title: donor procurement biopsy [D142_P]

tag: patient id

tag: donor biopsy ct

tag: donor biopsy ci

tag: donor biopsy ah


title: V182-CGND-HRA-02969-D

status: Public on Dec 22 2025

type: SRA

city: New York

first: Christopher

last: Jackson

state: NY

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

country: USA

institute: New York Genome Center

description: Library name: V182-CGND-HRA-02969-D

library_source: transcriptomic

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

molecule: polyA RNA

organism: Homo sapiens

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: tissue

tag: sample id

tag: donor id

tag: Sex

value: Male

tag: age

tag: disease duration

tag: pmi

tag: phenotype

value: ALSci


title: 786O_day3_rep1

city: Cambridge

first: Niek

last: Wit

state: Not US or Canada

address: Puddicombe Way

department: Department of Medicine

country: United Kingdom

institute: University of Cambridge

description: 786O CRISPR screen

library_source: other

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 null


title: HPC-Rat19-E4-Female-PBS

city: New Brunswick

first: Chadni

last: Patel

state: NJ

address: 195 Little Albany Street

institute: Rutgers Cancer Institute

description:
Library name: Sample 25
HPC-E4-PBS-vs-HPC-E4-DOXO-Differential_expression_analysis_table.csv
HPC-E4-PBS-vs-HPC-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

molecule: total RNA

organism: Rattus norvegicus

source_name: brain hippocampus

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).

value: brain hippocampus

tag: treatment

value: PBS


title: 786O_day25_rep1

description: 786O CRISPR screen


title: 786O+VHL_day29_rep1

description: 786O CRISPR screen

value: VHL positive


title: V182-CGND-HRA-02955-A

description: Library name: V182-CGND-HRA-02955-A


title: donor procurement biopsy [D142_L]

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.

value: left kidney

tag: donor age

tag: donor category

value: DBD - SCD

tag: donor bmi

tag: donor hypertension

tag: donor biopsy cv


title: donor procurement biopsy [D141_P]

tag: patient id

value: right kidney

value: DBD - ECD

tag: donor biopsy ct

tag: donor biopsy ci

tag: donor biopsy ah


title: HPC-Rat18-E4-Male-DOXO

description:
Library name: Sample 24
HPC-E4-PBS-vs-HPC-E4-DOXO-Differential_expression_analysis_table.csv
HPC-E4-PBS-vs-HPC-E4-DOXO-raw_counts.csv

tag: tissue

value: doxorubicin


title: 786O+VHL_day19_rep1

description: 786O CRISPR screen


title: donor procurement biopsy [D140_P]


title: V175-CGND-HRA-02959-B

description: Library name: V175-CGND-HRA-02959-B

tag: sample id

tag: donor id

tag: Sex

tag: age


title: donor procurement biopsy [D141_L]


title: V175-CGND-HRA-02959-A

description: Library name: V175-CGND-HRA-02959-A

tag: disease duration

tag: pmi

tag: phenotype


title: 786O_day17_rep1

description: 786O CRISPR screen

tag: cell line

tag: genotype


title: HPC-Rat11-E4-Male-DOXO

description:
Library name: Sample 22
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: HPC-Rat13-E4-Male-DOXO

description:
Library name: Sample 23
HPC-E4-PBS-vs-HPC-E4-DOXO-Differential_expression_analysis_table.csv
HPC-E4-PBS-vs-HPC-E4-DOXO-raw_counts.csv


title: MZKO 3 10 dpf

first: M. Chiara

last: Manzini

address: 89 French Street, Child Health Institute of New Jersey

department: Neuroscience and Cell Biology

institute: Rutgers Robert Wood Johnson Me

description: Library name: Sample 21

data_processing:
Raw sequence reads were trimmed (10/150 bp) for adapter sequence bias and base calling quality with TrimGalore
Trimmed sequence reads were aligned to DanRer11 with HISAT2 and resulting BAM files were sorted and indexed with Samtools
Aligned sequence reads were counted with FeatureCounts
Raw counts were normalized using DESeq2
Assembly: DanRer11
Supplementary files format and content: .csv files include raw counts for each sample

organism: Danio rerio

source_name: Whole larvae

extract_protocol:
RNA was extracted from composite samples of 4-6 whole zebrafish using RNAzol reagent
Performed by NovoGene Corporation as follows: "Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification."

value: Whole larvae

value: 10 days-post fertilization

tag: strain

value: EK

tag: female parent_genotype

tag: batch


title: V182-CGND-HRA-02969-C

description: Library name: V182-CGND-HRA-02969-C


title: V175-CGND-HRA-02955-C

description: Library name: V175-CGND-HRA-02955-C


title: donor procurement biopsy [D138_L]

tag: patient id

tag: donor age

tag: donor category

tag: donor bmi

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ct


title: donor procurement biopsy [D137_P]

tag: tissue

tag: donor biopsy ci

tag: donor biopsy ah


title: V174-CGND-HRA-02969-B

description: Library name: V174-CGND-HRA-02969-B

tag: sample id

tag: donor id

tag: Sex

tag: age

tag: disease duration

tag: pmi

tag: phenotype


title: MZKO 2 10 dpf

description: Library name: Sample 20

tag: strain

tag: genotype

tag: female parent_genotype

tag: batch


title: HPC-Rat7-E4-Male-PBS

description:
Library name: Sample 20
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: V174-CGND-HRA-02964-C

description: Library name: V174-CGND-HRA-02964-C

value: Female


title: MZKO 1 10 dpf

description: Library name: Sample 19


title: MHet 3 10 dpf

description: Library name: Sample 18


title: HPC-Rat4-E4-Male-PBS

description:
Library name: Sample 19
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 [D140_L]

tag: patient id

tag: donor age

tag: donor category

tag: donor bmi

tag: donor hypertension

tag: donor biopsy cv


title: V174-CGND-HRA-02964-D

description: Library name: V174-CGND-HRA-02964-D

tag: tissue

tag: sample id

tag: donor id


title: MHet 2 10 dpf

description: Library name: Sample 17

tag: age


title: HPC-Rat3-E4-Male-PBS

description:
Library name: Sample 18
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 [D136_P]

tag: donor biopsy ct

tag: donor biopsy ci

tag: donor biopsy ah


title: HPC-Rat1-E4-Male-PBS

description:
Library name: Sample 17
HPC-E4-PBS-vs-HPC-E4-DOXO-Differential_expression_analysis_table.csv
HPC-E4-PBS-vs-HPC-E4-DOXO-raw_counts.csv

tag: genotype


title: V173-CGND-HRA-02955-B

description: Library name: V173-CGND-HRA-02955-B

tag: Sex

tag: disease duration

tag: pmi

tag: phenotype


title: V172-CGND-HRA-02955-B

description: Library name: V172-CGND-HRA-02955-B


title: HPC-Rat10-E4-Male-DOXO

description:
Library name: Sample 21
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: HPC-Rat72-E3-Female-DOXO

description:
Library name: Sample 16
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv


title: HPC-Rat68-E3-Female-DOXO

description:
Library name: Sample 15
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv


title: MZKO 3 5 dpf

description: Library name: Sample 15

value: 5 days post-fertilization

tag: strain

tag: female parent_genotype

tag: batch


title: V171-CGND-HRA-02988-C

description: Library name: V171-CGND-HRA-02988-C


title: donor procurement biopsy [D136_L]

tag: patient id

tag: donor age

tag: donor category

tag: donor bmi

tag: donor hypertension

tag: donor biopsy cv


title: MZKO 2 5 dpf

description: Library name: Sample 14

tag: tissue

tag: age


title: donor procurement biopsy [D135_L]

tag: donor biopsy ct

tag: donor biopsy ci

tag: donor biopsy ah


title: donor procurement biopsy [D137_L]


title: MHet 3 5 dpf

description: Library name: Sample 12

tag: genotype


title: V170-CGND-HRA-02988-D

description: Library name: V170-CGND-HRA-02988-D

tag: sample id

tag: donor id

tag: Sex

tag: disease duration

tag: pmi

tag: phenotype


title: donor procurement biopsy [D133_P]

tag: patient id

tag: donor age


title: donor procurement biopsy [D134_L]

tag: donor category

tag: donor bmi


title: MHet 1 10 dpf

description: Library name: Sample 16

tag: strain

tag: female parent_genotype

tag: batch


title: HPC-Rat61-E3-Female-PBS

description:
Library name: Sample 12
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv

tag: tissue

tag: treatment


title: HPC-Rat65-E3-Female-DOXO

description:
Library name: Sample 13
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv


title: V171-CGND-HRA-02959-B

description: Library name: V171-CGND-HRA-02959-B

tag: age


title: MHet 2 5 dpf

description: Library name: Sample 11

tag: genotype


title: HPC-Rat59-E3-Female-PBS

description:
Library name: Sample 11
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv


title: V170-CGND-HRA-02988-C

description: Library name: V170-CGND-HRA-02988-C

tag: sample id


title: donor procurement biopsy [D130_L]

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci

tag: donor biopsy ah


title: donor procurement biopsy [D131_P]

tag: patient id


title: V171-CGND-HRA-02988-D

description: Library name: V171-CGND-HRA-02988-D

tag: donor id

tag: Sex

tag: disease duration

tag: pmi

tag: phenotype


title: MHet 1 5 dpf

description: Library name: Sample 10

tag: strain

tag: female parent_genotype

tag: batch


title: HPC-Rat66-E3-Female-DOXO

description:
Library name: Sample 14
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv

tag: tissue

tag: treatment


title: V101-CGND-HRA-02999-B

description: Library name: V101-CGND-HRA-02999-B

tag: sample id

tag: age

value: Control


title: HPC-Rat58-E3-Female-PBS

description:
Library name: Sample 10
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv

tag: genotype


title: donor procurement biopsy [D131_L]

tag: donor age

tag: donor category

tag: donor bmi

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ct


title: ZKO 3 5 dpf

description: Library name: Sample 9


title: HPC-Rat56-E3-Female-PBS

description:
Library name: Sample 9
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv


title: MZKO 1 5 dpf

description: Library name: Sample 13


title: ZKO 2 5 dpf

description: Library name: Sample 8


title: V101-CGND-HRA-02999-A

description: Library name: V101-CGND-HRA-02999-A

tag: donor id

tag: Sex

value: Male


title: ZKO 1 5 dpf

description: Library name: Sample 7


title: donor procurement biopsy [D128_P]

tag: patient id

tag: donor biopsy ci

tag: donor biopsy ah


title: donor procurement biopsy [D129_L]


title: donor procurement biopsy [D132_P]


title: HPC-Rat52-E3-Male-DOXO

description:
Library name: Sample 8
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv


title: HPC-Rat51-E3-Male-DOXO

description:
Library name: Sample 7
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv


title: V170-CGND-HRA-02959-B

description: Library name: V170-CGND-HRA-02959-B

tag: disease duration

tag: pmi

tag: phenotype

value: ALSci


title: donor procurement biopsy [D129_P]

tag: tissue


title: Het 3 5 dpf

description: Library name: Sample 6

tag: age

tag: strain

tag: female parent_genotype

tag: batch


title: HPC-Rat49-E3-Male-DOXO

description:
Library name: Sample 6
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv

tag: genotype

tag: treatment


title: V100-CGND-HRA-02999-B

description: Library name: V100-CGND-HRA-02999-B

tag: sample id


title: donor procurement biopsy [D127_P]

tag: donor age

tag: donor category

tag: donor bmi

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ct


title: HPC-Rat47-E3-Male-DOXO

description:
Library name: Sample 5
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv


title: V099-CGND-HRA-02970-D

description: Library name: V099-CGND-HRA-02970-D

tag: donor id

tag: Sex

tag: disease duration

value: ALS


title: Het 2 5 dpf

description: Library name: Sample 5

tag: tissue


title: Het 1 5 dpf

description: Library name: Sample 4

tag: age


title: WT 3 5 dpf

description: Library name: Sample 3

tag: strain


title: donor procurement biopsy [D125_P]

tag: patient id

tag: donor biopsy ci

tag: donor biopsy ah


title: donor procurement biopsy [D125_L]


title: V099-CGND-HRA-02970-C

description: Library name: V099-CGND-HRA-02970-C

tag: pmi

tag: phenotype


title: donor procurement biopsy [D124_L]

