title: grass carp sperm, biological repeat 5

city: WuHan

first: Yi-Xuan

last: Tu

state: HuBei

address: 1 Shizishan Rd

department: College of Life Science and Technology

institute: Huazhong agricultural university

data_processing:
Illumina Casava software used for basecalling.
FastQC was used to check the quality of the raw sequence fastq files. High-quality pruning was performed using fastp.
Paired end reads were mapped to the reference genome of NCBI (HZGC01) using HISAT2. And SAMtools is used to sort and index aligned BAM files.
Reads were counted using the featureCounts program in the Subread.
Assembly: HZGC01
Supplementary files format and content: counts

organism: Ctenopharyngodon idella

source_name: sperm

extract_protocol:
Sperm samples were collected from five zebrafish, three GSCT zebrafish and five wild-type grass carps. 0.5 μL sperm from each fish was diluted into 20 μL Hank’s buffer. For one sample, 1μL of diluted sperm was used to extract RNA and synthetize cDNA in one reaction using the single cell full length mRNA-amplification kit (N712, Vazyme) following manufacturer's protocols.
cDNA was used to prepare DNA library for sequencing using the DNA Library Prep Kit for Illumina (TD504, Vazyme) following manufacturer's protocols.

value: sperm

value: wildtype


title: BV-2 cells LPS+NMN 2

status: Public on Mar 01 2025

type: SRA

city: Yinchuan

first: Yin

last: Wang

address: 1160 Shengli St

country: China

institute: Ningxia Medical University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software is used for base-calling.
Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12)
The MACS2 (version 2.1.0) peak calling software was used to identify regions of IP enrichment over the background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level, and peak summit number per peak were all displayed.
Homer (Heinz et al., 2010) was used to detect the denovo sequence motif and the matched known motifs.
Peak related genes can be confirmed by PeakAnnotator
Assembly: GRCm38
Supplementary files format and content: FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: BV-2 cell line

extract_protocol:
RNA were harvested using Trizol reagent. 1.5ug total RNA were used for constracution of sequencing library.
RNA library were prepared for sequecing using standard illumina protocols

tag: cell line

value: BV-2 cell line

tag: cell type

value: macroglia

tag: treatment

value: LPS+NMN


title: iSAM hESCs after CRISPRa screen interrogation to discover CCRs using high MOI gRNA library (gRNA library)

city: New York

first: Julian

last: Pulecio

state: NY

department: Developmental Biology

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: Multiplex array (high MOI) gRNA library
Custom gRNA library

library_source: other

data_processing:
FASTQ files were pre-processed via 10x Genomics CellRanger -8.0.0. The files were aligned to GRCh38 (refdata-gex-GRCh38-2024-A) and counted by ‘cellranger count’
For the single array samples we combined the alignment results files from the seven 10X reactions into one, by employing ‘cellranger aggr --normalize=none’ to obtain the filtered count matrix.
Assembly: hg38 h.sapiens
Supplementary files format and content: CellRanger Matrix Files combining the gRNA library and Transciptome library results

molecule: other

organism: Homo sapiens

source_name: Embryo

growth_protocol: hESC iSAM line was cultured in Essential 8 (E8) medium (Thermo Fisher Scientific) on vitronectin (Thermo Fisher Scientific) pre-coated plates at 37 °C with 5% CO2. Medium was changed every day.

extract_protocol:
mCherry+ hESCs transduced with the 4 different library conditions were FACS-sorted and 2 cellular mixes were prepared as it follows: 1.) 500000 cells at 97:3 ratio = low MOI candidate CCR-library transduced hESCs : low MOI negative control transduced hESCs. 2.) 100000 cells at 97:3 ratio = high MOI candidate CCR-library transduced hESCs : high MOI negative control transduced hESCs. Cellular suspensions were loaded on a Chromium Controller targeting 30000 cells per reaction. Seven reactions for the low MOI condition and one reaction for the high MOI condition were loaded.
Single-cell 3′ transcriptome libraries were generated following the manufacturer’s instructions (10x Genomics Chromium Single Cell 3′ Reagent Kit v3.1-Dual Index User Guide). gRNA libraries were generated by amplifying the fragment that contains the gRNA sequence from the MS2-CROP construct (see oligos in table S9), and a second PCR to add index adaptors from the Chromium Single Cell 3′ Reagent Kit v3.1-Dual Index.

treatment_protocol: iSAM cells were transduced with a gRNA library targeting candidate CCRs at a low and high MOI. In parallel, iSAM cells were independently transduced at high and low MOIs with the libraries of the candidate CCRs + promoters and the “control gRNA libraries” ( a total of 4 independent transductions). After selection 4 days with puromycin, cells were treated with doxycycline for 3 additional days, washed with PBS and treated with TrypLE Select for 2 minutes, washed 2 times with PBS containing 0.04%BSA and filtered through CellTrics™ (20μm, Sysmex) to be sorted in a Flow Cytomete using the mCherry live marker (see Addgene #153457).

tag: tissue

value: Embryo

value: Embryonic Stem Cells

value: Multiplex-Array gRNA library transduced


title: HCC tumor, IMQNP_3

city: Hsinchu

first: Hsin mei

last: Lee

address: Guangfu Rd.

country: Taiwan

institute: National Tsing Hua University

description: Library name: IMQNP_3

data_processing:
Illumina Casava software used for basecalling.
FastQC and MultiQC were used to check fastq files for quality.The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0).
FeatureCounts (v2.0.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Relative Log Expression” normalization (RLE) was performed DEGseq2 (v1.26.0).
Assembly: mm_GRChm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TMM values for each Sample

source_name: tumor

growth_protocol: Murine HCC HCA-1 cells were orthotopically implanted in the liver of 6–8-week-old male C3H mice. 1 × 10^6 HCA-1 cells were injected in the subcapsular region through a 28-gauge needle.

extract_protocol:
The integrity of RNA extracted from the treatment and control groups using the RNeasy Kit (Qiagen) was evaluated with the RNA Nano6000 assay kit (Agilent Technologies, CA, USA)
RNA libraries were prepared for sequencing using KAPA mRNA HyperPrep Kit Illumina® Platforms protocol

treatment_protocol: The experimental design involved orthotopically implanting murine HCC (HCA-1) cells in C3H mice, followed by IV administration of PFSUV-IMQ on day 17. Subsequent transcriptome analysis of the tumors was performed after 3-hour circulation.

value: tumor

value: HCC


title: BV-2 cells LPS+NMN 3


title: BV-2 cells LPS+NMN 1


title: grass carp sperm, biological repeat 4

molecule: polyA RNA

tag: genotype


title: iSAM hESCs after CRISPRa screen interrogation to discover CCRs using high MOI gRNA library (transcriptome)

description:
Library name: Multiplex array (high MOI) transcriptome library
10x genomic

library_source: transcriptomic single cell


title: HCC tumor, IMQNP_2

description: Library name: IMQNP_2


title: BV-2 cells NMN 3

value: NMN


title: grass carp sperm, biological repeat 3


title: iSAM hESCs after CRISPRa screen interrogation to discover CCRs using low MOI gRNA library (gRNA library)

description:
Library name: Single array (low MOI) gRNA library
Custom gRNA library

value: Single-Array gRNA library transduced


title: HCC tumor, IMQNP_1

description: Library name: IMQNP_1


title: grass carp sperm, biological repeat 2


title: iSAM hESCs after CRISPRa screen interrogation to discover CCRs using low MOI gRNA library (transcriptome)

description:
Library name: Single array (low MOI) transcriptome library
10x genomic


title: HCC tumor, Control_5

description: Library name: Control_5


title: BV-2 cells NMN 1


title: BV-2 cells NMN 2


title: grass carp sperm, biological repeat 1


title: HCC tumor, Control_4

description: Library name: Control_4


title: GSCT sperm, biological repeat 3

value: surrogate reproduction


title: HCC tumor, Control_3

description: Library name: Control_3


title: CGND-HRA-03760

first: Christopher

last: Jackson

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

description: Library name: M143

data_processing:
Sequenced 10x libraries were aligned to a standard reference genome (hg38; GENCODE v32/Ensembl98) and counted (Cellranger-ARC v2.0.2). ATAC peaks were aligned between samples for quantification (Cellranger-ARC aggr v2.0.2)
Cell type annotations and low-quality/doublet cells were determined with a pre-trained ML model of snRNA-seq prefrontal cortex expression
Assembly: hg38
Supplementary files format and content: aggr.csv is a CSV file identifying sample libraries in cellranger-arc aggregated file filtered_feature_bc_matrix.h5
Supplementary files format and content: filtered_feature_bc_matrix.h5 is cellranger-arc aggregated GEX/ATAC file for all samples
Supplementary files format and content: BA44_BA46_COUNTS.h5ad is a scanpy/anndata file with integer gene expression counts and associated metadata for all cells
Supplementary files format and content: BA44_BA46_ATAC_COUNTS is a scanpy/anndata file with integer ATAC peak counts and associated metadata for all cells which pass ATAC filtering

extract_protocol:
Nuclei isolation protocol was adapted from previously described methods (PMID: 31042697; PMID: 36385529). All procedures were carried out on ice unless otherwise stated. Frozen post-mortem brain tissue was retrieved from storage at -80 °C and equilibrated on dry ice for 20–30 minutes before being transferred to a cryostat at -18 °C. Tissue samples were left for 15–20 minutes inside the cryostat before sectioning. We collected 20-50 mg of tissue per preparation, taking care to avoid excessive sampling of white matter. Tissue cuts were placed in a pre-chilled Dounce homogenizer containing 700 µL of ice-cold homogenization buffer (320 mM sucrose, 5 mM CaCl2 [#21115; Millipore Sigma], 3 mM magnesium acetate [#63052; Millipore Sigma], 10 mM Tris HCl [pH 7.8; prepared from Thermo Fisher’s #AM9850G and #AM9855G], 0.1 mM EDTA [pH 8.0; Thermo Fisher #AM9260G], 0.1% IGEPAL CA-630 [#I8896; Millipore Sigma], 1 mM DTT [#646563, Millipore Sigma], and 0.4 U/µl Protector RNase inhibitor [#03335402001, Millipore Sigma]). Homogenization was performed with 10 strokes of the loose pestle followed by 10 strokes of the tight pestle. After a 5-minute incubation on ice, the homogenized tissue was passed through a 70-µm Flowmi Cell Strainer (Bel-Art; H13680-0070) and combined with an equal volume of a solution made of 50% OptiPrep (#07820, STEMCELL Technologies), 5 mM CaCl2, 3 mM magnesium acetate, 10 mM Tris HCl (pH 7.8), 0.1 mM EDTA (pH 8.0), and 1 mM DTT. Using a 15-mL conical tube, this mixture was then layered onto a density gradient made up of 750 µL of a 30% OptiPrep solution supplemented with 134 mM sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 10 mM Tris HCl (pH 7.8), 0.1 mM EDTA (pH 8.0), 1 mM DTT, 0.04% IGEPAL CA-630, and 0.17 U µl−1 RNase inhibitor) over 300 µL of 40% OptiPrep solution supplemented with 96 mM sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 10 mM Tris HCl (pH 7.8), 0.1 mM EDTA (pH 8.0), 1 mM DTT, 0.03% IGEPAL CA-630, and 0.12 U µl−1 RNase inhibitor. Nuclei were separated by centrifugation at 3,000 × g for 20 minutes at 4 °C using a pre-chilled swinging-bucket rotor with the brake off. Approximately 150 µL of nuclei were collected from the 30%/40% gradient interphase and subsequently washed in PBS containing 1% BSA and 1 U µl-1 RNase inhibitor. Following a 5-minute incubation on ice, the nuclei were centrifuged at 450 × g for 3 minutes at 4 °C, and the pellet resuspended in 15 µL of diluted 10X Genomics Nuclei Buffer. Nuclei counting was performed using a Countess II FL instrument (Thermo Fisher) by staining with SYTOX Green (ThermoFisher; S7020). Additional quality control measures included Trypan Blue staining (#EBT-001, NanoEntek) to evaluate adequate permeabilization (cutoff: >95% of ‘dead cells’) and the assessment of nuclear morphology before proceeding with transposition.
Matched snRNA-seq and snATAC-seq libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (#PN-1000283) according to the protocol provided by 10X Genomics. Nuclei (16,100 per reaction; targeted recovery: 10,000 nuclei) from a single donor were used for each library preparation. Partitioning of nuclei was performed on a Chromium X instrument (10X Genomics). Quality control of cDNAs and libraries was conducted using Agilent High Sensitivity DNA Kits and a BioAnalyzer instrument. Final library quantification prior to pooling utilized KAPA Biosystems’ Library Quantification Kit for Illumina Platforms (KK4824). Libraries were sequenced on a NovaSeq X system using a 2 × 100 bp configuration run on a 10B flow cell. BA44/45 and BA46 libraries (n = 48) were prepared and sequenced in independent batches.

