title: Submucosa, Uninflamed small intestine, Crohn's disease, biol rep 3

description: Library name: CD3_2_Uninf


title: Lamina propria, Uninflamed small intestine, Crohn's disease, biol rep 4

status: Public on Jul 01 2026

type: SRA

city: Seoul

first: Yoonho

last: Lee

address: 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea

department: Department of Biochemistry and Molecular Biology

country: South Korea

institute: University of Ulsan College of Medicine

description: Library name: CD4_1_Uninf

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Rnager software v6.1.2.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: Lamina propria of the uninflamed small intestine

extract_protocol:
Small intestinal tissues were rinsed with ice cold 1× phosphate buffered saline, and the mesenteric fat and epithelial layer were mechanically removed. We meticulously isolated the lamina propria-enriched fraction (LP) and the submucosa/muscularis propria-enriched fraction (SM/MP) for uninflamed small intestinal tissues. Curved iris scissors (AC 451/10, Nopa Instruments, Tuttlingen, Germany) were used with precision to dissect within the submucosal layer, following a technique similar to that used in endoscopic submucosal dissection. The dissected LP and SM/MP fractions were minced into small pieces (<1 mm in diameter) and placed in digestion medium (0.05% collagenase IV (Sigma-Aldrich, St. Louis, MO, USA), 0.01% DNase I (Roche, Basel, Swiss) and 10% fetal bovine serum [FBS] in RPMI 1640). Tissues were digested in an incubator at 37°C for 30 min followed by 40 min with 90 rpm agitation for each LP and SM/MP. Dissociated cells were filtered through a 70 µm cell strainer (Falcon, Durham, NC, USA) and washed with RPMI 1640 containing 2% FBS following centrifugation at 400 relative centrifugal force for 10 min. Cell pellets were suspended in RPMI 1640 containing 2% FBS and filtered through a 40 µm cell strainer followed by centrifugation at 400 relative centrifugal force for 10 min. The same protocol was performed using inflamed intestinal tissues as a whole, without separating them into the LP and the SM/MP. We processed all samples by isolating CD3+ or CD45+ cells using magnetic bead sorting. Whole blood was drawn into Heparin vacutainer tube (BD, NJ, USA) and PBMCs were isolated by Ficoll-Paque® PLUS (density = 1.077 ± 0.001 g/ml; GE Healthcare, UK), according to the manufacturer’s protocol. Briefly, 5 ml of whole blood was diluted with an equal volume of 1× phosphate-buffered saline (PBS), and the diluted blood sample (10 ml) was carefully layered on 5 ml of Ficoll-Paque® PLUS and centrifuged at 400× g for 30 min at 20°C without breaks. The cell interface layer was carefully collected, followed by washing twice with 10 ml of 1× PBS (400× g for 10 min), and the cell pellet was resuspended in CELLBANKER® Cell Freezing Media (Amsbio, UK) and store at -80℃ before multiplex RNA sequencing. Frozen PBMCs were thawed and washed prior to library preparation. Cells were resuspended in 1 x PBS containing 0.04% BSA and the concentration of each sample was adjusted to 900–1,600 cells/μL. The samples were pooled into mixtures of 2–4 donors per batch (total of 3 batches).
We utilized the 10x Genomics Chromium Instrument and cDNA synthesis kit (Chromium Next GEM Single Cell 5ʹ Kit v2 & Chromium Next GEM Chip K Single Cell Kit) to generate a barcoded cDNA library for cells isolated from intestinal tissues. cDNA library quality was determined using an Agilent Bioanalyzer. Pooled PBMCs from patients with CD were loaded on Chromium platform (10x Genomics) with a target of capturing 12,000–16,000 cells. Single cell capturing and library construction were performed using Chromium Next GEM Single Cell 5’ kit v2 (10x Genomics, PN1000263) and Chromium Single Cell Human V(D)J Reagent kit (10x Genomics, PN1000252 and PN1000253). Single-cell libraries were constructed according to the manufacturer’s protocol (10x Genomics, CG000331). All libraries were sequenced on the NovaSeq 6000 platform using S2 sequencing reagent, with a target of ~600 million reads per library using dual indexing.

tag: tissue

tag: cell type

value: CD45+ T-cells


title: 118_CC_2019_04_30_1, rep3

city: Villenave d Ornon

first: mathieu

last: fouché

state: Gironde

address: 71 avenue Edouard Bourlaux

department: UMR BFP

country: France

institute: INRAE

description: Library name: 118_cold_deprivation, 118_GACGTCTT-GGTGAACC-AHGKC2BBXY_L006

library_source: transcriptomic

data_processing:
trimming: Trimmomatic 0.36 (Bolger et al., 2014) with following settings fa:2:10:5:1 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to the sweet cherry ‘Regina’ reference genome v.1 (Vimont et al., 2021) using STAR (Dobin et al., 2013)
Raw read count was performed using HTSeq count (Anders et al., 2015)
Assembly: sweet cherry ‘Regina’ reference genome v.1 (Le Dantec et al, 2022)
Supplementary files format and content: the format is .txt and include raw counts of each gene for each sample

organism: Prunus avium

source_name: flower bud

growth_protocol: adult potted trees

extract_protocol:
Total RNA was extracted from 100 mg of frozen and grinded flower buds using RNeasy Plant Mini kit (Qiagen) with minor modification: 1.5% PVP-40 was added in the extraction buffer RLT
Library preparation was performed on 1 μg of high quality RNA (RNA integrity number equivalent superior or equivalent to 8.5) using the TruSeq Stranded mRNA Library Prep Kit High Throughput (Illumina cat. no. RS-122-2103)

value: flower bud

value: plant

tag: genotype

value: Regina

tag: treatment

tag: batch


title: Lamina propria, Uninflamed small intestine, Crohn's disease, biol rep 3

description: Library name: CD3_1_Uninf

value: Lamina propria of the uninflamed small intestine

value: CD3+ T-cells


title: T2-high asthma_8040254012

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

country: United Kingdom

institute: University of  Oxford

description: Library name: 8040254012

data_processing:
Sequences in fastq files (in single and pair ends) were aligned using STAR aligner (version 2.7.1a)
R package (17)Rsubread was employed for quantification of reads assigned to genes
Assembly: GRCh38
Supplementary files format and content: Raw_counts_B_BR_Pl.txt
Supplementary files format and content: Normalized_counts_B_BR_Pl.txt

source_name: BRUSHING

extract_protocol:
Total RNA was extracted from subjects biopsies and brushing using RNeasy mini kits (Qiagen).
TruSeq library preparation kits were used for RNA samples. Starting with total RNA, the messenger RNA was first purified using polyA.
Single and paired-ends library were prepared.

value: BRUSHING

tag: sample group

value: T2-high asthma


title: HIP from animal_14

city: Tempe

first: Noah

last: Snyder-Mackler

state: Arizona

address: 214 Life Sciences C

department: School of Life Sciences

country: USA

institute: Arizona State University

description:
Library name: NSM1175
3 lvl sciRNAseq

data_processing:
Converts base calls to fastq files with bcl2fastq/ v.2.20 (RRID:SCR_015058) (Illumina), merge read 1 which contains the barcode to read 2 files.
Removes polyA tails using Trim Galore/v.0.6.7 (RRID:SCR_011847)
Aligns trimmed reads to a reference genome with STAR/v.2.7.6 (RRID:SCR_004463)
Extracts mapped reads and removes duplicates.
Generates UMI counts for exonic and intronic regions of each gene, tabulated according to the unique three-level barcode design in sci-RNA-seq3.
Assembly: rhesus macaque reference genome (Mmul_10)
Supplementary files format and content: all_regions_cell_annotate.csv
Supplementary files format and content: all_regions_count.npz
Supplementary files format and content: all_regions_gene_annotate.csv

molecule: nuclear RNA

organism: Macaca mulatta

source_name: hippocampus

growth_protocol: free-ranging population

extract_protocol:
Briefly, tissue was manually pulverized on dry ice, transferred to pre-chilled tubes, and stored at −80°C. For lysis, pulverized tissue was suspended in hypotonic lysis buffer A (0.3 M sucrose, 0.1% Triton X-100, 3 mM MgCl₂, 0.025% IGEPAL CA-630, 1% DEPC in PBS) for 10 min, filtered (40-μm), pelleted, and resuspended in SPBSTM buffer (0.3 M sucrose, 1X PBS, 0.1% TritonX-100, 3 mM MgCl₂, and 1% DEPC). Nuclei were fixed for 10 min in 1.5 mM dithiobis(succinimidyl propionate) (DSP), diluted from a 123 mM stock in DMSO into methanol. After washing in 0.3 M SPBSTM, nuclei were layered onto a 10:1 volume of 1.4 M SPBSTM, centrifuged (3,000 x g, 20 min, 4°C), and resuspended. Nuclei were filtered (20-μm), counted, aliquoted, and cryopreserved in 90% 0.3 M SPBSTM with 10% anhydrous DMSO at -80°C. One library per region was generated using the optimized sci-RNA-seq3 protocol with the following modifications: nuclei were counted using the ImageExpress Pico System (Molecular Devices), and 15,000-20,000 nuclei were loaded per reverse transcription well. Tagmentation used N7 adaptor-loaded Tn5 transposase (Diagenode, C01070010-20), with 6-9 μL of Tn5 per 550 μL of 2X TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl₂, 20% dimethylformamide), distributed at 5uL per well.
sci-RNA-seq3

treatment_protocol: Following veterinary euthanasia, a necropsy was immediately performed during which the brain was perfused by transcardial perfusion with sterile saline. The brain was then removed from the cranium and sagittally sectioned into left and right hemispheres. The left hemisphere was fixed in 10% formalin and not used for this study. The right hemisphere was further sectioned prior to cryopreservation. First, the cerebellum was separated from the cerebrum. The cerebrum was then placed on a custom mold and sectioned coronally into 11 ~0.5 cm-thick slices. All 12 slices (including the cerebellar hemisphere) were individually stored in Whirl-pak bags and flash frozen in a dry-ice/ethanol bath immediately before storage in ultralow (-80°C) freezers. Regions of interest were dissected in sterile, RNase-free conditions on dry ice to minimize RNA degradation. Six 1-mm tissue biopsies were then collected by biopsy punch.

value: hippocampus


title: HIP from animal_13

description:
Library name: NSM1174
3 lvl sciRNAseq


title: T2-high asthma_8040254009

description: Library name: 8040254009


title: Submucosa, Uninflamed small intestine, Crohn's disease, biol rep 2

description: Library name: CD2_2_Uninf

source_name: Submucosa of the uninflamed small intestine


title: 118_CC_2019_04_30_1, rep2

description: Library name: 118_cold_deprivation, 118_GACGTCTT-GGTGAACC-AHGKC2BBXY_L005


title: 118_CC_2019_04_30_1, rep1

description: Library name: 118_cold_deprivation, 118_GACGTCTT-GGTGAACC-AHGKC2BBXY_L004


title: T2-high asthma_8040253996

description: Library name: 8040253996


title: Lamina propria, Uninflamed small intestine, Crohn's disease, biol rep 2

description: Library name: CD2_1_Uninf


title: T2-high asthma_8040253987

description: Library name: 8040253987


title: Submucosa, Uninflamed small intestine, Crohn's disease, biol rep 1

description: Library name: CD1_2_Uninf

value: Submucosa of the uninflamed small intestine


title: 114_CC2MAR_2019_03_28_3, rep2

description: Library name: 114_cold_deprivation, 114_AGTACTCC-AACAGGTT-AHGKC2BBXY_L005


title: HIP from animal_10

description:
Library name: NSM1171
3 lvl sciRNAseq


title: Lamina propria, Uninflamed small intestine, Crohn's disease, biol rep 1

description: Library name: CD1_1_Uninf


title: T2-high asthma_8040253976

description: Library name: 8040253976


title: HIP from animal_11

description:
Library name: NSM1172
3 lvl sciRNAseq


title: T2-high asthma_8040253973

description: Library name: 8040253973


title: 113_CC2MAR_2019_03_28_2, rep3

description: Library name: 113_cold_deprivation, 113_TGGCCGGT-GCGCTCTA-AHGKC2BBXY_L006


title: RNAseq of LUAD cancer-associated fibroblast

city: Singapore

first: Damien

last: Chua

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University, Singapore

description: Library name: Fibroblast

data_processing:
STAR for alignment, FeatureCounts for quantification.
Assembly: GRCh37
Supplementary files format and content: For RNAseq: Tab-delimited filed with TPM normalised gene expression quantification

molecule: polyA RNA

source_name: LUAD

extract_protocol: For RNAseq: RNA-seq was conducted by Chi Biotech (Shenzhen, China)

value: LUAD


title: RNAseq of LUAD tumoroid

description: Library name: LCO


title: 113_CC2MAR_2019_03_28_2, rep2

description: Library name: 113_cold_deprivation, 113_TGGCCGGT-GCGCTCTA-AHGKC2BBXY_L005


title: HIP from animal_7

description:
Library name: NSM1168
3 lvl sciRNAseq


title: T2-high asthma_8040253972

description: Library name: 8040253972


title: RNAseq of LUAD adjacent-normal tissue biopsy 3

description: Library name: Normal_3

source_name: LUAD adjacent normal

value: LUAD adjacent normal


title: T2-high asthma_8040253960

description: Library name: 8040253960


title: RNAseq of LUAD adjacent-normal tissue biopsy 2

description: Library name: Normal_2


title: 113_CC2MAR_2019_03_28_2, rep1

description: Library name: 113_cold_deprivation, 113_TGGCCGGT-GCGCTCTA-AHGKC2BBXY_L004


title: 112_CC2MAR_2019_03_28_1, rep3

description: Library name: 112_cold_deprivation, 112_CAATTAAC-ATATCTCG-AHGKC2BBXY_L006


