title: 1257 myo primary HMGA2-V5 V5

city: Chicago

first: Debabrata

last: Chakravarti

state: IL

address: 303 E Superior St.

department: Obstetrics and Gynecology

institute: Northwestern University

data_processing:
For basecalls, RTA v.2.4.11 was utilized on Nextseq instrument.
Quality control of the sequenced reads was done by FastQC. Reads were then aligned to human genome (hg38) using Bowtie2 with options --end-to-end --sensitive --score-min L,-1.5,-0.3
The program HOMER was used to make tag directories (-tbp 1), peak calling (-style histone (for H3K27ac)) and annotating peaks (default settings). For V5-tagged HMGA2, bam alignment files were combined into a single file prior to peak calling which performed with options -style histone -F 2 -L 2 -fdr 0.01
Assembly: hg38
Supplementary files format and content: bed files of peaks (except for input sample)

source_name: Uterine myometrium

growth_protocol: Normal myometrial tissues were enzymatically digested to obtain primary cells. Primary cells were then plated and grown at 37°C in a humidified cell culture incubator conatining 5% CO2. Cells were used in experiment after two passages.

extract_protocol:
Cross-linking with 1% formaldehyde was performed for 10 min for each condition. To quench cross-linking, glycine was added to a final concentration of 119 mM for 5 min. Cells were washed 3 times with ice-cold 1X PBS and then scraped and pelleted by spinning at 1000xg for 10 min at 4°C. The cell pellet was flash-frozen in liquid nitrogen and stored at -80°C. For further processing, the thawed cell pellet was resuspended in 3 ml of LB1 (50 mM HEPES-KOH [pH 7.6], 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% glycerol, 0.5% IGEPAL-CA630, and 0.25% Triton X-100) and mixed end-over-end on a rotator for 10 min at 4°C. The cell suspension was pelleted by centrifugation at 2000xg for 5 min at 4°C. The pellet was resuspended in 3 ml of LB2 (10 mM Tris-HCl [pH 8.0], 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA) and mixed on a rotator for 10 min at 4°C. The nuclei pellet was then resuspended in 500 μl of LB3 (10 mM Tris-HCl [pH 8.0], 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, and 0.5% sarkosyl) and chromatin was solubilized by 15 pulses of sonication at Misonix sonicator at 5 W with 15 s on and 45 s off. 10% Triton X-100 was added to a final concentration of 1%. The sonicated chromatin was pelleted by centrifugation (20,000xg) for 25 min at 4°C to remove cell debris. Protein concentration was determined by BCA (Thermo Fisher Scientific, 23209), and approximately 400 μg of chromatin was incubated overnight with end-over-end mixing with 3 µg antibodies for ChIP. Antibodies used for ChIP were anti-H3K27ac (Active motif, 39133) and anti-V5 epitope-specific antibodies (Thermo Fisher Scientific, R96025).
Library preparation was carried out with the KAPA Hyper Prep Kit (Kapa biosystems, KK8502). 1 to 5 ng of immunoprecipitated DNA was used. Adapter ligation was carried out for 15 min followed by 0.6X - 0.8X double-sided size selection with Ampure XP beads (Beckman Coulter, A63881). The libraries were then amplified and the profile was checked with an Agilent Bioanalyzer (Agilent Technologies, 5067). Libraries were diluted to 2 nM, pooled, and quantified with the Kapa quantification kit (Kapa biosystems, KK4835) for single-end sequencing with the Nextseq 500/550 high-output kit (v2, 75 cycles).

treatment_protocol: Primary myometrial cells were transduced with lentivirus containing either empty or V5-tagged HMGA2 construct in the presence of 6ug/ml polybrene for 18 hours. Fresh SmGM complete media was added then after 24 hours, cells were selected in 2ug/ml puromycin.

value: Uterine myometrium

value: Primary cells

tag: chip antibody

value: Thermo Fisher Scientific, R96025 (V5)

value: Lentiviral transduction of V5-tagged HMGA2 vector


title: NHA_Neg_Library_RepA_300ng, Batch1_10

status: Public on Oct 01 2025

type: RNA

city: Kensington

first: Irina

last: Voineagu

state: NSW

address: High St

department: Biotechnology and Biomolecular Sciences

country: Australia

institute: The University of New South Wales

hyb_protocol: TagSet Hyb setup NanoString MAN-10057-03.  A normalisation plate was prepared for 150 ng input. Prepared working (30x) stock dilutions of Master stock probe pools for 12 reactions,  See table 4 of protocol TagSet Hyb setup MAN-10057-03.  Creating working pools is also in Manual LBL-10241-04 June 2018 nCounter Elements XT reagents user manual.  Hyb set up as per protocol page 5. Hyb for 20 hours at 67'C. Samples were cleaned up on a nanoString Max Flex PrepStation. See MAN-C0035, nCounter Analysis System User Manual for details

scan_protocol: NanoString cartridges were scanned on a nanoString Digital Analyser: nCounter Analysis System User Manual MAN-C0035-07 July 18.

data_processing: Raw RCCs were processed following the nSolver pipeline implemented in NanoTube (Class et al., Bioinformatics, 2023), which normalizes expression across samples by relative housekeeping gene (n=6) and positive control probe (n=6) expression scale. BEST1 was was filtered out during preprocessing, as it fell below the minimum expression threshold (2SD above the mean of negative control probes) in 57.4% of samples.

molecule: total RNA

organism: Homo sapiens

source_name: NHA, transduced with CRISPRi sgRNA targeting enhancer

growth_protocol: NHA cells stably expressing dCas9-KRAB were grown in DMEM media supplemented with 10% foetal bovine serum and 1% streptomycin/penicillin at 37°C, 5% CO2

extract_protocol: 7 days after transduction, RNA was extracted using the miRNeasy Mini Kit (Qiagen, 217004)

treatment_protocol: NHA-dCas9-KRAB cells were transduced with 1-3 sgRNA that target enhancers linked to one gene at an MOI of 1 per sgRNA. After 4 days, cells were selected with 3 µg/mL of puromycin and 10 µg/mL blasticidine S hydrochloride

tag: cell line

value: Normal Human Astrocytes (Lonza, #CC-2565)

tag: enhancer crispri target

value: Negative control - no enhancer target

tag: gene regulated by targeted enhancer

tag: replicate

value: RepA

tag: amount of input rna


title: testis, Control-1

type: SRA

city: Jiang Su

first: ke

last: Ren

address: 608A, Chemistry Building, Northwest Gate, Gulou Campus, Nanjing University, Gulou District, Nanjing City, Jiangsu Province

department: medical college

country: China

institute: Nanjing University

description:
Library name: sample1
Column name in processed data.txt: Control_1

library_source: transcriptomic

data_processing:
Quality control was performed using the fastp software (version 0.23.0) [@fastp], with the following specific quality control steps: 1. Remove adapter sequences from reads and filter out reads shorter than 15 bp; 2. Filter out low-quality reads (discard if the proportion of bases with a quality score below Q20 exceeds 0.08); 3. Filter out reads with excessive N bases (discard if the number of N bases in a read exceeds 5).
Assembly: GRCm39_release110
Supplementary files format and content: The tab-delimited xls file contains the RPKM values for each sample

organism: Mus musculus

source_name: testis

extract_protocol:
Total RNA was extracted from mouse testicular tissue using the Trizol reagent kit, and a sequencing library was constructed using 2400 ng of total RNA.
During library preparation, total RNA was used as input, and the RNA sequencing library was constructed using the KCTM mRNA Library Prep Kit (Wuhan Kangce) following the manufacturer's instructions.

tag: tissue

value: testis


title: NHA_Neg_Library_RepA_150ng, Batch1_9


title: MD8HB1_2

city: Xiamen

first: Chunlan

last: Xie

address: Daxue

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a pvalue cutoff of 0.05 to judge statistically significant enrichment. Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

source_name: cell line

growth_protocol: MC3T3-E1 were cultivated with complete α-MEM essential medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1 % penicillin/ streptomycin (BI, Beit Haemek, Israel) at a temperature of 37°C and a CO2 concentration of 5%.

extract_protocol:
The total RNA of each of above listed samples was isolated using the Trizol Kit (Promega, USA) following by the manufacturer’ s instructions. 2 μg of total RNAs were utilized for the preparation of stranded RNA sequencing libraries with the KCTM Stranded mRNA Library Prep Kit (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China)
RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

treatment_protocol: Under the induction conditions of 50 μg/mL ascorbic acid and 5 mM β-glycerophosphate, MC3T3-E1 were exposed to VDC (5 μM) for 3, 5 and 8 days. 0.1% DMSO was the control treatment.

value: cell line

tag: cell type

value: Multipotent precursor cells

tag: genotype

tag: treatment

value: D5+Osteogenic differentiation+HB-1


title: NHA_Neg_Library_RepB_150ng, Batch1_11

value: RepB


title: MD8HB1_3


title: 1257 myo primary HMGA2-V5 input

country: USA

library_source: genomic

molecule: genomic DNA


title: lung, SD-ZT12, bio rep1

city: Dalian

first: jinxin

last: lu

state: Liaoning

address: lvshunkou district lvshun south goad west sector No.9

institute: Dalian Medical University

data_processing:
The RNA-seq data were mapped to the reference genome mm10 using the software Hisat2 v2.0.5 based on the default parameters.
The expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) estimated each gene expression levels by featureCounts (v1.5.0-p3).
Assembly: mm10

source_name: lung

growth_protocol: All mice were kept at a strict 24-hour light-dark cycle, with lights being turned on from 8:00 am (ZT0) to 8:00 pm (ZT12). Food and water were provided ad libitum.

extract_protocol:
Total RNAs were extracted according to TRIzol manufacturer's protocols.1.5 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared according to the NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s recommendations.

treatment_protocol: Mice were pre-treated in SD cages or home cages for 20 hours a day (14:00-10:00) for 2 days. Then the lungs of C57BL/6J in Ctrl and SD group were collected per 4 h for 24h beginning at 8:00 am.

value: lung

value: WT

value: SD


title: NHA_Enh854_HSPB1_RepB_300ng, Batch1_8


title: lung, SD-ZT8, bio rep3


title: NHA_Enh854_HSPB1_RepB_150ng, Batch1_7


title: MD8HB1_1


title: NHA_Enh210_FTH1_RepA_150ng, Batch2_1


title: 1257 myo primary control H3K27ac

value: Active motif, 39133 (H3K27ac)

value: Lentiviral transduction of empty vector


title: MD8Diff_4

value: D8+Osteogenic differentiation


title: NHA_Neg_Library_RepB_300ng, Batch1_12


title: 1257 myo primary control input

value: Uterine myometrium

value: Primary cells


title: NHA_Enh854_HSPB1_RepA_300ng, Batch1_6


title: NHA_Enh854_HSPB1_RepA_150ng, Batch1_5


title: lung, SD-ZT8, bio rep1


title: 1257 myo primary HMGA2-V5 H3K27ac

value: Lentiviral transduction of V5-tagged HMGA2 vector


title: NHA_Enh210_FTH1_RepB_300ng, Batch1_4

value: Normal Human Astrocytes (Lonza, #CC-2565)


title: lung, SD-ZT4, bio rep2


title: MD8Diff_2


title: lung, SD-ZT4, bio rep3


title: MD8Diff_3


title: 1289 myo primary HMGA2-V5 input


title: lung, SD-ZT8, bio rep2


title: 1289 myo primary HMGA2-V5 H3K27ac


title: NHA_Enh210_FTH1_RepA_300ng, Batch1_2


title: NHA_Enh210_FTH1_RepB_150ng, Batch1_3


title: MD5HB1_3


title: 1289 myo primary control H3K27ac


title: lung, SD-ZT0, bio rep3


title: HEK-293T cells SLX4-XPF CRISPRCAS9 knockout_rep3_L02_15

city: Lyon

first: abdelakamel

last: chettab

address: 8 avenue Rockeffeler

department: centre de recherche en cancérologie de lyon

country: France

institute: université claude bernard lyon1

description:
Library name: HEK-293T cells SLX4-XPF CRISPRCAS9 knockout_rep3
Column name in raw_counts-All_Samples.txt:SLX4-XPF CRISPR/CAS9 knockout_rep3