tag: donor age


title: HPC-Rat43-E3-Male-PBS

description:
Library name: Sample 3
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv

value: brain hippocampus

tag: genotype

tag: treatment


title: donor procurement biopsy [D123_P]

tag: donor category

tag: donor bmi

tag: donor hypertension


title: V098-CGND-HRA-03002-B

description: Library name: V098-CGND-HRA-03002-B

tag: sample id

tag: donor id


title: WT 2 5 dpf

description: Library name: Sample 2

tag: female parent_genotype

tag: batch


title: HPC-Rat41-E3-Male-PBS

description:
Library name: Sample 2
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv

tag: tissue

value: PBS


title: donor procurement biopsy [D122_P]

tag: donor biopsy cv

tag: donor biopsy ct


title: WT 1 5 dpf

description: Library name: Sample 1

tag: age

tag: strain


title: HPC-Rat37-E3-Male-PBS

description:
Library name: Sample 1
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv


title: V098-CGND-HRA-03002-A

description: Library name: V098-CGND-HRA-03002-A

tag: Sex

tag: pmi


title: V099-CGND-HRA-03002-B

description: Library name: V099-CGND-HRA-03002-B

tag: phenotype


title: V098-CGND-HRA-02970-D

description: Library name: V098-CGND-HRA-02970-D

tag: disease duration


title: HPC-Rat45-E3-Male-PBS

description:
Library name: Sample 4
HPC-E3-PBS-vs-HPC-E3-DOXO-Differential_expression_analysis_table.csv
HPC-E3-PBS-vs-HPC-E3-DOXO-raw_counts.csv

tag: genotype

tag: treatment


title: V098-CGND-HRA-02970-C

description: Library name: V098-CGND-HRA-02970-C


title: V100-CGND-HRA-02999-A

description: Library name: V100-CGND-HRA-02999-A


title: OSTIR1-Auxin-rep2_LR

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: Sample31

data_processing:
Circular consensus sequences (CCS) from the Revio system were demultiplexed using lima with --hifi-preset SYMMETRIC option. Then Reverse transcription primer sequence flanking the mRNA sequences was removed using lima with --isoseq and --peek-guess to generate full-length reads. Concatemers and polyA tails were removed using isoseq3 refine with --require-polya to generate full-length non-concatemer reads. Full-length non-concatemer reads were merged using pbmerge, grouped into read cluster by hierarchical clustering using isoseq cluster2, aligned to genome using pbmm2 align, collapsed using isoseq3 collapse, and classified using SQANTI3. Short-read data were processed using kallisto bus. Short-read and long-read data were processed through standard MPAQT pipeline.
Assembly: hg38
Supplementary files format and content: isoformMetadata.csv is a dataframe containing the definition for each isoform in the transcriptome of this study, including the associated genes, associated transcripts, and SQANTI3 defined structural categories. MPAQT.(LR_)SR.tsv files for each sample contains the corrected TPMs of these isoforms in each sample.

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen, #74106) as per manufacturer’s instructions.
Long read RNA-seq libraries were prepared using NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification Module, Iso-Seq Express oligo kit, and SMRTbell® prep kit 3.0 per manufacturer’s instructions. Library quality was assessed on Agilent Femto Pulse before the libraries were loaded onto a Revio or Sequel II flow cell. Short read RNA-seq libaries were prepared using Takara Bio SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian kit (Cat.# 634485) per maufacturer's instructions. Library quality was assessed on Agilent DNA ScreenTape.

tag: cell line

value: Auxin 6hr


title: mouse_HSV1

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

country: China

institute: PICB

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking,RNA-seq data were mapped to the mouse genome (mm10) using Hisat2 using default parameters
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons using HTSeq
Genome_build: mm10 (mouse)
Supplementary_files_format_and_content: tab-delimited text files include gene ID and expression level in reads count for each sample

organism: Mus musculus

source_name: L929 cells

growth_protocol: Cells were were cultured in Dulbecco's modified Eagle's medium (DMEM) plus 10% fetal bovine serum (FBS) (Gibco), supplemented with 1% penicillin-streptomycin (Invitrogen).These cells were maintained in a humidified 5% CO2 incubator at 37˚C

extract_protocol:
Total RNA were extracted with Trizol reagent (Invitrogen).
A cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq4000 by a 2X150 bp run.

treatment_protocol: Transfection experiments were conducted in mouse L929 cells. Total RNA was prepared 6 hours after transfection. The RNA with polyA tails were isolated, ligated to the adapters, amplified, and sequenced following the standard RNAseq preparation protocol (Illumina, USA) with no modifications. The transfection experiments were conducted in duplicates.

value: mouse fibroblast cell line L929

value: HSV transfection


title: mouse_HSV2


title: mouse_G3-YSD2

value: G3-YSD transfection


title: mouse_G3-YSD1


title: V092-CGND-HRA-02992-C

description: Library name: V092-CGND-HRA-02992-C


title: donor procurement biopsy [D122_L]

tag: patient id

value: left kidney

tag: donor age

tag: donor category

value: DBD - ECD

tag: donor bmi

tag: donor hypertension

tag: donor biopsy ci

tag: donor biopsy ah


title: OSTIR1-Auxin-rep1_LR

description: Library name: Sample30


title: OSTIR1-DMSO-rep3_LR

description: Library name: Sample29

value: DMSO 6hr


title: donor procurement biopsy [D123_L]

tag: tissue

tag: donor biopsy cv

tag: donor biopsy ct


title: donor procurement biopsy [D119_P]

value: right kidney

value: DBD - SCD


title: V091-CGND-HRA-02992-D

description: Library name: V091-CGND-HRA-02992-D

tag: sample id

tag: donor id

tag: Sex

tag: age


title: OSTIR1-DMSO-rep2_LR

description: Library name: Sample28

tag: genotype


title: OSTIR1-Auxin-rep3_LR

description: Library name: Sample32

tag: treatment


title: mouse_cGAMP2

tag: cell line

value: cGAMP stimulation


title: V091-CGND-HRA-02992-C

description: Library name: V091-CGND-HRA-02992-C

tag: disease duration

tag: pmi

tag: phenotype


title: donor procurement biopsy [D118_L]

tag: patient id

tag: donor age

tag: donor category

tag: donor bmi


title: mouse_cGAMP1


title: OSTIR1-DMSO-rep1_LR

description: Library name: Sample27


title: V089-CGND-HRA-02764-D

description: Library name: V089-CGND-HRA-02764-D

tag: tissue

value: Female


title: mouse_hpRNA2

source_name: mouse fibroblast cell line

value: expressed RNA after hpRNA transfection


title: donor procurement biopsy [D118_P]

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ci

tag: donor biopsy ah


title: NELFC-AID-Auxin-ELOA-KO_rep2_LR

description:
Library name: Sample26
isoformMetadata.csv

value: sgELOA


title: donor procurement biopsy [D121_P]

tag: donor biopsy ct


title: NELFC-AID-Auxin-ELOA-KO_rep1_LR

description:
Library name: Sample25
isoformMetadata.csv


title: donor procurement biopsy [D117_L]


title: V092-CGND-HRA-02992-D

description: Library name: V092-CGND-HRA-02992-D

tag: sample id

tag: donor id

tag: Sex

value: Male

tag: age

value: ALSci


title: donor procurement biopsy [D116_P]


title: mouse_hpRNA1

tag: cell line

tag: treatment


title: V088-CGND-HRA-02763-D

description: Library name: V088-CGND-HRA-02763-D

tag: disease duration

tag: pmi

tag: phenotype

value: ALS


title: V088-CGND-HRA-02763-C

description: Library name: V088-CGND-HRA-02763-C


title: NELFC-AID-DMSO-ELOA-KO_rep2_LR

description:
Library name: Sample24
isoformMetadata.csv

tag: genotype


title: V088-CGND-HRA-02757-A

description: Library name: V088-CGND-HRA-02757-A


title: mouse_HT-DNA2

value: expressed RNA after HT-DNA transfection


title: mouse_HT-DNA1


title: NELFC-AID-DMSO-ELOA-KO_rep1_LR

description:
Library name: Sample23
isoformMetadata.csv


title: donor procurement biopsy [D115_P]

tag: patient id

tag: donor age

tag: donor category

tag: donor bmi


title: mouse_mock2

value: expressed RNA without treatment


title: NELFC-AID-Auxin_rep2_LR

description:
Library name: Sample22
isoformMetadata.csv

value: sgControl

value: Auxin 6hr


title: V087-CGND-HRA-02766-D

description: Library name: V087-CGND-HRA-02766-D

tag: tissue

value: Control


title: mouse_mock1


title: donor procurement biopsy [D115_L]

value: left kidney

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ci

tag: donor biopsy ah


title: V087-CGND-HRA-02766-C

description: Library name: V087-CGND-HRA-02766-C

tag: sample id

tag: donor id

tag: Sex


title: NELFC-AID-DMSO_rep2_LR

description:
Library name: Sample20
isoformMetadata.csv

tag: cell line

tag: treatment


title: V087-CGND-HRA-02762-B

description: Library name: V087-CGND-HRA-02762-B

tag: age

tag: disease duration

tag: pmi


title: donor procurement biopsy [D114_P]

tag: patient id

value: DBD - ECD

tag: donor biopsy ct


title: V087-CGND-HRA-02762-A

description: Library name: V087-CGND-HRA-02762-A

tag: phenotype


title: NELFC-AID-DMSO_rep1_LR

description:
Library name: Sample19
isoformMetadata.csv

tag: genotype

value: DMSO 6hr


title: donor procurement biopsy [D114_L]

tag: tissue

tag: donor age

tag: donor category

tag: donor bmi


title: donor procurement biopsy [D112_L]

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ci

tag: donor biopsy ah


title: V086-CGND-HRA-02765-D

description: Library name: V086-CGND-HRA-02765-D

tag: sample id

tag: donor id

tag: Sex


title: donor procurement biopsy [D113_L]


title: donor procurement biopsy [D116_L]


title: SPT6-AID-Auxin-rep3_LR

description:
Library name: Sample18
isoformMetadata.csv

tag: cell line

tag: treatment


title: donor procurement biopsy [D111_P]

tag: patient id

value: right kidney


title: V086-CGND-HRA-02765-C

description: Library name: V086-CGND-HRA-02765-C

tag: age

tag: pmi


title: Pig brain cervical spinal cord, Animal ID 15-5, male, UBE3A mat. deletion

city: College Station

first: Sarah

last: Christian

state: TX

address: 4467 TAMU

institute: Texas A&M University

description: Library name: CSC15-5

data_processing:
Qiagen IPA RNA-seq Analysis Portal was used for Sus scrofa 11.1 reference alignment and differential expression analysis with default parameters
Assembly: Ensembl Sus scrofa 11.1
Supplementary files format and content: Excel files that provide RPKM, TPM, and CPM for each sample.
Supplementary files format and content: A single Excel file that compares gene differential expression between wildtype (WT) and UBE3A maternal deletion (AS)

organism: Sus scrofa

source_name: Cervical Spinal Cord

extract_protocol:
Tissues were flash frozen on liquid nitrogen and stored at -80*C until use. RNA was extracted from 20 mg of tissue using the Qiagen RNeasy kit (74104) following the manufacturer’s protocol.
RNA quantity was verified using the Qubit RNA BR assay (Thermo Fisher Scientific, Q10210) and quality was checked using an Agilent TapeStation.  RNA libraries were prepared from 1 µg of total RNA with RIN > 6.1 by TIGSS using the TruSeq mRNA stranded kit (Illumina, 20020595).  Paired end, 150 base pair sequencing on the NovaSeq 6000 at a depth of 10-20 million reads per sample was performed.