title: HIP from animal_5

description:
Library name: NSM1166
3 lvl sciRNAseq


title: T2-high asthma_8040253952

description: Library name: 8040253952


title: RNAseq of LUAD adjacent-normal tissue biopsy 1

description: Library name: Normal_1


title: HIP from animal_9

description:
Library name: NSM1170
3 lvl sciRNAseq


title: 112_CC2MAR_2019_03_28_1, rep2

description: Library name: 112_cold_deprivation, 112_CAATTAAC-ATATCTCG-AHGKC2BBXY_L005


title: HIP from animal_4

description:
Library name: NSM1165
3 lvl sciRNAseq


title: T2-high asthma_8040253949

description: Library name: 8040253949


title: 112_CC2MAR_2019_03_28_1, rep1

description: Library name: 112_cold_deprivation, 112_CAATTAAC-ATATCTCG-AHGKC2BBXY_L004


title: Healthy control_8038915175

description: Library name: 8038915175

value: Healthy control


title: HIP from animal_3

description:
Library name: NSM1164
3 lvl sciRNAseq


title: RNAseq of LUAD tumor biopsy 2

description: Library name: Cancer_2


title: 108_CC2JAN_2019_03_28_3, rep3

description: Library name: 108_cold_deprivation, 108_GTCTACAC-ACCTTGGC-AHGKC2BBXY_L006


title: HIP from animal_2

description:
Library name: NSM1163
3 lvl sciRNAseq


title: Healthy control_8038915163

description: Library name: 8038915163


title: 108_CC2JAN_2019_03_28_3, rep2

description: Library name: 108_cold_deprivation, 108_GTCTACAC-ACCTTGGC-AHGKC2BBXY_L005


title: RNAseq of LUAD tumor biopsy 1

description: Library name: Cancer_1


title: HIP from animal_1

description:
Library name: NSM1162
3 lvl sciRNAseq


title: Healthy control_8038915162

description: Library name: 8038915162


title: CAMA-1 Ribociclib-Resistant, Ribociclib + Afatinib, Day18 Hr24

city: Duarte

first: Aritro

last: Nath

state: California

address: 1500 E Duarte Rd

department: Medical Oncology & Therapeutics Research

institute: City of Hope

description:
Library name: 90_CAMA1_Ribo_Afat
90_CAMA1_Ribo_Afat

data_processing:
Paired-end raw RNA-seq FASTQ files were processed using Kallisto version 0.48 to perform pseudoalignment and obtain estimates of transcript abundance. An index fo Kallisto was built using GENCODE release 43 (CRCh38.p13) trancript sequences and comprehensive gene annotations.
Assembly: GRCh38 (hg38)
Supplementary files format and content: TSV (tab-separated values) files with counts or transcripts per million. Genes in rows, samples in columns.

source_name: CAMA-1 Ribociclib-Resistant

growth_protocol: CAMA-1 and MCF-7 breast cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic-antimycotic and incubated in 5% CO2 at 37°C.

extract_protocol:
Cells were collected for bulk RNA-seq on days 0, 6, 12, and 18 at 0, 6, and 24 h after media change. Cells were pooled, washed with PBS, and pellets were frozen at -80°C for subsequent RNA isolation. RNA was isolated using the Qiagen RNeasy® Plus Mini Kit (Cat. No: 74136) following the manufacturer’s protocol.
Library preparation was performed on the samples using the Illumina TruSeq Stranded mRNA Kit following the manufacturer’s protocol.

treatment_protocol: CAMA-1 cells were treated with 0.2µM ribociclib (Selleck Chemicals, Cat. No: S7440), 1.25μM afatinib (Selleck Chemicals, Cat. No: S1011), or a combination of ribociclib and afatinib. MCF-7 cells were treated with 0.5μM ribociclib, 1.5µM afatinib, or a combinatin of ribociclib and afatinib. Cells were treated for a total of 21 days with media change performed every three days.

tag: cell line

value: CAMA-1 Ribociclib-Resistant

value: ER+ Breast Cancer

value: WT

value: Ribociclib + Afatinib

tag: time

value: Day18 Hr24


title: 108_CC2JAN_2019_03_28_3, rep1

description: Library name: 108_cold_deprivation, 108_GTCTACAC-ACCTTGGC-AHGKC2BBXY_L004

value: flower bud


title: lCb from animal_55

description:
Library name: NSM1161
3 lvl sciRNAseq

source_name: lateral cerebellum

value: lateral cerebellum


title: Healthy control_8038915149

description: Library name: 8038915149


title: 107_CC2JAN_2019_03_28_2, rep3

description: Library name: 107_cold_deprivation, 107_ACTCGTGT-GTTCCAAT-AHGKC2BBXY_L006

value: plant

value: Regina


title: lCb from animal_54

description:
Library name: NSM1160
3 lvl sciRNAseq


title: Healthy control_8038915148

description: Library name: 8038915148


title: CAMA-1 Ribociclib-Resistant, Ribociclib, Day18 Hr24

description:
Library name: 88_CAMA1_Ribo_Afat
88_CAMA1_Ribo_Afat

value: Ribociclib


title: lCb from animal_53

description:
Library name: NSM1159
3 lvl sciRNAseq


title: 107_CC2JAN_2019_03_28_2, rep2

description: Library name: 107_cold_deprivation, 107_ACTCGTGT-GTTCCAAT-AHGKC2BBXY_L005


title: CAMA-1 Ribociclib-Resistant, DMSO, Day18 Hr24

description:
Library name: 87_CAMA1_Ribo_Afat
87_CAMA1_Ribo_Afat

value: DMSO


title: 107_CC2JAN_2019_03_28_2, rep1

description: Library name: 107_cold_deprivation, 107_ACTCGTGT-GTTCCAAT-AHGKC2BBXY_L004


title: lCb from animal_52

description:
Library name: NSM1158
3 lvl sciRNAseq


title: Healthy control_8038915139

description: Library name: 8038915139

value: BRUSHING


title: CAMA-1 Sensitive, Ribociclib + Afatinib, Day18 Hr24

description:
Library name: 86_CAMA1_Ribo_Afat
86_CAMA1_Ribo_Afat

source_name: CAMA-1 Sensitive

value: CAMA-1 Sensitive


title: 106_CC2JAN_2019_03_28_1, rep3

description: Library name: 106_cold_deprivation, 106_ATTGTGAA-GCAATGCA-AHGKC2BBXY_L006


title: lCb from animal_50

description:
Library name: NSM1157
3 lvl sciRNAseq


title: Healthy control_8038915138

description: Library name: 8038915138


title: CAMA-1 Sensitive, Afatinib, Day18 Hr24

description:
Library name: 85_CAMA1_Ribo_Afat
85_CAMA1_Ribo_Afat

value: Afatinib


title: T2-high asthma_8040253984

description: Library name: 8040253984

value: T2-high asthma


title: 106_CC2JAN_2019_03_28_1, rep2

description: Library name: 106_cold_deprivation, 106_ATTGTGAA-GCAATGCA-AHGKC2BBXY_L005


title: Healthy control_8038915134

description: Library name: 8038915134


title: lCb from animal_49

description:
Library name: NSM1156
3 lvl sciRNAseq


title: CAMA-1 Sensitive, Ribociclib, Day18 Hr24

description:
Library name: 84_CAMA1_Ribo_Afat
84_CAMA1_Ribo_Afat


title: 106_CC2JAN_2019_03_28_1, rep1

description: Library name: 106_cold_deprivation, 106_ATTGTGAA-GCAATGCA-AHGKC2BBXY_L004


title: lCb from animal_46

description:
Library name: NSM1155
3 lvl sciRNAseq


title: Healthy control_8038915147

description: Library name: 8038915147


title: CAMA-1 Sensitive, DMSO, Day18 Hr24

description:
Library name: 83_CAMA1_Ribo_Afat
83_CAMA1_Ribo_Afat


title: 102_CC2NOV_2019_03_28_3, rep3

description: Library name: 102_cold_deprivation, 102_GCCACAGG-ATGGCATG-AHGKC2BBXY_L006


title: lCb from animal_45

description:
Library name: NSM1154
3 lvl sciRNAseq


title: CAMA-1 Ribociclib-Resistant, Ribociclib + Afatinib, Day18 Hr6

description:
Library name: 82_CAMA1_Ribo_Afat
82_CAMA1_Ribo_Afat

value: Day18 Hr6


title: Healthy control_8038915124

description: Library name: 8038915124

value: Healthy control


title: 102_CC2NOV_2019_03_28_3, rep2

description: Library name: 102_cold_deprivation, 102_GCCACAGG-ATGGCATG-AHGKC2BBXY_L005


title: Healthy control_8038915122

description: Library name: 8038915122


title: lCb from animal_44

description:
Library name: NSM1153
3 lvl sciRNAseq


title: 102_CC2NOV_2019_03_28_3, rep1

description: Library name: 102_cold_deprivation, 102_GCCACAGG-ATGGCATG-AHGKC2BBXY_L004


title: lCb from animal_43

description:
Library name: NSM1152
3 lvl sciRNAseq


title: CAMA-1 Ribociclib-Resistant, Ribociclib, Day18 Hr6

description:
Library name: 80_CAMA1_Ribo_Afat
80_CAMA1_Ribo_Afat

value: CAMA-1 Ribociclib-Resistant


title: lCb from animal_42

description:
Library name: NSM1151
3 lvl sciRNAseq


title: Healthy control_8038915120

description: Library name: 8038915120


title: 101_CC2NOV_2019_03_28_2, rep3

description: Library name: 101_cold_deprivation, 101_CCTTCACC-GGAGCGTC-AHGKC2BBXY_L006


title: lCb from animal_41

description:
Library name: NSM1150
3 lvl sciRNAseq


title: CAMA-1 Sensitive, Ribociclib + Afatinib, Day18 Hr6

description:
Library name: 78_CAMA1_Ribo_Afat
78_CAMA1_Ribo_Afat

value: ER+ Breast Cancer


title: 101_CC2NOV_2019_03_28_2, rep1

description: Library name: 101_cold_deprivation, 101_CCTTCACC-GGAGCGTC-AHGKC2BBXY_L004


title: CAMA-1 Ribociclib-Resistant, Afatinib, Day18 Hr6

description:
Library name: 81_CAMA1_Ribo_Afat
81_CAMA1_Ribo_Afat

value: WT


title: lCb from animal_40

description:
Library name: NSM1149
3 lvl sciRNAseq


title: CAMA-1 Sensitive, Afatinib, Day18 Hr6

description:
Library name: 77_CAMA1_Ribo_Afat
77_CAMA1_Ribo_Afat


title: 100_CC2NOV_2019_03_28_1, rep3

description: Library name: 100_cold_deprivation, 100_TTCCTGTT-AAGATACT-AHGKC2BBXY_L006


title: CAMA-1 Sensitive, Ribociclib, Day18 Hr6

description:
Library name: 76_CAMA1_Ribo_Afat
76_CAMA1_Ribo_Afat


title: 100_CC2NOV_2019_03_28_1, rep2

description: Library name: 100_cold_deprivation, 100_TTCCTGTT-AAGATACT-AHGKC2BBXY_L005


title: lCb from animal_37

description:
Library name: NSM1147
3 lvl sciRNAseq


title: T2-low asthma_8038917367

description: Library name: 8038917367

source_name: BIOPSY

value: BIOPSY

value: T2-low asthma


title: Healthy control_8038915125

description: Library name: 8038915125


title: CAMA-1 Sensitive, DMSO, Day18 Hr6

description:
Library name: 75_CAMA1_Ribo_Afat
75_CAMA1_Ribo_Afat


title: CAMA-1 Ribociclib-Resistant, DMSO, Day18 Hr6

description:
Library name: 79_CAMA1_Ribo_Afat
79_CAMA1_Ribo_Afat


title: 100_CC2NOV_2019_03_28_1, rep1

description: Library name: 100_cold_deprivation, 100_TTCCTGTT-AAGATACT-AHGKC2BBXY_L004

value: flower bud


title: lCb from animal_36

description:
Library name: NSM1146
3 lvl sciRNAseq

value: lateral cerebellum


title: Healthy control_8038915121

description: Library name: 8038915121


title: T2-low asthma_8038917358

description: Library name: 8038917358


title: 96_CC_2019_03_28_3, rep3

description: Library name: 96_cold_deprivation, 96_GTGTCGGA-GCGCAAGC-AHGKC2BBXY_L006

value: plant


title: lCb from animal_35

description:
Library name: NSM1145
3 lvl sciRNAseq


title: CAMA-1 Ribociclib-Resistant, Ribociclib + Afatinib, Day18 Hr0

description:
Library name: 74_CAMA1_Ribo_Afat
74_CAMA1_Ribo_Afat

value: Ribociclib + Afatinib

value: Day18 Hr0


title: 101_CC2NOV_2019_03_28_2, rep2

description: Library name: 101_cold_deprivation, 101_CCTTCACC-GGAGCGTC-AHGKC2BBXY_L005

value: Regina


title: T2-low asthma_8038917355

description: Library name: 8038917355


title: Healthy control_8038915113

description: Library name: 8038915113

value: BRUSHING


title: CAMA-1 Ribociclib-Resistant, Afatinib, Day18 Hr0

description:
Library name: 73_CAMA1_Ribo_Afat
73_CAMA1_Ribo_Afat


title: 96_CC_2019_03_28_3, rep2

description: Library name: 96_cold_deprivation, 96_GTGTCGGA-GCGCAAGC-AHGKC2BBXY_L005


title: lCb from animal_34

description:
Library name: NSM1144
3 lvl sciRNAseq


title: CAMA-1 Ribociclib-Resistant, Ribociclib, Day18 Hr0

description:
Library name: 72_CAMA1_Ribo_Afat
72_CAMA1_Ribo_Afat

value: Ribociclib


title: T2-low asthma_8038917343

description: Library name: 8038917343


title: Healthy control_8038915091

description: Library name: 8038915091


title: 96_CC_2019_03_28_3, rep1

description: Library name: 96_cold_deprivation, 96_GTGTCGGA-GCGCAAGC-AHGKC2BBXY_L004


