title: DSP-1001660014616-A-B02

value: BCM-August

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: %laa950 whole.lung

tag: %laa950 lobe

tag: condition

value: copd

tag: roi

value: oct


title: C6-SF18103133-96h

status: Public on Nov 21 2023

type: SRA

city: Nashville

first: Taha

last: Jan

state: TN

address: 2220 Pierce Ave, PRB 752

department: Otolaryngology

country: USA

institute: VUMC

library_source: transcriptomic single cell

data_processing:
Illumina NextGen Sequencing
demultiplexing
STAR alignment v2.5.3a
read quantification: RSEM v1.3.0
Assembly: galGal6
Supplementary files format and content: RDS file with metadata, counts, normcounts, and logcounts in SingleCellExperiment object format for R

molecule: total RNA

organism: Gallus gallus

source_name: basilar papilla

extract_protocol:
FACS sorted into 96-well plates containing RNA lysis buffer
smartseq2

treatment_protocol: in vivo administration of sisomicin with harvesting of cells at indicated timepoints

tag: tissue

value: basilar papilla

tag: treatment


title: Fpt1-TAP ChIP-exo 5.0 NKI5632-1 Replicate 1

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

library_source: genomic

data_processing:
High-throughput DNA sequencing in paired-end mode was performed with Illumina NextSeq 500.
Sequence reads were aligned to the yeast genome (sacCer3) using bwa-mem (v0.7.9a). Reference: https://arxiv.org/pdf/1303.3997.pdf
Aligned reads obtained were filtered to remove PCR duplicates and non-unique alignments.
Assembly: sacCer3
Supplementary files format and content: Bedgraph, de-duplicated BAM files aligned to sacCer3
Library strategy: ChIP-exo

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Fpt1-TAP yeast

growth_protocol: Yeast strains were grown to an O.D600 of ~0.8 at 25°C.

extract_protocol:
Cells were crosslinked with formaldehyde to a final concentration of 1.0%. Lysates were clarified from sonicated nuclei and protein-DNA complexes were purified using appropriate antibody.
Libraries were prepared as described in PMID: 33692541
ChIP-exo 5.0

tag: strain

tag: chip antibody

value: IgG (Sigma i5006, Lot#SLBM2617V)

tag: cell type

value: Fpt1-TAP yeast

tag: genotype

value: MATa his3d1 leu2d0 ura3d0 met15d0 YKR011C-TAP-KanMX


title: iPSC-derived neurons (Subject #3, Clone #1), NDC

city: La Jolla

first: Shankar

last: Subramaniam

state: CA

address: 9500 Gilman Drive

department: Department of Bioengineering

institute: University of California, San Diego

library_source: transcriptomic

data_processing:
Preprocessing of both paired-end and single-end RNA-seq data was conducted using the Trimgalore! package v0.6.4 by removing adapters and low quality reads using CutAdapt v1.18.
Trimmed RNA-seq reads were then mapped to the GRCh38.104 human transcriptome using Kallisto v0.46.1 with the following options: -bias -rf-stranded -b 100 for the paired-end RNA-seq data
Transcript abundances from Kallisto were imported and summarized to the gene level using tximport v1.22.0.
A DGEList object was created from gene-level read counts using the DGEList function from edgeR v3.36.0.
Lowly expressed genes were filtered out using filterByExpr function in edgeR.
Then gene-level counts were normalized using the weighted mean trimmed of M values (TMM) in the calcNormFactors R package
Assembly: GRCh38.104 human transcriptome
Supplementary files format and content: comma-separated value (.csv) file includes unfiltered, raw counts matrix for all samples

organism: Homo sapiens

source_name: skin

growth_protocol: Patient and subject fibroblasts that were grown on a Trevigen Reduced Growth Factor Basement Membrane Extract (Trevigen Cat. No. 3433-005-01) with Stem Cell mTeSR-1 media (STEMCELL Technologies Cat. No. 05851) were then reprogrammed into iPSCs using Sendai Virus at the Salk Institute. Direct differentiation of iPSCs to a population of neurons was performed as previously described. Briefly, iPSCs were differentiated into neurons using two stages: First, iPSCs were differentiated into pluripotent neuronal cells (NPCs) using dual Suppressor of Mothers Against Decapentaplegic (SMAD) inhibitors SB431542 (StemRD No. 50176030; Final concentration = 10 uM), LDN193189 (BioVision No. 1995-5; Final concentration = 0.5 uM), and the recombinant protein Noggin (R&D Systems No. 1967-NG/CF; Final concentration = 0.5 ug/ml)) in 500ml of Neural Maintenance Media (NMM) based on previous methods. Next, NPCs were differentiated into mixed neuronal cell populations by basic-Fibroblast Growth Factor (bFGF) (Millipore Cat. No. GF003AF; Final concentration = 20 ng/ml) withdrawal for 3-4 weeks.

extract_protocol:
Total RNA was extracted from previously-harvested EOAD and NDC frozen neuron pellets (replicates, n=3) with cell counts ranging from 500,000 – 2 million cells using the RNeasy Plus Micro Kit protocol (Qiagen, catalog no. 74034) as previously described. Concentrations of total RNA were determined using the Nanodrop 2000c according to the manufacturer’s guidelines. QC measurements were performed at the UC San Diego IGM sequencing core to evaluate the RNA Integrity Numbers (RIN) using TapeStation (Agilent Technologies), which ranged from 7.8-9.8.
Libraries were generated for RNA-seq using the Illumina Ribo-Zero Plus rRNA Depletion kit with IDT for Illumina RNA UD Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions. Resulting libraries were multiplexed and sequenced on an Illumina NovaSeq 6000 generating paired-end, 100-bp (PE100) to a depth of approximately 25 million reads per sample at the UC San Diego IGM sequencing core. In addition, samples were demultiplexed using the bcl2fastq v.2.20 Conversion Software (Illumina, San Diego, CA).

value: skin

value: induced pluripotent stem cells

value: Non-demented control (NDC)

tag: age at_onset

tag: age at_skin_biopsy

tag: Sex

value: Female

tag: clinical diagnosis

tag: mri or_other_imaging

value: Negative amyloid PET scan (2019)

tag: csf biomarkers_for_ad

value: Low A-beta42, normal tau and P-tau (2014)

tag: cognition at_time_of_skin_biopsy

value: Normal

tag: apoe status

tag: rna rin_score

value: SMAD inhibition and bFGF withdrawal


title: Fpt1-TAP ChIP-exo 5.0 NKI5623 Replicate 1

value: MATalpha can1d::HphMX lyp1d::STE3pr-LEU his3d1 leu2d0 ura3d0 met15d0 Ykr011c-TAP-His3MX6


title: C5-SF18103138-96h


title: C5-SF18103137-96h


title: iPSC-derived neurons (Subject #2, Clone #2), NDC

value: Negative (2013)


title: iPSC-derived neurons (Subject #2, Clone #3), NDC


title: section E 1K cells rep 3

city: Vestec by Prague

first: Radek

last: Sindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

description: Sample 60

data_processing:
Low quality reads and adaptor sequences were removed using Trimmomatic PE (v. 0.36) . Ribosomal RNA sequences were removed using sortmerna (v. 2.1b) and the SILVA rRNA database (version 119). The A. mexicanum reads were then pseudo-aligned to the A. mexicanum transcriptome AmexT_v34 using kallisto (v. 0.43.1).
Normalized number of reads was generated using DESeq2.
Raw counts were initially filtered to keep transcripts with counts greater than 30 in at least one sample.
Assembly: A. mexicanum transcriptome AmexT_v34 (Axolotl-omics, 2018)
Supplementary files format and content: Excel files include non-normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column. "amexicanum_non_normalized.xlsx" contains the non-normalized reads while "amexicanum_altered_magnitudes_per_section_and_stage_normalized.xlsx" contains the normalized reads for all samples (all stage sections). "amexicanum_total_altered_counts_per_stage_non_normalized.xlsx" contains the non-normalized reads while "amexicanum_total_altered_counts_per_stage_normalized.xlsx" the normalized reads for the total transcripts within the whole stage. "amexicanum_alteration_between_the_sections_at_1cell_stage_normalized.xlsx", "amexicanum_alteration_between_the_sections_at_4cells_stage_normalized.xlsx", "amexicanum_alteration_between_the_sections_at_64cells_stage_normalized.xlsx", and "amexicanum_alteration_between_the_sections_at_1kcells_stage_normalized.xlsx" contain the normalized reads at a given stage. “ortholog_analysis_human_gene_symbols.xlsx” contains the most probable human gene symbols for the A. mexicanum transcripts based on gene symbol comparison and also similarity of the protein sequences to those from the human genome.

organism: Ambystoma mexicanum

source_name: 1000-cells stage

extract_protocol:
The samples were homogenized in 300 μl of TRIReagent® (Sigma-Aldrich, USA) and total RNA was extracted according to the manufacturer’s protocol. LiCl precipitation was performed to remove inhibitors present in the yolky vegetal hemisphere. The concentration of RNA was measured using NanoDrop-2000 (ThermoFisher, USA) and sample quality was assessed using 5200 Fragment Analyzer (Agilent, USA).
Libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, USA). 100 ng of a total RNA was used for library preparation. Ribosomal RNA depletion was performed using Ribocop rRNA Depletion Kit V1.3 (Lexogen, Austria).

tag: section

value: E

tag: biological replicate


title: C5-SF18103134-96h

tag: tissue


title: C5-SF18103133-96h

tag: treatment


title: iPSC-derived neurons (Subject #3, Clone #2), NDC


title: iPSC-derived neurons (Subject #2, Clone #1), NDC


title: C4-SF19013101-96h


title: iPSC-derived neurons (Subject #1, Clone #2), NDC

value: Negative (2011)


title: section A 1K cells rep 3

description: Sample 56

value: A


title: DSP-1001660014616-A-E11

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Fastq files were automatically generated with the Illumina BaseSpace Sequence Hub
Supplementary files format and content: Digital count conversion (.dcc) files produced from fastq files using the GeoMx NGS Pipeline 2.3.3.10 desktop application.

source_name: lung: lymphoid follicle

extract_protocol:
Default Nanostring GeoMx extraction protocol
Default Nanostring GeoMx library consruction protocol

value: lung

value: lymphoid follicle

tag: slide name

tag: processing date

value: BCM-August

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: patient

tag: %laa950 whole.lung

tag: %laa950 lobe

tag: condition

value: copd

tag: roi

tag: scan name

value: paraffin


title: C4-SF18103138-96h

value: basilar papilla


title: iPSC-derived neurons (Subject #1, Clone #3), NDC

value: skin

tag: cell type

value: induced pluripotent stem cells

tag: genotype

value: Non-demented control (NDC)

tag: age at_onset

tag: age at_skin_biopsy

tag: Sex

value: Female

tag: clinical diagnosis

tag: mri or_other_imaging

tag: csf biomarkers_for_ad


title: section D 1K cells rep 2

description: Sample 54

tag: section

value: D

tag: biological replicate


title: Fpt1-TAP ChIP-exo 5.0 NKI5623 Replicate 2

tag: strain

tag: chip antibody

value: IgG (Sigma i5006, Lot#SLBM2617V)

value: Fpt1-TAP yeast

value: MATalpha can1d::HphMX lyp1d::STE3pr-LEU his3d1 leu2d0 ura3d0 met15d0 Ykr011c-TAP-His3MX6


title: section B 1K cells rep 3

description: Sample 57

value: B


title: C4-SF18103134-96h

tag: tissue

tag: treatment


title: section C 1K cells rep 2

description: Sample 53

value: C


title: C4-SF18103137-96h


title: 3_8_119095_N2_Day-7_CSE-3%

city: San Diego

first: John

last: Walker

address: 10675 John Jay Hopkins Dr

institute: NIBR

data_processing:
Reads were generated from a NovaSeq instrument with bcl2fastq from Illumina, v 2.20.0.422-2 and were aligned to a combined human/mouse genome provided by 10xGenomics, version 2020-A with STAR aligner v2.7.3a
Gene counts were assessed with RSEM v1.3
Differential gene expression was assessed with DESeq2 v.1.28.0, in R version 4.0 (25)
Assembly: combined human/mouse genome provided by 10xGenomics, version 2020-A
Supplementary files format and content: a single Excel file includes DESEQ2-derived expression values for each Sample

source_name: HBEC

growth_protocol: Bronchospheres were differentiated in 384-well plates on 50% Matrigel for two weeks, after which they were exposed to cigarette smoke extract (CSE) at the indicated percentages (diluted in HBEC differentiation media) for 7, 14, and 21 Days. Then they were lysed directly in the plate with Qiagen buffer RLT

extract_protocol:
RNA was isolated from cell lysis using Qiagen RNEasy kit
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Prep Kit (Illumina 20020595) following manufacturer's protocols.

