title: ELOA-dTAG_DMSO_Input

description: Library name: ELOA-dTAG_DMSO_Input

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments. Pol2 samples were normalized to RPKMs, while pSer2, HA-ELOA, and NELFc chipped samples were normalized using drosophila spike-in and saved in a bigWig format.
Assembly: hg38 (dm6 spike-in as indicated)
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis,  the nuclei were transferred to 1ml milliTUBEs with AFA fibers (Covaris, 520130) and sonicated in a Covaris E220 focused ultrasonicator (duty factor: 10%, peak intensity pulse: 140, cycles per burst: 200, time: 500 seconds).
Libraries were made using the KAPA HTP Biosystems Library Prep kit (Roche, KK8234) using Perkin Elmer Unique Dual Index Barcodes for Illumina NextSeq 2000

treatment_protocol: ELOA-dTAG DLD-1 cells were treated with dTAG13 (2uM, 5h) or DMSO at 37°C to deplete the ELOA protein.

value: DLD-1 ELOA-dTAG

value: ELOA-dTAG

value: DMSO


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-F15

status: Public on Dec 22 2025

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: strain

tag: age

value: 18 months

tag: brain region

value: DHC

tag: gender

value: M


title: ELOA-dTAG_dTAG13_Input

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Library name: ELOA-dTAG_dTAG13_Input

organism: Homo sapiens

source_name: colon

growth_protocol: All cells were cultured in Dulbecco's modified Eagle's medium (DMEM) from Thermo Fisher (cat# 11965-118) supplemented with 15% fetal bovine serum (FBS) from Millipore Sigma (cat# F2442), 1x Glutamax from Thermo Fisher (cat# 35050-079) and 100 units/ml penicillin-streptomycin from Thermo Fisher (cat# 15140-163).

tag: tissue

value: colon

tag: cell line

tag: cell type

value: epithelial cell

tag: genotype

tag: treatment

tag: chip antibody


title: ELOA-dTAG_dTAG13_NELFC

description: Library name: ELOA-dTAG_dTAG13_NELFC

value: NELFC


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-E4


title: ELOA-dTAG_dTAG13_HA-ELOA

description: Library name: ELOA-dTAG_dTAG13_HA-ELOA

value: HA-ELOA


title: ChIP_NELFC-AID_TetELOA_Aux_HA-ELOA

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis,  the nuclei were transferred to 1ml milliTUBEs with AFA fibers (Covaris, 520130) and sonicated in a Covaris E220 focused ultrasonicator (duty factor: 10%, peak intensity pulse: 140, cycles per burst: 200, time: 500 seconds).
Libraries were made using the KAPA HTP Biosystems Library Prep kit (Roche, KK8234) using Perkin Elmer Unique Dual Index Barcodes for NovaSeq 6000.

treatment_protocol: NELF-C-AID DLD-1 cells were treated with 500 µM Auxin or H2O (duration as indicated in the text) at 37°C to deplete the NELF-C-AID protein. To select lentivirus-infected cells, puromycin (1.5 μg/ml) and hygromycin (250 μg/ml) were used.

value: DLD-1 NELFC-AID

value: TetELOA

value: Auxin


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-E15


title: ELOA-dTAG_dTAG13_pSer2

description: Library name: ELOA-dTAG_dTAG13_pSer2


title: ChIP_NELFC-AID_NT_TetELOA_SPT6

value: no treatment


title: ELOA-dTAG_dTAG13_POL2

description: Library name: ELOA-dTAG_dTAG13_POL2


title: ELOA-dTAG_DMSO_NELFC

description: Library name: ELOA-dTAG_DMSO_NELFC


title: ChIP_NELFC-AID_NT_TetELOA_HA-ELOA


title: ChIP_NELFC-AID_TetELOA3_Aux_HA-ELOA3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-D3


title: ELOA-dTAG_DMSO_pSer2

description: Library name: ELOA-dTAG_DMSO_pSer2


title: ChIP_NELFC-AID_Aux_TetGFP_SPT6

value: TetGFP


title: blastoids, feeder-free

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

country: Italy

institute: University of Padua

description:
Library name: ff
gene expression (GEX): 3' mRNA library: R1 file contains cell barcode and UMI; R2 file contains transcript

library_source: transcriptomic single cell

data_processing:
Initial processing of scRNA-seq data was performed using Cell Ranger (v 6.1.2; 10X Genomics). Dual-indexed RNA and single-indexed hashtag oligo (HTO) libraries were processed in separate instances of cellranger mkfastq, using bcl2fastq (v2.20.0.422; Illumina).
FASTQ files were aligned to the human reference genome (GRCh38, v 2020-A as provided by 10x Genomics) with cellranger multi (expect-cells 16500, min-assignment-confidence 0.9), assigning 4251 cells to the given sample.
The resulting sample-specific filtered feature-barcode matrix provided here has subsequently been filtered to include only features detected in at least three cells, and cells with at most 15% mitochondrial counts and at least 7000 UMIs, retaining 3260 high-quality cells.
Assembly: GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics)
Supplementary files format and content: filtered feature-barcode matrix (combined gene expression and HTO counts of this sample) in Market Exchange Format: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: polyA RNA

source_name: H9 (WA09, WiCell)

growth_protocol: hESC were cultured without feeders in PXGL on plates coated with 10%FBS (Merck Sigma Aldrich, F7524) in DMEM/F12 with GlutaMAX (Thermo Fisher Scientific, 31331028) for 24h at 37°C. hESC were collected by incubation at 37°C for 3 min with Accutase (Merck Sigma Aldrich, A6964). Single cells were plated at a density of 98-102 cells per micro-well of a 24-well AggreWell 400 plate in N2B27 supplemented with Y27632 (10 uM, Merck Millipore, 688000) to aggregate for 3h. Subsequently, medium was changed to PALLY medium consisting of N2B27 supplemented with PD0325901 (1 uM, Axon Medchem, Axon 1408), A83-01 (1 uM, Axon MedChem, Axon 1421), hLIF (10 ng/mL, Qkine, Qk036), oleoyl-L-alpha-lysophosphatidic acid sodium salt (LPA, 1 uM, Merck Sigma Aldrich, L7260) and Y27632 (10 uM, Merck Millipore, 688000). 24 hours and 48 hours later, half medium was changed with PALLY medium. After a total of 72h of PALLY culture, blastoids were maintained for 48 hours in LY medium consisting of N2B27 supplemented with LPA (1 uM, Merck Sigma Aldrich, L7260) and Y27632 (10 uM, Merck Millipore, 688000).

extract_protocol:
Blastoids were dissociated into a single cell suspension by incubation with a mixture of TrypLE™ 10x (1x, Thermo Fisher Scientific, A1217701) and Accutase (Merck Sigma Aldrich, A6964) for about 15 minutes with intermittent pipetting. Each sample was incubated with 0.5 μg of unique hashtag antibody for 20 min on ice. TotalSeq hashtag antibodies (A0255-A0256, Biolegend) were used to multiplex the samples (DOI: 10.1126/sciadv.adg4055). All samples were sorted on a BD FACSymphony S6 (BD Bioscences) resulting in a total cell recovery of around 8000 cells, which were loaded onto a Chromium Next GEM chip (10x Genomics).
Library preparation was performed according to the Chromium Next GEM Single Cell 3’ v3.1 user guide with the addition of the hashtag library for demultiplexing. Combined libraries were sequenced using the NextSeq2000 P2-100 kit (Illumina) with Paired-end sequencing

value: H9 (WA09, WiCell)

value: human embryonic stem cells


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-D16


title: ELOA-dTAG_DMSO_POL2

description: Library name: ELOA-dTAG_DMSO_POL2

value: DLD-1 ELOA-dTAG


title: Shef6 on serum, RNA-Seq, Replicate 2

description: Library name: Shef6_serum_Rep_2

library_source: transcriptomic

data_processing:
Transcript quantification was performed from raw reads using Salmon (v1.6.0) on transcripts defined in Ensembl 106.
Gene expression levels were estimated with tximport R package (v1.26.1).
Assembly: Human GRCh38.p13 Ensembl release 106.
Supplementary files format and content: Expression_raw counts.txt is a txt containing EnsemblID, official gene symbols and raw counts for each condition.

source_name: human embryonic pluripotent stem cells

growth_protocol:
Cultured on serum coating (10% Fetal Bovine Serum [Gibco A5256701] in DMEM high glucose [Gibco 41965039]) in PXGL medium (Bredenkamp et al, 2019) at 37°C, 5% CO2, 5% O2. The PXGL medium was prepared as follows: N2B27 (DMEM/F12 [Gibco 11320074], and Neurobasal in 1:1 ratio [Gibco 21103049], with 1:200 N2 Supplement [Gibco 17502048], and 1:100 B27 Supplement [Gibco 17504044], 2 mM L-glutamine [Gibco 25030024], 0.1 mM 2-mercaptoethanol [Sigma-Aldrich M3148]) supplemented with 1 µM PD0325901 (Axon Medchem), 2 μM XAV939 (Axon Medchem 1408), 2 μM Gö6983 (Axon Medchem 2466) and 10 ng/ml human LIF (Qkine Qk036). Cells were passaged every 3-4 days at a split ratio up to 1:12 using Accutase (Sigma-Aldrich, A6964) for 5 minutes at 37°C. 10 μM ROCK inhibitor was added to the naive medium for 24 hours after passaging.
Cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs; DR4 ATCC), or on serum coating (10% Fetal Bovine Serum [Gibco A5256701] in DMEM high glucose [Gibco 41965039]) in PXGL medium (Bredenkamp et al, 2019) at 37°C, 5% CO2, 5% O2. The PXGL medium was prepared as follows: N2B27 (DMEM/F12 [Gibco 11320074], and Neurobasal in 1:1 ratio [Gibco 21103049], with 1:200 N2 Supplement [Gibco 17502048], and 1:100 B27 Supplement [Gibco 17504044], 2 mM L-glutamine [Gibco 25030024], 0.1 mM 2-mercaptoethanol [Sigma-Aldrich M3148]) supplemented with 1 µM PD0325901 (Axon Medchem), 2 μM XAV939 (Axon Medchem 1408), 2 μM Gö6983 (Axon Medchem 2466) and 10 ng/ml human LIF (Qkine Qk036). Cells were passaged as single cells every 3-4 days following dissociation with TrypLE (Gibco 12563029) or Accutase (Sigma-Aldrich, A6964) for 3 minutes at room temperature. 10 μM ROCK inhibitor (ROCKi, Y27632, Axon Medchem 1683) was added to the naive medium for 24 hours after passaging.

extract_protocol:
Total RNA was isolated using Total RNA Purification Kit (Norgen Biotek 37500) following the manufacturer’s instructions for HPD06 and HPD03 lines; Total RNA was isolated with the ExtractMe kit (Blirt, EM15) following the manufacturer’s instructions for Shef6 line.
Quant Seq 3' mRNA-seq Library Prep kit (Lexogen) was used for library construction.

value: human embryonic pluripotent stem cells


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-E16


title: TTseq_H2O4h_NVP2_30m_ELOA-KO2_NELFC-AID_Rep2

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
Trimming of paired-end reads were performed using cutadapt 4.2. The resulting reads were aligned to the genome assemblies GRCh38 release 103 for human and BDGP6.28 release 102 for fly using STAR 2.7.5. The reads with primary alignment and MAPQ ≥ 20 were retained and used for the downstream analysis. TT-seq signal was normalized to the total mapped spike-in reads.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: TT-seq

molecule: nuclear RNA

extract_protocol:
TT-seq library was prepared as described previously (Schwalb et al., 2016; Rosencrance wt al., 2020) with these modifications:  after treatment cells were immediately lysed in TRIzol and the lysates were stored at –80°C. ~150 µg total RNA supplemented with 4sU-labeled fly S2 spike-in RNA was fragmented at 94°C for 2 min using NEBNext Magnesium RNA Fragmentation Module. The labeled RNA was biotinylated using 33 µg/ml MTSEA-biotin-XX in the presence of 20% DMF for 1 h at r.t. The biotinylated RNA was purified using Dynabeads MyOne Streptavidin C1 and eluted in 100 mM DTT.
rRNA was depleted using NEBNext rRNA Depletion Kit v2. Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: ELOA KO or WT NELF-C-AID DLD-1 cells were treated with 500 µM Auxin or H2O for 4 h at 37°C to deplete the NELF-C-AID protein. Cells were then treated with CDK9 inhibitor NVP-2 at 250 nM for 0 or 30 min at 37°C to synchronize RNAPII, followed by washout/media replacement to release RNAPII and RNA labelling with 500 µM 4-Thiouridine (4sU) for 10 min at 37°C.