title: lCb from animal_33

description:
Library name: NSM1143
3 lvl sciRNAseq


title: T2-low asthma_8038917321

description: Library name: 8038917321


title: CAMA-1 Ribociclib-Resistant, DMSO, Day18 Hr0

description:
Library name: 71_CAMA1_Ribo_Afat
71_CAMA1_Ribo_Afat

value: DMSO


title: 95_CC_2019_03_28_2, rep3

description: Library name: 95_cold_deprivation, 95_ACACTAAG-ATATGGAT-AHGKC2BBXY_L006


title: lCb from animal_32

description:
Library name: NSM1142
3 lvl sciRNAseq


title: CAMA-1 Sensitive, Ribociclib + Afatinib, Day18 Hr0

description:
Library name: 70_CAMA1_Ribo_Afat
70_CAMA1_Ribo_Afat

value: CAMA-1 Sensitive


title: T2-low asthma_8038917310

description: Library name: 8038917310


title: T2-low asthma_8038917379

description: Library name: 8038917379


title: HIP from animal_12

description:
Library name: NSM1173
3 lvl sciRNAseq

value: hippocampus


title: 95_CC_2019_03_28_2, rep2

description: Library name: 95_cold_deprivation, 95_ACACTAAG-ATATGGAT-AHGKC2BBXY_L005


title: lCb from animal_39

description:
Library name: NSM1148
3 lvl sciRNAseq


title: T2-low asthma_8038917309

description: Library name: 8038917309


title: 114_CC2MAR_2019_03_28_3, rep3

description: Library name: 114_cold_deprivation, 114_AGTACTCC-AACAGGTT-AHGKC2BBXY_L006


title: lCb from animal_31

description:
Library name: NSM1141
3 lvl sciRNAseq


title: CAMA-1 Sensitive, Afatinib, Day18 Hr0

description:
Library name: 69_CAMA1_Ribo_Afat
69_CAMA1_Ribo_Afat

value: Afatinib


title: lCb from animal_30

description:
Library name: NSM1140
3 lvl sciRNAseq


title: 95_CC_2019_03_28_2, rep1

description: Library name: 95_cold_deprivation, 95_ACACTAAG-ATATGGAT-AHGKC2BBXY_L004


title: 114_CC2MAR_2019_03_28_3, rep1

description: Library name: 114_cold_deprivation, 114_AGTACTCC-AACAGGTT-AHGKC2BBXY_L004


title: T2-low asthma_8038917308

description: Library name: 8038917308


title: HIP from animal_8

description:
Library name: NSM1169
3 lvl sciRNAseq


title: CAMA-1 Sensitive, Ribociclib, Day18 Hr0

description:
Library name: 68_CAMA1_Ribo_Afat
68_CAMA1_Ribo_Afat


title: T2-low asthma_8038917296

description: Library name: 8038917296


title: lCb from animal_29

description:
Library name: NSM1139
3 lvl sciRNAseq


title: 94_CC_2019_03_28_1, rep3

description: Library name: 94_cold_deprivation, 94_CCATTCGA-CGGACAAC-AHGKC2BBXY_L006


title: CAMA-1 Sensitive, DMSO, Day18 Hr0

description:
Library name: 67_CAMA1_Ribo_Afat
67_CAMA1_Ribo_Afat


title: 94_CC_2019_03_28_1, rep2

description: Library name: 94_cold_deprivation, 94_CCATTCGA-CGGACAAC-AHGKC2BBXY_L005


title: T2-low asthma_8038917294

description: Library name: 8038917294


title: lCb from animal_28

description:
Library name: NSM1138
3 lvl sciRNAseq


title: 94_CC_2019_03_28_1, rep1

description: Library name: 94_cold_deprivation, 94_CCATTCGA-CGGACAAC-AHGKC2BBXY_L004


title: CAMA-1 Ribociclib-Resistant, Ribociclib + Afatinib, Day12 Hr24

description:
Library name: 66_CAMA1_Ribo_Afat
66_CAMA1_Ribo_Afat

value: CAMA-1 Ribociclib-Resistant

value: Day12 Hr24


title: T2-intermediate asthma_8038917382

description: Library name: 8038917382

value: T2-intermediate asthma


title: lCb from animal_27

description:
Library name: NSM1137
3 lvl sciRNAseq


title: CAMA-1 Ribociclib-Resistant, Afatinib, Day12 Hr24

description:
Library name: 65_CAMA1_Ribo_Afat
65_CAMA1_Ribo_Afat

value: ER+ Breast Cancer

value: WT


title: 93_Control_2019_03_28_3, rep3

description: Library name: 93_cold_deprivation, 93_TTGCCTAG-TAAGTGGT-AHGKC2BBXY_L006

value: flower bud


title: HIP from animal_6

description:
Library name: NSM1167
3 lvl sciRNAseq


title: CAMA-1 Ribociclib-Resistant, Ribociclib, Day12 Hr24

description:
Library name: 64_CAMA1_Ribo_Afat
64_CAMA1_Ribo_Afat


title: lCb from animal_26

description:
Library name: NSM1136
3 lvl sciRNAseq

value: lateral cerebellum


title: 93_Control_2019_03_28_3, rep2

description: Library name: 93_cold_deprivation, 93_TTGCCTAG-TAAGTGGT-AHGKC2BBXY_L005

value: plant


title: T2-intermediate asthma_8038917380

description: Library name: 8038917380

value: BIOPSY


title: CAMA-1 Ribociclib-Resistant, DMSO, Day12 Hr24

description:
Library name: 63_CAMA1_Ribo_Afat
63_CAMA1_Ribo_Afat


title: lCb from animal_25

description:
Library name: NSM1135
3 lvl sciRNAseq


title: 93_Control_2019_03_28_3, rep1

description: Library name: 93_cold_deprivation, 93_TTGCCTAG-TAAGTGGT-AHGKC2BBXY_L004


title: lCb from animal_24

description:
Library name: NSM1134
3 lvl sciRNAseq


title: T2-intermediate asthma_8038917377

description: Library name: 8038917377


title: 92_Control_2019_03_28_2, rep3

description: Library name: 92_cold_deprivation, 92_TAAGGTCA-CTACGACA-AHGKC2BBXY_L006


title: T2-intermediate asthma_8038917366

description: Library name: 8038917366


title: lCb from animal_23

description:
Library name: NSM1133
3 lvl sciRNAseq


title: RNAseq of LUAD tumor biopsy 3

description: Library name: Cancer_3

value: LUAD


title: CAMA-1 Sensitive, Afatinib, Day12 Hr24

description:
Library name: 61_CAMA1_Ribo_Afat
61_CAMA1_Ribo_Afat


title: T2-intermediate asthma_8038917356

description: Library name: 8038917356


title: 92_Control_2019_03_28_2, rep1

description: Library name: 92_cold_deprivation, 92_TAAGGTCA-CTACGACA-AHGKC2BBXY_L004

value: Regina


title: lCb from animal_21

description:
Library name: NSM1131
3 lvl sciRNAseq


title: T2-intermediate asthma_8038917357

description: Library name: 8038917357


title: CAMA-1 Sensitive, Ribociclib, Day12 Hr24

description:
Library name: 60_CAMA1_Ribo_Afat
60_CAMA1_Ribo_Afat


title: lCb from animal_22

description:
Library name: NSM1132
3 lvl sciRNAseq


title: CAMA-1 Sensitive, DMSO, Day12 Hr24

description:
Library name: 59_CAMA1_Ribo_Afat
59_CAMA1_Ribo_Afat


title: lCb from animal_20

description:
Library name: NSM1130
3 lvl sciRNAseq


title: 91_Control_2019_03_28_1, rep3

description: Library name: 91_cold_deprivation, 91_CGGAACTG-TCGTAGTG-AHGKC2BBXY_L006


title: T2-intermediate asthma_8038917354

description: Library name: 8038917354


title: CAMA-1 Ribociclib-Resistant, Ribociclib + Afatinib, Day12 Hr6

description:
Library name: 58_CAMA1_Ribo_Afat
58_CAMA1_Ribo_Afat

value: Ribociclib + Afatinib

value: Day12 Hr6


title: T2-intermediate asthma_8038917381

description: Library name: 8038917381


title: lCb from animal_19

description:
Library name: NSM1129
3 lvl sciRNAseq


title: T2-intermediate asthma_8038917353

description: Library name: 8038917353


title: 91_Control_2019_03_28_1, rep2

description: Library name: 91_cold_deprivation, 91_CGGAACTG-TCGTAGTG-AHGKC2BBXY_L005


title: CAMA-1 Ribociclib-Resistant, Afatinib, Day18 Hr24

description:
Library name: 89_CAMA1_Ribo_Afat
89_CAMA1_Ribo_Afat

value: Day18 Hr24


title: CAMA-1 Ribociclib-Resistant, Afatinib, Day12 Hr6

description:
Library name: 57_CAMA1_Ribo_Afat
57_CAMA1_Ribo_Afat


title: CAMA-1 Sensitive, Ribociclib + Afatinib, Day12 Hr24

description:
Library name: 62_CAMA1_Ribo_Afat
62_CAMA1_Ribo_Afat

value: CAMA-1 Sensitive


title: T2-intermediate asthma_8038917352

description: Library name: 8038917352


title: CAMA-1 Ribociclib-Resistant, Ribociclib, Day12 Hr6

description:
Library name: 56_CAMA1_Ribo_Afat
56_CAMA1_Ribo_Afat

value: Ribociclib


title: lCb from animal_18

description:
Library name: NSM1128
3 lvl sciRNAseq


title: T2-intermediate asthma_8038917333

description: Library name: 8038917333


title: 92_Control_2019_03_28_2, rep2

description: Library name: 92_cold_deprivation, 92_TAAGGTCA-CTACGACA-AHGKC2BBXY_L005


title: CAMA-1 Ribociclib-Resistant, DMSO, Day12 Hr6

description:
Library name: 55_CAMA1_Ribo_Afat
55_CAMA1_Ribo_Afat

value: DMSO


title: lCb from animal_16

description:
Library name: NSM1126
3 lvl sciRNAseq


title: CAMA-1 Sensitive, Ribociclib + Afatinib, Day12 Hr6

description:
Library name: 54_CAMA1_Ribo_Afat
54_CAMA1_Ribo_Afat


title: lCb from animal_14

description:
Library name: NSM1125
3 lvl sciRNAseq


title: T2-intermediate asthma_8038917331

description: Library name: 8038917331


title: 87_CC2JAN_2019_02_28_3, rep1

description: Library name: 87_cold_deprivation, 87_AGCTCGCT-GATTCTGC-AHGKC2BBXY_L004


title: 87_CC2JAN_2019_02_28_3, rep2

description: Library name: 87_cold_deprivation, 87_AGCTCGCT-GATTCTGC-AHGKC2BBXY_L005


title: T2-intermediate asthma_8038917330

description: Library name: 8038917330


title: lCb from animal_12

description:
Library name: NSM1124
3 lvl sciRNAseq


title: CAMA-1 Sensitive, Ribociclib, Day12 Hr6

description:
Library name: 52_CAMA1_Ribo_Afat
52_CAMA1_Ribo_Afat


title: CAMA-1 Sensitive, Afatinib, Day12 Hr6

description:
Library name: 53_CAMA1_Ribo_Afat
53_CAMA1_Ribo_Afat

value: Afatinib


title: 86_CC2JAN_2019_02_28_2, rep2

description: Library name: 86_cold_deprivation, 86_GATCTATC-AGCCTCAT-AHGKC2BBXY_L005


title: T2-intermediate asthma_8038917329

description: Library name: 8038917329


title: lCb from animal_11

description:
Library name: NSM1123
3 lvl sciRNAseq


title: CAMA-1 Sensitive, DMSO, Day12 Hr6

description:
Library name: 51_CAMA1_Ribo_Afat
51_CAMA1_Ribo_Afat


title: 86_CC2JAN_2019_02_28_2, rep1

description: Library name: 86_cold_deprivation, 86_GATCTATC-AGCCTCAT-AHGKC2BBXY_L004


title: CAMA-1 Ribociclib-Resistant, Ribociclib + Afatinib, Day12 Hr0

description:
Library name: 50_CAMA1_Ribo_Afat
50_CAMA1_Ribo_Afat

value: CAMA-1 Ribociclib-Resistant

value: Day12 Hr0


title: T2-intermediate asthma_8038917320

description: Library name: 8038917320

value: T2-intermediate asthma


title: 85_CC2JAN_2019_02_28_1, rep3

description: Library name: 85_cold_deprivation, 85_CATAATAC-CGTTAGAA-AHGKC2BBXY_L006


title: lCb from animal_9

description:
Library name: NSM1121
3 lvl sciRNAseq


title: T2-intermediate asthma_8038917319

description: Library name: 8038917319


title: 85_CC2JAN_2019_02_28_1, rep2

description: Library name: 85_cold_deprivation, 85_CATAATAC-CGTTAGAA-AHGKC2BBXY_L005


title: CAMA-1 Ribociclib-Resistant, Afatinib, Day12 Hr0

description:
Library name: 49_CAMA1_Ribo_Afat
49_CAMA1_Ribo_Afat

value: ER+ Breast Cancer

value: WT


title: lCb from animal_10

description:
Library name: NSM1122
3 lvl sciRNAseq

value: lateral cerebellum


title: lCb from animal_8

description:
Library name: NSM1120
3 lvl sciRNAseq


title: T2-intermediate asthma_8038917311

description: Library name: 8038917311


title: CAMA-1 Ribociclib-Resistant, Ribociclib, Day12 Hr0

description:
Library name: 48_CAMA1_Ribo_Afat
48_CAMA1_Ribo_Afat


title: 85_CC2JAN_2019_02_28_1, rep1

description: Library name: 85_cold_deprivation, 85_CATAATAC-CGTTAGAA-AHGKC2BBXY_L004