tag: donor id

tag: als phenotype

value: ALS

tag: race

value: White

tag: Sex

value: Female

tag: age

tag: pmi


title: BV-2 cells LPS 3

value: LPS


title: CGND-HRA-02746

description: Library name: M141

value: ALSci

value: Male


title: BV-2 cells LPS 2

value: BV-2 cell line


title: GSCT sperm, biological repeat 2

value: sperm


title: P21 Mouse retina WGBS Tet1/2/3 tcKO Replicate 3

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

description: Library name: P21 Tet1/2/3 tcKO Replicate 3 WGBS

library_source: genomic

data_processing:
bACE-seq: Paired-end sequencing reads were processed with TrimGalore (v0.4.4_dev) to remove adapters and low-quality sequences using the parameters --paired --clip_R1 16 --clip_R2 16. The trimmed reads were independently aligned to the mouse genome (mm10) using Bismark (v0.18.2). Read 1 (R1) was aligned with Bowtie2 in PBAT mode (--pbat flag) and the following settings: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --directional. Read 2 (R2) was mapped using Bowtie2 with default parameters. Aligned reads were filtered to retain only those with a mapping quality score ≥ 10 using Samtools (v1.15.1) and PCR duplicates were removed using Picard’s MarkDuplicates tool (GATK v4.1.3). CpG methylation levels were extracted with MethylDackel (v0.6.1) using the --CHG and --CHH flags alongside default settings. Finally, strand-specific read counts were combined using a custom Python script.
WGBS: WGBS data were processed using the same pipeline as described for bACE-seq analysis (above), with modifications to the  alignment steps. Reads were aligned to the mouse genome (mm10) using Bismark (v0.18.2) with default alignment parameters (PBAT mode turned off).
Differentially Methylated Region (DMR) Analysis - DMRs were identified using DSS (v2.48.0). The DMLtest function was applied with smoothing=TRUE and default parameters. DMRs were called with a p-value threshold of 0.01. To define DMRs, a minimum length of 50 bp and at least 3 CpG sites were required, with DMRs within 50 bp merged (following DSS default settings). DMR annotation was performed using ChIPseeker (v1.36.0), with the transcription start site (TSS) Region set to +/- 2000 bp and default settings. Mouse gene annotations from TxDb.Mmusculus.UCSC.mm10.knownGene were used for the annotation process.
Assembly: mm10
Supplementary files format and content: diff.Methy .csv files

molecule: genomic DNA

source_name: Whole Retina

extract_protocol:
Retinas from P21 animals were dissected in PBS and homogenized in 1ml TRIZOL solution. 200µl of chloroform was added to homogenized TRIZOL solution, mixed by vortexing and incubated for 3 min at RT. Lysates were centrifuged for 10 min at 4C at max speed (16,000g). The aqueous phase with RNA was transferred into a fresh tube without disturbing the interphase. The rest of the volume, containing DNA and proteins was washed with 300µl 100% ethanol, inverted several times, and then centrifuged for 5 min at 4C at 2000g. The supernatant containing proteins was carefully removed so as to not disturb the precipitated DNA pellet. The DNA pellet was washed in 1mL of 100mM sodium citrate in 10% ethanol and incubated for 30 min at RT followed by centrifugation 5 min at 4ºC at 2000g and removal of the resulting supernatant. This step is repeated twice. 1.5mL of 75% ethanol was added to the DNA pellet and incubated for 20 min at RT using occasional mixing during the 20-minute incubation. The supernatant is discarded, and the DNA pellet is air dried for 10 min. 100µl of 8mM NaOH in 1mM EDTA pH 7-8 was added to resuspend the DNA pellet. After that, samples are centrifuged for 10 min at 4ºC and max speed (16,000g). The supernatant is transferred to a new tube and stored at -20ºC. DNA concentrations were measured in a Qubit fluorometer.
Genomic DNA was quantified using the Qubit fluorometer. 200ng of gDNA, including 0.2% Lambda DNA (N6-methyladenine-free; NEB) was fragmented in a final volume of 50uL using the Covaris LE220 targeting ~350bp inserts. A 1.5x AMPure clean-up was utilized after fragmentation to concentrate the sample. The fragmented gDNA was bisulfite converted with the EZ-96 DNA Methylation-Gold Mag Prep Kit (Zymo Research, Cat # D5043) according to the manufacturer’s recommendations. Bisulfite converted DNA was quantitated on the Qubit Fluorometer using the ssDNA Assay Kit (Thermo Fisher Scientific, Cat #Q10212). Whole genome bisulfite libraries were constructed with ~100ng of converted DNA using the xGen™ Methyl-Seq Library Prep Kit (Integrated DNA Technologies, Cat # 10009825) using unique dual indexes (IDT, 0008053) and eight PCR cycles for incorporation and amplification of indexed libraries, followed by a final 0.85x AMPure cleanup. Final libraries are quality checked for average library size and concentration. Molar concentration of libraries was determined using the KAPA Library Quantification kit (Roche Diagnostics). Libraries were sequenced on NovaSeq X using 150bp paired end reads.
bACE-seq: 10-15ng of RNAse treated, TRIZOL purified gDNA was used for each sample. Samples were diluted to 10µL in MilliQ water and pre-heated by incubating at 50C for 20 minutes on a thermocycler with a heated lid set to 95ºC. 32.5µL of CT Conversion Reagent (Zymo EZ DNA Methylation Direct Kit) was then added to each sample before running the the following program on a thermocycler (98ºC for 8min, 64ºC for 105 min, followed by 98ºC for 8 min, 64ºC for 105 min), with the lid set to 95ºC. Following the bisulfite reaction, the tubes were placed at -20ºC overnight, or for 16 hours. The bisulfite converted DNA was then purified using the Zymo EZ Methylation Direct Kit, eluting with 17µL of MilliQ water for a final elution volume of 16µL. Each sample was incubated at 95ºC for 3 minutes on a thermocycler, with the lid set to 105ºC. The samples were then immediately placed into a dry-ice ethanol bath to snap cool them and were left in the cooling bath for 5 minutes. The samples were then placed on a pre-chilled PCR rack and kept on ice. 8µL of premixed APOBEC reaction mixture (2.4µL APOBEC reaction buffer (E7134A, NEB), 0.48µL APOBEC (E7133AA, NEB), 0.48µL BSA (B9000S, NEB), water to 8µL) was added to each tube and samples were incubated at 37ºC on a thermocycler with the lid set to 95ºC. After 30 min, the samples were mixed and placed back on the thermocycler for two and a half hours at 37ºC with the lid set to 95ºC. DNA was purified from the reaction using 2X Agencourt AMPure XP SPRI beads (add 2X volume of SPRI beads, incubate at room temperature for 10 minutes, place samples on magnet and wash 2 times with fresh 80% ethanol, dry for 3 min, elute in 9µL Low EDTA TE (IDT). Sequencing libraries were constructed using the xGen Adaptase Module with minor modification. 250nM of random stubby index primer was added to each sample (xGen Adaptase Module, P5L_AD002_H). Samples were incubated at 95ºC on a thermocycler with the lid set to 105ºC for 3 min, then cooled on ice for 2 min. 10µL of BST-based random priming mixture (2µL 10X ISO AMP Buffer II (B0374S, NEB), 0.8µL BST 3.0 (M0374S, NEB), 1.2µL 200mM MgCl2, 2.8µL 10mM dNTP, 3.2 µL water) was then added to each sample and incubated at 60ºC for 1 hour on a thermocycler with the lid set to 95ºC. Fragment ends were blunted and dephosphorylated by adding 2µl Exonuclease I (M0293L, NEB) and 1µl shrimp alkaline phosphatase (M0371S, NEB) to each sample. The samples were then incubated at 37ºC for 30 min and purified using a 1.6X SPRI beads (add 1.6X volume of SPRI beads, incubate at room temperature for 10 minutes, place samples on magnet and wash 2 times with fresh 80% ethanol, dry for 3 min, elute) Samples were eluted in 10 µL Low EDTA TE (IDT). In brief, samples were denatured by incubating at 95ºC on a thermocycler with the lid set to 105ºC for 3 min, then cooled on ice for 2 min. Samples were indexed and amplified using the PCR protocol in the xGen Adaptase Module using 21 cycles. The indexed samples were purified using 1.6X SPRI beads (add 1.6X volume of SPRI beads, incubate at room temperature for 10 minutes, place samples on magnet and wash 2 times with fresh 80% ethanol, dry for 3 min, elute) and eluted in 12µL Low EDTA TE (IDT).

value: Whole Retina

tag: strain

value: C57 BL/6J

value: Tet tcKO


title: BV-2 cells LPS 1

value: macroglia


title: BV-2 cells Control 3

value: Control


title: CGND-HRA-03641

description: Library name: M124


title: P21 Mouse retina WGBS Tet1/2/3 tcKO Replicate 2

description: Library name: P21 Tet1/2/3 tcKO Replicate 2 WGBS


title: HCC tumor, Control_1

description: Library name: Control_1

value: tumor

value: HCC


title: BV-2 cells Control 2


title: GSCT sperm, biological repeat 1


title: CGND-HRA-03649

description: Library name: M137


title: CGND-HRA-03629

description: Library name: M144


title: P21 Mouse retina WGBS Cre- Replicate 3

description: Library name: P21 Cre- Replicate 3 WGBS

value: WT


title: KO4

city: Wenzhou

first: Shenmeng

last: Gao

state: Zhejiang Province

address: 1 Xuefubei Street, Ouhai District

department: Laboratory of Internal Medicine

institute: The First Affiliated Hospital of Wenzhou Medical University

description: mRNA Expression for all samples

data_processing:
miR-182 knockout type(182KO) and wild type(182WT) gene mice were constructed.
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Bone Marrow

growth_protocol: Mice aged 6-8 weeks were selected for bone marrow cell transplantation

extract_protocol:
ransfer to flow cytometry, and sort 2 * 106 GFP+B220+(182WT/182NC) BM cells to trizol.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The positive rate of GFP in peripheral blood of mice was detected regularly 3 weeks after bone marrow cell transplantation

value: Bone Marrow

value: acute lymphoblastic leukemia

value: miR-182 KO

tag: time

value: Day 0


title: P21 Mouse retina WGBS Cre- Replicate 2

description: Library name: P21 Cre- Replicate 2 WGBS


title: CGND-HRA-02964

description: Library name: M127

value: White

value: Female


title: CGND-HRA-02745

description: Library name: M134

value: ALSci


title: Rosette leaf_ 16hpi_Methanol_rep2

type: RNA

city: Hyderabad

first: Subhadeep

last: Chatterjee

address: Uppal, Hyderabad

country: India

institute: Center for DNA Fingerprinting and Diagnostics, Hyderabad

description: Gene expression after 16hpi Methanol treatment

hyb_protocol: Labeled cRNA sample were fragmented at 60ºC and hybridized on to Agilent Arabidopsis Gene Expression 8x60k Microarray. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method and gene based analysis was performed.