value: Cervical Spinal Cord

value: 140 days

value: male

tag: genotype

value: UBE3A maternal deletion


title: Pig brain cervical spinal cord, Animal ID 15-3, male, UBE3A mat. deletion

description: Library name: CSC15-3

tag: tissue


title: Pig brain cervical spinal cord, Animal ID 15-4, male, wildtype

description: Library name: CSC15-4

value: wildtype


title: Pig brain cervical spinal cord, Animal ID 15-2, male, wildtype

description: Library name: CSC15-2


title: donor procurement biopsy [D111_L]

tag: donor age

tag: donor biopsy ct


title: SPT6-AID-Auxin-rep2_LR

description:
Library name: Sample17
isoformMetadata.csv


title: Pig brain cervical spinal cord, Animal ID 14-9, male, UBE3A mat. deletion

description: Library name: CSC14-9


title: V086-CGND-HRA-02761-B

description: Library name: V086-CGND-HRA-02761-B

value: Female

tag: disease duration

tag: phenotype


title: NELFC-AID-Auxin_rep1_LR

description:
Library name: Sample21
isoformMetadata.csv


title: SPT6-AID-Auxin-rep1_LR

description:
Library name: Sample16
isoformMetadata.csv


title: V086-CGND-HRA-02761-A

description: Library name: V086-CGND-HRA-02761-A


title: Pig brain cervical spinal cord, Animal ID 14-2, male, wildtype

description: Library name: CSC14-2


title: SPT6-AID-DMSO-rep3_LR

description:
Library name: Sample15
isoformMetadata.csv


title: donor procurement biopsy [D110_P]

tag: donor category

tag: donor bmi

tag: donor hypertension


title: Pig brain cortex, Animal ID 15-5, male, UBE3A mat. deletion

description: Library name: Cortex15-5

source_name: Cortex

value: Cortex


title: donor procurement biopsy [D107_P]

value: DBD - SCD

tag: donor biopsy cv

tag: donor biopsy ci

tag: donor biopsy ah


title: donor procurement biopsy [D108_P]


title: Pig brain cortex, Animal ID 15-4, male, wildtype

description: Library name: Cortex15-4

tag: Sex


title: SPT6-AID-DMSO-rep2_LR

description:
Library name: Sample14
isoformMetadata.csv

tag: cell line

tag: treatment


title: V085-CGND-HRA-02760-C

description: Library name: V085-CGND-HRA-02760-C

tag: sample id

tag: donor id

value: Male

tag: age

value: ALS


title: V085-CGND-HRA-02756-B

description: Library name: V085-CGND-HRA-02756-B

tag: tissue

tag: pmi


title: donor procurement biopsy [D110_L]

tag: patient id

tag: donor age

tag: donor biopsy ct


title: SPT6-AID-DMSO-rep1_LR

description:
Library name: Sample13
isoformMetadata.csv

tag: genotype


title: Pig brain cortex, Animal ID 15-3, male, UBE3A mat. deletion

description: Library name: Cortex15-3


title: SPT5-AID-Auxin-rep2_LR

description:
Library name: Sample11
isoformMetadata.csv


title: Pig brain cortex, Animal ID 15-2, male, wildtype

description: Library name: Cortex15-2


title: V028-CGND-HRA-02749-B

description: Library name: V028-CGND-HRA-02749-B

tag: disease duration

tag: phenotype


title: Pig brain cortex, Animal ID 14-2, male, wildtype

description: Library name: Cortex14-2


title: Pig brain cortex, Animal ID 14-9, male, UBE3A mat. deletion

description: Library name: Cortex14-9


title: SPT5-AID-Auxin-rep1_LR

description:
Library name: Sample10
isoformMetadata.csv


title: V085-CGND-HRA-02760-D

description: Library name: V085-CGND-HRA-02760-D


title: SPT5-AID-Auxin-rep3_LR

description:
Library name: Sample12
isoformMetadata.csv


title: V027-CGND-HRA-02752-D

description: Library name: V027-CGND-HRA-02752-D


title: V028-CGND-HRA-02749-A

description: Library name: V028-CGND-HRA-02749-A


title: SPT5-AID-DMSO-rep3_LR

description:
Library name: Sample9
isoformMetadata.csv


title: V085-CGND-HRA-02756-A

description: Library name: V085-CGND-HRA-02756-A


title: SPT5-AID-DMSO-rep2_LR

description:
Library name: Sample8
isoformMetadata.csv


title: NPPO-1NE-KTX, multiome snATAC-seq

first: Jia

middle: Jessie

last: Li

department: Medicine

institute: Columbia University Irving Medical Center

description:
Library name: NPPO-1NE-KTX_multiome_snATAC-seq
10x Genomics

library_source: genomic single cell

data_processing:
The demultiplexes, alignment, filtering, barcode counting, peak calling, counting of both ATAC and gene expression molecules and generation of feature-barcode matrices of multiome snATAC-seq+snRNA-seq data were made using Cell Ranger ARC (v1.0.0: MJ018, MJ019, MJ020, MJ021, MJ022 and MJ023; v2.0.2: MJ024 and MJ025)
Assembly: mm10
Supplementary files format and content: CellRanger output files: snATAC_atac_fragments.tsv.gz, snATAC_atac_fragments.tsv.gz.tbi, snATAC_atac_peak_annotation.tsv, snATAC_atac_peaks.bed

molecule: genomic DNA

source_name: Prostate

extract_protocol:
For multiome snRNA-seq and snATAC-seq, organoids were digested into single cells using TrypLE, passed through 40 µM cell strainers three times, and cell numbers were quantified using an automated cell counter. Approximately 1 million cells in 0.04% BSA were used for single nuclei isolation. Cells were spun at 1000 rpm for 5 min at 4°C, dissociated for 5 min with 100 µl ice-cold lysis buffer, neutralized with 1 ml wash buffer, spun at 1000 rpm for 5 min at 4°C, and resuspended in chilled Nuclei buffer included in the Chromium Next GEM Multiome ATAC + Gene Expression Kit (10X Genomics). Wash buffer contained 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 1% BAS, 0.1% Tween-20, 1 mM DTT (Millipore-Sigma 646563), 1 U/µl RNase inhibitor (Millipore-Sigma 3335399001) in nuclease-free water. Lysis buffer contained 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 1% BAS, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin, 1 mM DTT, 1 U/µl RNase inhibitor in nuclease-free water. Nuclei concentration was determined using a Countess II FL Automated Cell Counter. Approximately 5,000 nuclei were loaded onto the Chromium Controller.
Multiome snATAC+snRNA-seq libraries were prepared following the manufacturer's instructions (Chromium Next GEM Single Cell Multiome Reagent Kit,10X Genomics). Briefly, nuclei suspensions are transposed, and adapters were added to the ends of the DNA fragments. Single Cell Multiome ATAC + GEX Gel Beads include a poly(dT) sequence that enables production of barcoded, full-length cDNA from poly-adenylated mRNA for gene expression (GEX) library and a Spacer sequence that enables barcode attachment to transposed DNA fragments for ATAC library. The GEMs are generated by combining barcoded Gel Beads, transposed nuclei, and a Master Mix. Barcoded transposed DNA and barcoded full-length cDNA from poly-adenylated mRNA are amplified via PCR. Libraries were prepared for paired-end sequencing, and data were processed with Cell Ranger ARC software (10x Genomics) by the Columbia University Single Cell Analysis Core.

value: Prostate

value: NPPO-1NE organoids

tag: cell type

value: Prostate NE tumor cells


title: donor procurement biopsy [D107_L]

value: left kidney

tag: donor category

tag: donor bmi

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ci


title: NPPO-1NE-DMSO, multiome snATAC-seq

description:
Library name: NPPO-1NE-DMSO_multiome_snATAC-seq
10x Genomics

tag: cell line

tag: treatment

value: DMSO


title: V027-CGND-HRA-02752-C

description: Library name: V027-CGND-HRA-02752-C

tag: sample id

tag: donor id

tag: Sex

tag: age


title: SPT5-AID-DMSO-rep1_LR

description:
Library name: Sample7
isoformMetadata.csv

value: DMSO 6hr


title: donor procurement biopsy [D106_P]

tag: patient id

tag: tissue

value: right kidney

tag: donor age

value: DBD - ECD


title: V027-CGND-HRA-02746-B

description: Library name: V027-CGND-HRA-02746-B

tag: disease duration

tag: pmi

value: ALSci


title: donor procurement biopsy [D104_P]

tag: donor biopsy ct

tag: donor biopsy ah


title: donor procurement biopsy [D106_L]

tag: donor category

tag: donor bmi


title: PAF1-AID-Auxin-rep3_LR

description:
Library name: Sample6
isoformMetadata.csv

tag: genotype

value: Auxin 6hr


title: donor procurement biopsy [D103_P]

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ci


title: NPPO-1NE-KTX, multiome snRNA-seq

description:
Library name: NPPO-1NE-KTX_multiome_snRNA-seq
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexes, alignment, filtering, barcode counting, peak calling, counting of both ATAC and gene expression molecules and generation of feature-barcode matrices of multiome snATAC-seq+snRNA-seq data were made using Cell Ranger ARC (v1.0.0: MJ018, MJ019, MJ020, MJ021, MJ022 and MJ023; v2.0.2: MJ024 and MJ025)
Assembly: mm10
Supplementary files format and content: CellRanger output files: snRNA_barcodes.tsv.gz, snRNA_features.tsv.gz, snRNA_matrix.mtx.gz

molecule: nuclear RNA

tag: cell line

tag: cell type

tag: treatment


title: V027-CGND-HRA-02746-A

description: Library name: V027-CGND-HRA-02746-A

tag: sample id

tag: donor id

tag: Sex

tag: age

tag: phenotype


title: donor procurement biopsy [D102_L]

tag: patient id

tag: tissue

tag: donor age


title: PAF1-AID-Auxin-rep2_LR

description:
Library name: Sample5
isoformMetadata.csv


title: NPPO-1NE-DMSO, multiome snRNA-seq

description:
Library name: NPPO-1NE-DMSO_multiome_snRNA-seq
10x Genomics


title: donor procurement biopsy [D105_P]

tag: donor category


title: V026-CGND-HRA-02750-D

description: Library name: V026-CGND-HRA-02750-D

tag: disease duration

tag: pmi


title: donor procurement biopsy [D101_P]

tag: donor bmi

tag: donor hypertension

tag: donor biopsy ct

tag: donor biopsy ah


title: PAF1-AID-Auxin-rep1_LR

description:
Library name: Sample4
isoformMetadata.csv

tag: cell line

tag: genotype


title: PAF1-AID-DMSO-rep3_LR

description:
Library name: Sample3
isoformMetadata.csv

tag: treatment


title: V026-CGND-HRA-02745-B

description: Library name: V026-CGND-HRA-02745-B

tag: sample id

tag: donor id


title: donor procurement biopsy [D101_L]

tag: donor biopsy cv

tag: donor biopsy ci


title: NPPO-1NE-sgNSD2, multiome snATAC-seq

description: 10x Genomics

data_processing:
The demultiplexes, filtering and alignment, barcode counting, identification of transposase cut sites, detection of accessible chromatin peaks, cell calling, and count matrix generation for peaks and transcription factors of snATAC-seq data was made using Cell Ranger ATAC v2.1.
The demultiplexes, alignment, filtering, barcode counting, peak calling, counting of both ATAC and gene expression molecules and generation of feature-barcode matrices of multiome snATAC-seq+snRNA-seq data were made using Cell Ranger ARC v2.0.2
Assembly: mm10
Supplementary files format and content: Tab seperated value files and matrix files