value: flower bud

value: plant


title: lCb from animal_7

description:
Library name: NSM1119
3 lvl sciRNAseq


title: T2-intermediate asthma_8038917307

description: Library name: 8038917307

value: BIOPSY


title: CAMA-1 Ribociclib-Resistant, DMSO, Day12 Hr0

description:
Library name: 47_CAMA1_Ribo_Afat
47_CAMA1_Ribo_Afat


title: T2-intermediate asthma_8038917299

description: Library name: 8038917299


title: CAMA-1 Sensitive, Ribociclib + Afatinib, Day12 Hr0

description:
Library name: 46_CAMA1_Ribo_Afat
46_CAMA1_Ribo_Afat


title: lCb from animal_5

description:
Library name: NSM1117
3 lvl sciRNAseq


title: T2-intermediate asthma_8038917298

description: Library name: 8038917298


title: CAMA-1 Sensitive, Afatinib, Day12 Hr0

description:
Library name: 45_CAMA1_Ribo_Afat
45_CAMA1_Ribo_Afat


title: 81_CC2NOV_2019_02_28_3, rep1

description: Library name: 81_cold_deprivation, 81_TGCGGCGT-TACCGAGG-AHGKC2BBXY_L004

value: Regina


title: lCb from animal_4

description:
Library name: NSM1116
3 lvl sciRNAseq


title: CAMA-1 Sensitive, Ribociclib, Day12 Hr0

description:
Library name: 44_CAMA1_Ribo_Afat
44_CAMA1_Ribo_Afat


title: 80_CC2NOV_2019_02_28_2, rep3

description: Library name: 80_cold_deprivation, 80_GAATGAGA-AATGCCTC-AHGKC2BBXY_L006


title: CAMA-1 Sensitive, DMSO, Day12 Hr0

description:
Library name: 43_CAMA1_Ribo_Afat
43_CAMA1_Ribo_Afat


title: lCb from animal_2

description:
Library name: NSM1114
3 lvl sciRNAseq


title: T2-high asthma_8038917378

description: Library name: 8038917378

value: T2-high asthma


title: CAMA-1 Ribociclib-Resistant, Ribociclib + Afatinib, Day6 Hr24

description:
Library name: 42_CAMA1_Ribo_Afat
42_CAMA1_Ribo_Afat

value: Ribociclib + Afatinib

value: Day6 Hr24


title: 81_CC2NOV_2019_02_28_3, rep2

description: Library name: 81_cold_deprivation, 81_TGCGGCGT-TACCGAGG-AHGKC2BBXY_L005


title: 80_CC2NOV_2019_02_28_2, rep2

description: Library name: 80_cold_deprivation, 80_GAATGAGA-AATGCCTC-AHGKC2BBXY_L005


title: lCb from animal_1

description:
Library name: NSM1113
3 lvl sciRNAseq


title: T2-high asthma_8038917376

description: Library name: 8038917376


title: CAMA-1 Ribociclib-Resistant, Afatinib, Day6 Hr24

description:
Library name: 41_CAMA1_Ribo_Afat
41_CAMA1_Ribo_Afat


title: 79_CC2NOV_2019_02_28_1, rep3

description: Library name: 79_cold_deprivation, 79_AGGCAGAG-GGCATTCT-AHGKC2BBXY_L006


title: T2-high asthma_8038917370

description: Library name: 8038917370


title: CAMA-1 Ribociclib-Resistant, Ribociclib, Day6 Hr24

description:
Library name: 40_CAMA1_Ribo_Afat
40_CAMA1_Ribo_Afat


title: 79_CC2NOV_2019_02_28_1, rep2

description: Library name: 79_cold_deprivation, 79_AGGCAGAG-GGCATTCT-AHGKC2BBXY_L005


title: IPP from animal_54

description:
Library name: NSM1062
3 lvl sciRNAseq

source_name: inferior posterior parietal cortex

value: inferior posterior parietal cortex


title: T2-high asthma_8038917369

description: Library name: 8038917369


title: 79_CC2NOV_2019_02_28_1, rep1

description: Library name: 79_cold_deprivation, 79_AGGCAGAG-GGCATTCT-AHGKC2BBXY_L004


title: T2-high asthma_8038917368

description: Library name: 8038917368


title: IPP from animal_53

description:
Library name: NSM1061
3 lvl sciRNAseq


title: CAMA-1 Sensitive, Ribociclib + Afatinib, Day6 Hr24

description:
Library name: 38_CAMA1_Ribo_Afat
38_CAMA1_Ribo_Afat

value: CAMA-1 Sensitive


title: 75_CC_2019_02_28_3, rep3

description: Library name: 75_cold_deprivation, 75_TGGTGGCA-TTACAGGA-AHGKC2BBXY_L006


title: T2-high asthma_8038917365

description: Library name: 8038917365


title: CAMA-1 Sensitive, Afatinib, Day6 Hr24

description:
Library name: 37_CAMA1_Ribo_Afat
37_CAMA1_Ribo_Afat


title: 75_CC_2019_02_28_3, rep2

description: Library name: 75_cold_deprivation, 75_TGGTGGCA-TTACAGGA-AHGKC2BBXY_L005


title: CAMA-1 Sensitive, Ribociclib, Day6 Hr24

description:
Library name: 36_CAMA1_Ribo_Afat
36_CAMA1_Ribo_Afat

value: Ribociclib


title: T2-high asthma_8038917364

description: Library name: 8038917364


title: T2-high asthma_8038917346

description: Library name: 8038917346


title: IPP from animal_50

description:
Library name: NSM1058
3 lvl sciRNAseq


title: IPP from animal_51

description:
Library name: NSM1059
3 lvl sciRNAseq


title: 75_CC_2019_02_28_3, rep1

description: Library name: 75_cold_deprivation, 75_TGGTGGCA-TTACAGGA-AHGKC2BBXY_L004


title: IPP from animal_49

description:
Library name: NSM1057
3 lvl sciRNAseq


title: 91_Control_2019_03_28_1, rep1

description: Library name: 91_cold_deprivation, 91_CGGAACTG-TCGTAGTG-AHGKC2BBXY_L004


title: 87_CC2JAN_2019_02_28_3, rep3

description: Library name: 87_cold_deprivation, 87_AGCTCGCT-GATTCTGC-AHGKC2BBXY_L006


title: T2-high asthma_8038917345

description: Library name: 8038917345


title: lCb from animal_17

description:
Library name: NSM1127
3 lvl sciRNAseq


title: T2-intermediate asthma_8038917332

description: Library name: 8038917332


title: CAMA-1 Ribociclib-Resistant, Ribociclib + Afatinib, Day6 Hr6

description:
Library name: 34_CAMA1_Ribo_Afat
34_CAMA1_Ribo_Afat

value: Day6 Hr6


title: CAMA-1 Sensitive, DMSO, Day6 Hr24

description:
Library name: 35_CAMA1_Ribo_Afat
35_CAMA1_Ribo_Afat

value: DMSO


title: 86_CC2JAN_2019_02_28_2, rep3

description: Library name: 86_cold_deprivation, 86_GATCTATC-AGCCTCAT-AHGKC2BBXY_L006


title: 74_CC_2019_02_28_2, rep2

description: Library name: 74_cold_deprivation, 74_CAACAATG-CCGTGAAG-AHGKC2BBXY_L005


title: IPP from animal_48

description:
Library name: NSM1056
3 lvl sciRNAseq


title: T2-high asthma_8038917342

description: Library name: 8038917342


title: 74_CC_2019_02_28_2, rep3

description: Library name: 74_cold_deprivation, 74_CAACAATG-CCGTGAAG-AHGKC2BBXY_L006


title: CAMA-1 Ribociclib-Resistant, Afatinib, Day6 Hr6

description:
Library name: 33_CAMA1_Ribo_Afat
33_CAMA1_Ribo_Afat

value: CAMA-1 Ribociclib-Resistant

value: Afatinib


title: 74_CC_2019_02_28_2, rep1

description: Library name: 74_cold_deprivation, 74_CAACAATG-CCGTGAAG-AHGKC2BBXY_L004


title: IPP from animal_47

description:
Library name: NSM1055
3 lvl sciRNAseq


title: T2-high asthma_8038917341

description: Library name: 8038917341


title: CAMA-1 Ribociclib-Resistant, Ribociclib, Day6 Hr6

description:
Library name: 32_CAMA1_Ribo_Afat
32_CAMA1_Ribo_Afat

value: ER+ Breast Cancer


title: 73_CC_2019_02_28_1, rep3

description: Library name: 73_cold_deprivation, 73_GGTGAACC-TCCAACGC-AHGKC2BBXY_L006


title: IPP from animal_46

description:
Library name: NSM1054
3 lvl sciRNAseq


title: T2-high asthma_8038917340

description: Library name: 8038917340


title: CAMA-1 Ribociclib-Resistant, DMSO, Day6 Hr6

description:
Library name: 31_CAMA1_Ribo_Afat
31_CAMA1_Ribo_Afat

value: WT


title: 73_CC_2019_02_28_1, rep2

description: Library name: 73_cold_deprivation, 73_GGTGAACC-TCCAACGC-AHGKC2BBXY_L005


title: IPP from animal_45

description:
Library name: NSM1053
3 lvl sciRNAseq


title: T2-high asthma_8038917334

description: Library name: 8038917334


title: lCb from animal_6

description:
Library name: NSM1118
3 lvl sciRNAseq

value: lateral cerebellum


title: 81_CC2NOV_2019_02_28_3, rep3

description: Library name: 81_cold_deprivation, 81_TGCGGCGT-TACCGAGG-AHGKC2BBXY_L006

value: flower bud


title: CAMA-1 Sensitive, Ribociclib + Afatinib, Day6 Hr6

description:
Library name: 30_CAMA1_Ribo_Afat
30_CAMA1_Ribo_Afat


title: 73_CC_2019_02_28_1, rep1

description: Library name: 73_cold_deprivation, 73_GGTGAACC-TCCAACGC-AHGKC2BBXY_L004

value: plant


title: IPP from animal_44

description:
Library name: NSM1052
3 lvl sciRNAseq


title: T2-high asthma_8038917322

description: Library name: 8038917322

value: BIOPSY


title: CAMA-1 Sensitive, Afatinib, Day6 Hr6

description:
Library name: 29_CAMA1_Ribo_Afat
29_CAMA1_Ribo_Afat


title: IPP from animal_43

description:
Library name: NSM1051
3 lvl sciRNAseq


title: T2-high asthma_8038917318

description: Library name: 8038917318


title: T2-intermediate asthma_8038917297

description: Library name: 8038917297

value: T2-intermediate asthma


title: 72_Control_2019_02_28_3, rep2

description: Library name: 72_cold_deprivation, 72_AACAGGTT-CTTGGTAT-AHGKC2BBXY_L005

value: Regina


title: IPP from animal_42

description:
Library name: NSM1050
3 lvl sciRNAseq


title: T2-high asthma_8038917317

description: Library name: 8038917317

value: T2-high asthma


title: CAMA-1 Sensitive, Ribociclib, Day6 Hr6

description:
Library name: 28_CAMA1_Ribo_Afat
28_CAMA1_Ribo_Afat


title: CAMA-1 Sensitive, DMSO, Day6 Hr6

description:
Library name: 27_CAMA1_Ribo_Afat
27_CAMA1_Ribo_Afat


title: 72_Control_2019_02_28_3, rep1

description: Library name: 72_cold_deprivation, 72_AACAGGTT-CTTGGTAT-AHGKC2BBXY_L004


title: T2-high asthma_8038917305

description: Library name: 8038917305


title: CAMA-1 Ribociclib-Resistant, Ribociclib + Afatinib, Day6 Hr0

description:
Library name: 26_CAMA1_Ribo_Afat
26_CAMA1_Ribo_Afat

value: Ribociclib + Afatinib

value: Day6 Hr0


title: T2-high asthma_8038917293

description: Library name: 8038917293


title: lCb from animal_3

description:
Library name: NSM1115
3 lvl sciRNAseq


title: 71_Control_2019_02_28_2, rep2

description: Library name: 71_cold_deprivation, 71_GCGCTCTA-GTCGGAGC-AHGKC2BBXY_L005


title: IPP from animal_40

description:
Library name: NSM1048
3 lvl sciRNAseq

value: inferior posterior parietal cortex


title: 71_Control_2019_02_28_2, rep3

description: Library name: 71_cold_deprivation, 71_GCGCTCTA-GTCGGAGC-AHGKC2BBXY_L006


title: IPP from animal_39

description:
Library name: NSM1047
3 lvl sciRNAseq


title: CAMA-1 Ribociclib-Resistant, Ribociclib, Day6 Hr0

description:
Library name: 24_CAMA1_Ribo_Afat
24_CAMA1_Ribo_Afat

value: Ribociclib


title: 72_Control_2019_02_28_3, rep3

description: Library name: 72_cold_deprivation, 72_AACAGGTT-CTTGGTAT-AHGKC2BBXY_L006


title: Healthy control_8038917328

description: Library name: 8038917328

value: Healthy control


title: CAMA-1 Ribociclib-Resistant, Afatinib, Day6 Hr0

description:
Library name: 25_CAMA1_Ribo_Afat
25_CAMA1_Ribo_Afat


title: IPP from animal_38

description:
Library name: NSM1046
3 lvl sciRNAseq


title: Healthy control_8038917316

description: Library name: 8038917316


title: Healthy control_8038917304

description: Library name: 8038917304


title: 70_Control_2019_02_28_1, rep3

description: Library name: 70_cold_deprivation, 70_ATATCTCG-ACTAAGAT-AHGKC2BBXY_L006


title: CAMA-1 Sensitive, Ribociclib + Afatinib, Day6 Hr0

description:
Library name: 22_CAMA1_Ribo_Afat
22_CAMA1_Ribo_Afat

value: CAMA-1 Sensitive


title: IPP from animal_36

description:
Library name: NSM1044
3 lvl sciRNAseq


title: Healthy control_8038917292

description: Library name: 8038917292


title: CAMA-1 Sensitive, Afatinib, Day6 Hr0

description:
Library name: 21_CAMA1_Ribo_Afat
21_CAMA1_Ribo_Afat


title: IPP from animal_35

description:
Library name: NSM1043
3 lvl sciRNAseq


title: Healthy control_8038915173

description: Library name: 8038915173


title: 69_CC2JAN_2019_02_01_3, rep3

description: Library name: 69_cold_deprivation, 69_ACCTTGGC-ATGAGGCC-AHGKC2BBXY_L006


