title: FOXG1 W308X control 1


title: FOXG1 W308X control 2

status: Public on Jun 06 2025

type: SRA

city: Sacramento

first: Julian

last: Halmai

state: CA

address: 2921 Stockton Blvd

department: Department of Neurology

country: USA

institute: UC Davis

library_source: transcriptomic

data_processing:
star align 2.7a
edgeR
Assembly: hg38
Supplementary files format and content: .xlsx with raw reads per gene

molecule: polyA RNA

organism: Homo sapiens

source_name: neuronal

extract_protocol:
Cells were lysed using TriZol Reagent and RNA extractions were performed on with the Direct-zol RNA Miniprep kit (Zymo Research). 500ng total RNA was used to construct libraries according to Novogene sample submission guidelines.
Library construction was performed by the UC Davis DNA Technologies Core and Novogene.

tag: tissue

value: neuronal

tag: cell line

value: patient-derived NSC

tag: cell type

value: NSC


title: LuNE, shP300, H3K27ac ChIP 1#

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

library_source: genomic

data_processing:
Reads were aligned to the hg19 reference human genome using bowtie2
bigwig generated from bam
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: Prostate

growth_protocol: Prostate cancer cell lines LNCaP, 22Rv1 and LuNE cells were maintained in RPMI1640 with 10% fetal bovine serum (FBS), 1% penicillin and streptomycin and  NCI-H660 cells were maintained in ATCC-formulated RPMI-1640 Medium (Catalog No.30-2001) with 0.005 mg/ml Insulin, 0.01 mg/ml Transferrin, 30nM Sodium selenite, 10 nM Hydrocortisone, 10 nM beta-estradiol, 5% fetal bovine serum. 2. LuCaP PDX were maintained in NOD SCID male mice which were purchased from Charles River

extract_protocol:
PCa cells were crosslinked with 1% formaldehyde (Thermo fisher, Cat#28908)) for 10 min at room temperature with gentle rotation and then quenched for 5 min with 0.125 M glycine. Chromatin was sonicated to an average length of 200–600 bp using an E220 focused-ultrasonicator (Covaris).
ChIP–seq libraries were prepared from 3–5 ng of ChIPed DNA using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions.

treatment_protocol: 1.LNCaP cells were co-infected with FOXA2 virus along with either sgNC or sgNKX2-1 virus and infected cells were collected at D7, D14, D21 and D28 for ChIP analysis  2. LuNE cells were infected gRNAs targeting control (sgNC), NKX2-1 (sgNKX2-1), FOXA2 (sgFOXA2) or shRNAs targeting control (shCtrl), P300 (shP300), CBP (shCBP), the cells were collected for ChIP analysis 5 days after infection. 3. LuNE cells were treated with DMSO or CCS1477 (500nM) for 24h and collected for ChIP analysis.

value: Prostate

value: LNCaP (LuNE)

value: Prostate cancer cell

tag: genotype

value: WT

tag: antibody

value: H3K27ac, Cst, Cat#8173S

tag: treatment


title: FOXG1 W308X CRISPRa 3


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample4

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

institute: United States Environmental Protection Agency

description:
Chem11_A_D4
Chem11_counts_matrix.txt

data_processing:
Sequencing was performed in a 1x100bp single read format using Illumina NovaSeq SP flow cells (Illumina, Inc., San Diego, CA, USA).
The R. subcapitata reference genome (GCA_003203535.1) was indexed using STAR v2.7.10a (Dobin et al., 2012) using the following parameters: genomeSAindexNbases = 11, sjdbOverhang = 99, and sjdbGTFfeatureExon = gene.
The raw, 1x100bp single end FASTQ sequence files were trimmed, quality filtered (Phred score <15), and had UMIs and adapter sequences removed after deduplication using fastp v0.23.2 (Chen 2023, Chen et al., 2018).
Quality reads were aligned and mapped to the indexed reference genome using STAR. The resulting alignment files were sorted by coordinates and indexed by sample using Samtools v1.15.1 (Danecek et al., 2021).
Aligned reads were quantified with respect to gene features using the “featureCounts” program (v2.0.6) of the subread package (Liao et al., 2014). A 1,400 bp extension was added to each read at the 5’ end as most reads aligned at unannotated 3’ untranslated regions (UTR) of the genome and gene features with the largest overlap were counted. The quantified reads were organized into separate (tab-delimited) count matrix files for each chemical treatment group where columns represented samples and rows represented genes.
Assembly: GCA_003203535.1
Supplementary files format and content: count matrices with rows as gene features and columns as samples

organism: Raphidocelis subcapitata

source_name: whole body

growth_protocol: not applicable

extract_protocol:
After a series of flash freezing and homogenization, algae total RNA was extracted using the Norgen Biotek Plant/Fungi Total RNA kit (Norgen) according to the manufacturer’s protocol. Sample quantity and quality was assessed using a NanoDrop Eight spectrophotometer (Thermo Scientific) and 4200 TapeStation (Agilent Technologies).
Sample libraries were prepared using QuantSeq 3’ mRNA-Seq V2 Library Prep Kits (Lexogen, GmbH, Austria) with Unique Dual Index (UDI) and QuantSeq Unique Molecular Identifiers (UMI). Preparation followed manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays.

treatment_protocol: 800 µL of algae was loaded into each well of 4 x 96-well plates (Beckman Cat #267007) using the Biomek robot. The algae were pelleted by centrifugation at 4000 rpm for 5 min and 400 µL of the supernatant (i.e., media) was removed. Final exposure concentrations were achieved by loading 400 µL of the 2X dosing solutions to the appropriate wells. After the dosing solutions were added, the plates were covered with optical adhesive covers, vortexed briefly to disrupt the algae pellet, and pulse centrifuged making sure to the algae did not pellet. The exposure plates, each containing 700 µL algae after 100 µL was removed for Time 0 apical measurements, were incubated for 24 h at 24ºC under a constant LED 4300 lux grow light and on a timed orbital shaker (Titramax 1000, Heidolph Instruments GmbH) turning on and off every 15 min so the algae remained in suspension.

value: whole body

tag: developmental stage

value: Exponential Growth Stage

value: Metolachlor OA


title: FOXG1 W308X CRISPRa 2


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample3

description:
Chem11_A_D3
Chem11_counts_matrix.txt


title: FOXG1 W308X CRISPRa 1


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample2

description:
Chem11_A_D2
Chem11_counts_matrix.txt


title: YCCEL1 OmniC

city: HK

first: Lai Shun Dittman

last: CHUNG

state: HK

address: 21 Sassoon Road, Pokfulam

department: Department of Clinical Oncology

country: Hong Kong

institute: the University of Hong Kong

data_processing:
The BWA-MEM alignment method with bwa mem -5SP -T0 -t16 was employed to align reads to both the human genome (hg19) and the EBV genome (NC_007605).
Valid ligation events were recorded using the parse function in pairtools, with ligation junctions documented under specific parameters, including --min-mapq 40, --walks-policy 5unique, and --max-inter-align-gap 30. Subsequently, pairtools was utilized to sort reads, eliminate PCR duplicates, and generate .pairs and .bam files using samtools.
Quality control and reproducibility checks were performed on sample replicates, followed by merging into a single file for subsequent analysis. To ensure comparability, the sample reads were normalised through random sampling using shuf -n , resulting in approximately 200 million paired reads.
Homer has been used to create a Paired-End Tag Directory, then analyzeHiC was used to normalised to background in 50kbp resolution. runHiCpca.pl was used to perform PCA analysis to identify AB compartments
Juicer tools (version 1.22.01) has been used to generate the contactmap matrix
Assembly: hg19 & EBV genome (NC_007605)
Supplementary files format and content: The .hic contactmap files can be visualised in juicer tool
Supplementary files format and content: The PCA generating .bw files can be visualised in IGV browser

source_name: EBV-associated gastric cancer (EBVaGC), detectable EBV copies in GC

growth_protocol: NP69 was cultured in Keratinocyte SFM (GIBCO Cat# 10744019) supplemented with Bovine Pituitary Extract (BPE), 1 ng/ml epidermal growth factor (EGF), and 1% penicillin. NP460 was cultured in a mixture of defined keratinocyte–serum-free medium and EpiLife (1:1) with supplements (GIBCO Cat# MEPI500CA) and 10% fetal bovine serum (FBS) (GIBCO Cat# 26140079), and 1% penicillin (GIBCO Cat# 10378016). C17, NPC43, NPC43noEBV, NPC53, and NPC38 were cultured in RPMI-1640 medium supplemented with 10% FBS, 1% penicillin, and 2 mM rock inhibitor Y-27632 (Enzo Life Sciences Cat# BML-EU299). YCCEL1 and C666 were cultured in RPMI-1640 (GIBCO Cat# 31800022) medium supplemented with 10% FBS and 1% penicillin. HK1 was cultured in RPMI-1640 (GIBCO Cat# 31800022) medium supplemented with 10% FBS and 1% penicillin. HK1EBV was cultured in RPMI-1640 (GIBCO Cat# 31800022) medium supplemented with 10% FBS, 1% penicillin, and 500ug/ml geneticin selective antibiotic (G418 sulfate Cat# 10131027). The cells were maintained in a 37°C incubator with 5% CO2.

extract_protocol:
A million cells were freshly harvested and subjected to chromatin cross-linking using disuccinimidyl glutarate (DSG) (Cat# 20593) and 37% formaldehyde. Chromatin digestion was carried out using an endonuclease enzyme, and the digestion efficiency was monitored, and quality controlled using a Bioanalyzer. With approximately 80% of the fragments falling within the 100-2500 bps range, the captured and ligated chromatin underwent reverse crosslinking and DNA purification. Subsequently, the libraries were constructed using the Dovetail™ Library Module for Illumina (Cat# 25004). The final libraries were sequenced with 150bp paired-end reads on the NovaSeq 6000 platform
modified Hi-C, with using endonuclease cutting
The Dovetail® Omni-C® Library Preparation Kit (Cat# 21005) was employed for sequencing library preparation.