tag: cell line

value: HBEC

value: Human Bronchial Epithelial Cells

value: cigarette smoke extract 3%

tag: time (days)


title: section C 1K cells rep 3

description: Sample 58


title: 3_9_119095_N2_Day-14_CSE-0%

value: cigarette smoke extract 0%


title: iPSC-derived neurons (Subject #1, Clone #1), NDC

value: Negative (2011)

tag: cognition at_time_of_skin_biopsy

value: Normal

tag: apoe status

tag: rna rin_score

value: SMAD inhibition and bFGF withdrawal


title: section B 1K cells rep 2

description: Sample 52

tag: cell type


title: 3_7_119095_N2_Day-7_CSE-0%


title: section D 1K cells rep 3

description: Sample 59


title: C3-SF19013101-96h

value: basilar papilla


title: 3_6_119095_N1_Day-21_CSE-3%


title: section A 1K cells rep 2

description: Sample 51

value: A


title: section E 1K cells rep 2

description: Sample 55

value: E


title: C3-SF18103138-96h


title: 3_4_119095_N1_Day-14_CSE-3%


title: C4-SF18103133-96h


title: section E 1K cells rep 1

description: Sample 50


title: 3_5_119095_N1_Day-21_CSE-0%


title: C3-SF18103134-96h


title: C2-SF19013101-96h


title: C3-SF18103137-96h


title: section D 1K cells rep 1

description: Sample 49


title: 3_3_119095_N1_Day-14_CSE-0%


title: section A 1K cells rep 1

description: Sample 46


title: 3_18_119095_N3_Day-21_CSE-3%


title: 3_17_119095_N3_Day-21_CSE-0%


title: section C 1K cells rep 1

description: Sample 48


title: section E 64 cells rep 3

description: Sample 45

source_name: 64-cells stage


title: 3_2_119095_N1_Day-7_CSE-3%


title: section D 64 cells rep 3

description: Sample 44


title: 3_16_119095_N3_Day-14_CSE-3%


title: section B 1K cells rep 1

description: Sample 47


title: section C 64 cells rep 3

description: Sample 43


title: 3_14_119095_N3_Day-7_CSE-3%


title: C2-SF18103138-96h


title: C2-SF18103133-96h


title: C2-SF18103137-96h


title: C12-SF19013101-96h


title: section B 64 cells rep 3

description: Sample 42


title: 3_13_119095_N3_Day-7_CSE-0%


title: C3-SF18103133-96h


title: C12-SF18103138-96h


title: C2-SF18103134-96h


title: 3_12_119095_N2_Day-21_CSE-3%


title: 3_11_119095_N2_Day-21_CSE-0%


title: section E 64 cells rep 2

description: Sample 40


title: section B 64 cells rep 2

description: Sample 37


title: C11-SF19013101-96h


title: 2_9_642823_N2_Day-14_CSE-0%


title: C12-SF18103134-96h


title: 3_15_119095_N3_Day-14_CSE-0%


title: 3_10_119095_N2_Day-14_CSE-3%


title: C12-SF18103133-96h


title: 3_1_119095_N1_Day-7_CSE-0%


title: 2_8_642823_N2_Day-7_CSE-3%


title: section E 64 cells rep 1

description: Sample 35


title: section A 64 cells rep 2

description: Sample 36


title: C11-SF18103138-96h


title: C11-SF18103137-96h


title: 2_7_642823_N2_Day-7_CSE-0%


title: section D 64 cells rep 1

description: Sample 34


title: 2_6_642823_N1_Day-21_CSE-3%


title: C11-SF18103134-96h


title: section A 64 cells rep 3

description: Sample 41


title: section C 64 cells rep 1

description: Sample 33


title: C11-SF18103133-96h


title: 2_5_642823_N1_Day-21_CSE-0%


title: C12-SF18103137-96h


title: section D 64 cells rep 2

description: Sample 39


title: C10-SF19013101-96h


title: section B 64 cells rep 1

description: Sample 32


title: section C 64 cells rep 2

description: Sample 38


title: 2_4_642823_N1_Day-14_CSE-3%


title: 2_3_642823_N1_Day-14_CSE-0%


title: C10-SF18103138-96h


title: section A 64 cells rep 1

description: Sample 31


title: C10-SF18103134-96h


title: 2_18_642823_N3_Day-21_CSE-3%


title: section C 4 cells rep 3

description: Sample 28

source_name: 4-cells stage


title: C10-SF18103137-96h


title: 2_2_642823_N1_Day-7_CSE-3%


title: section B 4 cells rep 3

description: Sample 27


title: C10-SF18103133-96h


title: 2_17_642823_N3_Day-21_CSE-0%


title: 2_16_642823_N3_Day-14_CSE-3%


title: section E 4 cells rep 2

description: Sample 25


title: 2_15_642823_N3_Day-14_CSE-0%


title: C1-SF19013101-96h


title: C1-SF18103137-96h


title: 2_14_642823_N3_Day-7_CSE-3%


title: section D 4 cells rep 2

description: Sample 24


title: C1-SF18103134-96h


title: section A 4 cells rep 3

description: Sample 26


title: section C 4 cells rep 2

description: Sample 23


title: 2_13_642823_N3_Day-7_CSE-0%


title: B9-SF19013101-96h


title: C1-SF18103133-96h


title: 2_11_642823_N2_Day-21_CSE-0%


title: 2_12_642823_N2_Day-21_CSE-3%


title: section B 4 cells rep 2

description: Sample 22


title: section A 4 cells rep 2

description: Sample 21


title: 2_10_642823_N2_Day-14_CSE-3%


title: B9-SF18103138-96h


title: section D 4 cells rep 3

description: Sample 29


title: section E 4 cells rep 3

description: Sample 30


title: B9-SF18103137-96h


title: 2_1_642823_N1_Day-7_CSE-0%


title: C1-SF18103138-96h


title: section D 4 cells rep 1

description: Sample 19


title: 1_9_646466_N3_Day-14_CSE-0%


title: section E 4 cells rep 1

description: Sample 20


title: B9-SF18103133-96h


title: section C 4 cells rep 1

description: Sample 18


title: section B 4 cells rep 1

description: Sample 17


title: section E 1 cell rep 3

description: Sample 15

source_name: fertilized egg stage

value: fertilized egg


title: section A 4 cells rep 1

description: Sample 16


title: 1_8_646466_N3_Day-7_CSE-3%


title: 1_7_646466_N3_Day-7_CSE-0%


title: 1_5_646466_N2_Day-21_CSE-0%


title: B8-SF18103138-96h


title: B8-SF18103137-96h


title: B8-SF19013101-96h


title: section D 1 cell rep 3

description:
Sample 14
Sample 14 was deemed an outlier and removed from the processed data.

value: D


title: B8-SF18103134-96h


title: B8-SF18103133-96h


title: section C 1 cell rep 3

description: Sample 13


title: 1_4_646466_N2_Day-14_CSE-3%


title: section B 1 cell rep 3

description: Sample 12


title: 1_3_646466_N2_Day-14_CSE-0%


title: 1_2_646466_N2_Day-7_CSE-3%


title: B7-SF19013101-96h


title: B9-SF18103134-96h


title: section A 1 cell rep 3

description: Sample 11


title: B7-SF18103138-96h


title: B7-SF18103137-96h


title: 1_18_646466_N4_Day-21_CSE-3%


title: section D 1 cell rep 2

description: Sample 9


title: 1_17_646466_N4_Day-21_CSE-0%


title: B7-SF18103134-96h


title: section C 1 cell rep 2

description: Sample 8


title: 1_16_646466_N4_Day-14_CSE-3%


title: 1_6_646466_N2_Day-21_CSE-3%


title: section B 1 cell rep 2

description: Sample 7


title: section A 1 cell rep 2

description: Sample 6


title: B6-SF19013101-96h


title: 1_12_646466_N3_Day-21_CSE-3%


title: B7-SF18103133-96h


title: section D 1 cell rep 1

description: Sample 4


title: B6-SF18103134-96h


title: B6-SF18103138-96h


title: B6-SF18103133-96h


title: 1_13_646466_N4_Day-7_CSE-0%


title: B6-SF18103137-96h


title: 1_10_646466_N3_Day-14_CSE-3%


title: section E 1 cell rep 2

description: Sample 10


title: section B 1 cell rep 1

description: Sample 2


title: section E 1 cell rep 1

description: Sample 5


title: section C 1 cell rep 1

description: Sample 3


title: 1_11_646466_N3_Day-21_CSE-0%


title: 1_14_646466_N4_Day-7_CSE-3%


title: B5-SF19013101-96h


title: B5-SF18103138-96h


title: section A 1 cell rep 1

description: Sample 1


title: HTG_3

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

country: China

institute: School of Pharmaceutical Sciences, Jilin University

description: Nonalcoholic fatty liver

data_processing:
Hisat2 for sequence alignment
Stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
Samtools tools for related file processing
Assembly: mRatBN7.2
Supplementary files format and content: Xls file include expression  values for each sample

organism: Rattus norvegicus

source_name: liver

extract_protocol:
Total RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified using the RNeasy Mini Kit (Qiagen, Carlsbad, USA) according to the manufacturer’s instructions
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: liver

value: high-fat diet + HCG treatment


title: 1_1_646466_N2_Day-7_CSE-0%


title: B5-SF18103134-96h


title: EMM2/1, day 34

city: East Lansing

first: Aitor

last: Aguirre

state: MI

address: 775 Woodlot Dr

department: Biomedical Engineering

institute: Michigan State University

description: 10X Genomics

data_processing:
Output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.
After demultiplexing reads from each of the sample libraries was further processed using 10x Genomics cellranger count (v6.1.2). This program uses the read 1 data to identify reads from individual cells and remove duplicate reads (based on UMIs) as well as align the corresponding read 2 to the reference transcriptome (GRCh38). Cellranger automatically combines reads across both lanes for each sample.
Assembly: reference transcriptome (GRCh38)
Supplementary files format and content: .mtx format, matrix files
Supplementary files format and content: .tsv format, barcodes and features files
Supplementary files format and content: cloupe format, 10X Loupe file

source_name: heart organoid

extract_protocol:
The libraries were prepared using the 10x Chromium Next GEM Single Cell 3' Kit, v3.1 and associated components.
Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS, Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays. The libraries were pool in equimolar proportions and the pool quantified again using the Invitrogen Collibri qPCR assay.
The pool was loaded onto two lanes of an Illumina NovaSeq 6000 SP flow cell (v1.5) and sequencing was performed in a custom paired end format, 28 cycles for read 1, 2 10 cycle index reads and 90 cycles for read 2. A v1.5, 100 cycle NovaSeq reagent cartridge was used for sequencing. The 28bp read 1 includes the 10x cell barcodes and UMIs, read 2 is the cDNA read.

value: heart organoid

tag: genotype

value: WT

value: cardiac organoid differentiation +EMM2/1 strategy


title: EMM1, day 34

description: 10X Genomics

value: cardiac organoid differentiation + EMM1 strategy


title: HTG_2

description: Nonalcoholic fatty liver


title: B5-SF18103137-96h


title: 1_15_646466_N4_Day-14_CSE-0%

value: HBEC

value: Human Bronchial Epithelial Cells


title: MM, day 34

description: 10X Genomics

value: cardiac organoid differentiation + MM strategy


title: HTG_1

description: Nonalcoholic fatty liver


title: B5-SF18103133-96h


title: HFD_3

description: Nonalcoholic fatty liver

value: high-fat diet


title: B4-SF18103138-96h


title: B4-SF19013101-96h


title: PAEC_OLA1NLS

city: Milwaukee

first: Adeleye

middle: James

last: Afolayan

state: WI

address: 8701 Watertown Plank road

department: Pediatrics

institute: Medical College of Wisconsin

data_processing:
Basecalls were performed using MACs 2.2.6 for Novaseq output
ChIP-seq reads were trimmed from 3' end until the final base had a quality score>/30, discarding reads left with<20bp
ChIP-seq reads were aligned to the UCSC hg19 genome using Bowtie version 1.1.2. Only uniquely mapped reads with at most two mismatches were retained
Peaks were called using MACs v 2.26 with the significance cut-off q value <=0.01
Bigwig files were generated using the genomic Ranges R package. Score represents the normalized coverage of DNA fragment at a given genomic cordinate. Narrow Peak files were generated using MACs vs 2.26 with default settings
annotated Peak list were generated using MASC2.26
Assembly: UCSC hg19
Supplementary files format and content: BigWig , narrow peak (except for input sample)

source_name: HPAEC cells

growth_protocol: Pulmonary-derived arterial endothelial cells (ATCC) were generated by plating on TC-treated plastic (typically 2–3 × 106 cells into a 100mm dish) with Vasculife EC Media (Lifeline Cell Technology, Frederick, MD, USA).