title: CAMA-1 Sensitive, Ribociclib, Day6 Hr0

description:
Library name: 20_CAMA1_Ribo_Afat
20_CAMA1_Ribo_Afat


title: IPP from animal_34

description:
Library name: NSM1042
3 lvl sciRNAseq


title: Healthy control_8038915172

description: Library name: 8038915172


title: 69_CC2JAN_2019_02_01_3, rep2

description: Library name: 69_cold_deprivation, 69_ACCTTGGC-ATGAGGCC-AHGKC2BBXY_L005


title: IPP from animal_33

description:
Library name: NSM1041
3 lvl sciRNAseq


title: Healthy control_8038915159

description: Library name: 8038915159


title: CAMA-1 Ribociclib-Resistant, Ribociclib + Afatinib, Day0 Hr24

description:
Library name: 18_CAMA1_Ribo_Afat
18_CAMA1_Ribo_Afat

value: CAMA-1 Ribociclib-Resistant

value: Day0 Hr24


title: 69_CC2JAN_2019_02_01_3, rep1

description: Library name: 69_cold_deprivation, 69_ACCTTGGC-ATGAGGCC-AHGKC2BBXY_L004


title: IPP from animal_32

description:
Library name: NSM1040
3 lvl sciRNAseq


title: IPP from animal_37

description:
Library name: NSM1045
3 lvl sciRNAseq


title: Healthy control_8038915157

description: Library name: 8038915157


title: 68_CC2JAN_2019_02_01_2, rep3

description: Library name: 68_cold_deprivation, 68_GTTCCAAT-GCAGAATT-AHGKC2BBXY_L006


title: IPP from animal_31

description:
Library name: NSM1039
3 lvl sciRNAseq


title: Healthy control_8038915156

description: Library name: 8038915156


title: IPP from animal_30

description:
Library name: NSM1038
3 lvl sciRNAseq


title: 68_CC2JAN_2019_02_01_2, rep2

description: Library name: 68_cold_deprivation, 68_GTTCCAAT-GCAGAATT-AHGKC2BBXY_L005


title: CAMA-1 Ribociclib-Resistant, DMSO, Day0 Hr24

description:
Library name: 15_CAMA1_Ribo_Afat
15_CAMA1_Ribo_Afat

value: ER+ Breast Cancer

value: DMSO


title: Healthy control_8038915144

description: Library name: 8038915144


title: 68_CC2JAN_2019_02_01_2, rep1

description: Library name: 68_cold_deprivation, 68_GTTCCAAT-GCAGAATT-AHGKC2BBXY_L004


title: IPP from animal_29

description:
Library name: NSM1037
3 lvl sciRNAseq


title: Healthy control_8038915126

description: Library name: 8038915126


title: CAMA-1 Ribociclib-Resistant, DMSO, Day6 Hr0

description:
Library name: 23_CAMA1_Ribo_Afat
23_CAMA1_Ribo_Afat

value: WT


title: 70_Control_2019_02_28_1, rep2

description: Library name: 70_cold_deprivation, 70_ATATCTCG-ACTAAGAT-AHGKC2BBXY_L005

value: flower bud


title: 67_CC2JAN_2019_02_01_1, rep3

description: Library name: 67_cold_deprivation, 67_GCAATGCA-AACGTTCC-AHGKC2BBXY_L006

value: plant


title: CAMA-1 Sensitive, Ribociclib + Afatinib, Day0 Hr24

description:
Library name: 14_CAMA1_Ribo_Afat
14_CAMA1_Ribo_Afat


title: IPP from animal_28

description:
Library name: NSM1036
3 lvl sciRNAseq


title: Healthy control_8038915104

description: Library name: 8038915104

value: BIOPSY


title: 70_Control_2019_02_28_1, rep1

description: Library name: 70_cold_deprivation, 70_ATATCTCG-ACTAAGAT-AHGKC2BBXY_L004


title: CAMA-1 Sensitive, Afatinib, Day0 Hr24

description:
Library name: 13_CAMA1_Ribo_Afat
13_CAMA1_Ribo_Afat

value: Afatinib


title: IPP from animal_27

description:
Library name: NSM1035
3 lvl sciRNAseq


title: 67_CC2JAN_2019_02_01_1, rep2

description: Library name: 67_cold_deprivation, 67_GCAATGCA-AACGTTCC-AHGKC2BBXY_L005

value: Regina


title: Healthy control_8038915100

description: Library name: 8038915100


title: CAMA-1 Sensitive, Ribociclib, Day0 Hr24

description:
Library name: 12_CAMA1_Ribo_Afat
12_CAMA1_Ribo_Afat


title: 67_CC2JAN_2019_02_01_1, rep1

description: Library name: 67_cold_deprivation, 67_GCAATGCA-AACGTTCC-AHGKC2BBXY_L004


title: CAMA-1 Sensitive, DMSO, Day6 Hr0

description:
Library name: 19_CAMA1_Ribo_Afat
19_CAMA1_Ribo_Afat


title: Healthy control_8038915099

description: Library name: 8038915099


title: IPP from animal_26

description:
Library name: NSM1034
3 lvl sciRNAseq


title: CAMA-1 Sensitive, DMSO, Day0 Hr24

description:
Library name: 11_CAMA1_Ribo_Afat
11_CAMA1_Ribo_Afat


title: Healthy control_8038915097

description: Library name: 8038915097


title: IPP from animal_25

description:
Library name: NSM1033
3 lvl sciRNAseq


title: 63_CC2NOV_2019_02_01_3, rep3

description: Library name: 63_cold_deprivation, 63_ATGGCATG-GGTACCTT-AHGKC2BBXY_L006


title: CAMA-1 Ribociclib-Resistant, Ribociclib + Afatinib, Day0 Hr6

description:
Library name: 10_CAMA1_Ribo_Afat
10_CAMA1_Ribo_Afat

value: Day0 Hr6


title: 63_CC2NOV_2019_02_01_3, rep2

description: Library name: 63_cold_deprivation, 63_ATGGCATG-GGTACCTT-AHGKC2BBXY_L005


title: IPP from animal_24

description:
Library name: NSM1032
3 lvl sciRNAseq


title: Healthy control_8038915096

description: Library name: 8038915096


title: 63_CC2NOV_2019_02_01_3, rep1

description: Library name: 63_cold_deprivation, 63_ATGGCATG-GGTACCTT-AHGKC2BBXY_L004


title: CAMA-1 Ribociclib-Resistant, Afatinib, Day0 Hr6

description:
Library name: 9_CAMA1_Ribo_Afat
9_CAMA1_Ribo_Afat


title: CAMA-1 Ribociclib-Resistant, Afatinib, Day0 Hr24

description:
Library name: 17_CAMA1_Ribo_Afat
17_CAMA1_Ribo_Afat


title: Healthy control_8038915090

description: Library name: 8038915090


title: IPP from animal_23

description:
Library name: NSM1031
3 lvl sciRNAseq


title: CAMA-1 Ribociclib-Resistant, Ribociclib, Day0 Hr6

description:
Library name: 8_CAMA1_Ribo_Afat
8_CAMA1_Ribo_Afat


title: CAMA-1 Ribociclib-Resistant, Ribociclib, Day0 Hr24

description:
Library name: 16_CAMA1_Ribo_Afat
16_CAMA1_Ribo_Afat


title: Healthy control_8038915089

description: Library name: 8038915089


title: 62_CC2NOV_2019_02_01_2, rep3

description: Library name: 62_cold_deprivation, 62_GGAGCGTC-GCACGGAC-AHGKC2BBXY_L006


title: IPP from animal_22

description:
Library name: NSM1030
3 lvl sciRNAseq


title: CAMA-1 Ribociclib-Resistant, DMSO, Day0 Hr6

description:
Library name: 7_CAMA1_Ribo_Afat
7_CAMA1_Ribo_Afat


title: 62_CC2NOV_2019_02_01_2, rep2

description: Library name: 62_cold_deprivation, 62_GGAGCGTC-GCACGGAC-AHGKC2BBXY_L005


title: IPP from animal_21

description:
Library name: NSM1029
3 lvl sciRNAseq


title: Healthy control_8038915087

description: Library name: 8038915087


title: CAMA-1 Sensitive, Ribociclib + Afatinib, Day0 Hr6

description:
Library name: 6_CAMA1_Ribo_Afat
6_CAMA1_Ribo_Afat

value: Ribociclib + Afatinib


title: 62_CC2NOV_2019_02_01_2, rep1

description: Library name: 62_cold_deprivation, 62_GGAGCGTC-GCACGGAC-AHGKC2BBXY_L004


title: IPP from animal_20

description:
Library name: NSM1028
3 lvl sciRNAseq


title: Healthy control_8038915086

description: Library name: 8038915086


title: CAMA-1 Sensitive, Afatinib, Day0 Hr6

description:
Library name: 5_CAMA1_Ribo_Afat
5_CAMA1_Ribo_Afat


title: 61_CC2NOV_2019_02_01_1, rep3

description: Library name: 61_cold_deprivation, 61_AAGATACT-ATGTAAGT-AHGKC2BBXY_L006


title: Patient 102 COAD 102

type: RNA

first: Chungyeop

address: Songpagu Olympicro 43gil

institute: Asan Medical Center

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software. Training cohort and validation cohort normalization were separately conducted.

source_name: Locally Advanced Rectal Cancer

label_protocol: No labeling was performed; digital barcoding system was used (NanoString).

extract_protocol: Total RNA was extracted from pretreatment FFPE biopsy tissues using the RNeasy FFPE Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol.

value: rectal cancer

tag: histology

value: Moderate


title: CAMA-1 Sensitive, Ribociclib, Day0 Hr6

description:
Library name: 4_CAMA1_Ribo_Afat
4_CAMA1_Ribo_Afat

value: Ribociclib


title: 61_CC2NOV_2019_02_01_1, rep2

description: Library name: 61_cold_deprivation, 61_AAGATACT-ATGTAAGT-AHGKC2BBXY_L005


title: IPP from animal_19

description:
Library name: NSM1027
3 lvl sciRNAseq

value: inferior posterior parietal cortex


title: IPP from animal_18

description:
Library name: NSM1026
3 lvl sciRNAseq


title: CAMA-1 Sensitive, DMSO, Day0 Hr6

description:
Library name: 3_CAMA1_Ribo_Afat
3_CAMA1_Ribo_Afat

value: CAMA-1 Sensitive


title: IPP from animal_17

description:
Library name: NSM1025
3 lvl sciRNAseq


title: 61_CC2NOV_2019_02_01_1, rep1

description: Library name: 61_cold_deprivation, 61_AAGATACT-ATGTAAGT-AHGKC2BBXY_L004


title: Patient 101 COAD 101

description: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software.

value: Total


title: CAMA-1 Ribociclib-Resistant, DMSO, Day0 Hr0

description:
Library name: 2_CAMA1_Ribo_Afat
2_CAMA1_Ribo_Afat

value: CAMA-1 Ribociclib-Resistant

value: Day0 Hr0


title: Patient 100 COAD 100


title: 57_CC_2019_02_01_3, rep3

description: Library name: 57_cold_deprivation, 57_GCGCAAGC-CGGCGTGA-AHGKC2BBXY_L006


title: IPP from animal_16

description:
Library name: NSM1024
3 lvl sciRNAseq


title: CAMA-1 Sensitive, DMSO, Day0 Hr0

description:
Library name: 1_CAMA1_Ribo_Afat
1_CAMA1_Ribo_Afat

value: ER+ Breast Cancer


title: 57_CC_2019_02_01_3, rep2

description: Library name: 57_cold_deprivation, 57_GCGCAAGC-CGGCGTGA-AHGKC2BBXY_L005


title: Patient 99 COAD 099

value: Minimal


title: IPP from animal_15

description:
Library name: NSM1023
3 lvl sciRNAseq


title: 57_CC_2019_02_01_3, rep1

description: Library name: 57_cold_deprivation, 57_GCGCAAGC-CGGCGTGA-AHGKC2BBXY_L004

value: flower bud


title: MCF-7 Ribociclib-Resistant, Ribociclib + Afatinib, Day18 Hr24

description:
Library name: 90_MCF7_Ribo_Afat
90_MCF7_Ribo_Afat

source_name: MCF-7 Ribociclib-Resistant

value: MCF-7 Ribociclib-Resistant

value: WT

value: Day18 Hr24


title: IPP from animal_14

description:
Library name: NSM1022
3 lvl sciRNAseq


title: Patient 98 COAD 098


title: MCF-7 Ribociclib-Resistant, Afatinib, Day18 Hr24

description:
Library name: 89_MCF7_Ribo_Afat
89_MCF7_Ribo_Afat

value: Afatinib


title: Patient 97 COAD 097


title: 56_CC_2019_02_01_2, rep3

description: Library name: 56_cold_deprivation, 56_ATATGGAT-TAATACAG-AHGKC2BBXY_L006

value: plant

value: Regina


title: IPP from animal_13

description:
Library name: NSM1021
3 lvl sciRNAseq


title: Patient 96 COAD 096

value: rectal cancer


title: MCF-7 Ribociclib-Resistant, Ribociclib, Day18 Hr24

description:
Library name: 88_MCF7_Ribo_Afat
88_MCF7_Ribo_Afat


title: 56_CC_2019_02_01_2, rep2

description: Library name: 56_cold_deprivation, 56_ATATGGAT-TAATACAG-AHGKC2BBXY_L005


title: IPP from animal_12

description:
Library name: NSM1020
3 lvl sciRNAseq


title: Patient 95 COAD 095

value: Moderate


title: MCF-7 Ribociclib-Resistant, DMSO, Day18 Hr24

description:
Library name: 87_MCF7_Ribo_Afat
87_MCF7_Ribo_Afat

value: DMSO


title: 56_CC_2019_02_01_2, rep1

description: Library name: 56_cold_deprivation, 56_ATATGGAT-TAATACAG-AHGKC2BBXY_L004


title: IPP from animal_11

description:
Library name: NSM1019
3 lvl sciRNAseq

value: inferior posterior parietal cortex


title: Patient 94 COAD 094


title: IPP from animal_10

description:
Library name: NSM1018
3 lvl sciRNAseq


title: 55_CC_2019_02_01_1, rep3

description: Library name: 55_cold_deprivation, 55_CGGACAAC-AATCCGGA-AHGKC2BBXY_L006


title: IPP from animal_41

description:
Library name: NSM1049
3 lvl sciRNAseq


title: MCF-7 Sensitive, Ribociclib + Afatinib, Day18 Hr24

description:
Library name: 86_MCF7_Ribo_Afat
86_MCF7_Ribo_Afat

source_name: MCF-7 Sensitive

value: MCF-7 Sensitive

value: Ribociclib + Afatinib


title: MCF-7 Sensitive, Afatinib, Day18 Hr24

description:
Library name: 85_MCF7_Ribo_Afat
85_MCF7_Ribo_Afat


title: Patient 93 COAD 093

value: Near total


title: 55_CC_2019_02_01_1, rep2

description: Library name: 55_cold_deprivation, 55_CGGACAAC-AATCCGGA-AHGKC2BBXY_L005


title: IPP from animal_9

description:
Library name: NSM1017
3 lvl sciRNAseq


title: MCF-7 Sensitive, Ribociclib, Day18 Hr24

description:
Library name: 84_MCF7_Ribo_Afat
84_MCF7_Ribo_Afat

value: Ribociclib


title: Patient 92 COAD 092

description: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software.