treatment_protocol: No treatment

value: cell line

value: Gastric adenocarcinoma

value: Wild-type


title: LNCaP, FOXA2-D21, sgNC, NKX2-1 ChIP

value: LNCaP

value: NKX2-1, Sigma-Aldrich, Cat#07-601

value: FOXA2-D21, sgNC


title: LNCaP, FOXA2-D21, sgNKX2-1, NKX2-1 ChIP

value: FOXA2-D21, sgNKX2-1


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample1

description:
Chem11_A_D1
Chem11_counts_matrix.txt


title: Xeno23 OmniC

source_name: Patient derived xenograft (PDX) with EBV copies detection

value: patient derived xenograft

value: nasopharyngeal cancer cells


title: LNCaP, FOXA2-D14, sgNKX2-1,NKX2-1 ChIP

value: Prostate

value: FOXA2-D14, sgNKX2-1


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample21

description:
Chem10_C_D7
Chem10_counts_matrix.txt

value: cis-nonachlordane


title: LNCaP, FOXA2-D14, sgNC, NKX2-1 ChIP

value: Prostate cancer cell

value: WT

value: FOXA2-D14, sgNC


title: HK1EBV OmniC

source_name: EBV+NPC, detectable EBV copies in NPC


title: C15 OmniC


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample20

description:
Chem10_C_D6
Chem10_counts_matrix.txt

value: whole body

value: Exponential Growth Stage


title: NPC38 OmniC

source_name: EBV-NPC, no detectable EBV copies

value: cell line


title: LNCaP, FOXA2-D28, sgNKX2-1, NKX2-1 ChIP

value: FOXA2-D28, sgNKX2-1


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample19

description:
Chem10_C_D5
Chem10_counts_matrix.txt


title: LNCaP, FOXA2-D7, sgNKX2-1, NKX2-1 ChIP

value: FOXA2-D7, sgNKX2-1


title: HK1 OmniC

value: Wild-type


title: NPC43noEBV OmniC


title: LNCaP, FOXA2-D7, sgNC, NKX2-1 ChIP

value: LNCaP

value: NKX2-1, Sigma-Aldrich, Cat#07-601

value: FOXA2-D7, sgNC


title: NPC43 OmniC


title: LNCaP, FOXA2-D28, sgNC, NKX2-1 ChIP

value: FOXA2-D28, sgNC


title: LNCaP, FOXA2-D28, sgNKX2-1, FOXA2 ChIP

value: FOXA2, Abcam, Cat#ab108422


title: C17 OmniC

value: nasopharyngeal cancer cells


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample18

description:
Chem10_C_D4
Chem10_counts_matrix.txt


title: C666 OmniC


title: NPC113 OmniC

value: patient derived xenograft


title: NP460 OmniC

source_name: Normal NPE

value: nasopharyngeal epithelial cells


title: Xeno32 OmniC


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample17

description:
Chem10_C_D3
Chem10_counts_matrix.txt

value: cis-nonachlordane


title: LNCaP, FOXA2-D28, sgNC, FOXA2 ChIP

value: Prostate

value: Prostate cancer cell

value: WT


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample16

description:
Chem10_C_D2
Chem10_counts_matrix.txt

value: whole body

value: Exponential Growth Stage


title: NP69 OmniC

value: cell line


title: well5, Feature barcode

city: Boston

first: Yuling

last: Ma

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

description: 10x Genomics

library_source: other

data_processing:
Cell demultiplexing, assignment, gene expression and TCR quantification were performed with cell Ranger v.7.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: GRCh38 and mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: protein

source_name: Bone Marrow

extract_protocol:
Cell suspensions following harvesting of bone marrow and spleen tissues from individual mice were cryopreserved. NSG mice had been injected with human T cells. Upon thawing, samples underwent dead cell removal (Miltenyi MACS kit) and human CD45 enrichment (Stem Cell Technologies).
5 spleen or bone marrow samples were pooled together (one sample per treatment group), and 32,000-40,000 cells were loaded in one channel of a Chromium Chip K (10x Genomics) and profiled using the Chromium Next GEM Single Cell 5' Kit v2 (10x Genomics). Full-length paired α/β TCR libraries were obtained using the Chromium Single Cell V(D)J Enrichment Human T Cell (10x Genomics). cDNA, gene expression, and TCR library quality was assessed using the DNA High Sensitivity Bioanalyzer Chip (Agilent). Gene expression or TCR libraries were pooled and sequenced on a NovaSeq 6000 sequencer (Illumina).

value: Bone Marrow


title: well7, Feature barcode

description: 10x Genomics


title: well6, Feature barcode

description: 10x Genomics


title: well8, Feature barcode

description: 10x Genomics


title: well3, Feature barcode

description: 10x Genomics

source_name: Spleen

value: Spleen


title: well4, Feature barcode

description: 10x Genomics


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample14

description:
Chem10_B_D7
Chem10_counts_matrix.txt


title: LNCaP, FOXA2-D14, sgNKX2-1,FOXA2 ChIP

value: LNCaP

value: FOXA2-D14, sgNKX2-1


title: LNCaP, FOXA2-D21, sgNKX2-1,FOXA2 ChIP

value: FOXA2-D21, sgNKX2-1


title: well2, Feature barcode

description: 10x Genomics


title: LNCaP, FOXA2-D21, sgNC, FOXA2 ChIP

value: FOXA2-D21, sgNC


title: LNCaP, FOXA2-D7, sgNKX2-1, FOXA2 ChIP

value: FOXA2, Abcam, Cat#ab108422

value: FOXA2-D7, sgNKX2-1


title: well8, TCR, BM.well8.1, BM.well8.2, BM.well8.3, BM.well8.4, BM.well8.5

description: 10x Genomics

data_processing:
Cell demultiplexing, assignment, gene expression and TCR quantification were performed with cell Ranger v.7.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: GRCh38 and mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-seq

molecule: total RNA


title: well7, TCR, BM.well7.1, BM.well7.2, BM.well7.3, BM.well7.4, BM.well7.5

description: 10x Genomics


title: well1, Feature barcode

description: 10x Genomics


title: LNCaP, FOXA2-D14, sgNC, FOXA2 ChIP

value: FOXA2-D14, sgNC


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample12

description:
Chem10_B_D5
Chem10_counts_matrix.txt


title: NPC53 OmniC

value: nasopharyngeal cancer cells

value: Wild-type


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample11

description:
Chem10_B_D4
Chem10_counts_matrix.txt

value: cis-nonachlordane


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample13

description:
Chem10_B_D6
Chem10_counts_matrix.txt


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample15

description:
Chem10_C_D1
Chem10_counts_matrix.txt


title: well6, TCR, BM.well6.1, BM.well6.3, BM.well6.4, BM.well6.5

description: 10x Genomics


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample10

description:
Chem10_B_D3
Chem10_counts_matrix.txt


title: LNCaP, FOXA2-D7, sgNC, FOXA2 ChIP

value: Prostate

value: Prostate cancer cell

value: FOXA2-D7, sgNC


title: well5, TCR, BM.well5.1, BM.well5.2, BM.well5.3, BM.well5.4, BM.well5.5

description: 10x Genomics


title: well4, TCR, Spleen.well4.1, Spleen.well4.2, Spleen.well4.3, Spleen.well4.4, Spleen.well4.5

description: 10x Genomics


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample9

description:
Chem10_B_D2
Chem10_counts_matrix.txt

value: whole body

value: Exponential Growth Stage


title: LNCaP, FOXA2-D2, FOXA2 ChIP

value: WT


title: well2, TCR, Spleen.well2.1, Spleen.well2.2, Spleen.well2.3, Spleen.well2.4, Spleen.well2.5

description: 10x Genomics

value: Spleen


title: LNCaP, FOXA2-D0, FOXA2 ChIP

value: LNCaP


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample8

description:
Chem10_B_D1
Chem10_counts_matrix.txt


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample7

description:
Chem10_A_D7
Chem10_counts_matrix.txt


title: LNCaP, FOXA2-D28, sgNKX2-1, H3K4me1 ChIP

value: H3K4me1, Abcam, Cat#ab8895

value: FOXA2-D28, sgNKX2-1


title: well8, GEX, BM.well8.1, BM.well8.2, BM.well8.3, BM.well8.4, BM.well8.5

description: 10x Genomics

library_source: transcriptomic single cell

value: Bone Marrow


title: well7, GEX, BM.well7.1, BM.well7.2, BM.well7.3, BM.well7.4, BM.well7.5

description: 10x Genomics


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample6

description:
Chem10_A_D6
Chem10_counts_matrix.txt


title: well1, TCR, Spleen.well1.1, Spleen.well1.4, Spleen.well1.5

description: 10x Genomics


title: well3, TCR, Spleen.well3.1, Spleen.well3.2, Spleen.well3.3, Spleen.well3.4, Spleen.well3.5

description: 10x Genomics


title: well5, GEX, BM.well5.1, BM.well5.2, BM.well5.3, BM.well5.4, BM.well5.5

description: 10x Genomics


title: LNCaP, FOXA2-D21, sgNKX2-1, H3K4me1 ChIP

value: FOXA2-D21, sgNKX2-1


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample5

description:
Chem10_A_D5
Chem10_counts_matrix.txt


title: well4, GEX, Spleen.well4.1, Spleen.well4.2, Spleen.well4.3, Spleen.well4.4, Spleen.well4.5

description: 10x Genomics


title: LuCaP145.1, Hi-C, repicate 2

description: instrument model: NovaSeq X plus

data_processing:
Reads were processed using runHiC pipeline with chromap as the aligner
Assembly: hg38
Supplementary files format and content: .mcool maps of chromatin contact

growth_protocol: 1.Prostate cancer cell lines LNCaP cells were maintained in RPMI1640 with 10% fetal bovine serum (FBS), 1% penicillin and streptomycin and NCI-H660 cells were maintained in ATCC-formulated RPMI-1640 Medium (Catalog No.30-2001) with 0.005 mg/ml Insulin, 0.01 mg/ml Transferrin, 30nM Sodium selenite, 10 nM Hydrocortisone, 10 nM beta-estradiol, 5% fetal bovine serum. 2. LuCaP PDX were maintained in NOD SCID male mice which were purchased from Charles River Laboratories.

extract_protocol:
FOXA2-D14, D21 and D28 LNCaP cells, NCI-H660 cells and the cells from LuCaP PDXs were fixed with 2% formaldehyde (final concentration) at room temperature for 10 min, followed by adding 2.5 M glycine to a final concentration of 0.2 M to quench the reaction.
Hi-C libraries were generated using the Arima-HiC+ kit (Arima Genomics, A510008) for cell line and PDXs, Arima-HiC+ FFPE Kit (Arima Genomics, A101060) for CRPC and NEPC FFPE samples. The Hi-C libraries were sequenced with paired-end 2 × 150 bp using Illumina NovaSeq6000.

treatment_protocol: LNCaP cells were infected with FOXA2 overexpression virus and fallowed up by 28 days, cells were collected at D14, D21 and D28 for Hi-C analysis.

value: LuCaP145.1 PDX


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample4

description:
Chem10_A_D4
Chem10_counts_matrix.txt


title: LNCaP, FOXA2-D14, sgNKX2-1, H3K4me1 ChIP

value: FOXA2-D14, sgNKX2-1


title: LuCaP145.1, Hi-C, repicate 1

description: instrument model: NovaSeq X plus


title: LuCaP77CR, Hi-C

description: instrument model: NovaSeq X plus

value: LuCaP77CR PDX


title: well1, GEX, Spleen.well1.1, Spleen.well1.4, Spleen.well1.5

description: 10x Genomics


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample3

description:
Chem10_A_D3
Chem10_counts_matrix.txt


title: LNCaP, FOXA2-D14, sgNC, H3K4me1 ChIP

value: FOXA2-D14, sgNC


title: LuCaP70CR, Hi-C

description: instrument model: NovaSeq X plus

value: LuCaP70CR PDX


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample2

description:
Chem10_A_D2
Chem10_counts_matrix.txt

value: cis-nonachlordane


title: LuCaP145.1, NKX2-1 ChIP

data_processing:
Reads were aligned to the hg19 reference human genome using bowtie2
Assembly: hg19
Supplementary files format and content: bigwig generated from bam

value: Prostate

value: LuCaP PDX

value: Prostate cancer cell

value: NKX2-1, Sigma-Aldrich, Cat#07-601


title: LNCaP, FOXA2-D7, sgNKX2-1, H3K4me1 ChIP

value: WT

value: FOXA2-D7, sgNKX2-1


title: LuCaP145.1, FOXA2 ChIP

value: FOXA2, Abcam, Cat#ab108422


title: LNCaP, FOXA2-D28, sgNC, H3K4me1 ChIP

value: LNCaP

value: H3K4me1, Abcam, Cat#ab8895

value: FOXA2-D28, sgNC


title: well6, GEX, BM.well6.1, BM.well6.3, BM.well6.4, BM.well6.5

description: 10x Genomics

value: Bone Marrow


title: LNCaP, FOXA2-D7, sgNC, H3K4me1 ChIP

value: FOXA2-D7, sgNC


title: LuCaP93, NKX2-1 ChIP


title: LuCaP77CR, H3K27me3 Cut&Tag

data_processing:
Reads were aligned to the hg19 reference human genome using bowtie2
Assembly: hg19
Supplementary files format and content: bigwig generated from bam
Library strategy: Cut&tag