extract_protocol:
Transfected cells were treated with 100uM H202 for 30 minutes, then fixed with 1% formaldehyde for 10 minutes. After quenching snf cell lysis, chromatin was sonicated using a E220 foucsed ultrasonicator (Covaris)
ChIP-seq library was prepare using TruSeq SBS Kit v3/HiSeq 2000 System User Guide Part # 15011190 Rev. V HCS 2.2.38.

treatment_protocol: Cells were transfected with OLA1-NLS constructs at ~50% confluency for 24 hours with Fugene 6 transfection reagent (Fugent, Middleton, WI, USA), followed by 24 hours rest.

value: HPAEC

value: Pulmonary-derived endothelial cells

tag: transfection


title: HFD_2

description: Nonalcoholic fatty liver


title: HFD_1

description: Nonalcoholic fatty liver


title: B4-SF18103137-96h

value: basilar papilla


title: PAEC_OLA1H2O2


title: Scramble siRNA, treated with vehicle, rep 2

first: Andrea

last: Wilderman

data_processing:
Raw data (raw reads) in fastq format was firstly processed through in-house (Novogen) perl scripts. In this step, clean data (clean reads) was obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene.
Assembly: Differential gene expression analysis using biological replicates was doneusing DESeq2 (v.1.20.0). P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Supplementary files format and content: rn6
Supplementary files format and content: excel spreadsheet of raw counts, fpkm, log2 fold-change values, p-values and BH adjusted p-values of each pairwise comparison of interest

source_name: NRVM

extract_protocol:
For siRNA knockdown, NRVMs were transfected with siRNA against rat Esrra (Dharmacon, M-085000-02-0005), rat Esrrb (Dharmacon, M-100126-01-0005), rat Esrrg (Dharmacon, M-100212-01-0005), rat E2f1 (Dharmacon, M-102754-00-0005) or scramble control siRNA (ThermoFisher, 4390843), using the Viromer BLUE Transfection Reagent (Lipocalyx, VB-01LB-01). Typically, 25 nM siRNA was used for NRVMs seeded in 24-well. For treatment with 915 or vehicle, cells were treated with 10uM 915 or equivalent volume of vehicle (DMSO) for 24h.
Total RNA was extracted using Qiagen miRNeasy kit according to the manufacturer's instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP, followed by end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
unstranded, dual indexed for paired-end sequencing 2x150

treatment_protocol: NRVM were isolated from rat pups (P3) as described in PMID:28878135. Following overnight incubation in 0.05% trypsin EDTA at 4°C, cardiomyocytes were dissociated with type 2 collagenase (Worthington, LS004176) in HBSS and neutralized with 10% FBS in DMEM. The cell suspension was further incubated in a tissue culture-treated plastic dish for 90 min to allow fibroblast attachment. Typically, NRVMs were seeded at 50-70% confluence in DMEM supplemented with 10% FBS, 1% penicillin/streptomycin and 100μM bromodeoxyuridine. 2 days after seeding, the medium was changed to DMEM supplemented with insulin/transferrin/selenium (Sigma-Aldrich, I3146) and cultures were used within 5 days.

value: NRVM

value: isolated cardiomyocyte

value: scramble siRNA

value: DMSO 24h


title: PAEC_OLA1CTR


title: Scramble siRNA, treated with vehicle, rep 1


title: B4-SF18103134-96h


title: B4-SF18103133-96h


title: BT2019110, Cell

city: Cambridge

first: Maxwell

last: Gold

state: MA

address: 21 Ames St

institute: MIT

data_processing:
Data was processed through the standard 10X genomics pipeline.
Filtered counts matrices were used and uploaded to Seurat for downstream processing.
Assembly: hg38
Supplementary files format and content: counts (h5)

source_name: Tumor cells

extract_protocol:
Nuclei were isolated from fresh, snap frozen tumor tissues as previously described in Nagy et al 2020. Tumor tissue was mechanically dissociated followed by collagenase-based enzymatic dissociation as previously described in Vladoiu et al 2019
Library construction was performed according to 10X genomics.

value: SHH MB tumors with MBEN histology

tag: assay

value: scRNA-Seq


title: Scramble siRNA, treated with vehicle, rep 3


title: Scramble siRNA, treated with 915, rep 2


title: MB3201, Nuc

source_name: Tumor nuclei

value: snRNA-Seq


title: MB3612, Nuc


title: B3-SF19013101-96h


title: Scramble siRNA, treated with 915, rep 3


title: B3-SF18103134-96h


title: B3-SF18103138-96h


title: B3-SF18103137-96h


title: Scramble siRNA, treated with 915, rep 1


title: MB4113, Nuc


title: Control, day 34

description: 10X Genomics

value: heart organoid

value: WT

value: cardiac organoid differentiation


title: Double knockdown treated with vehicle, rep 3

value: siRNA against ERRalpha and ERRgamma


title: MB3400, Nuc


title: B3-SF18103133-96h


title: PAEC_IGGNEG


title: MB2112, Nuc


title: Double knockdown treated with vehicle, rep 2


title: B2-SF19013101-96h


title: MB0601, Nuc


title: Double knockdown treated with 915, rep 3


title: B2-SF18103138-96h


title: Double knockdown treated with vehicle, rep 1


title: MB0595, Nuc


title: 1514_knockdown_DEX_poly

city: Edinburgh

first: Jennifer

last: Rynne

email: jrynne@ed.ac.uk, jenrynne@gmail.com

address: QMRI, Edinburgh BioQuarter, Little France Crescent

country: United Kingdom

institute: University of Edinburgh

data_processing:
CGC cloud platform for QC (multiQC), trimming (trimmomatic) and alignment (Salmon index & quant)
R studio for differential gene expression (DESeq2)
Assembly: gencode.v24
Supplementary files format and content: counts

source_name: bronchial epithelium

growth_protocol: BECs cultured in airway epithelial culture media (Promocell) supplemented with growth factors provided, on collagen coated plates

extract_protocol:
TRIzol & chloroform RNA extraction method, Qiagen on column Dnase digestion
NEB Ultra II directional library prep kit with polyA selection and unique dual indexes

treatment_protocol: siRNA transfection with interferrin transfection reagent. Dexamethasone at a concentration of 10-7 M

value: bronchial epithelium

value: bronchial epithelial cells

value: knockdown

value: DEX

tag: fraction

value: polysomal mRNA


title: Double knockdown treated with 915, rep 2


title: 1514_knockdown_noDEX_poly

value: noDEX


title: B2-SF18103134-96h

value: basilar papilla


title: B2-SF18103133-96h


title: 1514_control_DEX_poly

value: control


title: CutandRun_IgG_2_GIMEN_ASCL1_Neg_4TF_Pos

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

data_processing:
CUT&RUN-seq data were preprocess and analyzed using cutRunTools pipeline.
This pipeline automate the preprocessing and alignment of CUT&RUN-seq data to hg19 genome. CutRunTools utilized MACS2 and SEACR software to call peaks using the default optimized cutoff for each CUT&RUN-seq data.
The paired control data were further been utilized by the cutRunTools step2 script to normalize the MACS2 output peaks.
Each bedGraph output has been further normalize by subtract the treatment file to the correspondence control file using MACS2 bdgcmp and floored the signal to 0.1 before convert to bigWig using UCSC bedGraphToBigWig tool.
Assembly: hg19
Supplementary files format and content: Peak bed files of ASCL1 and H3K27ac
Supplementary files format and content: bigWig files of ASCL1 and H3K27ac
Library strategy: Cut&Run

source_name: GI-MEN cells

growth_protocol: All cells were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

extract_protocol:
Library construction from the Cut&Run-seq samples and sequencing of paired-end-150-bp-long reads by the  Illumina HiSeq sequencing of ~10 M paired-end 150-bp reads was performed at Genewiz.
Paired-end Cut&Run-Seq sequencing

treatment_protocol: All cells were freshly collected after DMSO or DOX treatment and subject to cut and run assay using an EpiCypher kit (SKU: 14-1048).

value: GI-MEN cells

value: Neuroblastoma

value: 4TF Overexpression

tag: antibody

value: Contol (input)


title: B12-SF18103138-96h

source_name: basilar papilla


title: B12-SF19013101-96h


title: CutandRun_PHOX2B_GIMEN_ASCL1_Pos_4TF_Pos

value: 4TF+ASCL1 Overexpression


title: CutandRun_PHOX2B_GIMEN_ASCL1_Neg_4TF_Pos


title: 1314_knockdown_DEX_poly


title: 1314_knockdown_noDEX_poly


title: 1514_control_noDEX_poly


title: B12-SF18103134-96h


title: CutandRun_MYCN_GIMEN_ASCL1_Pos_4TF_Pos

value: MYCN


title: 1314_control_DEX_poly


title: B12-SF18103133-96h


title: 1314_control_noDEX_poly


title: CutandRun_MYCN_GIMEN_ASCL1_Neg_4TF_Pos


title: 0941p3_knockdown_noDEX_poly


title: B11-SF19013101-96h


title: B2-SF18103137-96h


title: Double knockdown treated with 915, rep 1

value: NRVM

value: isolated cardiomyocyte


title: 0941p3_knockdown_DEX_poly


title: CutandRun_IgG_2_GIMEN_ASCL1_Pos_4TF_Pos


title: CutandRun_H3K27ac_GIMEN_ASCL1_Neg_4TF_Pos


title: CutandRun_H3K27ac_GIMEN_ASCL1_Pos_4TF_Pos


title: 0941p3_control_noDEX_poly


title: 0941p3_control_DEX_poly


title: CutandRun_IgG_GIMEN_ASCL1_Pos_4TF_Pos


title: B12-SF18103137-96h


title: B11-SF18103137-96h


title: 0941p2_knockdown_DEX_poly


title: ChIP_input_HA_GI-MEN_ASCL1_HA_tag

data_processing:
ChIP-seq reads were mapped to human hg19 reference genome using bowtie2 program with default parameters.
Aligned ChIP-seq reads were remove duplicate with Picard MarkDuplicate package.
ChIP-Seq peaks were called with MACS2 software version 2.2.7.1 with --keep-dup=1 --SPMR -p 1e-9 -f BAM.
The output bedGraph data were normalized by subtracting the corresponding background values using MACS2 bdgcmp -m subtract.
BedGraph signal were further floored to 0.1, then convert to bigWig format using UCSC bedGraphToBigWig tool
Assembly: hg19
Supplementary files format and content: Peak bed files of ASCL1 and H3K27ac
Supplementary files format and content: bigWig files of ASCL1 and H3K27ac

growth_protocol: GI-MEN DOX-ASCL1/ GI-MEN DOX-ASCL1-tag-HA cells cells were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

extract_protocol:
Library construction from the H3K27ac/HA ChIP-seq samples and sequencing of single-end 50-bp-long reads by the Illumina HiSeq 4000 were performed at BGI Biotech Solutions Co. Ltd (Hong Kong, China).
Single-end ChIP-Seq sequencing

treatment_protocol: Cells were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and H3K27ac/HA-DNA complexes were isolated with antibody.  A sample of whole cell extract (Input) was sequenced and used as the background to determine enrichment.