title: IPP from animal_8

description:
Library name: NSM1016
3 lvl sciRNAseq


title: 55_CC_2019_02_01_1, rep1

description: Library name: 55_cold_deprivation, 55_CGGACAAC-AATCCGGA-AHGKC2BBXY_L004


title: MCF-7 Sensitive, DMSO, Day18 Hr24

description:
Library name: 83_MCF7_Ribo_Afat
83_MCF7_Ribo_Afat

value: ER+ Breast Cancer


title: IPP from animal_7

description:
Library name: NSM1015
3 lvl sciRNAseq


title: 54_Control_2019_02_01_3, rep3

description: Library name: 54_cold_deprivation, 54_TAAGTGGT-GGCTTAAG-AHGKC2BBXY_L006


title: Patient 91 COAD 091

value: Total


title: 54_Control_2019_02_01_3, rep2

description: Library name: 54_cold_deprivation, 54_TAAGTGGT-GGCTTAAG-AHGKC2BBXY_L005

value: flower bud


title: MCF-7 Ribociclib-Resistant, Ribociclib + Afatinib, Day18 Hr6

description:
Library name: 82_MCF7_Ribo_Afat
82_MCF7_Ribo_Afat

value: MCF-7 Ribociclib-Resistant

value: Day18 Hr6


title: 71_Control_2019_02_28_2, rep1

description: Library name: 71_cold_deprivation, 71_GCGCTCTA-GTCGGAGC-AHGKC2BBXY_L004


title: Patient 90 COAD 090


title: IPP from animal_6

description:
Library name: NSM1014
3 lvl sciRNAseq


title: MCF-7 Ribociclib-Resistant, Afatinib, Day18 Hr6

description:
Library name: 81_MCF7_Ribo_Afat
81_MCF7_Ribo_Afat

value: WT


title: Patient 89 COAD 089


title: IPP from animal_5

description:
Library name: NSM1013
3 lvl sciRNAseq


title: 54_Control_2019_02_01_3, rep1

description: Library name: 54_cold_deprivation, 54_TAAGTGGT-GGCTTAAG-AHGKC2BBXY_L004


title: MCF-7 Ribociclib-Resistant, Ribociclib, Day18 Hr6

description:
Library name: 80_MCF7_Ribo_Afat
80_MCF7_Ribo_Afat


title: 53_Control_2019_02_01_2, rep3

description: Library name: 53_cold_deprivation, 53_CTACGACA-TTGGACTC-AHGKC2BBXY_L006


title: IPP from animal_4

description:
Library name: NSM1012
3 lvl sciRNAseq


title: Patient 88 COAD 088

value: Minimal


title: MCF-7 Ribociclib-Resistant, DMSO, Day18 Hr6

description:
Library name: 79_MCF7_Ribo_Afat
79_MCF7_Ribo_Afat


title: mGSCs-I-SB cells, shHSPA8-2

city: xian yang

first: donghui

last: Yang

state: shaanxi

address: No. 3rd, Taicheng Road, Yangling, Shaanxi

country: China

institute: Northwest A&F University

data_processing:
Trimmomatic (v0.36)
Raw sequencing data were first filtered using Trimmomatic (v0.36), with low-quality reads discarded and reads contaminated with adaptor sequences trimmed.
Clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster.  Reads in the same cluster were compared to each other by pairwise alignment and reads with sequence identity over 95% were then extracted to a new sub-cluster.
All sub-clusters were generated, multiple sequence alignments were performed to obtain one consensus sequence for each sub-cluster
Assembly: Capra
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Capra hircus

source_name: mGSCs-I-SB

growth_protocol: mGSCs-I-SB cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: mGSCs-I-SB

value: Spermatogonial stem cells

value: HSPA8 knockdown


title: IPP from animal_3

description:
Library name: NSM1011
3 lvl sciRNAseq


title: Patient 87 COAD 087

value: rectal cancer


title: MCF-7 Sensitive, Ribociclib + Afatinib, Day18 Hr6

description:
Library name: 78_MCF7_Ribo_Afat
78_MCF7_Ribo_Afat


title: Patient 86 COAD 086


title: mGSCs-I-SB cells, shHSPA8-1


title: IPP from animal_2

description:
Library name: NSM1010
3 lvl sciRNAseq


title: Patient 85 COAD 085


title: mGSCs-I-SB cells, shUCHL1-2

value: UCHL1 knockdown


title: MCF-7 Sensitive, Afatinib, Day18 Hr6

description:
Library name: 77_MCF7_Ribo_Afat
77_MCF7_Ribo_Afat

value: Afatinib


title: MCF-7 Sensitive, Ribociclib, Day18 Hr6

description:
Library name: 76_MCF7_Ribo_Afat
76_MCF7_Ribo_Afat

value: MCF-7 Sensitive


title: mGSCs-I-SB cells, shUCHL1-1


title: Patient 84 COAD 084


title: peaks HeLa cells, 24hrs Oligomycin + Antimycin, pS65Ub ChIPseq, rep 2

city: South San Francisco

first: Daniel

last: Le

state: CA

address: 1 DNA Way

institute: Genentech

description: Library name: SAM24456503_OA2_pS65Ub_bed

library_source: genomic

data_processing:
ChIP Seq: The ENCODE analysis pipeline (v2.2.1) was used, with Bowtie2 (v2.3.4.3) employed to align reads to the reference genome (hg38). Duplicated or low-quality reads were filtered out using Picard (Broad Institute - v2.20.7) and samtools (v1.9), with further filtering to remove regions where genome assembly introduces erroneous signal. The SPP data processing pipeline was used to call peaks, with the level of background signal assessed via reference to input sample. DiffBind (v3.12.0) was used to identify differential peaks as follows. RPKM-normalized ChIP Seq data was visualized using IGV (2.18.4) genome browser
CUT&RUN: Indexed libraries generated using NEBNext library prep kit 32 (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) as per manufacturers instructions. Paired-end reads were aligned to the reference genome (hg38) using Bowtie2 (-p 24 -X2000 -t -x) and sorted with Samtools (view -bS -F 4 -q 30 -u - | sort -T). PCR duplicates were marked using Picard MarkDuplicates (MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 REMOVE_DUPLICATES=true ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT). Genome-wide coverage was determined using Bedtools genomecov (-ibam -bg -scale -g), converted to a BigWig file with wigToBigWig -clip.
Assembly: hg38
Supplementary files format and content: bigwig files for each sample
Supplementary files format and content: bed files for each sample

molecule: genomic DNA

source_name: HeLa Cells

extract_protocol:
ChIP-Seq samples were extracted as follows: 50mM DSG (disuccinimidyl glutarate, #C1104 - ProteoChem) for 30 mins followed by 10 mins of 1% formaldehyde was used to double crosslink HeLa or iPSC-derived NGN2 neurons (5x106), followed by the addition of glycine to quench formaldehyde. Nuclei were released using ChIP Nuclear Isolation Buffer (20 mM Tris pH 8.0, 1% Triton X-100, 0.1% SDS, 150 mM NaCl and 1mM EDTA), and chromatin sheared via sonication (Covaris sonicator: Fill level – 10, Duty Cycle – 15, PIP – 350, Cycles/Burst – 200, Time – 8-mins). Solutions containing sheared chromatin were mixed with relevant antibodies and rotated at 4°C overnight before protein A magnetic beads were then added to isolate antibody-bound chromatin. The beads were washed twice in each of the following buffers: ChIP Wash Buffer #1 (20 mM Tris pH 8.0, 1% Triton X-100, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, and 0.1% NaDOC), ChIP Wash Buffer #2. (20 mM Tris pH 8.0, 1% Triton X-100, 0.1% SDS, 500 mM NaCl, 1 mM EDTA, and 0.1% NaDOC) and ChIP Wash Buffer #3 (0.25 M LiCl, 0.5% NP-40, 1mM EDTA, 20 mM Tris, pH 8.0, 0.5% NaDOC), followed by single wash in TE buffer (200 mM Tris pH 8.0 and 10 mM EDTA). The mixtures were then shaken for 20 mins in Elution Buffer (100mM NaHCO3, 1% SDS), before overnight incubation at 65°C to de-crosslink DNA. The DNA fragments were purified with MinElute PCR purification kit (Qiagen), then quantified by Qubit. CUT&RUN was performed using the CUTANA ChIC/CUT&RUN Kit (Epicypher) as per manufacturers instructions with the addition of DUB inhibitor PR-619 (100μM) to Wash and Antibody buffers.
ChIP-Seq libraries were generated using Ovation Ultralow Library System V2 (Tecan) using 2ng of each sample according to the manufacturer’s instructions, then sequenced using paired-end 50bp read configuration. CUT&RUN libraries were generated using NEBNext library prep kit 32 (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) as per manufacturers instructions.

value: HeLa Cells

value: Epithelial

value: 24hrs Oligomycin (1µM) + Antimycin (1µM)


title: Patient 83 COAD 083


title: mGSCs-I-SB cells, shCON-2


title: MCF-7 Sensitive, DMSO, Day18 Hr6

description:
Library name: 75_MCF7_Ribo_Afat
75_MCF7_Ribo_Afat

value: ER+ Breast Cancer

value: DMSO


title: peaks HeLa cells, 24hrs Oligomycin + Antimycin, pS65UbChIPseq, rep 1

description: Library name: SAM24456502_OA1_pS65Ub_bed


title: MCF-7 Ribociclib-Resistant, Ribociclib + Afatinib, Day18 Hr0

description:
Library name: 74_MCF7_Ribo_Afat
74_MCF7_Ribo_Afat

value: Ribociclib + Afatinib

value: Day18 Hr0


title: Patient 82 COAD 082

description: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software.

value: Moderate


title: mGSCs-I-SB cells, shCON-1

value: WT


title: peaks HeLa cells, 24hrs DMSO, pS65Ub ChIPseq, rep 2

description: Library name: SAM24456501_V2_pS65Ub_bed

value: 24hrs DMSO


title: MCF-7 Ribociclib-Resistant, Afatinib, Day18 Hr0

description:
Library name: 73_MCF7_Ribo_Afat
73_MCF7_Ribo_Afat

value: MCF-7 Ribociclib-Resistant


title: S3-GFP (+) mTmG(GFP-KRas-G12D) rep 3

city: Chicago

first: Jalees

last: Rehman

state: IL

address: 900 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

description: Library name: E3_S3_GFP_positive

data_processing:
Sequenced reads were mapped to the reference genome (GRCh38) and their abundances were quantified using Salmon v1.3.0 in quasi-mapping mode. Salmon produced transcript-level quantification files, which were subsequently aggregated into gene-level counts for downstream analysis.
Assembly: hg38
Supplementary files format and content: Gene level raw counts matrix per sample as quantified by salmon

source_name: HEK293T ATCC (CRL-3216)

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 5% fetal bovine serum (FBS) and 1% glutamine. Cells were maintained at 37 °C in a humidified incubator with 5% CO₂ and seeded onto plastic culture dishes coated with 1:200 poly-L-lysine. Cells were grown to approximately 70% confluency prior to transfection.

extract_protocol:
At the end points, the cells were harvested under safe red light for fluorescence-activated cell sorting (FACS) of GFP positive and GFP negative population. The cells were harvested as single cell suspensions and the GFP-positive and GFP-negative cells from these locally illuminated plates were sorted using the MoFlo Astrios (Beckman Coulter). The sorted cells were used for total RNA extraction by TRIzol Reagent (Invitrogen, 15596026), the RNA was treated with DNase, and its quality was evaluated with gel QC. All handling of the live cells was performed under safe red light, to avoid unwanted non-specific activity.
The RNAseq libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche)

treatment_protocol: About 70% confluent HEK293T cells were co-transfected with E-LightR-Cre-miRFP670 and one of the three constructs: pCA-mTmG(GFP-only), pCA-mTmG(GFP-KRas-WT), or pCA-mTmG(GFP-KRas-G12D) in 1:9 ratio and incubated in dark for 16-18 hours. Following incubation, local illumination was performed using Low_power µ-ILED devices operating at 10 W power, 10 Hz frequency, and 20% duty cycle for 6 hours. Following illumination, the plates were wrapped in aluminum foil and incubated at 37 °C and 5% CO2 for 18 hours in the dark.