title: R. subcapitata, 24 h exposure, DMSO, sample3

description:
Chem1_Chem2_C_CON
Chem1_counts_matrix.txt
Chem2_counts_matrix.txt

value: whole body

value: Exponential Growth Stage

value: DMSO


title: LNCaP, FOXA2-D2, H3K4me1 ChIP


title: NCI-H660, H3K27me3 Cut&Tag


title: LNCaP, FOXA2-D21, sgNC, H3K4me1 ChIP

value: FOXA2-D21, sgNC


title: well3, GEX, Spleen.well3.1, Spleen.well3.2, Spleen.well3.3, Spleen.well3.4, Spleen.well3.5

description: 10x Genomics

value: Spleen


title: well2, GEX, Spleen.well2.1, Spleen.well2.2, Spleen.well2.3, Spleen.well2.4, Spleen.well2.5

description: 10x Genomics


title: LuCaP145.1, H3K27me3 Cut&Tag

value: Prostate


title: LNCaP, FOXA2-D0, H3K4me1 ChIP


title: LuCaP70CR, H3K27me3 Cut&Tag

value: LuCaP PDX


title: LuCaP145.2, H3K27me3 Cut&Tag

value: Prostate cancer cell


title: LNCaP, FOXA2-D28, sgNKX2-1, H3K27ac ChIP

value: H3K27ac, Cst, Cat#8173S

value: FOXA2-D28, sgNKX2-1


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample21

description:
Chem1_C_D7
Chem1_counts_matrix.txt


title: LNCaP, FOXA2-D28, sgNC, H3K27ac ChIP

value: WT


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample20

description:
Chem1_C_D6
Chem1_counts_matrix.txt


title: LuCaP35CR, H3K27me3 Cut&Tag


title: LuCaP77CR, H3K27ac ChIP


title: LuCaP70CR, H3K27ac ChIP


title: R. subcapitata, 24 h exposure, cis-nonachlordane, sample1

description:
Chem10_A_D1
Chem10_counts_matrix.txt

value: cis-nonachlordane


title: LuCaP145.1, H3K4me1 ChIP


title: LuCaP145.1, H3K27ac ChIP


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample19

description:
Chem1_C_D5
Chem1_counts_matrix.txt


title: R. subcapitata, 24 h exposure, DMSO, sample2

description:
Chem1_Chem2_B_CON
Chem1_counts_matrix.txt
Chem2_counts_matrix.txt


title: LNCaP, FOXA2-D21, single-cell mutiome,  scATAC-seq

library_source: genomic single cell

data_processing:
Raw sequencing data were preprocessed and aligned using Cell Ranger ARC (2.0.2)
Assembly: hg38
Supplementary files format and content: gene and fragement matrices from Cell Ranger

growth_protocol: Prostate cancer cell lines LNCaP cells were maintained in RPMI1640 with 10% fetal bovine serum (FBS), 1% penicillin and streptomycin.

extract_protocol:
5,000 of D0, D14 and D21 LNCaP+FOXA2 cells were used for single-cell Multiome ATAC + Gene Expression assay, the multiome libraries were prepared using 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (Cat# 1000285) per manufacturer’s protocol.
single-cell Multiome ATAC + Gene Expression assay

treatment_protocol: LNCaP cells were infected with FOXA2 overexpression virus and fallowed up by 21 days, cells were collected at D0, D14 and D21 for single-cell Multiome ATAC + Gene Expression assay.

value: LNCaP


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample18

description:
Chem1_C_D4
Chem1_counts_matrix.txt


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample17

description:
Chem1_C_D3
Chem1_counts_matrix.txt


title: LNCaP, FOXA2-D21, sgNC, H3K27ac ChIP


title: LNCaP, FOXA2-D14, single-cell mutiome,  scATAC-seq


title: LNCaP, FOXA2-D0, single-cell mutiome,  scATAC-seq


title: R. subcapitata, 24 h exposure, DMSO, sample1

description:
Chem1_Chem2_A_CON
Chem1_counts_matrix.txt
Chem2_counts_matrix.txt


title: LNCaP, FOXA2-D21, single-cell mutiome,  scRNA-seq


title: LNCaP, FOXA2-D14, single-cell mutiome,  scRNA-seq


title: LuCaP147, H3K27me3 Cut&Tag


title: LuCaP93, H3K27me3 Cut&Tag


title: LNCaP, FOXA2-D0, single-cell mutiome,  scRNA-seq


title: LNCaP, FOXA2-D14, sgNC, H3K27ac ChIP

value: FOXA2-D14, sgNC


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample15

description:
Chem1_C_D1
Chem1_counts_matrix.txt


title: LNCaP, FOXA2-D7, sgNKX2-1, H3K27ac ChIP

value: FOXA2-D7, sgNKX2-1


title: LuNE, shP300+CBP 3#

data_processing:
Raw fastq files were aligned using STAR v2.6.0. Raw counts were calculated by STAR, RPKM/FPKM values were calculated by in-house perl script
Assembly: hg38
Supplementary files format and content: txt file of RPKM/FPKM values

growth_protocol: Prostate cancer cell lines LNCaP, 22Rv1 and LuNE cells were maintained in RPMI1640 with 10% fetal bovine serum (FBS), 1% penicillin and streptomycin

extract_protocol:
RNA was extracted using the nucleospin RNA kit (Takara) according to the manufacturer’s recommended protocol
RNA-seq libraries were prepared from 0.5 μg of high-quality DNA-free RNA using NEBNext Ultra RNA Library Prep Kit, according to the manufacturer’s instructions.

treatment_protocol: 1.LNCaP cells were infected with FOXA2 overexpression virus and fallowed up by 28 days, cells were collected at D0, D2, D7, D14, D21 and D28 for RNA analysis. 2.22Rv1 cells were infected with control (plv) or  FOXA2 overexpression virus and fallowed up by 28 days, cells were collected at week4 for RNA analysis. 3. LuNE cells were infected gRNAs targeting control (sgNC), NKX2-1 (sgNKX2-1), FOXA2 (sgFOXA2) and both NKX2-1/FOXA2 (sgFOXA2+NKX2-1) or shRNAs targeting control (shCtrl), P300 (shP300), CBP (shCBP) and both P300/CBP (shP300+CBP), the cells were collected for RNA analysis 5 days after infection. 4. LuNE cells were treated with DMSO or CCS1477 (250nM) for 72h and collected for RNA analysis.

value: LNCaP (LuNE)


title: LuNE, shP300+CBP 2#


title: LNCaP, FOXA2-D7, sgNC, H3K27ac ChIP

value: FOXA2-D7, sgNC


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample16

description:
Chem1_C_D2
Chem1_counts_matrix.txt

value: whole body


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample14

description:
Chem1_B_D7
Chem1_counts_matrix.txt

value: Exponential Growth Stage


title: LuNE, shP300+CBP 1#


title: LNCaP, FOXA2-D21, sgNKX2-1, H3K27ac ChIP

value: FOXA2-D21, sgNKX2-1


title: LNCaP, FOXA2-D2, H3K27ac ChIP


title: LuNE, shCBP 2#

value: shCBP


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample13

description:
Chem1_B_D6
Chem1_counts_matrix.txt


title: LuNE, shCBP 1#


title: LNCaP, FOXA2-D14, sgNKX2-1, H3K27ac ChIP

value: FOXA2-D14, sgNKX2-1


title: LNCaP, FOXA2-D0, H3K27ac ChIP

value: Prostate


title: LuNE, shP300 3#


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample12

description:
Chem1_B_D5
Chem1_counts_matrix.txt


title: LuNE, shP300 2#


title: LNCaP, FOXA2-D28 2# ATAC-seq

data_processing:
Reads were aligned using ENCODE pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline)
The pipeline trimmed, filtered, and aligned the reads using Bowtie2. Mapped reads were shifted to correct for transposase insertion. PCR duplicates and mitochondrial reads were removed
Assembly: hg38
Supplementary files format and content: narrowpeak files from peak calling was performed using MACS2 with blacklisted regions removed (output from ENCODE pipeline)

growth_protocol: Prostate cancer cell lines LNCaP cells were maintained in RPMI1640 with 10% fetal bovine serum (FBS), 1% penicillin and streptomycin

extract_protocol:
50,000 cells were washed once with 1 × PBS and resuspended in 100 μl lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP 40, 0.1% Tween-20, 0.01% Digitonin) for 3min on ice, followed by adding 1ml of wash buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20) to remove cytoplasm and mitochondria fraction.
The nuclei were resuspended in 25 μl transposition mix (12.5 ul 2x TD buffer, 2.5 μl Tn5 Transposome, 8.25 μl 1xPBS, 0.25 μl 1% digitonin, 0.25 μl 10% Tween-20, 1.25 μl H2O) and incubated at 37 °C for 30 min in a thermomixer with 300 r.p.m. mixing. The tagmented DNA was purified using the DNA Clean & Concentrator-5 kit (ZYMO Research). Libraries were amplified and adapter dimers and primer dimers were cleaned up. Paired-end reads (50 bp) were sequenced using an Illumina HiSeq 4000.

treatment_protocol: LNCaP cells were infected with FOXA2 overexpression virus and fallowed up by 28 days, cells were collected at D2, D7, D14, D21 and D28 for ATAC-seq analysis.


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample11

description:
Chem1_B_D4
Chem1_counts_matrix.txt


title: LuNE, shCtrl  3#

value: shCtrl


title: LuNE, shP300 1#

value: Prostate cancer cell


title: LNCaP, FOXA2-D14 2# ATAC-seq


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample10

description:
Chem1_B_D3
Chem1_counts_matrix.txt


title: LuNE, shCtrl  2#


title: LNCaP, FOXA2-D7 2# ATAC-seq


title: RNA in water, isolated from interleukin-6 treated adult mouse cardiomyocytes

city: Ann Arbor

first: Matthew

middle: Jacob

last: Brody

state: MI

address: 1150 MEDICAL CENTER DR, 1240A MSRBIII

department: Department of Pharmacology

institute: University of Michigan

description: Library name: ACMs_IL6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
HISAT2 (2.2.1) used to build the index of the reference genome, aligning paired-end clean reads to 3 the reference genome.
featureCounts (2.0.6) was used to count the reads numbers mapped to each gene.
Prior to differential gene expression analysis, for each sequencing library, read counts were 4 adjusted using the edgeR R package (4.0.16) by scaling normalization factors to eliminate differences in sequencing depth between samples, followed by differential expression analysis. The resulting P value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate. The threshold of significant differential expression： padj <= 0.05 ＆ |log2(foldchange)| >= 1.
Assembly: mm39
Supplementary files format and content: raw counts and fpkm values per sample.

organism: Mus musculus

source_name: Heart

growth_protocol: Cardiomyocytes were isolated from hearts of 8-10 weeks old mice using the Langendorff-free method as described previously (https://doi.org/10.1161/CIRCRESAHA.116.309202) and plated for 3-4 hours on laminin-coated dishes or 8-well chamber slides (BD Falcon) in M199 media  (Gibco) containing 5% fetal bovine serum (FBS, Sigma), 10 mM 2,3-butanedione monoxime (BDM, Sigma), and 1% penicillin-streptomycin (P/S, Hyclone) and then put in fresh serum-free M199 with 0.1% BSA, 10 mM BDM, 1X insulin-transferrin-selenium (ITS, Invitrogen), 1X CD lipid (Gibco), and 1% P/S.

