title: mHAR123, ECTO, Rep2

data_processing:
Reads were filtered for quality and aligned with STAR (2.5.2b) against the GRCh38 (Ensembl version 106).
The exon counts were aggregated for each gene to build a read count table using SubRead function featureCounts.
Differentially expressed genes (DEGs) were defined using DESeq2 using the following threshold: |Log2FC| > 1, and q-val < 0.01. The R package program pheatmap was used for clustering and generating heatmap plots. The R package program clusterProfiler was used for gene functional annotation.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited txt file including raw counts for each sample

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen), following the manufacturer’s protocol. Ribosomal RNAs were removed using NEBNext® rRNA Depletion Kit v2 (New England Biolabs).
Purified RNAs were used to make the library using the NEBNext Ultra II Directional RNA Library Prep kit (New England Biolabs), as per manufacturer's instructions. Libraries were sequenced (pair-end reads) with an Illumina NovaSeq 6000 platform for 100 cycles at the UCSD institute for Genomic Medicine (IGM) core.

treatment_protocol: hESCs were harvested and seeded as single cells at 6x104 cells per cm2. Once confluent, the hESCs were cultured in KnockOut™ DMEM (Gibco) medium containing 10% knockout serum replacement (Gibco) and supplemented with Noggin (500 ng/ml; R&D Systems) and SB431542 (10 μM; Selleck Chemicals) for 5 days.

value: human neuroecrtodermal cells

value: neuroectodermal differentiation


title: 23_D4_313

status: Public on Jul 15 2025

type: SRA

city: Gaithersburg

first: Binbin

last: Wang

state: MD

address: 408 Suffield Dr

country: USA

institute: NATIONAL CANCER INSTITUTE, NIH

description:
Library name: 23_D4_313
NonResponder

library_source: transcriptomic

data_processing:
RNAseq data was process with STAR
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text files containing TPM values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Blood

extract_protocol:
Mice were bled via retro-orbital puncture using heparinized EDTA-coated glass capillary tubes. Blood was immediately transferred into microcentrifuge tubes containing TRIzol reagent (Thermo Fisher Scientific) for RNA stabilization. Samples were processed according to the manufacturer's instructions for RNA extraction.
RNA libraries were prepared using the SMARTer mRNA-Seq Library Prep Kit following the manufacturer's protocols.

tag: tissue

value: Blood

tag: treatment


title: mHAR123, ECTO, Rep1

city: La Jolla

first: Kun

last: Tan

state: CA

address: 9500 Gilman Drive # 0695

department: Dept. of Obstetrics, Gynecology & Reproductive Science

institute: UCSD

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

value: replace hHAR123 with mHAR123


title: 22_D4_310

description:
Library name: 22_D4_310
NonResponder


title: 5929-606939_1-Day_S1_OVCAR3_ROI-010_Ciliated

city: Kansas City

first: Andrew

last: Godwin

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: Kansas University Medical Center

description: Library name: DSP-1001660010839-A-H09

data_processing:
FASTQ files downloaded from the NextSeq are converted into the DCC file format using the GeoMxNGSPipeline (version-2.3.3.10).
Initial quality control and data analyses were performed using the GeoMxWorkflows, NanoStringNCTools, and GeoMxTools packages provided on Bioconductor, following the vignette “Analyzing GeoMx-NGS RNA Expression Data with GeoMxTools” provided by NanoString.
Assembly: GRCh38.p13
Supplementary files format and content: .dcc: probe count data
Supplementary files format and content: .pkc: probe metadata linking probe barcodes with target genes IDs
Supplementary files format and content: .xlsx: annotation file containing segment annotation info
Library strategy: Spatial Transcriptomics

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) slides were prepared following the “RNA Slide Preparation Protocol” in MAN-10150 in the Manual Slide Preparation User Manual, available from NanoString. The RNA probe hybridization solution was prepared using the GeoMx® Cancer Transcriptome Atlas (CTA) RNA probe mix (NanoString), following the recommended dilution (10% probe mix + 10% DEPC water + 80% Buffer R).
Library prep was performed according to instructions provided in NanoString’s NGS Readout Library Prep User Manual (MAN-10117-05), followed by paired-end (27 x 27 ) sequencing on the Illumina NextSeq 550 sequencer using a high-output flow cell.

tag: patient

tag: roi

tag: days

tag: segment

value: Ciliated

tag: nuclei

tag: area


title: 5929-606939_1-Day_S1_OVCAR3_ROI-010_Secretory

description: Library name: DSP-1001660010839-A-H10

value: Secretory


title: 5929-606939_1-Day_S1_FT240_ROI-009_Secretory

description: Library name: DSP-1001660010839-A-H08


title: 5929-606939_1-Day_S1_FT240_ROI-011_Secretory

description: Library name: DSP-1001660010839-A-H12


title: 21_D4_308

description:
Library name: 21_D4_308
NonResponder


title: 5929-606939_1-Day_S1_FT240_ROI-009_Ciliated

description: Library name: DSP-1001660010839-A-H07


title: cHAR123, ECTO, Rep3

value: replace hHAR123 with cHAR123


title: 5929-606939_1-Day_S1_FT240_ROI-008_Secretory

description: Library name: DSP-1001660010839-A-H06


title: 27_D4_323

description:
Library name: 27_D4_323
NonResponder


title: 5929-606939_1-Day_S1_FT240_ROI-008_Ciliated

description: Library name: DSP-1001660010839-A-H05


title: 20_D4_305

description:
Library name: 20_D4_305
NonResponder


title: 5929-606939_1-Day_S1_FT240_ROI-007_Secretory

description: Library name: DSP-1001660010839-A-H04


title: 5929-606939_1-Day_S1_PBS_ROI-006_Secretory

description: Library name: DSP-1001660010839-A-H02

value: PBS


title: 5929-606939_1-Day_S1_FT240_ROI-007_Ciliated

description: Library name: DSP-1001660010839-A-H03


title: cHAR123, ECTO, Rep1


title: mHAR123, ECTO, Rep3


title: 25_D4_320

description:
Library name: 25_D4_320
NonResponder


title: 5929-606939_1-Day_S1_PBS_ROI-006_Ciliated

description: Library name: DSP-1001660010839-A-H01


title: 5929-606939_1-Day_S1_PBS_ROI-005_Secretory

description: Library name: DSP-1001660010839-A-G12


title: 19_D4_304

description:
Library name: 19_D4_304
NonResponder


title: DSP-1001660010837_NTC

description: Library name: DSP-1001660010837-B-A01

source_name: NTC

value: NTC


title: 5929-606939_1-Day_S1_FT240_ROI-011_Ciliated

description: Library name: DSP-1001660010839-A-H11


title: HAR123-KO, ECTO, Rep3


title: HAR123-KO, ECTO, Rep2


title: 5929-606939_1-Day_S1_PBS_ROI-005_Ciliated

description: Library name: DSP-1001660010839-A-G11


title: 18_D4_7222

description:
Library name: 18_D4_7222
NonResponder


title: 17_D4_7220

description:
Library name: 17_D4_7220
NonResponder


title: HAR123-KO, ECTO, Rep1


title: 5929-606939_1-Day_S1_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660010839-A-G09


title: 5929-606939_1-Day_S1_PBS_ROI-004_Secretory

description: Library name: DSP-1001660010839-A-G10


title: 16_D4_7203

description:
Library name: 16_D4_7203
NonResponder


title: 5929-606939_1-Day_S1_OVCAR3_ROI-003_Ciliated

description: Library name: DSP-1001660010839-A-G07


title: 15_D4_327

description:
Library name: 15_D4_327
Responder


title: cHAR123, ECTO, Rep2


title: hHAR123, ECTO, Rep2

value: WT


title: 14_D4_322

description:
Library name: 14_D4_322
Responder


title: hHAR123, ECTO, Rep3


title: 5929-606939_1-Day_S1_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660010839-A-G04


title: 5929-606939_1-Day_S1_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660010839-A-G06


title: 5929-606939_1-Day_S1_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660010839-A-G05


title: hHAR123, ECTO, Rep1


title: mHAR123, ESC, Rep3

value: human embryonic stem cells


title: 13_D4_315

description:
Library name: 13_D4_315
Responder


title: 12_D4_311

description:
Library name: 12_D4_311
Responder


title: 5929-606856_1-Day_S3_FT240_ROI-008_Ciliated

description: Library name: DSP-1001660010839-A-G01


title: 5929-606856_1-Day_S3_FT240_ROI-008_Secretory

description: Library name: DSP-1001660010839-A-F12


title: 5929-606856_1-Day_S3_PBS_ROI-009_Ciliated

description: Library name: DSP-1001660010839-A-G03


title: 5929-606856_1-Day_S3_FT240_ROI-007_Ciliated

description: Library name: DSP-1001660010839-A-F11


title: 5929-606856_1-Day_S3_FT240_ROI-007_Secretory

description: Library name: DSP-1001660010839-A-F10


title: mHAR123, ESC, Rep1


title: 5929-606856_1-Day_S3_PBS_ROI-009_Secretory

description: Library name: DSP-1001660010839-A-G02


title: 10_D4_7228

description:
Library name: 10_D4_7228
Responder


title: 5929-606856_1-Day_S3_FT240_ROI-006_Ciliated

description: Library name: DSP-1001660010839-A-F09


title: 5929-606856_1-Day_S3_FT240_ROI-006_Secretory

description: Library name: DSP-1001660010839-A-F08


title: 11_D4_7229

description:
Library name: 11_D4_7229
Responder


title: 5929-606939_1-Day_S1_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660010839-A-G08


title: cHAR123, ESC, Rep3


title: 9_D4_7227

description:
Library name: 9_D4_7227
Responder


title: 5929-606856_1-Day_S3_PBS_ROI-005_Ciliated

description: Library name: DSP-1001660010839-A-F07


title: 5929-606856_1-Day_S3_PBS_ROI-005_Secretory

description: Library name: DSP-1001660010839-A-F06


title: cHAR123, ESC, Rep2


title: 5929-606856_1-Day_S3_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660010839-A-F05


title: 5929-606856_1-Day_S3_PBS_ROI-004_Secretory

description: Library name: DSP-1001660010839-A-F04


title: 7_D4_7221

description:
Library name: 7_D4_7221
Responder


title: 5929-606856_1-Day_S3_OVCAR3_ROI-003_Ciliated

description: Library name: DSP-1001660010839-A-F03


title: HAR123-KO, ESC, Rep3


title: 8_D4_7226

description:
Library name: 8_D4_7226
Responder


title: 5929-606856_1-Day_S3_OVCAR3_ROI-002_Ciliated

description: Library name: DSP-1001660010839-A-F01


title: 6_D4_7210

description:
Library name: 6_D4_7210
Responder


title: 5929-606856_1-Day_S3_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660010839-A-E12


title: 5_D4_7208

description:
Library name: 5_D4_7208
Responder


title: HAR123-KO, ESC, Rep1


title: 5929-606856_1-Day_S3_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660010839-A-E10


title: 5929-606856_1-Day_S2_FT240_ROI-008_Ciliated

description: Library name: DSP-1001660010839-A-E08


title: 5929-606856_1-Day_S2_FT240_ROI-008_Secretory

description: Library name: DSP-1001660010839-A-E09


title: hHAR123, ESC, Rep3


title: 3_D4_7205

description:
Library name: 3_D4_7205
Responder


title: mHAR123, ESC, Rep2


title: 5929-606856_1-Day_S2_PBS_ROI-007_Secretory

description: Library name: DSP-1001660010839-A-E07


title: 2_D4_7202

description:
Library name: 2_D4_7202
Responder


title: hHAR123, ESC, Rep1


title: 1_D4_7201

description:
Library name: 1_D4_7201
Responder


title: 5929-606856_1-Day_S3_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660010839-A-F02


title: 4_D4_7206

description:
Library name: 4_D4_7206
Responder


title: hHAR123, ESC, Rep2


title: cHAR123, ESC, Rep1


title: 5929-606856_1-Day_S3_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660010839-A-E11


title: 5929-606856_1-Day_S2_FT240_ROI-005_Ciliated

description: Library name: DSP-1001660010839-A-E02


title: 5929-606856_1-Day_S2_PBS_ROI-006_Ciliated

description: Library name: DSP-1001660010839-A-E04


title: 5929-606856_1-Day_S2_FT240_ROI-005_Secretory

description: Library name: DSP-1001660010839-A-E03


title: scTCR_SCAF3507_61_7262_T4

description:
Library name: scTCR_SCAF3507_61_7262_T4
non-responder

library_source: transcriptomic single cell

data_processing:
Seurat
Assembly: mm10
Supplementary files format and content: Processed data include the Seurat object (.rds file) containing the filtered gene expression matrix, metadata annotations, dimensionality reduction results (e.g., PCA, UMAP), and clustering results for each sample.

extract_protocol:
For single-cell RNA sequencing, blood was diluted in PBS + 0.04% BSA, and cell concentration and viability were determined using the Countess II Automated Cell Counter, targeting 700–1,200 cells/µL for downstream analysis.
Single-cell suspensions were processed using the 10x Genomics Chromium Single Cell 5' Library & Gel Bead Kit and Chromium Single Cell V(D)J Enrichment Kit according to the manufacturer's protocol (10x Genomics).