extract_protocol:
For snATAC-seq, Organoids were digested into single cells using TrypLE, passed through a 40 µM cell strainer three times, and cell numbers were quantified using an automated cell counter. Approximately 1 million cells in 0.04% BSA/PBS (Miltenyi Biotec 130-091-376) were used for single nuclei isolation. Cells were spun at 1000 rpm for 5 min at 4°C, dissociated for 5 min with 100 µl ice-cold lysis buffer, neutralized with 1 ml chilled wash buffer, spun at 1000 rpm for 5 min at 4°C, and resuspended in chilled Nuclei buffer included in the Chromium Single Cell ATAC Library Kit (10X Genomics). Wash buffer contained 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 1% BAS, 0.1% Tween-20 in nuclease-free water. Lysis buffer contained 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin, 1% BAS in nuclease-free water. Nuclei concentration was determined using a Countess II FL Automated Cell Counter. Approximately 5,000 nuclei were loaded onto the Chromium Controller. For multiome snATAC-seq + snRNA-seq, organoids were digested into single cells using TrypLE, passed through a 40 µM cell strainer three times, and cell numbers were quantified using an automated cell counter. Approximately 1 million cells in 0.04% BSA were used for single nuclei isolation. Cells were spun at 1000 rpm for 5 min at 4°C, dissociated for 5 min with 100 µl ice-cold lysis buffer, neutralized with 1 ml wash buffer, spun at 1000 rpm for 5 min at 4°C, and resuspended in chilled Nuclei buffer included in the Single Cell Multiome ATAC Kit (10X Genomics). Wash buffer contained 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 1% BAS, 0.1% Tween-20, 1 mM DTT (Millipore-Sigma 646563), 1 U/µl RNase inhibitor (Millipore-Sigma 3335399001) in nuclease-free water. Lysis buffer contained 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 1% BAS, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin, 1 mM DTT, 1 U/µl RNase inhibitor in nuclease-free water. Nuclei concentration was determined using a Countess II FL Automated Cell Counter. Approximately 5,000 nuclei were loaded onto the Chromium Controller.
snATAC-seq libraries were prepared following the manufacturer's instructions (Chromium Next GEM Single Cell ATAC Reagent Kits v1.1, 10X Genomics). Briefly, nuclei were transposed and partitioned into GEMs. 10x Barcodes were added to index the transposed DNA of each individual nucleus. Libraries were generated via PCR and sequenced on the Illumina NextSeq 550 platform. Paired-end sequencing data were processed with Cell Ranger software (10x Genomics, version 2.1) by the Columbia University Single Cell Analysis Core. Multiome snATAC+snRNA-seq libraries were prepared following the manufacturer's instructions (Chromium Next GEM Single Cell Multiome Reagent Kit,10X Genomics). Briefly, nuclei suspensions are transposed and adapters were added to the ends of the DNA fragments. Single Cell Multiome ATAC + GEX Gel Beads include a poly(dT) sequence that enables production of barcoded, full-length cDNA from poly-adenylated mRNA for gene expression (GEX) library and a Spacer sequence that enables barcode attachment to transposed DNA fragments for ATAC library. The GEMs are generated by combining barcoded Gel Beads, transposed nuclei, and a Master Mix. Barcoded transposed DNA and barcoded full-length cDNA from poly-adenylated mRNA are amplified via PCR. Libraries were prepared for paired-end sequencing, and data were processed with Cell Ranger ARC software (10x Genomics, version v2.0.2) by the Columbia University Single Cell Analysis Core.

tag: cell type

value: Cas9+sgNSD2 guide RNA


title: donor procurement biopsy [D100_P]

tag: patient id

tag: tissue


title: NPPO-2-sgControl, multiome snATAC-seq

description: 10x Genomics

value: Cas9+sgControl guide RNA


title: V026-CGND-HRA-02750-C

description: Library name: V026-CGND-HRA-02750-C

tag: Sex

value: Female

tag: age

tag: phenotype


title: PAF1-AID-DMSO-rep2_LR

description:
Library name: Sample2
isoformMetadata.csv


title: donor procurement biopsy [D100_L]

tag: donor age

tag: donor category

tag: donor bmi


title: donor procurement biopsy [D099_L]

tag: donor hypertension

tag: donor biopsy ct

tag: donor biopsy ah


title: V025-CGND-HRA-02754-D

description: Library name: V025-CGND-HRA-02754-D

tag: pmi

value: Control


title: NPPO-2-sgNSD2, multiome snATAC-seq

description: 10x Genomics

tag: cell line

tag: genotype

tag: treatment


title: PAF1-AID-DMSO-rep1_LR

description:
Library name: Sample1
isoformMetadata.csv


title: V025-CGND-HRA-02754-C

description: Library name: V025-CGND-HRA-02754-C

tag: sample id

tag: donor id


title: NPPO-6-EV, multiome snATAC-seq

description: 10x Genomics

tag: cell type

value: empty vector transgene


title: NPPO-1NE-sgControl, multiome snATAC-seq

description: 10x Genomics


title: 786O CBFB overexpression rep3

description: Library name: OE_3

library_source: genomic

data_processing:
Snakemake workflow https://github.com/niekwit/chip-seq (https://doi.org/10.5281/zenodo.13801525)
Assembly: ENSEMBL hg38 build 113
Supplementary files format and content: BigWig

extract_protocol:
Two 70 % confluent 15 cm plates of WT and CBF- β overexpression 786O cells were used per replicate, fixed and sonicated. 1 ml of sonicated sample was diluted with 4 ml dilution buffer, put in 15 ml falcon tubes, and pre-cleared using 60 µl of IgG beads. For ChIP sequencing samples, 30 µl of primary CBF-β antibody (C15310002 Diagenode) was used per replicate. ChIPed DNA was eluted in 10 µl of elution buffer and submitted for sequencing.
ThruPLEX® DNA-Seq Kit and ThruPLEX DNA Unique Dual Index Kit


title: 786O CBFB overexpression input rep3

description: Library name: OE_3_in


title: NPPO-6-H3.3K36M, multiome snATAC-seq

description: 10x Genomics

value: H3.3K36M transgene


title: NPPO-1, snATAC-seq

description: 10x Genomics

source_name: NPPO-1 organoids

value: NPPO-1 organoids

value: No


title: V025-CGND-HRA-02751-B

description: Library name: V025-CGND-HRA-02751-B

tag: tissue

value: Male

tag: disease duration

value: ALS


title: 786O CBFB overexpression rep1

description: Library name: OE_1


title: V025-CGND-HRA-02751-A

description: Library name: V025-CGND-HRA-02751-A

tag: Sex

tag: age


title: V026-CGND-HRA-02745-A

description: Library name: V026-CGND-HRA-02745-A

tag: phenotype


title: donor procurement biopsy [D097_P]

tag: patient id

tag: donor age

tag: donor category

tag: donor biopsy cv

tag: donor biopsy ci


title: NPPO-1NE-sgNSD2, multiome snRNA-seq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation of scRNA-seq data were made using Cell Ranger software v2.1.
The demultiplexes, alignment, filtering, barcode counting, peak calling, counting of both ATAC and gene expression molecules and generation of feature-barcode matrices of multiome snATAC-seq+snRNA-seq data were made using Cell Ranger ARC v2.0.2
Assembly: mm10
Supplementary files format and content: Tab seperated value files and matrix files
Library strategy: multiome snRNA-seq

extract_protocol:
For scRNA-seq, organoids were dissociated by incubation with pre-warmed TrypLE at 37°C for 10 min, neutralization with 1:10 5% CS-FBS/PBS, centrifugation at 1000 rpm for 1 min, and filtration three times through a 40 µM cell strainer (Corning 431750). Cells were spun at 1000 rpm for 5 min, pellets were dissociated with 5% CS-FBS/PBS, and resuspended at 1000 cells/µl after counting using a Countess II FL Automated Cell Counter. Approximately 5,000 cells were loaded onto the Chromium Controller (10X Genomics). For multiome snATAC-seq + snRNA-seq, organoids were digested into single cells using TrypLE, passed through a 40 µM cell strainer three times, and cell numbers were quantified using an automated cell counter. Approximately 1 million cells in 0.04% BSA were used for single nuclei isolation. Cells were spun at 1000 rpm for 5 min at 4°C, dissociated for 5 min with 100 µl ice-cold lysis buffer, neutralized with 1 ml wash buffer, spun at 1000 rpm for 5 min at 4°C, and resuspended in chilled Nuclei buffer included in the Single Cell Multiome ATAC Kit (10X Genomics). Wash buffer contained 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 1% BAS, 0.1% Tween-20, 1 mM DTT (Millipore-Sigma 646563), 1 U/µl RNase inhibitor (Millipore-Sigma 3335399001) in nuclease-free water. Lysis buffer contained 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 1% BAS, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin, 1 mM DTT, 1 U/µl RNase inhibitor in nuclease-free water. Nuclei concentration was determined using a Countess II FL Automated Cell Counter. Approximately 5,000 nuclei were loaded onto the Chromium Controller.
scRNA-seq libraries were prepared following the manufacturer's instructions (Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1, 10X Genomics). Briefly, cells were loaded onto the Chromium Controller (10X Genomics) to generate Gel Beads-in-emulsion (GEMs), and barcoded, full-length cDNA from poly-adenylated mRNA was generated and amplified via PCR. scRNA-seq libraries were prepared for paired-end sequencing, and data were processed with Cell Ranger software (10x Genomics, version 2.1) by the Columbia University Single Cell Analysis Core. Multiome snATAC+snRNA-seq libraries were prepared following the manufacturer's instructions (Chromium Next GEM Single Cell Multiome Reagent Kit,10X Genomics). Briefly, nuclei suspensions are transposed and adapters were added to the ends of the DNA fragments. Single Cell Multiome ATAC + GEX Gel Beads include a poly(dT) sequence that enables production of barcoded, full-length cDNA from poly-adenylated mRNA for gene expression (GEX) library and a Spacer sequence that enables barcode attachment to transposed DNA fragments for ATAC library. The GEMs are generated by combining barcoded Gel Beads, transposed nuclei, and a Master Mix. Barcoded transposed DNA and barcoded full-length cDNA from poly-adenylated mRNA are amplified via PCR. Libraries were prepared for paired-end sequencing, and data were processed with Cell Ranger ARC software (10x Genomics, version v2.0.2) by the Columbia University Single Cell Analysis Core.

value: Prostate NE tumor cells


title: V024-CGND-HRA-02753-D

description: Library name: V024-CGND-HRA-02753-D

tag: pmi


title: NPPO-1NE-sgControl, multiome snRNA-seq

description: 10x Genomics

tag: cell line


title: 786O empty vector ip rep3

description: Library name: EV_3


title: V024-CGND-HRA-02753-C

description: Library name: V024-CGND-HRA-02753-C


title: donor procurement biopsy [D097_L]

value: left kidney

tag: donor bmi

tag: donor hypertension

tag: donor biopsy ct

tag: donor biopsy ah


title: donor procurement biopsy [D095_L]


title: NPPO-2-sgControl, multiome snRNA-seq

description: 10x Genomics

tag: cell type

tag: genotype

tag: treatment


title: donor procurement biopsy [D095_P]

tag: tissue


title: donor procurement biopsy [D094_P]

value: DBD - SCD


title: donor procurement biopsy [D099_P]

value: right kidney


title: donor procurement biopsy [D096_L]


title: V024-CGND-HRA-02748-B

description: Library name: V024-CGND-HRA-02748-B

tag: sample id

tag: donor id

tag: Sex

tag: age

tag: disease duration


title: V024-CGND-HRA-02748-A

description: Library name: V024-CGND-HRA-02748-A

tag: phenotype


title: 786O empty vector ip rep2

description: Library name: EV_2


title: NPPO-2-sgNSD2, multiome snRNA-seq

description: 10x Genomics


title: NPPO-6-EV, multiome snRNA-seq

description: 10x Genomics


title: V023-CGND-HRA-02747-C

description: Library name: V023-CGND-HRA-02747-C


title: 786O empty vector input rep2

description: Library name: EV_2_in


title: 786O CBFB overexpression input rep1

description: Library name: OE_1_in


title: 786O empty vector ip rep1

description: Library name: EV_1


title: donor procurement biopsy [D094_L]

tag: patient id

tag: donor age

tag: donor category

tag: donor biopsy cv

tag: donor biopsy ci


title: NPPO-6-H3.3K36M, multiome snRNA-seq

description: 10x Genomics

tag: cell line


title: donor procurement biopsy [D093_P]

tag: donor bmi

tag: donor hypertension

tag: donor biopsy ct

tag: donor biopsy ah


title: NPPO-1nonNE-LV-RFP, scRNA-seq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation of scRNA-seq data were made using Cell Ranger software v2.1.
The demultiplexes, alignment, filtering, barcode counting, peak calling, counting of both ATAC and gene expression molecules and generation of feature-barcode matrices of multiome snATAC-seq+snRNA-seq data were made using Cell Ranger ARC v2.0.2
Assembly: mm10
Supplementary files format and content: Tab seperated value files and matrix files

tag: cell type

tag: genotype

tag: treatment

value: H2B-RFP transgene (addgene26001)