value: ELOA-KO


title: ChIP_NELFC-AID_Aux_TetELOA_SPT6


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-D15

value: 18 months


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-C4

value: DHC


title: TTseq_H2O4h_NVP2_30m_ELOA-WT_NELFC-AID_Rep2

value: WT


title: MTB37

city: New York

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

institute: Columbia University

data_processing:
RNA-seq reads were mapped to the human reference genome version GRCh38 using Kallisto
Assembly: GCRh38
Supplementary files format and content: Tab-separated values file containing the count matrix of the 3 samples (genes entez-ID in the rows and sample IDs in the columns)

molecule: total RNA

source_name: untreated DIPG Tumor

extract_protocol:
Frozen tissue was sent to Ashion/Exact Sciences, and processed there to generate bulk RNA Sequencing. GEM ExTra®, a Next Generation Sequencing tumor/normal exome and tumor RNA Seq assay, provides for the detection of SNVs, indels, copy number events, and fusions in tumor tissue
Total RNA is extracted from the patient's tumor sample. The isolated RNA is then prepared using KAPA HyperPrep with Riboerase (Kapa Biosystems). Libraries are then clustered on a flow cell and sequenced using the Illumina NovaSeq 6000

tag: tissue type

value: Biopsy

value: untreated DIPG Tumor


title: MTB36


title: TTseq_H2O4h_NVP2_0m_ELOA-WT_NELFC-AID_Rep1

value: colon

value: epithelial cell

value: No treatment


title: TTseq_H2O4h_NVP2_0m_ELOA-WT_NELFC-AID_Rep2

value: DLD-1 NELFC-AID


title: TTseq_H2O4h_NVP2_30m_ELOA-KO1_NELFC-AID_Rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-C16

value: M


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-C3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-D4


title: TTseq_H2O4h_NVP2_0m_ELOA-KO2_NELFC-AID_Rep2


title: ELOA-dTAG_DMSO_HA-ELOA

description: Library name: ELOA-dTAG_DMSO_HA-ELOA

value: ELOA-dTAG

value: DMSO

value: HA-ELOA


title: Control, VH005, scRNASeq

description: 10x Genomics

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

source_name: DMG Cell Line (SU-DIPG-XVII) subcutaneously injected in mice

growth_protocol: All mice were maintained under barrier conditions and experiments were conducted under the protocol approved by the Columbia University Institute of Comparative Medicine (ICM) and the Institutional Animal Care and Use Committee (IACUC) under protocol AC-AABL655. Juvenile male and female NOD.Cg Prkdcscid/J (NSGTM) mice were inoculated with 500,000 SU-DIPG-17-luciferase tagged cells in 1:1 suspension (200 μl total) with full media (Knockout DMEM/F12, Stempro neural supplement, Human FGF2, Human EGF2, Glutamine and Penicillin/Streptomycin) and Matrigel (BD Bioscience) via subcutaneous injection in the left flanks. Two weeks post-injection, animals were injected intraperitoneally with luciferin and scanned with PerkinElmer IVIS Optical Imagingto monitor tumor growth.

extract_protocol:
After tumor isolation, fat, fibrous and necrotic areas were removed from the tumor sample in a tissue culture hood (within 2 minutes to avoid cell viability loss). Then, tumor was cut into 1-2 mm pieces and transferred to a gentleMACS C Tube containing 4.7 mL of sterile media (Knockout DMEM/F12), 200 μl of Enzyme H, 100 μl of Enzyme R, and 25 μl of Enzyme A). C Tubes were placed in the gentleMACS Dissociator under the “Medium” Tumor type (gentleMACS Program 37C_h_TDK_2) for 18 minutes. Then, samples were filtered through a 70μm strainer (previously primed with 2 ml of sterile media). Samples were centrifuged at 250 x g at 4°C for 8 minutes. Then, resuspended in 400 μl of red blood cell lysis buffer and incubated on ice. After 2 minutes, at least 3 times the volume of RBC was added to rebalance osmolarity and the sample was centrifuged at 250 x g at 4°C for 5 minutes and resuspended in HBBS + 0.04% BSA. Samples were then examined for cell viability and counts using the Countess II
Dissociated cells were processed for single-cell gene expression capture (scRNA-seq) using the 10X Chromium 3’ Library and Gel Bead Kit (10x Genomics), following the manufacturer’s user guide. After Gel bead-in-EMulsion Reverse Transcription (GEM-RT) reaction, 12-15 cycles of polymerase chain reaction (PCR) amplification were performed to obtain cDNAs used for RNA seq library generation
Libraries were prepared following the manufacturer’s user guide and sequenced on the Illumina NovaSeq 6000 Sequencing System at the Columbia University Single Cell Analysis Core

treatment_protocol: Animals were monitored biweekly until tumor size reached ~100 mm3 (range of volumes >75 – <185 mm3) and tumor-bearing mice were randomly assigned to distinct drug arms or vehicle control treated groups when they reached adequate size. Animals were treated for 5 days at the following doses: Vehicle (n=4) (N-Methyl-2-pyrrolidone (NMP) as solvent and 30%PEG-400 + 5% Tween 80 + 65% D5W (PTD) as vehicle, all drugs were dissolved in the same solvent and vehicle), Larotrectinib 200mg/kg PO (per os, oral gavages) QD (every day), Trametinib (n=2) 1mg/kg PO (5 days on, 2 off), Dinaciclib (n=2)40mg/kg (Monday-Wednesday-Friday), Avapritinib (n=3) 30mg/kg PO QD (5 days on, 2 days off), Ruxolitinib (n=2) 90mg/kg PO BID (180mg/kg/day), Venetoclax (n=3) 100 mg/kg PO QD (5 days on, 2 days off), Etoposide (n=3) 8mg/kg IP QD (5 days on, 2 days off), Mocetinostat (n=2) 50mg/kg PO QD (5 days on, 2 days off) and Napabucasin (n=3) 10mg/kg (Monday-Wednesday-Friday)

value: SU-DIPG-XVII

value: Vehicle


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-C15


title: TTseq_H2O4h_NVP2_0m_ELOA-KO1_NELFC-AID_Rep1


title: TTseq_Aux4h_NVP2_30m_ELOA-WT_NELFC-AID_Rep2


title: TTseq_H2O4h_NVP2_30m_ELOA-WT_NELFC-AID_Rep1


title: TTseq_Aux4h_NVP2_30m_ELOA-KO1_NELFC-AID_Rep1


title: TTseq_Aux4h_NVP2_30m_ELOA-KO2_NELFC-AID_Rep2


title: Napabucasin, JE029, scRNASeq

description: 10x Genomics

value: DMG Cell Line (SU-DIPG-XVII) subcutaneously injected in mice

value: Napabucasin


title: MTB41

value: Surgery


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-B4

value: 18 months

value: DHC


title: TTseq_Aux4h_NVP2_0m_ELOA-WT_NELFC-AID_Rep2

value: WT

value: Auxin


title: Trametinib, TR002, scRNASeq

description: 10x Genomics

value: Trametinib


title: Venetoclax, JE027, scRNASeq

description: 10x Genomics

value: Venetoclax


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-B16


title: Avapritinib, JE028, scRNASeq

description: 10x Genomics

value: Avapritinib


title: TTseq_Aux4h_NVP2_0m_ELOA-WT_NELFC-AID_Rep1

value: colon

value: DLD-1 NELFC-AID

value: epithelial cell


title: TTseq_Aux4h_NVP2_30m_ELOA-WT_NELFC-AID_Rep1


title: TTseq_Aux4h_NVP2_0m_ELOA-KO1_NELFC-AID_Rep1

value: ELOA-KO


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-B3

value: M


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-B15


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-A4


title: Shef6 on serum, RNA-Seq, Replicate 1

description: Library name: Shef6_serum_Rep_1

value: human embryonic pluripotent stem cells


title: Dinaciclib, JE026, scRNASeq

description: 10x Genomics

value: SU-DIPG-XVII

value: Dinaciclib


title: Venetoclax, JE025, scRNASeq

description: 10x Genomics

value: DMG Cell Line (SU-DIPG-XVII) subcutaneously injected in mice


title: Control_3A

city: Changchun, China

first: Hao

last: Wu

address: Xinjiang Street, Changchun, Jilin

country: China

institute: Jilin University

description: Library name: sample6

data_processing:
sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp 0.20.1
Trimmed sequence reads were mapped to GRCm38 using hisat2 2.2.1
read count extraction and normalization were performed using stringtie 2.1.5（-e -b）and R Package "ballgown"
Assembly: GCF_000001895.5_Rnor_6.0

organism: Rattus norvegicus

source_name: Primary cells

extract_protocol:
RNA extraction adopts traditional trizol method
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

value: Ovaries

value: Ovarian granulosa cells


title: Control_1A

description: Library name: sample4


title: ATR_3A

description: Library name: sample3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-A3

value: 18 months

value: DHC


title: Control_2A

description: Library name: sample5


title: ATR_2A

description: Library name: sample2


title: Ruxolitinib, JE024, scRNASeq

description: 10x Genomics

value: Ruxolitinib


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-A16


title: ATR_1A

description: Library name: sample1


title: Mocetinostat, JE024, scRNASeq

description: 10x Genomics

value: Mocetinostat


title: TTseq_Aux4h_NVP2_0m_ELOA-KO2_NELFC-AID_Rep2

value: Auxin


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-A15


title: WT recurrent acute pancreatitis, 6× protocol, replicate 2

city: Boston

first: Sahar

last: Nissim

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital

description:
Library name: RAP_6x_rep2
10x Genomics Chromium Single Cell 3' RNA-seq

data_processing:
FASTQ files were processed with Cell Ranger count (v7.0.0 / v8.0.1) to align reads to the mouse genome and generate feature–barcode matrices. Ambient RNA was removed using CellBender remove-background (v0.2.0). Cells were filtered by UMI count, gene count, mitochondrial content, and doublets (scDblFinder). Data were normalized using proportional fitting and log1p transformation. Dimensionality reduction, integration, clustering, and differential expression were performed using Scanpy, Harmony, and Triku.
Assembly: Mouse mm10 (2020-A) + mKate2
Supplementary files format and content: Cell-level gene-by-cell count matrices in MEX format (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz) for each library
Supplementary files format and content: CellBender cleaned, doublet removed h5ad scanpy files for each sample, as well as 10X output files (matrix, features, barcodes)

source_name: Pancreas

extract_protocol:
The FixNCut method was used to preserve pancreatic cells from harvested tissue. Fresh mouse pancreas tissue (~3×3 mm) was fixed in 1 mg/mL DSP (dithiobis(succinimidyl propionate)) at room temperature for 30 min and quenched with Tris-HCl. Tissue was dissociated with Liberase TM (200 µg/mL, 37 °C, 30 min), filtered (70 µm), washed in PBS + 1% BSA, and resuspended with RNase inhibitor. Single-cell suspensions were filtered (40 µm), counted, and loaded onto the 10x Chromium controller targeting ~10,000 cells.
Single-cell 3′ gene expression libraries were generated using the 10x Genomics Chromium Single Cell 3′ Reagent Kit v3.1 according to the manufacturer’s instructions. Libraries were sequenced on Illumina platforms using paired-end 100-cycle chemistry.

value: Pancreas

value: Pancreatic cells

value: WT

value: RAP (6 weeks)


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-P2


title: WT recurrent acute pancreatitis, 4× protocol, replicate 2

description:
Library name: RAP_4x_rep2
10x Genomics Chromium Single Cell 3' RNA-seq

value: RAP (4 weeks)


title: Mocetinostat, JE023, scRNASeq

description: 10x Genomics


title: WT recurrent acute pancreatitis, 6× protocol, replicate 1

description:
Library name: RAP_6x_rep1
10x Genomics Chromium Single Cell 3' RNA-seq


title: WT recurrent acute pancreatitis, 4× protocol, replicate 1

description:
Library name: RAP_4x_rep1
10x Genomics Chromium Single Cell 3' RNA-seq


title: Napabucasin, JE021, scRNASeq

description: 10x Genomics

value: Napabucasin


title: WT chronic pancreatitis, 4 weeks, mKate2+ epithelial cells, replicate 2

description:
Library name: CP4w_2C
10x Genomics Chromium Single Cell 3' RNA-seq

value: Pancreatic epithelial cells (mKate2+ sorted)

value: CP (4 weeks)