data_processing:
Partek™ Flow™ software version 12.8.0 was used to analyze the RNA seq data using the count matrix generated after the sequencing of the libraries
pre-alignment QA/QC was applied to assesses the quality of the unaligned reads. Reads with Phred scores below 35 were trimmed from 3’ end, and trimmed reads shorter than 25 nucleotides were excluded from further analysis
High-quality reads from each sample were aligned to the human genome (hg38) using the STAR aligner (version 2.7.8a) implemented in Partek Flow
Assembly: homo sapiens (hg38) using the STAR aligner (version 2.7.8a) implemented in Partek Flow
Supplementary files format and content: .txt file includes total reads of each samples

growth_protocol: All cell lines and CRISPR-Cas9-modified models are described in detail our previous publication (Cros-Perrial E, Beaumel S, Gimbert M, Camus N, Vicente C, Sekiou I, Figuet L, Duruisseaux M, Dumontet C and Jordheim LP. SLX4 and XPF are involved in cell migration and EMT in a cell-specific manner. Biochem Pharmacol. 2025;236:116885.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
mRNA was enriched from 200 ng of total RNA, then library preparation was realized with the MGIEasy RNA Directional Library Prep Set (MGI)

value: embryonic kidney cells

value: SLX4_XPF knockout


title: MD5HB1_1


title: lung, SD-ZT0, bio rep2


title: lung, SD-ZT4, bio rep1


title: MD5HB1_2


title: 1313 myo primary HMGA2-V5 V5

value: Thermo Fisher Scientific, R96025 (V5)


title: HEK-293T cells SLX4-XPF CRISPRCAS9 knockout_rep2_L02_64

description:
Library name: HEK-293T cells SLX4-XPF CRISPRCAS9 knockout_rep2
Column name in raw_counts-All_Samples.txt:SLX4-XPF CRISPR/CAS9 knockout_rep2


title: lung, SD-ZT0, bio rep1


title: HEK-293T cells SLX4-XPF CRISPRCAS9 knockout_rep1_L02_60

description:
Library name: HEK-293T cells SLX4-XPF CRISPRCAS9 knockout_rep1
Column name in raw_counts-All_Samples.txt:SLX4-XPF CRISPR/CAS9 knockout_rep1


title: 1313 myo primary HMGA2-V5 H3K27ac


title: 12898 myo primary HMGA2-V5 V5


title: lung, Ctrl-ZT24, bio rep3

value: Ctrl


title: MD5Diff_2

value: cell line

value: Multipotent precursor cells

value: D5+Osteogenic differentiation


title: lung, Ctrl-ZT24, bio rep2

value: lung


title: MD8Diff_1


title: MD5Diff_1


title: 1313 myo primary HMGA2-V5 input


title: HEK-293T cells XPF CRISPRCAS9 knockout_rep2_L02_63

description:
Library name: HEK-293T cells XPF CRISPRCAS9 knockout_rep2
Column name in raw_counts-All_Samples.txt:XPF CRISPR/CAS9 knockout_rep2

value: XPF knockout


title: 1313 myo primary control H3K27ac


title: lung, Ctrl-ZT24, bio rep1

value: WT


title: MD3HB1_4

value: D3+Osteogenic differentiation+HB-1


title: 1289 myo primary control input

value: Lentiviral transduction of empty vector


title: HEK-293T cells XPF CRISPRCAS9 knockout_rep3_L02_14

description:
Library name: HEK-293T cells XPF CRISPRCAS9 knockout_rep3
Column name in raw_counts-All_Samples.txt:XPF CRISPR/CAS9 knockout_rep3


title: NHA_Enh210_FTH1_RepA_150ng, Batch1_1

value: RepA


title: 1313 myo primary control input

value: Uterine myometrium


title: HEK-293T cells XPF CRISPRCAS9 knockout_rep1_L02_59

description:
Library name: HEK-293T cells XPF CRISPRCAS9 knockout_rep1
Column name in raw_counts-All_Samples.txt:XPF CRISPR/CAS9 knockout_rep1


title: lung, Ctrl-ZT20, bio rep3


title: 1257 myo primary  HMGA2 RNA-seq

data_processing:
For basecalls, RTA v.2.4.11 was utilized on Nextseq instrument.
The STAR aligner was used to align paired-end reads to the hg38 genome (with ENSEMBL GRCh38.92 annotations).
Gene counts were obtained using the STAR option –quantMode.
The fourth column of the quantmode output was extracted to obtain reads aligning to features in the correct orientation
Assembly: hg38
Supplementary files format and content: Tab deliminated files containing the output from STAR aligner in quantmode. The first column is the gene name and the fourth column is the number of reads aligning to the gene in the correct strand specific orientation.

extract_protocol:
RNeasy mini kit (Qiagen, 74104) was used for RNA isolation.
Approximately 100 ng of purified RNA was used for library generation using the TruSeq stranded mRNA kit (Illumina, 20020594). 2-nM libraries from three biological replicates were pooled, quantified, and sequenced as paired-end with 42 cycles using the Nextseq 500/550 high-output kit (v2, 75 cycles).

value: Primary cells


title: lung, Ctrl-ZT20, bio rep2


title: MD3HB1_1


title: MD5Diff_3


title: lung, Ctrl-ZT20, bio rep1


title: HEK-293T cells SLX4 CRISPRCAS9 knockout_rep2_L02_62

description:
Library name: HEK-293T cells SLX4 CRISPRCAS9 knockout_rep2_
Column name in raw_counts-All_Samples.txt:SLX4 CRISPR/CAS9 knockout_rep2

value: SLX4 knockout


title: HEK-293T cells SLX4 CRISPRCAS9 knockout_rep1_L02_58

description:
Library name: HEK-293T cells SLX4 CRISPRCAS9 knockout_rep1
Column name in raw_counts-All_Samples.txt:SLX4 CRISPR/CAS9 knockout_rep1


title: 1257 myo primary control RNA-seq


title: lung, Ctrl-ZT16, bio rep3


title: 1289 myo primary  HMGA2 RNA-seq

value: Lentiviral transduction of V5-tagged HMGA2 vector


title: 1289 myo primary control RNA-seq


title: MD3Diff_4

value: D3+Osteogenic differentiation


title: HEK-293T cells, WT_rep3_L03_65

description:
Library name: HEK-293T cells, WT_rep3_
Column name in raw_counts-All_Samples.txt:WT_rep3

value: embryonic kidney cells


title: HEK-293T cells, WT_rep2_L02_61

description:
Library name: HEK-293T cells, WT_rep2
Column name in raw_counts-All_Samples.txt:WT_rep2


title: lung, Ctrl-ZT12, bio rep3


title: HEK-293T cells, WT_rep1_L02_57

description:
Library name: HEK-293T cells, WT_rep1_
Column name in raw_counts-All_Samples.txt:WT_rep1


title: MD3HB1_3


title: lung, Ctrl-ZT16, bio rep1


title: lung, Ctrl-ZT16, bio rep2


title: MD3Diff_2


title: 1313 myo primary control RNA-seq


title: 1313 myo primary HMGA2 RNA-seq


title: MD3Diff_1


title: lung, Ctrl-ZT12, bio rep2


title: HEK-293T cells SLX4 CRISPRCAS9 knockout_rep3_L02_13

description:
Library name: HEK-293T cells SLX4 CRISPRCAS9 knockout_rep3
Column name in raw_counts-All_Samples.txt:SLX4 CRISPR/CAS9 knockout_rep3


title: MD3Diff_3


title: HT-29 cells SLX4-XPF CRISPRCAS9 knockout_rep3_L03_88_1

description:
Library name: HT-29 cells SLX4-XPF CRISPRCAS9 knockout_rep3
Column name in raw_counts-All_Samples.txt: SLX4-XPF CRISPR/CAS9 knockout_rep3

value: colon cancer cells

value: SLX4_XPF knockout


title: MD3HB1_2

value: cell line


title: L_ShamM_2

city: Seattle

first: Jianjun

last: Jiang

address: 401 Terry Ave N

institute: Institute for Systems Biology

description:
Total RNA was extracted for DNBSEQ sequencing
18m_gene_expression.xls
18m_gene_diff.xls

data_processing:
Raw data was preprocessed by SolexaQA to exclude too quanlity and short reads
Cleaned data was subjected to Hisat2 for mapping
SAM files generated by Hisat2 were converted and sorted to bam files by SAMTOOLs
Bam files were then subjected to Cufflinks packages for gene counts, FPKM values normalization and identifying differentially expressed genes.
FDR < 0.05 was applied as the cut-off value
Assembly: mm10
Supplementary files format and content: Tab-delimited txt file for the FPKM values and statistical significance data of 12week samples;
Supplementary files format and content: Microsoft Excel spreadsheets for the FPKM values statistical significance data of 18month samples.

source_name: liver

growth_protocol: Mice were breed in pathogen free facility with normal water and chow.

extract_protocol:
Total RNA was isolated from kidney and liver by Trizol
PolyA-tailed RNA was enriched for constructing 150bp pair-end RNA-sequencing libraries using MGISEQ-2000RS kit

treatment_protocol: Castration/sham procedure was processed in 8 weeks old WT C57BL6 mice, mice at 12weeks and 18 months old were scarified for sample collection.

value: liver

value: sham


title: L_ShamM_1


title: HT-29 cells SLX4-XPF CRISPRCAS9 knockout_rep1_L01_68_1

description:
Library name: HT-29 cells SLX4-XPF CRISPRCAS9 knockout_rep1
Column name in raw_counts-All_Samples.txt: SLX4-XPF CRISPR/CAS9 knockout_rep1


title: 1257 myo primary control ATAC-seq

data_processing:
For basecalls, RTA v.2.4.11 was utilized on Nextseq instrument.
Fastq files were first analyzed for quality by FastQC. Paired-end reads were aligned to the hg38 reference genome using Bowtie2 (v2.2.6) with options --very-sensitive -X 800. Mitochondrial reads were removed from the alignment files using sed, and adapters were removed with NGmerge.
Peaks were called using MACS2 (v2.2.6) with the DNase-seq enriched cut site method (--nomodel --shift -75 --extsize 150 --nolambda -p 0.01).
Assembly: hg38
Supplementary files format and content: MACS2 narrowPeak files

extract_protocol:
Cells from each condition were trypsinized. Approximately 1 million cells were washed in ice-cold PBS and ATAC-seq libraries were generated. cells were spun at 500xg for 5 min at 4°C and then resuspended in 1 ml of lysis mix (0.1% Tween 20, 0.1% IGEPAL, and 0.01% Digitonin) in ATAC resuspension buffer (10 mM Tris-HCl [pH 8.0], 10 mM NaCl, and 3 mM MgCl2). The cell suspension was kept on ice for 3 min for lysis to occur, then 4 ml of wash buffer (0.1% Tween 20 in ATAC resuspension buffer) was added and gently mixed. The nuclei pellet was obtained by centrifugation at 500xg for 10 min at 4°C and then resuspended in 125 μl of ice-cold PBS.
Nuclei were counted and approximately 12,500 nuclei were resuspended into the transposase tagmentation mix (2.5 μl TDE1 enzyme and 25 μl TD buffer [Illumina, FC-121-1030], 16.5 μl nuclei in ice-cold PBS, 0.5 μl 1% Digitonin, 0.5 μl 10% Tween 20, and 5 μl water). The tagmentation reaction was carried out in a thermomixer at 37°C for 30 min at 300 rpm. DNA was purified with the Zymo DNA clean and concentrator (Zymo Research, D4013) and amplified for 9 cycles with High Fidelity 2X PCR Master Mix (NEB, M0541S). The amplified libraries were then purified using the Zymo kit (Zymo Research, D4013), and size selected 0.6X - 1.8X using Ampure XP beads (Beckman Coulter, A63880). The library profile was checked with an Agilent 2100 Bioanalyzer, followed by paired-end sequencing (2 × 42 bp) using the Illumina NextSeq500.