title: ECTO, Rep2

library_source: genomic

data_processing:
Paired-end reads were aligned separately to the UCSC human genome (hg38) using bowtie2, with low mapping quality filtered, paired and PCR duplicates removed.
The output bam files were transformed into tag directories for further analysis in HOMER. We used the contact matrix in 1-kb and 10-kb resolution. Topological associated domains (TADs) were identified, and significant interactions (p < 1e-10, z-score>10) were identified by using HOMER program.
Assembly: hg38
Supplementary files format and content: Tab-delimited txt file including interactions

molecule: genomic DNA

extract_protocol:
DNA purification was performed following the manufacturer’s instructions of EpiTect® Hi-C (Qiagen) kit.
Indexed libraries were prepared using 2×106 cells, with EpiTect® Hi-C (Qiagen) according to the manufacturer’s instructions. The pooled library was sequenced using 2 x 150 paired-end sequencing protocol on an Illumina NovaSeq 6000 instrument.

treatment_protocol: hESCs and neuroectodermal cells were cross-linked with 1% formaldehyde for 10 min at room temperature and incubated with 3M Tris pH 7.5 for 5 min at room temperature and then on ice for 15 min to quench the formaldehyde. The cells were centrifugated for 10 min at 800×g at 4° C, the pellet was resuspended in cold 1X PBS, and the cell density was determined.

value: human neuroectodermal cells


title: 5929-606856_1-Day_S2_OVCAR3_ROI-004_Ciliated

description: Library name: DSP-1001660010839-A-D12


title: HAR123-KO, ESC, Rep2


title: scTCR_SCAF3554_45_7262_T3

description:
Library name: scTCR_SCAF3554_45_7262_T3
non-responder


title: 5929-606856_1-Day_S2_FT240_ROI-003_Secretory

description: Library name: DSP-1001660010839-A-D11


title: ESC, Rep2


title: 5929-606856_1-Day_S2_PBS_ROI-002_Ciliated

description: Library name: DSP-1001660010839-A-D08


title: ESC, Rep1


title: 5929-606856_1-Day_S2_PBS_ROI-006_Secretory

description: Library name: DSP-1001660010839-A-E05


title: 5929-606856_1-Day_S2_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660010839-A-D10


title: scTCR_SCAF3512_13_7262_T1

description:
Library name: scTCR_SCAF3512_13_7262_T1
non-responder


title: scTCR_SCAF3519_29_7262_T2

description:
Library name: scTCR_SCAF3519_29_7262_T2
non-responder


title: 5929-606856_1-Day_S2_PBS_ROI-002_Secretory

description: Library name: DSP-1001660010839-A-D09


title: scTCR_SCAF3470_60_7261_T4

description:
Library name: scTCR_SCAF3470_60_7261_T4
non-responder


title: 461-27444_1-Day_S1_FT240_ROI-009_Secretory

description: Library name: DSP-1001660010839-A-D05


title: 461-27444_1-Day_S1_FT240_ROI-009_Ciliated

description: Library name: DSP-1001660010839-A-D04


title: scTCR_SCAF3462_44_7261_T3_2

description:
Library name: scTCR_SCAF3462_44_7261_T3_2
non-responder


title: Plate6_M2

city: Stevenage

first: Carl

last: Fishwick

address: Gunnels Wood Road

country: United Kingdom

institute: GSK

data_processing:
library strategy: DRUG-seq (multiplexed 3' RNA-seq)
Reads quantification (assignment to genes and UMI-aware counting) and demultiplexing of well barcodes were performed along with the alignment using the extension STARsolo (R1 contains the well barcodes and UMI; 10nt long well barcode starting at position 1, 10nt along UMI starting at position 11, forward-strand-specific gene assignment, Gene quantification mode used accounting only for exonic overlaps).
The mRNA reads (R2) were trimmed for poly-A and poly-G tails (>=12nt) using Atropos and then aligned against the Human reference genome using STAR.
Assembly: GRCh38 (Ensembl 96)
Supplementary files format and content: PlateX_XX_barcodes.csv well barcodes used in the polyA primer
Supplementary files format and content: PlateX_XX_features.csv gene feature ID
Supplementary files format and content: PlateX_XX_matrix.mtx sparse matrix representation in a Matrix Market format including the raw counts in each well using Gene mode

source_name: iPSC Macrophage

extract_protocol:
Cells were lysed following the DRUG-seq protocol.
cDNA was generated per well following the DRUG-seq protocol. cDNA from each 384-well plate was then pooled and subjected to library preparation as per the DRUG-seq protocol.

value: iPSC Macrophage


title: 461-27444_1-Day_S1_PBS_ROI-008_Ciliated

description: Library name: DSP-1001660010839-A-D02


title: Plate5_M1


title: scTCR_SCAF3478_28_7261_T2

description:
Library name: scTCR_SCAF3478_28_7261_T2
non-responder


title: 461-27444_1-Day_S1_PBS_ROI-008_Secretory

description: Library name: DSP-1001660010839-A-D03


title: 461-27444_1-Day_S1_PBS_ROI-007_Ciliated

description: Library name: DSP-1001660010839-A-C12


title: 5929-606856_1-Day_S2_OVCAR3_ROI-004_Secretory

description: Library name: DSP-1001660010839-A-E01


title: 461-27444_1-Day_S1_PBS_ROI-007_Secretory

description: Library name: DSP-1001660010839-A-D01


title: 461-27444_1-Day_S1_FT240_ROI-006_Secretory

description: Library name: DSP-1001660010839-A-C11


title: scTCR_SCAF3480_12_7261_T1

description:
Library name: scTCR_SCAF3480_12_7261_T1
non-responder


title: 461-27444_1-Day_S1_FT240_ROI-006_Ciliated

description: Library name: DSP-1001660010839-A-C10


title: ECTO, Rep1


title: Plate3_M2


title: Plate2_M1


title: Plate4_M0


title: 461-27444_1-Day_S1_FT240_ROI-005_Secretory

description: Library name: DSP-1001660010839-A-C09


title: 5929-606856_1-Day_S2_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660010839-A-D07


title: 5929-606856_1-Day_S2_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660010839-A-D06


title: 461-27444_1-Day_S1_FT240_ROI-005_Ciliated

description: Library name: DSP-1001660010839-A-C08


title: scTCR_SCAF3520_35_7249_T3

description:
Library name: scTCR_SCAF3520_35_7249_T3
non-responder


title: Plate1_M0


title: 461-27444_1-Day_S1_PBS_ROI-004_Secretory

description: Library name: DSP-1001660010839-A-C07


title: 461-27444_1-Day_S1_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660010839-A-C06


title: SOX4i

city: Saint Louis

first: Patrick

last: DeSouza

state: MO

address: 4515 McKinley Ave.

department: Neurosurgery

institute: Washington University School of Medicine

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Total RNA was extracted from harvested cells using QIA shredder (Qiagen, 79656) and RNeasy Plus Mini Kit (Qiagen, 74134), following the manufacture's instructions. Single-cell suspensions were made using Brain Tumor Dissociation Kit (Miltenyi Biotec, 130-095-942), CD45- cell populations were enriched using CD45 MicroBead depeletion (Miltenyi Biotec, 130-052-301).
Library construction was done following manufacturer protocols (10X Genomics)

value: neural stem cells

value: PRO

value: shCtrl vs. 2x SOX4 RNAi


title: scTCR_SCAF3510_3_7249_T1

description:
Library name: scTCR_SCAF3510_3_7249_T1
non-responder


title: scTCR_SCAF3405_19_7249_T2

description:
Library name: scTCR_SCAF3405_19_7249_T2
non-responder


title: scTCR_SCAF3559_51_7249_T4

description:
Library name: scTCR_SCAF3559_51_7249_T4
non-responder


title: TCF4i

value: shCtrl vs. 2x TCF4 RNAi


title: 461-27444_1-Day_S1_OVCAR3_ROI-003_Ciliated

description: Library name: DSP-1001660010839-A-C04


title: 461-27444_1-Day_S1_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660010839-A-C01


title: INSM1i

value: shCtrl vs. 2x INSM1 RNAi


title: 461-27444_1-Day_S1_OVCAR3_ROI-002_Ciliated

description: Library name: DSP-1001660010839-A-C02


title: 461-27444_1-Day_S1_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660010839-A-C05


title: 461-27444_1-Day_S1_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660010839-A-B12


title: 5929-606939_1-Day_S1_PBS_ROI-002_Secretory

description: Library name: DSP-1001660010839-A-B11


title: scTCR_SCAF3515_41_7257_T3

description:
Library name: scTCR_SCAF3515_41_7257_T3
non-responder


title: mouse-42

source_name: glioblastoma

value: glioblastoma

value: tumor cells


title: scTCR_SCAF3471_57_7257_T4

description:
Library name: scTCR_SCAF3471_57_7257_T4
non-responder

value: Blood


title: scTCR_SCAF3514_25_7257_T2

description:
Library name: scTCR_SCAF3514_25_7257_T2
non-responder


title: 5929-606939_1-Day_S1_PBS_ROI-002_Ciliated

description: Library name: DSP-1001660010839-A-B10

value: Ciliated


title: mouse-38


title: 5929-606939_1-Day_S1_FT240_ROI-001_Secretory

description: Library name: DSP-1001660010839-A-B09

value: Secretory


title: 5929-606939_1-Day_S1_FT240_ROI-001_Ciliated

description: Library name: DSP-1001660010839-A-B08


title: DSP-1001660010839_NTC

description: Library name: DSP-1001660010839-A-A01


title: mouse-35


title: scTCR_SCAF3556_9_7257_T1

description:
Library name: scTCR_SCAF3556_9_7257_T1
non-responder


title: PRO, rep2 [GEX]


title: 461-27413_1-Day_S1_FT240_ROI-006_Ciliated

description: Library name: DSP-1001660010692-B-F03


title: 461-27413_1-Day_S1_OVCAR3_ROI-005_Secretory

description: Library name: DSP-1001660010692-B-F02


title: 461-27444_1-Day_S1_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660010839-A-C03


title: PRO, rep2 [ATAC]


title: 461-27413_1-Day_S1_OVCAR3_ROI-005_Ciliated

description: Library name: DSP-1001660010692-B-F01


title: PRO, rep1 [GEX]


title: 461-27413_1-Day_S1_OVCAR3_ROI-004_Secretory

description: Library name: DSP-1001660010692-B-E12


title: 461-27413_1-Day_S1_OVCAR3_ROI-004_Ciliated

description: Library name: DSP-1001660010692-B-E11


title: scTCR_SCAF3468_24_7256_T2

description:
Library name: scTCR_SCAF3468_24_7256_T2
non-responder


title: PRO, rep1 [ATAC]


title: 461-27413_1-Day_S1_FT240_ROI-003_Secretory

description: Library name: DSP-1001660010692-B-E10


title: 461-27413_1-Day_S1_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660010692-B-E09


title: scTCR_SCAF3509_8_7256_T1

description:
Library name: scTCR_SCAF3509_8_7256_T1
non-responder


title: WT, rep2 [GEX]


title: scTCR_SCAF3557_46_7263_T3

description:
Library name: scTCR_SCAF3557_46_7263_T3
non-responder


title: WT, rep2 [ATAC]


title: 461-27413_1-Day_S1_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660010692-B-E08


title: 461-27413_1-Day_S1_FT240_ROI-001_Ciliated

description: Library name: DSP-1001660010692-B-E05


title: 461-27413_1-Day_S1_FT240_ROI-001_Secretory

description: Library name: DSP-1001660010692-B-E06


title: 461-27413_1-Day_S1_OVCAR3_ROI-002_Ciliated

description: Library name: DSP-1001660010692-B-E07


title: NW71422_1-Day_S1_FT240_ROI-008_Secretory

description: Library name: DSP-1001660010692-B-E04


title: 461-27413_1-Day_S1_FT240_ROI-006_Secretory

description: Library name: DSP-1001660010692-B-F04


title: NW71422_1-Day_S1_FT240_ROI-008_Ciliated

description: Library name: DSP-1001660010692-B-E03


title: WT, rep1 [GEX]


title: scTCR_SCAF3479_14_7263_T1

description:
Library name: scTCR_SCAF3479_14_7263_T1
non-responder


title: scTCR_SCAF3555_56_7256_T4

description:
Library name: scTCR_SCAF3555_56_7256_T4
non-responder


title: NW71422_1-Day_S1_FT240_ROI-007_Secretory

description: Library name: DSP-1001660010692-B-E02


title: WT, rep1 [ATAC]


title: scTCR_SCAF3516_40_7256_T3

description:
Library name: scTCR_SCAF3516_40_7256_T3
non-responder


title: scTCR_SCAF3518_59_7259_T4

description:
Library name: scTCR_SCAF3518_59_7259_T4
non-responder


title: NW71422_1-Day_S1_FT240_ROI-007_Ciliated

description: Library name: DSP-1001660010692-B-E01


title: NW71422_1-Day_S1_OVCAR3_ROI-006_Secretory

description: Library name: DSP-1001660010692-B-D12


title: scTCR_SCAF3475_43_7259_T3

description:
Library name: scTCR_SCAF3475_43_7259_T3
non-responder


title: scTCR_SCAF3553_27_7259_T2

description:
Library name: scTCR_SCAF3553_27_7259_T2
non-responder


title: U2OS -Pi_3

city: Salt Lake City

first: Jordan

middle: A

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

department: Biochemistry

institute: University of Utah

description:
150 x 150 cycle paired end sequence
19821X18

data_processing:
NovaSeq S4 Reagent Kit v1.5_150x150 bp Sequencing (2500 M read-pairs/lane): Sequencing libraries were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP workflow (20043131).  Following transfer of the flowcell to an Illumina NovaSeq 6000 instrument, a 150 x 150 cycle paired end sequence run was performed using a NovaSeq 6000 S4 reagent Kit v1.5 (20028312).
Single base mismatch
XPRESSpipe v0.6.3 was used to process sequence files, with the following command: xpresspipe peRNAseq ... -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --sjdbOverhang 150 --quantification_method htseq --remove_rrna. See supplementary files for XPRESSpipe dependencies and settings used.
Assembly: Ensembl homo_sapiens release-106 (GRCh38)
Supplementary files format and content: Tab-delimited text file - sample counts

growth_protocol: DMEM

extract_protocol:
Total RNA samples (5-500 ng) were hybridized with NEBNext rRNA Depletion Kit v2 (Human, Mouse, Rat) (E7400) to substantially diminish rRNA from the samples.
Stranded RNA sequencing libraries were prepared as described using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L).  Purified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 5 nM in preparation for Illumina sequence analysis.