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-P14

value: M


title: WT chronic pancreatitis, 4 weeks, mKate2+ epithelial cells, replicate 1

description:
Library name: CP4w_1C
10x Genomics Chromium Single Cell 3' RNA-seq


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-P13


title: WT recurrent acute pancreatitis, 2× protocol, replicate 1

description:
Library name: RAP_2x_rep1
10x Genomics Chromium Single Cell 3' RNA-seq

value: RAP (2 weeks)


title: Larotrectinib, JE018, scRNASeq

description: 10x Genomics

value: DMG Cell Line (SU-DIPG-XVII) subcutaneously injected in mice

value: SU-DIPG-XVII

value: Larotrectinib


title: Etoposide, JE020, scRNASeq

description: 10x Genomics

value: Etoposide


title: WT chronic pancreatitis, 4 weeks, all cells, replicate 1

description:
Library name: CP4w_1
10x Genomics Chromium Single Cell 3' RNA-seq


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-P1

value: 18 months

value: DHC


title: WT chronic pancreatitis, 4 weeks, all cells, replicate 2

description:
Library name: CP4w_2
10x Genomics Chromium Single Cell 3' RNA-seq


title: K-AP 7 days, mKate2+ epithelial cells, replicate 2

description:
Library name: APK7d_2C
10x Genomics Chromium Single Cell 3' RNA-seq

value: APK (7 days)


title: Ruxolitinib, JE016, scRNASeq

description: 10x Genomics

value: Ruxolitinib


title: Avapritinib, JE017, scRNASeq

description: 10x Genomics

value: Avapritinib


title: K-AP 12 weeks, mKate2+ epithelial cells, replicate 2

description:
Library name: APK12w_2C
10x Genomics Chromium Single Cell 3' RNA-seq

value: Pancreas

value: APK (12 weeks)


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-O2


title: WT recurrent acute pancreatitis, 2× protocol, replicate 2

description:
Library name: RAP_2x_rep2
10x Genomics Chromium Single Cell 3' RNA-seq

value: Pancreatic cells

value: WT


title: Napabucasin, JE015, scRNASeq

description: 10x Genomics

value: Napabucasin


title: K-AP 12 weeks after caerulein, all cells, replicate 2

description:
Library name: APK12w_2
10x Genomics Chromium Single Cell 3' RNA-seq


title: K-AP 12 weeks after caerulein, all cells, replicate 1

description:
Library name: APK12w_1
10x Genomics Chromium Single Cell 3' RNA-seq


title: K-AP 7 days, mKate2+ epithelial cells, replicate 1

description:
Library name: APK7d_1C
10x Genomics Chromium Single Cell 3' RNA-seq

value: Pancreatic epithelial cells (mKate2+ sorted)


title: K-AP 6 weeks, mKate2+ epithelial cells, replicate 1

description:
Library name: APK6w_1C
10x Genomics Chromium Single Cell 3' RNA-seq

value: APK (6 weeks)


title: Trametinib, JE013, scRNASeq

description: 10x Genomics

value: Trametinib


title: K-AP 6 weeks, mKate2+ epithelial cells, replicate 2

description:
Library name: APK6w_2C
10x Genomics Chromium Single Cell 3' RNA-seq


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-O14

value: M


title: K-AP 6 weeks after caerulein, all cells, replicate 2

description:
Library name: APK6w_2
10x Genomics Chromium Single Cell 3' RNA-seq


title: K-AP 14 days, mKate2+ epithelial cells, replicate 1

description:
Library name: APK11
10x Genomics Chromium Single Cell 3' RNA-seq

value: APK (14 days)


title: K-AP 14 days after caerulein, KrasG12D, replicate 2

description:
Library name: APK10
10x Genomics Chromium Single Cell 3' RNA-seq


title: K-AP 6 weeks after caerulein, all cells, replicate 1

description:
Library name: APK6w_1
10x Genomics Chromium Single Cell 3' RNA-seq


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-N14


title: K-AP 14 days, mKate2+ epithelial cells, replicate 2

description:
Library name: APK12
10x Genomics Chromium Single Cell 3' RNA-seq


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-N13


title: K-AP 14 days after caerulein, KrasG12D, replicate 1

description:
Library name: APK9
10x Genomics Chromium Single Cell 3' RNA-seq


title: Larotrectinib, JE011, scRNASeq

description: 10x Genomics

value: DMG Cell Line (SU-DIPG-XVII) subcutaneously injected in mice

value: SU-DIPG-XVII

value: Larotrectinib


title: Venetoclax, JE012, scRNASeq

description: 10x Genomics

value: Venetoclax


title: Etoposide, JE009, scRNASeq

description: 10x Genomics

value: Etoposide


title: K-AP 12 weeks, mKate2+ epithelial cells, replicate 1

description:
Library name: APK12w_1C
10x Genomics Chromium Single Cell 3' RNA-seq


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-N1

value: 18 months

value: DHC


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-O13


title: Dinaciclib, JE008, scRNASeq

description: 10x Genomics

value: Dinaciclib


title: K-AP 7 days after caerulein, KrasG12D, replicate 1

description:
Library name: APK7
10x Genomics Chromium Single Cell 3' RNA-seq

value: Pancreas

value: APK (7 days)


title: K-AP 72 h after caerulein, KrasG12D, replicate 2

description:
Library name: APK6
10x Genomics Chromium Single Cell 3' RNA-seq

value: Pancreatic cells

value: APK (72 h)


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-M2


title: K-AP 72 h after caerulein, KrasG12D, replicate 1

description:
Library name: APK5
10x Genomics Chromium Single Cell 3' RNA-seq


title: K-AP 14 h after caerulein, KrasG12D, replicate 2

description:
Library name: APK4
10x Genomics Chromium Single Cell 3' RNA-seq

value: APK (14 h)


title: Control, JE004, scRNASeq

description: 10x Genomics

value: Vehicle


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-O1


title: Control, JE014, scRNASeq

description: 10x Genomics


title: K-AP 14 h after caerulein, KrasG12D, replicate 1

description:
Library name: APK3
10x Genomics Chromium Single Cell 3' RNA-seq


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-N2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-M14


title: K-AP 7 days after caerulein, KrasG12D, replicate 2

description:
Library name: APK8
10x Genomics Chromium Single Cell 3' RNA-seq


title: K-AP control, KrasG12D, replicate 2

description:
Library name: APK2
10x Genomics Chromium Single Cell 3' RNA-seq

value: APK (control)


title: K-AP control, KrasG12D, replicate 1

description:
Library name: APK1
10x Genomics Chromium Single Cell 3' RNA-seq


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-M13

value: M


title: Control, JE003, scRNASeq

description: 10x Genomics


title: HAEC, Sample REST2

city: Columbus

first: Marios

last: Arvanitis

state: OH

address: 473 W 12th Ave

institute: The Ohio State University

description: Library name: Sample REST2

data_processing:
CUT&Tag was performed using the CUT Tag-IT Assay Kit (Active Motif #53160) following the manufacturer’s protocol, using an anti-REST antibody (EMD Millipore #17-6410). Two biological replicates were used for CUT&Tag per the ENCODE CHIP-seq best practice guidelines. CUT&Tag sequences were aligned to the hg38 human genome using Bowtie2 and peaks were called using the MACS2 software
Assembly: Human
Supplementary files format and content: narrowpeak
Library strategy: CUT&Tag

source_name: Aorta

extract_protocol:
Primary HAEC were obtained from Lonza (#CC-25350) and cultured in complete endothelial cell media according to the manufacturer’s instructions. All experiments were performed using HAEC grown for no more than 10 passages. CUT&Tag was performed using the CUT Tag-IT Assay Kit (Active Motif #53160) following the manufacturer’s protocol
CUT$TAG libraries were prepared according to the manufacter's instructions

value: Aorta

value: Human Aortic Endothelial cells

value: Endothelial cells

tag: batch


title: HAEC, Sample REST1

description: Library name: Sample REST1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-L2


title: Adipocyte precursor cells, 6hr FICZ, Sample 4

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: Library name: FICZ_4

data_processing:
Reads were demultiplexed with Illumina's bll2fq
STAR (2.7.7 ) was used to aligne reads against UCSC mm10.
Gene based counting also done with STAR
Assembly: mm10
Supplementary files format and content: csv file includes Gene counts for each Sample

source_name: Perigonadal white adipose tissue

growth_protocol: Adipose tissue was collected in PBS with 0.5% BSA (fatty-acid-free; Sigma A3803-100G) and kept on ice until ready to process. Tissue was minced using scalpels and digested in DMEM (Thermo Fisher, 41965039) containing 2% BSA, 12.5 mM HEPES, 0.2 mg/ml liberase TL (Sigma, 5401020001) and 1/100 DNase (Sigma, 10104159001) for 30min at 37 oC with constant agitation at 180 rpm. The digestion was stopped by adding one volume DMEM, and the sample centrifuged at 250xg for 10min to separate the stromovascular (SVF) and adipocyte fractions. Cells were strained through a 100 μm cell strainer, centrifuged at 300xg for 3min to pellet and red blood cells lysed by resuspending in ACK lysis buffer (0.15 M NH4Cl, 1 mM KHCO3, 0.1 mM Na2EDTA, pH 7.4) for 2min. DMEM was added to stop the lysis, cells strained through a 40 μm cell strainer and centrifuged at 300xg for 3min to pellet. Cells were resuspended in DMEM and counted and an appropriate number of cells aliquoted per condition and panel. Cells were washed in FACS buffer (3% FBS, 2 mM EDTA) and pelleted at 300xg for 3min. Fc receptor blockade was carried out using TruStain Fc Block (1:500; Biolegend, 101320) for 15min on ice. Cells were incubated in antibody mix for 20min on ice (CD45 PerCP-Cy5.5, 1:200, Biolegend 103132; CD31 AF647, 1:200, Biolegend 102516; Pdgfrα BV605, 1:100, Biolegend 135916). After staining cells were passed through a 40 μm cell strainer and resuspended in FACS buffer containing 10 ng/ml DAPI (Sigma, D9542-1MG). 100 μm nozzle was used for sorting and sorted cells were collected in 100% FBS. Cells were then centrifuged at 300 x g for 5min and re-suspended in ITS medium (60% DMEM, 40% MCDB 201, 2% FBS, 0.02% ITS, 0.1mM L-ascorbic acid-2-2-phosphate, 10ng/ml FGF, 0.5% Pen/Strep, 0.2% Gentamycine) for counting and plating. Media was replaced every 2 days and cells used once confluent without passaging.

extract_protocol:
Cultured cells were washed once with PBS, lysed using Trizol and snap-frozen on dry ice. RNA was extracted from the lysates using the TRIzol™ Plus RNA Purification Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Once confluent FICZ (100nM) or vehicle (DMSO) was added to the cells and lysates collected 6hr after stimulation for bulk RNA sequencing.

value: Perigonadal white adipose tissue

value: WT

value: FICZ


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-L14

value: 18 months


title: Adipocyte precursor cells, 6hr FICZ, Sample 3

description: Library name: FICZ_3


title: Adipocyte precursor cells, 6hr DMSO, Sample 4

description: Library name: DMSO_4

value: DMSO


title: Adipocyte precursor cells, 6hr DMSO, Sample 3

description: Library name: DMSO_3


title: Adipocyte precursor cells, 6hr FICZ, Sample 5

description: Library name: FICZ_5


title: Adipocyte precursor cells, 6hr FICZ, Sample 2

description: Library name: FICZ_2


title: Adipocyte precursor cells, 6hr DMSO, Sample 2

description: Library name: DMSO_2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-L13

value: DHC


title: V360-CGND-HRA-03714-B

first: Christopher

last: Jackson

state: NY

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

description: Library name: V360-CGND-HRA-03714-B

data_processing:
Each sequenced 10X Visium library was aligned to a standard reference genome (hg38; GENCODE v32/Ensembl98) and counted with spaceranger
Assembly: hg38
Supplementary files format and content: ALS_FTD_SPATIAL_SPACERANGER_OUTPUT.h5ad AnnData object containing spaceranger count data and image arrays

extract_protocol:
Frozen tissue blocks, kept at -80°C prior to processing, were equilibrated to -16°C inside a Leica CM3050S cryostat, embedded in Tissue Plus OCT Compound (Fisher Healthcare, #4585), and sectioned in a perpendicular orientation with regard to the pial surface. Tissue sections (10 µm-thick) from quality controlled blocks (H&E staining and imaging) were collected onto prechilled Visium Spatial Gene Expression Slides (10X Genomics, #1000185) while briefly warming the back of the slide with a gloved finger to improve adherence and minimize artifacts. We sought to capture cortical layers 1 through 6 and white matter within each spatially barcoded array.
Visium libraries were prepared using unique Illumina-compatible PCR primers with Dual Index Kit TT Set A (10X Genomics, #1000215). Size distribution profiles of the final libraries were assessed by running Agilent High Sensitivity DNA chips (#5067-4626) on a 2100 Bioanalyzer system (Agilent, #G2939BA). Libraries outside the expected range (450 ± 50 bp) or that contained adapter dimer contaminants were discarded and reprocessed. Total yields were initially measured on a Qubit 3.0 fluorometer before final qPCR quantification (KAPA Library Quantification Kit for Illumina Platforms, KAPA Biosystems, #KK4824).