value: Control (input)


title: B11-SF18103134-96h


title: B10-SF19013101-96h


title: 0941p2_control_DEX_poly

value: bronchial epithelium


title: 0941p2_knockdown_noDEX_poly

value: bronchial epithelial cells


title: B10-SF18103138-96h


title: ChIP_input_H3K27ac_GI-MEN_ASCL1_pos_rep2

value: ASCL1 overexpression


title: B10-SF18103137-96h


title: B11-SF18103138-96h


title: ChIP_HA_GI-MEN_ASCL1_HA_tag

value: HA


title: 0941p2_control_noDEX_poly

value: polysomal mRNA


title: 0213_knockdown_DEX_poly

value: knockdown

value: DEX


title: B10-SF18103134-96h

value: basilar papilla


title: ChIP_input_H3K27ac_GI-MEN_ASCL1_neg_rep2

value: GI-MEN cells

value: control


title: ChIP_input_H3K27ac_GI-MEN_ASCL1_neg_rep1

value: Neuroblastoma


title: ChIP_input_H3K27ac_GI-MEN_ASCL1_pos_rep1


title: CutandRun_ASCL1_GIMEN_ASCL1_Pos_4TF_Pos


title: ChIP_H3K27ac_GI-MEN_ASCL1_pos_rep2


title: B10-SF18103133-96h


title: 0213_knockdown_noDEX_poly

value: noDEX


title: B11-SF18103133-96h


title: 0213_control_DEX_poly


title: B1-SF18103138-96h


title: B1-SF19013101-96h


title: ChIP_H3K27ac_GI-MEN_ASCL1_pos_rep1


title: 1514_knockdown_DEX_80S

value: monosomal mRNA


title: B1-SF18103137-96h


title: 0213_control_noDEX_poly


title: 1514_knockdown_noDEX_80S


title: B1-SF18103133-96h


title: ChIP_H3K27ac_GI-MEN_ASCL1_neg_rep1


title: 1514_control_DEX_80S


title: B1-SF18103134-96h


title: A9-SF19013101-96h


title: ATAC_GIMEN_ASCL1_Pos_4TF_Pos_Rep3

data_processing:
ATAC-seq reads were mapped to human hg19 reference genome using bowtie2 program with default parameters.
Aligned ATAC-seq reads were remove duplicate with Picard MarkDuplicates package. Multiple mapping reads were removed using samtools view -q 10
ATAC-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Threshold for the peaks called is p-value < 1e-5, keep-dup=all, --SPMR were used to normalized the bedGraph output.The signal has been floored to 0.1 after bdgcmp subtract function.
Assembly: hg19
Supplementary files format and content: narrowPeak files of ATAC-seq
Supplementary files format and content: bigWig files of ATAC-seq

growth_protocol: Different GI-MEN cell lines were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

extract_protocol:
Library construction from  ATAC-seq samples and sequencing of single-end 50-bp-long reads by the Illumina HiSeq 4000 were performed at BGI Biotech Solutions Co. Ltd (Hong Kong, China).
Paired-end ATAC-Seq sequencing

treatment_protocol: Cells were freshly collected to perform ATAC assay.  DNA was analyzed by Illumina Hiseq 4000.

value: 4TF + ASCL1 overexpression


title: A9-SF18103138-96h


title: 1514_control_noDEX_80S


title: ATAC_GIMEN_ASCL1_Neg_4TF_Pos_Rep3

value: 4TF overexpression


title: A9-SF18103134-96h


title: A9-SF18103137-96h


title: 1314_control_DEX_80S

description: Sample not represented in 80S_counts_txi.csv, as we removed one donor from the analysis due to it being an outlier.


title: 1314_knockdown_noDEX_80S


title: ATAC_GIMEN_ASCL1_Neg_Rep2

value: Control


title: ATAC_GIMEN_ASCL1_Pos_4TF_Pos_Rep2


title: 0941p3_knockdown_DEX_80S


title: ATAC_GIMEN_ASCL1_Neg_4TF_Pos_Rep2


title: 1314_knockdown_DEX_80S


title: A8-SF18103137-96h


title: A9-SF18103133-96h


title: ATAC_GIMEN_ASCL1_Neg_4TF_Pos_Rep1


title: ATAC_GIMEN_ASCL1_Pos_4TF_Pos_Rep1


title: 0941p3_knockdown_noDEX_80S


title: ChIP_H3K27ac_GI-MEN_ASCL1_neg_rep2


title: ATAC_GIMEN_ASCL1_Pos_Rep2

value: ASCL1 Overexpression


title: A8-SF19013101-96h


title: 0941p3_control_DEX_80S

value: bronchial epithelium


title: 0941p3_control_noDEX_80S

value: bronchial epithelial cells


title: QTMAN2_1

city: Hirosawa Wako city, Saitama prefecture, Japan

first: Shintaro

last: Iwasaki

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

data_processing:
Basecalling with illumina CASAVA bcl2fastq (v2.19)
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
rRNA and other non-coding RNA alignment with STAR(2.7.0a)
Alignment with STAR(2.7.0a)
Read quantitation using fp-count
Assembly: hg38
Supplementary files format and content: Text files contain three columns: 1. Transcript name;2. CDS length (nt);3. Read count

extract_protocol:
Cell extracts were prepared with lysis buffer, treated with DNase, and clarified by centrifugation.
RNA extraction, RNaseI footprinting, ribosome pelletting, 17-34 nt gel excision, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification
Ribosome profiling

value: epithelial

value: QTMAN KO


title: A8-SF18103134-96h


title: 0941p2_knockdown_DEX_80S


title: ATAC_GIMEN_ASCL1_Neg_Rep1


title: A8-SF18103133-96h


title: A7-SF19013101-96h


title: A8-SF18103138-96h


title: 1314_control_noDEX_80S


title: QTMAN1_2


title: ATAC_GIMEN_ASCL1_Pos_Rep1

value: ASCL1 overexpression


title: A7-SF18103138-96h


title: QTGAL1_1

value: QTGAL KO


title: 0213_knockdown_DEX_80S

value: knockdown

value: DEX


title: A7-SF18103137-96h

value: basilar papilla


title: 0941p2_control_DEX_80S

value: control


title: 14_GBM_617_periphery

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
Single-cell sequencing FASTQ files were processed using Salmon-Alevin (v1.2.1) for sample demultiplexing, barcode processing, pseudo-alignment to human transcriptome (Gencode v35) and UMI counting. The unfiltered output of Salmon-Alevin is provided for each sample as processed data file.
Filtering for high-quality cells was done using the cells library sizes, the number of detected genes and the percentage of reads mapping to mitochondrial genes, based on the distribution observed across cells. Low-abundance genes were filtered out. After quality filtering, the resulting dataset consisted of 15,523 genes and 45,466 cells derived from the 14 samples. The filtered UMI counts matrix for these genes and cells is provided in file UMIsMatrix.txt.gz.
Further quality controls and analyses were performed using the dropletUtils, scran, and scater Bioconductor packages (Bioconductor release 3.12), mostly following the steps of the OSCA book workflow (https://bioconductor.org/books/release/OSCA/).
Genome_build: hg38
Supplementary_files_format_and_content: UMIsMatrix.txt.gz: TSV file (tab separated values) with UMI counts for Gencode v35 gene models (after filtering out genes with low average expression level across cells) in retained good quality cells; columns correspond to: 1. Gencode gene ID, remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample name separated by a dot (e.g., "TCAGGTAGTACCCGCA.10_GBM_616_center")
Supplementary_files_format_and_content: colData.txt: TSV file (tab separated values) with metadata for retained good quality cells; columns correspond to: 1. Cell barcode sequence and sample name as used in UMIsMatrix.txt.gz; 2. Sample ID, 3. Inferred cell cycle phase, 4. Normalization size factor, 5. Final cell annotation, 6. Final cell annotation (finer level), 7. Number of detected genes, 8. Percent of reads originating from the mitochondria, 9. Percent of reads originating from the ribosomal genes, 10. and 11. tSNE coordinates
Supplementary_files_format_and_content: *Alevin.tar.gz: TAR archive including Alevin output files

molecule: polyA RNA

source_name: glioblastoma tumor

extract_protocol:
Resected GBM tissue samples were immediately placed on ice and transferred to the laboratory for single cell dissociation within 2-3 h after resection. Human brain tissue was manually minced using razor blades and enzymatically dissociated at 37°C for 30 minutes with collagenase-IV and DNAse1  in a buffer containing Hank’s Balanced Salt Solution (HBSS) with Ca2+/Mg2+, non-essential amino acids, sodium pyruvate, sodium bi-carbonate, HEPES, glutamine and antibiotic-antimycotic. Cells were filtered and separated from dead cells, debris and myelin by a 0.9 M sucrose density gradient centrifugation. Upon ACK-lysis for removal of erythrocytes the generated single-cell suspension was washed, counted and frozen in Bambanker for later use. Human peripheral blood mononuclear cells (PBMCs) were collected from venous blood of healthy donors, diluted 2x with 2% FBS in PBS and separated via Ficoll density gradient. Isolated PBMCs were cryopreserved in Bambanker. Cryopreserved tumor digests from GBM samples (center and periphery), as well as autologous PBMCs were thawed and washed with excess ice-cold 1xPBS and spun down at 350xg for 5 min. Subsequently, the cells were stained with Live/Dead  and a cocktail of fluorescently-conjugated antibodies CD11b (FITC, Biolegend, 101206) and CD45 (FITC, Biolegend, 302006), and large debris were removed with a 40-μm strainer . All samples were acquired on the BD FACS ARIA Fusion III (Becton Dickinson GmbH, Germany). For single-cell RNA-seq experiments, live and single gated cells were sorted into non-immune cell (CD45-CD11b-) and immune cell (CD45+CD11b+) populations. Both populations were directly sorted into eppendorf tubes with 1xPBS supplemented with 1% BSA for single cell RNA sequencing.
Cell suspensions from each sample (patient/site) were loaded each into a single well of a 10× Genomics Chromium Single Cell Controller for a targeted recovery of 10,000 cells. Single-cell capture and cDNA and library preparation were performed at Roche, Basel, with a Single Cell 3’ v3 Reagent Kit (10× Genomics) according to manufacturer’s instructions.

treatment_protocol: No treatment

value: tumor periphery

tag: patient

tag: tumor type

value: proneuronal

tag: idh1 status

value: IDH1 WT


title: QTGAL2_1


title: 0941p2_control_noDEX_80S

value: noDEX

value: monosomal mRNA


title: A6-SF18103138-96h

data_processing:
Illumina NextGen Sequencing
demultiplexing
STAR alignment v2.5.3a
read quantification: RSEM v1.3.0
Assembly: galGal6
Supplementary files format and content: RDS file with metadata, counts, normcounts, and logcounts in SingleCellExperiment object format for R

extract_protocol:
FACS sorted into 96-well plates containing RNA lysis buffer
smartseq2


title: A7-SF18103134-96h


title: 0213_control_noDEX_80S


title: A7-SF18103133-96h


title: 15_GBM_617_PBMC

source_name: blood

value: PBMC


title: QTRT1_1

value: QTRT1 KO


title: 0213_control_DEX_80S

value: bronchial epithelium


title: 12_GBM_616_PBMC


title: 1514_knockdown_DEX_total

value: bronchial epithelial cells

value: total mRNA


title: 1514_control_DEX_total


title: 0941p2_knockdown_noDEX_80S


title: A6-SF18103137-96h


title: 13_GBM_617_center

value: tumor center


title: 10_GBM_616_center


title: A5-SF18103138-96h


title: 11_GBM_616_periphery


title: 1514_knockdown_noDEX_total


title: 1514_control_noDEX_total


title: 0213_knockdown_noDEX_80S


title: A6-SF18103133-96h


title: A5-SF18103137-96h


title: 8_GBM_604_periphery

value: mesenchymal


title: 9_GBM_604_PBMC


title: A5-SF18103134-96h


title: A6-SF18103134-96h


title: A4-SF18103138-96h


title: A5-SF18103133-96h


title: 7_GBM_604_center


title: 6_GBM_622_PBMC

value: secondary GBM, high grade astrocytoma

value: IDH1 mutated


title: 1314_knockdown_noDEX_total

value: knockdown


title: A4-SF19013101-96h

value: basilar papilla


title: A4-SF18103137-96h


title: 5_GBM_622_periphery


title: 0941p3_knockdown_DEX_total

value: DEX


title: 1314_control_noDEX_total

value: control


title: 0941p3_knockdown_noDEX_total


title: 3_GBM_609_PBMC


title: A4-SF18103134-96h


title: 2_GBM_609_periphery

value: tumor periphery


title: 0941p3_control_DEX_total


title: 0941p3_control_noDEX_total


title: A3-SF19013101-96h


title: 0941p2_knockdown_DEX_total


title: TAC+Veh rep5

data_processing:
Fastq files were examined for QC with the package, fastp. The default setting was utilized with the fastp.
Then, filtered files were pseudo-alined with the tool, salmon using the single-end setting.
Salmon output files were loaded into R. DESeq2 was utilized for differential genes and downstream pathways.
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Mus musculus

source_name: Heart

extract_protocol:
Total RNA was extracted from left ventricle using Qiagen miRNeasy kit according to manufacturer's instructions
RNA (100–500 ng) was utilized for library preparation with the TruSeq RNA Sample Preparation Kit v2 (Illumina), according to the manufacturer’s protocol.