organism: Arabidopsis thaliana

source_name: Rosette leaf_ 16hpi_Methanol treatment

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Arabidopsis thaliana Col0 wild type seedings were initially germinated on sterile half strength Murashige and Skoog plant growth promotion medium. The seedlings with four leaves stage is then transplants into pots containing soilrite individually. The seedlings were grown for 4weeks in a plant growth chamber with controlled growth conditions mainaning a photoperiod of 12hours light and 12hours dark, 65% humidity, 22 deg C temperature and light of 200LUX until the rosette leaves are completely elongated for DSF infiltration.

extract_protocol: RNA was prepared using TRIZOL method following the manufacturer's recommendations.

treatment_protocol: Rosette leaves of 4 week old Arabidopsis thaliana seedlings were syringe infiltrated without a needle on their abaxial surface with 100uM DSF elicitor concentration prepared in a solvent of Methanol. Further, the treated seedlings were maintained in a plant growth chamber with controlled growth conditions with a photoperiod of 12hours light and 12hours dark, 65% humidity, 22 deg C temperature and light of 200LUX until excised for RNA extraction in TRIZOL at 4hpi, 8hpi and 16hpi. (hpi-hours post infiltration)

tag: ecotype

value: Leaf


title: CGND-HRA-03647

description: Library name: M138

value: Male


title: KO2

description: mRNA Expression for all samples


title: P21 Mouse retina WGBS Cre- Replicate 1

description: Library name: P21 Cre- Replicate 1 WGBS

value: Whole Retina


title: KO3

description: mRNA Expression for all samples


title: Huh7_control_3 rep3

city: shanghai

first: Wangl

middle: si

last: kai

address: fenglin road

institute: zhongshan hospital

data_processing:
SOAPnuke (Version 1.5.2)
SOAPnuke (Version 1.5.2) was performed to clean the sequencing data via removing reads which contained sequencing adapter, contained more than 20% of low-quality base ratio (ratio less than or equal to 5) and contained more than 5% unknow base (‘N’ base) ratio. The cleaned reads, consequently, were acquired and stored in FASTQ format.
HISAT270 was used to align the cleaned reads to the reference human genome.
Bowtie2 (Version 2.2.5) was used to align the cleaned reads to the reference coding gene set.
RSEM (Version 1.2.12) was used to compute the expression level of gene and Count data was generated.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes row counts for each sample.

growth_protocol: Cells were maintained in high glucose DMEM with10% fetal bovine serum and 1% penicillin and streptomycin with 5% CO2 at 37.

extract_protocol:
Cells were collected and total RNA of the cells were extracted by TRIzol reagent (Thermo Fisher)
Agilent 2100 Bioanalyzer (ABI) was performed to assessed quantity and quality of the cDNA libraries. The Double-stranded PCR products were treated with thermal denaturation and cyclization reaction using the splint oligo sequence and the final library was generated. Phi29 (Thermo Fisher) was utilized for amplifying the single-stranded circular DNA and then a DNA nanoball was generated.

treatment_protocol: Huh7 cells were exposure to HSP90 inhibitor 17-AAG.

value: Liver cancer cells

value: control group


title: Rosette leaf_ 16hpi_DSF_rep2

description: Gene expression after 16hpi DSF treatment

source_name: Rosette leaf_ 16hpi_DSF treatment


title: CGND-HRA-02985

description: Library name: M139


title: Rosette leaf_ 4hpi_DSF_rep2

description: Gene expression after 4hpi DSF treatment

source_name: Rosette leaf_ 4hpi_DSF treatment


title: Huh7_control_2 rep2


title: CGND-HRA-02747

description: Library name: M123

value: ALS


title: WT4

description: mRNA Expression for all samples


title: Rosette leaf_ 16hpi_Methanol_rep1


title: P21 Mouse retina WGBS Tet1/2/3 tcKO Replicate 1

description: Library name: P21 Tet1/2/3 tcKO Replicate 1 WGBS

value: C57 BL/6J

value: Tet tcKO


title: CGND-HRA-02749

description: Library name: M130


title: Huh7_control_1 rep1


title: BV-2 cells Control 1

value: BV-2 cell line

value: macroglia

value: Control


title: WT3

description: mRNA Expression for all samples

value: Bone Marrow

value: acute lymphoblastic leukemia

value: WT


title: WT1

description: mRNA Expression for all samples

value: Day 0


title: P16WT SCJ Squamous Replicate 3

city: Washington

first: Jorge

middle: Lemos

last: Sepulveda

state: DC

address: 2300 M Street NW, Suite 700

department: Pathology

institute: George Washington University

hyb_protocol: The fragmented and labeled ss-cDNA was hybridized to the GeneChip mouse WT Array for 16h at 45C and 60 rpm. After hybridization, arrays were washed, stained, and scanned.

scan_protocol: Followed manufacturer's instructions.

data_processing: Microarray data was analyzed with Transcriptome Analysis Console 4.0 (TAC) software version 4.0.2.15 (Applied Biosystems - Thermo Fisher Scientific, Waltham, MA).  First, data was normalized, summarized, and distributions adjusted for GC content and compression effects using the Signal Space Transformation-Robust Multichip Analysis (SST-RMA) algorithm. All samples were considered as passed after examination of all QC metrics. For all samples, all hybridization controls performed as expected. Principal component analysis with 3 components showed excellent separation between glandular and squamous samples. Comparisons of differentially expressed genes between groups were performed using the Empirical Bayes (eBayes) ANOVA method. A probeset (gene or exon) was considered expressed if ≥ 50% of the samples had "detected above background" (DABG) scores below the DABG threshold of ≤ 0.05. Microarray expression differential was further compared with RNASeq data using custom R code as described in the publication.

label: biotin

source_name: Mouse SCJ-Squamous

label_protocol: Briefly, 0.3 ng of purified total RNA was used for reverse transcription initiated at the poly-A tail and throughout the entire length of RNA to capture both coding and multiple forms of non-coding RNA. RNA amplification was achieved using low-cycle PCR followed by linear amplification using T7 in vitro transcription technology. Then, the cRNA was converted to biotinylated sense-strand DNA (ss-cDNA) hybridization targets for unbiased coverage of the transcriptome

growth_protocol: All mice were fed standard irradiated feed (LabDiet 5V75) and bedded in corn cob bedding (1/8” Bed-O-Cob) in individually ventilated cages (Tecniplast emerald line). Interventions were done during the light cycle.

extract_protocol: Total RNA was extracted with the RNeasy plus Micro Kit (QIAGEN, Germantown, MD) following the manufacturer protocol. RNA quality and quantity were assessed utilizing NanoDrop Spectrophotometer and qPCR and RNA integrity was analyzed with the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and then used for mouse Clariom D transcriptome microarray.

treatment_protocol: At the age of 6-8 weeks, all mice were treated with 133 mg/kg of tamoxifen (Sigma-Aldrich, St Louis, MO), administered via IP (intraperitoneal) injection every 48 hours, for a total of 3 injections.  Starting at the age of 3 months, mice were given 0.2% sodium deoxycholate (bile acid, BA) (Sigma-Aldrich) in their drinking water ad libitum.

value: SCJ squamous mucosa

tag: age (months)


title: CGND-HRA-03639

description: Library name: M128

value: White

value: Female


title: Huh7+17-AAG_3 rep3

value: 17-AAG group

value: 17-AAG treatment


title: P16WT SCJ Squamous Replicate 2


title: Huh7+17-AAG_2 rep2

value: Liver cancer cells


title: Colon, Candida tropicalis, 30days, rep2 [CT_R]

city: Taipei

first: Hao-Sen

last: Chiang

address: No.1, Roosevelt Road

department: Department of Life Science

institute: National Taiwan University

data_processing:
Data filtering was processed through in-house perl scripts.
Read alignment: TopHat v2.0.12
Read count: HTSeq v.6.1
Differential expression analysis: DESeq R package (1.18.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Colon

extract_protocol:
RNA was extracted from the colon using the RNeasy Mini kit (Qiagen). 3 μg RNA was used for the construction of sequencing libraries.
Sequencing libraries were produced using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (E7530L; New England BioLabs) following the manufacturer’s guidelines.

value: Colon

value: female

value: C. tropicalis MYA-3404


title: Rosette leaf_ 8hpi_DSF_rep2

description: Gene expression after 8hpi DSF treatment

source_name: Rosette leaf_ 8hpi_DSF treatment

value: Leaf


title: CGND-HRA-03653

description: Library name: M142

value: ALS

value: Male


title: Colon, Candida tropicalis, 30days, rep1 [CT_LL]


title: CGND-HRA-02751

description: Library name: M131


title: Rosette leaf_ 16hpi_DSF_rep1


title: P16WT SCJ Squamous Replicate 1


title: Huh7+17-AAG_1 rep1


title: Rosette leaf_ 4hpi_DSF_rep1


title: Rosette leaf_ 8hpi_DSF_rep1


title: Colon, Candida albicans, 30days, rep3 [CA_R]

value: C. albicans SC5314


title: P16KO SCJ Gland Replicate 3

source_name: Mouse SCJ-Glands

value: SCJ glandular mucosa


title: CGND-HRA-02972

description: Library name: M132


title: Colon, Candida albicans, 30days, rep1 [CA_L]


title: Colon, Candida albicans, 30days, rep2 [CA_LL]


title: CGND-HRA-02978

description: Library name: M126


title: P16WT SCJ Gland Replicate 2


title: Colon, control, 30days, rep3 [C_X]

value: control


title: P16KO SCJ Gland Replicate 2


title: CGND-HRA-02750

description: Library name: M129


title: Colon, control, 30days, rep2 [C_RR]

value: WT


title: Motor neurons under normal gravity NG3

city: 武汉市

first: yang

last: fei

address: 狮子山街道

institute: 无

data_processing:
Raw reads were adaptor trimmed and quality controled with trimiomatic
Clean reads were aligned and processed with Hisat2 and Samtools
Alignment result were counted with StrignTie and FeatureCount
Differential analysis were conducted with DeSeq2
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts of each sample

growth_protocol: Moter neuron progenitors were cultured in neural culture medium added with 0.01μM RA and 0.1μM SAG to differentiate to motor neurons.

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

treatment_protocol: Two-dimensional (2D) clinostat was used to simulate microgravity (SMG).

value: Motor neurons derived from embryonic stem cells

value: normal gravity


title: P16WT SCJ Gland Replicate 1


title: Motor neurons under normal gravity NG2


title: P16WT SCJ Gland Replicate 3


title: CGND-HRA-02754

description: Library name: M121

value: Control

value: White


title: Motor neurons under microgravity SMG3

value: microgravity


title: Colon, control, 30days, rep1 [C_R]


title: P16KO SCJ Gland Replicate 1

value: Female


title: R1/E cells shControl, H3K27me3

city: Guangzhou

first: Mangmang

last: Li

state: Baiyun District

address: 1023 Shatai South Road

institute: Southern Medical University

data_processing:
bwa mem -o {output} -t {threads} {params.reference} {input.r1} {input.r2} 1>{log.std} 2>{log.err}
samtools view -@ {threads} -bS -o {output} {input} 1>{log.std} 2>{log.err}
samtools sort -@ {threads} -o {output} {input} 1>{log.std} 2>{log.err}
samtools index -@ {threads} {input} 1>{log.std} 2>{log.err}
samtools view -F 1804 -f 2 -q 30 -bS -@ {threads} -o {output} {input} 1>{log.std} 2>{log.err}
bedtools intersect -v -a {input.bam} -b {input.blackList} 1>{output} 2>{log.err}
samtools index -@ {threads} {input} 1>{log.std} 2>{log.err}
bamCoverage --bam {input.bam} --outFileName {output} --outFileFormat bigwig --binSize 10 --numberOfProcessors {threads} 1>{log.std} 2>{log.err}
bigWig files were normalized using S3V2_IDEAS packages with binsize=50
Assembly: mm10
Supplementary files format and content: bigWig files normalized using S3V2_IDEAS packages with binsize=50

source_name: R5/E cells

extract_protocol:
40 million cells were fixed with 1% formaldehyde for 10 minutes at room temperature. Fixation was stopped with 0.125 M glycine, the cell pellets were washed with cold PBS three times. And cells were prepared using a step-by-step process involving Lysis buffer 1 (50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100), Lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA), and Lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholdate, and 0.5% N-lauroylsarcosine). All buffers were freshly supplemented with  1 mM PMSF, 5 mg/mL leupeptin, 5 mg/mL pepstatin, and 10 mg/mL aprotinin. Chromatin fraction was sonicated with a Bioruptor® Plus to shear DNA to a size of 300-500bp. Samples were centrifuged at 12,000 ×g for 10 min at 4°C and supernatants collected. Specific antibodies and protein A-agarose beads were used to immunoprecipitate the antibody/protein/DNA complexes. The protein-DNA-antibody complexes were washed 5 times with cold Wash buffer(50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, and 0.7% Na-Deoxycholdate), and eluted in elution buffer TES (10 mM Tris-HCl+1% SDS). Crosslinks were reversed overnight at 65°C. After RNase A and proteinase K treatment, the DNA was purified by phenol/chloroform extraction and ethanol precipitated and was quantified using QubitTM 3.0.
ChIPed DNA was reverse-crosslinked and purified for DNA library construction followed by sequencing. Libraries were sequenced on HiSeq PE150.