treatment_protocol: DMEM +/-Pi for 24 hr

value: Epithelial-like osteosarcoma (bone)

value: -phosphate for 24 hr


title: NW71422_1-Day_S1_OVCAR3_ROI-006_Ciliated

description: Library name: DSP-1001660010692-B-D11


title: NW71422_1-Day_S1_OVCAR3_ROI-005_Secretory

description: Library name: DSP-1001660010692-B-D10


title: serial mutants

value: WT; TERTp; TERTp+TP53; PRO


title: scTCR_SCAF3551_30_7263_T2

description:
Library name: scTCR_SCAF3551_30_7263_T2
non-responder


title: NW71422_1-Day_S1_OVCAR3_ROI-005_Ciliated

description: Library name: DSP-1001660010692-B-D09


title: scTCR_SCAF3404_11_7259_T1

description:
Library name: scTCR_SCAF3404_11_7259_T1
non-responder


title: U2OS -Pi_2

description:
150 x 150 cycle paired end sequence
19821X17


title: NW71422_1-Day_S1_PBS_ROI-003_Secretory

description: Library name: DSP-1001660010692-B-D06

value: PBS


title: NW71422_1-Day_S1_FT240_ROI-004_Secretory

description: Library name: DSP-1001660010692-B-D08


title: U2OS -Pi_1

description:
150 x 150 cycle paired end sequence
19821X16


title: NW71422_1-Day_S1_FT240_ROI-004_Ciliated

description: Library name: DSP-1001660010692-B-D07


title: NW71422_1-Day_S1_PBS_ROI-003_Ciliated

description: Library name: DSP-1001660010692-B-D05


title: scTCR_SCAF3047_39_7255_3

description:
Library name: scTCR_SCAF3047_39_7255_3
non-responder


title: NW71422_1-Day_S1_PBS_ROI-002_Ciliated

description: Library name: DSP-1001660010692-B-D03


title: scTCR_SCAF3511_55_7255_T4

description:
Library name: scTCR_SCAF3511_55_7255_T4
non-responder


title: NW71422_1-Day_S1_PBS_ROI-001_Secretory

description: Library name: DSP-1001660010692-B-D02


title: U2OS +Pi_2

description:
150 x 150 cycle paired end sequence
19821X14

value: +phosphate for 24 hr


title: NW71422_1-Day_S1_PBS_ROI-001_Ciliated

description: Library name: DSP-1001660010692-B-D01


title: scTCR_SCAF3477_23_7255_T2

description:
Library name: scTCR_SCAF3477_23_7255_T2
non-responder


title: UH000028_14-Day_S1_FT240_ROI-010_Secretory

description: Library name: DSP-1001660010692-B-C12


title: UH000028_14-Day_S1_FT240_ROI-010_Ciliated

description: Library name: DSP-1001660010692-B-C11


title: U2OS +Pi_1

description:
150 x 150 cycle paired end sequence
19821X13


title: scTCR_SCAF3473_7_7255_T1

description:
Library name: scTCR_SCAF3473_7_7255_T1
non-responder


title: UH000028_14-Day_S1_PBS_ROI-007_Secretory

description: Library name: DSP-1001660010692-B-C07


title: A375 -Pi_2

description:
150 x 150 cycle paired end sequence
19821X11

value: Epithelial-like malignant melanoma (skin)


title: A375 -Pi_3

description:
150 x 150 cycle paired end sequence
19821X12


title: scTCR_SCAF3522_54_7254_T4

description:
Library name: scTCR_SCAF3522_54_7254_T4
non-responder


title: UH000028_14-Day_S1_PBS_ROI-009_Secretory

description: Library name: DSP-1001660010692-B-C10


title: UH000028_14-Day_S1_PBS_ROI-009_Ciliated

description: Library name: DSP-1001660010692-B-C09


title: UH000028_14-Day_S1_OVCAR3_ROI-008_Secretory

description: Library name: DSP-1001660010692-B-C08


title: scTCR_SCAF3464_38_7254_T3_2

description:
Library name: scTCR_SCAF3464_38_7254_T3_2
non-responder


title: scTCR_SCAF3406_22_7254_T2

description:
Library name: scTCR_SCAF3406_22_7254_T2
non-responder


title: U2OS +Pi_3

description:
150 x 150 cycle paired end sequence
19821X15


title: UH000028_14-Day_S1_PBS_ROI-005_Secretory

description: Library name: DSP-1001660010692-B-C03


title: scTCR_SCAF3521_6_7254_T1

description:
Library name: scTCR_SCAF3521_6_7254_T1
non-responder


title: UH000028_14-Day_S1_PBS_ROI-006_Secretory

description: Library name: DSP-1001660010692-B-C05


title: UH000028_14-Day_S1_PBS_ROI-007_Ciliated

description: Library name: DSP-1001660010692-B-C06


title: A375 -Pi_1

description:
150 x 150 cycle paired end sequence
19821X10


title: A375 +Pi_3

description:
150 x 150 cycle paired end sequence
19821X9


title: UH000028_14-Day_S1_PBS_ROI-005_Ciliated

description: Library name: DSP-1001660010692-B-C02


title: NW71422_1-Day_S1_PBS_ROI-002_Secretory

description: Library name: DSP-1001660010692-B-D04


title: scTCR_SCAF3461_64_7265_T4_2

description:
Library name: scTCR_SCAF3461_64_7265_T4_2
responder


title: A375 +Pi_2

description:
150 x 150 cycle paired end sequence
19821X8


title: UH000028_14-Day_S1_FT240_ROI-004_Ciliated

description: Library name: DSP-1001660010692-B-B12


title: A375 +Pi_1

description:
150 x 150 cycle paired end sequence
19821X7


title: UH000028_14-Day_S1_FT240_ROI-004_Secretory

description: Library name: DSP-1001660010692-B-C01


title: UH000028_14-Day_S1_FT240_ROI-003_Secretory

description: Library name: DSP-1001660010692-B-B11


title: scTCR_SCAF3466_48_7265_T3

description:
Library name: scTCR_SCAF3466_48_7265_T3
responder


title: UH000028_14-Day_S1_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660010692-B-B10


title: UH000028_14-Day_S1_FT240_ROI-002_Secretory

description: Library name: DSP-1001660010692-B-B09


title: HEK293 -Pi_3

description:
150 x 150 cycle paired end sequence
19821X6

value: Epithelial-like embryonic kidney


title: scTCR_SCAF3048_16_7265_1

description:
Library name: scTCR_SCAF3048_16_7265_1
responder


title: UH000028_14-Day_S1_FT240_ROI-002_Ciliated

description: Library name: DSP-1001660010692-B-B08


title: scTCR_SCAF3517_32_7265_T2

description:
Library name: scTCR_SCAF3517_32_7265_T2
responder


title: HEK293 -Pi_2

description:
150 x 150 cycle paired end sequence
19821X5


title: UH000028_1-Day_S1_PBS_ROI-003_Ciliated

description: Library name: DSP-1001660010692-B-B06


title: HEK293 -Pi_1

description:
150 x 150 cycle paired end sequence
19821X4


title: UH000028_1-Day_S1_PBS_ROI-003_Secretory

description: Library name: DSP-1001660010692-B-B07


title: scTCR_SCAF3474_63_7264_T4

description:
Library name: scTCR_SCAF3474_63_7264_T4
responder


title: UH000028_1-Day_S1_PBS_ROI-002_Ciliated

description: Library name: DSP-1001660010692-B-B04


title: UH000028_1-Day_S1_PBS_ROI-002_Secretory

description: Library name: DSP-1001660010692-B-B05


title: scTCR_SCAF3476_47_7264_T3

description:
Library name: scTCR_SCAF3476_47_7264_T3
responder


title: UH000028_1-Day_S1_PBS_ROI-001_Secretory

description: Library name: DSP-1001660010692-B-B03


title: 5929-606856_1-Day_S2_PBS_ROI-007_Ciliated

description: Library name: DSP-1001660010839-A-E06


title: UH000028_14-Day_S1_PBS_ROI-006_Ciliated

description: Library name: DSP-1001660010692-B-C04


title: scTCR_SCAF3046_31_7264_2

description:
Library name: scTCR_SCAF3046_31_7264_2
responder


title: HEK293 +Pi_3

description:
150 x 150 cycle paired end sequence
19821X3


title: HEK293 +Pi_1

description:
150 x 150 cycle paired end sequence
19821X1


title: UH00022_14-Day_S1_OVCAR3_ROI-006_Ciliated

description: Library name: DSP-1001660010692-B-A12


title: UH00022_14-Day_S1_OVCAR3_ROI-005_Ciliated

description: Library name: DSP-1001660010692-B-A10


title: HEK293 +Pi_2

description:
150 x 150 cycle paired end sequence
19821X2


title: UH00022_14-Day_S1_OVCAR3_ROI-006_Secretory

description: Library name: DSP-1001660010692-B-B01


title: UH00022_14-Day_S1_OVCAR3_ROI-004_Secretory

description: Library name: DSP-1001660010692-B-A09


title: AB_17, Tumor_chemo_controldiet

city: Edmonton

first: Sambasivarao

last: Damaraju

state: Alberta

address: 11560 University Avenue

department: Laboratory Medicine and Pathology

country: Canada

institute: University of Alberta

description: Library name: AB_17

data_processing:
The TruSeq Stranded Total RNA with Ribo-ZeroTM Human/Mouse/Rat kit was used to make RNA-seq libraries, which were prepared according to the manufacturer's instructions. All samples were sequenced on an Illumina NextSeq 500 with high throughput 2x150 nt (paired-end sequencing) run.
Illumina CASAVA 1.9 with default parameters was used for base-calling and de-multiplexing. Trim Galore v.0.4.1 was used to trim the adapters. FastQC v.0.11.4 was used to check the quality of the sequenced reads. Tophat 2.0.10 and Bowtie2 were used to match the trimmed sequences to the rat reference genome. The rat genome (Rnor 6, Ensembl) was used as a reference genome and was downloaded from the iGENOME website. Sequences that were aligned were saved as .sam files, which were subsequently transformed to .bam files and used for further data processing.
Assembly: rnor6.0
Supplementary files format and content: tab-delimited file includes the raw counts for each sample

organism: Rattus norvegicus

source_name: Skeletal muscle tissue

extract_protocol:
The MagMax-96 total RNA isolation Kit (Ambion, Austin, TX, USA) was used to extract total RNA from gastrocnemius muscle (10 mg / n>5 per group) according to the manufacturer's protocol. The quantity and quality of extracted RNA were determined using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA Integrity Number (RIN) from Bioanalyzer were >9.0, indicating high quality of RNA isolated from muscle biopsies, and these were subjected to NGS analysis.
The TruSeq Stranded Total RNA with Ribo-ZeroTM Human/Mouse/Rat kit was used to make RNA-seq libraries, which were prepared according to the manufacturer's instructions.