tag: sample id

tag: donor id

tag: Sex

value: Male

tag: pmi

tag: phenotype

value: Control


title: V360-CGND-HRA-03714-A

description: Library name: V360-CGND-HRA-03714-A


title: V358-CGND-HRA-03630-D

description: Library name: V358-CGND-HRA-03630-D

value: Female

tag: disease duration

value: ALSci


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-L1

tag: strain

tag: age


title: NPPO-9, RNA-seq

first: Jia

middle: Jessie

last: Li

department: Medicine

institute: Columbia University Irving Medical Center

description: Library name: NPPO-9_RNA-seq

data_processing:
RNA-seq reads were aligned to the mouse reference genome (mm10) using HISAT2 (v2.1.0).
The mapped reads count of each gene was measured by featureCounts (v1.6.1).
The RNA-seq reads count matrix was combined with the CUT&Tag signal reads count matrix for all gene loci in R (v4.1.2).
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Prostate

extract_protocol:
Organoids were dissociated into single cells using TrypLE, and total RNA isolated using MagMAX™-96 for Microarrays Total RNA Isolation Kit (ThermoFisher Scientific AM1839). Briefly, cells were lysed in 1 ml TRI reagent per 5 million cells, and incubated for 5 min at RT. The homogenate was mixed with 0.1 volume 1-bromo-3-chloropropane (Millipore-Sigma B9673), incubated at RT for 5 min, and centrifuged at 12,000 g for 10 min at 4°C. 100 μl of the aqueous phase was transferred to an 8-strip EpiCypher tube (DNase/RNase-free), and 50 μl of 100% isopropanol (Millipore-Sigma I9516) added with shaking for 1 min. 10 μl of RNA Binding Beads were added, followed by shaking for 3 minutes. The RNA Binding Beads were then captured on a magnetic stand and the beads washed twice with 150 μl Wash Solution. The beads were dried for 2 min, and RNA eluted in 50 μl of Elution Buffer. All samples were DNase-treated prior to library treatment. Quality assessment was performed using the 4200 TapeStation system (Agilent), with a median RNA integrity number of 9.7 (range 9.5 to 10).
Libraries were generated using the Illumina Stranded mRNA Prep, and 150-bp paired-end sequencing was performed to a minimum of ~30 million reads per sample on the Illumina HiSeq platform.

value: Prostate

value: NPPO-9 organoids

value: Prostate non-NE tumor cells

value: No


title: V358-CGND-HRA-03630-C

description: Library name: V358-CGND-HRA-03630-C


title: NPPO-8, RNA-seq

description: Library name: NPPO-8_RNA-seq

value: NPPO-8 organoids


title: Adipocyte precursor cells, 6hr DMSO, Sample 5

description: Library name: DMSO_5


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-K2

tag: brain region

tag: gender

value: M


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-M1


title: NPPO-7, RNA-seq

description: Library name: NPPO-7_RNA-seq

tag: tissue

tag: cell line

value: NPPO-7 organoids


title: NPPO-1nonNE, RNA-seq

description: Library name: NPPO-1nonNE_RNA-seq

value: NPPO-1nonNE organoids

tag: cell type

tag: genotype


title: NPPO-6, RNA-seq

description: Library name: NPPO-6_RNA-seq

value: NPPO-6 organoids

value: Prostate NE tumor cells

tag: treatment


title: V357-CGND-HRA-03630-C

description: Library name: V357-CGND-HRA-03630-C


title: NPPO-4, RNA-seq

description: Library name: NPPO-4_RNA-seq

value: NPPO-4 organoids


title: V357-CGND-HRA-03630-D

description: Library name: V357-CGND-HRA-03630-D


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-K13

value: 18 months


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-K14

value: DHC


title: NPPO-2, RNA-seq

description: Library name: NPPO-2_RNA-seq

value: NPPO-2 organoids


title: NPPO-1NE, RNA-seq

description: Library name: NPPO-1NE_RNA-seq

value: NPPO-1NE organods


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-J2


title: San1_tile5_35_rep2

city: Copenhagen

first: Sven

last: Larsen-Ledet

state: N

address: Ole Maaloes Vej 5

country: Denmark

institute: University of Copenhagen

description:
Library name: San1_tile5_35_rep2
San1_tile5_35_rep2

library_source: other

data_processing:
Libraries were sequenced on a NextSeq 550 instrument (Illumina) and base called using the instrument's Real Time Analysis software.
Sequencing reads were converted to fastq format and demultiplexed using BaseSpace Sequence Hub.
Reads from each lane were merged and resulting R1 and R2 fastq files were trimmed. The trimmed fastq files were used as input to our in-house script to calculate a folding score for each indel variant using normalization to synonymous wild-type variants in WT strain, Ubr1 strain, San1 strain at 30C and 35C.
Assembly: atggttggttctttgaactgtatcgttgctgtttcacaaaacatgggtatcggtaaaaatggtgacttgccatggccaccattaagaaacgaattcagatacttccaaagaatgactacaacttcttcagttgaaggtaaacaaaatttggttattatgggtaaaaagacttggttctctatcccagaaaagaatagaccattgaagggtagaattaatttggttttgtcaagagaattgaaagaaccaccacaaggtgctcatttcttgtctagatcattggatgatgcattgaagttgacagaacaaccagaattggctaataaggttgatatggtttggattgttggtggttcttcagtttacaaagaagcaatgaaccatccaggtcatttgaagttgttcgttactagaatcatgcaagatttcgaatctgatactttctttccagaaatcgatttggaaaagtacaagttgttgccagaatacccaggtgttttatcagatgttcaagaagaaaagggtattaaatacaagttcgaagtttacgaaaagaatgat
Supplementary files format and content: A xlsx file with folding scores for each variant at 30C and 35C as well as and error for each score.

molecule: protein

source_name: Yeast cells

growth_protocol: Following library transformations, yeast cells were expanded in SC-LEU medium until saturation.

extract_protocol:
Plasmid DNA was extracted from 9 OD units of yeast cells using the ChargeSwitch Plasmid Yeast Mini kit (Invitrogen).
Tiled DHFR indel libraries comprised wild-type DHFR; a synonymous (silent) variant at each position; a nonsense (stop codon) mutation at each position; a single glycine insertion at each position; and a single amino acid deletion at each position. The libraries were cloned into pAG415GPD-ccdB.

treatment_protocol: For selection yeast cells were washed and grown on solid SC-LEU-URA medium at 30C and 35C for two days. Following selection, the cells were harvested and stored at -20C prior to plasmid DNA extraction.

value: Yeast cells

value: San1 KD strain

value: 35 °C


title: V355-CGND-HRA-03714-A

description: Library name: V355-CGND-HRA-03714-A

value: Male

value: Control


title: San1_tile5_35_rep3

description:
Library name: San1_tile5_35_rep3
San1_tile5_35_rep3


title: Adipocyte precursor cells, 6hr FICZ, Sample 1

description: Library name: FICZ_1

value: Perigonadal white adipose tissue

value: WT

value: FICZ


title: V355-CGND-HRA-03714-B

description: Library name: V355-CGND-HRA-03714-B


title: San1_tile5_35_rep1

description:
Library name: San1_tile5_35_rep1
San1_tile5_35_rep1


title: San1_tile5_30_rep2

description:
Library name: San1_tile5_30_rep2
San1_tile5_30_rep2

value: 30 °C


title: Adipocyte precursor cells, 6hr DMSO, Sample 1

description: Library name: DMSO_1

value: DMSO


title: V352-CGND-HRA-03661-C

description: Library name: V352-CGND-HRA-03661-C


title: San1_tile5_30_rep1

description:
Library name: San1_tile5_30_rep1
San1_tile5_30_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-J14

value: M


title: V351-CGND-HRA-03661-D

description: Library name: V351-CGND-HRA-03661-D


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-J13


title: San1_tile5_no_sele_rep3

description:
Library name: San1_tile5_no_sele_rep3
San1_tile5_no_sele_rep3

value: control


title: San1_tile5_no_sele_rep1

description:
Library name: San1_tile5_no_sele_rep1
San1_tile5_no_sele_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-J1


title: San1_tile5_no_sele_rep2

description:
Library name: San1_tile5_no_sele_rep2
San1_tile5_no_sele_rep2


title: V350-CGND-HRA-03752-B

description: Library name: V350-CGND-HRA-03752-B

value: Female


title: V350-CGND-HRA-03752-A

description: Library name: V350-CGND-HRA-03752-A


title: San1_tile4_35_rep3

description:
Library name: San1_tile4_35_rep3
San1_tile4_35_rep3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-I2

value: 18 months


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-I14

value: DHC


title: V338-CGND-HRA-03662-A

description: Library name: V338-CGND-HRA-03662-A


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-K1


title: San1_tile4_35_rep1

description:
Library name: San1_tile4_35_rep1
San1_tile4_35_rep1


title: San1_tile4_35_rep2

description:
Library name: San1_tile4_35_rep2
San1_tile4_35_rep2


title: San1_tile4_30_rep3

description:
Library name: San1_tile4_30_rep3
San1_tile4_30_rep3


title: San1_tile4_30_rep2

description:
Library name: San1_tile4_30_rep2
San1_tile4_30_rep2


title: San1_tile4_no_sele_rep3

description:
Library name: San1_tile4_no_sele_rep3
San1_tile4_no_sele_rep3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-I13


title: V337-CGND-HRA-03662-A

description: Library name: V337-CGND-HRA-03662-A


title: San1_tile4_30_rep1

description:
Library name: San1_tile4_30_rep1
San1_tile4_30_rep1


title: V337-CGND-HRA-03662-B

description: Library name: V337-CGND-HRA-03662-B


title: San1_tile5_30_rep3

description:
Library name: San1_tile5_30_rep3
San1_tile5_30_rep3


title: V310-CGND-HRA-03634-B

description: Library name: V310-CGND-HRA-03634-B

value: ALS


title: San1_tile4_no_sele_rep1

description:
Library name: San1_tile4_no_sele_rep1
San1_tile4_no_sele_rep1


title: San1_tile3_35_rep3

description:
Library name: San1_tile3_35_rep3
San1_tile3_35_rep3


title: V310-CGND-HRA-03634-A

description: Library name: V310-CGND-HRA-03634-A


title: San1_tile3_35_rep2

description:
Library name: San1_tile3_35_rep2
San1_tile3_35_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-H14


title: San1_tile3_30_rep3

description:
Library name: San1_tile3_30_rep3
San1_tile3_30_rep3


title: V310-CGND-HRA-03621-D

description: Library name: V310-CGND-HRA-03621-D


title: San1_tile3_30_rep2

description:
Library name: San1_tile3_30_rep2
San1_tile3_30_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-H13


title: San1_tile3_30_rep1

description:
Library name: San1_tile3_30_rep1
San1_tile3_30_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-H1


title: San1_tile3_no_sele_rep2

description:
Library name: San1_tile3_no_sele_rep2
San1_tile3_no_sele_rep2


title: San1_tile3_no_sele_rep3

description:
Library name: San1_tile3_no_sele_rep3
San1_tile3_no_sele_rep3


title: San1_tile3_no_sele_rep1

description:
Library name: San1_tile3_no_sele_rep1
San1_tile3_no_sele_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-G2


title: V310-CGND-HRA-03621-C

description: Library name: V310-CGND-HRA-03621-C


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-I1


title: San1_tile2_35_rep3

description:
Library name: San1_tile2_35_rep3
San1_tile2_35_rep3


title: V309-CGND-HRA-03634-B

description: Library name: V309-CGND-HRA-03634-B


title: San1_tile4_no_sele_rep2

description:
Library name: San1_tile4_no_sele_rep2
San1_tile4_no_sele_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-G14


title: V309-CGND-HRA-03621-D

description: Library name: V309-CGND-HRA-03621-D


title: San1_tile2_35_rep1

description:
Library name: San1_tile2_35_rep1
San1_tile2_35_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-H2


title: San1_tile2_30_rep2

description:
Library name: San1_tile2_30_rep2
San1_tile2_30_rep2


title: San1_tile3_35_rep1

description:
Library name: San1_tile3_35_rep1
San1_tile3_35_rep1


title: San1_tile2_30_rep3

description:
Library name: San1_tile2_30_rep3
San1_tile2_30_rep3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-G1


title: San1_tile2_30_rep1

description:
Library name: San1_tile2_30_rep1
San1_tile2_30_rep1


title: V309-CGND-HRA-03621-C

description: Library name: V309-CGND-HRA-03621-C


title: V308-CGND-HRA-03639-B

description: Library name: V308-CGND-HRA-03639-B


title: San1_tile2_no_sele_rep3

description:
Library name: San1_tile2_no_sele_rep3
San1_tile2_no_sele_rep3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-F2