value: R5/E cells

tag: antibody


title: R1/E cells shTrim28, H3K27me3

source_name: R6/E cells

value: R6/E cells


title: CGND-HRA-02753

description: Library name: M136


title: Rescued, scRNAseq

city: Dallas

first: Matt

last: Sieber

state: Texas

address: 5323 Harry Hines blvd, MC 9040 ND12.214

institute: UT Southwestern Medical Center

description: 10x Genomics

data_processing:
We used the cellranger 5 pipeline for counting as recommended by 10X genomics. All secondary data analysis was sone using 10XGenomics Cloupe browser.
Assembly: DM6
Supplementary files format and content: Tab-separated values files and matrix files

organism: Drosophila melanogaster

source_name: posterior midgut

extract_protocol:
The midgut region of 30 Drosophila intestines per sample was harvested in PBS with 2% BSA on ice. Samples were transferred into a tube containing 100µL trypsin (0.75%) and 100µL elastase (2mg/ml). Samples are incubated at 37C for 15 minutes with gentle pipetting in between. 250uL Schneider’s media is added into the tubes and tubes are transferred onto ice. Samples are filtered by using 40um strainer and centrifuged for 1.5 minutes at 1000 rcf at 4C. The supernatant was removed and cells were washed with 400uL PBS. After the second wash, 200uL PBS (0.4% BSA) was added to the pellet, and viability was measured using Trypan blue (viability should be close to 90%).
Libraries were constructed by the UTSW sequencing core using standardt 10XGenomics protocols.

value: posterior midgut

value: Progeny of MTD-GAL4/InR-DN crossed with OregonR

value: methionine feeding


title: Motor neurons under microgravity SMG2


title: CGND-HRA-03661

description: Library name: M140


title: R1/E cells siTop2a, H3K27me3

source_name: R4/E cells

value: R4/E cells


title: CGND-HRA-03562

description: Library name: M125


title: Motor neurons under normal gravity NG1


title: CGND-HRA-02987

description: Library name: M122

value: ALS

value: Male


title: Control, scRNAseq

description: 10x Genomics

value: Progeny of MTD-GAL4/+ crossed with OregonR


title: CGND-HRA-03763

description: Library name: M133


title: CGND-HRA-03760_ATAC

description: Library name: M119

library_source: genomic single cell


title: MUTYH tile 10, repair-positive, replicate #2

city: Ann Arbor

first: Jacob

last: Kitzman

state: MI

address: 4811 Med Sci II, 1241 E Catherine St

department: Department of Human Genetics

institute: University of Michigan

description: Library name: tile10_rep2_pos

data_processing:
Paired end reads were overlapped and an error-corrected consensus was taken by PEAR, and  aligned to MUTYH reference with bwa mem. Variant counts were tabulated by a custom pipeline (https://github.com/kitzmanlab/tileseq/). Amino acid level counts were processed by Rosace.
Supplementary files format and content: Tab delimited table with read counts for each single-residue mutation, for input to rosace or other modeling software.

organism: synthetic construct

growth_protocol: Human HEK-293 cells (ATCC) were cultured in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Invitrogen) and 1% penicillin-streptomycin (Invitrogen).  Mutant cell pools were seeded at 10^5 cells/cm2 in media containing 10 pg/ml doxycycline.

extract_protocol:
Genomic DNA from pre-sort and sorted cell populations was isolated using CleanNA Blood and Tissue magnetic bead kit (Bulldog Bio).
To amplify integrated MUTYH mutant libraries, ‘outer PCR’ was performed with primers flanking MUTYH cDNA using PrimeSTAR GXL kit (Takara). Each PCR reaction contained up to 500 ng gDNA as template; multiple reactions were performed and pooled as needed. Briefly, 1ul of outer PCR library product was diluted 1:25 and amplified in a limited (≤10) cycle-PCR, with primers directed at constant bases flanking the targeted tile within MUTYH cDNA. Primer 5’ tails contained constant sequencing adaptor stub sequences. Each resulting product was then diluted and further amplified to add sequencing adaptors and sample-specific unique dual 10bp index sequences.

treatment_protocol: At 24 hrs post seeding, cells were cotransfected with 1.8 ug 8OG GFP-off reporter plus 1.8 ug mCherry plasmid per plate, using Lipofectamine 3000. Repair positive and negative fractions were sorted at 72 hrs post-transfection using a Bigfoot Spectral cell sorter.


title: MUTYH tile 10, repair-negative, replicate #3

description: Library name: tile10_rep3_neg


title: MUTYH tile 10, repair-negative, replicate #2

description: Library name: tile10_rep2_neg


title: MUTYH tile 10, repair-positive, replicate #3

description: Library name: tile10_rep3_pos


title: R1/E cells shTrim28, H3K9me3

source_name: R2/E cells

value: R2/E cells


title: MUTYH tile 10, repair-positive, replicate #1

description: Library name: tile10_rep1_pos


title: CGND-HRA-03713

description: Library name: M135


title: MUTYH tile 10, repair-negative, replicate #1

description: Library name: tile10_rep1_neg


title: CGND-HRA-02746_ATAC

description: Library name: M117

value: ALSci


title: R1/E cells shControl, H3K9me3

source_name: R1/E cells

value: R1/E cells

value: WT


title: Motor neurons under microgravity SMG1

value: Motor neurons derived from embryonic stem cells


title: CGND-HRA-03649_ATAC

description: Library name: M113

value: White


title: Reprogrammed, scRNAseq

description: 10x Genomics


title: R1/E cells siTop2a, H3K9me3


title: MUTYH tile 9, repair-positive, replicate #3

description: Library name: tile09_rep3_pos


title: R1/E cells siControl, H3K9me3


title: R1/E cells siControl, H3K27me3

source_name: R3/E cells

value: R3/E cells


title: MUTYH tile 9, repair-negative, replicate #3

description: Library name: tile09_rep3_neg


title: CGND-HRA-03629_ATAC

description: Library name: M120

value: Female


title: R1/E cells shTrim28, H3K4me3


title: Reprogrammed intestines replicate 1

data_processing:
Reads were mapped using the tuxdeo suite (Tophat).  Differential gene expression anaylysus was done using EdgeR.
Assembly: DM6
Supplementary files format and content: tab delimeted text file includes tpm counts for each sample

source_name: intestine

extract_protocol:
RNA was extracted by trizol RNA extraction protocol (Ambion)
The mRNA-seq library was constructed using the miseq Library construction kit from illumina.

value: intestine


title: Control intestines replicate 3


title: R1/E cells shControl, H3K4me3


title: MUTYH tile 9, repair-negative, replicate #2

description: Library name: tile09_rep2_neg


title: R1/E cells siTop2a, H3K4me3


title: CGND-HRA-02964_ATAC

description: Library name: M103


title: MUTYH tile 9, repair-positive, replicate #1

description: Library name: tile09_rep1_pos


title: CGND-HRA-03647_ATAC

description: Library name: M114


title: CGND-HRA-02985_ATAC

description: Library name: M115


title: R1/E cells siControl, H3K4me3


title: R1/E cells shTrim28, H3K9ac


title: Control intestines replicate 1


title: MUTYH tile 8, repair-positive, replicate #3

description: Library name: tile08_rep3_pos


title: MUTYH tile 9, repair-negative, replicate #1

description: Library name: tile09_rep1_neg


title: CGND-HRA-02747_ATAC

description: Library name: M099


title: 22-month-old mouse kidney

city: Seoul

first: Donghwan

last: YUN

state: Jongno-gu

address: 103 Daehakro

country: South Korea

institute: Seoul National University Hospital

description:
Library name: Old mouse kidney
10X Genomics

data_processing:
The purified libraries were quantified using quantitative PCR (qPCR) according to the manufacturer’s protocol (Sigma-Aldrich) and were qualified using the Agilent 4200 TapeStation (Agilent Technologies) and sequenced using HiSeqX (Illumina) with a read length of 28 bp for read 1 (cell barcode and UMI), an 10 bp index read (sample barcode), and a read length of 90 bp for read 2 (RNA read). The Cell Ranger pipeline (version 3.1.0; 10× Genomics) was used to process the raw data set.
Assembly: m10
Supplementary files format and content: h5 format

source_name: Kidney

extract_protocol:
After digesting kidneys with 0.2 mg/ml liberase (Roche) at 37°C for 25 minutes in a shaking incubator, cells were filtered through a 70-μm and 40-μm strainer. The isolated cells were re-suspended in DMEM consist of 10% FBS.
Libraries were prepared using the chromium controller according to the 10× Chromium Next GEM Single Cell 5′ protocol (version 2; 10× Genomics).

treatment_protocol: No pharmacological treatments or chemical interventions were administered.

value: Kidney

value: Wild Type


title: Control intestines replicate 2


title: Reprogrammed intestines replicate 2

value: Progeny of MTD-GAL4/InR-DN crossed with OregonR


title: R1/E cells shControl, H3K9ac


title: PRO-seq of CH12F3: Csb-KO, 2 hours post UV, repeat1

city: Shanghai

first: Fei-Long

last: Meng

state: Shanghai

address: 320 Yue Yang Road

institute: Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

description: Library name: ELOF1_Lib207

data_processing:
Adapter sequences were trimed before alignment to mouse mm10 or mouse-human mixed (mm10-hg38) genome. The 16 bases at the 5’ end of the paired read which indicated the 3' end of the nascent RNA were used to generate bigwig files.
Assembly: mm10
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: PRO-Seq

molecule: nuclear RNA

extract_protocol:
Total nuclear RNA was extratcted from run-on reaction using TRIZol, then the bition NTP integrated nascent RNA was retrieved by C1 beads (thermofisher) and subjected to PRO-seq library prep.
A 3' adapter is first ligated to nascent RNA, 5' illumina adapter sequence is added in RT reaction using template switch. The full adapters are added by PCR.