value: Skeletal muscle tissue


title: scTCR_SCAF3562_58_7258_T4

description:
Library name: scTCR_SCAF3562_58_7258_T4
responder


title: UH00022_14-Day_S1_OVCAR3_ROI-004_Ciliated

description: Library name: DSP-1001660010692-B-A08


title: scTCR_SCAF3467_15_7264_T1

description:
Library name: scTCR_SCAF3467_15_7264_T1
responder


title: UH00022_14-Day_S1_OVCAR3_ROI-005_Secretory

description: Library name: DSP-1001660010692-B-A11


title: UH00022_14-Day_S1_FT240_ROI-003_Secretory

description: Library name: DSP-1001660010692-B-A07


title: scTCR_SCAF3472_42_7258_T3

description:
Library name: scTCR_SCAF3472_42_7258_T3
responder


title: UH00022_14-Day_S1_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660010692-B-A06


title: AB_15, Tumor_chemo_controldiet

description: Library name: AB_15


title: UH00022_14-Day_S1_FT240_ROI-002_Secretory

description: Library name: DSP-1001660010692-B-A05


title: AB_14, Tumor_chemo_controldiet

description: Library name: AB_14


title: scTCR_SCAF3403_10_7258_T1

description:
Library name: scTCR_SCAF3403_10_7258_T1
responder


title: UH000028_1-Day_S1_PBS_ROI-001_Ciliated

description: Library name: DSP-1001660010692-B-B02


title: AB_13, Tumor_chemo_controldiet

description: Library name: AB_13


title: DSP-1001660010692_NTC

description: Library name: DSP-1001660010692-B-A01

value: NTC


title: UH00022_14-Day_S1_FT240_ROI-001_Ciliated

description: Library name: DSP-1001660010692-B-A02


title: scTCR_SCAF3560_53_7252_T4

description:
Library name: scTCR_SCAF3560_53_7252_T4
responder


title: AB_12, Tumor_chemo_controldiet

description: Library name: AB_12


title: scTCR_SCAF3566_37_7252_T3

description:
Library name: scTCR_SCAF3566_37_7252_T3
responder


title: NW71422_1-Day_S2_OVCAR3_ROI-002_Ciliated

description: Library name: DSP-1001660010693-A-F03


title: NW71422_1-Day_S2_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660010693-A-F04


title: AB_11, Tumor_chemo_controldiet

description: Library name: AB_11


title: NW71422_1-Day_S2_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660010693-A-F01


title: scTCR_SCAF3045_21_7252_2

description:
Library name: scTCR_SCAF3045_21_7252_2
responder


title: NW71422_1-Day_S2_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660010693-A-F02


title: AB_10, Tumor_nochemo_controldiet

description: Library name: AB_10


title: 461-27413_1-Day_S2_PBS_ROI-003_Secretory

description: Library name: DSP-1001660010693-A-E12


title: scTCR_SCAF3552_5_7252_T1

description:
Library name: scTCR_SCAF3552_5_7252_T1
responder


title: AB_16, Tumor_chemo_controldiet

description: Library name: AB_16


title: 461-27413_1-Day_S2_PBS_ROI-002_Secretory

description: Library name: DSP-1001660010693-A-E11


title: 461-27413_1-Day_S2_PBS_ROI-001_Secretory

description: Library name: DSP-1001660010693-A-E10


title: AB_9, Tumor_nochemo_controldiet

description: Library name: AB_9


title: scTCR_SCAF3565_26_7258_T2

description:
Library name: scTCR_SCAF3565_26_7258_T2
responder


title: DSP-1001660010693_NTC

description: Library name: DSP-1001660010693-A-A01


title: UH00022_14-Day_S1_FT240_ROI-002_Ciliated

description: Library name: DSP-1001660010692-B-A04


title: UH00022_14-Day_S1_FT240_ROI-001_Secretory

description: Library name: DSP-1001660010692-B-A03


title: UH000025_1-Day_S1_PBS_ROI-012_Secretory

description: Library name: DSP-1001660010695-A-H11


title: AB_8, Tumor_nochemo_controldiet

description: Library name: AB_8


title: scTCR_SCAF3564_36_7251_T3

description:
Library name: scTCR_SCAF3564_36_7251_T3
responder


title: UH000025_1-Day_S1_OVCAR3_ROI-011_Secretory

description: Library name: DSP-1001660010695-A-H09


title: AB_7, Tumor_nochemo_controldiet

description: Library name: AB_7


title: scTCR_SCAF3469_20_7251_T2

description:
Library name: scTCR_SCAF3469_20_7251_T2
responder


title: UH000025_1-Day_S1_OVCAR3_ROI-011_Ciliated

description: Library name: DSP-1001660010695-A-H08


title: UH000025_1-Day_S1_OVCAR3_ROI-010_Secretory

description: Library name: DSP-1001660010695-A-H07


title: AB_6, Tumor_nochemo_controldiet

description: Library name: AB_6


title: scTCR_SCAF3508_50_7248_T4

description:
Library name: scTCR_SCAF3508_50_7248_T4
responder


title: UH000025_1-Day_S1_FT240_ROI-009_Secretory

description: Library name: DSP-1001660010695-A-H05


title: UH000025_1-Day_S1_FT240_ROI-009_Ciliated

description: Library name: DSP-1001660010695-A-H04


title: AB_5, healthy_controldiet

description: Library name: AB_5


title: UH000025_1-Day_S1_FT240_ROI-008_Secretory

description: Library name: DSP-1001660010695-A-H03


title: AB_4, healthy_controldiet

description: Library name: AB_4


title: scTCR_SCAF3513_18_7248_T2

description:
Library name: scTCR_SCAF3513_18_7248_T2
responder


title: scTCR_SCAF3558_2_7248_T1

description:
Library name: scTCR_SCAF3558_2_7248_T1
responder


title: scTCR_SCAF3569_33_7246_T3

description:
Library name: scTCR_SCAF3569_33_7246_T3
responder


title: scTCR_SCAF3561_49_7246_T4

description:
Library name: scTCR_SCAF3561_49_7246_T4
responder


title: scTCR_SCAF3463_52_7251_T4_2

description:
Library name: scTCR_SCAF3463_52_7251_T4_2
responder


title: UH000025_1-Day_S1_PBS_ROI-004_Secretory

description: Library name: DSP-1001660010695-A-G07


title: UH000025_1-Day_S1_FT240_ROI-007_Ciliated

description: Library name: DSP-1001660010695-A-G12


title: UH000025_1-Day_S1_OVCAR3_ROI-005_Secretory

description: Library name: DSP-1001660010695-A-G09


title: AB_3, healthy_controldiet

description: Library name: AB_3


title: UH000025_1-Day_S1_FT240_ROI-006_Ciliated

description: Library name: DSP-1001660010695-A-G10


title: AB_1, healthy_controldiet

description: Library name: AB_1


title: Global KO, rep 3

city: Riverside

first: Anusha

last: Iyengar

address: 900 University Ave

institute: University of California, Riverside

data_processing:
Genome alignment (STAR), HTSeq
Assembly: Caenorhabditis_elegans.WBcel235.112
Supplementary files format and content: HTSeq count table containing number of counts for each gene for each library

organism: Caenorhabditis elegans

source_name: Whole worm

extract_protocol:
Zymo research direct-zol RNA mini prep kit
NEBNext poly(A) mRNA magnetic isolation, and NEBNext ultra RNA library prep kit for Illumina

value: Whole worm

value: untreated


title: UH000025_1-Day_S1_FT240_ROI-007_Secretory

description: Library name: DSP-1001660010695-A-H01


title: AB_2, healthy_controldiet

description: Library name: AB_2


title: UH000025_1-Day_S1_PBS_ROI-012_Ciliated

description: Library name: DSP-1001660010695-A-H10


title: UH000025_1-Day_S1_PBS_ROI-002_Secretory

description: Library name: DSP-1001660010695-A-G05


title: UH000025_1-Day_S1_FT240_ROI-006_Secretory

description: Library name: DSP-1001660010695-A-G11


title: UH000025_1-Day_S1_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660010695-A-G06


title: scTCR_SCAF3570_17_7246_T2

description:
Library name: scTCR_SCAF3570_17_7246_T2
responder


title: scRNAseq_SCAF3507_61_7262_T4

description:
Library name: scRNAseq_SCAF3507_61_7262_T4
non-responder


title: UH000025_1-Day_S1_PBS_ROI-001_Secretory

description: Library name: DSP-1001660010695-A-G03


title: Global KO, rep 2


title: Global KO, rep 1


title: scTCR_SCAF3567_34_72248_T3

description:
Library name: scTCR_SCAF3567_34_72248_T3
responder


title: scTCR_SCAF3563_1_7246_T1

description:
Library name: scTCR_SCAF3563_1_7246_T1
responder


title: UH000025_1-Day_S1_PBS_ROI-002_Ciliated

description: Library name: DSP-1001660010695-A-G04


title: UH000025_1-Day_S1_OVCAR3_ROI-010_Ciliated

description: Library name: DSP-1001660010695-A-H06


title: UH000025_1-Day_S1_OVCAR3_ROI-005_Ciliated

description: Library name: DSP-1001660010695-A-G08


title: UH000025_1-Day_S1_FT240_ROI-008_Ciliated

description: Library name: DSP-1001660010695-A-H02


title: UH000025_1-Day_S1_OVCAR3_ROI-00_Secretory

description: Library name: DSP-1001660010695-A-G01


title: scRNAseq_SCAF3554_45_7262_T3

description:
Library name: scRNAseq_SCAF3554_45_7262_T3
non-responder


title: scRNAseq_SCAF3519_29_7262_T2

description:
Library name: scRNAseq_SCAF3519_29_7262_T2
non-responder


title: scRNAseq_SCAF3512_13_7262_T1

description:
Library name: scRNAseq_SCAF3512_13_7262_T1
non-responder


title: UH000025_14-Day_S1_PBS_ROI-012_Secretory

description: Library name: DSP-1001660010695-A-F11


title: UH000025_14-Day_S1_PBS_ROI-011_Secretory

description: Library name: DSP-1001660010695-A-F10


title: UH000025_14-Day_S1_PBS_ROI-009_Secretory

description: Library name: DSP-1001660010695-A-F08


title: UH000025_14-Day_S1_PBS_ROI-010_Secretory

description: Library name: DSP-1001660010695-A-F09


title: scRNAseq_SCAF3470_60_7261_T4

description:
Library name: scRNAseq_SCAF3470_60_7261_T4
non-responder


title: UH000025_1-Day_S1_PBS_ROI-001_Ciliated

description: Library name: DSP-1001660010695-A-G02


title: Muscle KO, rep 3


title: UH000025_14-Day_S1_FT240_ROI-008_Secretory

description: Library name: DSP-1001660010695-A-F07


title: UH000025_14-Day_S1_FT240_ROI-008_Ciliated

description: Library name: DSP-1001660010695-A-F06


title: Pan neuronal KO, rep 3


title: Muscle KO, rep 2


title: scRNAseq_SCAF3478_28_7261_T2

description:
Library name: scRNAseq_SCAF3478_28_7261_T2
non-responder


title: Pan neuronal KO, rep 1


title: UH000025_14-Day_S1_FT240_ROI-005_Secretory

description: Library name: DSP-1001660010695-A-F01


title: UH000025_14-Day_S1_FT240_ROI-007_Ciliated

description: Library name: DSP-1001660010695-A-F04


title: UH000025_14-Day_S1_FT240_ROI-007_Secretory

description: Library name: DSP-1001660010695-A-F05


title: UH000025_14-Day_S1_FT240_ROI-005_Ciliated

description: Library name: DSP-1001660010695-A-E12


title: scRNAseq_SCAF3462_44_7261_T3_2

description:
Library name: scRNAseq_SCAF3462_44_7261_T3_2
non-responder


title: UH000025_14-Day_S1_FT240_ROI-006_Secretory

description: Library name: DSP-1001660010695-A-F03


title: scRNAseq_SCAF3480_12_7261_T1

description:
Library name: scRNAseq_SCAF3480_12_7261_T1
non-responder


title: Muscle KO, rep 1


title: UH000025_14-Day_S1_FT240_ROI-006_Ciliated

description: Library name: DSP-1001660010695-A-F02


title: Intestinal KO, rep 3


title: UH000025_14-Day_S1_OVCAR3_ROI-004_Secretory

description: Library name: DSP-1001660010695-A-E11


title: UH000025_1-Day_S1_OVCAR3_ROI-00_Ciliated

description: Library name: DSP-1001660010695-A-F12


title: UH000025_14-Day_S1_OVCAR3_ROI-004_Ciliated

description: Library name: DSP-1001660010695-A-E10


title: Intestinal KO, rep 1


title: scRNAseq_SCAF3405_19_7249_T2

description:
Library name: scRNAseq_SCAF3405_19_7249_T2
non-responder


title: UH000025_14-Day_S1_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660010695-A-E09


title: scRNAseq_SCAF3559_51_7249_T4

description:
Library name: scRNAseq_SCAF3559_51_7249_T4
non-responder


title: UH000025_14-Day_S1_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660010695-A-E07


title: UH000025_14-Day_S1_OVCAR3_ROI-002_Ciliated

description: Library name: DSP-1001660010695-A-E06


title: WT, rep 3


title: UH000025_14-Day_S1_OVCAR3_ROI-003_Ciliated

description: Library name: DSP-1001660010695-A-E08


title: scRNAseq_SCAF3510_3_7249_T1

description:
Library name: scRNAseq_SCAF3510_3_7249_T1
non-responder


title: UH000025_14-Day_S1_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660010695-A-E05


title: WT, rep 2


title: UH00006_1-Day_S1_PBS_ROI-009_Secretory

description: Library name: DSP-1001660010695-A-E03


title: WT, rep 1


title: UH000025_14-Day_S1_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660010695-A-E04


title: scRNAseq_SCAF3471_57_7257_T4

description:
Library name: scRNAseq_SCAF3471_57_7257_T4
non-responder


title: UH00006_1-Day_S1_PBS_ROI-008_Secretory

description: Library name: DSP-1001660010695-A-E01


type: RNA

city: TLALPAN

first: SALVADOR

middle: GARCIA

last: CARMONA

state: CIUDAD DE MÉXICO

address: Calz. de Tlalpan 4502

department: INVESTIGACION

country: Mexico

institute: INSTITUTO NACIONAL DE ENFERMEDADES RESPIRATORIAS

description: Cell-free genomic DNA of induced sputum from without COPD subject 96