title: lung, Ctrl-ZT8, bio rep3

value: lung

value: Ctrl


title: lung, Ctrl-ZT12, bio rep1

value: WT


title: L_ShamM_3


title: HT-29 cells XPF CRISPRCAS9 knockout_rep3_L03_87_1

description:
Library name: HT-29 cells XPF CRISPRCAS9 knockout_rep3
Column name in raw_counts-All_Samples.txt: XPF CRISPR/CAS9 knockout_rep3

value: XPF knockout


title: 1289 myo primary  HMGA2 ATAC-seq


title: L_ShamF_1


title: 1289 myo primary control ATAC-seq

value: Lentiviral transduction of empty vector


title: lung, Ctrl-ZT8, bio rep2


title: HT-29 cells XPF CRISPRCAS9 knockout_rep2_L02_75_1

description:
Library name: HT-29 cells XPF CRISPRCAS9 knockout_rep2
Column name in raw_counts-All_Samples.txt: XPF CRISPR/CAS9 knockout_rep2


title: 1257 myo primary  HMGA2 ATAC-seq


title: L_ShamF_2


title: L_ShamF_3


title: lung, Ctrl-ZT8, bio rep1


title: HT-29 cells SLX4-XPF CRISPRCAS9 knockout_rep2_L02_76_1

description:
Library name: HT-29 cells SLX4-XPF CRISPRCAS9 knockout_rep2
Column name in raw_counts-All_Samples.txt: SLX4-XPF CRISPR/CAS9 knockout_rep2


title: 1313 myo primary HMGA2 ATAC-seq


title: HT-29 cells SLX4 CRISPRCAS9 knockout_rep3_L03_86_1

description:
Library name: HT-29 cells SLX4 CRISPRCAS9 knockout_rep3_
Column name in raw_counts-All_Samples.txt: SLX4 CRISPR/CAS9 knockout_rep3


title: 1313 myo primary control ATAC-seq


title: HT-29 cells SLX4 CRISPRCAS9 knockout_rep2_L02_74_1

description:
Library name: HT-29 cells SLX4 CRISPRCAS9 knockout_rep2
Column name in raw_counts-All_Samples.txt: SLX4 CRISPR/CAS9 knockout_rep2


title: L_Case2

value: castration


title: lung, Ctrl-ZT4, bio rep2


title: HT-29 cells XPF CRISPRCAS9 knockout_rep1_L01_67_1

description:
Library name: HT-29 cells XPF CRISPRCAS9 knockout_rep1
Column name in raw_counts-All_Samples.txt: XPF CRISPR/CAS9 knockout_rep1


title: lung, Ctrl-ZT4, bio rep1


title: S1423, VS2, snRNAseq

city: Bethesda

first: Prashant

last: Chittiboina

state: MD

address: 3D20, 10 Center Drive

department: NINDS

institute: NIH

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
library strategy: snRNA-seq
Sequencing reads were demultiplexed and aligned to the hg38 reference genome using the 10X Genomics CellRanger software (arc v2.0.1) mkfastq function with default settings, and counts were generated using the CellRanger-arc count function. Individual datasets were integrated using the CCA integration method from the Seurat v4 R-package integration workflow to remove batch effects while preserving biological variation.
Assembly: GRCh38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Tumor

extract_protocol:
OCT-embedded hemangioblastoma samples were removed from -80°C storage and placed in a cryostat. A clean razor blade was used to cut away OCT fragments. Nuclei were isolated from the frozen tissues using an adaptation of a previously established protocol. Samples was placed on a clean petri dish and washed with 800uL of Detergent-Lysis Buffer (0.1% Triton-X). Tissues were chopped into small pieces, homogenized in a 7mL Dounce Homogenizer on ice (Fisher Scientific # 501945204), and passed through a 70 m MACS strainer (Miltenyi Biotec # 130-098-462).
Library was performed according to the manufacter’s instructions (single nucleus protocol, 10x Genomics).

tag: patient id

value: Patient 1

value: After Vorinostat treatment

value: vestibular schwannoma

value: Tumor


title: lung, Ctrl-ZT0, bio rep3


title: HT-29 cells SLX4 CRISPRCAS9 knockout_rep1_L01_66_1

description:
Library name: HT-29 cells SLX4 CRISPRCAS9 knockout_rep1
Column name in raw_counts-All_Samples.txt: SLX4 CRISPR/CAS9 knockout_rep1

value: SLX4 knockout


title: HT-29 cells, WT_rep3_L03_85_1

description:
Library name: HT-29 cells, WT_rep3
Column name in raw_counts-All_Samples.txt: WT_rep3


title: S1581, VS4, snRNAseq

description: 10x Genomics

value: Patient 2


title: S1285, VS1, snRNAseq

description: 10x Genomics

value: Before Vorinostat treatment


title: L_Case3


title: lung, Ctrl-ZT0, bio rep2


title: S1510, VS3, snRNAseq

description: 10x Genomics


title: L_Case5


title: L_Case4


title: HT-29 cells, WT_rep2_L02_73_1

description:
Library name: HT-29 cells, WT_rep2
Column name in raw_counts-All_Samples.txt: WT_rep2

value: colon cancer cells


title: lung, Ctrl-ZT0, bio rep1


title: HDMEC-KTR3

city: Wuerzburg

first: Natalie

last: Burkard

address: Oberduerrbacherstr. 6

department: Experimentelle Viszeralchirurgie

country: Germany

institute: Universitätsklinikum Würzburg

data_processing:
Base calling with NextSeq Control/RTA v2 and FASTQ file generation with bcl2fastq v2.20.0.422
Adapter clipping and trimming with cutadapt 2.5.
Mapping to RefSeq the human genome GRCh38.p19  with STAR version 2.7.2b and raw read counting with featureCounts v 1.6.4 using the RefSeq annotation.
Differential Expression analysis with DESeq2_1.24.0
Assembly: GRCh38.p19
Supplementary files format and content: CSV: Raw read table

source_name: human primary endothelial (HDMEC) cells

extract_protocol:
RNA was isolated using TRIZOL. 0.5µl of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA kit (Illumina) with total RNA as input for mRNA capture with oligo-dT beads

value: human primary endothelial (HDMEC) cells

value: control


title: HDMEC-KTR2


title: L_Case1

value: liver


title: K_ShamM_1

source_name: kidney

value: kidney

value: sham


title: HAPC, spleen, MNC, replicate1, scRNAseq

city: Tianjin

first: Peng

last: Wu

address: 288 Nanjing Road

institute: IHCAMS

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
FACS-sorted MNC spleen
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

treatment_protocol: hypoxia exposure

value: Spleen

value: MNC

value: Hypoxia


title: HAPC, spleen, MNC, replicate2, scRNAseq

description: 10x Genomics


title: COLO-357 cells SLX4-XPF CRISPRCAS9 knockout_rep3_L01_4

description:
Library name: COLO-357 cells SLX4-XPF CRISPRCAS9 knockout_rep3
Column name in raw_counts-All_Samples.txt: SLX4-XPF CRISPR/CAS9 knockout_rep3

value: pancreatic cancer cells

value: SLX4_XPF knockout


title: K_ShamM_2

value: WT


title: HDMEC-KTR1


title: HDMEC-sVE3

value: sVE

value: Soluble VE-cadherinEC1-5 treatment


title: Control, spleen, MNC, replicate2, scRNAseq

description: 10x Genomics

value: Control


title: lung, Ctrl-ZT4, bio rep3

value: lung

value: Ctrl


title: COLO-357 cells SLX4-XPF CRISPRCAS9 knockout_rep2_L01_48

description:
Library name: COLO-357 cells SLX4-XPF CRISPRCAS9 knockout_rep2
Column name in raw_counts-All_Samples.txt: SLX4-XPF CRISPR/CAS9 knockout_rep2


title: K_ShamM_3


title: HDMEC-sVE2


title: K_ShamF_1


title: COLO-357 cells SLX4-XPF CRISPRCAS9 knockout_rep1_L01_44

description:
Library name: COLO-357 cells SLX4-XPF CRISPRCAS9 knockout_rep1
Column name in raw_counts-All_Samples.txt: SLX4-XPF CRISPR/CAS9 knockout_rep1


title: Control, spleen, MNC, replicate1, scRNAseq

description: 10x Genomics


title: HDMEC-sVE1


title: COLO-357 cells XPF CRISPRCAS9 knockout_rep3_L01_3

description:
Library name: COLO-357 cells XPF CRISPRCAS9 knockout_rep3
Column name in raw_counts-All_Samples.txt: XPF CRISPR/CAS9 knockout_rep3

value: XPF knockout


title: COLO-357 cells XPF CRISPRCAS9 knockout_rep2_L01_47

description:
Library name: COLO-357 cells XPF CRISPRCAS9 knockout_rep2
Column name in raw_counts-All_Samples.txt: XPF CRISPR/CAS9 knockout_rep2


title: C57BL6 mouse,sham,24hours,rep3

city: HANGZHOU

first: MINGJIE

last: FU

state: ZHEJIANG

address: 79#QINGCHUN ROAD

institute: THE FIRST AFFILIATED HOSPITAL OF ZHEJIANG UNIVERSITY

description: Library name: S3

data_processing:
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 file include RPKM values for each Sample

source_name: Kidney

extract_protocol:
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.

value: Kidney

value: C57BL6 wild

value: Just open the abdominal cavity


title: K_ShamF_2

value: kidney


title: F-GAS41_Y74A W93A_IP

city: 长春市

last: Liu

state: 吉林省

address: 东民主大街519转化医学院

institute: 1st hospital

data_processing:
Raw sequence reads were trimmed to remove both poor-quality calls and adapters using Trim Galore (v0.6.5, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Cutadapt version 1.8.1).
The reads were aligned to human genome reference hg19 using bowtie
Sam files were then converted into bam files using samtools (version 1.12)
To create heatmaps, reads within -5000 ~ 5000 bps regions were quantified and visualized using deeptools (version 3.4.3)
Peak calling were performed using MACS2
Peaks were annotated were using R package ChIPseeker
Peak associated genes were quantified and visualized using R package BioVenn.
the alignment and coverage of ChIP-seq data were visualized by integrative genomics viewer (IGV)
Assembly: hg 19
Supplementary files format and content: bigWig files

source_name: Homo sapiens HCT116 cell line

growth_protocol: HCT116 cells were cultured in RPMI-1640 contained 10% fetal calf serum , 100 units of penicillin  and 100 µg/ml streptomycin.

extract_protocol:
Fixed cells were sonicated and clear cell lysate was incubated with antibody. Dynabeads was added to isolate protein-DNA complexes.
DNA elute was sent to BGI for ChIP sequencing. Briefly, ChIP DNA was end repaired and purified for A-Tailing followed by adaptor ligation. Then, the adapter-ligated DNA was enriched by PCR amplification and 100-300bp PCR products were selected. DNA library preparation was qualified and DNA sequencing was performed on BGISEQ-500 platform (BGI-Shenzhen, China).

treatment_protocol: GAS41 was knocked out in HCT116 cells. Flag-GAS41 was transiently or stably expressed in HCT116 GAS41 KO cells.