value: B cell

value: UV 20J/m2


title: MUTYH tile 8, repair-negative, replicate #3

description: Library name: tile08_rep3_neg


title: CGND-HRA-03641_ATAC

description: Library name: M100


title: CGND-HRA-02749_ATAC

description: Library name: M106

value: ALS


title: MUTYH tile 9, repair-positive, replicate #2

description: Library name: tile09_rep2_pos


title: CGND-HRA-02745_ATAC

description: Library name: M110


title: PRO-seq of CH12F3: Elof1-KO, 2 hours post UV, repeat2

description: Library name: ELOF1_Lib206

value: UV 20J/m2, Clone2


title: Reprogrammed intestines replicate 3


title: R1/E cells siTop2a, H3K9ac


title: MUTYH tile 8, repair-positive, replicate #2

description: Library name: tile08_rep2_pos


title: R1/E cells siControl, H3K9ac


title: PRO-seq of CH12F3: WT, 2 hours post UV, repeat2

description: Library name: ELOF1_Lib205


title: CGND-HRA-03639_ATAC

description: Library name: M104


title: MUTYH tile 8, repair-negative, replicate #2

description: Library name: tile08_rep2_neg


title: CGND-HRA-03653_ATAC

description: Library name: M118

value: Male


title: L5 IT_replicate 3_P10

city: London

first: Julie

last: Jezequel

address: Newcomen Street

department: Centre for Developmental Neurobiology

country: United Kingdom

institute: King's College London

data_processing:
FASTQ files were processed using Nextflow's RNAseq pipeline (v3.2) to output aligned sequence reads and gene-level expression matrix files.
Gene expression matrix was imported into R and analysed for differential gene expression analysis using DESeq2 package.
Assembly: GRCm38
Supplementary files format and content: Julie_raw_counts.tsv; Tab-delimted file. Gene-level read counts
Supplementary files format and content: Julie_TpM.tsv; Tab-delimted file. Normalised gene expression values (transcripts per million)

source_name: Cortex (Somatosensory)

extract_protocol:
RNA was extracted using RNeasy Plus Micro kit (Qiagen) according to the manufacturer's instructions. Quality of RNA were checked using Bioanalyzer.
Sequencing libraries were prepared using SMARTer v4 Ultra low input kit according to the manufacturer's protocols.

value: Cortex (Somatosensory)

value: L5 IT Pyramidal neurons_P10, males + females

value: Red RetroBeads IX (Lumafluor)


title: PRO-seq of CH12F3: Csb-KO, Non-UV, repeat1

description: Library name: ELOF1_Lib204

value: Non-UV


title: MUTYH tile 8, repair-positive, replicate #1

description: Library name: tile08_rep1_pos


title: L5 IT_replicate 2_P10

value: WT


title: PRO-seq of CH12F3: Elof1-KO, Non-UV, repeat2

description: Library name: ELOF1_Lib203

value: Non-UV, Clone2


title: MUTYH tile 8, repair-negative, replicate #1

description: Library name: tile08_rep1_neg


title: L5 IT_replicate 1_P10


title: CGND-HRA-02987_ATAC

description: Library name: M098

value: White


title: CGND-HRA-02972_ATAC

description: Library name: M108

value: Female


title: MUTYH tile 7, repair-positive, replicate #3

description: Library name: tile07_rep3_pos


title: L5 ET_replicate 3_P10

value: L5 ET Pyramidal neurons (Pons-projecting)_P10, males + females


title: PRO-seq of CH12F3: WT, Non-UV, repeat2

description: Library name: ELOF1_Lib202


title: L5 ET_replicate 2_P10


title: PRO-seq of CH12F3: Elof1-KO, 2 hours post UV, repeat1

description: Library name: ELOF1_Lib201

value: UV 20J/m2, Clone1


title: MUTYH tile 7, repair-negative, replicate #3

description: Library name: tile07_rep3_neg


title: CGND-HRA-02978_ATAC

description: Library name: M102


title: PRO-seq of CH12F3: WT, 2 hours post UV, repeat1

description: Library name: ELOF1_Lib200


title: MUTYH tile 7, repair-positive, replicate #2

description: Library name: tile07_rep2_pos


title: CGND-HRA-02750_ATAC

description: Library name: M105


title: L5 ET_replicate 1_P10


title: MUTYH tile 7, repair-negative, replicate #2

description: Library name: tile07_rep2_neg


title: CGND-HRA-03661_ATAC

description: Library name: M116

value: Control


title: AIR_MPLA rep3

city: Beijing

first: Zebin

last: Liao

address: 27 Taiping Road

institute: Beijing Institute of Radiation Medicine

data_processing:
Double-terminal sequencing data with 125 bp or 150 bp was obtained through Illumina HiSeq 2500 sequencer
Adaptor and low-grade reads removal, low-quality bases elimination from 3' or 5' ends, original and effective sequencing quantity analysis, as well as guanine and cytosine statistics were subjected
Differential expression genes were selected via correlation test, principal component analysis and cluster analysis
Differential expression genes were clustered into pathways of intestinal crypts through KEGG
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Raw data (raw reads) were processed using Trimmomatic
Supplementary_files_format_and_content: The reads containing ploy-N and the low quality reads were removed to obtain the clean reads
Supplementary_files_format_and_content: Then the clean reads were mapped to reference genome using hisat2
Supplementary_files_format_and_content: FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.

source_name: Intestinal crypt

extract_protocol:
Intestinal crypts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Intestinal crypt

value: 3 days post abdominal body irradiation


title: MUTYH tile 7, repair-positive, replicate #1

description: Library name: tile07_rep1_pos


title: CGND-HRA-02753_ATAC

description: Library name: M112


title: PRO-seq of CH12F3: WT, Non-UV, repeat1

description: Library name: ELOF1_Lib198

value: B cell


title: AIR_MPLA rep1


title: PRO-seq of CH12F3: Elof1-KO +ELOF1 repeat2

description: Library name: ELOF1_Lib157

value: CIT day1.5, Clone4


title: CGND-HRA-02751_ATAC

description: Library name: M107

value: ALS


title: MUTYH tile 7, repair-negative, replicate #1

description: Library name: tile07_rep1_neg


title: CGND-HRA-02754_ATAC

description: Library name: M097

value: Male


title: CGND-HRA-03713_ATAC

description: Library name: M111


title: MUTYH tile 6, repair-positive, replicate #3

description: Library name: tile06_rep3_pos


title: PRO-seq of CH12F3: Elof1-KO +Vector repeat2

description: Library name: ELOF1_Lib156


title: PRO-seq of CH12F3: Elof1-KO +ELOF1 repeat1

description: Library name: ELOF1_Lib155

value: CIT day1.5, Clone3


title: MUTYH tile 6, repair-negative, replicate #3

description: Library name: tile06_rep3_neg


title: CGND-HRA-03763_ATAC

description: Library name: M109


title: Control rep3

value: without abdominal body irradiation


title: PRO-seq of CH12F3: Elof1-KO +Vector repeat1

description: Library name: ELOF1_Lib154


title: CGND-HRA-03562_ATAC

description: Library name: M101


title: MUTYH tile 6, repair-positive, replicate #2

description: Library name: tile06_rep2_pos


title: PRO-seq of CH12F3: Elof1-KO, Non-UV, repeat1

description: Library name: ELOF1_Lib199

value: Non-UV, Clone1


title: MUTYH tile 6, repair-negative, replicate #2

description: Library name: tile06_rep2_neg


title: Control rep2


title: PRO-seq of CH12F3: WT repeat1

description: Library name: ELOF1_Lib153

value: CIT day1.5


title: PRO-seq of CH12F3: Elof1-KO repeat2

description: Library name: ELOF1_Lib152


title: AAV9_SaCas9_KKH_Plasma_BiolRep4

city: Charlestown

first: Koen

last: Breyne

state: MA

address: Building 149 149 13th Street

institute: MGH

description: Library name: AAV9 SaCas9-KKH Mouse Plasma Biol Rep 4

data_processing:
Data was processed using CRISPResso2 analysis software
Assembly: The reference sequence used for read alignment consisted of the region of the DYT1 mutant allele sequence associated with the appropriate primers used for sequencing.
Supplementary files format and content: the processed data files are jpg images of the CRISPResso2 software's detected allele edits for each sample
Library strategy: CRISPR Screen

source_name: Plasma

extract_protocol:
For RNA isolation, cultured NPCs and EVs from conditioned media were processed using the miRNeasy Micro Kit (Qiagen, #217084, Germantown, MD, USA). For the isolation of exRNA from conditioned media, as little as 500 mL from a confluent 48-well plate to 50 mLs from multiple T75 flasks can be used. Conditioned media should on the cells for 48 hours before isolation. Nanodrop was employed for RNA sample quantification, followed by reverse transcription using the Superscript IV VILO gDNA extraction from cultured hNPCs utilized the remaining sample post-removal of the aqueous layer during RNA isolation. The protocol, adapted with modifications from the TRIzolTM Reagent. Experimental protocol for DNA isolation involved the addition of 300 μL of 100% Isopropanol to the sample. After a 30-min incubation at RT, the sample underwent centrifugation for 5 min at 2000 x g at 4°C to pellet the DNA. The DNA pellet was resuspended in 1 mL of 0.1M Sodium Citrate in 10% ethanol and incubated for 30 min and then spun at 2000 x g for 5 min at 4°C. This step was repeated once. The pellet was then resuspended in 1 mL of 75% ethanol and incubated for 10-20 min. Following a 5-min centrifugation at 2000 x g at 4°C, the pellet was air-dried and resuspended in 8 mM NaOH. pH adjustments were made as needed with HEPES.
Isolated gDNA and cDNA were amplified for NGS analysis using appropriate primers. A portion of the PCR product was run on a gel to check for band size and appropriate amplification. PCR product was cleaned using the QIAquick PCR purification kit (Qiagen, #28106) and eluted in 35 μL of RNAase free water. Samples were sent for Next Generation sequencing (MGH CCIB DNA Core). After sequencing, the results were analyzed using CRISPResso2.

value: Plasma


title: CGND-HRA-03640

city: New York

description: Library name: M048

data_processing:
Sequenced 10x libraries were aligned to a standard reference genome (hg38; GENCODE v32/Ensembl98) and counted (Cellranger-ARC v2.0.2). ATAC peaks were aligned between samples for quantification (Cellranger-ARC aggr v2.0.2)
Cell type annotations and low-quality/doublet cells were determined with a pre-trained ML model of snRNA-seq prefrontal cortex expression
Assembly: hg38
Supplementary files format and content: aggr.csv is a CSV file identifying sample libraries in cellranger-arc aggregated file filtered_feature_bc_matrix.h5
Supplementary files format and content: filtered_feature_bc_matrix.h5 is cellranger-arc aggregated GEX/ATAC file for all samples
Supplementary files format and content: BA44_BA46_COUNTS.h5ad is a scanpy/anndata file with integer gene expression counts and associated metadata for all cells
Supplementary files format and content: BA44_BA46_ATAC_COUNTS is a scanpy/anndata file with integer ATAC peak counts and associated metadata for all cells which pass ATAC filtering

extract_protocol:
Nuclei isolation protocol was adapted from previously described methods (PMID: 31042697; PMID: 36385529). All procedures were carried out on ice unless otherwise stated. Frozen post-mortem brain tissue was retrieved from storage at -80 °C and equilibrated on dry ice for 20–30 minutes before being transferred to a cryostat at -18 °C. Tissue samples were left for 15–20 minutes inside the cryostat before sectioning. We collected 20-50 mg of tissue per preparation, taking care to avoid excessive sampling of white matter. Tissue cuts were placed in a pre-chilled Dounce homogenizer containing 700 µL of ice-cold homogenization buffer (320 mM sucrose, 5 mM CaCl2 [#21115; Millipore Sigma], 3 mM magnesium acetate [#63052; Millipore Sigma], 10 mM Tris HCl [pH 7.8; prepared from Thermo Fisher’s #AM9850G and #AM9855G], 0.1 mM EDTA [pH 8.0; Thermo Fisher #AM9260G], 0.1% IGEPAL CA-630 [#I8896; Millipore Sigma], 1 mM DTT [#646563, Millipore Sigma], and 0.4 U/µl Protector RNase inhibitor [#03335402001, Millipore Sigma]). Homogenization was performed with 10 strokes of the loose pestle followed by 10 strokes of the tight pestle. After a 5-minute incubation on ice, the homogenized tissue was passed through a 70-µm Flowmi Cell Strainer (Bel-Art; H13680-0070) and combined with an equal volume of a solution made of 50% OptiPrep (#07820, STEMCELL Technologies), 5 mM CaCl2, 3 mM magnesium acetate, 10 mM Tris HCl (pH 7.8), 0.1 mM EDTA (pH 8.0), and 1 mM DTT. Using a 15-mL conical tube, this mixture was then layered onto a density gradient made up of 750 µL of a 30% OptiPrep solution supplemented with 134 mM sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 10 mM Tris HCl (pH 7.8), 0.1 mM EDTA (pH 8.0), 1 mM DTT, 0.04% IGEPAL CA-630, and 0.17 U µl−1 RNase inhibitor) over 300 µL of 40% OptiPrep solution supplemented with 96 mM sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 10 mM Tris HCl (pH 7.8), 0.1 mM EDTA (pH 8.0), 1 mM DTT, 0.03% IGEPAL CA-630, and 0.12 U µl−1 RNase inhibitor. Nuclei were separated by centrifugation at 3,000 × g for 20 minutes at 4 °C using a pre-chilled swinging-bucket rotor with the brake off. Approximately 150 µL of nuclei were collected from the 30%/40% gradient interphase and subsequently washed in PBS containing 1% BSA and 1 U µl-1 RNase inhibitor. Following a 5-minute incubation on ice, the nuclei were centrifuged at 450 × g for 3 minutes at 4 °C, and the pellet resuspended in 15 µL of diluted 10X Genomics Nuclei Buffer. Nuclei counting was performed using a Countess II FL instrument (Thermo Fisher) by staining with SYTOX Green (ThermoFisher; S7020). Additional quality control measures included Trypan Blue staining (#EBT-001, NanoEntek) to evaluate adequate permeabilization (cutoff: >95% of ‘dead cells’) and the assessment of nuclear morphology before proceeding with transposition.
Matched snRNA-seq and snATAC-seq libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (#PN-1000283) according to the protocol provided by 10X Genomics. Nuclei (16,100 per reaction; targeted recovery: 10,000 nuclei) from a single donor were used for each library preparation. Partitioning of nuclei was performed on a Chromium X instrument (10X Genomics). Quality control of cDNAs and libraries was conducted using Agilent High Sensitivity DNA Kits and a BioAnalyzer instrument. Final library quantification prior to pooling utilized KAPA Biosystems’ Library Quantification Kit for Illumina Platforms (KK4824). Libraries were sequenced on a NovaSeq X system using a 2 × 100 bp configuration run on a 10B flow cell. BA44/45 and BA46 libraries (n = 48) were prepared and sequenced in independent batches.