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina EPIC Infinium Methylation microarray Beadchip using standard Illumina protocol

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

data_processing: The whole process of the data obtained from the microarray from the intensity data files (IDAT), the quality control of the intensity detection values, the elimination of non-hybridized probes and the results of differentially methylated sites were analyzed using the Rstudio environment version 3.5. 1, using different packages installed in Rstudio, for data normalization and differentially methylated sites analysis the limma package was used implementing a quantile normalization procedure, generating M values and B values used for statistical analysis of methylation data and data visualization. Comparison between the methylation of the 2 groups included in the study was performed by analyzing the m-value matrix in limma obtaining moderated t-statistics and associated p-values for each CpG site by adjusting the p-values for multiple testing, the data obtained in the study were exported from the Rstudio environment as csv files.

label: Cy3 and Cy5

source_name: induced sputum

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was isolated with the Blood DNA Preparation - Solution Kit, Jena Bioscience (Jena, Germany).

value: induced sputum

tag: Sex

value: Famale

value: induced sputum cells

tag: disease state

value: without COPD subject 96


title: scRNAseq_SCAF3515_41_7257_T3

description:
Library name: scRNAseq_SCAF3515_41_7257_T3
non-responder

value: Blood


description: Cell-free genomic DNA of induced sputum from without COPD subject 95

value: without COPD subject 95


title: UH00006_1-Day_S1_PBS_ROI-008_Ciliated

description: Library name: DSP-1001660010695-A-D12

value: Ciliated


title: UH00006_1-Day_S1_PBS_ROI-007_Secretory

description: Library name: DSP-1001660010695-A-D11

value: Secretory


title: scRNAseq_SCAF3514_25_7257_T2

description:
Library name: scRNAseq_SCAF3514_25_7257_T2
non-responder


title: UH00006_1-Day_S1_PBS_ROI-007_Ciliated

description: Library name: DSP-1001660010695-A-D10


title: UH00006_1-Day_S1_FT240_ROI-006_Secretory

description: Library name: DSP-1001660010695-A-D09


title: Intestinal KO, rep 2


title: scRNAseq_SCAF3520_35_7249_T3

description:
Library name: scRNAseq_SCAF3520_35_7249_T3
non-responder


description: Cell-free genomic DNA of induced sputum from without COPD subject 92

value: without COPD subject 92


title: UH00006_1-Day_S1_FT240_ROI-006_Ciliated

description: Library name: DSP-1001660010695-A-D08


title: scRNAseq_SCAF3556_9_7257_T1

description:
Library name: scRNAseq_SCAF3556_9_7257_T1
non-responder


description: Cell-free genomic DNA of induced sputum from without COPD subject 91

value: without COPD subject 91


title: UH00006_1-Day_S1_FT240_ROI-005_Secretory

description: Library name: DSP-1001660010695-A-D07


title: scRNAseq_SCAF3555_56_7256_T4

description:
Library name: scRNAseq_SCAF3555_56_7256_T4
non-responder


title: UH00006_1-Day_S1_FT240_ROI-005_Ciliated

description: Library name: DSP-1001660010695-A-D06


description: Cell-free genomic DNA of induced sputum from without COPD subject 90

value: without COPD subject 90


title: UH00006_1-Day_S1_FT240_ROI-004_Secretory

description: Library name: DSP-1001660010695-A-D05


title: UH00006_1-Day_S1_PBS_ROI-009_Ciliated

description: Library name: DSP-1001660010695-A-E02

value: PBS


title: UH00006_1-Day_S1_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660010695-A-D03


description: Cell-free genomic DNA of induced sputum from without COPD subject 89

value: without COPD subject 89


title: UH00006_1-Day_S1_OVCAR3_ROI-003_Ciliated

description: Library name: DSP-1001660010695-A-D02


title: UH00006_1-Day_S1_OVCAR3_ROI-002_Ciliated

description: Library name: DSP-1001660010695-A-C12


title: induced sputum from COPD patient 87

description: Cell-free genomic DNA of induced sputum from COPD patient 87

value: COPD patient 87


title: scRNAseq_SCAF3557_46_7263_T3

description:
Library name: scRNAseq_SCAF3557_46_7263_T3
non-responder


title: UH00006_1-Day_S1_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660010695-A-C11


title: UH00006_1-Day_S1_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660010695-A-D01


title: UH00006_14-Day_S1_PBS_ROI-009_Ciliated

description: Library name: DSP-1001660010695-A-C08


title: UH00006_1-Day_S1_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660010695-A-C10


title: scRNAseq_SCAF3509_8_7256_T1

description:
Library name: scRNAseq_SCAF3509_8_7256_T1
non-responder


title: scRNAseq_SCAF3551_30_7263_T2

description:
Library name: scRNAseq_SCAF3551_30_7263_T2
non-responder


title: induced sputum from COPD patient 86

description: Cell-free genomic DNA of induced sputum from COPD patient 86

value: COPD patient 86


title: scRNAseq_SCAF3468_24_7256_T2

description:
Library name: scRNAseq_SCAF3468_24_7256_T2
non-responder


title: UH00006_14-Day_S1_PBS_ROI-008_Ciliated

description: Library name: DSP-1001660010695-A-C06


title: scRNAseq_SCAF3479_14_7263_T1

description:
Library name: scRNAseq_SCAF3479_14_7263_T1
non-responder


title: UH00006_1-Day_S1_FT240_ROI-004_Ciliated

description: Library name: DSP-1001660010695-A-D04


title: scRNAseq_SCAF3516_40_7256_T3

description:
Library name: scRNAseq_SCAF3516_40_7256_T3
non-responder


title: induced sputum from COPD patient 82

description: Cell-free genomic DNA of induced sputum from COPD patient 82

value: COPD patient 82


title: scRNAseq_SCAF3518_59_7259_T4

description:
Library name: scRNAseq_SCAF3518_59_7259_T4
non-responder


title: UH00006_14-Day_S1_PBS_ROI-007_Secretory

description: Library name: DSP-1001660010695-A-C05


title: induced sputum from COPD patient 84

description: Cell-free genomic DNA of induced sputum from COPD patient 84

value: COPD patient 84


title: UH00006_14-Day_S1_PBS_ROI-008_Secretory

description: Library name: DSP-1001660010695-A-C07


title: UH00006_14-Day_S1_PBS_ROI-007_Ciliated

description: Library name: DSP-1001660010695-A-C04


title: induced sputum from COPD patient 88

description: Cell-free genomic DNA of induced sputum from COPD patient 88

value: induced sputum

value: COPD patient 88


title: induced sputum from COPD patient 81

description: Cell-free genomic DNA of induced sputum from COPD patient 81

value: Famale

value: induced sputum cells

value: COPD patient 81


title: scRNAseq_SCAF3475_43_7259_T3

description:
Library name: scRNAseq_SCAF3475_43_7259_T3
non-responder

value: Blood


title: UH00006_14-Day_S1_FT240_ROI-006_Secretory

description: Library name: DSP-1001660010695-A-C03


title: UH00006_14-Day_S1_FT240_ROI-006_Ciliated

description: Library name: DSP-1001660010695-A-C02

value: Ciliated


title: UH00006_14-Day_S1_FT240_ROI-005_Secretory

description: Library name: DSP-1001660010695-A-C01

value: Secretory


description: Cell-free genomic DNA of induced sputum from without COPD subject 80

value: without COPD subject 80


title: scRNAseq_SCAF3553_27_7259_T2

description:
Library name: scRNAseq_SCAF3553_27_7259_T2
non-responder


title: UH00006_14-Day_S1_FT240_ROI-005_Ciliated

description: Library name: DSP-1001660010695-A-B12


title: UH00006_14-Day_S1_PBS_ROI-009_Secretory

description: Library name: DSP-1001660010695-A-C09


title: UH00006_14-Day_S1_FT240_ROI-004_Secretory

description: Library name: DSP-1001660010695-A-B11


description: Cell-free genomic DNA of induced sputum from without COPD subject 79

value: without COPD subject 79


title: scRNAseq_SCAF3404_11_7259_T1

description:
Library name: scRNAseq_SCAF3404_11_7259_T1
non-responder


title: UH00006_14-Day_S1_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660010695-A-B09


description: Cell-free genomic DNA of induced sputum from without COPD subject 78

value: without COPD subject 78


title: UH00006_14-Day_S1_OVCAR3_ROI-003_Ciliated

description: Library name: DSP-1001660010695-A-B08


title: scRNAseq_SCAF3047_39_7255_3

description:
Library name: scRNAseq_SCAF3047_39_7255_3
non-responder


title: UH00006_14-Day_S1_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660010695-A-B07


title: scRNAseq_SCAF3511_55_7255_T4

description:
Library name: scRNAseq_SCAF3511_55_7255_T4
non-responder


description: Cell-free genomic DNA of induced sputum from without COPD subject 76

value: without COPD subject 76


title: UH00006_14-Day_S1_OVCAR3_ROI-002_Ciliated

description: Library name: DSP-1001660010695-A-B06


description: Cell-free genomic DNA of induced sputum from without COPD subject 77

value: without COPD subject 77


title: UH00006_14-Day_S1_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660010695-A-B04


title: scRNAseq_SCAF3477_23_7255_T2

description:
Library name: scRNAseq_SCAF3477_23_7255_T2
non-responder


title: UH00006_14-Day_S1_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660010695-A-B05


description: Cell-free genomic DNA of induced sputum from without COPD subject 75

value: without COPD subject 75


title: scRNAseq_SCAF3473_7_7255_T1

description:
Library name: scRNAseq_SCAF3473_7_7255_T1
non-responder


title: scRNAseq_SCAF3522_54_7254_T4

description:
Library name: scRNAseq_SCAF3522_54_7254_T4
non-responder


title: UH00006_14-Day_S2_FT240_ROI-006_Secretory

description: Library name: DSP-1001660010695-A-B01


title: UH00006_14-Day_S2_FT240_ROI-007_Secretory

description: Library name: DSP-1001660010695-A-B03


title: UH00006_14-Day_S2_FT240_ROI-006_Ciliated

description: Library name: DSP-1001660010695-A-A12


description: Cell-free genomic DNA of induced sputum from without COPD subject 73

value: without COPD subject 73


title: UH00006_14-Day_S2_FT240_ROI-005_Secretory

description: Library name: DSP-1001660010695-A-A11


title: UH00006_14-Day_S2_FT240_ROI-007_Ciliated

description: Library name: DSP-1001660010695-A-B02


title: scRNAseq_SCAF3464_38_7254_T3_2

description:
Library name: scRNAseq_SCAF3464_38_7254_T3_2
non-responder


title: UH00006_14-Day_S2_FT240_ROI-005_Ciliated

description: Library name: DSP-1001660010695-A-A10


title: UH00006_14-Day_S2_OVCAR3_ROI-004_Secretory

description: Library name: DSP-1001660010695-A-A09


title: induced sputum from COPD patient 71

description: Cell-free genomic DNA of induced sputum from COPD patient 71

value: COPD patient 71


title: scRNAseq_SCAF3406_22_7254_T2

description:
Library name: scRNAseq_SCAF3406_22_7254_T2
non-responder


title: UH00006_14-Day_S1_FT240_ROI-004_Ciliated

description: Library name: DSP-1001660010695-A-B10


title: induced sputum from COPD patient 70

description: Cell-free genomic DNA of induced sputum from COPD patient 70

value: COPD patient 70


title: UH00006_14-Day_S2_OVCAR3_ROI-003_Ciliated

description: Library name: DSP-1001660010695-A-A06


title: scRNAseq_SCAF3521_6_7254_T1

description:
Library name: scRNAseq_SCAF3521_6_7254_T1
non-responder


title: induced sputum from COPD patient 69

description: Cell-free genomic DNA of induced sputum from COPD patient 69

value: induced sputum

value: COPD patient 69


title: UH00006_14-Day_S2_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660010695-A-A07


title: Pan neuronal KO, rep 2

value: Whole worm

value: untreated


title: scRNAseq_SCAF3461_64_7265_T4_2

description:
Library name: scRNAseq_SCAF3461_64_7265_T4_2
responder


title: UH00006_14-Day_S2_OVCAR3_ROI-002_Ciliated

description: Library name: DSP-1001660010695-A-A04


title: UH00006_14-Day_S2_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660010695-A-A05


title: scRNAseq_SCAF3466_48_7265_T3

description:
Library name: scRNAseq_SCAF3466_48_7265_T3
responder


title: UH00006_14-Day_S2_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660010695-A-A03


title: induced sputum from COPD patient 68

description: Cell-free genomic DNA of induced sputum from COPD patient 68

value: Famale

value: induced sputum cells

value: COPD patient 68


title: UH00006_14-Day_S2_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660010695-A-A02

value: Ciliated


description: Cell-free genomic DNA of induced sputum from without COPD subject 74