treatment_protocol: we performed TAC or sham surgery and treated mice with 332 (IP injection) for 6 weeks following surgery.

value: Heart

value: WT

value: TAC+Vehicle


title: TAC+Veh rep4


title: 1314_knockdown_DEX_total


title: 1314_control_DEX_total


title: A3-SF18103138-96h


title: 4_GBM_622_center


title: TAC+Veh rep3


title: 0941p2_control_DEX_total


title: 0213_knockdown_DEX_total


title: A3-SF18103134-96h


title: A3-SF18103133-96h


title: TAC+332 rep5


title: TAC+Veh rep1


title: TAC+Veh rep2


title: 0941p2_control_noDEX_total

value: noDEX


title: 0213_control_DEX_total


title: A4-SF18103133-96h


title: TAC+332 rep3


title: A2-SF19013101-96h


title: A2-SF18103137-96h


title: 0213_control_noDEX_total


title: 0213_knockdown_noDEX_total


title: A2-SF18103138-96h


title: A5-SF19013101-96h


title: HC-9

city: Pittsburgh

first: Patrizia

last: Fuschiotti

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

data_processing:
Chromium scRNA-seq data produced by the 10X Chromium Platform were processed to generate sample-specific fastq files.
Processed reads were then examined by quality metrics, mapped to a reference human genome using RNA-seq aligner STAR and assigned to individual cells of origin according to the cell specific barcodes, using the Cell Ranger pipeline (10X Genomics).
To ensure that PCR amplified transcripts were counted only once, only single UMIs were counted for gene expression level 10. In this way, cell x gene UMI counting matrices were generated for downstream analyses.
Seurat, an R package developed for single-cell analysis, was used to identify distinct cell populations and visualize cell clusters in graphs. Specifically, the UMI matrix was filtered such that only cells expressing at least 200 genes were utilized in downstream analysis.
Unwanted sources of variation were regressed out of the data by constructing linear models to predict gene expression based on the number of UMIs per cell as well as the percentage of mitochondrial gene content.
Assembly: GrCh38A genome
Supplementary files format and content: H5 files for gene expression

source_name: Skin tissue

extract_protocol:
Skin biopsies were minced and digested enzymatically (Whole Dissociation Skin Kit, Miltenyi Biotec) for 2 hours at 37°C and further dispersed using the Miltenyi gentleMACS Octo Dissociator. Certain skin biopsies were hashed together per protocol: https://www.biolegend.com/en-us/protocols/totalseq-b-or-c-with-10x-feature-barcoding-technology . HC8 is hashed with 2 SSc samples. Barcodes used in this analysis are reported in the SC348barcodes.csv file.
Experimental procedures followed established techniques using the Chromium Single Cell 5’ Library V1 kit (10x Genomics) or Chromium Single Cell 3’ Library V2  kit. Experimental procedures followed established techniques using the Chromium Single Cell 5’ Library V1 kit +V(D)J Enrichment Kit, Human T Cell (10x Genomics).

tag: chemistry

tag: disease state

value: Healthy control


title: TAC+332 rep1

tag: tissue

tag: treatment


title: A2-SF18103133-96h


title: A2-SF18103134-96h


title: TAC+332 rep2


title: HC-8


title: 0941p2_knockdown_noDEX_total

value: bronchial epithelium


title: A3-SF18103137-96h


title: A12-SF19013101-96h


title: Sham+Vehicle rep2

value: Sham+Vehicle


title: HC-7


title: Sham+Vehicle rep3


title: TAC+332 rep4


title: Sham+Vehicle rep1


title: Sham+332 rep5


title: HC-5


title: UCMSC-scRNAseq

city: Macau

first: Ren-He

last: Xu

state: Macau

address: N22 Research Building, University of Macau, Taipa

department: Faculty of Health Sciences

institute: University of Macau

data_processing:
Bulk RNA sequenced reads were trimmed for short or low-quality sequence, then mapped to hg38 whole genome using hisat2 with defalut parameters
Single-cell squenced reads were analyzed using Drop-seq pipeline with parameters NUM_CORE_BARCODES=10000
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample of bulk RNA-seq,

source_name: UC-MSCs

growth_protocol: MSCs were cultured in α-MEM with 20%FBS.

extract_protocol:
Bulk mRNA was extracted using RNeasy mini kit (QIAGEN). Smart-seq samples were lysed in lysis buffer containing Triton X-100, RNase inhibitor, dNTPs and miliQ H2O preparing for expansion. Single cell mRNA was captured in Nadia platform (Dolomite) using ChemGenes Barcoded beads for Drop-seq (Macosko-2011-10)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: UC-MSCs

tag: strain

value: Wildtype


title: A12-SF18103138-96h

first: Taha

last: Jan


title: HC-4 [reanalyzed]

description: Healthy control


title: HC-6


title: A12-SF18103134-96h


title: Sham+332 rep4


title: EnvyNCMSC-scRNAseq

source_name: ENVY NC-MSC scRNA-seq

value: NC-MSCs

value: ENVY cell line


title: Sham+332 rep3


title: HC-3 [reanalyzed]

description: Healthy control


title: EnvyTMSC-scRNAseq

source_name: ENVY T-MSC scRNA-seq

value: T-MSCs


title: BMSC#4-scRNAseq

source_name: BM-MSCs

value: BM-MSCs


title: A12-SF18103137-96h

value: basilar papilla


title: HC-2 [reanalyzed]

description: Healthy control


title: A12-SF18103133-96h


title: A11-SF19013101-96h


title: EnvyES-scRNAseq

source_name: ENVY hESC single cell RNA sequencing (scRNA-seq)

value: hESCs


title: Sham+332 rep1


title: UCMSC

source_name: Umbilical cord mesenchymal stem cells (UC-MSCs)


title: HC-1 [reanalyzed]

description: Healthy control


title: A11-SF18103137-96h


title: CTCL-12 [reanalyzed]

source_name: Skin tumor

tag: tumor stage

value: CTCL tumor


title: BMSC#4

source_name: Bone marrow mesenchymal stem cells (BM-MSCs)


title: Brown Adipose Tissue, RT, WT,  bio rep3

city: New Brunswick

first: Tracy

middle: G

last: Anthony

state: NJ

address: 59 Dudley Rd

department: Nutritional Sciences

institute: Rutgers University

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. 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: GRCm39
Supplementary files format and content: Processed data contains the Deseq output of comparisons between our experimental groups.

source_name: Brown Adipose Tissue

extract_protocol:
Total RNA was isolated using the Direct-zol™ RNA MiniPrep Plus Kit (Zymo Research) following instructions provided by the manufacturer.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s instructions. Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’-ends and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated with the TapeStation System (Agilent Technologies) and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific). Further validation of the libraries was carried out by quantitative PCR (KAPA Biosystems) of selected genes.

treatment_protocol: Animals were reared at 23°C. Prior to cold exposure, animals were individually housed and kept at room temperature (RT) (23°C) or a 5-day acclimation period and subsequently exposed to 4°C (Cold). Room temperture treated animals were held at 23°C and killed at the same time of day.

value: Brown Adipose Tissue

tag: temperature


title: CTCL-8 [reanalyzed]

value: IIB T3N0B0M0


title: A11-SF18103134-96h

city: Nashville

institute: VUMC


title: Brown Adipose Tissue, RT, WT, bio rep2

value: WT


title: EnvyNCMSC

source_name: ENVY hESC-derived MSCs via neural crest cells (NCCs)

value: EMSCs via NCCs


title: CTCL-6 [reanalyzed]

value: F IIB T3NxB0M0


title: A10-SF18103138-96h


title: Sham+332 rep2

value: Heart


title: TW03 MTSS1 rep3

city: Stockholm

first: Ingemar

last: Ernberg

address: Solnavagen 9 C8

department: Department of Microbiology, Tumor and Cell Biology

country: Sweden

institute: Karolinska Institutet

description: TW03 MTSS1 rep3

data_processing:
The quality control was evaluated by Q30.
Normalization was performed as counts per million plus weighted trimmed mean of M-values.
Downstream analysis was performed using a combination of programs, which included TapeStation Analysis Software A.02.02 (SR1), STAR, HTseq, Cufflink, and wrapped scripts.
Alignments were analyzed using the Tophat program, and differential expression was determined using DESeq2, with Wald tests.
A few different approaches were used for this analysis. One used the general linear model approach and the Voom approach, where samples and genes are assigned weights and then modeled using linear models.
The genes were filtered to remove non/low expressed genes. Filtering was carried out by keeping genes that had one count per million in three or more samples (cpm1_3).
Assembly: hg18
Supplementary files format and content: Excel file includes normalized abundance measurements for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Homo

source_name: NPC cells

growth_protocol: All cells were cultured in Modified Eagles Medium/High glucose (DMEM) medium supplemented with 10% fetal bovine serum (FBS) in the presence of penicillin-streptomycin. All of the cell lines were maintained in a humidified incubator with an atmosphere of 5% CO2 at 37 °C.

extract_protocol:
RNA was purified using the RNeasy mini kit and cDNA was synthesized using the high capacity cDNA reverse transcription kit with RNase inhibitor according to the manufacturer’s protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were plated the day before transfection to reach ~50% confluency on the day of transfection. The FuGENE HD transfection reagent was mixed with plasmid DNA solution at a 3 uL:1 ug ratio and then diluted in the correct volume of reduced-serum medium, according to the manufacturer instructions. The diluted mixture was incubated for 10 min at room temperature before being added to the plates containing the cells. The cells were assayed 36 h after transfection.

tag: tag

value: Myc

value: MTSS1 overexpressed

value: EBV negative NPC cells


title: Brown Adipose Tissue, GCN2 KO, WT,  bio rep3

value: GCN2 KO


title: EnvyTMSC

source_name: ENVY hESC-derived mesenchymal stem cells via trophoblasts (T-MSCs)

tag: cell type

value: EMSCs via trophoblasts

value: Wildtype


title: A10-SF19013101-96h

address: 2220 Pierce Ave, PRB 752

source_name: basilar papilla


title: Brown Adipose Tissue, RT, WT, bio rep1

tag: genotype


title: Brown Adipose Tissue, Cold, GCN2 KO, bio rep2


title: TW03 MTSS1 rep2

description: TW03 MTSS1 rep2


title: Brown Adipose Tissue, Cold, GCN2 KO, bio rep1


title: A11-SF18103138-96h


title: TW03 MTSS1 rep1

description: TW03 MTSS1 rep1


title: A10-SF18103134-96h


title: A10-SF18103137-96h


title: TW03 rep3

description: TW03 rep3

value: wild type


title: Brown Adipose Tissue, Cold, WT,  bio rep3


title: A10-SF18103133-96h


title: Caco-2 cells expressing FAM46A-shRNA#4, biological rep1

type: RNA

city: Kyoto

first: Toshiyasu

last: Suzuki

address: Sakyo-ku

department: Department of Cell and Developmental Biology, Graduate school of Biostudies

institute: Kyoto University

description: Caco-2 cells were infected with lentivirus expressing FAM46A-shRNA#4. Caco-2 cells were harvested at 17 days after infection.

hyb_protocol: 3.5 ug of fragmented and biotin-labeled ss-cDNA was hybridized for 16 hr at 45°C on the Human Gene 2.0 ST Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Styation 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner.

data_processing: The CEL files were analyzed with ExonRMA16 algorithm on GeneSpring GX with default analysis settings.

label: biotin

source_name: Caco-2 cell, FAM46A-shRNA#4 expressing

label_protocol: Fragmented and biotin-labeled ss-cDNA was prepared from 100 ng total RNA using the GeneChip WT PLUS Reagent Kit (Affymetrix) according to the manufacturer’s instruction.

growth_protocol: Caco-2 cells were maintained in DMEM supplemented with 10% FCS, 100 U/ml of penicillin and 100 U/ml of streptomycin.

extract_protocol:
Total RNA was extracted from Caco-2 cells using NucleoSpin RNA kit (MACHEREY-NAGEL).
The quality of total RNA was assessed using the Agilent 2100 BioAnalyser. Amplified and biotinylated sense-strand DNA (ss-DNA) was prepared from total RNA using the GeneChip WT PLUS Reagent Kit (Affymetrix).

treatment_protocol: Subconfluent Caco-2 cells were infected with lentivirus and cultured for 17 days before sampling.