title: MUTYH tile 6, repair-positive, replicate #1

description: Library name: tile06_rep1_pos


title: CGND-HRA-03662

description: Library name: M047


title: AAV9_SaCas9_KKH_Plasma_BiolRep3

description: Library name: AAV9 SaCas9-KKH Mouse Plasma Biol Rep 3


title: MUTYH tile 6, repair-negative, replicate #1

description: Library name: tile06_rep1_neg


title: PRO-seq of CH12F3: Elof1-KO repeat1

description: Library name: ELOF1_Lib151


title: AAV9_SaCas9_KKH_Plasma_BiolRep2

description: Library name: AAV9 SaCas9-KKH Mouse Plasma Biol Rep 2


title: CGND-HRA-02762

description: Library name: M045


title: AIR rep3


title: MUTYH tile 5, repair-positive, replicate #3

description: Library name: tile05_rep3_pos


title: AIR rep1


title: PADD-seq of CH12F3: WT NVP-2 30 min repeat2

description: Library name: ELOF1_Lib285

data_processing:
See the paper.
Assembly: mm10
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Sonication and IP
ChIP-seq library was prepared using NEB Ultral II DNA prep kit. Other seq library was prepared using home-made protocol (refer to our paper).

value: 250nM NVP-2, UV 20J/m2, Anti-pan-RPB1 (Bethyl A304-405A), Anti-cyclobutane pyrimidine dimers (Cosmo Bio NMDND001)


title: AAV9_SaCas9_KKH_Plasma_BiolRep1

description: Library name: AAV9 SaCas9-KKH Mouse Plasma Biol Rep 1

source_name: Brain

value: Brain


title: PADD-seq of CH12F3: WT NVP-2 60 min repeat2

description: Library name: ELOF1_Lib284


title: MUTYH tile 5, repair-negative, replicate #3

description: Library name: tile05_rep3_neg


title: PADD-seq of CH12F3: Elof1-KO NVP-2 30 min repeat2

description: Library name: ELOF1_Lib283


title: MUTYH tile 5, repair-positive, replicate #2

description: Library name: tile05_rep2_pos


title: CGND-HRA-03750

description: Library name: M044

value: White

value: Female


title: CGND-HRA-03646

description: Library name: M043

value: ALSci


title: AAV9_SaCas9_KKH_Brain_BiolRep4

description: Library name: AAV9 SaCas9-KKH Mouse Brain Biol Rep 4


title: PADD-seq of CH12F3: Elof1-KO NVP-2 60 min repeat2

description: Library name: ELOF1_Lib282


title: CGND-HRA-02765

description: Library name: M042

value: Control


title: AAV9_SaCas9_KKH_Brain_BiolRep3

description: Library name: AAV9 SaCas9-KKH Mouse Brain Biol Rep 3


title: MUTYH tile 5, repair-negative, replicate #2

description: Library name: tile05_rep2_neg


title: MUTYH tile 5, repair-positive, replicate #1

description: Library name: tile05_rep1_pos


title: PADD-seq of CH12F3: Elof1-Csb-KO NVP-2 30 min repeat2

description: Library name: ELOF1_Lib281


title: PADD-seq of CH12F3: Elof1-Csb-KO NVP-2 60 min repeat2

description: Library name: ELOF1_Lib280


title: CGND-HRA-03634

description: Library name: M041


title: AAV9_SaCas9_KKH_Brain_BiolRep2

description: Library name: AAV9 SaCas9-KKH Mouse Brain Biol Rep 2


title: MUTYH tile 5, repair-negative, replicate #1

description: Library name: tile05_rep1_neg


title: CGND-HRA-03756

description: Library name: M046


title: PADD-seq of CH12F3: Csb-KO NVP-2 30 min repeat2

description: Library name: ELOF1_Lib279


title: CGND-HRA-03753

description: Library name: M040


title: AAV9_Null_Plasma_BiolRep3

description: Library name: AAV9 Null Mouse Plasma Biol Rep 3


title: MUTYH tile 4, repair-negative, replicate #3

description: Library name: tile04_rep3_neg


title: AAV9_Null_Plasma_BiolRep4

description: Library name: AAV9 Null Mouse Plasma Biol Rep 4


title: CGND-HRA-03752

description: Library name: M039


title: PADD-seq of CH12F3: Csb-KO NVP-2 60 min repeat2

description: Library name: ELOF1_Lib278


title: AAV9_SaCas9_KKH_Brain_BiolRep5

description: Library name: AAV9 SaCas9-KKH Mouse Brain Biol Rep 5


title: CGND-HRA-03630

description: Library name: M038


title: PADD-seq of CH12F3: Elof1-KO NVP-2 60 min repeat1

description: Library name: ELOF1_Lib197


title: AAV9_Null_Plasma_BiolRep2

description: Library name: AAV9 Null Mouse Plasma Biol Rep 2


title: CGND-HRA-02959

description: Library name: M037


title: MUTYH tile 4, repair-negative, replicate #2

description: Library name: tile04_rep2_neg


title: U54-HRA-059

description: Library name: M036


title: AAV9_Null_Plasma_BiolRep1

description: Library name: AAV9 Null Mouse Plasma Biol Rep 1


title: PADD-seq of CH12F3: Elof1-Csb-KO NVP-2 60 min repeat1

description: Library name: ELOF1_Lib195


title: MUTYH tile 4, repair-positive, replicate #1

description: Library name: tile04_rep1_pos


title: PADD-seq of CH12F3: Elof1-Csb-KO NVP-2 30 min repeat1

description: Library name: ELOF1_Lib194


title: CGND-HRA-02756

description: Library name: M034


title: PADD-seq of CH12F3: Csb-KO NVP-2 60 min repeat1

description: Library name: ELOF1_Lib193


title: AAV9_Null_Brain_BiolRep5

description: Library name: AAV9 Null Mouse Brain Biol Rep 5


title: AAV9_Null_Brain_BiolRep4

description: Library name: AAV9 Null Mouse Brain Biol Rep 4


title: MUTYH tile 3, repair-positive, replicate #3

description: Library name: tile03_rep3_pos


title: U54-HRA-058

description: Library name: M035


title: AAV9_Null_Brain_BiolRep3

description: Library name: AAV9 Null Mouse Brain Biol Rep 3


title: AAV9_SaCas9_KKH_Brain_BiolRep1

description: Library name: AAV9 SaCas9-KKH Mouse Brain Biol Rep 1


title: PADD-seq of CH12F3: Csb-KO NVP-2 30 min repeat1

description: Library name: ELOF1_Lib192


title: CGND-HRA-02763

description: Library name: M033


title: MUTYH tile 3, repair-positive, replicate #2

description: Library name: tile03_rep2_pos


title: AAV9_Null_Brain_BiolRep2

description: Library name: AAV9 Null Mouse Brain Biol Rep 2


title: MUTYH tile 3, repair-negative, replicate #3

description: Library name: tile03_rep3_neg


title: PADD-seq of CH12F3: WT NVP-2 60 min repeat1

description: Library name: ELOF1_Lib191


title: CGND-HRA-03638

description: Library name: M031


title: MUTYH tile 4, repair-positive, replicate #3

description: Library name: tile04_rep3_pos


title: MUTYH tile 4, repair-positive, replicate #2

description: Library name: tile04_rep2_pos


title: CGND-HRA-02757

description: Library name: M032


title: PADD-seq of CH12F3: Elof1-KO NVP-2 30 min repeat1

description: Library name: ELOF1_Lib196


title: AAV9_Null_Brain_BiolRep1

description: Library name: AAV9 Null Mouse Brain Biol Rep 1


title: PADD-seq of CH12F3: WT NVP-2 30 min repeat1

description: Library name: ELOF1_Lib190


title: MUTYH tile 3, repair-negative, replicate #2

description: Library name: tile03_rep2_neg


title: RPB1 S2-p ChIP-seq of CH12F3: +Vector NVP-2 60 min, repeat2

description: Library name: ELOF1_Lib189

value: Aicda-Elof1-KO Clone2, +3xHA, CIT day1.5, K562 cells were used as spike-in, anti-RPB1 S2-p (Abcam ab5095)


title: MUTYH tile 4, repair-negative, replicate #1

description: Library name: tile04_rep1_neg


title: MUTYH tile 3, repair-positive, replicate #1

description: Library name: tile03_rep1_pos


title: CGND-HRA-03642

description: Library name: M030


title: CGND-HRA-03718

description: Library name: M029


title: RPB1 S2-p ChIP-seq of CH12F3: +Vector NVP-2 0 min, repeat2

description: Library name: ELOF1_Lib187


title: MUTYH tile 2, repair-positive, replicate #3

description: Library name: tile02_rep3_pos


title: MUTYH tile 3, repair-negative, replicate #1

description: Library name: tile03_rep1_neg


title: MDA-MB-231/Res antiIGF2BP2 Replicate 3

city: chengdu

first: PAN

last: YiTong

address: Wangjiang Street

institute: Sichuan University

description: Library name: GJW105

data_processing:
Average RPM in the MDA-MB-231/Sens IgG or MDA-MB-231/Res IgG was calculated
Enrichment of circRNA was caluculated by duducting average RPM of IgG group
Delta enrichment of circRNA was calculated by minusing Enrichment/Sens from Enrichment/Res, P value by students' t-test were calculated.
Assembly: GRCh37
Supplementary files format and content: csv

source_name: TNBC

extract_protocol:
For the RIP-seq experiment, MDA-MB-231/Sens and MDA-MB-231/Res cells were harvested in RIP lysis buffer. The equivalent lysates were firstly incubated with 5μg anti-IGF2BP2 mAb or 5μg rabbit IgG overnight, and then captured by Protein A/G agarose for additional 4 hours at 4°C. Next, the rinsed agaroses were probed to TRIzol RNA extraction. The purified RNA was qualified and quantified.
Equivalent amount of RNA was mixed with spike-in (Invitrogen #4456740) to generate RIP-IGF2BP2 libraries using VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme #NRM604-01), according to the manufacture instructions. The libraries were probed to sequencing. For bioinformatic analysis, the sequencing data were normalized to the signal of spike-in (ERCC mixture) using RUVSeq’s method and the circRNA enrichment was calculated by comparing the reads numbers in IGF2BP2 groups (Sens and Res) to the IgG counterparts.