title: San1_tile2_no_sele_rep2

description:
Library name: San1_tile2_no_sele_rep2
San1_tile2_no_sele_rep2


title: San1_tile2_no_sele_rep1

description:
Library name: San1_tile2_no_sele_rep1
San1_tile2_no_sele_rep1


title: V308-CGND-HRA-03639-A

description: Library name: V308-CGND-HRA-03639-A


title: San1_tile1_35_rep3

description:
Library name: San1_tile1_35_rep3
San1_tile1_35_rep3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-F14


title: V308-CGND-HRA-03638-D

description: Library name: V308-CGND-HRA-03638-D


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-F13


title: San1_tile1_35_rep2

description:
Library name: San1_tile1_35_rep2
San1_tile1_35_rep2


title: San1_tile1_35_rep1

description:
Library name: San1_tile1_35_rep1
San1_tile1_35_rep1


title: V309-CGND-HRA-03634-A

description: Library name: V309-CGND-HRA-03634-A


title: San1_tile2_35_rep2

description:
Library name: San1_tile2_35_rep2
San1_tile2_35_rep2


title: V308-CGND-HRA-03638-C

description: Library name: V308-CGND-HRA-03638-C


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-G13


title: San1_tile1_30_rep2

description:
Library name: San1_tile1_30_rep2
San1_tile1_30_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-F1


title: San1_tile1_30_rep1

description:
Library name: San1_tile1_30_rep1
San1_tile1_30_rep1


title: San1_tile1_no_sele_rep3

description:
Library name: San1_tile1_no_sele_rep3
San1_tile1_no_sele_rep3


title: V307-CGND-HRA-03639-B

description: Library name: V307-CGND-HRA-03639-B


title: San1_tile1_30_rep3

description:
Library name: San1_tile1_30_rep3
San1_tile1_30_rep3


title: V307-CGND-HRA-03639-A

description: Library name: V307-CGND-HRA-03639-A


title: San1_tile1_no_sele_rep2

description:
Library name: San1_tile1_no_sele_rep2
San1_tile1_no_sele_rep2


title: San1_tile1_no_sele_rep1

description:
Library name: San1_tile1_no_sele_rep1
San1_tile1_no_sele_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-E14


title: Ubr1_tile5_35_rep3

description:
Library name: Ubr1_tile5_35_rep3
Ubr1_tile5_35_rep3

value: Ubr1 KD strain


title: Ubr1_tile5_35_rep2

description:
Library name: Ubr1_tile5_35_rep2
Ubr1_tile5_35_rep2

value: Yeast cells


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-E13


title: V307-CGND-HRA-03638-C

description: Library name: V307-CGND-HRA-03638-C


title: V307-CGND-HRA-03638-D

description: Library name: V307-CGND-HRA-03638-D


title: Ubr1_tile5_35_rep1

description:
Library name: Ubr1_tile5_35_rep1
Ubr1_tile5_35_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-E1


title: Ubr1_tile5_30_rep3

description:
Library name: Ubr1_tile5_30_rep3
Ubr1_tile5_30_rep3


title: Ubr1_tile5_30_rep2

description:
Library name: Ubr1_tile5_30_rep2
Ubr1_tile5_30_rep2


title: Ubr1_tile5_30_rep1

description:
Library name: Ubr1_tile5_30_rep1
Ubr1_tile5_30_rep1


title: Ubr1_tile5_no_sele_rep3

description:
Library name: Ubr1_tile5_no_sele_rep3
Ubr1_tile5_no_sele_rep3


title: V306-CGND-HRA-03646-C

description: Library name: V306-CGND-HRA-03646-C

value: ALSci


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-D14


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-D2


title: Ubr1_tile5_no_sele_rep2

description:
Library name: Ubr1_tile5_no_sele_rep2
Ubr1_tile5_no_sele_rep2


title: V306-CGND-HRA-03646-D

description: Library name: V306-CGND-HRA-03646-D


title: V306-CGND-HRA-03645-B

description: Library name: V306-CGND-HRA-03645-B


title: Ubr1_tile5_no_sele_rep1

description:
Library name: Ubr1_tile5_no_sele_rep1
Ubr1_tile5_no_sele_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-E2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-D13


title: Ubr1_tile4_35_rep3

description:
Library name: Ubr1_tile4_35_rep3
Ubr1_tile4_35_rep3

value: 35 °C


title: Ubr1_tile4_35_rep2

description:
Library name: Ubr1_tile4_35_rep2
Ubr1_tile4_35_rep2


title: V306-CGND-HRA-03645-A

description: Library name: V306-CGND-HRA-03645-A

value: Male


title: Ubr1_tile4_35_rep1

description:
Library name: Ubr1_tile4_35_rep1
Ubr1_tile4_35_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-D1


title: Ubr1_tile4_30_rep3

description:
Library name: Ubr1_tile4_30_rep3
Ubr1_tile4_30_rep3


title: V305-CGND-HRA-03646-D

description: Library name: V305-CGND-HRA-03646-D


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-C2


title: Ubr1_tile4_30_rep2

description:
Library name: Ubr1_tile4_30_rep2
Ubr1_tile4_30_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-C14


title: Ubr1_tile4_no_sele_rep3

description:
Library name: Ubr1_tile4_no_sele_rep3
Ubr1_tile4_no_sele_rep3


title: Ubr1_tile4_30_rep1

description:
Library name: Ubr1_tile4_30_rep1
Ubr1_tile4_30_rep1


title: Ubr1_tile4_no_sele_rep2

description:
Library name: Ubr1_tile4_no_sele_rep2
Ubr1_tile4_no_sele_rep2


title: Ubr1_tile4_no_sele_rep1

description:
Library name: Ubr1_tile4_no_sele_rep1
Ubr1_tile4_no_sele_rep1


title: V305-CGND-HRA-03646-C

description: Library name: V305-CGND-HRA-03646-C


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-C13


title: V305-CGND-HRA-03645-A

description: Library name: V305-CGND-HRA-03645-A


title: V305-CGND-HRA-03645-B

description: Library name: V305-CGND-HRA-03645-B


title: Ubr1_tile3_35_rep2

description:
Library name: Ubr1_tile3_35_rep2
Ubr1_tile3_35_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-C1


title: Ubr1_tile3_35_rep3

description:
Library name: Ubr1_tile3_35_rep3
Ubr1_tile3_35_rep3


title: Ubr1_tile3_35_rep1

description:
Library name: Ubr1_tile3_35_rep1
Ubr1_tile3_35_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-B2


title: V304-CGND-HRA-03648-D

description: Library name: V304-CGND-HRA-03648-D


title: Ubr1_tile3_30_rep3

description:
Library name: Ubr1_tile3_30_rep3
Ubr1_tile3_30_rep3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-B14


title: Ubr1_tile3_30_rep1

description:
Library name: Ubr1_tile3_30_rep1
Ubr1_tile3_30_rep1


title: V304-CGND-HRA-03648-C

description: Library name: V304-CGND-HRA-03648-C


title: Ubr1_tile3_no_sele_rep3

description:
Library name: Ubr1_tile3_no_sele_rep3
Ubr1_tile3_no_sele_rep3


title: Ubr1_tile3_30_rep2

description:
Library name: Ubr1_tile3_30_rep2
Ubr1_tile3_30_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-B13


title: V304-CGND-HRA-03647-B

description: Library name: V304-CGND-HRA-03647-B


title: Ubr1_tile3_no_sele_rep2

description:
Library name: Ubr1_tile3_no_sele_rep2
Ubr1_tile3_no_sele_rep2


title: V304-CGND-HRA-03647-A

description: Library name: V304-CGND-HRA-03647-A


title: Ubr1_tile2_35_rep3

description:
Library name: Ubr1_tile2_35_rep3
Ubr1_tile2_35_rep3


title: Ubr1_tile2_35_rep2

description:
Library name: Ubr1_tile2_35_rep2
Ubr1_tile2_35_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-B1


title: V303-CGND-HRA-03648-D

description: Library name: V303-CGND-HRA-03648-D


title: Ubr1_tile3_no_sele_rep1

description:
Library name: Ubr1_tile3_no_sele_rep1
Ubr1_tile3_no_sele_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-A2


title: V303-CGND-HRA-03648-C

description: Library name: V303-CGND-HRA-03648-C


title: Ubr1_tile2_30_rep3

description:
Library name: Ubr1_tile2_30_rep3
Ubr1_tile2_30_rep3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-A13


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-A14


title: V303-CGND-HRA-03647-B

description: Library name: V303-CGND-HRA-03647-B


title: Ubr1_tile2_35_rep1

description:
Library name: Ubr1_tile2_35_rep1
Ubr1_tile2_35_rep1


title: Ubr1_tile2_30_rep2

description:
Library name: Ubr1_tile2_30_rep2
Ubr1_tile2_30_rep2


title: Ubr1_tile2_30_rep1

description:
Library name: Ubr1_tile2_30_rep1
Ubr1_tile2_30_rep1


title: V303-CGND-HRA-03647-A

description: Library name: V303-CGND-HRA-03647-A


title: Ubr1_tile2_no_sele_rep2

description:
Library name: Ubr1_tile2_no_sele_rep2
Ubr1_tile2_no_sele_rep2


title: V302-CGND-HRA-03659-B

description: Library name: V302-CGND-HRA-03659-B

value: Control


title: Ubr1_tile1_35_rep3

description:
Library name: Ubr1_tile1_35_rep3
Ubr1_tile1_35_rep3


title: Ubr1_tile1_35_rep2

description:
Library name: Ubr1_tile1_35_rep2
Ubr1_tile1_35_rep2


title: V302-CGND-HRA-03659-A

description: Library name: V302-CGND-HRA-03659-A


title: Ubr1_tile1_30_rep3

description:
Library name: Ubr1_tile1_30_rep3
Ubr1_tile1_30_rep3


title: Ubr1_tile1_35_rep1

description:
Library name: Ubr1_tile1_35_rep1
Ubr1_tile1_35_rep1


title: Ubr1_tile1_30_rep2

description:
Library name: Ubr1_tile1_30_rep2
Ubr1_tile1_30_rep2


title: V302-CGND-HRA-03649-D

description: Library name: V302-CGND-HRA-03649-D


title: Ubr1_tile1_30_rep1

description:
Library name: Ubr1_tile1_30_rep1
Ubr1_tile1_30_rep1


title: Ubr1_tile1_no_sele_rep3

description:
Library name: Ubr1_tile1_no_sele_rep3
Ubr1_tile1_no_sele_rep3


title: Ubr1_tile1_no_sele_rep2

description:
Library name: Ubr1_tile1_no_sele_rep2
Ubr1_tile1_no_sele_rep2


title: V302-CGND-HRA-03649-C

description: Library name: V302-CGND-HRA-03649-C


title: WT_tile5_35_rep3

description:
Library name: WT_tile5_35_rep3
WT_tile5_35_rep3

value: WT strain


title: WT_tile5_35_rep2

description:
Library name: WT_tile5_35_rep2
WT_tile5_35_rep2


title: Ubr1_tile2_no_sele_rep3

description:
Library name: Ubr1_tile2_no_sele_rep3
Ubr1_tile2_no_sele_rep3


title: WT_tile5_35_rep1

description:
Library name: WT_tile5_35_rep1
WT_tile5_35_rep1


title: V301-CGND-HRA-03649-C

description: Library name: V301-CGND-HRA-03649-C


title: V301-CGND-HRA-03659-A

description: Library name: V301-CGND-HRA-03659-A


title: WT_tile5_30_rep3

description:
Library name: WT_tile5_30_rep3
WT_tile5_30_rep3


title: Ubr1_tile2_no_sele_rep1

description:
Library name: Ubr1_tile2_no_sele_rep1
Ubr1_tile2_no_sele_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-1-P17-A1


title: V300-CGND-HRA-03663-B

description: Library name: V300-CGND-HRA-03663-B


title: WT_tile5_30_rep1

description:
Library name: WT_tile5_30_rep1
WT_tile5_30_rep1


title: donor procurement biopsy [D202_P]

type: RNA

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Prime View Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000 7G.

data_processing: The data were analyzed using the “limma”package and R studio version 4.2.2.

label: biotin

source_name: kidney biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA

extract_protocol: Trizol-chloroform extraction of total RNA was performed according to the manufacturer's instructions.