value: without COPD subject 74


title: induced sputum from COPD patient 67

description: Cell-free genomic DNA of induced sputum from COPD patient 67

value: COPD patient 67


title: scRNAseq_SCAF3517_32_7265_T2

description:
Library name: scRNAseq_SCAF3517_32_7265_T2
responder

value: Blood


title: DSP-1001660010695_NTC

description: Library name: DSP-1001660010695-A-A01

value: NTC


title: 461-27304_14-Day_S4_PBS_ROI-011_Secretory

description: Library name: DSP-1001660005136-B-H03

value: PBS

value: Secretory


title: 461-27304_14-Day_S4_OVCAR3_ROI-010_Secretory

description: Library name: DSP-1001660005136-B-H02


title: scRNAseq_SCAF3048_16_7265_1

description:
Library name: scRNAseq_SCAF3048_16_7265_1
responder


title: 461-27304_14-Day_S4_OVCAR3_ROI-010_Ciliated

description: Library name: DSP-1001660005136-B-H01


title: 461-27304_14-Day_S4_PBS_ROI-009_Secretory

description: Library name: DSP-1001660005136-B-G12


title: UH00006_14-Day_S2_OVCAR3_ROI-004_Ciliated

description: Library name: DSP-1001660010695-A-A08


title: scRNAseq_SCAF3474_63_7264_T4

description:
Library name: scRNAseq_SCAF3474_63_7264_T4
responder


title: 461-27304_14-Day_S4_PBS_ROI-008_Secretory

description: Library name: DSP-1001660005136-B-G10


description: Cell-free genomic DNA of induced sputum from without COPD subject 64

value: without COPD subject 64


title: 461-27304_14-Day_S4_PBS_ROI-008_Ciliated

description: Library name: DSP-1001660005136-B-G09


title: scRNAseq_SCAF3476_47_7264_T3

description:
Library name: scRNAseq_SCAF3476_47_7264_T3
responder


title: 461-27304_14-Day_S4_PBS_ROI-007_Secretory

description: Library name: DSP-1001660005136-B-G08


description: Cell-free genomic DNA of induced sputum from without COPD subject 63

value: without COPD subject 63


description: Cell-free genomic DNA of induced sputum from without COPD subject 62

value: without COPD subject 62


title: scRNAseq_SCAF3046_31_7264_2

description:
Library name: scRNAseq_SCAF3046_31_7264_2
responder


title: 461-27304_14-Day_S4_PBS_ROI-007_Ciliated

description: Library name: DSP-1001660005136-B-G07


title: induced sputum from COPD patient 66

description: Cell-free genomic DNA of induced sputum from COPD patient 66

value: induced sputum

value: COPD patient 66


title: scRNAseq_SCAF3562_58_7258_T4

description:
Library name: scRNAseq_SCAF3562_58_7258_T4
responder


title: 461-27304_14-Day_S4_FT240_ROI-005_Secretory

description: Library name: DSP-1001660005136-B-G04


title: 461-27304_14-Day_S4_FT240_ROI-005_Ciliated

description: Library name: DSP-1001660005136-B-G03


title: 461-27304_14-Day_S4_FT240_ROI-006_Ciliated

description: Library name: DSP-1001660005136-B-G05


title: 461-27304_14-Day_S4_FT240_ROI-004_Ciliated

description: Library name: DSP-1001660005136-B-G01


title: 461-27304_14-Day_S4_FT240_ROI-004_Secretory

description: Library name: DSP-1001660005136-B-G02


description: Cell-free genomic DNA of induced sputum from without COPD subject 61

value: without COPD subject 61


title: 461-27304_14-Day_S4_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660005136-B-F12


title: scRNAseq_SCAF3472_42_7258_T3

description:
Library name: scRNAseq_SCAF3472_42_7258_T3
responder


description: Cell-free genomic DNA of induced sputum from without COPD subject 59

value: without COPD subject 59


title: 461-27304_14-Day_S4_FT240_ROI-006_Secretory

description: Library name: DSP-1001660005136-B-G06


title: scRNAseq_SCAF3565_26_7258_T2

description:
Library name: scRNAseq_SCAF3565_26_7258_T2
responder


title: 461-27304_14-Day_S4_PBS_ROI-009_Ciliated

description: Library name: DSP-1001660005136-B-G11


description: Cell-free genomic DNA of induced sputum from without COPD subject 60

value: Famale

value: without COPD subject 60


title: induced sputum from COPD patient 65

description: Cell-free genomic DNA of induced sputum from COPD patient 65

value: induced sputum cells

value: COPD patient 65


title: 461-27304_14-Day_S4_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660005136-B-F10


description: Cell-free genomic DNA of induced sputum from without COPD subject 58

value: without COPD subject 58


title: 461-27304_14-Day_S4_OVCAR3_ROI-002_Ciliated

description: Library name: DSP-1001660005136-B-F09

value: Ciliated


title: scRNAseq_SCAF3403_10_7258_T1

description:
Library name: scRNAseq_SCAF3403_10_7258_T1
responder

value: Blood


title: 461-27304_14-Day_S4_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660005136-B-F08


description: Cell-free genomic DNA of induced sputum from without COPD subject 57

value: without COPD subject 57


title: 461-27304_14-Day_S3_PBS_ROI-010_Secretory

description: Library name: DSP-1001660005136-B-F07

value: PBS


title: scRNAseq_SCAF3560_53_7252_T4

description:
Library name: scRNAseq_SCAF3560_53_7252_T4
responder


title: scRNAseq_SCAF3467_15_7264_T1

description:
Library name: scRNAseq_SCAF3467_15_7264_T1
responder


title: 461-27304_14-Day_S3_PBS_ROI-010_Ciliated

description: Library name: DSP-1001660005136-B-F06


title: induced sputum from COPD patient 56

description: Cell-free genomic DNA of induced sputum from COPD patient 56

value: COPD patient 56


title: scRNAseq_SCAF3566_37_7252_T3

description:
Library name: scRNAseq_SCAF3566_37_7252_T3
responder


title: induced sputum from COPD patient 55

description: Cell-free genomic DNA of induced sputum from COPD patient 55

value: COPD patient 55


title: scRNAseq_SCAF3045_21_7252_2

description:
Library name: scRNAseq_SCAF3045_21_7252_2
responder


title: 461-27304_14-Day_S3_PBS_ROI-008_Secretory

description: Library name: DSP-1001660005136-B-F03

value: Secretory


title: induced sputum from COPD patient 54

description: Cell-free genomic DNA of induced sputum from COPD patient 54

value: COPD patient 54


title: 461-27304_14-Day_S3_PBS_ROI-008_Ciliated

description: Library name: DSP-1001660005136-B-F02


title: 461-27304_14-Day_S3_FT240_ROI-007_Secretory

description: Library name: DSP-1001660005136-B-F01


title: induced sputum from COPD patient 53

description: Cell-free genomic DNA of induced sputum from COPD patient 53

value: induced sputum

value: COPD patient 53


title: scRNAseq_SCAF3552_5_7252_T1

description:
Library name: scRNAseq_SCAF3552_5_7252_T1
responder


title: 461-27304_14-Day_S3_FT240_ROI-007_Ciliated

description: Library name: DSP-1001660005136-B-E12


title: 461-27304_14-Day_S3_FT240_ROI-006_Secretory

description: Library name: DSP-1001660005136-B-E11


title: scRNAseq_SCAF3463_52_7251_T4_2

description:
Library name: scRNAseq_SCAF3463_52_7251_T4_2
responder


title: 461-27304_14-Day_S3_FT240_ROI-006_Ciliated

description: Library name: DSP-1001660005136-B-E10


title: 461-27304_14-Day_S3_PBS_ROI-009_Ciliated

description: Library name: DSP-1001660005136-B-F04


title: scRNAseq_SCAF3564_36_7251_T3

description:
Library name: scRNAseq_SCAF3564_36_7251_T3
responder


title: induced sputum from COPD patient 52

description: Cell-free genomic DNA of induced sputum from COPD patient 52

value: COPD patient 52


title: 461-27304_14-Day_S3_FT240_ROI-005_Ciliated

description: Library name: DSP-1001660005136-B-E08


title: 461-27304_14-Day_S3_FT240_ROI-005_Secretory

description: Library name: DSP-1001660005136-B-E09


title: induced sputum from COPD patient 51

description: Cell-free genomic DNA of induced sputum from COPD patient 51

value: COPD patient 51


title: scRNAseq_SCAF3469_20_7251_T2

description:
Library name: scRNAseq_SCAF3469_20_7251_T2
responder


title: 461-27304_14-Day_S3_FT240_ROI-004_Ciliated

description: Library name: DSP-1001660005136-B-E06


title: 461-27304_14-Day_S4_OVCAR3_ROI-003_Ciliated

description: Library name: DSP-1001660005136-B-F11


title: 461-27304_14-Day_S3_FT240_ROI-004_Secretory

description: Library name: DSP-1001660005136-B-E07


title: 461-27304_14-Day_S3_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660005136-B-E05


title: induced sputum from COPD patient 50

description: Cell-free genomic DNA of induced sputum from COPD patient 50

value: Famale

value: COPD patient 50


title: scRNAseq_SCAF3568_4_7251_T1

description:
Library name: scRNAseq_SCAF3568_4_7251_T1
responder


title: 461-27304_14-Day_S3_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660005136-B-E04


title: 461-27304_14-Day_S3_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660005136-B-E03


title: 461-27304_14-Day_S3_PBS_ROI-009_Secretory

description: Library name: DSP-1001660005136-B-F05


title: induced sputum from COPD patient 49

description: Cell-free genomic DNA of induced sputum from COPD patient 49

value: induced sputum cells

value: COPD patient 49


description: Cell-free genomic DNA of induced sputum from without COPD subject 48

value: without COPD subject 48


title: scRNAseq_SCAF3567_34_72248_T3

description:
Library name: scRNAseq_SCAF3567_34_72248_T3
responder


description: Cell-free genomic DNA of induced sputum from without COPD subject 47

value: without COPD subject 47


title: 461-27304_1-Day_S2_OVCAR3_ROI-008_Ciliated

description: Library name: DSP-1001660005136-B-D12

value: Ciliated


title: scRNAseq_SCAF3513_18_7248_T2

description:
Library name: scRNAseq_SCAF3513_18_7248_T2
responder

value: Blood


title: 461-27304_1-Day_S2_OVCAR3_ROI-008_Secretory

description: Library name: DSP-1001660005136-B-E01


title: 461-27304_1-Day_S2_OVCAR3_ROI-007_Secretory

description: Library name: DSP-1001660005136-B-D11


description: Cell-free genomic DNA of induced sputum from without COPD subject 46

value: without COPD subject 46


title: scRNAseq_SCAF3558_2_7248_T1

description:
Library name: scRNAseq_SCAF3558_2_7248_T1
responder


title: 461-27304_1-Day_S2_OVCAR3_ROI-007_Ciliated

description: Library name: DSP-1001660005136-B-D10


title: 461-27304_1-Day_S2_PBS_ROI-006_Secretory

description: Library name: DSP-1001660005136-B-D09

value: PBS


title: 461-27304_1-Day_S2_PBS_ROI-006_Ciliated

description: Library name: DSP-1001660005136-B-D08


title: 461-27304_1-Day_S2_PBS_ROI-005_Secretory

description: Library name: DSP-1001660005136-B-D07


title: scRNAseq_SCAF3508_50_7248_T4

description:
Library name: scRNAseq_SCAF3508_50_7248_T4
responder


description: Cell-free genomic DNA of induced sputum from without COPD subject 44

value: without COPD subject 44


description: Cell-free genomic DNA of induced sputum from without COPD subject 43

value: without COPD subject 43


title: 461-27304_1-Day_S2_PBS_ROI-005_Ciliated

description: Library name: DSP-1001660005136-B-D06


title: scRNAseq_SCAF3561_49_7246_T4

description:
Library name: scRNAseq_SCAF3561_49_7246_T4
responder


title: 461-27304_14-Day_S3_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660005136-B-E02


title: scRNAseq_SCAF3569_33_7246_T3

description:
Library name: scRNAseq_SCAF3569_33_7246_T3
responder


description: Cell-free genomic DNA of induced sputum from without COPD subject 42

value: without COPD subject 42


title: scRNAseq_SCAF3570_17_7246_T2

description:
Library name: scRNAseq_SCAF3570_17_7246_T2
responder


title: 461-27304_1-Day_S2_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660005136-B-D04


title: 461-27304_1-Day_S3_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660005136-B-D02


title: 461-27304_1-Day_S3_FT240_ROI-003_Secretory

description: Library name: DSP-1001660005136-B-D03

value: Secretory


description: Cell-free genomic DNA of induced sputum from without COPD subject 41

value: induced sputum

value: without COPD subject 41


title: scRNAseq_SCAF3563_1_7246_T1

description:
Library name: scRNAseq_SCAF3563_1_7246_T1
responder


title: 461-27304_1-Day_S3_FT240_ROI-002_Ciliated

description: Library name: DSP-1001660005136-B-C12


title: 461-27304_1-Day_S3_FT240_ROI-001_Secretory

description: Library name: DSP-1001660005136-B-C11


title: 461-27304_1-Day_S3_FT240_ROI-002_Secretory

description: Library name: DSP-1001660005136-B-D01


title: ND630_4_S8

city: Minneapolis

first: Michael

last: Zaiken

state: MN

address: East River Parkway

department: Pediatrics

institute: University of Minnesota

description: Library name: Sample 8

data_processing:
FASTQ reads were entered into the Collection of Hierarchical UMII/RIS Pipelines for quality control, trimming, confirming viability, aligning reads using HISAT2, filtering alignments using SAMtools and generating output matrices using Subread FeatureCounts.
Assembly: mm10 (GRCm38)
Supplementary files format and content: tab-delineated-text file includes raw counts for each sample

source_name: T Regulatory Cells

growth_protocol: Human Treg (CD4+CD25hiCD127loCD45RA+) were sorted from leukapheresis products (Memorial Blood Center, St. Paul, MN). Sorted cells were incubated with irradiated K562 cells line (KT86/64) as previously described(2). Treg were cultured in XVivo-15 medium (Lonza) containing 10% human serum (Valley Biomedical), 1x Pen/Strep and GlutaMAX (Thermo), N-acetyl cysteine (USP), and rH-IL-2 (300 IU/mL).

