP-1001660020371-A-C12

description:
Library name: DSP-1001660020371-A-C12
spatial transcriptomic sequencing

value: COPD


title: DSP-1001660020371-A-C10

description:
Library name: DSP-1001660020371-A-C10
spatial transcriptomic sequencing


title: Sample: D5-547 , Mother: 965 , Day: 41

description: Library name: D5-547


title: Sample: D6-221 , Mother: 94E , Day: 55

description: Library name: D6-221


title: DSP-1001660020371-A-C11

description:
Library name: DSP-1001660020371-A-C11
spatial transcriptomic sequencing


title: Sample: D6-575 , Mother: 94E , Day: 41

description: Library name: D6-575


title: DSP-1001660020371-A-C09

description:
Library name: DSP-1001660020371-A-C09
spatial transcriptomic sequencing


title: DSP-1001660020371-A-C04

description:
Library name: DSP-1001660020371-A-C04
spatial transcriptomic sequencing


title: Sample: D5-200 , Mother: 965 , Day: 55

description: Library name: D5-200


title: DSP-1001660020371-A-C03

description:
Library name: DSP-1001660020371-A-C03
spatial transcriptomic sequencing


title: Sample: D4-539 , Mother: 965 , Day: 41

description: Library name: D4-539


title: DSP-1001660020371-A-C02

description:
Library name: DSP-1001660020371-A-C02
spatial transcriptomic sequencing


title: Sample: D4-192 , Mother: 965 , Day: 55

description: Library name: D4-192


title: DSP-1001660020371-A-C01

description:
Library name: DSP-1001660020371-A-C01
spatial transcriptomic sequencing


title: Sample: D3-274 , Mother: 965 , Day: 20

description: Library name: D3-274


title: Sample: D3-134 , Mother: FD247 , Day: 34

description: Library name: D3-134


title: DSP-1001660020371-A-B12

description:
Library name: DSP-1001660020371-A-B12
spatial transcriptomic sequencing


title: DSP-1001660020371-A-B11

description:
Library name: DSP-1001660020371-A-B11
spatial transcriptomic sequencing


title: Sample: D2-179 , Mother: 965 , Day: 13

description: Library name: D2-179


title: DSP-1001660020371-A-B10

description:
Library name: DSP-1001660020371-A-B10
spatial transcriptomic sequencing


title: Sample: D2-126 , Mother: 94E , Day: 34

description: Library name: D2-126


title: DSP-1001660020371-A-B09

description:
Library name: DSP-1001660020371-A-B09
spatial transcriptomic sequencing


title: DSP-1001660020371-A-B08

description:
Library name: DSP-1001660020371-A-B08
spatial transcriptomic sequencing


title: Sample: D12-66 , Mother: 94E , Day: 27

description: Library name: D12-66


title: DSP-1001660020371-A-B07

description:
Library name: DSP-1001660020371-A-B07
spatial transcriptomic sequencing


title: Sample: D11-655 , Mother: FD247 , Day: 48

description: Library name: D11-655


title: Sample: D10-647 , Mother: 94E , Day: 48

description: Library name: D10-647


title: DSP-1001660020371-A-B05

description:
Library name: DSP-1001660020371-A-B05
spatial transcriptomic sequencing


title: DSP-1001660020371-A-B06

description:
Library name: DSP-1001660020371-A-B06
spatial transcriptomic sequencing


title: DSP-1001660020371-A-B04

description:
Library name: DSP-1001660020371-A-B04
spatial transcriptomic sequencing


title: Sample: D1-151 , Mother: 94E , Day: 6

description: Library name: D1-151


title: Sample: C9-618 , Mother: 965 , Day: 48

description: Library name: C9-618


title: DSP-1001660020371-A-B03

description:
Library name: DSP-1001660020371-A-B03
spatial transcriptomic sequencing


title: DSP-1001660020371-A-A08

description:
Library name: DSP-1001660020371-A-A08
spatial transcriptomic sequencing


title: Sample: C8-743 , Mother: 965 , Day: 34

description: Library name: C8-743


title: Sample: C8-610 , Mother: 965 , Day: 48

description: Library name: C8-610


title: DSP-1001660020371-A-B02

description:
Library name: DSP-1001660020371-A-B02
spatial transcriptomic sequencing


title: Sample: C7-228 , Mother: FD247 , Day: 55

description: Library name: C7-228


title: Sample: C6-574 , Mother: 94E , Day: 41

description: Library name: C6-574


title: DSP-1001660020371-A-A07

description:
Library name: DSP-1001660020371-A-A07
spatial transcriptomic sequencing


title: DSP-1001660020371-A-A06

description:
Library name: DSP-1001660020371-A-A06
spatial transcriptomic sequencing


title: Sample: C7-582 , Mother: FD247 , Day: 41

description: Library name: C7-582


title: Sample: C5-546 , Mother: 965 , Day: 41

description: Library name: C5-546


title: Sample: C6-220 , Mother: 94E , Day: 55

description: Library name: C6-220


title: DSP-1001660020371-A-A05

description:
Library name: DSP-1001660020371-A-A05
spatial transcriptomic sequencing


title: Sample: C5-199 , Mother: 965 , Day: 55

description: Library name: C5-199


title: DSP-1001660020371-A-A03

description:
Library name: DSP-1001660020371-A-A03
spatial transcriptomic sequencing


title: DSP-1001660020371-A-A04

description:
Library name: DSP-1001660020371-A-A04
spatial transcriptomic sequencing


title: DSP-1001660020370-C-H12

description:
Library name: DSP-1001660020370-C-H12
spatial transcriptomic sequencing