value: Large intestine; Colon

value: human colorectal carcinoma cell

value: GAS41 knockout and stable transfection of Flag-GAS41 Y74A W93A


title: HT-29 cells, WT_rep1_L01_65_1

description:
Library name: HT-29 cells, WT_rep1
Column name in raw_counts-All_Samples.txt: WT_rep1

value: colon cancer cells


title: F-GAS41_Y74A W93A_Input

address: 东民主大街519转化医学院


title: COLO-357 cells XPF CRISPRCAS9 knockout_rep1__L01_43

description:
Library name: COLO-357 cells XPF CRISPRCAS9 knockout_rep1
Column name in raw_counts-All_Samples.txt: XPF CRISPR/CAS9 knockout_rep1

value: pancreatic cancer cells


title: C57BL6 mouse,sham,24hours,rep2

description: Library name: S2


title: K_Case4

description:
Total RNA was extracted for DNBSEQ sequencing
18m_gene_expression.xls
18m_gene_diff.xls

value: castration


title: IP_H3K27Ac

address: 东民主大街519转化医学院

data_processing:
Raw sequence reads were trimmed to remove both poor-quality calls and adapters using Trim Galore (v0.6.5, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Cutadapt version 1.8.1).
The reads were aligned to human genome reference hg19 using bowtie
Sam files were then converted into bam files using samtools (version 1.12)
To create heatmaps, reads within -5000 ~ 5000 bps regions were quantified and visualized using deeptools (version 3.4.3)
Peak calling were performed using MACS2
Peaks were annotated were using R package ChIPseeker
Peak associated genes were quantified and visualized using R package BioVenn.
the alignment and coverage of ChIP-seq data were visualized by integrative genomics viewer (IGV)
Genome_build: hg 19
Supplementary_files_format_and_content: bigWig files

source_name: HCT116 cell line

tag: tissue source

value: human colorectal carcinoma cell line

tag: genotype/variation

value: untreated


title: K_ShamF_3

value: WT

value: sham


title: COLO-357 cells SLX4 CRISPRCAS9 knockout_rep3-2

description:
Library name: COLO-357 cells SLX4 CRISPRCAS9 knockout_rep3
Column name in raw_counts-All_Samples.txt: SLX4 CRISPR/CAS9 knockout_rep3

value: SLX4 knockout


title: 18m_K_Case1


title: K_Case5


title: C57BL6 mouse,CLP,24hours,rep3

description: Library name: C3

value: cecal ligation and puncture


title: Input_H3K27Ac

address: 东民主大街519转化医学院


title: F-GAS41_T_IP

address: 东民主大街519转化医学院

value: GAS41 knockout and transient transfection of Flag-GAS41

value: Flag


title: F-GAS41_T_Input

address: 东民主大街519转化医学院


title: COLO-357 cells SLX4 CRISPRCAS9 knockout_rep1_L01_42

description:
Library name: COLO-357 cells SLX4 CRISPRCAS9 knockout_rep1
Column name in raw_counts-All_Samples.txt: SLX4 CRISPR/CAS9 knockout_rep1


title: ATAC-seq, E7.75, Lhx1-epiCKO, rep 2

city: Westmead

first: Riley

last: McMahon

address: 214 Hawkesbury Road

institute: Children's Medical Research Institute

data_processing:
Raw reads from each sample were mapped to the mm10 Mus musculus genome by Galaxy platform Bowtie2 v2.3.4
Three biological replicates for each sample were merged (samples were pre-processed to discard multimappers, duplicated and mitochondria associated reads). Differentially accessible regions (DARs) were then detected using MACS2 (v.2.1.1.20160309.4) .
Assembly: mm10
Supplementary files format and content: bw

source_name: E7.75 mouse embryo

growth_protocol: E7.25 and E7.75 embryos were collected from Lhx1flox/flox mice crossed with Lhx1+/del, Meox+/Cre mice and genotyped for Lhx1 as wild-type (control): Lhx1flox/+, or Lhx1-epiCKO: Meox2Cre/+;Lhx1flox/del. Embryos were imaged washed in PBS.

extract_protocol:
Genomic DNA from each embryo was extracted in 50 μL of cold lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630) and gently pipetted up and down to lyse the cells.
The Nextera XT DNA Library Preparation Kit (Illumina) was then used to generate ATAC-seq libraries for each individual embryo. Samples were submitted for 100 bp paired end sequencing on a HiSeq2500 with 60M reads per sample.

value: E7.75 mouse embryo


title: F-GAS41_S_IP

address: 东民主大街519转化医学院

value: GAS41 knockout and stable transfection of Flag-GAS41


title: 18m_K_Case3

value: kidney


title: C57BL6 mouse,sham,24hours,rep1

description: Library name: S1

value: Kidney

value: C57BL6 wild

value: Just open the abdominal cavity


title: C57BL6 mouse,CLP,24hours,rep2

description: Library name: C2


title: C57BL6 mouse,CLP,24hours,rep1

description: Library name: C1


title: COLO-357 cells, WT_rep1_L01_41

description:
Library name: COLO-357 cells, WT_rep1
Column name in raw_counts-All_Samples.txt: WT_rep1


title: 12w_shamF3_liver

description:
Total RNA was extracted for DNBSEQ sequencing
12w_RNA_seq_expression_FPKM_Mean.txt
12w_liver_exp_diff.txt

value: liver


title: F-GAS41_S_Input

address: 东民主大街519转化医学院

value: Large intestine; Colon


title: COLO-357 cells, WT_rep3-1

description:
Library name: COLO-357 cells, WT
Column name in raw_counts-All_Samples.txt: WT_rep3

value: pancreatic cancer cells


title: 12w_shamF2_liver


title: 12w_shamF1_liver


title: ATAC-seq, E7.75, Lhx1-epiCKO, rep 3


title: COLO-357 cells SLX4 CRISPRCAS9 knockout_rep2_L01_46

description:
Library name: COLO-357 cells SLX4 CRISPRCAS9 knockout_rep2
Column name in raw_counts-All_Samples.txt: SLX4 CRISPR/CAS9 knockout_rep2


title: ATAC-seq, E7.75, control, rep 3


title: NCI-H1703 cells SLX4-XPF CRISPRCAS9 knockout_rep3_L03_92_1

description:
Library name: NCI-H1703 cells SLX4-XPF CRISPRCAS9 knockout_rep3
Column name in raw_counts-All_Samples.txt: SLX4-XPF CRISPR/CAS9 knockout_rep3

value: lung squamous carcinoma epithelial Cells

value: SLX4_XPF knockout


title: Blank

city: Nanjing

first: Yaotang

address: Nanjing Agricultural University, Wei gang 1

institute: Nanjing Agricultural University

description: Library name: Blank

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: GCA_000003025.6
Supplementary files format and content: raw and norm expression profiles

organism: Sus scrofa

source_name: PAM

growth_protocol: Marc-145 cells were maintained in RPMI 1640  supplemented with 10% FBS, penicillin (100 U/ml), and streptomycin (100 mg/mL) at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (v4.2) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: PAM

value: Macrophage

value: WT

value: Blank


title: 18m_K_Case2

value: castration


title: COLO-357 cells, WT_rep2_L01_45

description:
Library name: COLO-357 cells, WT_rep2
Column name in raw_counts-All_Samples.txt: WT_rep2


title: 12w_shamF3_kidney

description:
Total RNA was extracted for DNBSEQ sequencing
12w_RNA_seq_expression_FPKM_Mean.txt
12w_kidney_gene_exp_diff.txt

value: sham


title: NCI-H1703 cells SLX4-XPF CRISPRCAS9 knockout_rep1_L01_72_1

description:
Library name: NCI-H1703 cells SLX4-XPF CRISPRCAS9 knockout_rep1
Column name in raw_counts-All_Samples.txt: SLX4-XPF CRISPR/CAS9 knockout_rep1


title: PRRSV

description: Library name: PRRSV

value: PRRSV


title: 12w_shamF2_kidney


title: 12w_shamF1_kidney


title: NCI-H1703 cells SLX4-XPF CRISPRCAS9 knockout_rep2_L02_80_1

description:
Library name: NCI-H1703 cells SLX4-XPF CRISPRCAS9 knockout_rep2
Column name in raw_counts-All_Samples.txt: SLX4-XPF CRISPR/CAS9 knockout_rep2


title: 12w_shamM3_liver


title: ATAC-seq, E7.25, Lhx1-epiCKO, rep 3

source_name: E7.25 mouse embryo

value: E7.25 mouse embryo


title: NCI-H1703 cells XPF CRISPRCAS9 knockout_rep2_L02_79_1

description:
Library name: NCI-H1703 cells XPF CRISPRCAS9 knockout_rep2
Column name in raw_counts-All_Samples.txt: XPF CRISPR/CAS9 knockout_rep2

value: XPF knockout


title: NCI-H1703 cells XPF CRISPRCAS9 knockout_rep1_L01_71_1

description:
Library name: NCI-H1703 cells XPF CRISPRCAS9 knockout_rep1
Column name in raw_counts-All_Samples.txt: XPF CRISPR/CAS9 knockout_rep1


title: NCI-H1703 cells SLX4 CRISPRCAS9 knockout_rep3_L03_90_1

description:
Library name: NCI-H1703 cells SLX4 CRISPRCAS9 knockout_rep3
Column name in raw_counts-All_Samples.txt: SLX4 CRISPR/CAS9 knockout_rep3

value: SLX4 knockout


title: ATAC-seq, E7.75, Lhx1-epiCKO, rep 1

value: E7.75 mouse embryo


title: H1-CAR DN biol rep 3

city: Los Angeles

first: Gay

middle: Miriam

last: Crooks

state: California

address: 610 Charles E. Young Drive, East

department: Pathology & Laboratory Med

institute: University of California Los Angeles

description: human embryonic stem cells  (H1 line) transduced with a CD19-targeted CAR

data_processing:
The STAR ultrafast universal RNA-seq aligner v2.5.2b (Dobin et al., 2013) was used to generate the genome index and perform paired-end alignments. Reads were aligned to a genome index that includes both the genome sequence (GRCh38 primary assembly) and the exon/intron structure of known gene models (Gencode v26 basic genome annotation).
Alignment files were used to generate strand-specific, gene-level count summaries with STAR's built-in gene counter. Only protein-coding, long-noncoding, anti-sense and T-cell receptor genes in the Gencode v26 annotation were considered (98% of total counts on average). Independent filtering was applied as follows: genes with less than one count per sample on average, count outliers or low mappability were filtered out for downstream analysis
Counts were normalized per-sample in units of FPKMs after correcting for gene mappable length and sample total counts.
Assembly: GRCh38 primary assembly
Supplementary files format and content: Tab delimited. Table of per-gene and per-sample expression estimates in units of FPKMs

source_name: human embryonic stem cells  (H1 line)

growth_protocol: PSC (CAR)-ATOs were generated using purified hEMPs and followed a two-step procedure including a hematopoietic induction phase and a T-cell differentiation phase.  MS5-hDLL4 cells were harvested by trypsinization and resuspended in hematopoietic induction medium composed of EGM2 (Lonza Ref CC-4176) supplemented with ROCK inhibitor Y-27632 dihydrochloride (10uM) (Tocris Bioscience, Cat. 1254) and TGF-βRI inhibitor SB-431542 (“SB blocker”) (10 uM) (Tocris Bioscience, Cat. 1614). 5x105 MS5-hDLL4 cells were combined with 0.5-1x104 purified hEMP per PSC-ATO in 1.5 ml Eppendorf tubes and centrifuged at 300 g for 5 min at 4˚C in a swinging bucket centrifuge. Multiple (up to 12) PSC-ATO cell volumes were prepared per tube. Supernatants were carefully removed and the cell pellet was resuspended by brief vortexing, and resuspended in hematopoietic induction medium at a volume of 6 µl per PSC-ATO. 6 µl of cells were plated as PSC-ATOs on a 0.4 µm Millicell transwell insert (EMD Millipore, Billerica, MA; Cat. PICM0RG50) (up to 2 PSC-ATOs per insert were plated) and placed in 6-well plates containing 1 ml hematopoietic induction medium per well. Medium was changed completely every 2-3 days for 1 weekM with medium composed of EGM2 with SB blocker (10uM). At day 7, medium was change to EGM2 + SB blocker (10uM) with the hematopoietic cytokines TPO 5ng/ml (Peprotech, Cat. 300-18), FLT3L 5ng/ml (Peprotech, Cat. 300-19), and SCF 50ng/ml (Peprotech, Cat. 300-07). This medium was changed every 2-3 days for an additional 7 days. At day 14, T cell differentiation was induced by changing the medium to “RB27” (described above) supplemented with 10 ng/ml SCF, 5 ng/ml FLT3L, and 5 ng/ml IL-7 (Peprotech, Cat. 200-07). Medium was changed completely every 3-4 days. PSC-ATO cells were harvested by adding MACS buffer (PBS/0.5% bovine serum album/2mM EDTA) to each well and briefly disaggregating the ATO by pipetting with a 1 ml “P1000” pipet, followed by passage through a 50 µm nylon strainer. Flow cytometry cell sorting of PSC (CAR)-ATO derived DN cell population used the following surface phenotypes: H1-CAR-DN (DAPI-eGFP+CD3-TCRαβ-CD8α-CD4-)

extract_protocol:
All samples were extracted using miRNeasy Micro Kit (Qiagen).
1.5ng of total RNA was input to generate sequencing libraries with SMARTer Stranded Total RNA-Seq (Pico) Kit (Clonetech, Cat. 635005).
Paired-end 150 bp sequencing was performed on an Illumina HiSeq 3000.