extract_protocol:
Qiagen RNAeasy Plus Kit
Takara Bio’s SMARTer Stranded Total RNA-Seq–Pico Mammalian Kit v2

value: T Regulatory Cells

value: WT

tag: batch


title: ND630_3_S7

description: Library name: Sample 7


title: ND630_2_S6

description: Library name: Sample 6


title: 461-27304_14-Day_S5_PBS_ROI-009_Secretory

description: Library name: DSP-1001660005136-B-C09


title: induced sputum from COPD patient 37

description: Cell-free genomic DNA of induced sputum from COPD patient 37

value: Famale

value: COPD patient 37


title: 461-27304_14-Day_S5_PBS_ROI-008_Secretory

description: Library name: DSP-1001660005136-B-C07


title: 461-27304_14-Day_S5_PBS_ROI-008_Ciliated

description: Library name: DSP-1001660005136-B-C06


title: 461-27304_14-Day_S5_FT240_ROI-007_Ciliated

description: Library name: DSP-1001660005136-B-C04


title: 461-27304_14-Day_S5_PBS_ROI-009_Ciliated

description: Library name: DSP-1001660005136-B-C08


title: induced sputum from COPD patient 36

description: Cell-free genomic DNA of induced sputum from COPD patient 36

value: induced sputum cells

value: COPD patient 36


title: ND630_1_S5

description: Library name: Sample 5


title: 461-27304_14-Day_S5_FT240_ROI-007_Secretory

description: Library name: DSP-1001660005136-B-C05


title: DMSO_4_S4

description: Library name: Sample 4

value: DMSO


title: induced sputum from COPD patient 35

description: Cell-free genomic DNA of induced sputum from COPD patient 35

value: COPD patient 35


title: induced sputum from COPD patient 38

description: Cell-free genomic DNA of induced sputum from COPD patient 38

value: COPD patient 38


title: DMSO_3_S3

description: Library name: Sample 3


title: 461-27304_14-Day_S5_FT240_ROI-005_Secretory

description: Library name: DSP-1001660005136-B-C01


title: 461-27304_14-Day_S5_FT240_ROI-006_Ciliated

description: Library name: DSP-1001660005136-B-C02

value: Ciliated


title: 461-27304_14-Day_S5_FT240_ROI-005_Ciliated

description: Library name: DSP-1001660005136-B-B12


title: induced sputum from COPD patient 34

description: Cell-free genomic DNA of induced sputum from COPD patient 34

value: COPD patient 34


title: induced sputum from COPD patient 40

description: Cell-free genomic DNA of induced sputum from COPD patient 40

value: COPD patient 40


title: 461-27304_14-Day_S5_FT240_ROI-004_Secretory

description: Library name: DSP-1001660005136-B-B11


title: induced sputum from COPD patient 39

description: Cell-free genomic DNA of induced sputum from COPD patient 39

value: COPD patient 39


title: 461-27304_1-Day_S3_FT240_ROI-001_Ciliated

description: Library name: DSP-1001660005136-B-C10


title: DMSO_2_S2

description: Library name: Sample 2


title: 461-27304_14-Day_S5_FT240_ROI-004_Ciliated

description: Library name: DSP-1001660005136-B-B10


title: induced sputum from COPD patient 33

description: Cell-free genomic DNA of induced sputum from COPD patient 33

value: COPD patient 33


description: Cell-free genomic DNA of induced sputum from without COPD subject 32

value: without COPD subject 32


title: DMSO_1_S1

description: Library name: Sample 1


title: 461-27304_14-Day_S5_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660005136-B-B07

value: Secretory


title: 461-27304_14-Day_S5_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660005136-B-B08


title: ME11_Facial_10um_RNA

city: Philadelphia

first: Hongxiang

last: Fu

state: PA

address: 3501 Civic Center Blvd

institute: University of Pennsylvania

description: Library name: SpMETSLE23R

data_processing:
For RNA sequencing data, we refined read 2 to extract barcode A, barcode B, and the Unique Molecular Identifier (UMI). Using the Spatial Transcriptomics (ST) pipeline version 1.7.2, this processed data was mapped against the appropriate mouse (mm10) genome references. The gene matrix was then read into Seurat v.5.1.0 as a Seurat object. For DNA methylation sequencing data, we first trimmed adaptors and demultiplexed the fastq files. Biscuit was then used to align to the mouse (mm10) genome references, and CG/CH levels were called. MethSCAn was used to identify variable methylation regions. The methylation level and residual matrices were then read into Seurat v.5.1.0 as Seurat objects for downstream analysis.
Assembly: mm10
Supplementary files format and content: File format: rds. Content: Seurat object that contains RNA counts, VMR methylation levels, methylation residuals matrices

source_name: Embryo

extract_protocol:
Frozen tissue slides were thawed at 37°C for 2 minutes, fixed with 1% formaldehyde in PBS with RNase inhibitor for 10 minutes, and quenched with glycine for 5 minutes. The tissue was washed with DPBS-RI and DI water, then permeabilized with Triton X-100 and RNase inhibitor for 30 minutes. After washing with DPBS-RI, the tissue was treated with HCl to disrupt protein structure and remove histones, then washed with a buffer containing RNase inhibitor. A transposition mixture was added and incubated at 37°C for 60 minutes twice. The reaction was stopped with EDTA and RNase inhibitor, and the tissue was washed with NEB3.1 buffer and DPBS-RI before proceeding to the in-situ reverse transcription reaction. mRNAs were then captured by the biotinylated RT-primer (poly-dT primer with UMIs and a universal linker sequence, followed by reverse transcription to synthesize the complementary DNA (cDNA). Both genomic fragments and cDNA in the tissue were then ligated to spatial barcodes A and B sequentially. Barcoded gDNA fragments and cDNA were then released after reverse crosslinking. Afterward, the biotin-labeled cDNA was enriched by the streptavidin bead and separated from the gDNA-contained supernatant.
cDNA was followed by template switching, and the cDNA library construction, whereas, gDNA was followed by Enzymatic Methyl-seq conversion, splint ligation, and DNA library construction. In brief, 200 µl of supernatant was collected for methylated gDNA detection and library construction. The supernatant was purified and eluted in 84 µl of nuclease-free water. The Enzymatic Methylation-seq Conversion module was used to convert unmethylated cytosines to uracil. The DNA sample was divided into PCR tubes, and a TET2 reaction mixture was added. After incubation at 37°C, the sample was purified with SPRI beads and eluted. The separated beads containing cDNA were used to generate a cDNA library. Beads were washed, then incubated in a TSO solution with agitation at room temperature and 42°C. PCR was run, and the clear PCR solution was transferred to qPCR tubes with Evagreen dye. After qPCR, the amplified product was purified with SPRI beads and eluted in nuclease-free water. The Nextera XT DNA Library Prep Kit was used for cDNA library preparation.
Library Strategy: Spatial-DMT-seq (Spatial DNA Methylation and RNA Transcriptomic Sequencing)

value: Embryo


title: 461-27304_14-Day_S5_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660005136-B-B06


title: 461-27304_14-Day_S3_OVCAR3_ROI-009_Secretory

description: Library name: DSP-1001660005136-B-B05


title: ME11_Facial_10um_DNAm

description: Library name: SpMETSLE23D


description: Cell-free genomic DNA of induced sputum from without COPD subject 30

value: induced sputum

value: without COPD subject 30


title: 461-27304_14-Day_S5_FT240_ROI-006_Secretory

description: Library name: DSP-1001660005136-B-C03


title: ME11_Replicate_50um_RNA

description: Library name: SpMETSLE21R


title: 461-27304_14-Day_S3_OVCAR3_ROI-007_Secretory

description: Library name: DSP-1001660005136-B-B02


description: Cell-free genomic DNA of induced sputum from without COPD subject 31

value: Famale

value: without COPD subject 31


title: 461-27304_14-Day_S3_OVCAR3_ROI-008_Secretory

description: Library name: DSP-1001660005136-B-B03


title: 461-27304_14-Day_S3_OVCAR3_ROI-008_Ciliated

description: Library name: DSP-1001660005136-B-B04


title: ME11_Replicate_50um_DNAm

description: Library name: SpMETSLE21D


title: 461-27304_14-Day_S3_PBS_ROI-006_Ciliated

description: Library name: DSP-1001660005136-B-B01

value: PBS


description: Cell-free genomic DNA of induced sputum from without COPD subject 28

value: induced sputum cells

value: without COPD subject 28


title: KKO3_D2

first: Kalyani

last: Pyaram

state: KS

address: 2060 W 39th Ave

institute: University of Kansas Medical Center

description: Library name: KKO3_D2

data_processing:
For bioinformatics analysis, raw data underwent quality processing through FastQC and were aligned to the mouse reference genome using RSEM (RNA-Seq by Expectation-Maximization), resulting in the creation of a gene count matrix.
Assembly: mm10
Supplementary files format and content: CSV count matrix

source_name: CD4+ T-cells

extract_protocol:
RNA was harvested at 24, 48hrs of activation of CD4+ T-cells. Total RNA was extracted using RNeasy Plus Micro kit (Qiagen). 1.5ug of RNA was used for construction of sequencing libraries.
100ng of the RNA was used to perform Agilent TapeStation QC analysis to verify RNA integrity and generate RNA Integrity number (RIN). Using Nova-Seq 6000 S1 200 cycle reagent kit, 25 million pair-ended reads were recorded for construction of mRNA libraries.

value: CD4+ T-cells

tag: timepoint

value: 48 hours

value: Keap-1 KO


title: 461-27304_14-Day_S3_PBS_ROI-005_Secretory

description: Library name: DSP-1001660005136-B-A10


title: 461-27304_14-Day_S3_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660005136-B-A09

value: Ciliated


description: Cell-free genomic DNA of induced sputum from without COPD subject 27

value: without COPD subject 27


title: KKO2_D2

description: Library name: KKO2_D2


title: 461-27304_14-Day_S5_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660005136-B-B09


title: 461-27304_14-Day_S3_PBS_ROI-004_Secretory

description: Library name: DSP-1001660005136-B-A08


title: KKO1_D2

description: Library name: KKO1_D2


description: Cell-free genomic DNA of induced sputum from without COPD subject 25

value: without COPD subject 25


title: 461-27304_14-Day_S3_FT240_ROI-003_Secretory

description: Library name: DSP-1001660005136-B-A06


title: 461-27304_14-Day_S3_FT240_ROI-002_Ciliated

description: Library name: DSP-1001660005136-B-A05


title: WT3_D2

description: Library name: WT3_D2

value: WT


title: induced sputum from COPD patient 24

description: Cell-free genomic DNA of induced sputum from COPD patient 24

value: COPD patient 24


title: 461-27304_14-Day_S3_FT240_ROI-002_Secretory

description: Library name: DSP-1001660005136-B-A04

value: Secretory


title: 461-27304_14-Day_S3_FT240_ROI-001_Ciliated

description: Library name: DSP-1001660005136-B-A03


description: Cell-free genomic DNA of induced sputum from without COPD subject 29

value: without COPD subject 29


title: WT2_D2

description: Library name: WT2_D2


title: 461-27304_14-Day_S3_FT240_ROI-001_Secretory

description: Library name: DSP-1001660005136-B-A02


title: 461-27304_14-Day_S3_PBS_ROI-006_Secretory

description: Library name: DSP-1001660005136-B-A12


title: 461-27304_14-Day_S3_PBS_ROI-005_Ciliated

description: Library name: DSP-1001660005136-B-A11


title: DSP-1001660005136_NTC

description: Library name: DSP-1001660005136-B-A01

value: NTC


title: induced sputum from COPD patient 22

description: Cell-free genomic DNA of induced sputum from COPD patient 22

value: induced sputum

value: COPD patient 22


title: KKO3_D1

description: Library name: KKO3_D1

value: 24 hours


title: 5929-606994_1-Day_S1_PBS_ROI-006_Secretory

description: Library name: DSP-1001660006709-D-F08

value: PBS


title: WT1_D2

description: Library name: WT1_D2


title: induced sputum from COPD patient 23

description: Cell-free genomic DNA of induced sputum from COPD patient 23

value: Famale

value: induced sputum cells

value: COPD patient 23


title: KKO2_D1

description: Library name: KKO2_D1

value: CD4+ T-cells


title: 5929-606994_1-Day_S1_PBS_ROI-004_Secretory

description: Library name: DSP-1001660006709-D-F06


title: induced sputum from COPD patient 20

description: Cell-free genomic DNA of induced sputum from COPD patient 20

value: COPD patient 20


title: induced sputum from COPD patient 21

description: Cell-free genomic DNA of induced sputum from COPD patient 21

value: COPD patient 21


title: 5929-606994_1-Day_S1_OVCAR3_ROI-003_Ciliated

description: Library name: DSP-1001660006709-D-F04

value: Ciliated


description: Cell-free genomic DNA of induced sputum from without COPD subject 26