tag: patient id

value: right kidney

tag: donor age

tag: donor category

value: DBD - SCD

tag: donor bmi

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci

tag: donor biopsy ah


title: WT_tile5_no_sele_rep3

description:
Library name: WT_tile5_no_sele_rep3
WT_tile5_no_sele_rep3


title: donor procurement biopsy [D202_L]

value: left kidney


title: donor procurement biopsy [D200_P]

value: DBD - ECD


title: WT_tile5_no_sele_rep2

description:
Library name: WT_tile5_no_sele_rep2
WT_tile5_no_sele_rep2


title: V300-CGND-HRA-03663-A

description: Library name: V300-CGND-HRA-03663-A

tag: sample id

tag: donor id

tag: Sex

tag: age

tag: pmi

tag: phenotype


title: Ubr1_tile1_no_sele_rep1

description:
Library name: Ubr1_tile1_no_sele_rep1
Ubr1_tile1_no_sele_rep1

tag: cell line

tag: cell type


title: donor procurement biopsy [D205_p]

tag: patient id

tag: tissue


title: donor procurement biopsy [D199_L]

tag: donor age

tag: donor category


title: WT_tile5_no_sele_rep1

description:
Library name: WT_tile5_no_sele_rep1
WT_tile5_no_sele_rep1

tag: treatment


title: donor procurement biopsy [D201_P]

tag: donor bmi

tag: donor hypertension

tag: donor biopsy cv


title: V301-CGND-HRA-03649-D

description: Library name: V301-CGND-HRA-03649-D

tag: disease duration


title: donor procurement biopsy [D203_L]

tag: donor biopsy ct

tag: donor biopsy ci

tag: donor biopsy ah


title: WT_tile4_35_rep3

description:
Library name: WT_tile4_35_rep3
WT_tile4_35_rep3


title: WT_tile4_35_rep2

description:
Library name: WT_tile4_35_rep2
WT_tile4_35_rep2


title: V300-CGND-HRA-03660-C

description: Library name: V300-CGND-HRA-03660-C

tag: sample id

tag: donor id

tag: Sex

tag: age


title: WT_tile4_35_rep1

description:
Library name: WT_tile4_35_rep1
WT_tile4_35_rep1

tag: cell line

tag: cell type


title: WT_tile4_30_rep2

description:
Library name: WT_tile4_30_rep2
WT_tile4_30_rep2

value: 30 °C


title: V300-CGND-HRA-03660-D

description: Library name: V300-CGND-HRA-03660-D

tag: tissue

tag: pmi

tag: phenotype


title: WT_tile4_30_rep1

description:
Library name: WT_tile4_30_rep1
WT_tile4_30_rep1

tag: treatment


title: WT_tile4_no_sele_rep3

description:
Library name: WT_tile4_no_sele_rep3
WT_tile4_no_sele_rep3

value: control


title: WT_tile5_30_rep2

description:
Library name: WT_tile5_30_rep2
WT_tile5_30_rep2


title: V299-CGND-HRA-03663-A

description: Library name: V299-CGND-HRA-03663-A

value: Female


title: WT_tile4_30_rep3

description:
Library name: WT_tile4_30_rep3
WT_tile4_30_rep3


title: donor procurement biopsy [D194_P]

tag: patient id

tag: donor age

tag: donor category

tag: donor bmi


title: donor procurement biopsy [D194_L]

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ct


title: WT_tile4_no_sele_rep2

description:
Library name: WT_tile4_no_sele_rep2
WT_tile4_no_sele_rep2


title: donor procurement biopsy [D193_P]

tag: donor biopsy ci

tag: donor biopsy ah


title: donor procurement biopsy [D200_L]


title: WT_tile4_no_sele_rep1

description:
Library name: WT_tile4_no_sele_rep1
WT_tile4_no_sele_rep1


title: WT_tile3_35_rep3

description:
Library name: WT_tile3_35_rep3
WT_tile3_35_rep3


title: donor procurement biopsy [D193_L]


title: V299-CGND-HRA-03660-C

description: Library name: V299-CGND-HRA-03660-C

tag: sample id

tag: donor id

tag: Sex


title: V299-CGND-HRA-03663-B

description: Library name: V299-CGND-HRA-03663-B

tag: age


title: V299-CGND-HRA-03660-D

description: Library name: V299-CGND-HRA-03660-D

tag: tissue


title: WT_tile3_35_rep2

description:
Library name: WT_tile3_35_rep2
WT_tile3_35_rep2

tag: cell line

tag: cell type


title: WT_tile3_35_rep1

description:
Library name: WT_tile3_35_rep1
WT_tile3_35_rep1

tag: treatment


title: WT_tile3_30_rep3

description:
Library name: WT_tile3_30_rep3
WT_tile3_30_rep3


title: V234-CGND-HRC-00021-D

description: Library name: V234-CGND-HRC-00021-D

tag: pmi

tag: phenotype


title: WT_tile3_30_rep2

description:
Library name: WT_tile3_30_rep2
WT_tile3_30_rep2


title: WT_tile3_30_rep1

description:
Library name: WT_tile3_30_rep1
WT_tile3_30_rep1


title: WT_tile3_no_sele_rep3

description:
Library name: WT_tile3_no_sele_rep3
WT_tile3_no_sele_rep3


title: donor procurement biopsy [D192_L]

tag: patient id

tag: donor age

tag: donor category


title: donor procurement biopsy [D192_P]

tag: donor bmi

tag: donor hypertension

tag: donor biopsy cv


title: WT_tile2_35_rep3

description:
Library name: WT_tile2_35_rep3
WT_tile2_35_rep3


title: V234-CGND-HRC-00021-C

description: Library name: V234-CGND-HRC-00021-C


title: WT_tile3_no_sele_rep1

description:
Library name: WT_tile3_no_sele_rep1
WT_tile3_no_sele_rep1


title: V234-CGND-HRC-00021-B

description: Library name: V234-CGND-HRC-00021-B


title: WT_tile3_no_sele_rep2

description:
Library name: WT_tile3_no_sele_rep2
WT_tile3_no_sele_rep2


title: V234-CGND-HRC-00021-A

description: Library name: V234-CGND-HRC-00021-A


title: donor procurement biopsy [D191_L]

tag: donor biopsy ct

tag: donor biopsy ci

tag: donor biopsy ah


title: WT_tile2_35_rep2

description:
Library name: WT_tile2_35_rep2
WT_tile2_35_rep2


title: WT_tile2_35_rep1

description:
Library name: WT_tile2_35_rep1
WT_tile2_35_rep1


title: V224-CGND-HRC-00018-C

description: Library name: V224-CGND-HRC-00018-C

tag: sample id

tag: donor id

tag: Sex

tag: disease duration


title: V224-CGND-HRC-00018-D

description: Library name: V224-CGND-HRC-00018-D

tag: tissue

tag: age


title: V223-CGND-HRC-00018-D

description: Library name: V223-CGND-HRC-00018-D

tag: pmi


title: WT_tile2_30_rep2

description:
Library name: WT_tile2_30_rep2
WT_tile2_30_rep2

tag: cell line

tag: cell type

tag: treatment


title: WT_tile2_30_rep1

description:
Library name: WT_tile2_30_rep1
WT_tile2_30_rep1


title: donor procurement biopsy [D189_P]

tag: patient id

tag: donor age

tag: donor category


title: donor procurement biopsy [D190_P]

tag: donor bmi

tag: donor hypertension


title: donor procurement biopsy [D189_L]

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: WT_tile2_no_sele_rep2

description:
Library name: WT_tile2_no_sele_rep2
WT_tile2_no_sele_rep2


title: donor procurement biopsy [D191_P]

tag: donor biopsy ah


title: V223-CGND-HRC-00018-C

description: Library name: V223-CGND-HRC-00018-C

tag: sample id

tag: donor id

tag: Sex

tag: phenotype


title: WT_tile2_no_sele_rep3

description:
Library name: WT_tile2_no_sele_rep3
WT_tile2_no_sele_rep3


title: WT_tile1_35_rep3

description:
Library name: WT_tile1_35_rep3
WT_tile1_35_rep3


title: donor procurement biopsy [D187_L]

tag: tissue


title: donor procurement biopsy [D186_P]


title: WT_tile1_35_rep2

description:
Library name: WT_tile1_35_rep2
WT_tile1_35_rep2

tag: cell line


title: WT_tile1_30_rep3

description:
Library name: WT_tile1_30_rep3
WT_tile1_30_rep3

tag: cell type


title: WT_tile2_30_rep3

description:
Library name: WT_tile2_30_rep3
WT_tile2_30_rep3

tag: treatment


title: V222-CGND-HRC-00016-C

description: Library name: V222-CGND-HRC-00016-C

tag: age

tag: pmi


title: donor procurement biopsy [D186_L]

tag: patient id

tag: donor age

tag: donor category


title: WT_tile1_30_rep1

description:
Library name: WT_tile1_30_rep1
WT_tile1_30_rep1


title: V222-CGND-HRC-00015-B

description: Library name: V222-CGND-HRC-00015-B


title: WT_tile1_no_sele_rep2

description:
Library name: WT_tile1_no_sele_rep2
WT_tile1_no_sele_rep2


title: WT_tile1_no_sele_rep1

description:
Library name: WT_tile1_no_sele_rep1
WT_tile1_no_sele_rep1


title: WT_tile2_no_sele_rep1

description:
Library name: WT_tile2_no_sele_rep1
WT_tile2_no_sele_rep1


title: V222-CGND-HRC-00016-D

description: Library name: V222-CGND-HRC-00016-D


title: Ram ID 871868, tail mid, rep.2

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

description:
Library name: ram_13_tail_middle_2
Improved Jezersko Solčava sheep breed

data_processing:
Quality of the sequencing data was checked using FastQC (version 0.11.9)
RNA-seq reads were mapped against the sheep genome (ARS-UI_Ramb_v3.0, NCBI RefSeq assembly GCF_016772045.2) and rRNA sequences using ContextMap 2 (version 2.7.9)
The number of read counts per gene and exon was determined from the mapped RNA-seq reads in a strand-specific manner using featureCounts  and gene annotations from NCBI RefSeq (GCF_016772045.2-RS_2023_10)
Assembly: ARS-UI_Ramb_v3.0, NCBI RefSeq assembly GCF_016772045.2
Supplementary files format and content: tab separated file, gene read counts for RefSeq GCF_016772045.2-RS_2023_10

organism: Ovis aries

source_name: Skin

extract_protocol:
The skin tissue was homogenized in TRIzol™ using Precellys® beads.  Total RNA was extracted with the PureLink™ RNA Mini Kit, including optional DNase treatment. RNA quality and concentration were assessed using LabChip® GXII system, with an average RQS of 7.1 ± 0.9.
The isolated total RNA was further purified with Ampure XP beads (Beckman Coulter, Brea, USA) and quality controlled on a Bioanalyzer (Agilent, Santa Clara, USA) RNA nano chip. 100 ng of the purified total RNA was converted into RNA-seq libraries using the CorALL kit (Lexogen, Vienna, Austria) according to the manufacturer's instructions.