value: TNBC

value: Established BETi resistance

value: Continuous BETi treatment till harvest

tag: rip antibody

value: anti-IGF2BP2 mAb


title: MDA-MB-231/Res IgG Replicate 3

description: Library name: GJW104

tag: cell line

value: Normal rabbit IgG


title: CGND-HRA-02766

first: Christopher

last: Jackson

address: 101 Avenue of the Americas

institute: New York Genome Center

description: Library name: M026

value: Male


title: MDA-MB-231/Sens antiIGF2BP2 Replicate 3

description: Library name: GJW103

tag: cell type

value: WT


title: CGND-HRA-02759

description: Library name: M027

value: ALS


title: RPB1 S2-p ChIP-seq of CH12F3: +ELOF1 NVP-2 30 min, repeat2

description: Library name: ELOF1_Lib185

value: B cell

tag: treatment

value: Aicda-Elof1-KO Clone2, +ELOF1-3xHA, CIT day1.5, K562 cells were used as spike-in, anti-RPB1 S2-p (Abcam ab5095)


title: MUTYH tile 2, repair-negative, replicate #3

description: Library name: tile02_rep3_neg


title: MUTYH tile 2, repair-positive, replicate #2

description: Library name: tile02_rep2_pos


title: RPB1 S2-p ChIP-seq of CH12F3: +ELOF1 NVP-2 0 min, repeat2

description: Library name: ELOF1_Lib184


title: MDA-MB-231/Res antiIGF2BP2 Replicate 2

description: Library name: GJW101

tag: tissue


title: MUTYH tile 2, repair-negative, replicate #2

description: Library name: tile02_rep2_neg


title: CGND-HRA-03640_ATAC

description: Library name: M024


title: RPB1 S2-p ChIP-seq of CH12F3: +Vector NVP-2 60 min, repeat1

description: Library name: ELOF1_Lib183

value: Aicda-Elof1-KO Clone1, +3xHA, CIT day1.5, K562 cells were used as spike-in, anti-RPB1 S2-p (Abcam ab5095)


title: MDA-MB-231/Sens IgG Replicate 3

description: Library name: GJW102

tag: genotype


title: CGND-HRA-03648

description: Library name: M028

tag: donor id


title: MDA-MB-231/Res IgG Replicate 2

description: Library name: GJW100


title: MouseOvary_3days_TachykininReceptorAgonists

city: 相楽郡

first: Tsuyoshi

last: Kawada

state: Kyoto

address: 精華町精華台8－1－1

country: Japan

institute: Suntory Foundation for Life Sciences

description: Gene expression of the mouse ovary treated with tachykinin agonists for 3 days

hyb_protocol: 0.6 mg Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes. Subsequently, fragmented cRNA was hybridized at 65 °C for 17 hr with Agilent Expression Array.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters.

source_name: Mouse ovary, 3 days, tachykinin receptor agonists

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using Low Input Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instructions.

extract_protocol: Each total RNA was extracted from the cultured ovaries using RNeasy Plus Mini kit (Qiagen, Hilden, Germany).

treatment_protocol: Half-portion of 2-weeks mouse ovary cultured with each ligand at 37 °C in 5 % CO2 in air and 100 % humidity for 3 days.

value: ovary

value: 2 weeks


title: CGND-HRA-03662_ATAC

description: Library name: M023

tag: als phenotype

value: White


title: CGND-HRA-03756_ATAC

description: Library name: M022

value: ALSci

tag: race


title: MUTYH tile 2, repair-negative, replicate #1

description: Library name: tile02_rep1_neg


title: RPB1 S2-p ChIP-seq of CH12F3: +Vector NVP-2 30 min, repeat2

description: Library name: ELOF1_Lib188


title: RPB1 S2-p ChIP-seq of CH12F3: +Vector NVP-2 30 min, repeat1

description: Library name: ELOF1_Lib182


title: MDA-MB-231/Sens antiIGF2BP2 Replicate 2

description: Library name: GJW99


title: MouseOvary_3days_TachykininReceptorAntagonists

description: Gene expression of the mouse ovary treated with tachykinin antagonists for 3 days

source_name: Mouse ovary, 3 days, tachykinin receptor antagonists


title: RPB1 S2-p ChIP-seq of CH12F3: +Vector NVP-2 0 min, repeat1

description: Library name: ELOF1_Lib181


title: CGND-HRA-02762_ATAC

description: Library name: M021

tag: Sex

value: Female


title: RPB1 S2-p ChIP-seq of CH12F3: +ELOF1 NVP-2 60 min, repeat1

description: Library name: ELOF1_Lib180

value: Aicda-Elof1-KO Clone1, +ELOF1-3xHA, CIT day1.5, K562 cells were used as spike-in, anti-RPB1 S2-p (Abcam ab5095)


title: MUTYH tile 1, repair-negative, replicate #3

description: Library name: tile01_rep3_neg


title: MDA-MB-231/Sens IgG Replicate 2

description: Library name: GJW98

value: TNBC


title: RPB1 S2-p ChIP-seq of CH12F3: +ELOF1 NVP-2 60 min, repeat2

description: Library name: ELOF1_Lib186


title: CGND-HRA-03750_ATAC

description: Library name: M020

tag: age


title: MUTYH tile 2, repair-positive, replicate #1

description: Library name: tile02_rep1_pos


title: MUTYH tile 1, repair-negative, replicate #2

description: Library name: tile01_rep2_neg


title: MDA-MB-231/Res IgG Replicate 1

description: Library name: GJW96

value: Established BETi resistance


title: RPB1 S2-p ChIP-seq of CH12F3: +ELOF1 NVP-2 0 min, repeat1

description: Library name: ELOF1_Lib178


title: CGND-HRA-02966

description: Library name: M025

tag: pmi


title: MDA-MB-231/Res antiIGF2BP2 Replicate 1

description: Library name: GJW97

value: Continuous BETi treatment till harvest


title: MUTYH tile 1, repair-positive, replicate #1

description: Library name: tile01_rep1_pos


title: CPD damage-seq of CH12F3: WT, 8 hours post UV, repeat2

description: Library name: ELOF1_Lib150

value: UV 20J/m2, Anti-cyclobutane pyrimidine dimers (Cosmo Bio NMDND001)


title: MUTYH tile 1, repair-positive, replicate #2

description: Library name: tile01_rep2_pos


title: RPB1 S2-p ChIP-seq of CH12F3: +ELOF1 NVP-2 30 min, repeat1

description: Library name: ELOF1_Lib179


title: CGND-HRA-03646_ATAC

description: Library name: M019


title: MDA-MB-231/Sens antiIGF2BP2 Replicate 1

description: Library name: GJW95

value: anti-IGF2BP2 mAb


title: MDA-MB-231/Sens IgG Replicate 1

description: Library name: GJW94

value: Normal rabbit IgG


title: MUTYH tile 1, repair-negative, replicate #1

description: Library name: tile01_rep1_neg


title: Post_treatment _5

city: Fuzhou

first: Aling

last: Shen

state: Fujian

address: 1 Qiuyang road, Minhou Shangjie

institute: Fujian university of Traditional Chinese Medicine

description:
Library name: Sample 10
Gastric tissue of reg patients afterJPQHSYY treatment for 8-12 weeks

data_processing:
StringTie software was used to reconstruct transcripts in each sample based on probability model.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each sample

source_name: Gastric tissue

extract_protocol:
The tissues were dissected and cardiac tissues were stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total of 3 µg RNA per sample was used as initial material to construct lncRNA and mRNA libraries. The NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer's instructions.

value: Gastric tissue

value: after JPQHSYY treatment


title: CPD damage-seq of CH12F3: WT, 0 hour post UV, repeat2

description: Library name: ELOF1_Lib149

value: B cell


title: CGND-HRA-03634_ATAC

description: Library name: M017

value: ALS


title: MUTYH tile 1, repair-positive, replicate #3

description: Library name: tile01_rep3_pos


title: CGND-HRA-03753_ATAC

description: Library name: M016

value: Male


title: 72 hours post inoculation, uninfected, biorep 4

city: Winnipeg

first: Mark

last: Belmonte

state: MB

address: 50 Sifton Road

country: Canada

institute: University of Manitoba

description:
Library name: 72hUTC4
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 72hUTC4

data_processing:
Read quality was determined using FastQC
Reads were aligned using HISAT2 and raw counts were generated using featureCounts
DESeq2 was used to conduct differencial gene expression analysis
Assembly: C. sativa genome - RefSeq assembly accession: GCF_029168945.1 (Kim et al,. 2023)
Assembly: S. sclerotiorum genome - RefSeq assembly accession: GCF_000146945.2 (Amselem et al., 2011)
Supplementary files format and content: C.sativa_raw_counts.txt - tab delimited txt file including raw counts for each sample aligned to C. sativa
Supplementary files format and content: S.sclerotiorum_raw_counts.txt - tab delimited txt file including raw counts for each sample aligned to S. sclerotiorum

organism: Cannabis sativa

source_name: Inflorescence

extract_protocol:
RNA was extracted using Purelink Invitrogen PlantRNA reagent with the addition of Qiagen's on-column DNAse treatment. 1µg of RNA was sent to Genome Québec for library construction.
Genome Québec constructed cDNA libraries according to their mRNA stranded library preparation protocol. Paired-end 100bp reads were sequenced (Illumina NovaSeq 6000).

value: Inflorescence

value: Cultivar - Kona

value: 72h control


title: Post_treatment _4

description:
Library name: Sample 9
Gastric tissue of reg patients afterJPQHSYY treatment for 8-12 weeks


title: CPD damage-seq of CH12F3: Csb-KO, 8 hours post UV, repeat2

description: Library name: ELOF1_Lib148


title: CGND-HRA-03752_ATAC

description: Library name: M015

value: Control

value: White


title: CPD damage-seq of CH12F3: Csb-KO, 0 hour post UV, repeat2

description: Library name: ELOF1_Lib147


title: 72 hours post inoculation, uninfected, biorep 3

description:
Library name: 72hUTC3
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 72hUTC3


title: Post_treatment _3

description:
Library name: Sample 8
Gastric tissue of reg patients afterJPQHSYY treatment for 8-12 weeks


title: CGND-HRA-03630_ATAC

description: Library name: M014

value: ALSci

value: Female


title: CPD damage-seq of CH12F3: WT, 8 hours post UV, repeat1

description: Library name: ELOF1_Lib146


title: Post_treatment _2

description:
Library name: Sample 7
Gastric tissue of reg patients afterJPQHSYY treatment for 8-12 weeks


title: CGND-HRA-02959_ATAC

description: Library name: M013


title: CPD damage-seq of CH12F3: WT, 0 hour post UV, repeat1

description: Library name: ELOF1_Lib145


title: 72 hours post inoculation, uninfected, biorep 2

description:
Library name: 72hUTC2
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 72hUTC2


title: U54-HRA-059_ATAC

description: Library name: M012


title: CGND-HRA-02765_ATAC

description: Library name: M018


title: Pre_treatment_5

description:
Library name: Sample 5
Gastric tissue of reg patients

value: before JPQHSYY treatment


title: 72 hours post inoculation, uninfected, biorep 1

description:
Library name: 72hUTC1
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 72hUTC1


title: Post_treatment _1

description:
Library name: Sample 6
Gastric tissue of reg patients afterJPQHSYY treatment for 8-12 weeks


title: 24 hours post inoculation, uninfected, biorep 4

description:
Library name: 24hUTC4
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 24hUTC4

value: 24h control


title: 24 hours post inoculation, uninfected, biorep 3

description:
Library name: 24hUTC3
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 24hUTC3


title: CPD damage-seq of CH12F3: Elof1-KO, 8 hours post UV, repeat2

description: Library name: ELOF1_Lib144

value: UV 20J/m2, Anti-cyclobutane pyrimidine dimers (Cosmo Bio NMDND001), Clone2