title: V022-CGND-HRA-02759-B

description: Library name: V022-CGND-HRA-02759-B

tag: tissue

tag: sample id

tag: donor id

tag: Sex

tag: pmi


title: DIPG6_RNA_Combo_rep3

city: Kensington

first: Holly

last: Holliday

address: Lowy Cancer Research Centre

country: Australia

institute: Children's Cancer Institute

description:
Library name: DIPG6_RNA_Combo_rep3
120min.combo.C
DIPG6_total_tpm.csv
DIPG6_nascent_tpm.csv

data_processing:
Reads were quality and adapter trimmed using trim-galore 0.6.10 using options –quality 20 -j 4 –paired
Trimmed reads were aligned to the human reference genome hg38 with star [122] 2.7.10 using options --runThreadN 23 --runMode alignReads --readFilesCommand zcat --outReadsUnmapped Fastx --outSAMattributes nM MD –outFileNamePrefix --peOverlapNbasesMin 10 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --alignEndsType EndToEnd --outFilterMismatchNoverReadLmax 0.3 --outSAMtype BAM SortedByCoordinate and indexed using samtools 1.6.
BAM files were converted to CIT format using the gedi Bam2CIT function. 4sU induced conversions were called using GrandSlam using options -plot  -full -D -allGenes -trim5p 5 -trim3p 5
The gene-wise estimates for the new-to-total ratio were input into GrandR
Nascent differential expression was performed using the PairwiseDESeq2 function, with normalization with respect to total
Assembly: hg38
Supplementary files format and content: raw counts for each sample
Supplementary files format and content: TPM counts for each sample

source_name: Diffuse Midline Glioma

growth_protocol: Cells were maintained in Tumour Stem Cell (TSM) media consisting of a 1:1 mixture of DMEM/F12 and Neurobasal medium (Invitrogen) supplemented with Glutamax, Pyruvate, non-essential amino acids, HEPES buffer, antibiotic/antimycotic, B-27 (Invitrogen), Heparin (0.0002%), EGF (20 ng/mL), bFGF (20 ng/mL), PDGF-AA (10 ng/mL) and PDGF-BB (10 ng/mL) (StemCell Technologies).

extract_protocol:
Total RNA was extracted from treated cells using a modified version of the RNeasy protocol (Qiagen) and 4SU was coverted to C as described in DOI: 10.1038/nmeth.4582
cDNA libraries were prepared using the Illumina Stranded Total RNA plus RIboZero Plus kit

treatment_protocol: Cells were treated with 100µM 4-Thiouridine (4sU) and DMSO, CBL0137 (1µM for DIPG7 and 2µM for DIPG6) or JQ1 (1µM) as single agents and in combination for 2h. DMSO concentrations were normalised across the 4 treatment groups.

value: Diffuse Midline Glioma

value: SU-DIPGVI


title: NPPO-1-LV-RFP, scRNA-seq

description: 10x Genomics


title: 786O empty vector input rep3

description: Library name: EV_3_in


title: V021-CGND-HRA-02764-D

description: Library name: V021-CGND-HRA-02764-D

tag: age

tag: disease duration

tag: phenotype


title: NPPO-1nonNE, scRNA-seq

description: 10x Genomics

source_name: NPPO-1nonNE organoids

value: NPPO-1nonNE organoids


title: donor procurement biopsy [D092_P]

tag: patient id

tag: donor age

tag: donor category

value: DBD - ECD

tag: donor biopsy cv

tag: donor biopsy ci


title: donor procurement biopsy [D093_L]

tag: donor bmi

tag: donor hypertension

tag: donor biopsy ct

tag: donor biopsy ah


title: DIPG6_RNA_Combo_rep2

description:
Library name: DIPG6_RNA_Combo_rep2
120min.combo.B
DIPG6_total_tpm.csv
DIPG6_nascent_tpm.csv

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: donor procurement biopsy [D091_P]


title: NPPO-6, scRNA-seq

description: 10x Genomics

source_name: NPPO-6 organoids

value: NPPO-6 organoids


title: V021-CGND-HRA-02764-C

description: Library name: V021-CGND-HRA-02764-C

tag: sample id

tag: donor id

tag: Sex

value: Female

tag: age

tag: pmi


title: donor procurement biopsy [D092_L]

tag: patient id

tag: donor age

tag: donor category


title: 786O empty vector input rep1

description: Library name: EV_1_in

value: WT


title: V022-CGND-HRA-02759-A

description: Library name: V022-CGND-HRA-02759-A

tag: disease duration

tag: phenotype


title: DIPG6_RNA_Combo_rep1

description:
Library name: DIPG6_RNA_Combo_rep1
120min.combo.A
DIPG6_total_tpm.csv
DIPG6_nascent_tpm.csv


title: V020-CGND-HRA-02757-B

description: Library name: V020-CGND-HRA-02757-B

value: ALSci


title: V020-CGND-HRA-02757-A

description: Library name: V020-CGND-HRA-02757-A


title: DIPG6_RNA_JQ1_rep2

description:
Library name: DIPG6_RNA_JQ1_rep2
120min.jq1.B
DIPG6_total_tpm.csv
DIPG6_nascent_tpm.csv

value: JQ1 + 4SU


title: NPPO-5, scRNA-seq

description: 10x Genomics

source_name: NPPO-5 organoids

value: NPPO-5 organoids

value: No


title: NPPO-2, scRNA-seq

description: 10x Genomics

source_name: NPPO-2 organoids

value: NPPO-2 organoids


title: V011-CGND-HRA-02766-D

description: Library name: V011-CGND-HRA-02766-D

value: Male

value: Control


title: donor procurement biopsy [D091_L]

value: left kidney

tag: donor bmi

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: V011-CGND-HRA-02766-C

description: Library name: V011-CGND-HRA-02766-C

tag: tissue


title: NPPO-4, scRNA-seq

description: 10x Genomics

source_name: NPPO-4 organoids

tag: cell line

value: NPPO-4 organoids

tag: cell type

value: Prostate NE tumor cells

tag: genotype

tag: treatment


title: NPPO-1, scRNA-seq

description: 10x Genomics

value: NPPO-1 organoids


title: DIPG6_RNA_CBL0137_rep3

description:
Library name: DIPG6_RNA_CBL0137_rep3
120min.cbl.C
DIPG6_total_tpm.csv
DIPG6_nascent_tpm.csv

value: Diffuse Midline Glioma

value: SU-DIPGVI


title: DIPG6_RNA_JQ1_rep1

description:
Library name: DIPG6_RNA_JQ1_rep1
120min.jq1.A
DIPG6_total_tpm.csv
DIPG6_nascent_tpm.csv


title: donor procurement biopsy [D090_P]

value: right kidney

value: DBD - ECD

tag: donor biopsy ah


title: V011-CGND-HRA-02762-B

description: Library name: V011-CGND-HRA-02762-B

tag: sample id

tag: donor id

tag: Sex

value: Female

tag: age

tag: pmi

value: ALS


title: donor procurement biopsy [D090_L]

tag: patient id

tag: donor age

tag: donor category


title: DIPG6_RNA_JQ1_rep3

description:
Library name: DIPG6_RNA_JQ1_rep3
120min.jq1.C
DIPG6_total_tpm.csv
DIPG6_nascent_tpm.csv


title: Zebra finch embryo 33 medial hypothalamus E13 control male

city: Clemson

first: Prakrit

last: Subba

state: SC

address: 132 Long Hall, 230 Parkway Drive

department: Biological Sciences

institute: Clemson University

description:
Library name: sample_33
Medial coronal punch from E13 zebra finch embryo exposed to control call playback (E9–E12, 9h/day); male

data_processing:
Trimmomatic v0.39 was used for quality control and adapter trimming.
Quality-trimmed reads were mapped to the zebra finch reference transcriptome (bTaeGut1.4.pri) and quantified using Salmon v1.5.2 in quasi-mapping mode.
Transcript-level counts were imported and aggregated to gene-level using tximport, with tx2gene mapping derived from the reference GTF file.
Gene-level differential expression analysis was performed using DESeq2 v1.30.1 with negative binomial generalized linear models, adjusting for sex as a covariate. P-values were adjusted using the Benjamini-Hochberg FDR method.
Variance-stabilizing transformation (VST) was applied for downstream analyses including principal component analysis and weighted gene co-expression network analysis (WGCNA).
Assembly: bTaeGut1.4.pri
Supplementary files format and content: CSV file includes raw gene-level counts for each sample (19 columns: gene_id + 19 samples).
Supplementary files format and content: CSV file includes normalized counts (DESeq2 size-factor normalized) for each sample.
Supplementary files format and content: CSV file includes variance-stabilized expression values (VST) for each sample.

organism: Taeniopygia guttata

source_name: hypothalamus

growth_protocol: Zebra finch eggs were incubated at 37.7°C in experimental incubators and exposed to either heat call or control call playback (9 hours/day) from embryonic day 9 to embryonic day 12.

extract_protocol:
On embryonic day 13, embryos were decapitated and medial hypothalamic punches (1 mm diameter) were collected from 100 μm coronal cryosections (10 sections per brain) using a micro-punching technique. Total RNA was extracted using the Zymo Quick-RNA Microprep Kit (cat #R1050). RNA quality and concentration were assessed using NanoDrop spectrophotometry and Agilent 2100 Bioanalyzer.
The Genome Centre and Queen Mary University of London prepared mRNA stranded libraries from total RNA using a custom method. Libraries were sequenced on an Illumina NextSeq 500 platform (75 bp paired-end).

treatment_protocol:
Heat call playback group (n=10): Eggs exposed to whine + heat call audio stimuli for 9 hours per day from E9-E12 via speakers attached to incubators.
Control call playback group (n=9): Eggs exposed to whine + tet call audio stimuli for 9 hours per day from E9-E12 via speakers attached to incubators.

value: hypothalamus

value: male

value: wild type

value: Control call playback E9–E12


title: Zebra finch embryo 32 medial hypothalamus E13 control female

description:
Library name: sample_32
Medial coronal punch from E13 zebra finch embryo exposed to control call playback (E9–E12, 9h/day); female

value: female


title: V011-CGND-HRA-02762-A

description: Library name: V011-CGND-HRA-02762-A

tag: disease duration

tag: phenotype


title: DIPG6_RNA_CBL0137_rep1

description:
Library name: DIPG6_RNA_CBL0137_rep1
120min.cbl.A
DIPG6_total_tpm.csv
DIPG6_nascent_tpm.csv


title: donor procurement biopsy [D089_L]

tag: donor bmi

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: V010-CGND-HRA-02761-B

description: Library name: V010-CGND-HRA-02761-B

tag: tissue


title: Zebra finch embryo 31 medial hypothalamus E13 heat call male

description:
Library name: sample_31
Medial coronal punch from E13 zebra finch embryo exposed to chronic heat call playback (E9–E12, 9h/day); male

tag: genotype

tag: treatment

value: Heat call playback E9–E12


title: V010-CGND-HRA-02761-A

description: Library name: V010-CGND-HRA-02761-A

tag: sample id

tag: donor id


title: donor procurement biopsy [D088_L]

tag: donor biopsy ah


title: Zebra finch embryo 30 medial hypothalamus E13 control male

description:
Library name: sample_30
Medial coronal punch from E13 zebra finch embryo exposed to control call playback (E9–E12, 9h/day); male

tag: Sex


title: donor procurement biopsy [D087_L]

tag: patient id

value: DBD - SCD


title: DIPG6_RNA_Veh_rep3

description:
Library name: DIPG6_RNA_Veh_rep3
120min.vehicle.C
DIPG6_total_tpm.csv
DIPG6_nascent_tpm.csv

tag: cell line

tag: cell type

value: DMSO + 4SU


title: donor procurement biopsy [D086_L]

value: left kidney

tag: donor age

tag: donor category


title: donor procurement biopsy [D086_P]

tag: donor bmi


title: V009-CGND-HRA-02760-D

description: Library name: V009-CGND-HRA-02760-D

value: Male

tag: age

tag: disease duration

tag: pmi

tag: phenotype


title: DIPG6_RNA_Veh_rep2

description:
Library name: DIPG6_RNA_Veh_rep2
120min.vehicle.B
DIPG6_total_tpm.csv
DIPG6_nascent_tpm.csv

tag: tissue


title: V009-CGND-HRA-02760-C

description: Library name: V009-CGND-HRA-02760-C


title: donor procurement biopsy [D085_L]