extract_protocol:
RNA was isolated from cultured adult cardiomyocytes with Trizol reagent (Invitrogen), samples pooled and cleaned up with the RNeasy Mini kit (Qiagen, #74104)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. Library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Cardiomyocytes were treated with 10 ng/mL mouse OSM (R&D systems), 10ng/mL human IL6 (R&D systems), or vehicle control in serum-free M199 media with 0.1% BSA, 10 mM BDM, 1X ITS, 1X CD lipid for 16 hours and then harvested for RNA isolation.

value: Heart

value: Cardiomyocytes

value: 10ng/mL human Interleukin-6


title: LuNE, shCtrl  1#

value: WT


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample9

description:
Chem1_B_D2
Chem1_counts_matrix.txt


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample8

description:
Chem1_B_D1
Chem1_counts_matrix.txt


title: LNCaP, FOXA2-D0 2# ATAC-seq

value: LNCaP


title: LuNE, shCBP 3#


title: RNA in water, isolated from vehicle-treated adult mouse cardiomyocytes

description: Library name: ACMs_BSA

value: Vehicle (0.1% BSA)


title: LuNE, sgFOXA2+NKX2-1 3#


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample7

description:
Chem1_A_D7
Chem1_counts_matrix.txt


title: LuNE, sgFOXA2+NKX2-1 2#


title: LNCaP, FOXA2-D28 1# ATAC-seq


title: LNCaP, FOXA2-D21 2# ATAC-seq


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample6

description:
Chem1_A_D6
Chem1_counts_matrix.txt


title: scRNA_lung_shNKX2-1_Vehicle

city: Taipei

first: Pinghsing

last: Tsai

state: Taiwan

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

country: Taiwan

institute: Taipei Veterans General Hospital

data_processing:
RNA seq
sequence reads were trimmed for adaptor sequence / low-quality sequence using basespace defult process
read count extraction and normalization were performed using R and EdgeR
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each sample
ATAC-Seq
The ATAC-seq pipeline was employed for processing and analyzing sequencing data, utilizing default parameters. The raw ATAC-seq fastq reads were aligned to the hg19 reference genome using the BWA Aligner (v1.1.4) on the basespace platform. The signal intensity present in the bedgraph files was determined as the fold enrichment of the signal per million reads within a sample compared to a modeled local background, utilizing the bdgcmp function in MACS2. Differential accessible peaks were detected using the MACS2 package and annotated with the ChIPseeker package.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files contain information on the distribution and enrichment of intersected peaks for both the control and shNKX2-1 samples.
Spatial Transcriptomics
The raw sequencing reads undergo processing using Space Ranger pipeline version 2.0.1. Sequences were aligned to mm10 genome.
Assembly: mm10
Supplementary files format and content: Spaceranger count pipline output files (Tab-separated values files and matrix files) Aligned tissue images: Spatial_lung_parental.tif; Spatial_lung_shNkx2-1.tif Cytassist image: Spatial_lung_parental_cytassist.tif; Spatial_lung_shNkx2-1_cytassist.tif Scalefactors in json format: Spatial_lung_parental_alignment.json; Spatial_lung_shNkx2-1_alignment.json
scRNA-seq
The raw sequencing reads undergo processing using Cell Ranger pipeline version 6.1.2. Sequences were aligned to mm10 genome.
Assembly: mm10
Supplementary files format and content: Cellranger count pipline output files (Tab-separated values files and matrix files)

growth_protocol: Lewis lung carcinoma (LL2) cells were cultured in DMEM media supplemented with 10% Fetal Bovine Serum (FBS), 100 mg/mL streptomycin, and 100 U/mL penicillin in a humidified atmosphere at 37°C.

extract_protocol:
Single-cell RNA sequencing libraries were generated by using a Chromium Controller instrument (10x Genomics, Pleasanton, CA, USA) and Chromium Single Cell 3’ Reagent Kits v2 according to the manufacturer’s instructions.
The library preparation was conducted in accordance with the manufacturer's guidelines using the single-cell 3’ v2 protocol from 10x Genomics. In summary, cells were suspended in a master mix and combined with partitioning oil and gel beads in a chip to create gel bead-in-emulsion (GEM) structures. The poly-A RNA from each GEM was reverse transcribed into cDNA, incorporating an Illumina R1 primer sequence, a Unique Molecular Identifier (UMI), and a 10x Barcode. The pooled barcoded cDNA was purified using Silane DynaBeads, PCR amplified, and fragments of appropriate sizes were selected using SPRIselect reagent for subsequent library construction. During library construction, the Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were introduced.

value: NKX2-1 Knockdown

value: vehicle


title: scRNA_lung_shNKX2-1_SB225002


title: scRNA_lung_shCtrl_Vehicle


title: LuNE, sgFOXA2+NKX2-1 1#

value: LNCaP (LuNE)


title: LNCaP, FOXA2-D14 1# ATAC-seq


title: LuNE, sgFOXA2 3#


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample5

description:
Chem1_A_D5
Chem1_counts_matrix.txt

value: whole body


title: RNA in water, isolated from oncostatin-M treated adult mouse cardiomyocytes

description: Library name: ACMs_OSM

value: 10ng/mL mouse oncostatin-M


title: LuNE, sgFOXA2 2#


title: Spatial_lung-shNkx2-1

data_processing:
RNA seq
sequence reads were trimmed for adaptor sequence / low-quality sequence using basespace defult process
read count extraction and normalization were performed using R and EdgeR
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each sample
ATAC-Seq
The ATAC-seq pipeline was employed for processing and analyzing sequencing data, utilizing default parameters. The raw ATAC-seq fastq reads were aligned to the hg19 reference genome using the BWA Aligner (v1.1.4) on the basespace platform. The signal intensity present in the bedgraph files was determined as the fold enrichment of the signal per million reads within a sample compared to a modeled local background, utilizing the bdgcmp function in MACS2. Differential accessible peaks were detected using the MACS2 package and annotated with the ChIPseeker package.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files contain information on the distribution and enrichment of intersected peaks for both the control and shNKX2-1 samples.
Spatial Transcriptomics
The raw sequencing reads undergo processing using Space Ranger pipeline version 2.0.1. Sequences were aligned to mm10 genome.
Assembly: mm10
Supplementary files format and content: Spaceranger count pipline output files (Tab-separated values files and matrix files) Aligned tissue images: Spatial_lung_parental.tif; Spatial_lung_shNkx2-1.tif Cytassist image: Spatial_lung_parental_cytassist.tif; Spatial_lung_shNkx2-1_cytassist.tif Scalefactors in json format: Spatial_lung_parental_alignment.json; Spatial_lung_shNkx2-1_alignment.json
scRNA-seq
The raw sequencing reads undergo processing using Cell Ranger pipeline version 6.1.2. Sequences were aligned to mm10 genome.
Assembly: mm10
Supplementary files format and content: Cellranger count pipline output files (Tab-separated values files and matrix files)
Library strategy: Spatial Transcriptomics

extract_protocol: Spatial transcriptomics sequencing libraries were prepared using 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit according to the manufacturer's instruction.


title: LNCaP, FOXA2-D7 1# ATAC-seq


title: LNCaP, FOXA2-D2 2# ATAC-seq


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample3

description:
Chem1_A_D3
Chem1_counts_matrix.txt

value: Exponential Growth Stage


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample4

description:
Chem1_A_D4
Chem1_counts_matrix.txt


title: Spatial_lung_parental


title: LuNE, sgFOXA2 1#


title: validation, Dnmt3a-/- Tx 5xFAD, rep2

city: Houston

first: Hu

last: Chen

state: TX

address: 1250 Moursund St,

department: Pediatrics

institute: Baylor College of Medicine

description: Library name: Validation_Dnmt3a_br15

data_processing:
We generated gene-level UMI counts for each sample using cellranger (V8.0.0), with the GRCm39 mouse genome (GRCm39-2024-A) downloaded from 10X Genomics. We applied EmptyDrops available through DropletUtils (V1.22.0) to identify empty droplets with default parameters, and droplets with an FDR lower than 0.01 were considered real cells. We further removed cells whose mitochondrial DNA (mtDNA) UMI count proportion was less than 20%. We employed Scrublet to calculate a doublet score for the retained cells and removed potential doublets with a score greater than 0.125. Each sample was manually reviewed by overlaying the total UMI count, mtDNA proportions, empty droplet scores, doublet scores, and gene markers to confirm the quality of the filtered cells for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: h5 from cellranger pipeline

source_name: brain

growth_protocol: Single cell suspensions were generated from whole brain preps using dissociation buffer following by Percoll gradient separation.

extract_protocol:
Mice were perfused with 20mL cold PBS prior to brain extraction. Brains were minced in dissociation buffer and incubated for 45mins at 37˚C. Homogenized cells were then subjected to a Percoll gradient to remove myelin. Cells were then filtered and enriched for either CD11a or CD45 using magnetic beads.
Library preparation was carried out using 10X Genomics manufacturers protocol CG000317_ChromiumNextGEMSingleCell3_v3.1_CellSurfaceProtein. Briefly, GEMs (Gel Beads-in-emulsion) were generated by combining barcoded Single Cell 3’ v3.1 Gel Beads, a Master Mix with cell surface protein labeled cells, and Partitioning Oil onto Chromium Chip G. Immediately following GEM generation, the Gel Bead is dissolved releasing the three types of primers and any co-partitioned cell is lysed. The poly(dT) and one of the capture sequence primers in the gel bead are engaged simultaneously in two different reactions inside individual GEMs. Both are mixed with cell lysate and Master Mix containing RT reagents. Incubation of the GEMs produces barcoded, full-length cDNA from poly-adenylated mRNA and barcoded DNA from the cell surface protein Feature Barcode. After incubation, GEMs are broken and pooled fractions are recovered. Silane magnetic beads are used to purify the cell barcoded products from the post GEM-RT reaction mixture. The cell barcoded cDNA molecules are amplified via PCR to generate sufficient mass for library constructions. Size selection is used to separate the amplified cDNA molecules for 3’ Gene Expression and Cell Surface Protein library construction. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina amplification.

treatment_protocol: Cells were enriched using magnetic beads for either CD11a (main) or CD45 (validation)

value: brain


title: LNCaP, FOXA2-D0 1# ATAC-seq


title: LNCaP, FOXA2-D21 1# ATAC-seq


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample1

description:
Chem1_A_D1
Chem1_counts_matrix.txt


title: validation, Tet2-/- Tx 5xFAD, rep2

description: Library name: Validation_Tet2_br5


title: BynRas3

city: Nicosia

first: Yiorgos

last: Apidianakis

address: 1 Panepistimiou Ave.

department: Biological Sciences

country: Cyprus

institute: University of Cyprus

description: Library name: Sample 6

data_processing:
Base calling was performed using bcl2fastq software.
Raw reads were aligned to the Drosophila genomic build dm6 through in two steps. Firstly, reads were mapped with hisat2 (https://www.nature.com/articles/s41587-019-0201-4) using the default parameters and then, the unmapped reads were mapped with bowtie2 (https://pubmed.ncbi.nlm.nih.gov/22388286/) using the local and very sensitive parameters.
Prior to the statistical testing procedure, the gene read counts were filtered for possible artifacts that could affect the subsequent statistical testing procedures. Genes presenting any of the following were excluded from further analysis: i) genes with zero reads (6531), ii) genes with length less than 500 (817    genes), iii) genes whose average reads per 100 bp was less than the 25th quantile of the total normalized distribution of average reads per 100bp (824    genes with cutoff value 0.26135    average reads per 100 bp), iv) genes with read counts below the median read counts of the total normalized count distribution (3931 genes with cutoff value) normalized read counts. The total (unified) number of genes excluded due to the application of all filters was 12055. The resulting gene counts were subjected to differential expression analysis for the contrasts Byn versus Byn>RasV12 using the Bioconductor packagemetaseqR2 with the DESeq algorithm and the utr parameter (https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbaa156/5890504). Differentially expressed genes were identified based on an absolute log2 fold change (|log2(FC)| > 1) and a p-value < 0.05. Code is available in https://github.com/alex-galaras/panagi_et.al.2025 .
Assembly: dm6
Supplementary files format and content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene for Quant-Seq data.