value: without COPD subject 26


title: 5929-606994_1-Day_S1_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660006709-D-F03


title: 5929-606994_1-Day_S1_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660006709-D-F05


title: 461-27304_14-Day_S3_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660005136-B-A07


title: 5929-606994_1-Day_S1_OVCAR3_ROI-002_Ciliated

description: Library name: DSP-1001660006709-D-F02


title: induced sputum from COPD patient 19

description: Cell-free genomic DNA of induced sputum from COPD patient 19

value: COPD patient 19


title: KKO1_D1

description: Library name: KKO1_D1

value: Keap-1 KO


title: 5929-606994_1-Day_S1_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660006709-D-F01

value: Secretory


title: WT3_D1

description: Library name: WT3_D1

value: WT


title: induced sputum from COPD patient 18

description: Cell-free genomic DNA of induced sputum from COPD patient 18

value: COPD patient 18


title: 5929-607267_1-Day_S1_OVCAR3_ROI-009_Secretory

description: Library name: DSP-1001660006709-D-E11


title: WT2_D1

description: Library name: WT2_D1


title: induced sputum from COPD patient 17

description: Cell-free genomic DNA of induced sputum from COPD patient 17

value: induced sputum

value: COPD patient 17


title: WT1_D1

description: Library name: WT1_D1

value: 24 hours


title: 5929-606994_1-Day_S1_PBS_ROI-005_Secretory

description: Library name: DSP-1001660006709-D-F07

value: PBS


title: 5929-607267_1-Day_S1_OVCAR3_ROI-008_Secretory

description: Library name: DSP-1001660006709-D-E09


title: 5929-607267_1-Day_S1_OVCAR3_ROI-009_Ciliated

description: Library name: DSP-1001660006709-D-E10


description: Cell-free genomic DNA of induced sputum from without COPD subject 16

value: Famale

value: without COPD subject 16


title: 5929-607267_1-Day_S1_OVCAR3_ROI-008_Ciliated

description: Library name: DSP-1001660006709-D-E08


description: Cell-free genomic DNA of induced sputum from without COPD subject 15

value: induced sputum cells

value: without COPD subject 15


title: 5929-607267_1-Day_S1_OVCAR3_ROI-007_Ciliated

description: Library name: DSP-1001660006709-D-E06


title: Knock-out 2

description: Library name: KKO2

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Signal maps and peak locations were used as input data to Active Motif’s proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations, and gene annotations.
Assembly: mm10
Supplementary files format and content: BigWig

extract_protocol:
Stimulated CD4+T-cells from WT and Keap1-KO mice were harvested after 36 h. Cells were transferred to a 15mL or 50mL conical tube and centrifuged at 500 x g for 5 minutes. The media was aspirated, and cells were resuspended in 10mL of pre-warmed growth media, followed by the addition of 1:100 volume of 100x DNase buffer and DNase solution (250mM MgCl2 and 50mM CaCl2 in dH2O). Incubated the cells at 37°C for 30 minutes and centrifuged again at 500 x g for 5 minutes at 4°C, resuspended in 5mL ice-cold PBS (or 500µL for Eppendorf tubes), and 300,000 cells were quantified using a hemocytometer for cryopreservation. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay.
The cells were then thawed in a 37oC water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al. 2013), with some modifications based on (Corces et al. 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the ATAC-Seq Kit (Active Motif cat# 53150). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the iSeq (Illumina) and sequenced with PE42 sequencing on the NovaSeq 6000 sequencer (Illumina).

value: CD4+ T-cells

value: Untreated


title: Knock-out 1

description: Library name: KKO1


title: 5929-607267_1-Day_S1_PBS_ROI-006_Secretory

description: Library name: DSP-1001660006709-D-E05


description: Cell-free genomic DNA of induced sputum from without COPD subject 14

value: without COPD subject 14


title: 5929-607267_1-Day_S1_PBS_ROI-006_Ciliated

description: Library name: DSP-1001660006709-D-E04

value: Ciliated


description: Cell-free genomic DNA of induced sputum from without COPD subject 13

value: without COPD subject 13


title: 5929-607267_1-Day_S1_PBS_ROI-005_Ciliated

description: Library name: DSP-1001660006709-D-E02


title: 5929-606994_1-Day_S1_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660006709-D-E12


title: 5929-607267_1-Day_S1_PBS_ROI-004_Secretory

description: Library name: DSP-1001660006709-D-E01


description: Cell-free genomic DNA of induced sputum from without COPD subject 12

value: without COPD subject 12


title: 5929-607267_1-Day_S1_PBS_ROI-005_Secretory

description: Library name: DSP-1001660006709-D-E03

value: Secretory


title: Wildtype 2

description: Library name: WT2


title: 5929-607267_1-Day_S1_FT240_ROI-003_Secretory

description: Library name: DSP-1001660006709-D-D11


title: 5929-607267_1-Day_S1_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660006709-D-D12


title: 5929-607267_1-Day_S1_FT240_ROI-002_Secretory

description: Library name: DSP-1001660006709-D-D09


title: 5929-607267_1-Day_S1_OVCAR3_ROI-007_Secretory

description: Library name: DSP-1001660006709-D-E07


description: Cell-free genomic DNA of induced sputum from without COPD subject 11

value: without COPD subject 11


title: 5929-607267_1-Day_S1_FT240_ROI-002_Ciliated

description: Library name: DSP-1001660006709-D-D08


description: Cell-free genomic DNA of induced sputum from without COPD subject 10

value: without COPD subject 10


title: mRNA-seq of motor neuron axons treated with primary muscle EVs, rep 2

city: ראשון לציון

first: Iddo

last: Magen

state: Not in US

address: בן אליעזר 32, 17

country: Israel

institute: Weizmann Institute

description:
Library name: Sample 17
column name in MARS_Seq_corrected_UTAP_GenCode_Axon_only.txt: Axon_EV2

data_processing:
Read alignment using GeneGlobe pipeline (Qiagen) for small RNA, or GenCode for mRNA
low-abudnant sample filtering
DESEq2 for differential expression
Assembly: GRCm38 for small RNA, GRCm39 for mRNA
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Comma-separated values file includes differential expression analysis

source_name: motor neuron

extract_protocol:
RNA extraction MN axonal RNA was extracted from outer compartment of radial MFCs at 14DIV. Axonal RNA was extracted by removing the PBS (from prior wash) from the outer compartment and adding 100µL Qiazol lysis reagent (Qiagen). Inner well was filled with higher volume of PBS to disable the inward flow of lysis reagent towards the inner (soma) compartment and prevent soma contamination. Axons washed off the plate by pipetting the Qiazol around the outer well for 30 seconds. RNA from somata in the inner compartment was extracted with 100µL Qiazol reagent, and lysate was collected in a similar manner. cDNA for axon and soma was prepared with High-Capacity Reverse Transcription Kit (Thermo; Cat. 4368814). Exosomal RNA was extracted by dissolving the exosomal pellet in 700µL Qiazol. RNA was extracted using the RNAeasy micro kit (Qiagen) according to manufacturer’s protocols and RNA yield was quantified using Qubit fluorometer Qubit fluorometer (RNA broad range assay kit; ThermoFisher Scientific). For standard whole-cell RNA preparations from MN / muscle cultures, cultures were lysed in 700µL TRI reagent, and RNA was isolated with ordinary chloroform, isopropanol precipitation protocol.
small RNA libraries were constructed using the QIAseq miRNA library kit following manufacturer's instructions. mRNA libraries were constructed with the MARS-seq protocol (Keren-Shaul et al., Nat. Prot. 2019)

value: motor neuron

value: motor neuron axons

value: WT

value: muscle-derived extracellular vesicles


title: 5929-607267_1-Day_S1_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660006709-D-D10


title: 5929-607267_1-Day_S1_FT240_ROI-001_Secretory

description: Library name: DSP-1001660006709-D-D07


title: 5929-607267_1-Day_S1_FT240_ROI-001_Ciliated

description: Library name: DSP-1001660006709-D-D06


title: mRNA-seq of motor neuron axons treated with primary muscle EVs, rep 1

address: בן אליעזר 32, 17

description:
Library name: Sample 16
column name in MARS_Seq_corrected_UTAP_GenCode_Axon_only.txt: Axon_EV1


description: Cell-free genomic DNA of induced sputum from without COPD subject 9

value: induced sputum

value: Famale

value: without COPD subject 9


title: mRNA-seq of motor neuron axons treated with vehicle, rep 3

address: בן אליעזר 32, 17

description:
Library name: Sample 15
column name in MARS_Seq_corrected_UTAP_GenCode_Axon_only.txt: Axon3

value: vehicle


title: 5929-606950_1-Day_S1_OVCAR3_ROI-007_Secretory

description: Library name: DSP-1001660006709-D-D05


title: 5929-606950_1-Day_S1_PBS_ROI-006_Secretory

description: Library name: DSP-1001660006709-D-D03

value: PBS


title: induced sputum from COPD patient 8

description: Cell-free genomic DNA of induced sputum from COPD patient 8

value: induced sputum cells

value: COPD patient 8


title: mRNA-seq of motor neuron axons treated with vehicle, rep 2

address: בן אליעזר 32, 17

description:
Library name: Sample 14
column name in MARS_Seq_corrected_UTAP_GenCode_Axon_only.txt: Axon2


title: induced sputum from COPD patient 7

description: Cell-free genomic DNA of induced sputum from COPD patient 7

value: COPD patient 7


title: 5929-606950_1-Day_S1_PBS_ROI-006_Ciliated

description: Library name: DSP-1001660006709-D-D02

value: Ciliated


title: 5929-606950_1-Day_S1_OVCAR3_ROI-007_Ciliated

description: Library name: DSP-1001660006709-D-D04


title: Wildtype 1

description: Library name: WT1

value: CD4+ T-cells

value: Untreated


title: mRNA-seq of motor neuron axons treated with primary muscle EVs, rep 3

address: בן אליעזר 32, 17

description:
Library name: Sample 18
column name in MARS_Seq_corrected_UTAP_GenCode_Axon_only.txt: Axon_EV3


title: mRNA-seq of motor neuron axons treated with vehicle, rep 1

address: בן אליעזר 32, 17

description:
Library name: Sample 13
column name in MARS_Seq_corrected_UTAP_GenCode_Axon_only.txt: Axon1


title: 5929-606950_1-Day_S1_PBS_ROI-005_Ciliated

description: Library name: DSP-1001660006709-D-C12


title: induced sputum from COPD patient 6

description: Cell-free genomic DNA of induced sputum from COPD patient 6

value: COPD patient 6


title: miRNA-seq of motor neuron axons treated with primary muscle EVs, rep 3

address: בן אליעזר 32, 17

description:
Library name: Sample 12
column name in miRNA_axons_EVs.txt: Axon_EV3


title: 5929-606950_1-Day_S1_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660006709-D-C10


title: 5929-606950_1-Day_S1_PBS_ROI-004_Secretory

description: Library name: DSP-1001660006709-D-C11

value: Secretory


title: induced sputum from COPD patient 4

description: Cell-free genomic DNA of induced sputum from COPD patient 4

value: COPD patient 4


title: 5929-606950_1-Day_S1_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660006709-D-C08


title: 5929-606950_1-Day_S1_FT240_ROI-003_Secretory

description: Library name: DSP-1001660006709-D-C09


title: induced sputum from COPD patient 3

description: Cell-free genomic DNA of induced sputum from COPD patient 3

value: COPD patient 3


title: miRNA-seq of motor neuron axons treated with primary muscle EVs, rep 1

address: בן אליעזר 32, 17

description:
Library name: Sample 10
column name in miRNA_axons_EVs.txt: Axon_EV1

value: motor neuron

value: motor neuron axons

value: WT


title: 5929-606950_1-Day_S1_FT240_ROI-002_Ciliated

description: Library name: DSP-1001660006709-D-C06


title: 5929-606950_1-Day_S1_FT240_ROI-002_Secretory

description: Library name: DSP-1001660006709-D-C07


title: miRNA-seq of motor neuron axons treated with primary muscle EVs, rep 2

address: בן אליעזר 32, 17

description:
Library name: Sample 11
column name in miRNA_axons_EVs.txt: Axon_EV2

value: muscle-derived extracellular vesicles


title: miRNA-seq of motor neuron axons treated with vehicle, rep 3

address: בן אליעזר 32, 17

description:
Library name: Sample 9
column name in miRNA_axons_EVs.txt: Axon3


title: induced sputum from COPD patient 2

description: Cell-free genomic DNA of induced sputum from COPD patient 2

value: induced sputum

value: Famale

value: COPD patient 2


title: 5929-606950_1-Day_S1_FT240_ROI-001_Secretory

description: Library name: DSP-1001660006709-D-C05


title: 5929-606950_1-Day_S1_FT240_ROI-001_Ciliated

description: Library name: DSP-1001660006709-D-C04


title: induced sputum from COPD patient 1

description: Cell-free genomic DNA of induced sputum from COPD patient 1

value: induced sputum cells

value: COPD patient 1