value: human embryonic stem cells  (H1 line)

value: in-vitro differentiated double-negative lymphocytes

tag: phenotype

value: lymphoid diffentiation in artificial thymic organoids (ATO)

tag: time

value: week 6


title: NCI-H1703 cells XPF CRISPRCAS9 knockout_rep3_L03_91_1

description:
Library name: NCI-H1703 cells XPF CRISPRCAS9 knockout_rep3
Column name in raw_counts-All_Samples.txt: XPF CRISPR/CAS9 knockout_rep3

value: lung squamous carcinoma epithelial Cells


title: H1-CAR DN biol rep 2


title: 12w_shamM1_liver

value: liver


title: HPPRRSV

description: Library name: HPPRRSV

value: PAM

value: HPPRRSV


title: WT_UV_nakedDNA_replicate1

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description:
Library name: WT_UV_nakedDNA_replicate1
Replicate 1

data_processing:
Base calling by Azenta and separated based on barcoded adapters
Read1 Fastq files were trimmed using either Trimmomatic v0.39 (BOLGER et al. 2014) or BBDuk version 38.95, with the parameters “ILLUMINACLIP:[XR-seq_adapter_file]:2:30:10”
Read1 fastq files were aligned to the Saccharomyces cerevisiae genome (saccer3) using bowtie2 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl scripts
Only reads mapping to dipyrimidine sequences (i.e., TT, TC, CT, CC), corresponding to CPD lesions were retained in BED files using a custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools or custom perl script
Assembly: saccer3
Supplementary files format and content: WIG files containing counts of DNA CPD lesion reads in dipyrimidine-mapping sequences and their position coordinates are included.

organism: Saccharomyces cerevisiae

source_name: Genomic DNA derived from Yeast cells

growth_protocol: Wild-type (WT) and hap5 yeast were grown overnight in rich (YPD) medium at normal growth temperature (30C), subcultured in YPD to midlog phase to an OD600 ~0.8, and harvested for UV exposure.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with approximately equal volumes of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 7.5-8.0, 1 mM EDTA) and PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and approximately 0.5 volumes of acid-washed glass beads. Beads were vortexed vigorously for about 4 min. After adding TE (10mM Tris-HCl, pH 7.5-8.0, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 2.5-3 volumes of 100% ethanol and stored at -20C to precipitate the DNA.  DNA pellets were washed with 75-80% ethanol, dissolved in mixture of 1xTE (pH7.5) and 0.2 μg/μl RNase A, and incubated at 37C for approximately 1 hr. The purified genomic DNA was then used for each sequencing library preparation.
The CPD-seq method was employed as previously described (Mao et al., PNAS 2016, 113 (32) 9057-9062). Briefly, approximately 50ug of yeast genomic DNA (gDNA; as measured by NanoDrop spectrophotometry) was extracted from UV-exposed cells via the phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation method. Genomic DNA was then sonicated (30s ON/OFF; 25 cycles; Diagenode Biorupter 300) to generate ~200-600bp fragments and ethanol precipitated. Fragmented DNA was converted to blunt-ended DNA with 5' phosphates and 3' hydroxyls with the NEBNext End Repair Module (NEB) and dA-tailed for ligation with the NEBNext dA-Tailing Module (NEB). A first double-stranded i7 Illumina adapter was ligated onto blunted 3' hydroxyls. Any remaining free 3' hydroxyls were blocked via incubation with terminal transferase (NEB) and either dideoxy ATP or GTP.  T4 endonuclease V (NEB) and APE1 were used to cleave at sites of CPDs and generate new ligatable 3' hydroxyl ends. A second double-stranded, biotinylated i7 Illumina adapter was ligated to these free 3' hydroxyls. Streptavidin beads were used to capture fragments containing the biotinylated second adapter, a wash with 1X SSC (saline sodium citrate) buffer removed non-specific binding, and 0.15M NaOH was used to elute the DNA prior to ethanol precipitation. The complementary strand was synthesized with EconoTaq (Lucigen) and the resulting libraries were amplified with 5 cycles of PCR containing unique barcoded primers for each sample. Libraries were pooled and submitted to Azenta for either Illumina HiSeq 4000 or Illumina NovaSeq X Plus sequencing. Cytiva SeraMag Select beads were used to purify DNA between enzyme incubation steps.

treatment_protocol: Cells were washed with water and exposed to either 90 or 125 J/m^2 UVC radiation (naked DNA vs cells, respectively). Cells were then spun down to obtain cell pellets for the 0h timepoint.

value: Genomic DNA derived from Yeast cells

value: WT

value: UV irradiated 90 J/m2

tag: repair time

value: 0 min


title: ATAC-seq, E7.75, control, rep 1


title: WT_UV_nakedDNA_replicate2

description:
Library name: WT_UV_nakedDNA_replicate2
Replicate 2


title: ATAC-seq, E7.75, control, rep 2


title: NCI-H1703 cells SLX4 CRISPRCAS9 knockout_rep2_L02_78_1

description:
Library name: NCI-H1703 cells SLX4 CRISPRCAS9 knockout_rep2
Column name in raw_counts-All_Samples.txt: SLX4 CRISPR/CAS9 knockout_rep2


title: ATAC-seq, E7.25, Lhx1-epiCKO, rep 2


title: ATAC-seq, E7.25, Lhx1-epiCKO, rep 1


title: ATAC-seq, E7.25, control, rep 3


title: WT_UV_0hr_cellular_replicate2

description:
Library name: WT_UV_0hr_cellular_replicate2
Replicate 2

source_name: Yeast cells

value: Yeast cells

value: UV irradiated 125 J/m2


title: H1-CAR DN biol rep 1


title: 12w_shamM3_kidney

value: kidney

value: sham


title: NCI-H1703 cells SLX4 CRISPRCAS9 knockout_rep1_L01_70_1

description:
Library name: NCI-H1703 cells SLX4 CRISPRCAS9 knockout_rep1
Column name in raw_counts-All_Samples.txt: SLX4 CRISPR/CAS9 knockout_rep1

value: SLX4 knockout


title: 12w_shamM2_liver

description:
Total RNA was extracted for DNBSEQ sequencing
12w_RNA_seq_expression_FPKM_Mean.txt
12w_liver_exp_diff.txt


title: 12w_shamM2_kidney


title: ATAC-seq, E7.25, control, rep 2

value: E7.25 mouse embryo


title: rad14_cdc13-1_cellular_6h

description:
Library name: rad14_cdc13-1_cellular_6h
Replicate 3

data_processing:
Base calling by Azenta
Read1 Fastq files were trimmed using Trimmomatic v0.39 (BOLGER et al. 2014), with the parameters “ILLUMINACLIP:[XR-seq_adapter_file]:2:30:10”
Read1 fastq files were aligned to the Saccharomyces cerevisiae genome (saccer3) using bowtie2 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to cytosine bases in dipyrimidine sequence contexts (i.e., TC, CT, CC), corresponding to deaminated CPD lesions, were retained in BED file using custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools or custom perl script
Assembly: saccer3
Supplementary files format and content: WIG files containing counts of DNA dCPD lesion reads filtered for only cytosines in dipyrimidine mapping sequences and the counts for the trinucleotide context of lesion sites associated with dCPD-seq reads are included. For the No UV sample, only the trinucleotide file is provided.
Library strategy: dCPD-seq

growth_protocol: rad14∆ cdc13-1 yeast were grown overnight in rich (YPD or YPDA) medium at a permissive temperature (~23C), diluted with pre-warmed (37C) fresh YPDA medium, and incubated with shaking at 37C for six hours to induce G2/M arrest.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with approximately equal volumes of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 7.5-8.0, 1 mM EDTA) and PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and approximately 0.5 volumes of acid-washed glass beads. Beads were vortexed vigorously twice for about 2 min each time. After adding TE (10mM Tris-HCl, pH 7.5-8.0, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 2.5-3 volumes of 100% ethanol and stored at -20C to allow DNA precipitiation to occur.  DNA pellets were washed with 75-80% ethanol, dissolved in mixture of 1xTE (pH7.5) and 0.2 μg/μl RNase A, and incubated at 37C for about 15 minutes. The purified genomic DNA was then used for each sequencing library preparation.
The dCPD-seq protocol was adapted from the CPDseq 2.0 method (Duan et al. PNAS 2024, 121 (4) e2310854121). Briefly, genomic DNA isolated from irradiated and deaminated yeast was incubated with TdT (NEB) and either ddATP or ddGTP to block free 3’ OH ends. After phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation, the DNA was resuspended in water and 10x CPD photolyase buffer (100mM NaCl, 50mM Tris HCl pH 7.5, 20mM DTT, 1mM EDTA, 50% glycerol) to a final concentration of ~1x buffer, and E. coli CPD photolyase and UDG were added to reverse CPDs and excise uracil bases. Reactions were incubated under 365nm light (Spectroline EA-160) to reverse CPDs and then phenol:chloroform:isoamyl alcohol extracted and ethanol precipitated. APE1 (NEB) was then used to cleave the abasic sugar backbone to yield free 3’OH ends that were ligated to a biotinylated dsS2 splint adaptor that was linked to biotin on the complementary 5’ end. Ligated DNA was fragmented via sonication and then purified with size selection beads (Cytiva). Adaptor-ligated DNA fragments were then captured with streptavidin beads (Invitrogen), washed with 1x SCC (saline sodium citrate) buffer to remove nonspecific binding, and the non-biotinylated strand containing the ligated 3’ S2 adaptor was eluted with 0.15M NaOH. After synthesis of the complementary strand with EconoTaq (Lucigen) and preparation of DNA ends with NEBNext end repair and NEBNExt dA-tailing modules, a second adaptor ligation with dsF1 adaptors was performed. The library was then amplified 10 cycles in a PCR reaction with a unique set of barcoded primers that were also complementary to the S2 and F1 adaptors. Following amplification and cleaning, libraries were submitted to Azenta (Genewiz) for Illumina sequencing.

treatment_protocol: Cells were washed with water and exposed to ~600 J/m^2 UVC radiation. Cells were then incubated in the dark at 37C for a designated deamination timepoint (0h, 6h, 24h, or 48h), before spinning down the cells to obtain cell pellets. For full deamination control, RNase A treated genomic DNA from 48 hr sample was further incubated 16 hr in a thermocycler set to 67C. Genomic DNA was either immediately extracted from cells following UV exposure, or cell pellets were frozen at -80C until all deamination timepoints were complete.

value: rad14 cdc13-1

value: UV irradiated 600 J/m2

tag: deamination time

value: 6 hr


title: 12w_shamM1_kidney


title: 12w_casM6_liver

value: castration


title: WT_UV_0hr_cellular_replicate1

description:
Library name: WT_UV_0hr_cellular_replicate1
Replicate 1


title: 12w_casM5_liver

value: liver


title: A549 cells SLX4-XPF CRISPRCAS9 knockout_rep3_L03_84_1

description:
Library name: A549 cells SLX4-XPF CRISPRCAS9 knockout_rep3
Column name in raw_counts-All_Samples.txt: SLX4-XPF CRISPR/CAS9 knockout_rep3

value: lung carcinoma epithelial cells

value: SLX4_XPF knockout


title: Day 6 EB, Kctd1-KO rep 3

data_processing:
Nucleotide sequences were mapped to the Mus Musculus (mm10) reference genome using the splice-aware aligner, STAR v020201
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Day 6 EB

growth_protocol: Naïve ESCs were grown on gelatin coated plates for two passages before being passaged and counted for embryoid body differentiation. AggreWell™ 400 24-wells (Stem Cell Technologies) were filled with 1 mL of EB media (DMEM, 15% FBS, 1x NEAA, 1x pen/strep, 0.1 mM  b-mercaptoethanol) and spun at 3000 g for 30 seconds to remove air bubbles. 2 x 106 ESCs per Aggrewell in 1mL of EB media were then added and the plate was spun at 500 g for 3 minutes. The plates were incubated at 37°C, 5% CO2 for 24 hours before the EBs were gently dislodged from the wells using a 1 mL pipette and transferred to a non-adherence 10 cm plate in 10mL of EB media. EBs were then incubated on a rocking plate and media was replaced every two days.

extract_protocol:
Total RNA was extracted using RNA Mini kit (Qiagen). 3ug of RNA was used for sequencing libraries
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®).