tag: cell line

value: human colon carcinoma cells


title: A11-SF18103133-96h

value: basilar papilla


title: Brown Adipose Tissue, Cold, WT, bio rep2


title: A1-SF18103138-96h


title: Caco-2 cells expressing FAM46A-shRNA#4, biological rep2


title: Caco-2 cells expressing FAM46A-shRNA#2, biological rep2

description: Caco-2 cells were infected with lentivirus expressing FAM46A-shRNA#2. Caco-2 cells were harvested at 17 days after infection.

source_name: Caco-2 cell, FAM46A-shRNA#2 expressing


title: TW03 rep1

description: TW03 rep1


title: A1-SF18103137-96h


title: EnvyES

source_name: ENVY human embryonic stem cells (hESCs)

value: hESCs

value: ENVY cell line


title: A1-SF18103134-96h


title: Brown Adipose Tissue, Cold, WT, bio rep1

value: Brown Adipose Tissue


title: 5-8F MTSS1 rep2

description: 5-8F MTSS1 rep2


title: XR-seq C. elegans xpc-1 CPD 48h

city: College Station

first: Yuchao

last: Jiang

address: 3143 TAMU

institute: Texas A&M University

library_source: other

data_processing:
For XR-seq, cutadapt was used to trim reads with adaptor sequence TGGAATTCTCGGGTGCCAAGGAACTCCAGTNNNNNNACGATCTCGTATGCCGTCTTCTGCTTG at the 3′-end and to discard untrimmed reads. Bowtie 2 was used for read alignment to the ce11 reference genome, followed by filtering, sorting, deduplication, and indexing. Post-alignment filtering steps were adopted using Rsamtools. We only keep reads that: (i) have mapping quality greater than 20; (ii) are from chromosome I, II, III, IV, V, and X; and (iii) are of length 19-24 bp. For plotting strand-based average repair profiles of the genes, we selected 7061 genes longer than 1 kilobase pair, situated at least 500 base pairs away from neighboring genes. Each gene was evenly divided into 100 bins from the Transcription Start Site (TSS) to the Transcription End Site (TES), and 25 bins (2 kbp) upstream of TSS, 25 bins (2 kbp) downstream of TES. Bed files of the reads were intersected to the 150 bin-divided-gene list by Bedtools intersect with the following commands -d -wa -F 0.5 -S or -s for TS and NTS, respectively22. We present the descriptive properties of our data in Supplementary Table 1. For RNA-seq, reads were aligned using STAR, followed by a filtering step to remove unmapped reads, reads with unmapped mates, reads that do not pass quality controls, reads that are unpaired, and reads that are not properly paired. We only kept the first read from the mate pair to ensure independent measures. Read counts for each gene were obtained using FeatureCounts.
Assembly: ce11
Supplementary files format and content: bigwig

molecule: other

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: The C. elegans wild-type (N2 ancestral) and xpc-1 (tm3886) strains were obtained from the Caenorhabditis Genetics Center and were cultured under standard conditions at room temperature on nematode growth media plates with E. coli strain OP50.

extract_protocol:
For XR-seq, supernatants were incubated with 5μL RNase A and then 5μL Proteinase K, purified, and then immunoprecipitated with either anti-CPD or anti-(6-4)PP antibodies. For RNA-seq, L1 stage wild-type (WT) and xpc-1 C. elegans were collected in M9 and washed until the supernatant was clear, followed by incubation with TRizol and chloroform. After centrifugation at 14,000g for 15min at 4°C, the aqueous phase was mixed with an equal volume of isopropanol. Following centrifugation, the RNA pellet was washed several times and then resuspended in RNase-free water.
For XR-seq, immunoprecipitations were ligated to the adaptors, purified with the antibody used in the first purification, and DNA damage was reversed by either CPD or (6-4)PP photolyase. After PCR amplification, the library was sequenced. For RNA-seq, quality control, followed by stranded and poly(A) enriched library preparation and sequencing, was performed by Novogene.
Single-end for XR-seq, paired-end for poly(A) RNA-seq.

treatment_protocol: To obtain L1 larvae, eggs were collected from adult animals by hypochlorite treatment, and kept in M9 buffer at 22℃ for 16 hours with gentle rotation. L1 larvae were exposed to 4,000 J/m2 of UVB radiation (313 nm). The animals were collected in M9 buffer at 5 minutes, 1 hour, 8 hours, 16 hours, 24 hours, and 48 hours after irradiation, and washed until the supernatant became clear. The pelleted C. elegans (~50 μl for each) were then incubated for 2 hours at 62°C with 450 μl of Worm Hirt Lysis Buffer (0.15M Tris pH 8.5, 0.1M NaCl, 5mM EDTA, 1% SDS) and 20 μl of Proteinase K (NEB, cat. no. P8107S). Subsequently, 120 μl of 5M NaCl was added, and the mixture was inverted to ensure proper mixing, followed by an overnight incubation and one hour centrifugation at 4°C.

value: L1 larvae

value: UV irradiation induced CPD


title: 5-8F MTSS1 rep3

description: 5-8F MTSS1 rep3


title: 5-8F rep3

description: 5-8F rep3


title: 5-8F MTSS1 rep1

description: 5-8F MTSS1 rep1


title: Caco-2 cells expressing FAM46A-shRNA#2, biological rep1


title: A1-SF18103133-96h


title: XR-seq C. elegans xpc-1 CPD 24h


title: Caco-2 cells expressing scramble shRNA, biological rep2

description: Caco-2 cells were infected with lentivirus expressing scramble shRNA. Caco-2 cells were harvested at 17 days after infection.

source_name: Caco-2 cell, scramble shRNA expressing

value: scramble shRNA


title: T3.

city: Jinan

first: jianhua

last: zhang

address: gongyebei street No. 23788

institute: Shandong Academy of Agricultural Sciences

data_processing:
coding and non-coding RNAs-Seq: Firstly, Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined
coding and non-coding RNAs: We used Bowtie2 and Tophat2 to map reads to the genome of species. Remaining reads (unmapped reads) were still mapped to genome using tophat-fusion
Assembly: Zm-TPD-CSHL-1.0
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

organism: Zea mays

source_name: four leaf stage leaves

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
coding and non-coding RNAs-Seq

value: four leaf stage leaves

value: after one day of Spodoptera frugiperda feeding


title: T1.


title: 5-8F rep2

description: 5-8F rep2

value: Myc


title: CK3.

value: control


title: XR-seq C. elegans xpc-1 CPD 8h


title: TW03 rep2

description: TW03 rep2

value: EBV negative NPC cells


title: XR-seq C. elegans xpc-1 CPD 5min


title: XR-seq C. elegans xpc-1 CPD 1h


title: CK1.


title: MCF10CA1H_M3b

status: Public on Nov 20 2023

city: Greenville

first: Kyle

middle: D.

last: Mansfield

state: NC

address: 600 Moye Blvd, MS622

department: Biochemistry and Molecular Biology

institute: East Carolina University, Brody School of Medicine

data_processing:
Sequence reads of each sample were pseudo-aligned to the human hg38 reference transcriptome and transcript abundance was quantified by using Kallisto (v.0.46.1).
Differential gene expression analyses were achieved by using tximport (v1.20.0) and DESeq2 (v1.26.0) packages in R Studio (Build 351 with R v4.1.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text file with normalized read counts for all genes in all samples/replicate

growth_protocol: MCF10-A, MCF10-AT1 and MCF10-CA1H cell lines were obtained from the Karmanos Cancer center and maintained in DMEM/F12 supplemented with 5% Horse serum, 1% Penn/Strep, 0.2% Sodium Chloride, Insulin and Hydrocortisone respectively, 0.07% Cholera toxin and 0.04% Epidermal Growth Factor.

extract_protocol:
Total RNA was isolated with TRIzol reagent (Ambion) according to manufacturer protocol. RNA quality was examined by the 4200 TapeStation (Agilent Technologies) and RNA concentration was determined using the Qubit Fluorometric Quantitation (Thermo Fisher).
Stranded cDNA libraries were prepared using the TruSeq Stranded Total RNA prep, Ligation with Ribo-Zero Plus kit (Illumina) in accordance with the manufacturer’s protocol, with ribosomal RNA depletion.

value: Human Breast Epithelial cell

value: METTL3 CRISPR knockdown


title: Caco-2 cells expressing scramble shRNA, biological rep1


title: MCF10CA1H_WTc

value: Control Negative CRISPR


title: MCF10CA1H_M3a


title: XR-seq C. elegans xpc-1 CPD 16h


title: MCF10CA1H_WTb


title: MCF10CA1H_M3c


title: MCF10CA1H_WTa


title: 5-8F rep1

description: 5-8F rep1

value: wild type


title: MCF10AT1_M3b


title: MCF10AT1_WTb


title: MCF10AT1_WTc


title: MCF10AT1_M3a


title: MCF10A_M3b


title: MCF10A_M3c


title: MCF10AT1_WTa


title: MCF10AT1_M3c


title: MCF10A_WTc


title: MCF10A_WTb


title: PBSC_plusDox_Rep2

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

data_processing:
*library strategy: shRNA dropout screen
To calculate read counts from shRNA experiments, 75bp single-end reads in fastq format were first processed to remove the first and last 25bp from each sequence, corresponding to the regions flanking the shRNA sequence that are common across all reads.
The shRNA sequences were then compared to the library of oligonucleotide sequences used in the experiment, allowing for only a single base mismatch.
Assembly: hg38
Supplementary files format and content: Tab-delimited files of shRNA sequence IDs, target gete ID, shRNA sequences used and counts

source_name: PBSC

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 1% L-glutamine and 20% heat-inactivated FBS. For culture maintenance cells were split to 0.5x106 cells/ml every 3 days to not exceed 1-2 x 106 cells/ml. For the in vitro screen after sorting the media was also supplemented with 1% Penicillin/Streptomycin. HEK293T cells (DSMZ, ACC305) were used to produce lentivirus. These cells are cultured in HEPES-modified DMEM medium supplemented with 10% FBS, 4mM L-glutamine and 1mM sodium pyruvate. Cells were split using trypsin every 3 days to not exceed a confluency of 70%. All cells were cultured and treated in an incubator at 37C with 5% CO2.

extract_protocol:
PCR of genomic DNA was performed using ExTaq (Takara) using custom designed primers with Nextera i5 and i7 index sequences (supplementary table X) to amplify the mir30 insert containing the shRNA. Amplicons were electrophoresed on an agarose gel and DNA was purified using the QIAquick gel extraction kit (QIAGEN) according to manufacturers instructions and further purified by ampure (Beckman Coulter).
Samples were pooled and analysed on a Next Seq 2000 75 using a NextSeq 500/550 High output kit

treatment_protocol: MV4-11 and MOLM-14 cells were transduced following the protocol described in Martinez et al 5. As a summary, cells at 106 cells/ml were transduced with the pooled library shRNA lentivirus particles present in the supernatant using Polybrene at a final concentration of 8 µg/ml. Afterwards, the plate was centrifuged at 34C for 50 min at 900xg. After centrifugation, cells were incubated for 3 days. The transduction was performed at a low MOI (0.3 TU/cell) to produce a population of cells with one integration event per cell.  Following lentiviral transduction, cells successfully carrying the fluorescent Venus constitutive expressed were purified using fluorescence activated cell sorting (FACS) in an ARIA II. Most cells that remained after selection carried a single copy of the inducible shRNA. Cells were then used to perform the screening as described.

value: PBSC

value: Wild-Type

value: plus Dox


title: PBSC_minusDox_Rep2

value: minus Dox


title: PBSC_minusDox_Rep1


title: PBSC_plusDox_Rep1


title: MCF10A_M3a


title: MV411_InVitro_plusDox_Rep2


title: MOLM14_InVivo_plusDox_Rep5


title: MV411_InVitro_plusDox_Rep1


title: MV411_InVitro_minusDox_Rep1


title: MV411_InVitro_minusDox_Rep2


title: MOLM14_InVivo_plusDox_Rep4


title: MOLM14_InVivo_plusDox_Rep2


title: MOLM14_InVivo_plusDox_Rep1


title: MCF10A_WTa


title: MOLM14_InVivo_minusDox_Rep5


title: MOLM14_InVivo_minusDox_Rep3


title: MOLM14_InVivo_minusDox_Rep4


title: MOLM14_InVivo_minusDox_Rep1


title: MOLM14_InVitro_plusDox_Rep1


title: MOLM14_InVivo_minusDox_Rep2


title: ITD-NPM1-6-PDX_FLT3i_Rep2 [RNA-seq]

data_processing:
Raw paired-end reads were trimmed to remove low-quality sequences and adaptors using Trimmomatic v0.39 (Bolger et al. 2014; PMID:24695404).
Reads were then aligned to the human genome (version hg38) using HISAT2 v2.2.1 (Kim et al. 2019; PMID:31375807) with default settings.
Counts were generated with featureCounts v2.0.1 (Liao et al. 2014; PMID:24227677) using gene models from ensembl as the reference transcriptome.
Assembly: hg38
Supplementary files format and content: Tab-delimited files of gene IDs and expression values

source_name: CD34 positive AML primary cells

growth_protocol: Primary human AML blast cells were cultured on primary human mesenchymal stem cells (hMSCs). Primary hMSCs from “normal” bone marrow were cultured in alpha-MEM (Lonza) supplemented with 10 % fetal calf serum (Gibco) and 2 mM L-Glutamine (Gibco). 24 h prior to addition of primary AML cells hMSCs were seeded at 5000 cells/cm2 in tissue culture plates pre-treated for 20 minutes with 0.1% glycine.