organism: Drosophila melanogaster

source_name: Intestine

growth_protocol: Flies were reared at 18°C and adult flies were transferred to 29°C for 7 days to induce the RasV12 transgene

extract_protocol:
Hindgut dissection and RNA extraction using Triazol reagent
QuantSeq-LEXOGEN (3’ mRNA-seq Library Prep Kit for Illumina)
RNA quality was assessed on a Bioanalyzer (Agilent Technologies) with RNA 6000 Nano Kit reagents and protocol (Agilent Technologies), followed by use of the 3′ mRNA-Seq Library Prep Kit protocol for Ion Torrent (QuantSeq-LEXOGEN Vienna, Austria) according to manufacturer’s instructions. Briefly, up to 500 ng of RNA was used for first and second-strand synthesis, followed by amplification. Library quality and quantity were assessed on a Bioanalyzer with DNA High Sensitivity Kit reagents and protocol (Agilent Technologies). The libraries were pooled together and templated and enriched on an Ion Proton One Touch system. Templating was performed using the Ion PI Hi-Q OT-II 200 Kit (ThermoFisher Scientific), followed by sequencing with the Ion PI Hi-Q Sequencing 200 Kit on Ion Proton PI V2 chips (ThermoFisher Scientific) on an Ion Proton System, according to the manufacturer’s instructions.

treatment_protocol: RasV12 oncogene expression in the adult Drosophila enterocytes

value: Intestine

value: Enterocytes-muscle

value: byn-G4 tub-G80ts U-gfp / U-RasV12

tag: group


title: LuNE, sgNKX2-1 2#

value: Prostate

value: Prostate cancer cell


title: LuNE, sgNKX2-1 3#


title: LuNE, sgNKX2-1 1#


title: R. subcapitata, 24 h exposure, 1(2H)-Phthalazinone, sample2

description:
Chem1_A_D2
Chem1_counts_matrix.txt


title: validation, Dnmt3a-/- Tx 5xFAD, rep1

description: Library name: Validation_Dnmt3a_br14


title: validation, Tet2-/- Tx 5xFAD, rep1

description: Library name: Validation_Tet2_br2


title: BynRas2

description: Library name: Sample 5


title: LuNE, sgNC 3#

value: sgNC


title: validation, WT Tx 5xFAD, rep2

description: Library name: Validation_WT_br7

value: Wildtype


title: BynRas1

description: Library name: Sample 4


title: HMB914

city: Toledo

first: Bina

last: Joe

state: OH

address: Block health Science building

institute: University of Toledo health science center

description: Library name: HMB914

data_processing:
The targeted sequencing depth for the ATAC-seq was 50-65 million pair-end reads per direction per sample, which aligns with the established guidelines for ATAC-seq (https://www.encodeproject.org/atac-seq/). Data preprocessing and quality controlling were performed using the bioinformatics pipeline, snakemake2. FastQC (FastQC) (v0.11.8) was used for Quality control of raw reads and trimmed reads3.
Assembly: TrimGalore (TrimGalore) (v0.4.5) and cutadapt (Martin) (v1.15) were used for adapter trimming and filtering of low-quality bases. Trimmed reads were aligned to rn6 with Bowtie24. Alignment quality control was performed using samtools5. Reads completely overlapping blacklisted regions (ENCODE Blacklist Regions) were removed with bedtools6. Sample-wise peaks were called with macs27. Peaks over all samples were merged with bedops8 for principal component analysis and unsupervised clustering to assess the similarity of samples. Finally, a report was generated by MultiQC9. For ATAC specific QC metrics, ataqv (Ataqv) was used10.
Supplementary files format and content: .bed and HMB_vs_HMC_merged_peaks.bed
Supplementary files format and content: .xlsx and HMB_vs_HMC_diff.xlsx
Supplementary files format and content: .xlsx and HMB_vs_HMC_annotations.xlsx
Supplementary files format and content: .xlsx and HMB_vs_HMC_annotations_summary.xlsx

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
Flash frozen renal tissues were transported to the UM Epigenomics Core for ATAC-Seq library preparation. Briefly, the tissues were cryo-pulverized with a Covaris CryoPREP2 (Covaris,). Frozen tissue powder (100mg) was aliquoted and processed for isolation of nuclei, enriched using an Optiprep discontinuous gradient and tagmented according to the Omni-ATAC-Seq protocol
The concentration of nuclei was assessed and a total of 50,000 nuclei were used for tagmentation. The final libraries were cleaned using Qiagen MinElute columns and AMPure XP beads before quantitation with the Qubit HS dsDNA kit, and quality assessment on a TapeStation HS D1000 kit. The libraries were pooled and quantitated by qPCR using KAPA’s Illumina Library quantitation kit before PE-150 sequencing on a NovaSeq6000 S4 at the University of Michigan Advanced Genomics Core.

value: Kidney

value: Dahl S (SS/Jr)

value: 1,3-Butanediol (20% w water)


title: validation, WT Tx 5xFAD, rep1

description: Library name: Validation_WT_br6


title: Byn3

description: Library name: Sample 3

value: byn-G4 tub-G80ts U-gfp

value: Control


title: LuNE, sgNC 1#

value: LNCaP (LuNE)

value: WT


title: HMC950

description: Library name: HMC950


title: main, Dnmt3a-/- Tx 5xFAD, rep2

description: Library name: main_Dnmt3a_2

value: LPS


title: LuNE, sgNC 2#


title: main, Dnmt3a-/- Tx 5xFAD, rep1

description: Library name: main_Dnmt3a_1


title: HMC946

description: Library name: HMC946


title: NCI-H660, Hi-C


title: Byn1

description: Library name: Sample 1


title: LNCaP, FOXA2-D2 1#  ATAC-seq

value: LNCaP


title: LuCaP147, Hi-C

value: LuCaP147 PDX


title: main, Tet2-/- Tx 5xFAD, rep2

description: Library name: main_Tet2_3

value: brain


title: Byn2

description: Library name: Sample 2

value: Intestine

value: Enterocytes-muscle


title: J18-IG-8

city: Toulouse

first: Ludovic

last: Martinet

state: Toulouse

address: 2 av Hubert Curien

country: France

institute: INSERM UMR 1037

data_processing:
TrimGalore(v0.6.5), default parameters
STAR (v2.6.0c), --alignIntronMax 1
samtools (v1.9),   -q 255
MarkDuplicates of Picard package (v1.88), REMOVE_DUPLICATES=true
MAC2 (v2.1.0.20150731), --call-summits
bamCoverage function of deeptools (v3.3.1), --normalizeUsing None  --blackListFileName
ChIPin package (v0.1.0) for quantile normalization
Assembly: GRCm39
Supplementary files format and content: Bed file: peaks merged from all samples identified using MAC2
Supplementary files format and content: Bigwig file: normalized ATAC signal in each condition

extract_protocol:
CD8+ T cells were isolated from the spleen using mouse CD8+ T cell isolation kit (Miltenyi Biotec) and FACSaria™ Fusion (BD biosciences). ATAC-seq was performed as previously described . Briefly, 50 000 cells pooled from 5 independent mice were lysed in ice-cold lysis buffer and the transposition reaction was performed using the Tn5 transposase at 37°C for 30 min. DNA was purified using the QIAGEN MinElute kit (QIAGEN).
The libraries were prepared using the Nextera DNA Library Prep Kit (Illumina) and purified using AMPure XP beads (Beckman) following a double-sided protocol to remove primer dimers and large fragments. Samples were performed in duplicates, multiplexed and sequenced on NextSeq-500 (75 bp paired-end reads).

treatment_protocol: C57BL/6 mice were treated with anti-CD137 (100 µg, 3H3, BioXcell, twice a week) or with control IgG (100 µg, HRPN, BioXcell).

value: Spleen

value: T cells

value: CD8+ T cells

value: IgG


title: HMB915

description: Library name: HMB915

value: Kidney


title: main, Tet2-/- Tx 5xFAD, rep1

description: Library name: main_Tet2_2


title: LCS8987_HB915

description: Library name: LCS8987_HB915

data_processing:
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.
To get high quality clean reads, reads were further filtered by Cutadapt. The parameters were as follows: 1. removing reads containing adapter, 2. removing reads containing poly A  and poly G, 3. removing reads containing more than 5% of unknown nucleotides (N), 4. removing low quality reads  containing more than 20% of low quality  (Q-valueless than or equal 20) bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: We aligned reads of all samples to the Rattus norvegicus reference genome using HISAT2 package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
Supplementary files format and content: .tar.gz and Report.tar.gz
Supplementary files format and content: .tar.gz and Summary.tar.gz

extract_protocol:
Total RNA was extracted from control and 1, 3-Butanediol fed rat kidneys using Trizol (Invitrogen).
Two rounds of mRNA purification were conducted from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA). Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Next, the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were then used to synthesize U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol. The sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9) 14,15. The sequence depth for RNAseq was 20M pair-end reads per sample (about 6Gb per sample).

value: Dahl S (SS/Jr)


title: LuCaP145.2, Hi-C

value: Prostate

value: LuCaP145.2 PDX

value: Prostate cancer cell


title: main, WT Tx 5xFAD, rep2

description: Library name: main_WT_2

value: Wildtype


title: LuCaP35CR, Hi-C

value: LuCaP 35CR PDX

value: WT


title: LCS8987_HB916

description: Library name: LCS8987_HB916

value: 1,3-Butanediol (20% w water)


title: J18-IG-7


title: LuCaP93, Hi-C

value: LuCaP93 PDX


title: HMB916

description: Library name: HMB916


title: J18-IG-6


title: LCS8987_HB914

description: Library name: LCS8987_HB914


title: J18-IG-5


title: main, WT Tx 5xFAD, rep1

description: Library name: main_WT_1

value: brain

value: LPS


title: LNCaP, FOXA2-D21, Hi-C

value: LNCaP


title: LNCaP, FOXA2-D28, Hi-C


title: LCS8987_HC950

description: Library name: LCS8987_HC950


title: J18-CD137-7

value: Spleen


title: HMC945

description: Library name: HMC945


title: LCS8987_HC946

description: Library name: LCS8987_HC946


title: LNCaP, FOXA2-D14, Hi-C


title: FLASH_D7_2

city: Beijing

first: Changzhen

last: Wang

address: No 27. Taiping Road

country: China

institute: Beijing Institute of Radiation Medicine

description:
Library name: 231468B_F_7D_2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregationwere made using the Cell Ranger software v7.2.0.(https://www.10xgenomics.com/support/jp/software/cell-ranger/8.0/getting-started/cr-what-is-cell-ranger)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
Once the samples were obtained during surgery, the tissue were washed twice with 1× PBS and minced into approximately 1mm3 fragments with sharp scissors and digested with collagenase Ⅱ (Sigma V900892, 2 mg/mL) and DNase I (Sigma DN25-100MG10 μg/mL) at 37℃ for 1h. Then, the single cell suspensions were collected through a 40 μm strainer (MACS® SmartStrainer 40μm, Miltenyi Biotec, Germany), and centrifuged at 500 g for 5 min, the supernatant was completely aspirated and cells were resuspended with 1ml 1 × PBS containing 0.04% weight/volume BSA. Finally, the cell number and viability were assessed by an automatic cell counter.
scRNA-seq libraries were constructed using the 10x Genomics Chromium platform 3′ library and Gel Bead Kit V3.1 according to manufacturer’s instructions, with an estimated 10,000 single cells per sample. Next-generation sequencing was performed on an Illumina Novaseq 6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy.