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: Zebra finch embryo 27 medial hypothalamus E13 control female

description:
Library name: sample_27
Medial coronal punch from E13 zebra finch embryo exposed to control call playback (E9–E12, 9h/day); female

tag: genotype

tag: treatment


title: DIPG6_RNA_Veh_rep1

description:
Library name: DIPG6_RNA_Veh_rep1
120min.vehicle.A
DIPG6_total_tpm.csv
DIPG6_nascent_tpm.csv


title: DIPG6_RNA_Veh_no4su_rep3

description:
Library name: DIPG6_RNA_Veh_no4su_rep3
0min.vehicle.C
DIPG6_total_tpm.csv
DIPG6_nascent_tpm.csv

value: DMSO


title: V009-CGND-HRA-02756-B

description: Library name: V009-CGND-HRA-02756-B

tag: sample id

tag: donor id

tag: Sex


title: Zebra finch embryo 26 medial hypothalamus E13 heat call female

description:
Library name: sample_26
Medial coronal punch from E13 zebra finch embryo exposed to chronic heat call playback (E9–E12, 9h/day); female


title: DIPG6_RNA_CBL0137_rep2

description:
Library name: DIPG6_RNA_CBL0137_rep2
120min.cbl.B
DIPG6_total_tpm.csv
DIPG6_nascent_tpm.csv

value: Diffuse Midline Glioma

tag: cell line

tag: cell type


title: Zebra finch embryo 25 medial hypothalamus E13 control male

description:
Library name: sample_25
Medial coronal punch from E13 zebra finch embryo exposed to control call playback (E9–E12, 9h/day); male


title: DIPG6_RNA_Veh_no4su_rep2

description:
Library name: DIPG6_RNA_Veh_no4su_rep2
0min.vehicle.B
DIPG6_total_tpm.csv
DIPG6_nascent_tpm.csv

value: SU-DIPGVI


title: donor procurement biopsy [D084_P]

tag: patient id

value: right kidney

tag: donor age

tag: donor category

tag: donor bmi

tag: donor biopsy ah


title: donor procurement biopsy [D084_L]

tag: tissue


title: Zebra finch embryo 28 medial hypothalamus E13 heat call female

description:
Library name: sample_28
Medial coronal punch from E13 zebra finch embryo exposed to chronic heat call playback (E9–E12, 9h/day); female


title: DIPG6_RNA_Veh_no4su_rep1

description:
Library name: DIPG6_RNA_Veh_no4su_rep1
0min.vehicle.A
DIPG6_total_tpm.csv
DIPG6_nascent_tpm.csv


title: V008-CGND-HRA-02749-B

description: Library name: V008-CGND-HRA-02749-B

tag: age

tag: disease duration

tag: pmi

tag: phenotype


title: Zebra finch embryo 24 medial hypothalamus E13 heat call male

description:
Library name: sample_24
Medial coronal punch from E13 zebra finch embryo exposed to chronic heat call playback (E9–E12, 9h/day); male

tag: genotype


title: donor procurement biopsy [D083_P]

value: DBD - ECD

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: DIPG7_RNA_Combo_rep3

description:
Library name: DIPG7_RNA_Combo_rep3
120min.combo.C
DIPG7_total_tpm.csv
DIPG7_nascent_tpm.csv

tag: cell line

tag: treatment


title: donor procurement biopsy [D083_L]

tag: patient id


title: V008-CGND-HRA-02749-A

description: Library name: V008-CGND-HRA-02749-A

tag: sample id

tag: donor id

tag: Sex

value: Female


title: Zebra finch embryo 22 medial hypothalamus E13 heat call female

description:
Library name: sample_22
Medial coronal punch from E13 zebra finch embryo exposed to chronic heat call playback (E9–E12, 9h/day); female


title: DIPG7_RNA_Combo_rep2

description:
Library name: DIPG7_RNA_Combo_rep2
120min.combo.B
DIPG7_total_tpm.csv
DIPG7_nascent_tpm.csv

tag: cell type


title: V007-CGND-HRA-02752-D

description: Library name: V007-CGND-HRA-02752-D

tag: tissue

value: ALS


title: V007-CGND-HRA-02752-C

description: Library name: V007-CGND-HRA-02752-C

tag: age


title: donor procurement biopsy [D082_P]

tag: donor age

tag: donor category

tag: donor bmi

tag: donor biopsy ah


title: Zebra finch embryo 20 medial hypothalamus E13 heat call female

description:
Library name: sample_20
Medial coronal punch from E13 zebra finch embryo exposed to chronic heat call playback (E9–E12, 9h/day); female

value: hypothalamus

tag: genotype


title: DIPG7_RNA_JQ1_rep3

description:
Library name: DIPG7_RNA_JQ1_rep3
120min.jq1.C
DIPG7_total_tpm.csv
DIPG7_nascent_tpm.csv

value: JQ1 + 4SU


title: V009-CGND-HRA-02756-A

description: Library name: V009-CGND-HRA-02756-A

tag: disease duration

tag: pmi

tag: phenotype


title: V007-CGND-HRA-02746-B

description: Library name: V007-CGND-HRA-02746-B

value: ALSci


title: Zebra finch embryo 16 medial hypothalamus E13 heat call male

description:
Library name: sample_16
Medial coronal punch from E13 zebra finch embryo exposed to chronic heat call playback (E9–E12, 9h/day); male

value: male

value: wild type


title: donor procurement biopsy [D080_L]

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: DIPG7_RNA_JQ1_rep2

description:
Library name: DIPG7_RNA_JQ1_rep2
120min.jq1.B
DIPG7_total_tpm.csv
DIPG7_nascent_tpm.csv

tag: cell line

tag: treatment


title: donor procurement biopsy [D078_P]

tag: patient id


title: V007-CGND-HRA-02746-A

description: Library name: V007-CGND-HRA-02746-A

tag: tissue

tag: sample id

tag: donor id

tag: Sex


title: DIPG7_RNA_JQ1_rep1

description:
Library name: DIPG7_RNA_JQ1_rep1
120min.jq1.A
DIPG7_total_tpm.csv
DIPG7_nascent_tpm.csv

tag: cell type


title: Zebra finch embryo 15 medial hypothalamus E13 heat call female

description:
Library name: sample_15
Medial coronal punch from E13 zebra finch embryo exposed to chronic heat call playback (E9–E12, 9h/day); female

value: female

value: Heat call playback E9–E12


title: Zebra finch embryo 14 medial hypothalamus E13 control male

description:
Library name: sample_14
Medial coronal punch from E13 zebra finch embryo exposed to control call playback (E9–E12, 9h/day); male

value: Control call playback E9–E12


title: donor procurement biopsy [D077_P]

tag: donor age

tag: donor category

tag: donor bmi

tag: donor biopsy ah


title: V006-CGND-HRA-02750-D

description: Library name: V006-CGND-HRA-02750-D

tag: age

tag: disease duration

tag: pmi

tag: phenotype


title: V006-CGND-HRA-02750-C

description: Library name: V006-CGND-HRA-02750-C


title: Zebra finch embryo 21 medial hypothalamus E13 control male

description:
Library name: sample_21
Medial coronal punch from E13 zebra finch embryo exposed to control call playback (E9–E12, 9h/day); male

tag: genotype


title: DIPG7_RNA_Combo_rep1

description:
Library name: DIPG7_RNA_Combo_rep1
120min.combo.A
DIPG7_total_tpm.csv
DIPG7_nascent_tpm.csv

tag: cell line


title: DIPG7_RNA_CBL0137_rep2

description:
Library name: DIPG7_RNA_CBL0137_rep2
120min.cbl.B
DIPG7_total_tpm.csv
DIPG7_nascent_tpm.csv

tag: treatment


title: V006-CGND-HRA-02745-B

description: Library name: V006-CGND-HRA-02745-B


title: Zebra finch embryo 12 medial hypothalamus E13 control male

description:
Library name: sample_12
Medial coronal punch from E13 zebra finch embryo exposed to control call playback (E9–E12, 9h/day); male


title: DIPG7_RNA_CBL0137_rep3

description:
Library name: DIPG7_RNA_CBL0137_rep3
120min.cbl.C
DIPG7_total_tpm.csv
DIPG7_nascent_tpm.csv


title: donor procurement biopsy [D075_L]

tag: patient id

value: left kidney

value: DBD - SCD

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: donor procurement biopsy [D073_P]

tag: tissue


title: donor procurement biopsy [D072_L]

tag: donor age


title: DIPG7_RNA_CBL0137_rep1

description:
Library name: DIPG7_RNA_CBL0137_rep1
120min.cbl.A
DIPG7_total_tpm.csv
DIPG7_nascent_tpm.csv

tag: cell type


title: donor procurement biopsy [D073_L]

tag: donor category

tag: donor bmi


title: DIPG7_RNA_Veh_rep3

description:
Library name: DIPG7_RNA_Veh_rep3
120min.vehicle.C
DIPG7_total_tpm.csv
DIPG7_nascent_tpm.csv

value: DMSO + 4SU


title: Zebra finch embryo 10 medial hypothalamus E13 heat call female

description:
Library name: sample_10
Medial coronal punch from E13 zebra finch embryo exposed to chronic heat call playback (E9–E12, 9h/day); female

tag: Sex


title: V005-CGND-HRA-02754-D

description: Library name: V005-CGND-HRA-02754-D

tag: sample id

tag: donor id

value: Male

tag: age

value: Control


title: Zebra finch embryo 08 medial hypothalamus E13 heat call female

description:
Library name: sample_08
Medial coronal punch from E13 zebra finch embryo exposed to chronic heat call playback (E9–E12, 9h/day); female

tag: genotype


title: DIPG7_RNA_Veh_rep2

description:
Library name: DIPG7_RNA_Veh_rep2
120min.vehicle.B
DIPG7_total_tpm.csv
DIPG7_nascent_tpm.csv

value: Diffuse Midline Glioma

tag: cell line


title: DIPG7_RNA_Veh_rep1

description:
Library name: DIPG7_RNA_Veh_rep1
120min.vehicle.A
DIPG7_total_tpm.csv
DIPG7_nascent_tpm.csv

tag: treatment


title: donor procurement biopsy [D071_L]

tag: patient id

value: DBD - ECD

tag: donor biopsy ah


title: V005-CGND-HRA-02754-C

description: Library name: V005-CGND-HRA-02754-C

tag: pmi

tag: phenotype


title: DIPG7_RNA_Veh_no4su_rep3

description:
Library name: DIPG7_RNA_Veh_no4su_rep3
0min.vehicle.C
DIPG7_total_tpm.csv
DIPG7_nascent_tpm.csv

value: DMSO


title: Tet-TOR1 R2

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

country: Canada

institute: Universite de Montreal

description: Library name: Tet-TOR1 R2

data_processing:
Sequencing reads were filtered with fastp version 0.23.2
Sequences were trimmed to remove adapters using TRIMMOMATIC with options “TRAILING:30”. Filtered reads were mapped to the reference genome sequence of strain SC5314 with STAR version 2.7.9a
For RNA-seq, the number of reads mapping on each of the genes was calculated by featurecount version 2.0.1. Differential gene expression was calculated with DESeq2 version 1.26.0.
For the CheC-seq and MNase-seq experiment, reads were mapped to the C. albicans genome (Candida_albicans_SC5314 assembly 22) using Bowtie2 with “-q --phred33 --no-unal” options. Peaks were determined using MACS2 algorithm with options “-BAM -nomodel-extsize 200-keep-dup all.”.
Assembly: Reference genome of the C. albicans SC5314 strain assembly 22 were used (http://www.candidagenome.org).
Supplementary files format and content: RNA-seq processed data files contain the raw counts for each sequencing experiment.

organism: Candida albicans

source_name: Yeast cells

growth_protocol: For RNA-seq, MNase-seq and ChEC-seq experiments, overnight cultures were diluted to an OD600 of 0.1 in 100 ml of fresh SC medium, grown at 30˚C to logarithmic phase (OD600 of 0.6) under normoxia. Cells were then harvested by centrifugation, washed once with PBS, and resuspended in 400 μl of SC medium.