extract_protocol:
RNA was extracted from primary cells using a RNeasy Micro Plus kit (QIAGEN) where less than 50,000 cells were harvested, and a RNeasy Micro Plus kit (QIAGEN) for larger cell numbers. After quantification by nanodrop and QC using an Agilent RNA 6000 Pico Kit (Agilent, bioanalyser), libraries for next generation sequencing were prepared using the NEBnext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) with the NEBNext® rRNA Depletion Kit v2 for low RNA input (<100 ng RNA), or the Total RNA Ribo-zero library preparation kit (with ribosomal RNA depletion) (Illumina) for higher RNA input.
Libraries were quantified using the High Sensitivity DNA kit (Agilent) and Kapa Library Quantification kit (Roche) prior to paired end sequencing on a Next Seq 2000 (PE 75) with a NextSeq High 150 v2.5 kit.

value: CD34 positive AML primary cells


title: MOLM14_InVitro_minusDox_Rep1


title: ITD-NPM1-6-PDX_DMSO_Rep1 [RNA-seq]

value: DMSO


title: ITD-NPM1-6-PDX_DMSO_Rep2 [RNA-seq]


title: MOLM14_InVitro_minusDox_Rep2


title: ITD-NPM1-6-PDX_FLT3i_Rep1 [RNA-seq]


title: ITD-14_Untreated_Rep2 [RNA-seq]

value: Untreated


title: ITD-13_Untreated_Rep1 [RNA-seq]


title: ITD-14_CBFBi_Rep2 [RNA-seq]

value: CBFBi


title: ITD-14_Untreated_Rep1 [RNA-seq]


title: ITD-13_CBFBi_Rep1 [RNA-seq]


title: ITD-13_CBFBi_Rep2 [RNA-seq]


title: ITD-14_CBFBi_Rep1 [RNA-seq]


title: ITD-13_Untreated_Rep2 [RNA-seq]


title: ITD-12_Untreated_Rep2 [RNA-seq]


title: ITD-12_shRUNX1_Rep2 [RNA-seq]


title: MOLM14_InVitro_plusDox_Rep2


title: ITD-12_Untreated_Rep1 [RNA-seq]


title: ITD-12_shRUNX1_Rep1 [RNA-seq]


title: ITD-12_shNFIX_Rep1 [RNA-seq]

value: shNFIX


title: ITD-12_NTC_Rep2 [RNA-seq]

value: NTC


title: ITD-12_NTC_Rep1 [RNA-seq]


title: ITD-12_EmptyVector [RNA-seq]

value: Empty Vector


title: ITD-12_dnFOS [RNA-seq]

value: dnFOS


title: ITD-12_dnCEBP [RNA-seq]

value: dnCEBP


title: ITD-12_DMSO_Rep2 [RNA-seq]


title: ITD-12_DMSO_Rep1 [RNA-seq]


title: ITD-12_CBFBi_Rep1 [RNA-seq]


title: ITD-14_CBFBi_RUNX1_ChIPseq

data_processing:
Reads were trimmed to remove low-quality sequences using Trimmomatic and aligned to the human genome (version hg38) using Bowtie2 with the --very-sensitive-local paramter.
Potential PCR duplicates were identified and removed from alignments using Picard MarkDuplicates.
Peaks were then called using MACS2 with the settings -B --trackline.
Assembly: hg38
Supplementary files format and content: bedGraph files of read pileups produced by MACS2

growth_protocol: Primary AML cells were cultured on hMSC feeders as described above in the following media: SFEMII (StemCell Technologies), 1 μM UM729 (StemCell Technologies), 750 nM StemReginin 1 (StemCell Technologies) supplemented with 150 ng/ml SCF, 100 ng/ml TPO, 10 ng/ml IL-3, 10 ng/ml G-CSF (Perpro tech). After 1 passage (1 week) in culture cells were treated for 24 h with 10 μM CBFβi or 0.1 % DMSO in the absence of UM729 and StemReginin 1. 2 million cells were harvested and crosslinked in 1% formaldehyde solution (methanol-free from Pierce, Thermo Scientific). 400 mM of glycine (Merck) was added, and cells were washed twice with PBS (Merck) after which pellets were frozen at -80 °C.

extract_protocol:
Libraries for next generation sequencing were prepared using a Kapa Hyper prep kit (Roche) according to manufacturers instructions. 16 cycles of PCR amplification were used and 200-450 bp fragments were size selected by gel electrophoresis.
Libraries were validated by qPCR and quantified using the High Sensitivity DNA kit (Agilent) and Kapa Library Quantification kit (Roche) prior to sequencing on a Nextseq 2000 75 using a NextSeq 500/550 High output kit.

treatment_protocol: Crosslinked cells were resuspended at 1x107 cells/ml in Buffer A (10 mM HEPES, 10 mM EDTA, 0.5 mM MEGTA, 0.25 % Triton- 100, 1x complete mini protease inhibitor cocktail (PIC) (Merck) pH 8.0) and incubated at 4 °C for 10 minutes prior to centrifugation at 500 xG for 10 min. This step was repeated with Buffer B (10 mM HEPES, 200 mM NaCl, 1 mM EDTA, 0.5 mM MEGTA, 0.01 % Triton-X 100, 1x PIC, pH 8.0) and after centrifugation 2 x 106 cells were resuspended in 300 μl IP buffer I (25 mM Tris-HCl, 150 mM NaCl, 2 mM EDTA, 1 % Triton-X 100, 0.25 % SDS, 1x PIC, pH 8.0) and sonicated using a Diagenode Bioruptor Pico sonicator for 4 cycles (30 sec on 30 sec off) before centrifugation for 10 min at 16,000 xG. The supernatant was then collected and 600 μl IP Buffer II (25 mM Tris-HCl, 150 mM NaCl, 2 mM EDTA, 1 % Triton-X 100, 7.5 % Glycerol, 1x PIC, pH 8.0) was added prior to immunoprecipitation.For immunoprecipitations 15 μl of Dynabeads-Protein G were washed twice with 500 μl 50 mM citrate phosphate buffer pH 5 and resupended in 15 μl citrate phosphate buffer with 4 μg anti-RUNX1 antibody (ab23980, Abcam) and 0.5% acetyl-BSA before incubation at 4 °C for 2 h. After incubation, dynabeads were washed with 500 μl pH 5 citrate phosphate buffer and resuspended in 15 μl citrate phosphate buffer with 0.5 % BSA before 555 μl of sonicated chromatin was added and incubated at 4 °C for ~ 16 h. After the incubation the dynabeads are washed sequentially with 500 μl of: Wash buffer 1 (20 mM Tris-HCl, 150 mM NaCl, 2 mM EDTA, 1% Triton-X 100, 0.1% SDS, pH 8.0) once, Wash buffer 2 (20 mM Tris-HCl, 500 mM NaCl, 20 mM EDTA, 1 % Triton-X 100, 0.1 % SDS, pH 8) twice, LiCl buffer (10 mM Tris-HCl,250 mM LiCl, 1 mM EDTA, 0.5 % NP-40, 0.5 % Na-deoxycholate, pH 8.0) once, TE/NaCl wash buffer (10 mM Tris-HCl, 50 mM NaCl, 1 mM EDTA, pH 8.0) twice. After these washes DNA was eluted from the dynabeads using 100 μl elution buffer (100 mM NaHCO3, 1% SDS). 200 mM NaCl and 500 μg/ml proteinase K were added to the eluant and the sample was reverse crosslinked at 65 °C for >4h. DNA was then purified by ampure (1.8x).

tag: target

value: ab23980, Abcam


title: ITD-14_CBFBi_Rep1 [ATAC-seq]

data_processing:
Single-end reads from ATAC-Seq experiments were processed to remove low-quality sequences and Nextera ATAC adaptors using Trimmomatic
Reads were then aligned to the human genome (version hg38) using Bowtie2 v2.2.5 (Langmead and Salzberg. 2012; PMID:22388286) with the option --very-sensitive-local.
Potential PCR duplicates were identified and removed from alignments using Picard MarkDuplicates v2.26.10 (http://broadinstitute.github.io/picard).
Peaks were called using MACS2 v2.2.7.1 (Zhang et al. 2008; PMID:18798982) with the parameters --nomodel -B --trackline.
Assembly: hg38
Supplementary files format and content: bedGraph files of read pileups produced by MACS2

extract_protocol:
Omni ATAC seq was performed on primary cells as described in Corces et al 2017.  Omni ATAC-seq was performed as in Corces et al. (2017). Briefly, cells were washed in ATAC resuspension buffer (RSB) (10mM Tris-HCl pH7.5, 10mM NaCl and 3mM MgCl2) and then lyzed for 3 minutes on ice in RSB buffer with 0.1% NP-40, 0.1% Tween-20. Then the cells were washed with 1ml of ATAC wash buffer consisting of RSB with 0.1% Tween-20. Then the nuclear pellet was resuspended in ATAC transposition buffer consisting of 25μl TD buffer and a concentration of Tn5 transposase enzyme (Illumina) related to the number of input cells, 16.5 μl PBS, 5 μl water, 0.1% tween-20 and 0.01% digitonin and then incubated on a thermomixer at 37°C for 30 minutes. The transposed DNA was then amplified by PCR amplification up to ½ of maximum amplification, as assessed by a qPCR side reaction.
The library was purified using a QIAquick PCR cleanup kit (QIAGEN) followed by ampure (Beckman Coulter) and analysed on a Next Seq 2000 75 using a NextSeq 500/550 High output kit.


title: ITD-14_Untreated_Rep2 [ATAC-seq]


title: ITD-14_Untreated_Rep1 [ATAC-seq]


title: ITD-14_CBFBi_Rep2 [ATAC-seq]


title: ITD-12_shRUNX1 [ATAC-seq]


title: ITD-12_dnFOS [ATAC-seq]


title: ITD-12_dnCEBP [ATAC-seq]


title: ITD-12_DMSO_Rep2 [ATAC-seq]


title: ITD-12_NTC [ATAC-seq]


title: ITD-12_EmptyVector [ATAC-seq]


title: ITD-12_shNFIX_Rep2 [RNA-seq]


title: Large preB cell, IKDN, Input

city: Charlestown

first: Katia

last: Georgopoulos

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

data_processing:
Read alignment was performed on the mm10 assembly with the STAR 5.02 genome alignment algorithm (--alignIntronMax 1 --alignEndsType EndToEnd) on the DNAnexus platform (https://www.dnanexus.com/)
Picard-tools 4.0.3 (Broad Institute) were used to remove PCR duplicates.
Peak calling was performed using MACS2 2.1.1 (Zhang et al., 2008) with input chromatin as control and with a q-value (minimum FDR) cutoff of 0.05. Model building with --mfold of 5, 50 was used for transcription factors, H3K4me3and H3K27ac. The –broad flag was used to identify enriched regions for spreading histone marks such as H3K4me1, H3K27ac, H3K9me3.
Normalized “pileup.bedgraphs” were used after indexing for browser visualization.
Bigwigs were obtained from the “pileup” files for visualization using bedGraphToBigWig v4.
Assembly: mm10

source_name: mouse large pre-B cell (CD19+CD43+BP1+)

growth_protocol: Sorted large pre-B cells were cultured on OP9 stroma in DMEM ( D-5671; Sigma) supplemented with 10% FBS (2442; Sigma), 50 μM 2-mercaptoethanol, 100 μg/ml penicillin, 100 μg/ml streptomycin, 1× Glutamax (35050-062; Gibco), 10 mM HEPES (156-30-80; Gibco) and 1× sodium pyruvate (11360-070; Gibco) in the presence of 5ng/ml of IL-7. Stroma adherent large pre-B cells from WT or IKDN cultures were detached with 0.2% trypsin (EDTA free) for 2 minutes at room temperature. Large pre-B cells were ~ 99% of the cells in suspension as determined by flow cytometry.