value: Skin

tag: genotype

value: HOXB13 D/D


title: WT_tile1_35_rep1

description:
Library name: WT_tile1_35_rep1
WT_tile1_35_rep1


title: V221-CGND-HRC-00016-D

description: Library name: V221-CGND-HRC-00016-D


title: V222-CGND-HRC-00015-A

description: Library name: V222-CGND-HRC-00015-A


title: donor procurement biopsy [D185_P]

tag: donor bmi

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ct


title: V221-CGND-HRC-00016-C

description: Library name: V221-CGND-HRC-00016-C

tag: sample id

tag: donor id


title: WT_tile1_30_rep2

description:
Library name: WT_tile1_30_rep2
WT_tile1_30_rep2


title: Ram ID 871868, tail mid, rep.1

description:
Library name: ram_13_tail_middle_1
Improved Jezersko Solčava sheep breed


title: donor procurement biopsy [D184_P]

value: DBD -ECD


title: Ram ID 871868, tail tip, rep. 1

description:
Library name: ram_13_tail_end_1
Improved Jezersko Solčava sheep breed


title: Ram ID 871868, tail base, rep. 2

description:
Library name: ram_13_tail_base_2
Improved Jezersko Solčava sheep breed


title: Ram ID 871868, tail base, rep. 1

description:
Library name: ram_13_tail_base_1
Improved Jezersko Solčava sheep breed


title: WT_tile1_no_sele_rep3

description:
Library name: WT_tile1_no_sele_rep3
WT_tile1_no_sele_rep3


title: donor procurement biopsy [D183_P]

tag: donor biopsy ci

tag: donor biopsy ah


title: Ram ID 871869, tail mid, rep.1

description:
Library name: ram_12_tail_middle_1
Improved Jezersko Solčava sheep breed

tag: tissue


title: donor procurement biopsy [D185_L]


title: V221-CGND-HRC-00015-B

description: Library name: V221-CGND-HRC-00015-B

tag: Sex

tag: phenotype


title: V221-CGND-HRC-00015-A

description: Library name: V221-CGND-HRC-00015-A

tag: age


title: donor procurement biopsy [D183_L]


title: Ram ID 871869, tail tip, rep. 2

description:
Library name: ram_12_tail_end_2
Improved Jezersko Solčava sheep breed


title: Ram ID 871869, tail base, rep. 2

description:
Library name: ram_12_tail_base_2
Improved Jezersko Solčava sheep breed


title: Ram ID 871869, tail tip, rep. 1

description:
Library name: ram_12_tail_end_1
Improved Jezersko Solčava sheep breed


title: Ram ID 871869, tail base, rep. 1

description:
Library name: ram_12_tail_base_1
Improved Jezersko Solčava sheep breed


title: V220-CGND-HRC-00016-C

description: Library name: V220-CGND-HRC-00016-C

tag: pmi


title: donor procurement biopsy [D181_P]

tag: patient id


title: Ram ID 871787, tail tip, rep. 2

description:
Library name: ram_11_tail_end_2
Improved Jezersko Solčava sheep breed


title: V220-CGND-HRC-00016-D

description: Library name: V220-CGND-HRC-00016-D


title: donor procurement biopsy [D180_L]

tag: donor age


title: V220-CGND-HRC-00015-A

description: Library name: V220-CGND-HRC-00015-A


title: donor procurement biopsy [D181_L]

tag: donor category


title: donor procurement biopsy [D180_P]


title: Ram ID 871787, tail mid, rep.2

description:
Library name: ram_11_tail_middle_2
Improved Jezersko Solčava sheep breed

tag: genotype


title: Ram ID 871787, tail base, rep. 2

description:
Library name: ram_11_tail_base_2
Improved Jezersko Solčava sheep breed


title: Ram ID 871868, tail tip, rep. 2

description:
Library name: ram_13_tail_end_2
Improved Jezersko Solčava sheep breed


title: Ram ID 871772, tail mid, rep.2

description:
Library name: ram_10_tail_middle_2
Improved Jezersko Solčava sheep breed

value: HOXB13 A/A


title: Ram ID 871772, tail mid, rep.1

description:
Library name: ram_10_tail_middle_1
Improved Jezersko Solčava sheep breed


title: Ram ID 871787, tail base, rep. 1

description:
Library name: ram_11_tail_base_1
Improved Jezersko Solčava sheep breed


title: donor procurement biopsy [D178_P]

tag: donor bmi


title: donor procurement biopsy [D179_P]

tag: donor hypertension


title: V199-CGND-HRA-02759-B

description: Library name: V199-CGND-HRA-02759-B

tag: disease duration

value: ALS


title: Ram ID 871772, tail tip, rep. 2

description:
Library name: ram_10_tail_end_2
Improved Jezersko Solčava sheep breed


title: Ram ID 871787, tail mid, rep.1

description:
Library name: ram_11_tail_middle_1
Improved Jezersko Solčava sheep breed


title: V199-CGND-HRA-02744-D

description: Library name: V199-CGND-HRA-02744-D

value: ALSci


title: Ram ID 871772, tail tip, rep. 1

description:
Library name: ram_10_tail_end_1
Improved Jezersko Solčava sheep breed


title: V220-CGND-HRC-00015-B

description: Library name: V220-CGND-HRC-00015-B


title: Ram ID 871772, tail base, rep. 2

description:
Library name: ram_10_tail_base_2
Improved Jezersko Solčava sheep breed


title: Ram ID 871772, tail base, rep. 1

description:
Library name: ram_10_tail_base_1
Improved Jezersko Solčava sheep breed


title: V199-CGND-HRA-02759-A

description: Library name: V199-CGND-HRA-02759-A


title: V199-CGND-HRA-02744-C

description: Library name: V199-CGND-HRA-02744-C


title: donor procurement biopsy [D179_L]

tag: donor biopsy cv

tag: donor biopsy ct


title: donor procurement biopsy [D176_P]


title: Ram ID 871784, tail mid, rep.1

description:
Library name: ram_9_tail_middle_1
Improved Jezersko Solčava sheep breed


title: Ram ID 871784, tail mid, rep.2

description:
Library name: ram_9_tail_middle_2
Improved Jezersko Solčava sheep breed


title: Ram ID 871787, tail tip, rep. 1

description:
Library name: ram_11_tail_end_1
Improved Jezersko Solčava sheep breed


title: V198-CGND-HRA-02977-B

description: Library name: V198-CGND-HRA-02977-B

tag: sample id

tag: donor id


title: Ram ID 871784, tail tip, rep. 2

description:
Library name: ram_9_tail_end_2
Improved Jezersko Solčava sheep breed


title: Ram ID 871784, tail tip, rep. 1

description:
Library name: ram_9_tail_end_1
Improved Jezersko Solčava sheep breed


title: V198-CGND-HRA-02977-A

description: Library name: V198-CGND-HRA-02977-A


title: donor procurement biopsy [D178_L]

tag: donor biopsy ci

tag: donor biopsy ah


title: Ram ID 871784, tail base, rep. 2

description:
Library name: ram_9_tail_base_2
Improved Jezersko Solčava sheep breed

tag: tissue


title: Ram ID 871784, tail base, rep. 1

description:
Library name: ram_9_tail_base_1
Improved Jezersko Solčava sheep breed


title: V198-CGND-HRA-02763-D

description: Library name: V198-CGND-HRA-02763-D

tag: Sex

tag: phenotype


title: Ram ID 871932, tail mid, rep.2

description:
Library name: ram_8_tail_middle_2
Improved Jezersko Solčava sheep breed


title: donor procurement biopsy [D175_P]


title: Ram ID 871932, tail mid, rep.1

description:
Library name: ram_8_tail_middle_1
Improved Jezersko Solčava sheep breed


title: V198-CGND-HRA-02763-C

description: Library name: V198-CGND-HRA-02763-C

tag: age

tag: pmi


title: donor procurement biopsy [D176_L]

tag: patient id

tag: donor age


title: Ram ID 871932, tail tip, rep. 1

description:
Library name: ram_8_tail_end_1
Improved Jezersko Solčava sheep breed

tag: genotype


title: Ram ID 871932, tail base, rep. 2

description:
Library name: ram_8_tail_base_2
Improved Jezersko Solčava sheep breed


title: V197-CGND-HRA-02991-D

description: Library name: V197-CGND-HRA-02991-D


title: V197-CGND-HRA-02991-C

description: Library name: V197-CGND-HRA-02991-C


title: donor procurement biopsy [D172_P]

tag: donor category

tag: donor bmi


title: Ram ID 871932, tail base, rep. 1

description:
Library name: ram_8_tail_base_1
Improved Jezersko Solčava sheep breed


title: donor procurement biopsy [D175_L]

tag: donor hypertension


title: donor procurement biopsy [D174_P]

tag: donor biopsy cv


title: V197-CGND-HRA-02978-B

description: Library name: V197-CGND-HRA-02978-B

tag: disease duration


title: Ram ID 835507, tail tip, rep. 2

description:
Library name: ram_7_tail_end_2
Improved Jezersko Solčava sheep breed


title: Ram ID 835507, tail mid, rep.1

description:
Library name: ram_7_tail_middle_1
Improved Jezersko Solčava sheep breed


title: Ram ID 835507, tail mid, rep.2

description:
Library name: ram_7_tail_middle_2
Improved Jezersko Solčava sheep breed


title: V197-CGND-HRA-02978-A

description: Library name: V197-CGND-HRA-02978-A

tag: sample id


title: Ram ID 835507, tail tip, rep. 1

description:
Library name: ram_7_tail_end_1
Improved Jezersko Solčava sheep breed


title: Ram ID 871932, tail tip, rep. 2

description:
Library name: ram_8_tail_end_2
Improved Jezersko Solčava sheep breed


title: Ram ID 835507, tail base, rep. 2

description:
Library name: ram_7_tail_base_2
Improved Jezersko Solčava sheep breed


title: Ram ID 835507, tail base, rep. 1

description:
Library name: ram_7_tail_base_1
Improved Jezersko Solčava sheep breed


title: donor procurement biopsy [D171_P]

tag: donor biopsy ct


title: V196-CGND-HRA-02979-D

description: Library name: V196-CGND-HRA-02979-D

tag: donor id


title: V196-CGND-HRA-02979-C

description: Library name: V196-CGND-HRA-02979-C


title: donor procurement biopsy [D172_L]

tag: donor biopsy ci

tag: donor biopsy ah


title: donor procurement biopsy [D171_L]

tag: tissue


title: V196-CGND-HRA-02979-B

description: Library name: V196-CGND-HRA-02979-B

tag: Sex

tag: phenotype


title: donor procurement biopsy [D170_P]


title: Patient ID 30012-Post

city: Madison

first: Douglas

last: McNeel

state: WI

address: 1111 highland ave, 7007

department: UW Carbone Cancer Center

institute: University of Wisconsin Madison

data_processing: Processed using nSolver software version 4.0.70

source_name: Metastatic Prostate Cancer Bone Biopsy

extract_protocol: Slides with tissue sections were processed according to the manufacturer’s protocol to be analyzed using nCounter technology. A pre-defined panel of 780 genes called “Tumor-signaling 360” (Cat# XT-CSO-H-TS360-12) from Nanostring was used for this analysis. The data generated were then normalized and presented as volcano plots using nSolver (Nanostring, version 4.0.70) software

tag: treatment arm

tag: biopsy time

value: Post

tag: clinical psa response

value: No

tag: irae status


title: Patient ID 30005-Post

description: nCounter® NanoString Tumor Signaling 360™ Panel

value: Yes


title: Patient ID 30008-Post


title: Patient ID 30002-Post


title: V195-CGND-HRA-02977-D

description: Library name: V195-CGND-HRA-02977-D

tag: age

tag: pmi


title: donor procurement biopsy [D173_L]

tag: patient id

tag: donor age

tag: donor category

tag: donor bmi

tag: donor hypertension


title: V195-CGND-HRA-02977-C

description: Library name: V195-CGND-HRA-02977-C

tag: sample id

tag: donor id

tag: disease duration


title: V194-CGND-HRA-02975-D

description: Library name: V194-CGND-HRA-02975-D

tag: tissue


title: Patient ID 20013-Post


title: donor procurement biopsy [D167_L]

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci

tag: donor biopsy ah


title: Patient ID 10004-Post

tag: treatment arm

tag: biopsy time

tag: clinical psa response


title: V194-CGND-HRA-02975-C

description: Library name: V194-CGND-HRA-02975-C

tag: Sex

tag: age

tag: pmi

tag: phenotype


title: V193-CGND-HRA-02975-D

description: Library name: V193-CGND-HRA-02975-D


title: Patient ID 20009-Post

tag: irae status


title: Patient ID 20011-Post


title: Patient ID 10003-Post


title: donor procurement biopsy [D170_L]

tag: patient id

tag: donor age

tag: donor category

tag: donor bmi

tag: donor hypertension


title: donor procurement biopsy [D177_P]

tag: tissue

tag: donor biopsy cv


title: donor procurement biopsy [D164_P]

tag: donor biopsy ct

tag: donor biopsy ci


title: Patient ID 10001-Post

tag: treatment arm


title: Patient ID 30008-Pre

tag: biopsy time

value: Pre


title: Patient ID 10011-Post

tag: clinical psa response


title: donor procurement biopsy [D164_L]

tag: donor biopsy ah


title: donor procurement biopsy [D165_L]


title: Patient ID 20008-Post


title: V192-CGND-HRA-03001-D

description: Library name: V192-CGND-HRA-03001-D

tag: sample id

tag: donor id

tag: Sex

value: Male

tag: age

value: Control


title: Patient ID 30002-Pre

tag: irae status


title: Patient ID 30005-Pre


title: V193-CGND-HRA-02975-C

description: Library name: V193-CGND-HRA-02975-C

tag: disease duration

tag: pmi

tag: phenotype


title: V192-CGND-HRA-03001-C

description: Library name: V192-CGND-HRA-03001-C


title: donor procurement biopsy [D167_P]

tag: patient id

value: right kidney

tag: donor age

tag: donor category

tag: donor bmi

tag: donor hypertension


title: Patient ID 20011-Pre

tag: treatment arm


title: donor procurement biopsy [D162_P]

tag: tissue

value: DBD - SCD

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: Patient ID 20013-Pre

tag: biopsy time

tag: clinical psa response


title: V192-CGND-HRA-02995-B

description: Library name: V192-CGND-HRA-02995-B

tag: sample id

tag: donor id

tag: Sex

tag: age


title: donor procurement biopsy [D162_L]

value: left kidney

tag: donor biopsy ah


title: Patient ID 20008-Pre

tag: irae status


title: Patient ID 30012-Pre


title: V192-CGND-HRA-02995-A

description: Library name: V192-CGND-HRA-02995-A

tag: pmi

tag: phenotype


title: Patient ID 10011-Pre


title: Patient ID 10004-Pre


title: PND 10 SAMPLE 3

city: Seattle

first: Edward

last: Kelly

state: Washington

address: 1959 NE Pacific St

institute: University of Washington

description: Library name: P10_3C

data_processing:
quality checked by FastQC
Assembly: mRatBN7.2
Supplementary files format and content: raw counts in excel sheet

source_name: testis

extract_protocol:
RNA was isolated using trizol after lysing in Qiagen RLT lysis buffer.
RNA-seq libraries were prepared as 250bp paire-end reads by Novogene.