extract_protocol:
Total RNA was extracted using an RNAeasy purification kit (Qiagen) and glass bead lysis in a Biospec Mini 24 bead-beater. For ChEC-seq, DNA was purified using the MasterPure Yeast DNA Purification Kit (Epicentre) following the manufacturer’s instructions and resuspended in 50µl of 10 mM Tris-HCl buffer (pH 8.0). For MNase-seq, DNA was extracted using phenol-chloroform-isoamyl alcohol and precipited with sodium acetate and ethanol.
The NEBNext UltraTM II RNA Library Prep Kit for Illumina was used to construct the RNA-seq library. For the ChEC-seq and Mnase-seq, sequencing libraries were prepared using the KAPA HyperPrep Kits.

treatment_protocol: For RNA-seq, MNase-seq and ChEC-seq experiments, cultures were incubated at 30 °C with shaking at 220 rpm for 15 min in 6-well plates under hypoxic (5% O2) conditions using the Cytation 5 plate reader equipped with O2 and CO2 gas controllers. Cells were then centrifuged for 2 min at 3,500 rpm and pellets were rapidly frozen and stored at -80°C.

value: Yeast cells

value: 15 min under hypoxia (5% O2)


title: V006-CGND-HRA-02745-A

description: Library name: V006-CGND-HRA-02745-A

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

value: Female

tag: disease duration


title: donor procurement biopsy [D069_L]

tag: tissue

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: V004-CGND-HRA-02753-D

description: Library name: V004-CGND-HRA-02753-D

tag: Sex


title: DIPG7_RNA_Veh_no4su_rep2

description:
Library name: DIPG7_RNA_Veh_no4su_rep2
0min.vehicle.B
DIPG7_total_tpm.csv
DIPG7_nascent_tpm.csv

tag: cell type


title: donor procurement biopsy [D068_P]

value: right kidney

tag: donor age

tag: donor category

tag: donor bmi


title: V005-CGND-HRA-02751-A

description: Library name: V005-CGND-HRA-02751-A

tag: sample id

tag: donor id

tag: age

value: ALS


title: donor procurement biopsy [D070_P]

tag: patient id

tag: donor biopsy ah


title: Tet-TOR1 R1

description: Library name: Tet-TOR1 R1

tag: cell line

tag: genotype

tag: treatment


title: donor procurement biopsy [D071_P]

tag: tissue

tag: donor hypertension


title: V004-CGND-HRA-02748-B

description: Library name: V004-CGND-HRA-02748-B

tag: disease duration

tag: pmi

tag: phenotype


title: V004-CGND-HRA-02753-C

description: Library name: V004-CGND-HRA-02753-C

tag: Sex


title: Zebra finch embryo 13 medial hypothalamus E13 control male

description:
Library name: sample_13
Medial coronal punch from E13 zebra finch embryo exposed to control call playback (E9–E12, 9h/day); male

value: hypothalamus

value: male

value: wild type


title: PDX305_Vacto 1uM_3

city: Seattle

first: Emma

last: Wrenn

state: WA

address: 1920 Terry Ave

institute: Seattle Children's Research Institute

description: Library name: E48

data_processing:
Fastq file quality scored by FASTQC 0.11.9
Reads trimmed using Trimgalore 0.6.7
Reads aligned with STAR Align 2.7.10a
Duplicates marked with Picard markduplicates 3.0.0
rlog normalized counts generated in DESeq2 (v1.44.0) from STAR raw counts matrix
Assembly: GRCh38
Supplementary files format and content: TC71_A673_CHLA10_PDX305_rld.csv contains an rlog normalized counts matrix of ENSEMBL gene IDs (rows) by library name (columns). See https://github.com/LawlorLab/ for code used to generate raw and normalized counts.

source_name: cell line

growth_protocol: TC71 and A673 cell lines grown in RPMI1640 + 10% FBS + 2mM L-glutamine, CHLA10 and PDX305 cells grown in IMDM + 20% FBS + 2 mM L-glutamine + 1X ITS-X

extract_protocol:
Total RNA was collected using a Qiagen RNEasy kit
mRNA library (polyA enrichment) preparation was performed by Novogene prior to sequencing on a NovaSeq X Plus (paired end 150 bp reads, 6B data per sample)

treatment_protocol: 100,000 cells were plated in 12wp, 24 hours later they were were treated with TGFβ1 (10 ng/mL), TGFβ2 (10 ng/mL), vactosertib (1uM), or vehicle controls. 24hrs after treatment total RNA was collected using Quiagen RNEasy kit.

value: cell line

tag: cell type

value: Ewing sarcoma cell line

value: 1 uM vactosertib

tag: batch


title: Tet-INO80+doxycycline R1

description: Library name: Tet-INO80+doxycycline R1


title: Tet-TOR1+doxycycline R2

description: Library name: Tet-TOR1+doxycycline R2


title: PDX305_TGFB2_3

description: Library name: E47

value: 10 ng per mL human TGFB2


title: V005-CGND-HRA-02751-B

description: Library name: V005-CGND-HRA-02751-B

value: Male


title: Tet-TOR1+doxycycline R1

description: Library name: Tet-TOR1+doxycycline R1


title: donor procurement biopsy [D067_L]

source_name: kidney biopsy

value: left kidney

tag: donor age

tag: donor category

value: DBD - SCD

tag: donor bmi

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: donor procurement biopsy [D065_L]

tag: patient id

value: DBD - ECD

tag: donor biopsy ah


title: V004-CGND-HRA-02748-A

description: Library name: V004-CGND-HRA-02748-A

tag: sample id

tag: donor id

tag: age


title: Tet-INO80+doxycycline R2

description: Library name: Tet-INO80+doxycycline R2

tag: tissue

tag: cell line

tag: genotype

tag: treatment


title: donor procurement biopsy [D064_L]

tag: donor hypertension


title: PDX305_TGFB1_3

description: Library name: E46

tag: cell type

value: 10 ng per mL human TGFB1

tag: batch


title: V003-CGND-HRA-02747-D

description: Library name: V003-CGND-HRA-02747-D

tag: Sex

tag: disease duration

tag: pmi

tag: phenotype


title: DIPG7_RNA_Veh_no4su_rep1

description:
Library name: DIPG7_RNA_Veh_no4su_rep1
0min.vehicle.A
DIPG7_total_tpm.csv
DIPG7_nascent_tpm.csv

value: Diffuse Midline Glioma

value: DMSO


title: donor procurement biopsy [D063_P]

tag: donor age

tag: donor category

tag: donor bmi

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: PDX305_Vacto 1uM_2

description: Library name: E44

tag: tissue


title: V003-CGND-HRA-02744-B

description: Library name: V003-CGND-HRA-02744-B

tag: sample id

tag: donor id

tag: age

value: ALSci


title: WT_Ino80-MNase R1

description: Library name: WT_Ino80-MNase R1

data_processing:
Sequencing reads were filtered with fastp version 0.23.2
Sequences were trimmed to remove adapters using TRIMMOMATIC with options “TRAILING:30”. Filtered reads were mapped to the reference genome sequence of strain SC5314 with STAR version 2.7.9a
For RNA-seq, the number of reads mapping on each of the genes was calculated by featurecount version 2.0.1. Differential gene expression was calculated with DESeq2 version 1.26.0.
For the CheC-seq and MNase-seq experiment, reads were mapped to the C. albicans genome (Candida_albicans_SC5314 assembly 22) using Bowtie2 with “-q --phred33 --no-unal” options. Peaks were determined using MACS2 algorithm with options “-BAM -nomodel-extsize 200-keep-dup all.”.
Assembly: Reference genome of the C. albicans SC5314 strain assembly 22 were used (http://www.candidagenome.org).
Supplementary files format and content: RNA-seq processed data files contain the raw counts for each sequencing experiment.
Library strategy: ChEC-seq

value: Yeast cells

tag: cell line

tag: genotype

value: SN148- INO80/INO80::Mnase

tag: treatment

value: 15 min under hypoxia (5% O2)


title: PDX305_TGFB2_2

description: Library name: E43

tag: cell type

tag: batch


title: donor procurement biopsy [D063_L]

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

tag: patient id

tag: donor hypertension

tag: donor biopsy ah


title: SN148-Cip-Act_Mnase-free R2

description: Library name: WT_Mnase-free R2


title: V003-CGND-HRA-02744-A

description: Library name: V003-CGND-HRA-02744-A

tag: Sex

tag: disease duration

tag: pmi

tag: phenotype


title: donor procurement biopsy [D061_L]

tag: donor age

tag: donor category

tag: donor bmi

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: Tet-INO80 R1

description: Library name: Tet-INO80 R1

tag: tissue

tag: cell line

tag: genotype

value: 15 min under normoxia (21% O2)


title: PDX305_veh_2

description: Library name: E41

tag: cell type

tag: treatment

value: vehicle

tag: batch


title: Tet-INO80 R2

description: Library name: Tet-INO80 R2


title: SN148-Cip-Act_Mnase-free R1

description: Library name: WT_Mnase-free R1


title: CU034-U54-HRA-058-B

description: Library name: CU034-U54-HRA-058-B

tag: sample id

tag: donor id

value: Female

tag: age

value: Control


title: WT_NRMX_R2

description: Library name: WT_NRMX_R2

value: WT


title: PDX305_TGFB1_2

description: Library name: E42

value: cell line

value: Ewing sarcoma cell line


title: PDX305_veh_3

description: Library name: E45


title: PDX305_Vacto 1uM_1

description: Library name: E40

value: 1 uM vactosertib


title: WT_NRMX_R1

description: Library name: WT_NRMX_R1


title: V003-CGND-HRA-02747-C

description: Library name: V003-CGND-HRA-02747-C

tag: Sex

value: Male

tag: disease duration

tag: pmi

value: ALS


title: donor procurement biopsy [D059_P]

tag: patient id

value: right kidney

tag: donor age

tag: donor category

value: DBD - SCD

tag: donor hypertension

tag: donor biopsy ah


title: WT_Ino80-MNase R2

description: Library name: WT_Ino80-MNase R2

tag: tissue


title: donor procurement biopsy [D060_L]

value: left kidney

tag: donor bmi

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: CU033-U54-HRA-058-B

description: Library name: CU033-U54-HRA-058-B

tag: phenotype


title: donor procurement biopsy [D058_P]

value: DBD - ECD


title: donor procurement biopsy [D059_L]


title: PDX305_TGFB2_1

description: Library name: E39

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: 10 ng per mL human TGFB2

tag: batch


title: PDX305_TGFB1_1

description: Library name: E38

value: 10 ng per mL human TGFB1


title: ino80_HPX_R1

description: Library name: ino80_HPX_R1

value: Yeast cells

value: 15 min under hypoxia (5% O2)


title: CU034-U54-HRA-058-A

description: Library name: CU034-U54-HRA-058-A

tag: sample id

tag: donor id

tag: Sex

tag: age

tag: pmi


title: CU031-U54-HRA-059-B

description: Library name: CU031-U54-HRA-059-B


title: PDX305_veh_1

description: Library name: E37

value: vehicle


title: CU031-U54-HRA-059-A

description: Library name: CU031-U54-HRA-059-A

value: Female


title: donor procurement biopsy [D057_P]

tag: patient id

tag: donor age

tag: donor category

tag: donor hypertension

tag: donor biopsy ah


title: WT_HPX_R1

description: Library name: WT_HPX_R1

tag: tissue


title: CU030-U54-HRA-059-B

description: Library name: CU030-U54-HRA-059-B

tag: phenotype

value: Control


title: CHLA10_TGFB2_3

description: Library name: E35

tag: cell line


title: CU030-U54-HRA-059-A

description: Library name: CU030-U54-HRA-059-A


title: CHLA10_Vacto 1uM_3

description: Library name: E36

tag: cell type


title: CU023-U54-HRA-003-B

description: Library name: CU023-U54-HRA-003-B


title: CHLA10_TGFB1_3

description: Library name: E34

tag: genotype


title: donor procurement biopsy [D055_L]

tag: donor bmi

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: donor procurement biopsy [D058_L]


title: CU033-U54-HRA-058-A

description: Library name: CU033-U54-HRA-058-A

tag: sample id

tag: donor id

tag: Sex


title: ino80_HPX_R2

description: Library name: ino80_HPX_R2

tag: treatment


title: donor procurement biopsy [D054_P]

tag: patient id

tag: donor age


title: donor procurement biopsy [D057_L]

tag: donor category

tag: donor hypertension


title: donor procurement biopsy [D054_L]

tag: tissue

tag: donor biopsy ah


title: CU023-U54-HRA-003-A

description: Library name: CU023-U54-HRA-003-A

tag: age

tag: pmi

tag: phenotype


title: Combo

description: Multimodal Cell Segmentation

hyb_protocol: Priming oligos were hybridized to the target RNA, followed by site-specific cleavage using RNase treatment to release the RNA strand from the hybridized oligo. The 5000-gene panel was then added to the sections to hybridize with the RNA, followed by ligation to generate circular DNA probes, which were subsequently amplified via rolling circle amplification.