value: HEK293T ATCC (CRL-3216)


title: Patient 81 COAD 081

value: Total


title: peaks HeLa cells, 24hrs DMSO, pS65Ub ChIPseq, rep 1

description: Library name: SAM24456500_V1_pS65Ub_bed


title: Patient 80 COAD 080

value: rectal cancer


title: MCF-7 Ribociclib-Resistant, Ribociclib, Day18 Hr0

description:
Library name: 72_MCF7_Ribo_Afat
72_MCF7_Ribo_Afat

value: Ribociclib


title: S3-GFP (+) mTmG(GFP-KRas-G12D) rep 2

description: Library name: E2_S3_GFP_positive


title: IPP from animal_1

description:
Library name: NSM1009
3 lvl sciRNAseq

value: inferior posterior parietal cortex


title: peaks HeLa cells, 24hrs Oligomycin + Antimycin, H2AK119Ub ChIPseq, rep 2

description: Library name: SAM24456499_OA2_H2AK119ub_bed


title: MCF-7 Ribociclib-Resistant, DMSO, Day18 Hr0

description:
Library name: 71_MCF7_Ribo_Afat
71_MCF7_Ribo_Afat


title: S3-GFP (+) mTmG(GFP-KRas-G12D) rep 1

description: Library name: E1_S3_GFP_positive


title: peaks HeLa cells, 24hrs Oligomycin + Antimycin, H2AK119Ub ChIPseq, rep 1

description: Library name: SAM24456498_OA1_H2AK119ub_bed


title: Patient 79 COAD 079


title: Blood, Crohn's disease, biol rep 7

description: Library name: CD14_4_Blood

source_name: Blood

value: Blood

value: CD45+ T-cells


title: MCF-7 Sensitive, Ribociclib + Afatinib, Day18 Hr0

description:
Library name: 70_MCF7_Ribo_Afat
70_MCF7_Ribo_Afat

value: MCF-7 Sensitive


title: HIP from animal_48

description:
Library name: NSM1208
3 lvl sciRNAseq

value: hippocampus


title: Patient 78 COAD 078

value: Minimal


title: S3-GFP (-) mTmG(GFP-KRAS-G12D) rep 3

description: Library name: E3_S3_GFP_negative


title: peaks HeLa cells, 24hrs DMSO, H2AK119ub ChIPseq, rep 2

description: Library name: SAM24456497_V2_H2AK119ub_bed

value: HeLa Cells

value: Epithelial


title: Patient 77 COAD 077


title: S3-GFP (-) mTmG(GFP-KRAS-G12D) rep 2

description: Library name: E2_S3_GFP_negative


title: MCF-7 Sensitive, Afatinib, Day18 Hr0

description:
Library name: 69_MCF7_Ribo_Afat
69_MCF7_Ribo_Afat

value: ER+ Breast Cancer

value: Afatinib

value: Day18 Hr0


title: peaks HeLa cells, 24hrs DMSO, H2AK119ub ChIPseq, rep 1

description: Library name: SAM24456496_V1_H2AK119ub_bed

value: WT

value: 24hrs DMSO


title: Patient 76 COAD 076

value: Moderate


title: S3-GFP (-) mTmG(GFP-KRAS-G12D) rep 1

description: Library name: E1_S3_GFP_negative

value: HEK293T ATCC (CRL-3216)


title: HeLa cells, 24hrs Oligomycin + Antimycin, pS65Ub ChIPseq, rep 2

description: Library name: SAM24456503_OA2_pS65Ub_bw

value: 24hrs Oligomycin (1µM) + Antimycin (1µM)


title: MCF-7 Sensitive, Ribociclib, Day18 Hr0

description:
Library name: 68_MCF7_Ribo_Afat
68_MCF7_Ribo_Afat

value: Ribociclib


title: S2-GFP (+) mTmG(GFP-KRas-WT) rep 3

description: Library name: E3_S2_GFP_positive


title: HeLa cells, 24hrs Oligomycin + Antimycin, pS65UbChIPseq, rep 1

description: Library name: SAM24456502_OA1_pS65Ub_bw


title: MCF-7 Sensitive, DMSO, Day18 Hr0

description:
Library name: 67_MCF7_Ribo_Afat
67_MCF7_Ribo_Afat

value: DMSO


title: Patient 75 COAD 075

value: rectal cancer


title: Patient 74 COAD 074


title: MCF-7 Ribociclib-Resistant, Ribociclib + Afatinib, Day12 Hr24

description:
Library name: 66_MCF7_Ribo_Afat
66_MCF7_Ribo_Afat

value: MCF-7 Ribociclib-Resistant

value: Ribociclib + Afatinib

value: Day12 Hr24


title: S2-GFP (+) mTmG(GFP-KRas-WT) rep 2

description: Library name: E2_S2_GFP_positive


title: HeLa cells, 24hrs DMSO, pS65Ub ChIPseq, rep 2

description: Library name: SAM24456501_V2_pS65Ub_bw


title: Patient 73 COAD 073

value: Total


title: S2-GFP (+) mTmG(GFP-KRas-WT) rep 1

description: Library name: E1_S2_GFP_positive


title: MCF-7 Ribociclib-Resistant, Afatinib, Day12 Hr24

description:
Library name: 65_MCF7_Ribo_Afat
65_MCF7_Ribo_Afat


title: HeLa cells, 24hrs DMSO, pS65Ub ChIPseq, rep 1

description: Library name: SAM24456500_V1_pS65Ub_bw

value: HeLa Cells


title: MCF-7 Ribociclib-Resistant, Ribociclib, Day12 Hr24

description:
Library name: 64_MCF7_Ribo_Afat
64_MCF7_Ribo_Afat


title: HeLa cells, 24hrs Oligomycin + Antimycin, H2AK119Ub ChIPseq, rep 2

description: Library name: SAM24456499_OA2_H2AK119ub_bw

value: Epithelial


title: Patient 72 COAD 072


title: S2-GFP (-) mTmG(GFP-KRAS-WT) rep 3

description: Library name: E3_S2_GFP_negative


title: S2-GFP (-) mTmG(GFP-KRAS-WT) rep 2

description: Library name: E2_S2_GFP_negative


title: MCF-7 Ribociclib-Resistant, DMSO, Day12 Hr24

description:
Library name: 63_MCF7_Ribo_Afat
63_MCF7_Ribo_Afat

value: ER+ Breast Cancer


title: HeLa cells, 24hrs Oligomycin + Antimycin, H2AK119Ub ChIPseq, rep 1

description: Library name: SAM24456498_OA1_H2AK119ub_bw


title: Patient 70 COAD 070

description: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software.


title: S2-GFP (-) mTmG(GFP-KRAS-WT) rep 1

description: Library name: E1_S2_GFP_negative


title: 145_CC_2019_05_31_1, rep1

description: Library name: 145_cold_deprivation, 145_TCATCCTT-AGCTCGCT-AHGV5KDRXY_L001

source_name: flower bud

value: flower bud

value: plant

value: Regina


title: 140_CC2MAR_2019_05_31_2, rep3

description: Library name: 140_cold_deprivation, 140_AGGTTATA-CGGAACTG-AHGKC2BBXY_L006


title: Patient 71 COAD 071


title: MCF-7 Sensitive, Ribociclib + Afatinib, Day12 Hr24

description:
Library name: 62_MCF7_Ribo_Afat
62_MCF7_Ribo_Afat

value: MCF-7 Sensitive

value: WT


title: MCF-7 Sensitive, Afatinib, Day12 Hr24

description:
Library name: 61_MCF7_Ribo_Afat
61_MCF7_Ribo_Afat

value: Afatinib


title: HeLa cells, 24hrs DMSO, H2AK119ub ChIPseq, rep 2

description: Library name: SAM24456497_V2_H2AK119ub_bw

value: 24hrs DMSO


title: S1-GFP (+) mTmG(GFP-Only) rep 3

description: Library name: E3_S1_GFP_positive

value: HEK293T ATCC (CRL-3216)


title: MCF-7 Sensitive, Ribociclib, Day12 Hr24

description:
Library name: 60_MCF7_Ribo_Afat
60_MCF7_Ribo_Afat

value: Ribociclib


title: HeLa cells, 24hrs DMSO, H2AK119ub ChIPseq, rep 1

description: Library name: SAM24456496_V1_H2AK119ub_bw


title: Patient 69 COAD 069

value: rectal cancer

value: Minimal


title: MERFISH Yap 4wk

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: MERFISH Yap 4wk

data_processing: The average of the median volume was calculated across all the libraries, and the large cells with greater than three times of the average volume were filtered out. Next, the doublets were removed using tool Scrublet.

organism: Mus musculus

source_name: liver

label_protocol: All MERFISH sample preparation was performed under RNase-free conditions. Frozen embedded livers were cryo-sectioned at 10 μm thickness at -16°C and mounted onto room temperature (RT) MERSCOPE beaded coverslips (Vizgen, Cat: 10500001). After adherence, sections were refrozen for 5 to 15 minutes, then fixed in 4% PFA diluted in 1x PBS for 15 minutes. Sections were washed three times with 1x PBS for 5 minutes each, then stored in 70% ethanol (EtOH) overnight at 4°C to permeabilize the tissue. Sections were stored in 70% EtOH for a maximum of 3 weeks.  Sample preparation was performed using the sample prep kit (Vizgen, 10400012) and Vizgen manufacturer instructions for unfixed tissue. First, for cell boundary staining, sections were washed with 1x PBS, incubated in blocking solution (1:20 RNase inhibitor (NEB M0314L) in Cell Boundary Blocking Buffer Premix (Vizgen, 20300012)) for 1 hr at room temperature, incubated in primary staining solution (1:100 Cell Boundary Primary Staining Mix (Vizgen, 20300010) in blocking solution) for 1 hr at room temperature, washed three times with 1x PBS for 5 minutes each on a rocking platform, incubated in secondary staining solution (3:100 Cell Boundary Secondary Staining Mix (Vizgen, 20300011) in blocking solution) for 1 hr at room temperature, washed three times with 1x PBS for 5 minutes each on a rocking platform, fixed in 4% PFA diluted in 1x PBS for 15 minutes, and washed two times with 1x PBS for 5 minutes, each. Next, sections were washed with Sample Prep Wash Buffer (Vizgen, 20300001), incubated in Formamide Wash Buffer (Vizgen, 20300002) for 30 minutes at 37°C, then incubated in the gene panel mix for 42-46 hrs at 37°C. Sections were then incubated two times in Formamide Wash Buffer for 30 minutes each at 47°C, and washed with sample prep wash buffer for at least 2 minutes. Sections were coated in gel embedding solution (0.05% w/v ammonium persulfate, 0.05% v/v N,N,N’,N'-tetramethylethylenediaminutese in Gel Embedding Premix (Vizgen, 20300004)) and incubated at RT for 1.5 hr, cleared in 1:5 concentration proteinase K in Clearing Premix (Vizgen, 20300003) at 37°C, then stored in 1:100 proteinase K in Clearing Premix at 37°C overnight or for a maximum of 7 days to clear lipids and proteins that may contribute to auto-fluorescence background noise.   Prior to imaging, sections were washed two times with Sample Prep Wash Buffer, incubated in DAPI and PolyT Staining Reagent (Vizgen, 20300021) for 15 minutes on a rocking platform, incubated in Formamide Wash Buffer for 10 minutes, and washed again with Sample Prep Wash Buffer.  Imaging was performed on the MERSCOPE platform (Vizgen, 10000001) according to manufacturer instructions. Briefly, samples were loaded into the flow chamber of the instrument and the desired region for imaging was selected using a low-resolution mosaic of DAPI and Poly-T stains. Samples were then imaged at high-resolution with a 7-plane z-stack and 1.5 μm spacing between adjacent z-planes to capture the entire 10 μm thickness of the tissue sections. Samples were then automatically imaged according to MERSCOPE imaging presets.

treatment_protocol: Adeno-associated virus (AAV8)- thyroid hormone-binding globulin (TBG)- cyclization recombinase (CRE) (AAV-CRE; Addgene, 107787-AAV8, 105535-AAV8) was delivered to the indicated genotypes retro-orbitally at 1011 pfu/mouse; AAV8-TBG-GFP (Addgene) or AAV8-TBG-NULL (Addgene) were used as controls. To induce expression of TetOYAP, 3 days after AAV-CRE injections, mice were given 1mg/mL doxycycline ad libitum in drinking water. These mice are referred to as “YAP-Tg” in the text.

tag: condition

value: MERFISH Yap 4wk


title: S1-GFP (+) mTmG(GFP-Only) rep 2

description: Library name: E2_S1_GFP_positive


title: MCF-7 Sensitive, DMSO, Day12 Hr24

description:
Library name: 59_MCF7_Ribo_Afat
59_MCF7_Ribo_Afat

value: DMSO

value: Day12 Hr24


title: Patient 67 COAD 067


title: Patient 68 COAD 068


title: MCF-7 Ribociclib-Resistant, Ribociclib + Afatinib, Day12 Hr6

description:
Library name: 58_MCF7_Ribo_Afat
58_MCF7_Ribo_Afat

value: MCF-7 Ribociclib-Resistant

value: Ribociclib + Afatinib

value: Day12 Hr6


title: MERFISH Yap 1wk region2

description: MERFISH Yap 1wk region2

value: MERFISH Yap 1wk


title: S1-GFP (-) mTmG(GFP-Only) rep 3

description: Library name: E3_S1_GFP_negative


title: S1-GFP (+) mTmG(GFP-Only) rep 1

description: Library name: E1_S1_GFP_positive


title: MERFISH Yap 1wk region1

description: MERFISH Yap 1wk region1


title: MCF-7 Ribociclib-Resistant, Afatinib, Day12 Hr6

description:
Library name: 57_MCF7_Ribo_Afat
57_MCF7_Ribo_Afat

value: ER+ Breast Cancer


title: Patient 66 COAD 066


title: Patient 65 COAD 065

value: Total


title: S1-GFP (-) mTmG(GFP-Only) rep 2

description: Library name: E2_S1_GFP_negative


title: MERFISH Lats 4wk

description: MERFISH Lats 4wk

value: MERFISH Lats 4wk


title: MERFISH Lats 1wk

description: MERFISH Lats 1wk

value: MERFISH Lats 1wk


title: CD34cells_CBU4_HTO

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

description:
Library name: CB554_hto
Hashtag-derived oligonucleotide
HTO library
Processed files contain combined GEX+HTO matrices for CBU4
CB554.barcodes.tsv.gz
CB554.features.tsv.gz
CB554.matrix.mtx.gz

library_source: other

data_processing:
Files were aligned, quality control filtered, and combined into GEX+HTO matrices using PIPseeker version 3.2 software.
Sensitivity matrix level 3 generated by PIPseeker software was used for further downstream analysis.
Seurat was used for demultiplexing and downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Combined GEX+HTO matrices: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: umbilical cord blood

growth_protocol: CD34+ cells derived from human umbilical cord blood were isolated using magnetic separation technology. Purified CD34+ cells were cultured in serum free media in the presence of growth factors in variable oxygen conditions using controlled oxygen incubators.