value: lung


title: LCS8987_HC945

description: Library name: LCS8987_HC945


title: FLASH_D7_1

description:
Library name: 231468B_F_7D_1
10x Genomics


title: J18-CD137-6

value: T cells

value: CD8+ T cells


title: FLASH_D7_3

description:
Library name: 231468B_F_7D_3
10x Genomics


title: CONV_D7_3

description:
Library name: 231468B_C_7D_3
10x Genomics


title: cdc5-3

city: Tai’ an

first: Xin

last: Xin

address: 61 Daizong Street

institute: Shandong Agricultural University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: Rosette leaves

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Rosette leaves


title: J18-CD137-5


title: LuNE, FOXA2 ChIP 1#

data_processing:
Reads were aligned to the hg19 reference human genome using bowtie2
bigwig generated from bam
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
PCa cells were crosslinked with 1% formaldehyde (Thermo fisher, Cat#28908)) for 10 min at room temperature with gentle rotation and then quenched for 5 min with 0.125 M glycine. Chromatin was sonicated to an average length of 200–600 bp using an E220 focused-ultrasonicator (Covaris).
ChIP–seq libraries were prepared from 3–5 ng of ChIPed DNA using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions.

value: LNCaP (LuNE)

value: FOXA2, Abcam, Cat#ab108422


title: J5-CD137-4


title: cdc5-2


title: LuNE, FOXA2 ChIP 2#

value: Prostate


title: LuNE, sgFOXA2, H3K27ac  ChIP 2#

value: Prostate cancer cell

value: H3K27ac, Cst, Cat#8173S


title: CONV_D7_2

description:
Library name: 231468B_C_7D_2
10x Genomics


title: J5-CD137-3


title: cdc5-1


title: LuNE, sgNKX2-1, H3K27ac ChIP 2#


title: CONV_D7_1

description:
Library name: 231468B_C_7D_1
10x Genomics


title: Col-3


title: J18-CD137-8


title: LuNE, sgNC, H3K27ac ChIP 2#

value: sgNC


title: FLASH_D1_3

description:
Library name: 231468A_Flash3
10x Genomics


title: FLASH_D1_2

description:
Library name: 231468A_Flash2
10x Genomics


title: J5-CD137-2

value: WT


title: Col-2


title: Aorta-P11_HET_replicate 6

city: Bethesda

first: Olivier

last: Duverger

state: MD

address: 30 Convent Drive - Bldg 30 - Room 202

institute: National Institute of Dental and Craniofacial Research

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to a custom GRCm38.vM11 mouse genome that was modified to include common mouse transgenes, ERCCs and SIRVs using STAR v2.5.2a in  single-pass mode with the --quantMode GeneCounts parameter.
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a GRCm38.vM11 genome annotation GTF which included common mouse transgenes, ERCCs and SIRVs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: GRCm38.vM11
Supplementary files format and content: Raw gene counts in tab-delimited txt format.
Supplementary files format and content: Filtered raw gene counts in tab-delimited txt format, after removal of genes with less that 5 reads in at least 1 sample.
Supplementary files format and content: TMM-normalized annotated gene expression matrix in counts per million reads units, tab-delimited txt format.

source_name: Aortic arch

extract_protocol:
Total RNA was isolated using TriPure™ Isolation Reagents (Sigma-Aldrich) followed by PureLink™ RNA Mini Kit (Thermo Fisher Scientific).
Library preparation was performed according to the manufacturer’s instructions for the Illumina Nextera XT unstranded library kit. The libraries were then pooled and sequenced on tow separate runs on a NextSeq 500 sequencer (Illumina) on 75bp single  mode.

value: Aortic arch

tag: age

value: Postnatal day 11

value: VSMC and EC

value: Het


title: Col-1


title: LuNE, sgNKX2-1, H3K27ac ChIP 1#


title: J5-CD137-1


title: LuNE, sgNC, H3K27ac ChIP 1#


title: CONV_D1_3

description:
Library name: 231468A_CONV3
10x Genomics


title: 6, CTRL Treated

city: Rockville

first: Resat

last: Cinar

state: Maryland

address: 5625 Fishers lane

institute: National Institute on Alcohol Abuse and Alcoholism

data_processing:
Kallisto with index generated from GRCm39 Protein_coding transcripts were summed to get the gene expression levels
Assembly: GRCm39
Supplementary files format and content: Estimated counts and TPM in tab-separated format

source_name: Lung

extract_protocol:
The right middle lobe of the lung tissues was immediately placed in RNAlater solution, then held on ice for 4–5 h, and then stored at -80°C until the RNA extraction procedure. RNA extraction was performed using RNeasy Mini Kits from Qiagen (Valencia, CA). RNA concentrations were measured with a NanoDrop One (ThermoFisher). One microgram of total RNA was reverse transcribed to cDNA using Bio-Rad iScript cDNA synthesis kit (Hercules, CA) according to the manufacturer’s instructions.
RNA Quality control, library preparations, sequencing reactions, and initial bioinformatic analysis were conducted at GENEWIZ, LLC (South Plainfield, NJ, USA). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA-sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer's instructions (NEB, Ipswich, MA, USA).

tag: strain

value: Lung

value: CTRL


title: LuNE, sgFOXA2, H3K27ac  ChIP 1#

source_name: Prostate


title: 40, VEH Treated

value: VEHICLE


title: FLASH_D1_1

description:
Library name: 231468A_Flash1
10x Genomics

value: lung


title: LuCaP145.2, H3K4me1 ChIP 2#

value: LuCaP PDX

value: H3K4me1, Abcam, Cat#ab8895


title: 39, VEH Treated


title: Aorta-P11_HET_replicate 5


title: Aorta-P11_HET_replicate 2


title: 5, CTRL Treated


title: Aorta-P11_HET_replicate 4


title: NCI-H660, H3K4me3 ChIP

value: H3K4me4, Cst, Cat#9751


title: NCI-H660, H3K27ac ChIP


title: CONV_D1_1

description:
Library name: 231468A_CONV1
10x Genomics


title: Aorta-P11_HET_replicate 3


title: Aorta-P11_WT_replicate 5


title: CONV_D1_2

description:
Library name: 231468A_CONV2
10x Genomics


title: Sham_3

description:
Library name: 231468A_Sham3
10x Genomics


title: LuCaP145.2, H3K4me1 ChIP 1#


title: Sham_2

description:
Library name: 231468A_Sham2
10x Genomics


title: Aorta-P11_HET_replicate 1


title: 37, RIMO Treated

value: RIMONABANT


title: NCI-H660, H3K4me1 ChIP 1#

value: Prostate


title: NCI-H660, H3K4me1 ChIP 2#

value: Prostate cancer cell


title: SOX2 KO organoids CUT&RUN with SOX2 ab

city: St. Louis

first: Ramon

last: Jin

address: 600 S Euclid

institute: Washington University School of Medicine

description: Library name: 26SOX2

data_processing:
Data analysis was performed on Galaxy platform using Cutadapt for adapter and bad quality base removal, Bowtie2 for mapping to reference genome GRCm38 (mm10). MACS2 was performed for peak calling.
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigWig
Library strategy: CUT&Run

source_name: Forestomach

growth_protocol: Mouse foregut squamous tissues fromand forestomachs were dissected, manually disrupted, and enzymatically digested with collagenase IX (Sigma-Aldrich) and dispase (Gibco). Dissociated squamous cells were then plated in Matrigel (Corning) droplets and supplemented with keratinocyte-SFM (KSFM) media supplemented with 50 µg/mL Bovin pituitary extract (Gibco), 10 µM Y-27632 (Sigma-Aldrich), 1 ng/mL EGF (Gibco), and 0.6 mM calcium chloride (Sigma-Aldrich). Organoids were expanded and passaged every 7-10 days by mechanical dissociation from Matrigel, dispersed using 0.05% Trypsin-EDTA (Thermo Fisher) and manual pipetting, and transferred into new Matrigel and plated in 24-well plates (Greiner Bio-One).

extract_protocol:
Mouse squamous organoids were mechanically dissociated from Matrigel, dispersed using 0.05% Trypsin-EDTA (Thermo Fisher) and manual pipetting. 400,000 cells were used per condition according to the CUTANA CUT&RUN Kit (EpiCypher). Briefly, ConA beads were activated and dissociated cells were bound to beads and incubated with antibodies (0.1 µg H3K27me3, MA5-11198, Invitrogen; 0.5 µg SOX2, ab97959, Abcam; IgG 0.5 µg, 13-0042, EpiCypher) on nutator overnight at 4°C. The slurry was washed with cold digitonin (0.01%) buffer prior to binding of pAG-MNase (EpiCypher) and incubation for 10 minutes at room temperature. 100 mM of CaCl2 was added to activate pAG-MNase for 2 hours at 4°C prior to stop buffer chelating of calcium and DNA purification with the CUTANA DNA Purification Kit.
Illumina NGS libraries were prepared using 5 ng of DNA from each condition and the CUTANA CUT&RUN Library Prep Kit. Agilent TapeStation was used to calculate molarity of DNA fragments. DNA libraries were pooled for a final concentration of 10 nM.

value: Forestomach

value: Organoid

value: SOX2 KO


title: 36, RIMO Treated

value: WT


title: Sham_1

description:
Library name: 231468A_Sham1
10x Genomics


title: 21, VEH Treated


title: Aorta-P11_WT_replicate 4

value: Aortic arch

value: Postnatal day 11


title: LuNE, shCBP, H3K27ac ChIP 2#

value: LNCaP (LuNE)

value: H3K27ac, Cst, Cat#8173S

value: shCBP


title: SOX2 KO organoids CUT&RUN with H3K27 ab

description: Library name: 26H3K27


title: SOX2 KO organoids CUT&RUN with IgG

description: Library name: 26IGG


title: 27, RIMO Treated

value: Lung


title: 18, MRI Treated


title: Aorta-P11_WT_replicate 2

value: VSMC and EC


title: Enamel-Organ-P11_Het_replicate 4

source_name: Enamel Organ

value: Enamel Organ

value: Dental epithelial cells

value: Het


title: LuNE, shP300, H3K27ac ChIP 2#


title: WT Control organoids CUT&RUN with SOX2 ab

description: Library name: 23SOX2


title: LuNE, DMSO, H3K27ac ChIP 2#

value: DMSO


title: WT Control organoids CUT&RUN with H3K27 ab

description: Library name: 23H3K27


title: 29, CTRL Treated

value: CTRL


title: 19, 1400W Treated


title: Enamel-Organ-P11_Het_replicate 5


title: LuNE, CCS1477, H3K27ac ChIP 2#

value: Prostate

value: Prostate cancer cell


title: LuCaP145.2, NKX2-1 ChIP

value: LuCaP PDX

value: NKX2-1, Sigma-Aldrich, Cat#07-601


title: LuCaP145.2, FOXA2 ChIP

value: WT

value: FOXA2, Abcam, Cat#ab108422


title: 12, MRI Treated


title: Enamel-Organ-P11_Het_replicate 2

value: Postnatal day 11


title: 15, 1400W Treated


title: 28, RIMO Treated

value: RIMONABANT


title: Mouse lung, Alternaria + Nucleosome 3

city: Denver

first: Rafeul

last: Alam

state: Colorado

address: 1400 Jackson Street

department: Medicine

institute: National Jewish Health

description:
Library name: Sample12
Coloum name in raw_counts_All_Samples.txt

data_processing:
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR and assigned count estimates to genes.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvested using Rneasy mini kit. Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Hyper mRNA-Seq kit for whole transcriptome libraries following manufacturer's protocols.