scan_protocol: Xenium In Situ Analyzer

data_processing: Xenium output from the four treatment conditions were merged into a single Seurat object (Seurat v5.2.1). Cells with transcript counts <10 and above the 98th percentile were filtered, and data were normalized with the median transcript count.  The Seurat object was down sampled (25,000 cells per sample) using SketchData and LeverageScore to retain rare cell populations for subsequent scaling and clustering. From the subsetted data, variable features (n = 2000 genes) were identified using FindVariableFeatures, data were scaled using ScaleData and Dimensionality reduction performed using RunPCA. Batch correction was performed using Harmony Integration, followed by UMAP projection and clustering in Harmony space. Clustering was then projected to all cells.

label: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel

source_name: mouse brain, CBL0137 and JQ1 treated

growth_protocol: 5-7 weeks old female C57BL6 mice were intracranially injected into the brainstem with IUE 24B7 cells that harbor H3.3K27M mutation generated in (doi: 10.1093/neuonc/noz197 and 10.1093/noajnl/vdac079). The timing of treatment initiation was 18 days post intracranial surgery.

extract_protocol: Brain samples were collected on the final day of treatment and fixed in a 10% formalin neutral buffered solution then embedded in paraffin wax (FFPE)

treatment_protocol: The drug treatments were as follows: CBL0137 - dissolved in 5% dextrose, CBL0137 was administered intravenously at a dosage of 40 mg/kg/day. The treatment was given once every four days for a total of three weeks. JQ1 - dissolved in DMSO and subsequently in a solution containing 0.9% saline with 5% PEG400 and 5% TWEEN-80, JQ1 was administered at a dosage of 50 mg/kg/day intraperitoneally. The treatment was given five days a week over three weeks.

value: 5-7 weeks

tag: gender

tag: strain

tag: glioma cell line


title: WT_HPX_R2

description: Library name: WT_HPX_R2

tag: cell line

tag: cell type

tag: genotype

value: WT


title: CU022-U54-HRA-003-B

description: Library name: CU022-U54-HRA-003-B

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


title: CHLA10_Vacto 1uM_2

description: Library name: E32

value: cell line

value: Ewing sarcoma cell line

tag: treatment

tag: batch


title: JQ1

description: Multimodal Cell Segmentation

source_name: mouse brain, JQ1 treated

label_protocol: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel


title: CHLA10_TGFB2_2

description: Library name: E31


title: CBL0137

description: Multimodal Cell Segmentation

source_name: mouse brain, CBL0137 treated


title: CHLA10_TGFB1_2

description: Library name: E30


title: CHLA10_veh_3

description: Library name: E33


title: CU022-U54-HRA-003-A

description: Library name: CU022-U54-HRA-003-A

value: Male


title: donor procurement biopsy [D053_P]

tag: patient id

tag: donor age

tag: donor category

tag: donor bmi

tag: donor hypertension

tag: donor biopsy cv

tag: donor biopsy ct

tag: donor biopsy ci


title: NCI-H889 si-NC

city: Toyoake

first: Kouhei

last: Sakurai

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Department of Joint Research Laboratory of Clinical Medicine, School of Medicine

country: Japan

institute: Fujita Health University

hyb_protocol: 2.3 ug fragmented and labeled cDNA was hybridized for 16 h at 45 °C on Human Clariom S Array. The GeneChip was washd using the GeneChip Fluidics Station 450.

scan_protocol: The GeneChip was scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were processed with SST-RMA using the Transcriptome Analysis Console (TAC) software.

label_protocol: Biotinylated cDNA was prepared according to the protocol starting from 250 ng of total RNA using the GeneChip WT PLUS Reagent Kit.

growth_protocol: NCI-H889 cells were cultured in RPMI medium containing 10% fetal calf serum.

extract_protocol: Total RNA was isolated using NucleoSpin RNA reagent according to the manufacturer's instruction.

treatment_protocol: NCI-H889 cells were transfected with si-NC or si-BAF53B, and incubated for 72 h.

value: small cell lung cancer cell


title: Colonoid line #11 hypoxia

city: Baltimore

first: Maged

last: Zeineldin

state: MD

address: 1812 Ashland Ave

institute: Johns Hopkins University School of Medicine

description:
Library name: H11_PH
Column name in colonoid_hypoxia_gene_count.txt: H11_PH

data_processing:
FastQC software was used to exclude low-quality reads
Mapping HISAT2 software (version 2.0.5)
Counted and normalized as FPKM using featureCounts (version 1.5.0-p3)
Differentially expressed genes (DEG) were generated using DESeq2 (version 1.20.0) and edgeR (version 3.22.5)
Assembly: hg19
Supplementary files format and content: Tab delimited text file includeing raw counts for every sample

source_name: Colon

growth_protocol: Colonoids grow in organoid medium, no medium change for the organoids in hypoxia and normoxia for one week

extract_protocol:
Rna extraction was done using Trizol Reagent manufacturer’s protocol, 500-ng were used for library prep
PolyA enrichment library prep was done by Novogene

treatment_protocol: Colonoids grow either in abient oxygen concentration or at 0.2% oxygen for one week no medium change

tag: tissue

value: Colon

value: Organoids

value: Epithelial cells

value: hypoxia


title: donor procurement biopsy [D053_L]

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

value: left kidney

value: DBD - ECD

tag: donor biopsy ah


title: NCI-H889 si-BAF53B

tag: cell type


title: CHLA10_Vacto 1uM_1

description: Library name: E28

tag: cell line

tag: genotype

value: 1 uM vactosertib


title: donor procurement biopsy [D051_L]


title: Colonoid line #4 hypoxia

description:
Library name: H4_DH
Column name in colonoid_hypoxia_gene_count.txt: H4_DH


title: CHLA10_veh_2

description: Library name: E29


title: donor procurement biopsy [D052_P]

value: right kidney


title: 5d_S22_Fetal-Brain_Multi-Pathogen-Free_Male

city: Columbia

first: Trupti

last: Joshi

state: Missouri

address: 103 Math Science Building

department: Department of Biomedical Informatics, Biostatistics and Medical Epidemiology (BBME)

institute: University of Missouri-Columbia

description: Library name: 5d_S22

data_processing:
The trimmed sequence reads ere mapped to GRCm39 using Hisat2
fpkm files are estimted using cufflinks
Assembly: mm39
Supplementary files format and content: gene_fpkm

source_name: Fetal-Brain

extract_protocol:
Total RNA was extracted by using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit (Cat. No. 80224; Qiagen, MD, USA) in accordance with the manufacturer’s protocol.
Libraries were constructed following the manufacturer’s protocol with reagents supplied in the Illumina mRNA Stranded Library Preparation Kit and sequenced at the University of Missouri Genomics Technology Core.

value: Fetal-Brain

value: Multi-Pathogen-Free


title: donor procurement biopsy [D050_P]


title: donor procurement biopsy [D064_P]

value: DBD - SCD


title: donor procurement biopsy [D049_P]


title: Colonoid line #12 hypoxia

description:
Library name: H12_DH
Column name in colonoid_hypoxia_gene_count.txt: H12_DH


title: donor procurement biopsy [D050_L]


title: Colonoid line #12 normoxia

description:
Library name: H12_DN
Column name in colonoid_hypoxia_gene_count.txt: H12_DN

value: Normoxia


title: Vehicle

description: Multimodal Cell Segmentation

source_name: mouse brain, vehicle treated

tag: age

value: 5-7 weeks

tag: gender

value: Female

tag: strain

tag: glioma cell line

value: Vehicle (0.9% saline, 5% PEG400 and 5% TWEEN-80)


title: 4c_S5_Placenta_Multi-Pathogen-Free_Female

description: Library name: 4c_S5

source_name: Placenta

value: Placenta

tag: treatment


title: CHLA10_TGFB1_1

description: Library name: E26

value: cell line

value: Ewing sarcoma cell line

value: 10 ng per mL human TGFB1

tag: batch


title: Colonoid line #11 normoxia

description:
Library name: H11_PN
Column name in colonoid_hypoxia_gene_count.txt: H11_PN

value: Colon

value: Organoids

value: Epithelial cells

value: WT


title: 41d_S20_Fetal-Brain_Germ-Free_Male

description: Library name: 41d_S20

value: Male

value: Germ-Free


title: CHLA10_veh_1

description: Library name: E25

value: vehicle


title: Colonoid line #4 normoxia

description:
Library name: H4_DN
Column name in colonoid_hypoxia_gene_count.txt: H4_DN


title: Colonoid line #3 hypoxia

description:
Library name: H3_PH
Column name in colonoid_hypoxia_gene_count.txt: H3_PH

value: hypoxia


title: CHLA10_TGFB2_1

description: Library name: E27

value: 10 ng per mL human TGFB2


title: A673_Vacto 1uM_3

description: Library name: E24

value: 1 uM vactosertib


title: 5c_S11_Placenta_Multi-Pathogen-Free_Male

description: Library name: 5c_S11

value: Multi-Pathogen-Free


title: A673_TGFB2_3

description: Library name: E23


title: 3c_S4_Placenta_Multi-Pathogen-Free_Female

description: Library name: 3c_S4

value: Female


title: Colonoid line #3 normoxia

description:
Library name: H3_PN
Column name in colonoid_hypoxia_gene_count.txt: H3_PN

value: Normoxia


title: 39c_S9_Placenta_Germ-Free_Male

description: Library name: 39c_S9

value: Placenta


title: NELFC-AID-Auxin-ELOA-KO_rep2_SR

description:
Library name: Sample58
isoformMetadata.csv

data_processing:
Circular consensus sequences (CCS) from the Revio system were demultiplexed using lima with --hifi-preset SYMMETRIC option. Then Reverse transcription primer sequence flanking the mRNA sequences was removed using lima with --isoseq and --peek-guess to generate full-length reads. Concatemers and polyA tails were removed using isoseq3 refine with --require-polya to generate full-length non-concatemer reads. Full-length non-concatemer reads were merged using pbmerge, grouped into read cluster by hierarchical clustering using isoseq cluster2, aligned to genome using pbmm2 align, collapsed using isoseq3 collapse, and classified using SQANTI3. Short-read data were processed using kallisto bus. Short-read and long-read data were processed through standard MPAQT pipeline.
Assembly: hg38
Supplementary files format and content: isoformMetadata.csv is a dataframe containing the definition for each isoform in the transcriptome of this study, including the associated genes, associated transcripts, and SQANTI3 defined structural categories. MPAQT.(LR_)SR.tsv files for each sample contains the corrected TPMs of these isoforms in each sample.

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen, #74106) as per manufacturer’s instructions.
Long read RNA-seq libraries were prepared using NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification Module, Iso-Seq Express oligo kit, and SMRTbell® prep kit 3.0 per manufacturer’s instructions. Library quality was assessed on Agilent Femto Pulse before the libraries were loaded onto a Revio or Sequel II flow cell. Short read RNA-seq libaries were prepared using Takara Bio SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian kit (Cat.# 634485) per maufacturer's instructions. Library quality was assessed on Agilent DNA ScreenTape.

value: sgELOA

value: Auxin 6hr


title: A673_TGFB1_3

description: Library name: E22

value: cell line

value: Ewing sarcoma cell line

value: 10 ng per mL human TGFB1


title: donor procurement biopsy [D046_L]

tag: patient id

value: left kidney

tag: donor age

tag: donor category

value: DBD - ECD