value: Day 6 EB

value: R1 ESC

value: mouse embryonic stem cell


title: NCI-H1703 cells, WT_rep2_L02_77_1

description:
Library name: NCI-H1703 cells, WT_rep2
Column name in raw_counts-All_Samples.txt: WT_rep2

value: lung squamous carcinoma epithelial Cells

value: WT


title: Day 6 EB, Kctd1-KO rep 1


title: rad14_cdc13_naked_post_UV_48h

description:
Library name: rad14_cdc13_naked_post_UV_48h
Replicate 1

data_processing:
Base calling by Azenta
Read1 Fastq files were trimmed using Trimmomatic v0.39 (BOLGER et al. 2014), with the parameters “ILLUMINACLIP:[XR-seq_adapter_file]:2:30:10”
Read1 fastq files were aligned to the Saccharomyces cerevisiae genome (saccer3) using bowtie2 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to cytosine bases in dipyrimidine sequence contexts (i.e., TC, CT, CC), corresponding to deaminated CPD lesions, were retained in BED file using custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools or custom perl script
Assembly: saccer3
Supplementary files format and content: WIG files containing counts of DNA dCPD lesion reads filtered for only cytosines in dipyrimidine mapping sequences and the counts for the trinucleotide context of lesion sites associated with dCPD-seq reads are included.
Library strategy: dCPD-seq

growth_protocol: rad14∆ cdc13-1 yeast were grown overnight in YPDA medium at a permissive temperature (~23C), diluted ~1:7 with pre-warmed (37C) fresh YPDA medium, and incubated with shaking at 37C for six hours to induce G2/M arrest.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with approximately equal volumes of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 7.5-8.0, 1 mM EDTA) and PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and approximately 0.5-0.7 volumes of acid-washed glass beads. Beads were vortexed vigorously twice for 2-3 min each time. After adding additional 1-5xTE buffer (pH7.5), cell lysates were centrifuged and supernatants were mixed with approximately 3-4 volumes of 100% ethanol and stored at -20C to allow DNA precipitation to occur.  After centrifugation, DNA pellets were washed with 75-80% ethanol, dissolved in either 10mM Tris (pH 8) + 0.2 μg/μl RNase A (replicate 1) or 1xTE (pH7.5) + 0.2 μg/μl RNase A (replicate 2) and incubated at 37C for about 15 minutes. This DNA was then quantified using a NanoDrop spectrophotometer.
The dCPD-seq protocol was adapted from the CPDseq 2.0 method (Duan et al. PNAS 2024, 121 (4) e2310854121). Briefly, approximately genomic DNA that had been irradiated in cells and then deaminated at 37C in vitro was incubated with TdT (NEB) and either ddATP or ddGTP to block free 3’ OH ends. After phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation, the DNA was resuspended in water and 10x CPD photolyase buffer (100mM NaCl, 50mM Tris HCl pH 7.5, 20mM DTT, 1mM EDTA, 50% glycerol) to a final concentration of ~1x buffer, and E. coli CPD photolyase and UDG were added to reverse CPDs and excise uracil bases. Reactions were incubated under 365nm light (Spectroline EA-160) to reverse CPDs and then phenol:chloroform:isoamyl alcohol extracted and ethanol precipitated. APE1 (NEB) was then used to cleave the abasic sugar backbone to yield free 3’OH ends that were ligated to a dsS2 splint adaptor labeled with biotin on the complementary 5’ end. Ligated DNA was then fragmented via sonication and cleaned with size selection beads (Cytiva). Adaptor-ligated DNA fragments were captured with streptavidin beads (Invitrogen), washed with 1x SCC (saline sodium citrate) buffer to remove nonspecific binding, and the non-biotinylated strand containing the ligated 3’ A adaptors was eluted with 0.15M NaOH. After synthesis of the complementary strand with EconoTaq (Lucigen) and preparation of DNA ends with NEBNext end repair and NEBNExt dA-tailing modules, a second adaptor ligation with dsF1 adaptors was performed. Each sample was then amplified 10 cycles in a PCR reaction with a primer set containing a unique barcode. Following amplification, libraries were cleaned and submitted to Azenta (Genewiz) for sequencing.

treatment_protocol: Cells were washed with water and exposed to ~600 J/m^2 UVC radiation (duration of exposure was 96 seconds). Genomic DNA was extracted from cells before subjecting them to deamination. For deamination of replicate 1, purified genomic DNA that had been resuspended in 10mM Tris, pH 8.0 was diluted 1:1 with 1xTE, pH 7.5 and either refrozen (0 hr) or incubated in a thermocycler at 37C for the designated length of time (6 hr, 24 hr, or 48 hr). After 48 hr of incubation, this sample was then incubated overnight at 67C to promote complete deamination of the DNA. Samples that had finished incubation were stored at -20C until all samples had finished their designated incubation period. For deamination of replicate 2, purified genomic DNA had been previously resuspended in 1xTE, pH7.5 and was not further diluted. For deamination timepoints, this DNA was incubated at 37C for 6 hr, 24 hr, or 48hr. After 48 hr of incubation, this sample was then incubated overnight at 67C to promote complete deamination of the DNA.

value: Yeast cells

value: 48 hr


title: 12w_casM3_liver


title: Day 6 EB, Lhx1-KO rep 3


title: 12w_casM4_liver


title: rad14_cdc13-1_cellular_24h

description:
Library name: rad14_cdc13-1_cellular_24h
Replicate 3

value: 24 hr


title: A549 cells SLX4-XPF CRISPRCAS9 knockout_rep1_L01_16_1

description:
Library name: A549 cells SLX4-XPF CRISPRCAS9 knockout_rep1
Column name in raw_counts-All_Samples.txt: SLX4-XPF CRISPR/CAS9 knockout_rep1

data_processing:
Partek™ Flow™ software version 12.8.0 was used to analyze the RNA seq data using the count matrix generated after the sequencing of the libraries
pre-alignment QA/QC was applied to assesses the quality of the unaligned reads. Reads with Phred scores below 35 were trimmed from 3’ end, and trimmed reads shorter than 25 nucleotides were excluded from further analysis
High-quality reads from each sample were aligned to the human genome (hg38) using the STAR aligner (version 2.7.8a) implemented in Partek Flow
Assembly: homo sapiens (hg38) using the STAR aligner (version 2.7.8a) implemented in Partek Flow
Supplementary files format and content: .txt file includes total reads of each samples


title: rad14_cdc13_naked_post_UV_24h

description:
Library name: rad14_cdc13_naked_post_UV_24h
Replicate 1


title: 12w_casM2_liver


title: Day 6 EB, Lhx1-KO rep 2


title: rad14_cdc13_naked_post_UV_6h

description:
Library name: rad14_cdc13_naked_post_UV_6h
Replicate 1


title: NCI-H1703 cells, WT_rep1_L01_69_1

description:
Library name: NCI-H1703 cells, WT_rep1
Column name in raw_counts-All_Samples.txt: WT_rep1


title: A549 cells XPF CRISPRCAS9 knockout_rep3_L03_83_1.

description:
Library name: A549 cells XPF CRISPRCAS9 knockout_rep3
Column name in raw_counts-All_Samples.txt: XPF CRISPR/CAS9 knockout_rep3

value: XPF knockout


title: A549 cells SLX4-XPF CRISPRCAS9 knockout_rep2_L02_4_1

description:
Library name: A549 cells SLX4-XPF CRISPRCAS9 knockout_rep2
Column name in raw_counts-All_Samples.txt: SLX4-XPF CRISPR/CAS9 knockout_rep2


title: Day 6 EB, Lhx1-KO rep 1


title: NCI-H1703 cells, WT_rep3_L03_89_1

description:
Library name: NCI-H1703 cells, WT_rep3
Column name in raw_counts-All_Samples.txt: WT_rep3


title: ATAC-seq, E7.25, control, rep 1

value: E7.25 mouse embryo


title: rad14_cdc13_naked_post_UV_0h

description:
Library name: rad14_cdc13_naked_post_UV_0h
Replicate 1

value: rad14 cdc13-1

value: 0 hr


title: 12w_casM1_liver


title: rad14_cdc13-1_cellular_48h

description:
Library name: rad14_cdc13-1_cellular_48h
Replicate 3

value: UV irradiated 600 J/m2


title: Day 6 EB, Kctd1-KO rep 2


title: A549 cells XPF CRISPRCAS9 knockout_rep2_L02_3_1

description:
Library name: A549 cells XPF CRISPRCAS9 knockout_rep2
Column name in raw_counts-All_Samples.txt: XPF CRISPR/CAS9 knockout_rep2


title: Day 6 EB, R1 ESC, rep 3


title: 12w_casM6_kidney

description:
Total RNA was extracted for DNBSEQ sequencing
12w_RNA_seq_expression_FPKM_Mean.txt
12w_kidney_gene_exp_diff.txt

value: kidney

value: castration


title: 12w_casM5_kidney


title: 12w_casM4_kidney


title: Day 6 EB, R1 ESC, rep 2


description:
Library name: yeast naked DNA deamination 6h replicate 2
Replicate 2

data_processing:
Base calling by Azenta
Read1 Fastq files were trimmed using Trimmomatic v0.39 (BOLGER et al. 2014), with the parameters “ILLUMINACLIP:[XR-seq_adapter_file]:2:30:10”
Read1 fastq files were aligned to the Saccharomyces cerevisiae genome (saccer3) using bowtie2 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to cytosine bases in dipyrimidine sequence contexts (i.e., TC, CT, CC), corresponding to deaminated CPD lesions, were retained in BED file using custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools or custom perl script
Assembly: saccer3
Supplementary files format and content: WIG files containing counts of DNA dCPD lesion reads filtered for only cytosines in dipyrimidine mapping sequences and the counts for the trinucleotide context of lesion sites associated with dCPD-seq reads is indicated.
Library strategy: dCPD-seq

growth_protocol: Wild type (i.e. BY4741) yeast were grown overnight in YPDA medium and subcultured the next day into fresh YPDA medium. Cells were then grown to log phase (OD600 ~1-2) before harvesting for genomic dna isolation.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with approximately equal volumes of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 7.5-8.0, 1 mM EDTA) and PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and approximately 0.7 volumes of acid-washed glass beads. Beads were vortexed vigorously twice for 2-3 min each time. After adding approximately 0.1 volume 5xTE (50mM Tris-HCl, pH 7.5, 5 mM EDTA) buffer, cell lysates were centrifuged and supernatants were mixed with approximately 3 volumes of 100% ethanol and stored at -20C to allow DNA precipitiation to occur.  After centrifugation, DNA pellets were washed with 80% ethanol, dissolved in a mixture of 0.1xTE (pH7.5) and 0.17 μg/μl RNase A, and incubated at 37C for 30-40 minutes. This DNA was then quantified using a NanoDrop spectrophotometer prior to irradiation of samples.
The dCPD-seq protocol was adapted from the CPDseq 2.0 method (Duan et al. PNAS 2024, 121 (4) e2310854121). Briefly, approximately 170-230mg of irradiated naked genomic wild type DNA was incubated with TdT (NEB) and either ddATP or ddGTP to block free 3’ OH ends. After phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation, the DNA was resuspended in water and 10x CPD photolyase buffer (100mM NaCl, 50mM Tris HCl pH 7.5, 20mM DTT, 1mM EDTA, 50% glycerol) to a final concentration of ~1x buffer, and E. coli CPD photolyase and UDG were added to reverse CPDs and excise uracil bases. Reactions were incubated under 365nm light (Spectroline EA-160) to reverse CPDs and then phenol:chloroform:isoamyl alcohol extracted and ethanol precipitated. APE1 (NEB) was then used to cleave the abasic sugar backbone to yield free 3’OH ends that were ligated to a dsS2 splint adaptor labeled with biotin on the complementary 5’ end. Ligated DNA was captured with streptavidin beads (Invitrogen), washed with 1x SCC (saline sodium citrate) buffer to remove nonspecific binding, and the non-biotinylated strand containing the ligated 3’ A adaptors was eluted with 0.15M NaOH. After synthesis of the complementary strand with EconoTaq (Lucigen) and preparation of DNA ends with NEBNext end repair and NEBNExt dA-tailing modules, a second adaptor ligation with dsF1 adaptors was performed. Each sample was then amplified 10 cycles in a PCR reaction with a primer set containing a unique barcode. Following amplification, libraries were cleaned and submitted to Azenta (Genewiz) for sequencing.