value: Alternaria + Nucleosome


title: Aorta-P11_WT_replicate 1

value: Aortic arch


title: 11, MRI Treated

value: Lung


title: Mouse lung, Alternaria 3

description:
Library name: Sample9
Coloum name in raw_counts_All_Samples.txt

value: Alternaria


title: Enamel-Organ-P11_Het_replicate 3

value: Enamel Organ


title: 16, 1400W Treated


title: Enamel-Organ-P11_WT_replicate 8

value: Dental epithelial cells


title: WT Control organoids CUT&RUN with IgG

description: Library name: 23IGG

value: Forestomach

value: Organoid


title: Enamel-Organ-P11_Het_replicate 1

value: Het


title: Mouse lung, Alternaria 2

description:
Library name: Sample8
Coloum name in raw_counts_All_Samples.txt


title: Enamel-Organ-P11_WT_replicate 7


title: NCI-H660, NKX2-1 ChIP 2#

value: Prostate


title: LNCaP, FOXA2-D0 scNanoRNA-Seq

description: Library name: NP81

data_processing:
base calling and alignment: guppy/6.4.6
Assembly: hg38
Supplementary files format and content: matrix.tsv: Gene count matrix table.
Supplementary files format and content: matrix_SNV_dp.tsv.gz: Single Nucleotide Variant (SNV) depth matrix table.

growth_protocol: 1.Prostate cancer cell lines LNCaP cells were maintained in RPMI1640 with 10% fetal bovine serum (FBS), 1% penicillin and streptomycin

extract_protocol:
Barcoded full-length cDNAs of single cells were prepared using 10x Genomics Next GEM Single Cell 3’ gene expression kit with elongation time extending to 3 min to enrich longer molecules
full-length cDNA libraries were prepared for nanopore long-read sequencing using SQK-LSK114 ligation sequencing kit (Oxford Nanopore).
final sequencing was run on PromethION flow cell (R10.4) with one sample per flow cell

treatment_protocol: LNCaP cells were infected with FOXA2 overexpression virus and followed up by 28 days, cells were collected at D0 and D28 for scNanoRNA-seq

value: LNCaP

value: Prostate cancer cell


title: LuNE, shCtrl, H3K27ac ChIP 2#

value: LNCaP (LuNE)

value: H3K27ac, Cst, Cat#8173S

value: shCtrl


title: Mouse lung, Alternaria 1

description:
Library name: Sample7
Coloum name in raw_counts_All_Samples.txt


title: Aorta-P11_WT_replicate 3

value: Postnatal day 11

value: VSMC and EC

value: WT


title: Mouse lung, Alternaria + Nucleosome 1

description:
Library name: Sample10
Coloum name in raw_counts_All_Samples.txt

value: Alternaria + Nucleosome


title: LNCaP, FOXA2-D28 scNanoRNA-Seq

description: Library name: NP83


title: LuNE, sgFOXA2, P300 ChIP


title: LuNE, sgNC, P300 ChIP

value: sgNC


title: Inulin 5

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Mus musculus genome (GRCm39)
DEG assessed using DeSeq2
Assembly: GRCm39
Supplementary files format and content: excel file with count data and gene symbol for each sample

source_name: Caecum

extract_protocol:
Total RNA was extracted using mRNAeasy kits (Qiagen)
Standard Illumina

value: Caecum


title: Mouse lung, Alternaria + Nucleosome 2

description:
Library name: Sample11
Coloum name in raw_counts_All_Samples.txt

value: Lung


title: Enamel-Organ-P11_WT_replicate 6

value: Enamel Organ

value: Dental epithelial cells


title: Enamel-Organ-P11_WT_replicate 5


title: Mouse lung, Nucleosome 3

description:
Library name: Sample6
Coloum name in raw_counts_All_Samples.txt

value: Nucleosome


title: NCI-H660, FOXA2 ChIP 2#

city: Atlanta

first: Jindan

last: Yu

address: E330, 1760 Haygood Dr NE

institute: Emory University

value: FOXA2, Abcam, Cat#ab108422


title: Mouse lung, Nucleosome 2

description:
Library name: Sample5
Coloum name in raw_counts_All_Samples.txt


title: LNCaP, FOXA2+NKX2-1-D14, FOXA2 ChIP

value: Prostate


title: Enamel-Organ-P11_WT_replicate 4


title: Enamel-Organ-P11_WT_replicate 3


title: SSD 6


title: Mouse lung, Saline 3

description:
Library name: Sample3
Coloum name in raw_counts_All_Samples.txt

value: Saline


title: Inulin, Tm day7 4


title: LNCaP, FOXA2-D28, H3K27me3 Cut&tag

data_processing:
Reads were aligned to the hg19 reference human genome using bowtie2
bigwig generated from bam
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&TAG

value: LNCaP

value: Prostate cancer cell


title: Mouse lung, Nucleosome 1

description:
Library name: Sample4
Coloum name in raw_counts_All_Samples.txt


title: Enamel-Organ-P11_WT_replicate 1


title: LuNE, sgNKX2-1, P300 ChIP

value: LNCaP (LuNE)


title: LNCaP, FOXA2-D14, H3K27me3 Cut&tag


title: Inulin, Tm day7 3


title: Enamel-Organ-P11_WT_replicate 2


title: Inulin, Tm day7 5


title: LNCaP, FOXA2-D21, H3K27me3 Cut&tag


title: Mouse lung, Saline 2

description:
Library name: Sample2
Coloum name in raw_counts_All_Samples.txt


title: Inulin, Tm day7 1


title: Mouse lung, Saline 1

description:
Library name: Sample1
Coloum name in raw_counts_All_Samples.txt


title: Tcf4(CTG)100/(CTG)100 mice, Tcf4 knockin, rep4

city: Kyotanabe

first: Taisuke

last: Numao

state: Kyoto

department: Department of Biomedical Engineering, Faculty of Life and Medical Sciences

country: Japan

institute: Doshisha University

description: Library name: KI4

data_processing:
Raw sequencing data quality was assessed using FastQC (v0.23.2)
Reads were mapped to mouse reference genome (GRCm39) using STAR (v2.7.11a)
Gene expression quantification using RSEM (v1.3.1)
Differential expression analysis using DESeq2 (Bioconductor v3.14)
Gene expression patterns were visualized using volcano plots with ggplot2 in R
Protein-coding differentially expressed genes (DEGs) were identified using biomaRt (v2.50.3)
Assembly: GRCm39
Supplementary files format and content: RNA-seq data will be deposited in the Gene Expression Omnibus (GEO) database.

source_name: cornea

growth_protocol: Mice were housed under standard laboratory conditions with a 12-hour light/dark cycle.

extract_protocol:
Total RNA was extracted from corneal endothelial cells using RNAlater and the RNeasy Micro Kit (QIAGEN) according to the manufacturer's protocol. RNA quantity and quality were assessed using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit.
RNA sequencing libraries were prepared using the SMART-Seq HT Kit (Takara Bio Inc.) following the manufacturer's protocol. After full-length cDNA synthesis, Illumina libraries were prepared using NexteraXT (Illumina Inc.).

value: cornea

value: primary

value: corneal endothelial cells

value: Tcf4 100×CTG repeat　knockin


title: NCI-H660, FOXA2 ChIP 1#

value: WT


title: SSD 5


title: Tcf4(CTG)100/(CTG)100 mice, Tcf4 knockin, rep5

description: Library name: KI5


title: LNCaP, FOXA2-D2,   H3K27me3 Cut&tag


title: SSD, Tm day7 5


title: Tcf4(CTG)100/(CTG)100 mice, Tcf4 knockin, rep3

description: Library name: KI3


title: SSD, Tm day7 4


title: LuCaP145.2, H3K27ac ChIP

value: LuCaP PDX

value: H3K27ac, Cst, Cat#8173S


title: Tcf4(CTG)100/(CTG)100 mice, Tcf4 knockin, rep2

description: Library name: KI2


title: NCI-H660, NKX2-1 ChIP 1#

value: NKX2-1, Sigma-Aldrich, Cat#07-601


title: SSD, Tm day7 3

value: Caecum


title: Inulin, Tm day7 2


title: LuCaP93, H3K27ac ChIP


title: WU016

type: RNA

description: human BE WU016

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized onto Gene 2.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C. GeneChip were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: An Affymetrix GeneChip Scanner 7G 3000 was used to scan the probe arrays. Gene expression intensities were calculated using Affymetrix AGCC software.

data_processing:
Data were processed using the Affymetrix Transcriptome Analysis Console (TAC; Thermo Fisher).
HuGene-2_0-st-v1.r4.pgf
HuGene-2_0-st-v1.r4.mps

label: biotin

source_name: human BE WU016

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system. Per RNA labeling, 50 nanograms of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip 2.0 ST chips.

growth_protocol: Barrett’s esophagus or normal adjacent esophageal squamous organoids were derived from de-identified tissue from patients undergoing Barrett’s esophagus surveillance EGD

extract_protocol: Human Barrett’s esophagus organoids were pelleted, and RNA was extracted using the AllPrep DNA/RNA/Protein Mini Kit (Qiagen) per manufacturer’s protocol.

value: BE


title: Tcf4(CTG)100/(CTG)100 mice, Tcf4 knockin, rep1

description: Library name: KI1


title: LuCaP147CR, H3K27ac ChIP


title: SSD, Tm day7 2


title: WU017

description: human BE WU017

source_name: human BE WU017


title: Wild type mice, control, rep4

description: Library name: WT4

value: Wild type


title: WU014 SQM

description: human adjacent esophagus WU014 SQM

source_name: human adjacent esophagus WU014 SQM

value: squamous esophagus


title: Wild type mice, control, rep5

description: Library name: WT5


title: WU014

description: human BE WU014

source_name: human BE WU014


title: SSD, Tm day7 1


title: LuCaP35CR, H3K27ac ChIP

value: Prostate


title: WU015

description: human BE WU015

source_name: human BE WU015


title: WU013 SQM

description: human adjacent esophagus WU013 SQM

source_name: human adjacent esophagus WU013 SQM


title: LNCaP, FOXA2-D28, CTCF ChIP

value: CTCF, Sigma-Aldrich, Cat#07-729


title: Inulin 4


title: SSD 4


title: Wild type mice, control, rep3

description: Library name: WT3


title: Inulin 3


title: SSD 3


title: RIDTumor13 rep2

city: Dallas

first: Philipp

last: Scherer

state: Texas

address: 5323 Harry Hines Blv

department: Touchstone Diabetes Center

institute: UT Southwestern Medical Center

description:
all_compare_Tumor vs RIDTumor.txt
RIDTumor_13

data_processing:
Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5).
Alignments were parsed using Tophat program
differential expressions were determined through DESeq2/edgeR
HTSeq v0.6.1 was used to count the read numbers mapped of each gene.
Supplementary_files_format_and_content: count, fpkm
Assembly: mm10
Supplementary files format and content: Supplementary_files_format_and_content: count, fpkm

source_name: PyMT breast tumor

extract_protocol:
RNA isolated from mammary fat pad or tumor tissues was used to prepare an RNAseq library by enrichment from total RNA using oligo(dT) beads
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PyMT breast tumor

value: (12-weeks) Dox-HFD regimen


title: LNCaP, FOXA2-D21, CTCF ChIP

value: LNCaP

value: Prostate cancer cell


title: Wild type mice, control, rep2

description: Library name: WT2

value: cornea

value: primary


title: Inulin, Tm day11 6


title: Spinal 3

city: Chengdu

first: Cheng

last: Zhou

state: Sichuan

address: No.37, guoxue lane, wuhou district, chengdu city, sichuan province

institute: West China Hospital of Sichuan University

data_processing:
Basecalls performed using  bcl2fastq tools
Raw single-cell RNA-seq data were processed using 10X Genomics Cell Ranger (v5.0.1), including demultiplexing the FASTQ reads, aligning them to the human reference genome (GRCh38, v3.0.0, from 10X Genomics), and counting the unique molecular identifier (UMI) (by using ‘cellranger count’ function).
Assembly: GRCh38
Supplementary files format and content: Tab separated values files with barcode sequences corresponding to column indices, features corresponding to row indices
Supplementary files format and content: peak text files

source_name: Spinal cord

extract_protocol:
Nuclei were isolated using a Nucleus Isolation Kit (catalogue no. 52009-10, SHBIO, China) according to the manufacturer’s instructions. Nuclei suspension was loaded onto a Chromium single cell controller (10x Genomics) to generate single-nucleus gel beads in the emulsion (GEM) using single cell 3' Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074) according to the manufacturer’s protocols.
The 10x snRNA-seq library was established using Single Cell 3’ Library and Gel Bead Kit V3.1, according to the manufacturer’s instructions.