value: testis

tag: genotype

value: WT


title: donor procurement biopsy [D163_L]

tag: patient id

tag: donor age

tag: donor category

tag: donor bmi

tag: donor hypertension


title: PND 10 SAMPLE 2

description: Library name: P10_2B

tag: tissue


title: Patient ID 10003-Pre

tag: treatment arm

tag: biopsy time


title: V191-CGND-HRA-03001-D

description: Library name: V191-CGND-HRA-03001-D

tag: sample id


title: V191-CGND-HRA-03001-C

description: Library name: V191-CGND-HRA-03001-C

tag: donor id


title: PND 5 SAMPLE 3

description: Library name: P5_3C


title: PND 10 SAMPLE 1

description: Library name: P10_1A


title: Patient ID 10001-Pre

tag: clinical psa response


title: donor procurement biopsy [D160_L]

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: donor procurement biopsy [D157_L]

value: DBD - ECD

tag: donor biopsy ah


title: Patient ID 20009-Pre

tag: irae status


title: PND 5 SAMPLE 1

description: Library name: P5_1A

tag: genotype


title: V191-CGND-HRA-02995-B

description: Library name: V191-CGND-HRA-02995-B

tag: Sex

tag: age

tag: pmi

tag: phenotype


title: V191-CGND-HRA-02995-A

description: Library name: V191-CGND-HRA-02995-A


title: donor procurement biopsy [D160_P]

tag: patient id

tag: donor age

tag: donor category

tag: donor bmi

tag: donor hypertension


title: CE-Rat34-E4-Female-DOXO

city: New Brunswick

first: Chadni

last: Patel

state: NJ

address: 195 Little Albany Street

institute: Rutgers Cancer Institute

description:
Library name: Sample 64
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv

data_processing:
The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality. The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes.
Assembly: Rnor6.0
Supplementary files format and content: Differential expression analysis table was generated as a csv file by DESeq2
Supplementary files format and content: Raw counts table as csv file for each sample in that comparison

source_name: brain cortex

extract_protocol:
Total RNA was extracted from frozen cell samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
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: tissue

value: brain cortex

tag: treatment

value: doxorubicin


title: donor procurement biopsy [D159_P]

tag: donor biopsy cv


title: CE-Rat31-E4-Female-DOXO

description:
Library name: Sample 62
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv


title: donor procurement biopsy [D155_P]

tag: donor biopsy ct


title: V190-CGND-HRA-02978-B

description: Library name: V190-CGND-HRA-02978-B

tag: sample id

tag: donor id

value: Female

tag: disease duration


title: donor procurement biopsy [D157_P]

tag: donor biopsy ci

tag: donor biopsy ah


title: CE-Rat24-E4-Female-PBS

description:
Library name: Sample 59
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv

tag: genotype

value: PBS


title: CE-Rat26-E4-Female-PBS

description:
Library name: Sample 60
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv


title: donor procurement biopsy [D155_L]


title: CE-Rat29-E4-Female-DOXO

description:
Library name: Sample 61
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv


title: V190-CGND-HRA-02978-A

description: Library name: V190-CGND-HRA-02978-A

tag: Sex

tag: age

tag: pmi

value: ALS


title: donor procurement biopsy [D154_L]

tag: patient id

tag: donor age


title: CE-Rat22-E4-Female-PBS

description:
Library name: Sample 58
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv


title: CE-Rat19-E4-Female-PBS

description:
Library name: Sample 57
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv


title: V189-CGND-HRA-02978-B

description: Library name: V189-CGND-HRA-02978-B

tag: phenotype


title: V188-CGND-HRA-02987-D

description: Library name: V188-CGND-HRA-02987-D


title: CE-Rat18-E4-Male-DOXO

description:
Library name: Sample 56
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv


title: PND 5 SAMPLE 2

description: Library name: P5_2B


title: CE-Rat13-E4-Male-DOXO

description:
Library name: Sample 55
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv


title: CE-Rat11-E4-Male-DOXO

description:
Library name: Sample 54
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv


title: CE-Rat32-E4-Female-DOXO

description:
Library name: Sample 63
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv


title: donor procurement biopsy [D151_L]

tag: donor category

tag: donor bmi

tag: donor hypertension


title: CE-Rat10-E4-Male-DOXO

description:
Library name: Sample 53
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv

tag: tissue

tag: treatment


title: donor procurement biopsy [D150_P]

tag: donor biopsy cv

tag: donor biopsy ct


title: donor procurement biopsy [D152_P]


title: V188-CGND-HRA-02987-C

description: Library name: V188-CGND-HRA-02987-C

tag: sample id

tag: donor id

tag: disease duration


title: V188-CGND-HRA-02985-B

description: Library name: V188-CGND-HRA-02985-B

value: ALSci


title: CE-Rat1-E4-Male-PBS

description:
Library name: Sample 49
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv

tag: genotype


title: CE-Rat4-E4-Male-PBS

description:
Library name: Sample 51
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv


title: CE-Rat72-E3-Female-DOXO

description:
Library name: Sample 48
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv


title: CE-Rat7-E4-Male-PBS

description:
Library name: Sample 52
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv


title: V187-CGND-HRA-02987-D

description: Library name: V187-CGND-HRA-02987-D

tag: Sex


title: CE-Rat66-E3-Female-DOXO

description:
Library name: Sample 46
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv


title: CE-Rat3-E4-Male-PBS

description:
Library name: Sample 50
CE-E4-PBS-vs-CE-E4-DOXO-Differential_expression_analysis_table.csv
CE-E4-PBS-vs-CE-E4-DOXO-raw_counts.csv


title: donor procurement biopsy [D150_L]

tag: donor biopsy ci

tag: donor biopsy ah


title: CE-Rat65-E3-Female-DOXO

description:
Library name: Sample 45
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv


title: donor procurement biopsy [D149_L]

tag: patient id


title: CE-Rat68-E3-Female-DOXO

description:
Library name: Sample 47
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv


title: V188-CGND-HRA-02985-A

description: Library name: V188-CGND-HRA-02985-A

tag: age

tag: pmi


title: V187-CGND-HRA-02987-C

description: Library name: V187-CGND-HRA-02987-C

tag: phenotype


title: CE-Rat61-E3-Female-PBS

description:
Library name: Sample 44
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv


title: donor procurement biopsy [D147_P]

tag: donor age

tag: donor category

tag: donor bmi


title: V187-CGND-HRA-02985-A

description: Library name: V187-CGND-HRA-02985-A

tag: tissue


title: donor procurement biopsy [D149_P]

tag: donor hypertension

tag: donor biopsy cv


title: V187-CGND-HRA-02985-B

description: Library name: V187-CGND-HRA-02985-B

tag: sample id


title: CE-Rat52-E3-Male-DOXO

description:
Library name: Sample 40
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv

tag: treatment


title: CE-Rat59-E3-Female-PBS

description:
Library name: Sample 43
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv


title: V186-CGND-HRA-02991-B

description: Library name: V186-CGND-HRA-02991-B

tag: donor id

tag: disease duration


title: donor procurement biopsy [D147_L]

tag: donor biopsy ct


title: V186-CGND-HRA-02972-D

description: Library name: V186-CGND-HRA-02972-D

tag: Sex


title: CE-Rat56-E3-Female-PBS

description:
Library name: Sample 41
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv

tag: genotype


title: CE-Rat51-E3-Male-DOXO

description:
Library name: Sample 39
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv


title: CE-Rat45-E3-Male-PBS

description:
Library name: Sample 36
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv


title: CE-Rat47-E3-Male-DOXO

description:
Library name: Sample 37
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv


title: V186-CGND-HRA-02972-C

description: Library name: V186-CGND-HRA-02972-C


title: CE-Rat49-E3-Male-DOXO

description:
Library name: Sample 38
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv


title: V185-CGND-HRA-02972-D

description: Library name: V185-CGND-HRA-02972-D


title: CE-Rat41-E3-Male-PBS

description:
Library name: Sample 34
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv


title: CE-Rat58-E3-Female-PBS

description:
Library name: Sample 42
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv


title: CE-Rat37-E3-Male-PBS

description:
Library name: Sample 33
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv


title: CE-Rat43-E3-Male-PBS

description:
Library name: Sample 35
CE-E3-PBS-vs-CE-E3-DOXO-Differential_expression_analysis_table.csv
CE-E3-PBS-vs-CE-E3-DOXO-raw_counts.csv


title: donor procurement biopsy [D148_P]

tag: patient id

tag: donor biopsy ci

tag: donor biopsy ah


title: HPC-Rat32-E4-Female-DOXO

description:
Library name: Sample 31
HPC-E4-PBS-vs-HPC-E4-DOXO-Differential_expression_analysis_table.csv
HPC-E4-PBS-vs-HPC-E4-DOXO-raw_counts.csv

source_name: brain hippocampus

value: brain hippocampus


title: HPC-Rat34-E4-Female-DOXO

description:
Library name: Sample 32
HPC-E4-PBS-vs-HPC-E4-DOXO-Differential_expression_analysis_table.csv
HPC-E4-PBS-vs-HPC-E4-DOXO-raw_counts.csv


title: HPC-Rat31-E4-Female-DOXO

description:
Library name: Sample 30
HPC-E4-PBS-vs-HPC-E4-DOXO-Differential_expression_analysis_table.csv
HPC-E4-PBS-vs-HPC-E4-DOXO-raw_counts.csv


title: donor procurement biopsy [D146_P]


title: HPC-Rat29-E4-Female-DOXO

description:
Library name: Sample 29
HPC-E4-PBS-vs-HPC-E4-DOXO-Differential_expression_analysis_table.csv
HPC-E4-PBS-vs-HPC-E4-DOXO-raw_counts.csv


title: V183-CGND-HRA-02979-D

description: Library name: V183-CGND-HRA-02979-D

tag: age

tag: pmi

tag: phenotype


title: donor procurement biopsy [D146_L]

tag: donor age

tag: donor category

tag: donor bmi


title: donor procurement biopsy [D143_L]

tag: tissue

tag: donor hypertension

tag: donor biopsy cv


title: donor procurement biopsy [D144_P]


title: donor procurement biopsy [D143_P]


title: HPC-Rat26-E4-Female-PBS

description:
Library name: Sample 28
HPC-E4-PBS-vs-HPC-E4-DOXO-Differential_expression_analysis_table.csv
HPC-E4-PBS-vs-HPC-E4-DOXO-raw_counts.csv

tag: treatment


title: V183-CGND-HRA-02979-C

description: Library name: V183-CGND-HRA-02979-C

tag: sample id

tag: donor id

tag: disease duration


title: 786O+VHL_day3_rep1

city: Cambridge

first: Niek

last: Wit

state: Not US or Canada

address: Puddicombe Way

department: Department of Medicine

institute: University of Cambridge

description: 786O CRISPR screen

data_processing:
Vector sequence removed with cutadapt
sgRNA sequences were counted with HISAT2 and sort/uniq Unix commands
Assembly: Toronto KO library v3
Supplementary files format and content: Each line in the txt files has the count and name of an sgRNA

molecule: other

extract_protocol:
QIAGEN Puregene Cell kit
Two-step PCR method

tag: cell line

tag: genotype

value: VHL positive


title: HPC-Rat24-E4-Female-PBS

description:
Library name: Sample 27
HPC-E4-PBS-vs-HPC-E4-DOXO-Differential_expression_analysis_table.csv
HPC-E4-PBS-vs-HPC-E4-DOXO-raw_counts.csv


title: HPC-Rat22-E4-Female-PBS

description:
Library name: Sample 26
HPC-E4-PBS-vs-HPC-E4-DOXO-Differential_expression_analysis_table.csv
HPC-E4-PBS-vs-HPC-E4-DOXO-raw_counts.csv


title: V185-CGND-HRA-02972-C

description: Library name: V185-CGND-HRA-02972-C

tag: Sex