treatment_protocol: Quantified genomic DNA was diluted to ~0.8 μg/μl with sterile Millipore water, spotted onto glass coverslips, and exposed on ice to approximately 600 J/m2 UVC radiation (duration ~96 seconds). Irradiated DNA was then returned to a fresh tube, vortexed, and subdivided into aliquots. These irradiated samples were either directly frozen or allowed to incubate in a thermocycler set to 37C for 6, 24, or 48 hours. After incubation was complete, the samples were incubated by the thermocycler at 4C until they were put -20C for storage until all incubations were complete. When all designated incubation times had finished, the samples were jointly processed for library construction.

value: Genomic DNA derived from Yeast cells

value: Wild Type

value: 6 hr


title: A549 cells SLX4 CRISPRCAS9 knockout_rep3_L03_82_1

description:
Library name: A549 cells SLX4 CRISPRCAS9 knockout_rep3
Column name in raw_counts-All_Samples.txt:SLX4 CRISPR/CAS9 knockout_rep3

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
mRNA was enriched from 200 ng of total RNA, then library preparation was realized with the MGIEasy RNA Directional Library Prep Set (MGI)

value: lung carcinoma epithelial cells

value: SLX4 knockout


title: A549 cells XPF CRISPRCAS9 knockout_rep1_L01_15_1

description:
Library name: A549 cells XPF CRISPRCAS9 knockout_rep1
Column name in raw_counts-All_Samples.txt: XPF CRISPR/CAS9 knockout_rep1


title: Naïve-4

city: Chengdu

first: chen

last: li

address: Renmin South Road

institute: Sichuan Univercity

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.32) (default parameters)
Trimmed sequence reads were mapped to Mus musculus genome (mm10) using STAR (v2.7.1a) with default parameters
Read count extraction were performed using GenomicAlignments (v1.24.0)
Read count extraction were normalization using DESeq2 (v1.24.0)
Assembly: mm10
Supplementary files format and content: Tab-delimited text file contains raw counts, with genes as rows and samples as columns

source_name: Lung

extract_protocol:
After samples thawed at 4°C, total RNA from purified cells was extracted using TRIzol (MiRNeasy Micro Kit, QIAGEN, #1071023) according to the manufacturer’s recommendation. All samples had high-quality RNA (Agilent 2100 Bioanalyzer RNA Integrity Number (RIN) >7). The RNA sequencing library was prepared using the Illumina TruSeq PE Cluster Kit V3-cBot-HS (Illumina) following the provided protocol
Sequencing was performed on the Illumina HiSeq platform (Illumina, San Diego, USA), generating standard 125 bp/150 bp paired-end reads.

value: Lung

value: Total lung cells

value: Mixed lung cell types

value: noninfection


description:
Library name: yeast naked DNA deamination 24h replicate 2
Replicate 2

value: 24 hr


description:
Library name: yeast naked DNA deamination 48h replicate 2
Replicate 2


title: A549 cells SLX4 CRISPRCAS9 knockout_rep1_L01_14_1

description:
Library name: A549 cells SLX4 CRISPRCAS9 knockout_rep1
Column name in raw_counts-All_Samples.txt:SLX4 CRISPR/CAS9 knockout_rep1


title: Naïve-3

value: WT


title: 12w_casM3_kidney

data_processing:
Raw data was preprocessed by SolexaQA to exclude too quanlity and short reads
Cleaned data was subjected to Hisat2 for mapping
SAM files generated by Hisat2 were converted and sorted to bam files by SAMTOOLs
Bam files were then subjected to Cufflinks packages for gene counts, FPKM values normalization and identifying differentially expressed genes.
FDR < 0.05 was applied as the cut-off value
Assembly: mm10
Supplementary files format and content: Tab-delimited txt file for the FPKM values and statistical significance data of 12week samples;
Supplementary files format and content: Microsoft Excel spreadsheets for the FPKM values statistical significance data of 18month samples.

extract_protocol:
Total RNA was isolated from kidney and liver by Trizol
PolyA-tailed RNA was enriched for constructing 150bp pair-end RNA-sequencing libraries using MGISEQ-2000RS kit


title: A549 cells, WT_rep3_L03_81_1

description:
Library name: A549 cells, WT_rep3
Column name in raw_counts-All_Samples.txt:WT_rep3


description:
Library name: yeast naked DNA deamination 0h replicate 2
Replicate 2


title: 12w_casM2_kidney


title: Day 6 EB, R1 ESC, rep 1

value: Day 6 EB

value: R1 ESC

value: mouse embryonic stem cell


title: A549 cells SLX4 CRISPRCAS9 knockout_rep2_L02_2_1

description:
Library name: A549 cells SLX4 CRISPRCAS9 knockout_rep2
Column name in raw_counts-All_Samples.txt:SLX4 CRISPR/CAS9 knockout_rep2


title: yeast naked DNA deamination 48h

description:
Library name: yeast naked DNA deamination 48h
Replicate 1

value: UV irradiated 600 J/m2


title: Naïve-2


title: 12w_casM1_kidney

value: kidney


title: Naïve-1


title: A549 cells, WT_rep2_L02_1_2

description:
Library name: A549 cells, WT_rep2
Column name in raw_counts-All_Samples.txt:WT_rep2


title: Mss11,FLAG-tagged,ChIP,input

city: Shanghai

first: Lu Ling

last: Wang

address: 170 Danshui Road

institute: Ruijin hospital,school of medicine,shanghai jiaotong university

data_processing:
Basecalls performed using CASAVA version 1.4
The initial quality control was conducted using Q30. After adaptor trimming and low-quality read removal by using cutadapt (version 1.9.3), high-quality clean reads were generated.
ChIP-seq reads were then aligned to the C. glabrata reference genome (ASM254v2) using bowtie2 (version 2.2.4)
Peak calling was performed with MACS (version 2.2.7.1).
Differentially enriched regions between the FLAG-tagged and untagged Mss11 strains were identified using diffReps (version 1.55.4). A threshold of P value <0.05 and fold change≥2 was set for differential enrichment.
Assembly: Candida glabrata CBS 138 RefSeq Genome,GCF_000002545.3
Supplementary files format and content: MSS11-IP_vs_MSS11-Input_peaks,xlsx,peak calling results and peak annotations
Supplementary files format and content: MSS11-FLAG-IP_vs_MSS11-FLAG-Input_peaks,xlsx, peak calling results and peak annotations

organism: Nakaseomyces glabratus

source_name: yeast cells

extract_protocol:
Lysates were clarified from sonicated nuclei and the Mss11-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: chip antibody

value: input

value: yeast cells


title: A549 cells, WT_rep1_L01_13_1

description:
Library name: A549 cells, WT_rep1
Column name in raw_counts-All_Samples.txt:WT_rep1

tag: cell line


title: NK65-E_Day 9-5

value: Pb NK88-E infection


title: yeast naked DNA deamination 6h

description:
Library name: yeast naked DNA deamination 6h
Replicate 1

value: Genomic DNA derived from Yeast cells

value: Wild Type

value: 6 hr


title: yeast naked DNA deamination 24h

description:
Library name: yeast naked DNA deamination 24h
Replicate 1


title: yeast naked DNA deamination 0h

description:
Library name: yeast naked DNA deamination 0h
Replicate 1

value: Wild Type (MATa his3 leu2 met15 ura3)

value: 0 hr


title: NK65-E_Day 9-4

value: Lung

value: Total lung cells

value: Mixed lung cell types

value: Pb NK87-E infection


title: Mss11,FLAG-tagged,ChIP

value: DYKDDDDK Tag Rabbit mAb(CST, lot 14793S)


title: NK65-E_Day 9-3

value: WT

value: Pb NK86-E infection


title: atf4_Sl1344_replicate4

city: Spokane

first: Yiyong

address: 412 E Spokane Falls Blvd

description: atf4_SL1344_vs_WT_SL1344_diffexpr_results.csv

data_processing:
bcl2fastq2 Conversion Software was used to convert base-calling files to fastq files and to trim adaptors.
HISAT2 v2.2.1 was used for alignment
featureCounts (from Subrea v2.0.1) was used to quantify genes and transcripts.
DESeq2 v1.31.16 was used for differential gene expression analysis.
Assembly: UCSC ce10
Supplementary files format and content: comma-delimited text files including read counts in genes and differential gene expression

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans was cultured under standard conditions and fed E. coli strain OP50.

extract_protocol:
Total RNA was extracted using QIAzol lysis reagent (QIAGEN) and purified with Rneasy Plus Universal Kit (QIAGEN).
Library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Synchronized L1 larvae were grown on E. coli OP50 at 20⁰C until they reached young adult stage.  The worms were transferred to NGM plates seeded with S. enterica SL1344 or E. coli OP50 (control) for 24 hrs at 25⁰C.  The worms were then collected and washed with M9 buffer.  Total RNA was extracted.

value: whole animal

value: infected

tag: batch

value: same batch


title: atf4_Sl1344_replicate3


title: Mss11,untagged,ChIP

value: yeast cells


title: BeWo cells, DMSO-treated

city: Utrecht

first: Mehrdad

last: Azarmi Aghajan

address: Universiteit Utrecht David de Wied gebouw  Universiteitsweg 99

department: Pharmaceutical Science

country: Netherlands

institute: Utrecht University

description: Library name: Sample13

data_processing:
This dataset was analyzed using two independent pipelines. First, raw reads were aligned to the hg38 assembly of the human reference genome using the HISAT2 algorithm, and a count matrix was generated with FeatureCounts. Second, the Salmon pipeline was used to perform both alignment and count matrix generation simultaneously.
Sequence reads were quality checked, trimed and aligned to the human genome GRCh38 using Hisat2 aligner and Salmon.
Read counts extaction was performed by FeatureCounts and Salmon and normalization was perfomed by DESeq2 package in R. Data visualization and statistical analysis was done in R.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Supplementary files format and content: Tab-delimited text file includes raw and normalized counts for each sample

source_name: Placenta

growth_protocol: BeWo cells were cultured in F-12K Nut mix (1x) medium supplemented with 10% FCS and kept in humidified incubator with 5% Co2 at 37C.

extract_protocol:
RNA was isolated from BeWo cells using SV total RNA isolation system (Promega). The isolation has been done based on manufacture protocol.
RNA libraries for RNA sequencing were prepared by MGIEasy RNA directional library kit following the manufacture protocol.

treatment_protocol: BeWo cells were exposed to sulfamethoxazole (200ug/ml), trimethoprim (50ug/ml) and co-trimoxazole (50ug/ml) and DMSO (1%) for 24 hrs in culture medium.