value: spinal cord

value: 46 years old


title: WU012

description: human BE WU012

source_name: human BE WU012


title: Inulin, Tm day11 5


title: LNCaP, FOXA2-D14, CTCF ChIP

value: WT


title: WU010

description: human BE WU010

source_name: human BE WU010


title: Spinal 1

value: 35 years old


title: WU012 SQM

description: human adjacent esophagus WU012 SQM

source_name: human adjacent esophagus WU012 SQM


title: Inulin, Tm day11 4


title: Tumor30 rep2

description:
all_compare_Tumor vs RIDTumor.txt
Tumor_30


title: LNCaP, FOXA2-D2, CTCF ChIP


title: Wild type mice, control, rep1

description: Library name: WT1

value: corneal endothelial cells


title: SSD, Tm day11 6

value: Caecum


title: RIDiWAT3 rep3

description:
all_compare_iWAT vs RIDiWAT.txt
RIDiWAT3

source_name: Mammary fat (adipose tissue)

value: Mammary fat (adipose tissue)

value: (4-weeks) Dox-HFD regimen


title: patient 210701 untreated

city: PARIS

first: Alexandre

last: Boissonnas

address: 91 boulevard de l'hôpital

institute: Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris)

description:
Library name: N210701
10X Genomics

data_processing:
Sequencing data for human samples underwent processing via the Cell Ranger 6.1 pipeline. Utilizing the cellranger count function, we transformed FASTQ files and conducted alignment, filtering, barcode, and unique molecular identifier (UMI) counting. Reads were aligned with count against the GRCh38 human genome for human samples. This process harnesses Chromium cellular barcodes to generate feature-barcode matrices, ascertain clusters, and conduct gene expression analysis. Cellranger count was run with default parameters.
Assembly: GRCh38 human genome
Supplementary files format and content: barcode.tsv.gz, features.tsv.gz and matrix.mtx.gz files obtained from CellRanger alignment.

source_name: NSCLC

extract_protocol:
For cell sorting, the fresh NSCLC samples were cut into small pieces with scalpels 28 in a Petri dish and enzymatic digested at 37°C for 1h by 1mg/mL Collagenase A (Roche) and 29 0.1mg/mL DNAse I (Roche). Samples were filtered using 70µm cell strainer and washed in 30 RPMI (Gibco). After staining, cells were resuspended in PBS 0.5% BSA with 0.1mg/mL DNase for cell sorting. 10,000 Lymphocytes B cells (defined as CD45+ CD19+), 45,000 Lymphocytes T (defined as CD45+ CD3+), and 45,000 myeloid cells (defined as CD45+ HLA-DR+ CD64+) were sorted in FBS for each NSCLC sample. After centrifugation, cells were resuspended in PBS 0.5% BSA.
Samples were processed for single-cell encapsulation and cDNA library generation according to the manufacturer’s instructions using the 10x Genomics Single Cell 3′v2 Reagent Kit.

value: NSCLC

value: untreated

tag: batch


title: SSD, Tm day11 5


title: RIDiWAT1 rep1

description:
all_compare_iWAT vs RIDiWAT.txt
RIDiWAT1


title: patient 220804 treated by neoadjuvant chemotherapy

description:
Library name: CH220804
10X Genomics

value: neoadjuvant chemotherapy


title: Inulin 2


title: SSD, Tm day11 4


title: patient 220927 treated by neoadjuvant chemotherapy

description:
Library name: CH220927
10X Genomics


title: WU011 SQM

description: human adjacent esophagus WU011 SQM

source_name: human adjacent esophagus WU011 SQM

value: squamous esophagus


title: iWAT5 rep3

description:
all_compare_iWAT vs RIDiWAT.txt
iWAT5


title: patient 210414 untreated

description:
Library name: N210414
10X Genomics


title: RIDTumor5 rep1

description:
all_compare_Tumor vs RIDTumor.txt
RIDTumor_5

value: PyMT breast tumor

value: (12-weeks) Dox-HFD regimen


title: WU007

description: human BE WU007

source_name: human BE WU007

value: BE


title: Spinal 2

value: 38 years old


title: WU011

description: human BE WU011

source_name: human BE WU011


title: WU009

description: human BE WU009

source_name: human BE WU009


title: patient 210323 treated by neoadjuvant chemotherapy

description:
Library name: CH210323
10X Genomics


title: WU002

description: human BE WU002

source_name: human BE WU002


title: WU006

description: human BE WU006

source_name: human BE WU006


title: patient 2110143 treated by neoadjuvant chemotherapy

description:
Library name: CH211014
10X Genomics


title: Tumor1 rep1

description:
all_compare_Tumor vs RIDTumor.txt
Tumor_1


title: 23 WT Control Organoids

description: 23 WT Control Organoids

data_processing: Data were processed using the Affymetrix Transcriptome Analysis Console (TAC; Thermo Fisher).

source_name: 23 WT Control Organoids

label_protocol: RNA was submitted to the Genome Technology Access Center at Washington University in St. Louis. cDNA was prepared according to the standard Affymetrix protocol using at least 1 µg RNA per sample using the WT Plus assay.

extract_protocol: Mouse squamous organoids were mechanically dissociated from Matrigel, dispersed using 0.05% Trypsin-EDTA and manual pipetting. RNA was isolated using RNeasy Mini Kit following the manufacturer’s protocol.

treatment_protocol: SOX2 KO forestomach organoids and WT control forestomach organoids generated from mouse forestomach tissues from Krt5CreER/+; Sox2∆/∆; ROSA26tdTomato/+ mice and wildtype control mice were harvested.

value: Control


title: 131-B SOX2 KO

data_processing:
Data were processed using the Partek Flow Genomic Analysis Software.
MoGene-2_0-st-v1.r4.pgf
MoGene-2_0-st-v1.r4.mps
RMA normalized linear gene level expression values from Partek Flow Genomic Analysis Software.

source_name: 131-B SOX2 KO

growth_protocol: 4 SOX2 KO and 3 control mice were injected with “low-dose” tamoxifen (1 mg/20 g body weight) intraperitoneally for 7 consecutive days. Mouse forestomach tissues from four Krt5CreER/+; Sox2∆/∆; ROSA26tdTomato/+ mice and three wildtype control mice were harvested.

extract_protocol: Forestomaches were harvested and flushed with PBS. Corpus and antrum were removed. The forestomach tissues were mechanically dissociated using a tissue Homogenizer 850. RNA was isolated using RNeasy Mini Kit, following the manufacturer’s protocol.

value: SOX2 KO


title: 128-2 SOX2 KO

treatment_protocol: 4 SOX2 KO and 3 control mice were injected with “low-dose” tamoxifen (1 mg/20 g body weight) intraperitoneally for 7 consecutive days. Mouse forestomach tissues from four Krt5CreER/+; Sox2∆/∆; ROSA26tdTomato/+ mice and three wildtype control mice were harvested.


title: 26 SOX2 KO Organoids

description: 26 SOX2 KO Organoids

source_name: 26 SOX2 KO Organoids


title: SSD 1

source_name: Caecum


title: iWAT2 rep2

description:
all_compare_iWAT vs RIDiWAT.txt
iWAT2


title: Hippocampus infected SFRS8 knockdown virus, KD3

city: Hefei

first: d

last: z

address: shushan

institute: University of Science and Technology of China

data_processing:
DEGSeq
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files includes RPKM values for each Sample

source_name: hippocampus

extract_protocol:
RNA was harvested using MagZol Reagent (Magen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
(1) Total RNA samples were tested and then enriched for eukaryotic mRNA by Oligo(dT) magnetic beads; (2) Add Fragmentation Buffer for mRNA fragmentation; (3) One strand of cDNA was synthesised using a six-base random primer using mRNA as a template, followed by the synthesis of the second strand of cDNA using buffer, dNTPs, DNA polymerase I and RNase H, and cDNA purification; (4) Purified double-stranded cDNA was subjected to end repair, base A was added, sequencing junctions were added, and fragments were screened to recover cDNA around 350 bp; (5) PCR enrichment was performed to obtain cDNA libraries.

value: hippocampus


title: RIDiWAT2 rep2

description:
all_compare_iWAT vs RIDiWAT.txt
RIDiWAT2


title: Inulin 1


title: iWAT1 rep1

description:
all_compare_iWAT vs RIDiWAT.txt
iWAT1


title: 131-7 SOX2 KO


title: 128-1 SOX2 KO


title: patient 210218 untreated

description:
Library name: N210218
10X Genomics


title: blood28_T1

city: Malaga

first: Mora

last: Guardamagna

state: --- Select One ---

address: Severo Ochoa 35

country: Spain

institute: IBIMA

description: barcoded probe hybridization

hyb_protocol: Hybridization was performed using the NanoString nCounter PanCancer Immune Profiling Panel™ according to the manufacturer’s protocol, with 100 ng of total RNA per sample and overnight hybridization at 65°C.

scan_protocol: Hybridized samples were processed and scanned using the NanoString nCounter® Digital Analyzer following the manufacturer's instructions.

data_processing: Raw data (RCC files) were processed using NanoString nSolver™ and the NanoTube R package. Normalization was performed using the RUVg method (Remove Unwanted Variation using control genes). Differential expression analysis was performed using Limma™. Genes with log2 fold change > 1 and adjusted p-value < 0.05 were considered significant.

label_protocol: Not applicable. NanoString technology uses fluorescent barcoded probe pairs for direct hybridization and does not require labeling of RNA samples.

growth_protocol: Not applicable. Peripheral blood samples were collected directly from human patients without in vitro culture.

extract_protocol: RNA was extracted from peripheral blood samples using the RNAEasy Plus Universal Mini Kit™ (for frozen samples) or the QIAamp RNA Blood Mini Kit™ (for fresh samples) according to the manufacturer’s instructions. RNA quality and quantity were assessed using NanoDrop™ spectrophotometry.

treatment_protocol: atients were treated with first-line BRAF/MEK inhibitors for BRAF V600-mutated metastatic melanoma. Blood samples were collected at baseline (T0) and at the first radiological evaluation (T1).

tag: Sex

value: female

tag: responder

value: yes

tag: timepoint


title: Hippocampus infected SFRS8 knockdown virus, KD2


title: Hippocampus infected SFRS8 knockdown virus, KD1


title: 130-24 WT Control

source_name: 130-24 WT Control

value: WT Control


title: Inulin swtiched to SSD, Tm day11 4

value: Caecum


title: 131-13 WT Control

source_name: 131-13 WT Control


title: SSD 2


title: Hippocampus infected control virus, Ctrl3


title: 131-10 WT Control

source_name: 131-10 WT Control


title: blood28_baseline

description: barcoded probe hybridization

value: BASELINE


title: blood27_T1

description: barcoded probe hybridization


title: Inulin swtiched to SSD, Tm day11 2


title: Hippocampus infected control virus, Ctrl2