extract_protocol:
Cells originating from the same cord blood unit were pooled into the same unit. Cells were captured using PIPseq fluidics free emulsification technology.
Single cell libraries were prepared using the PIPseq T20 kit.

treatment_protocol: Cells were grown in 1%, 3%, 5%, 14%, and 21% oxygen and were harvested two days or seven days following seeding or were isolated fresh as input control. Prior to single cell RNA-seq library prep, cells were stained with TotalSeq-A cell hashing antibodies based on their treatment condition to allow for multiplexing. Cells were washed twice and counted prior to pooling. This procedure was performed in a hypoxia chamber set to 3% oxygen for 1%, 3%, and 5% oxygen conditions or was performed in ambient air for 14% and 21% conditions.

value: umbilical cord blood

value: CD34 Cells

value: mixed sample (unmanipulated control, 1% oxygen, 3% oxygen, 5% oxygen, 14% oxygen, 21% oxygen)

tag: days in_culture

tag: library type

value: HTO

tag: hto

value: TotalSeq-A0251 anti human Hashtag 1 (1% oxygen); TotalSeq-A0252 anti human Hashtag 2 (3% oxygen); TotalSeq-A0253 anti human Hashtag 3 (5% oxygen); TotalSeq-A0254 anti human Hashtag 4 (14% oxygen); TotalSeq-A0255 anti human Hashtag 5 (21% oxygen); TotalSeq-A0256 anti human Hashtag 6 (unmanipulated control)


title: Patient 64 COAD 064

value: rectal cancer


title: MCF-7 Ribociclib-Resistant, Ribociclib, Day12 Hr6

description:
Library name: 56_MCF7_Ribo_Afat
56_MCF7_Ribo_Afat

value: WT

value: Ribociclib


title: MCF-7 Ribociclib-Resistant, DMSO, Day12 Hr6

description:
Library name: 55_MCF7_Ribo_Afat
55_MCF7_Ribo_Afat

value: DMSO


title: Patient 63 COAD 063


title: MERFISH WT region2

description: MERFISH WT region2

value: MERFISH WT


title: MCF-7 Sensitive, Ribociclib + Afatinib, Day12 Hr6

description:
Library name: 54_MCF7_Ribo_Afat
54_MCF7_Ribo_Afat

value: MCF-7 Sensitive

value: Ribociclib + Afatinib


title: MERFISH WT region1

description: MERFISH WT region1


title: CD34cells_CBU4_GEX

description:
Library name: CB554_mrna
polyA RNA
GEX library
Processed files contain combined GEX+HTO matrices for CBU4

value: mRNA


title: MCF-7 Sensitive, Afatinib, Day12 Hr6

description:
Library name: 53_MCF7_Ribo_Afat
53_MCF7_Ribo_Afat

value: ER+ Breast Cancer

value: Afatinib

value: Day12 Hr6


title: 131_CC2MAR_2019_04_30_2, rep2

description: Library name: 131_cold_deprivation, 131_CTGCTTCC-GATCTATC-AHGKC2BBXY_L005

value: flower bud

value: plant

value: Regina


title: Patient 61 COAD 061

description: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software.

value: Total


title: CD34cells_CBU3_HTO

description:
Library name: CB523_hto
Hashtag-derived oligonucleotide
HTO library
Processed files contain combined GEX+HTO matrices for CBU3
CB523.barcodes.tsv.gz
CB523.features.tsv.gz
CB523.matrix.mtx.gz

value: umbilical cord blood

value: CD34 Cells

value: mixed sample (unmanipulated control, 1% oxygen, 3% oxygen, 5% oxygen, 14% oxygen, 21% oxygen)

value: HTO


title: T2-low asthma_8040253986

description: Library name: 8040253986

source_name: BRUSHING

value: BRUSHING

value: T2-low asthma


title: Patient 62 COAD 062

value: rectal cancer


title: MCF-7 Sensitive, DMSO, Day12 Hr6

description:
Library name: 51_MCF7_Ribo_Afat
51_MCF7_Ribo_Afat

value: MCF-7 Sensitive

value: WT

value: DMSO


title: CD34cells_CBU3_GEX

description:
Library name: CB523_mrna
polyA RNA
GEX library
Processed files contain combined GEX+HTO matrices for CBU3

value: mRNA


title: MCF-7 Sensitive, Ribociclib, Day12 Hr6

description:
Library name: 52_MCF7_Ribo_Afat
52_MCF7_Ribo_Afat

value: ER+ Breast Cancer

value: Ribociclib


title: Patient 60 COAD 060


title: NHEK-sgTEDAR#4

city: Uppsala

first: Andor

last: Pivarcsi

address: BMC B11:3

department: Department of Medical Biochemistry and Microbiology

country: Sweden

institute: Uppsala Univesrity

hyb_protocol: Hybridization was performed according to the manufacturer’s instructions for the Affymetrix Clariom D Human array.

scan_protocol: Arrays were scanned according to the manufacturer’s instructions.

data_processing: Raw image files (CEL files) were processed using Affymetrix Expression Console software (version 1.4) with SST-RMA (Signal Space Transformation, Robust Multi-array Average) summarization. Expression data were annotated with Clariom_D_Human.r1.na36.hg38.a1.transcript.csv. Differential expression analysis was performed in R.

label: biotin

source_name: sgTEDAR

label_protocol: Biotin-labeled sense-strand cDNA was generated from total RNA according to the manufacturer’s instructions.

growth_protocol: Primary adult keratinocytes were cultured in EpiLife medium (p3) at 60-70% confluence until transfection.

extract_protocol: Total RNA from keratinocytes growing in monolayer was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. Total RNA from organotypic skin cultures was isolated using the RNeasy Plus mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Cells were transfected with sgRNA (MS2), MS2-P65-HSF1_GFP and dCAS9-VP64-GFP plasmids (100 ng of each plasmid per well in 24-well plate) with Lipofectamine™ 2000 (ThermoFisher Scientific). Differentiation was induced by switching to growth factor-depleted EpiLife containing 1.5 mM Calcium Chloride (Sigma).

value: sgTEDAR


title: Patient 59 COAD 059


title: NHEK-sgTEDAR#3


title: JB-161, 5-FU-5

city: Suita

first: Tomoaki

last: Hara

address: Yamadaoka 2-2

country: Japan

institute: The University of Osaka

description: Library name: Sample 29

data_processing:
Sequencing was performed on an Illumina NovaSeqX Plus platform in a 151-base single-end mode.
The NovaSeq control software operated base calling analysis software and delivered raw sequencing data.
Sequence quality of the FASTQ files was assessed using FastQC, and reads were trimmed based on quality scores using Trimmomatic. Trimmed reads were aligned to the human reference genome sequences (GRCh38.p5) using Hisat2.
SAM files were converted to BAM format with Samtools, and gene-level read counts were generated using featureCounts.
Assembly: GRCh38.p5
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: tumor

extract_protocol:
A moderate amount of tumor was placed in ISOGEN (NIPPON GENE), crushed with a mixer, and RNA was extracted according to ISOGEN protocol.
Ribosomal RNA was depleted using Ribo-Zero Plus rRNA Depletion Kit (Illumina) and the library was prepared using a TruSeq stranded mRNA Library Prep Kit (Illumina).

value: tumor


title: NHEK-sgTEDAR#2


title: MCF-7 Ribociclib-Resistant, Ribociclib + Afatinib, Day12 Hr0

description:
Library name: 50_MCF7_Ribo_Afat
50_MCF7_Ribo_Afat

value: MCF-7 Ribociclib-Resistant

value: Ribociclib + Afatinib

value: Day12 Hr0


title: Patient 58 COAD 058

value: Moderate


title: S1-GFP (-) mTmG(GFP-Only) rep 1

description: Library name: E1_S1_GFP_negative

value: HEK293T ATCC (CRL-3216)


title: JB-161, 5-FU-4

description: Library name: Sample 28


title: NHEK-sgTEDAR#1


title: MCF-7 Ribociclib-Resistant, Afatinib, Day12 Hr0

description:
Library name: 49_MCF7_Ribo_Afat
49_MCF7_Ribo_Afat

value: Afatinib


title: Patient 57 COAD 057

value: Total


title: JB-161, 5-FU-3

description: Library name: Sample 27


title: NHEK-sgCTRL#4

source_name: sgCTRL

value: sgCTRL


title: MCF-7 Ribociclib-Resistant, Ribociclib, Day12 Hr0

description:
Library name: 48_MCF7_Ribo_Afat
48_MCF7_Ribo_Afat


title: JB-161, 5-FU-2

description: Library name: Sample 26


title: Patient 56 COAD 056

value: rectal cancer


title: JB-161, 5-FU-1

description: Library name: Sample 25


title: Patient 55 COAD 055


title: MCF-7 Ribociclib-Resistant, DMSO, Day12 Hr0

description:
Library name: 47_MCF7_Ribo_Afat
47_MCF7_Ribo_Afat


title: NHEK-sgCTRL#3


title: NHEK-sgCTRL#2


title: Patient 54 COAD 054

value: Minimal


title: MCF-7 Sensitive, Ribociclib + Afatinib, Day12 Hr0

description:
Library name: 46_MCF7_Ribo_Afat
46_MCF7_Ribo_Afat

value: MCF-7 Sensitive

value: WT


title: JB-157, 5-FU-5

description: Library name: Sample 24


title: MCF-7 Sensitive, Afatinib, Day12 Hr0

description:
Library name: 45_MCF7_Ribo_Afat
45_MCF7_Ribo_Afat


title: NHEK-sgCTRL#1


title: Patient 53 COAD 053


title: JB-157, 5-FU-4

description: Library name: Sample 23


title: sws-mut-2

city: St. Petersburg

first: Artem

middle: Evgenevich

last: Komissarov

address: Kotelnikova Alley 2a

country: Russia

institute: PNPI

description:
Library name: Sample-4
Column name in data_raw_ABS.csv: sample_4

data_processing:
Trimmomatic was used to clean low-quality reads.
Hisat2 was used to map the filtered reads to the Drosophila melanogaster reference genome
Htseq-count was used to count the number of reads that were currently mapped to the transcript.
Assembly: dmel-all-transcript-r6.57.fasta
Supplementary files format and content: csv file containing transcript-level expression estimates. Rows represent Drosophila transcripts (FlyBase IDs), and columns represent individual samples.

organism: Drosophila melanogaster

source_name: testicles

growth_protocol: Flies were maintained on standard semolina media. Crosses were cultured at 25°C (12 h night/12 h day).

extract_protocol:
Total RNA for RNA-seq libraries was isolated from Canton S and sws1 mutant testes with the Quick-RNA MiniPrep kit. Ribosomal RNA was removed by hybridization of total RNA with biotinylated oligonucleotides complementary to different regions of rRNA followed by binding to Dynabeads™ MyOne™ Streptavidin C3 (Invitrogen by ThermoFisher Scientific, Waltham, MA, USA).
RNA libraries were prepared utilizing the MGIEasy RNA Directional Library Prep Set (MGI, Shenzhen, China) according to the manufacturer’s protocol. Sequencing was conducted on the DNB-SEQ-G400 platform (MGI, Shenzhen, China) in paired-end reading mode, with a read length of 150 bp.

value: testicles

value: SWS-mut

value: 5 day


title: MCF-7 Sensitive, Ribociclib, Day12 Hr0

description:
Library name: 44_MCF7_Ribo_Afat
44_MCF7_Ribo_Afat

value: ER+ Breast Cancer

value: Ribociclib


title: Patient 52 COAD 052


title: JB-157, 5-FU-3

description: Library name: Sample 22

value: tumor


title: MCF-7 Sensitive, DMSO, Day12 Hr0

description:
Library name: 43_MCF7_Ribo_Afat
43_MCF7_Ribo_Afat

value: DMSO


title: JB-157, 5-FU-2

description: Library name: Sample 21


title: MCF-7 Ribociclib-Resistant, Ribociclib + Afatinib, Day6 Hr24

description:
Library name: 42_MCF7_Ribo_Afat
42_MCF7_Ribo_Afat

value: MCF-7 Ribociclib-Resistant

value: Ribociclib + Afatinib

value: Day6 Hr24


title: sws-mut-1

description:
Library name: Sample-3
Column name in data_raw_ABS.csv: sample_3


title: Patient 51 COAD 051

value: Moderate


title: 40_CC_2019_01_02_1, rep1

description: Library name: 40_cold_deprivation, 40_GGCATTCT-CAAGCTAG-AHGKC2BBXY_L004

value: flower bud

value: plant

value: Regina


title: control-2

description:
Library name: Sample-2
Column name in data_raw_ABS.csv: sample_2


title: Patient 50 COAD 050

description: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software.

value: rectal cancer


title: control-1

description:
Library name: Sample-1
Column name in data_raw_ABS.csv: sample_1


title: MCF-7 Ribociclib-Resistant, Afatinib, Day6 Hr24

description:
Library name: 41_MCF7_Ribo_Afat
41_MCF7_Ribo_Afat

value: Afatinib


title: Patient 49 COAD 049

value: Minimal


title: JB-157, 5-FU-1

description: Library name: Sample 20