title: Sample: D1-105 , Mother: 965 , Day: 34

description: Library name: D1-105


title: DSP-1001660020370-C-H11

description:
Library name: DSP-1001660020370-C-H11
spatial transcriptomic sequencing


title: Sample: C4-191 , Mother: 965 , Day: 55

description: Library name: C4-191


title: Sample: C3-133 , Mother: FD247 , Day: 34

description: Library name: C3-133


title: DSP-1001660020370-C-H10

description:
Library name: DSP-1001660020370-C-H10
spatial transcriptomic sequencing


title: Sample: C3-273 , Mother: 965 , Day: 20

description: Library name: C3-273


title: DSP-1001660020370-C-H09

description:
Library name: DSP-1001660020370-C-H09
spatial transcriptomic sequencing


title: Sample: C2-125 , Mother: 94E , Day: 34

description: Library name: C2-125


title: DSP-1001660020370-C-H06

description:
Library name: DSP-1001660020370-C-H06
spatial transcriptomic sequencing


title: Sample: C11-654 , Mother: FD247 , Day: 48

description: Library name: C11-654


title: DSP-1001660020370-C-H08

description:
Library name: DSP-1001660020370-C-H08
spatial transcriptomic sequencing


title: DSP-1001660020370-C-H07

description:
Library name: DSP-1001660020370-C-H07
spatial transcriptomic sequencing


title: Sample: C12-65 , Mother: 94E , Day: 27

description: Library name: C12-65


title: DSP-1001660020370-C-H05

description:
Library name: DSP-1001660020370-C-H05
spatial transcriptomic sequencing


title: Sample: C2-178 , Mother: 965 , Day: 13

description: Library name: C2-178


title: DSP-1001660020370-C-H04

description:
Library name: DSP-1001660020370-C-H04
spatial transcriptomic sequencing


title: Sample: C10-646 , Mother: 94E , Day: 48

description: Library name: C10-646


title: DSP-1001660020370-C-H03

description:
Library name: DSP-1001660020370-C-H03
spatial transcriptomic sequencing


title: Sample: C1-104 , Mother: 965 , Day: 34

description: Library name: C1-104


title: DSP-1001660020370-C-G11

description:
Library name: DSP-1001660020370-C-G11
spatial transcriptomic sequencing

value: Copd4RUL_Airway_005 002


title: Sample: C1-109 , Mother: 965 , Day: 6

description: Library name: C1-109


title: Sample: B8-609 , Mother: 965 , Day: 48

description: Library name: B8-609


title: DSP-1001660020370-C-G10

description:
Library name: DSP-1001660020370-C-G10
spatial transcriptomic sequencing


title: Sample: B9-617 , Mother: 965 , Day: 48

description: Library name: B9-617


title: Sample: B8-742 , Mother: 965 , Day: 34

description: Library name: B8-742


title: Sample: B7-581 , Mother: FD247 , Day: 41

description: Library name: B7-581


title: DSP-1001660020370-C-G08

description:
Library name: DSP-1001660020370-C-G08
spatial transcriptomic sequencing


title: DSP-1001660020370-C-G09

description:
Library name: DSP-1001660020370-C-G09
spatial transcriptomic sequencing


title: DSP-1001660020370-C-G07

description:
Library name: DSP-1001660020370-C-G07
spatial transcriptomic sequencing


title: Sample: B7-227 , Mother: FD247 , Day: 55

description: Library name: B7-227


title: Sample: B6-219 , Mother: 94E , Day: 55

description: Library name: B6-219


title: Sample: B6-573 , Mother: 94E , Day: 41

description: Library name: B6-573


title: Sample: B5-198 , Mother: 965 , Day: 55

description: Library name: B5-198


title: Sample: B5-545 , Mother: 965 , Day: 41

description: Library name: B5-545


title: Sample: B4-335 , Mother: FD247 , Day: 20

description: Library name: B4-335


title: DSP-1001660020370-C-G05

description:
Library name: DSP-1001660020370-C-G05
spatial transcriptomic sequencing


title: DSP-1001660020370-C-G06

description:
Library name: DSP-1001660020370-C-G06
spatial transcriptomic sequencing


title: Sample: B3-132 , Mother: FD247 , Day: 34

description: Library name: B3-132


title: DSP-1001660020370-C-F12

description:
Library name: DSP-1001660020370-C-F12
spatial transcriptomic sequencing


title: DSP-1001660020370-C-F11

description:
Library name: DSP-1001660020370-C-F11
spatial transcriptomic sequencing


title: DSP-1001660020370-C-G03

description:
Library name: DSP-1001660020370-C-G03
spatial transcriptomic sequencing


title: DSP-1001660020370-C-G02

description:
Library name: DSP-1001660020370-C-G02
spatial transcriptomic sequencing


title: DSP-1001660020370-C-G01

description:
Library name: DSP-1001660020370-C-G01
spatial transcriptomic sequencing


title: Sample: B2-177 , Mother: 965 , Day: 13

description: Library name: B2-177


title: Sample: B3-249 , Mother: FD247 , Day: 13

description: Library name: B3-249


title: DSP-1001660020370-C-F10

description:
Library name: DSP-1001660020370-C-F10
spatial transcriptomic sequencing


title: DSP-1001660020370-C-F09

description:
Library name: DSP-1001660020370-C-F09
spatial transcriptomic sequencing


title: DSP-1001660020370-C-F08

description:
Library name: DSP-1001660020370-C-F08
spatial transcriptomic sequencing