extract_protocol:
Cells were fixed in 1% of fresh formaldehyde for 10 minutes at room temperature, quenched with glycine and washed twice with ice-cold PBS. Cells were re-suspended in lysis buffer 1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) for 10 minutes at 4°C, pelleted, and then re-suspended in lysis buffer 2 (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH8) for 5 minutes at 4°C. Cells were finally re-suspended in RIPA buffer (50mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Nadeoxycholate, 0.2% SDS, 0.5 mM PMSF, and 1x Protease inhibitor cocktail (Roche)) to a final concentration of 5x107 cells/ml. Chromatin was sonicated to an average size of 350bp with a Branson Sonifier 450 equipped with a micro probe. Chromatin was cleared by centrifugation at 20,000xg for 10 minutes, and then incubated with 5-10μg of antibodies pre-bound to Dynabeads protein G (Life technologies) and rotated overnight at 4°C. After extensive washing on beads, bound chromatin was eluted and de-crosslinked in 300μl of elution buffer (50 mM Tris pH8, 10 mM EDTA, 1% SDS, 0.3M NaCl) overnight at 65°C. Proteinases K was added to a final concentration of 200 μg/ml and incubated at 45°C for 2 hours. DNA was ethanol precipitated, re-suspended in TE and purified using the DNA Clean & Concentrator-5 kit (Zymo Research).
Purified ChIP DNA was end repaired, end adenylated, and then ligated with Illumina Truseq indexed adaptors. The ligated DNA was purified with AMPure XP beads (Beckman Coulter) and then amplified with KAPA HiFi DNA Polymerase (KAPA Biosystems) for 8 to 13 cycles. After amplification, the library DNA was size selected with AMPurex XP beads to 200-600 bp range, and the purified libraries were multiplexed for sequencing in house with an Illumina NextSeq 550 system.

treatment_protocol: To induce IkE5 deletion in the incucible IkE5 deletion large preB cells (IkE5 fl/fl, Rosa26-ERT2-Cre), 4-OHT (Sigma H7904, final concentration 0.2 μM ) or an equal volume of DMSO as control were added into the medium; and cells were harvested at Day 3 and D12 post induction.

value: mouse large pre-B cell (CD19+CD43+BP1+)

value: IkE5D/D (IKE5 fl/fl, Cd2-cre)

tag: chip antibody


title: ITD-12_CBFBi_Rep2 [ATAC-seq]


title: Large preB cell, WT, Input

value: Wild-type (IKE5 fl/fl, Cre-)


title: ITD-12_DMSO_Rep1 [ATAC-seq]


title: ITD-12_CBFBi_Rep1 [ATAC-seq]


title: Large preB cell, IKDN, H3K4me1

value: H3K4me1 (Active Motif AM39297)


title: Large preB cell, WT, H3K4me1


title: ITD-12_CBFBi_Rep2 [RNA-seq]


title: Large preB cell, IKDN, H3K27ac,rep2

value: H3K27ac (Abcam, ab4729)


title: ITD-14_Untreated_RUNX1_ChIPseq

tag: antibody


title: Large preB cell, WT, H3K27ac, rep2


title: Large preB cell, IKDN, H3K27ac,rep1


title: ITD-12_shNFIX [ATAC-seq]

tag: patient


title: Large preB cell, WT, IL7 withdrawal day2 H3K4me3, rep2

value: H3K4me3 (Active Motif AM39155)


title: Large preB cell, WT, H3K27ac, rep1


title: PC3 cell，shCTSZ-4

city: Chongqing

first: Saipeng

last: Chen

address: Gaotan Yan Street

institute: The First Affiliated Hospital of the Army Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to GRCh38.p13 human genome
Read count extraction and normalization were performed using RSEM software
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited table includes TPM values for all sample

growth_protocol: PC3 Cell cultures were maintained in a CO2 incubator at 37° C with either 1640 or DMEM with 10%  FBS and 1% penicillin‒streptomycin solution

extract_protocol:
Total RNA was extracted using TRIzol reagent (Ambion 317908) and use for RNA-seq.
RNA libraries for RNA-seq were prepared using SMAARTER mRNA-seq library prep kit following manufacture‘s protocols

treatment_protocol: ShRAN was transfected into PC3 cells by lentivirus and screened with different concentrations of purinomycin to obtain stable CTSZ knockdown and Vector cells

value: Tumor cell

value: shCTSZ


title: Large preB cell, IKDN, H3K4me3, rep2


title: PC3 cell，shCTSZ-6


title: PC3 cell，shControl-3

value: NC


title: C57BL6/N_HSP27Overexpression Transgenic(TG)_Bleomcyin (1.25mg/kg)

city: Seoul

first: Yun-Sil

last: Lee

address: 52, Ewhayeodae-gil, Seodaemun-gu

department: College of Pharmacy

country: South Korea

institute: Ewha Womans University

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Canine Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: Data was extracted using GeneSpringGX 7.3 (Agilent Technology, USA). Raw intensity data was globally normalized (Cheadle et al.(2003).

source_name: Whole lung_14days_1.25mg/kg

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: gender

value: male

tag: age

value: 6 weeks


title: PC3 cell，shCTSZ-5


title: C57BL6/N_Bleomcyin (1.25mg/kg)


title: Large preB cell, WT, H3K4me3, rep1


title: PC3 cell，shControl-1


title: Cell line Exon 11partc Ola Pool2 Replicate 1

city: Frederick

first: Shyam

last: Sharan

state: MD

address: Building 560, Room 32-33

institute: Mouse Cancer Genetics Program

data_processing:
The paired end reads were aligned to the reference sequence using the Needleman-Wunsch alignment algorithm after the reads were demultiplexed using bcl2fastq (Illumina), generation of fastq files, and merging using FLASH.
The total number of aligned reads were quantified using CRISPResso2 http://crispresso.pinellolab.org/submission. Iindividual unique alignments were annotated with a custom-made variant caller modified from ANNOVAR (64) (release 2019-10-21) and the R/Bioconductor Biostrings package in R version 4.1.2 https://bioconductor.org/packages/Biostrings. Merged reads containing “N” bases were removed from the analysis.
Abundances of SNVs were quantified when the reads contained a single-nucleotide substitution. Read counts for each SNVs were then normalized to the total read coverage of the sequencing library after adding a pseudocount of 1 to all reads for all conditions. Individual variants with a read count of more than 1 in 1,000 reads in the M15 condition were used for further analysis. Dropout or enrichment scores were calculated by taking the ratio of frequency of SNV after HAT, cisplatin, or olaparib treatment over that in M15.
The scores were expressed in log2 scale, which we define as the functional scores of SNVs in HAT, cisplatin, and olaparib. The functional scores, averaged between independent replicates (2-4), were used to calculate the the probabilities of impact on function (PIF) for all the variants in the data set.
Assembly: GRCh38
Supplementary files format and content: xlsx: Excel files include PIF and function scores for all variants.
Library strategy: Amplicon sequencing

extract_protocol:
Genomic DNA was extracted from the cell pellets using Zymo Genomic DNA Extraction kit
DNA libraries were prepared using TruSeq Nano DNA Library Prep kit

value: Embryonic stem cell

value: Olaparib


title: Large preB cell, WT, H3K4me3, rep2


title: Cell line Exon 11partc-2 HAT Pool1 Replicate 1

value: HAT


title: Large preB cell, WT, CTCF, rep1

value: CTCF (CST, 2899s)


title: Cell line Exon 11partc-2 M15 Pool1 Replicate 2


title: Cell line Exon 11partc-2 M15 Pool1 Replicate 1


title: PC3 cell，shControl-2


title: Large preB cell, IKDN, H3K4me3, rep1


title: Large preB cell, WT, IKAROS, rep1

description:
WTLpreB_IKAROS_R1_R2.pileup.bedgraph.gz
WTLpreB_IKAROS_R1_R2.pileup.bedgraph.gz.tbi

value: IKAROS (EMD Millipore, MABE912 & MABE913)


title: Large preB cell, WT, IKAROS, rep2

value: IKAROS (Abcam, ab191394)


title: Cell line Exon 11partc Ola Pool2 Replicate 2


title: Cell line Exon 11partc Cis Pool2 Replicate 2

value: Cisplatin


title: Cell line Exon 11partc HAT Pool2 Replicate 2


title: Cell line Exon 11partc Cis Pool2 Replicate 1


title: Large preB cell, IKDN, CTCF, rep1

value: mouse large pre-B cell (CD19+CD43+BP1+)

value: IkE5D/D (IKE5 fl/fl, Cd2-cre)


title: Large preB cell, IKDN, rep1

data_processing:
Alignment to the mouse mm10 assembly was conducted by STAR 5.02 (Dobin et al., 2013) on the DNAnexus platform
Normalization and differential expression by  DESeq2 were performed through a HOMER v4.10.4 implementation of the package in R.
Assembly: mm10

growth_protocol: Sorted wild-type and IkE5Δ/Δ large pre-B cells were cultured on OP9 stroma in DMEM ( D-5671; Sigma) supplemented with 10% FBS (2442; Sigma), 50 μM 2-mercaptoethanol, 100 μg/ml penicillin, 100 μg/ml streptomycin, 1× Glutamax (35050-062; Gibco), 10 mM HEPES (156-30-80; Gibco) and 1× sodium pyruvate (11360-070; Gibco) in the presence of 5ng/ml of IL-7. Stroma adherent large pre-B cells from WT or IKDN cultures were detached with 0.2% trypsin (EDTA free) for 2 minutes at room temperature. Large pre-B cells were ~ 99% of the cells in suspension as determined by flow cytometry.

extract_protocol:
Total RNAs were prepared using the Direct-zol RNA Miniprep (Zymo Research) and 1mg of total RNA was used for the construction of sequencing libraries.
The TruSeq Stranded mRNA Library prep kit was used for construction of cDNA libraries for RNA-sequencing (Illumina). The cDNA libraries were ligated with indexed primers and amplified by PCR for 10 cycles, multiplexed and sequenced in house with an Illumina NextSeq550 system.


title: Large preB cell, WT, rep2

value: Wild-type (IKE5 fl/fl, Cre-)


title: Large preB cell, IKDN, rep2


title: Large preB cell, WT, IL7 withdrawal day2, H3K4me3, rep1


title: Cell line Exon 11partc Cis Pool1 Replicate 2


title: Cell line Exon 11partc Ola Pool1 Replicate 2


title: Cell line Exon 11partc M15 Pool2 Replicate 1


title: Cell line Exon 11partc HAT Pool1 Replicate 1


title: Cell line Exon 11partc M15 Pool1 Replicate 2


title: Cell line Exon 11partc Ola Pool1 Replicate 1


title: Cell line Exon 11partc Cis Pool1 Replicate 1


title: Cell line Exon 11partc HAT Pool2 Replicate 1


title: Cell line Exon 11partc M15 Pool2 Replicate 2


title: Cell line Exon 25 batch2 Ola Pool2 Replicate 1


title: Late exponential 2308, biological rep 3

city: Pittsford

first: Paul

last: M Dunman

state: NY

address: 695 W. Bloomfield Rd

institute: University of Rochester

description: Gene expression data from late exponential phase wildtype 2308 cells

hyb_protocol: 1.5 ug of cDNA were hybrized for 16 hr at 45C on a B. abortus Affymetrix GeneChip.  GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.

scan_protocol: GeneChips were scanned in an Affymetrix 7G GeneArray Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.

label: Biotin

organism: Brucella abortus

source_name: Brucella abortus late exponential phase

label_protocol: cDNA was synthesized, fragmented and biotinylated according to the manufacturer's protocol for prokaryotic antisense labeling (Affymetrix)

growth_protocol: Cells were grown to late exponential phase in brucella broth at 37C with aeration

extract_protocol: Total bacterial RNA was isolated using Trizol according to the manufacturer's recommendations (Invitrogen)

treatment_protocol: Once reaching late exponential phase (measured by colony forming unit counts) 1:1 acetone-ethanol was added to inhibit cellular ribonucleases

tag: sample

value: Whole cell

value: Wildtype

tag: growth phase

value: Late exponential


title: Late exponential 2308, biological rep 2


title: Cell line Exon 11partc HAT Pool1 Replicate 2


title: Late exponential mavR, biological rep 3

description: Gene expression data from stationary phase 2308 cells containing mavR mutation

value: mavR