value: Placenta

value: BeWo

value: Trophoblast

value: DMSO 1%


title: BeWo cells, Co-trimoxazole-treated, Replicate 2

description: Library name: Sample11

value: CTX 50 µg/ml


title: NK65-E_Day 9-2

value: Pb NK85-E infection


title: NK65-E_Day 9-1

value: Lung

value: Pb NK84-E infection


title: BeWo cells, Co-trimoxazole-treated, Replicate 1

description: Library name: Sample10


title: atf4_Sl1344_replicate2


title: BeWo cells, Co-trimoxazole-treated, Replicate 3

description: Library name: Sample12


title: mESC_WT_rep6

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH

data_processing:
The paired-end reads from bulk RNA-seq datasets were processed to remove the Illumina universal adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) using Cutadapt (v4.4) with the parameters “-q 25 -m 25”. The resulting filtered reads were aligned to their respective reference genome using STAR aligner (v2.7.10b) with default parameters. Coordinate-sorted alignment files were indexed using SAMtools (v1.17). Exon mapped reads were counted using featureCounts from the subread package (v2.0.6). ATAC-seq datasets were processed to remove the Nextera adapter (CTGTCTCTTATACACATCT) using Cutadapt (v4.4) with the parameters “-q 25 -m 25”115. The resulting filtered reads were aligned to reference human genome using bowtie2 aligner (v2.5.1) with the parameter “--very-sensitive” (Bowtie2122). The alignment file was sorted by coordinate, indexed and filtered for mitochondrial reads using SAMtools (v1.17). The filtered alignment file was further processed to keep only uniquely mapped, non-duplicated reads using sambamba (v1.0.1). Reads were further processed using alignmentSieve from deepTools (v3.5.5) to account for transposon dimerization before insertion. Positive and negative strand alignments were shifted by +4 bp and −5 bp, respectively. Additionally, fragments of 100 bp, corresponding to nucleosome-free regions (NFRs), were retained with the parameters “--minMappingQuality 25 --maxFragmentLength 100 --ATACshift --BED”. Peaks were called on the resulting BEDPE files using MACS3 (v3.0.1) MACS3 with the parameters “--call-summits --bdg --nomodel --nolambda --gsize hs --keep-dup all --format BEDPE --qvalue 0.05”. The predicted peaks were filtered for ENCODE project blacklisted regions using BEDTools (v2.31.0) intersect.
Assembly: The reference genomes for human (GRCh38; annotation version 108) and mouse (GRCm39; annotation version 112) were obtained from ENSEMBL
Supplementary files format and content: HCT116_all_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr and nucleosomes.
Supplementary files format and content: HCT116_nfr_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr only.
Supplementary files format and content: HCT116_rna_seq_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.
Supplementary files format and content: HCT116_si11_all_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr and nucleosomes.
Supplementary files format and content: HCT116_si11_nfr_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr only.
Supplementary files format and content: HCT116_si11_rna_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.
Supplementary files format and content: mESC_all_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr and nucleosomes.
Supplementary files format and content: mESC_diff_rna_seq_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.
Supplementary files format and content: mESC_nfr_atac_raw_counts.tsv  is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr only.
Supplementary files format and content: mESC_rna_seq_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.

source_name: mESC

growth_protocol: HCT116 (CCL-247; ATCC), were grown in Dulbecco’s Modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal calf serum (FCS; Eurobio Scientific) and 100 µg/mL penicillin/streptomycin (Corning) at 37°C, 5% CO2. ES-E14TG2a mESCs (CRL-1821; ATCC) were grown in Dulbecco’s Modified Eagle’s medium (DMEM; Sigma) supplemented with 13% fetal calf serum (FCS; Sigma), 0.32% 2-mercaptoethanol (Gibco), and 100 µg/mL penicillin/streptomycin (Corning). Media was freshly supplemented with 1000 units/mL recombinant mouse LIF protein (ESGRO®), 1 µM of the MEK/ERK inhibitor PD0325901 (Sigma), and 3 µM of the GSK inhibitor CHIR99021 (Sigma) (2i). Cells were plated at a density of 2.65 x 105 cells per cm2 on plates coated with 0.2% gelatin from porcine skin (Sigma). Cells were grown at 37°C, 8% CO2, and passaged every 48 hours using 0.05% Trypsin-EDTA for detachment (Gibco). Cells were frozen in fetal calf serum (FCS; Sigma) supplemented with 10% DMSO (Gibco).

extract_protocol:
To prepare samples for RNA-seq, 3 individual batches of cells were plated on the same day and further processed in parallel. Freshly harvested cells were lysed with 500 µL of QIAzol lysis reagent (QIAGEN #79306) and mixed by gentle pipetting. Subsequently, 100 µL of chloroform (Sigma) was added, samples were vortexed for 10 s and spun at 12’000 x g for 15 s at 4°C. The upper phase was transferred into a new tube, 600 μL of isopropanol (Sigma) added and samples incubated O/N at -20°C. After centrifugation at 16’000 x g for 10 min at 4°C, the RNA pellet was washed in 75% ethanol and resuspended in RNase-free water (Invitrogen). DNase digestion of RNA was performed using RNase-Free DNase Set (QIAGEN) following the manufacturer’s instructions. RNA was then precipitated by adding sodium acetate (Sigma) to a final concentration of 0.3 M, and adding 3 volumes of 100% ethanol O/N at -20°C. RNA was recovered by centrifugation at 16’000 x g for 10 min and washed two times with 70% ethanol. RNA was dissolved in RNase-free water (Invitrogen). To prepare ATAC-seq samples, 3 individual batches of cells were plate on the same day in 6-wells (for si-11) or 10 cm plates (for KO cells). Cell batches were then further processed in parallel, during all subsequent steps. For harvest, cells were washed twice with 1x PBS and detached using 0.5 mM EDTA in 1x PBS. Cells were counted and 80’000 cells were pelleted. Pellets were resuspended in 200 µL of freezing medium (10% DMSO in FCS) and slowly frozen at -80°C. ATAC-seq was performed at QuickBiology (Monrovia, California). Here, cells were washed and lysed to generate a crude preparation of nuclei. This crude extract was then treated with Tn5 Transposase. Tn5 transposase tagmentation simultaneously fragments the genome and tags the resulting DNA with Illumina sequencing adapters. DNA fragments were PCR-amplified and subsequently purified using the MinElute PCR Purification Kit (Qiagen, Maryland, USA).
The ATAC-seq library was prepared as described in Corces, M.R. et al.Nat Methods, 2017. After quality control using an Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA) and Life Technologies Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA), the libraries were sequenced (150 bp paired-end reads) on an Illumina HiSeq Sequencer (Illumina Inc., San Diego, CA). For RNA-seq, the quality of the isolated RNA was determined using a Fragment Analyzer (Agilent, Santa Clara, California, USA). Only samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further used for library preparation. The Illumina Ribo Zero Plus (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (25-1000 ng) were depleted of ribosomal RNA and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired, and adenylated before ligation of an anchor. Fragments containing the anchor on both ends were selectively enriched with PCR at the same time adding the index with unique dual indexes (UDI). The quality and quantity of the enriched libraries were validated using the Fragment Analyzer (Agilent, Santa Clara, California, USA). The libraries were normalized to 10 nM in Tris-HCl 10 mM, pH8.5 with 0.1% Tween20.

value: mESC


title: atf4_Sl1344_replicate1


title: mESC_WT_rep4


title: BeWo cells, TMP-treated, Replicate 3

description: Library name: Sample9

value: TMP 50 µg/ml


title: mESC_WT_rep3


title: BeWo cells, TMP-treated, Replicate 2

description: Library name: Sample8


title: NK65-E_Day 7-3

value: Total lung cells

value: Mixed lung cell types

value: Pb NK82-E infection


title: NK65-E_Day 7-4

value: WT

value: Pb NK83-E infection


title: atf4_OP50_replicate4

description: atf4_OP50_vs_WT_OP50_diffexpr_results.csv

value: whole animal

value: uninfected

value: same batch


title: atf4_OP50_replicate3


title: mESC_WT_rep2


title: BeWo cells, TMP-treated, Replicate 1

description: Library name: Sample7

value: Placenta

value: BeWo


title: atf4_OP50_replicate2


title: NK65-E_Day 7-2

value: Pb NK81-E infection


title: BeWo cells, SMZ-treated, Replicate 3

description: Library name: Sample6

value: Trophoblast

value: SMZ 200 µg/ml


title: mESC_LBR_TMPO_LMNA_KO_rep3


title: Mss11,untagged,ChIP,input

value: input

value: yeast cells


title: NK65-E_Day 7-1

value: Lung

value: Pb NK80-E infection


title: mESC_LBR_TMPO_LMNA_KO_rep2

value: mESC


title: atf4_OP50_replicate1


title: mESC_LBR_TMPO_LMNA_KO_rep1


title: WT_Sl1344_replicate4

value: wild-type N2

value: infected


title: mESC_LBR_TMPO_KO_rep3


title: NK65-E_Day 5-2

value: Total lung cells

value: Mixed lung cell types

value: WT

value: Pb NK77-E infection


title: WT_Sl1344_replicate3

value: whole animal

value: same batch


title: mESC_LBR_TMPO_KO_rep2


title: WT_Sl1344_replicate2


title: BeWo cells, Control, Replicate 2

description: Library name: Sample2

value: Placenta

value: BeWo

value: No treatment.


title: NK65-E_Day 5-1

value: Pb NK76-E infection


title: mESC_LBR_TMPO_KO_rep1


title: BeWo cells, Control, Replicate 1

description: Library name: Sample1

value: Trophoblast


title: WT_OP50_replicate4

value: uninfected


title: NK65-E_Day 3-3

value: Lung

value: Pb NK75-E infection


title: mESC_diff_WT_rep3

source_name: Differentiated mESC

value: Differentiated mESC


title: WT_OP50_replicate3

value: wild-type N2


title: Clone I-2

city: Nedlands

first: Kevin

middle: Guangxing

last: Chen

address: Hospital Avenue

institute: The Kids Research Institute Australia

description:
Library name: Run73_23_SH112_MED12_ND3_CloneI_iPSC_cDNA
Molecule: PCR amplicon

library_source: other

data_processing:
Amplicon sequencing: reads were aligned to either WT or VUS amplicon using CRISPResso2
Assembly: WT and VUS amplicon
Supplementary files format and content: Run72_S57_Alleles_frequency_table_MED12_Clone_D_gDNA.txt shows all reads and alignments to the reference and genetic variant amplicons
Supplementary files format and content: Run72_S58_Alleles_frequency_table MED12_Clone_I_gDNA.txt shows all reads and alignments to the reference and genetic variant amplicons
Supplementary files format and content: Run73_S22_Alleles_frequency_table MED12_Clone_D_cDNA.txt shows all reads and alignments to the reference and genetic variant amplicons
Supplementary files format and content: Run73_S23_Alleles_frequency_table MED12_Clone_I_cDNA.txt shows all reads and alignments to the reference and genetic variant amplicons

molecule: other

source_name: Patient-derived, Day 0

growth_protocol: Patient-derived iPSCs were grown in Matrigel-coated plates in TeSR-E8 media. The STEMdiff SMADi Neural Induction Kit was used to stimulate differentiation of iPSCs into NPCs

extract_protocol:
cDNA for amplicon sequencing was prepared using SuperScript IV reverse transcriptase. Primers designed to bind across genetic variant region in gDNA and cDNA were used to prepare amplicons for sequencing.
PCR amplicon products corresponding to the SNV sites in WT and VUS MED12 were prepared from extracted gDNA with forward and reverse amplicon primers and Phusion High-Fidelity PCR Master Mix with HF Buffer (Thermo Scientific). Purified samples were barcoded with TruSeq primers (IDT) and MED12 sequences determined with paired-end, 250bp DNA amplicon sequencing with a MiniSeq Mid-Output Kit, 300 cycles.

value: induced pluripotent stem cell

tag: clone

value: I


title: NK65-E_Day 3-2

value: Total lung cells

value: Mixed lung cell types

value: Pb NK74-E infection


title: NK65-E_Day 3-1

value: WT

value: Pb NK73-E infection


title: mESC_diff_WT_rep2


title: WT_Sl1344_replicate1

value: whole animal

value: infected

value: same batch


title: WT_OP50_replicate2


title: Clone D-2

description:
Library name: Run73_22_SH112_MED12_ND3_CloneD_iPSC_cDNA
Molecule: PCR amplicon

value: D


title: NK65-E_Day 5-4

value: Pb NK79-E infection


title: mESC_diff_WT_rep1


title: NK65-E_Day 13-4

value: Pb NK72-E infection


title: NK65-E_Day 5-3

value: Lung

value: Pb NK78-E infection


title: Clone I-1

description:
Library name: Run72_58_NS0104_MED12_clone_I_iPSC_ND1_conf gDNA
Molecule: PCR amplicon


title: BeWo cells, Control, Replicate 3

description: Library name: Sample3

value: Placenta

value: BeWo

value: Trophoblast

value: No treatment.


title: BeWo cells, SMZ-treated, Replicate 2

description: Library name: Sample5

value: SMZ 200 µg/ml


title: BeWo cells, SMZ-treated, Replicate 1

description: Library name: Sample4


title: WT_OP50_replicate1

value: wild-type N2

value: uninfected


title: NK65-E_Day 13-3

value: Total lung cells

value: Mixed lung cell types

value: WT

value: Pb NK71-E infection


title: NK65-E_Day 13-2

value: Pb NK70-E infection


title: mESC_diff_LBR_TMPO_LMNA_KO_rep3

value: Differentiated mESC


title: mESC_diff_LBR_TMPO_LMNA_KO_rep2