title: CGND-HRA-02756_ATAC

description: Library name: M010


title: Pre_treatment_4

description:
Library name: Sample 4
Gastric tissue of reg patients


title: 24 hours post inoculation, uninfected, biorep 2

description:
Library name: 24hUTC2
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 24hUTC2


title: CPD damage-seq of CH12F3: Elof1-KO, 8 hours post UV, repeat1

description: Library name: ELOF1_Lib142

value: UV 20J/m2, Anti-cyclobutane pyrimidine dimers (Cosmo Bio NMDND001), Clone1


title: CGND-HRA-02763_ATAC

description: Library name: M009


title: Pre_treatment_3

description:
Library name: Sample 3
Gastric tissue of reg patients


title: 24 hours post inoculation, uninfected, biorep 1

description:
Library name: 24hUTC1
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 24hUTC1


title: CPD damage-seq of CH12F3: Elof1-KO, 0 hour post UV, repeat1

description: Library name: ELOF1_Lib141


title: Pre_treatment_2

description:
Library name: Sample 2
Gastric tissue of reg patients


title: CGND-HRA-02757_ATAC

description: Library name: M008


title: CPD damage-seq of CH12F3: Csb-KO, 8 hours post UV, repeat1

description: Library name: ELOF1_Lib140

value: UV 20J/m2, Anti-cyclobutane pyrimidine dimers (Cosmo Bio NMDND001)


title: 168 hours post inoculation, uninfected, biorep 4

description:
Library name: 168hUTC4
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 168hUTC4

value: 168h control


title: CPD damage-seq of CH12F3: Csb-KO, 0 hour post UV, repeat1

description: Library name: ELOF1_Lib139


title: CGND-HRA-03642_ATAC

description: Library name: M006


title: 168 hours post inoculation, uninfected, biorep 3

description:
Library name: 168hUTC3
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 168hUTC3


title: 168 hours post inoculation, uninfected, biorep 2

description:
Library name: 168hUTC2
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 168hUTC2


title: U54-HRA-058_ATAC

description: Library name: M011


title: Y27632_3

first: Wei

last: Zhang

address: No.180 Fengling Road, Xuhui

department: Vascular Surgery

institute: Zhongshan Hospital, Fudan University

data_processing:
Reads that contained the sequence of adaptor, high content of unknown bases, and low-quality reads were filtered and stored in FASTQ format.
RNA-seq reads were aligned to mouse GRCh38 with Bowtie2 and then raw reads were obtained with RSEM.
The FPKM method was used to calculate gene expression for direct comparison among samples.
the DESeq2 method was used to screen differentially expressed genes (DEGs) between two groups according to the following default criteria: fold change ≥ 2 and Q value (adjusted P value) ≤ 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each samples
Supplementary files format and content: tab-delimited text file includes FPKM for each samples

source_name: aorta

growth_protocol: Normal human primary aortic smooth muscle cell were cultured in SMCM supplemented with 2% fetal bovin serum and antibiotics in humidifieid atmosphere with 5% CO2 at 37℃

extract_protocol:
Whole RNA was extracted using the TRIzol Plus RNA Purification Kit (Thermo Fisher Scientific) following the manufacturer’s protocol
SBS50 sequencing was performed at DNBSEQ using illumine HiseqTM 2000.

treatment_protocol: Y27632 dissolved in PBS (20μM) was added to PBS treated celltjns for overnight

value: aorta

value: primary human aortic smooth muscle cell


title: Pre_treatment_1

description:
Library name: Sample 1
Gastric tissue of reg patients

value: Gastric tissue


title: CGND-HRA-03638_ATAC

description: Library name: M007

value: ALS


title: BMDM, NS2A, rep3

city: Jiangsu suzhou

first: Jingfei

last: Zhu

state: CN

address: Chongwen Road 215123

institute: ISM

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: BMDM

extract_protocol:
The cell samples were lysed in TRIzol and extract total RNA for RNA-seq
RNA libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit following standard Illumina protocol

value: BMDM

value: Mouse primary macrophage

value: NS2A knock-in

value: untreat


title: CGND-HRA-03648_ATAC

description: Library name: M004

value: White

value: Male


title: CGND-HRA-03718_ATAC

description: Library name: M005

value: ALSci


title: CPD damage-seq of CH12F3: Elof1-KO, 0 hour post UV, repeat2

description: Library name: ELOF1_Lib143

value: B cell


title: BMDM, NS2A, rep2


title: Y27632_1


title: Y27632_2


title: BMDM, NS2A, rep1


title: 168 hours post inoculation, uninfected, biorep 1

description:
Library name: 168hUTC1
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 168hUTC1

value: Inflorescence

value: Cultivar - Kona


title: CGND-HRA-02759_ATAC

description: Library name: M003


title: 120 hours post inoculation, uninfected, biorep 4

description:
Library name: 120hUTC4
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 120hUTC4

value: 120h control


title: 120 hours post inoculation, uninfected, biorep 3

description:
Library name: 120hUTC3
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 120hUTC3


title: CGND-HRA-02766_ATAC

description: Library name: M002

value: Control


title: NC_2

value: PBS


title: NC_3

value: aorta


title: BMDM, WT, rep2

value: wide type


title: NC_1

value: primary human aortic smooth muscle cell


title: CGND-HRA-02966_ATAC

description: Library name: M001

value: Female


title: BMDM, WT, rep1

value: BMDM


title: 120 hours post inoculation, uninfected, biorep 1

description:
Library name: 120hUTC1
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 120hUTC1


title: 60M-15006

status: Public on Feb 28 2025

type: genomic

first: Hwan Young

last: Lee

address: 103, Daehak-ro, Jongno-gu

institute: Seoul National University College of Medicine

description: Illumina Infinium MethylationEPIC BeadChip kits

hyb_protocol: Bisulfite converted DNA was amplified, fagmented and hybridised to Infinium HumanMethylation EPIC BeadChip using standard Illumina protocol

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles. Background intensity computed from a set of negative controls was subtracted from each analytical data point. The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100). The ß-value reflects the methylation level of each CpG site. A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

label: Cy5 and Cy3

source_name: semen

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using Qiagen DNA Mini Kit (Qiagen, Hilden, Germany) based on the manufacturers’ instructions

value: semen

tag: ethnicity

value: Korean-Asian


title: 60M-15003


title: 50M-15018


title: 60M-15008


title: 50M-15002


title: 60M-15002


title: 50M-15008


title: 60M-15007


title: BMDM, WT, rep3

value: Mouse primary macrophage

value: untreat


title: 50M-15013

value: Male


title: 40M-15021


title: 40M-15017


title: 40M-15020


title: 50M-15011


title: A549

city: Novosibirsk

first: Nikita

last: Torgunakov

address: Prospekt Lavrentyeva 10

country: Russia

institute: Institute of Cytology and Genetics

description:
Library name: A549
Chromatin fragmentation by DNase I

data_processing:
merged_nodups.txt files were obtained using modified version of the Juicer 1.6 (https://github.com/genomech/juicer1.6_compact)
Assembly: hg19
Supplementary files format and content: merged_nodups.txt.gz files containing valid Hi-C pairs (described as "Long format" in Juicer documentation here: https://github.com/aidenlab/juicer/wiki/Pre#long-format), modified to remove fields <cigar1> <sequence1> <cigar2> <sequence2> <readname1> <readname2> due to patient privacy concerns. Fields <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> remain.

extract_protocol:
Extraction protocol was performed as described in Gridina. et. al 2021 (PMID: 33743768).
Exo-C protocol includes a 3C part followed by exome enrichment. The 3C part was performed either following DNase I protocol as described in Gridina. et. al 2021 (PMID: 33743768), or S1 as described in Gridina. et. al 2023 (PMID: 38072950).


title: 40M-15032


title: 40M-17001


title: 50M-15010


title: 120 hours post inoculation, uninfected, biorep 2

description:
Library name: 120hUTC2
Column name in "C.sativa_raw_counts" and "S.sclerotiorum_raw_counts": 120hUTC2


title: 40M-15008


title: 30M-15001


title: 40M-17002


title: 30M-17001


title: 30M-15007


title: 30M-15017


title: 50M-15009


title: 60M-15004


title: 30M-15028


title: 30M-17006


title: 30M-15010


title: 30M-15044


title: 30M-15004


title: 30M-15027


title: 30M-17002


title: 30M-17005


title: 40M-15024


title: 30M-15012


title: 30M-15020


title: 30M-15015


title: 30M-15019


title: 30M-15014


title: 20M-15039


title: 30M-15040


title: 20M-17003


title: 20M-15032


title: 20M-15041


title: 20M-15036


title: 40M-15035


title: 20M-17002


title: 30M-17004


title: 20M-15019


title: 20M-15005


title: 20M-15004


title: 20M-15017


title: 20M-15003


title: HCT8 cells, Control,H3K9me3(ChIP)

first: Tanxing

last: Cai

state: Guangdong

address: 26 Erheng Road, Yuancun, Tianhe District

department: Department of General Surgery

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

description: Library name: CON_K9

data_processing:
Basecalls were performed for Illumina NovaSeq 6000 output.
ChIP-seq reads were trimmed using Trimmomatic v0.38.
ChIP-seq reads were aligned to the Homo sapiens reference genome GRCh37 using BowTie v1.1.2.
Peaks were called using MACS2 v2.1.1.20160309 and duplicate reads were processed using Picard v0.118.
Peaks annotated using ChIPseeker 1.16.1.
Assembly: GRCh37
Supplementary files format and content: bigwig

growth_protocol: HCT8 cells were mainteined in DMEM supplemented with 10 fetal bovine serum(FBS) and antibodics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Cells were fixed with 37% formaldehyde for 10 minutes. After quenching and cell lysis, chrmatin was sonicated using a SimpleChIP® Plus Sonication Chromatin IP Kit(CST,56383S)
Libraries were constructed using the Rapid Plus DNA Lib Prep Kit for Illumina V2 (RK20255, ABclonal, China). Procedures included DNA end repair, 3'-end adenylation, adapter ligation, and PCR amplification.

treatment_protocol: HCT8 cells transfected with control plasmid or KDM4A overexpression plasmid

value: colorectal cancer

value: WT

tag: chip antibody


title: 30M-15033


title: 20M-15020


title: HCT8 cells, KDM4A overexpression,H3K9me3(ChIP)

description: Library name: OE_K9

value: KDM4A overexpression

value: HCT8 cells transfected with KDM4A plasmid


title: HN35 Pre TCR-Seq data

status: Public on Feb 24 2025

city: Chapel Hill

first: Robert

middle: L

last: Ferris

state: NC

address: 450 West Drive

institute: UNC Lineberger Comprehensive Cancer Center

description: Library name: HN35_Pre_VDJ

data_processing:
Fastq files were demultiplexed using Cellranger mkfastq
Demultiplexed data (GEX,ADT and VDJ) were processed using Cellranger Multi pipeline
Assembly: GRCh38
Supplementary files format and content: Cellranger output files for GEX, ADT and VDJ libraries
Library strategy: TCR-Seq

source_name: Tumor

extract_protocol:
FACS sorting was used to extract CD45+ CD3+ or CD45+ cells from baseline and post treatment samples of HNSCC patients
10x genomics protocol for GEX, ADT and VDJ libraries was followed

value: Tumor

value: CD45+ CD3+ T cells

tag: library type

value: VDJ


title: HN35 Post CITE-Seq expression data

description: Library name: HN35_Post_ADT

data_processing:
Fastq files were demultiplexed using Cellranger mkfastq
Demultiplexed data (GEX,ADT and VDJ) were processed using Cellranger Multi pipeline
Assembly: GRCh38
Supplementary files format and content: Cellranger output files for GEX, ADT and VDJ libraries
Library strategy: CITE-Seq

molecule: protein

value: CD45+ cells

value: ADT


title: HN34 Post TCR-Seq data

description: Library name: HN34_Post_VDJ


title: HN35 Pre CITE-Seq expression data

description: Library name: HN35_Pre_ADT