title: sgNT/T618I_3


title: Healthy donor 1, 28delta CAR, un-stimulated

status: Public on Jan 22 2025

type: SRA

city: Xi'an

first: Pengju

last: Wang

state: Shaanxi

address: Changle West Road

department: Immunology

country: China

institute: Fourth Military Medical University

library_source: transcriptomic

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 files include RPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: T cell

growth_protocol: Primary T cells were stimulated with CD3/CD28 dynabeads (Gibco) at a T cell to bead ratio of 1:3, and cultured in X-VIVO15 medium (Lonza, Bend, OR, USA) supplemented with 10% FBS and 100 IU/ml recombinant IL-2 (PeproTech, Rocky Hill, NJ, USA). Twenty-four hours after stimulation, T cells were infected with lentiviruses for 24 h. At day 5 after stimulation, CD3/CD28 dynabeads were removed, T cells were cultured continuously, and medium and IL-2 was changed every second day.

extract_protocol:
RNA was isolated using the QIAGEN Rneasy following manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 10 days of transduction, 3 x 106 CAR T cells were stimulated 36 h with targrt cells at a ratio of 1:1 while 3 x 106 CAR T cells were maintained without stimulation.

tag: cell line

value: T cell

tag: cell type

value: Primary human T cells

tag: genotype

value: T cells expressing 28delta CAR

tag: treatment

value: un-stimulated


title: sgB2/T618I_1

city: Portland

first: Julia

last: Maxson

state: Oregon

address: 3181 SW Sam Jackson Park Rd

country: USA

institute: Oregon Health and Science University

library_source: genomic

data_processing:
Adapters were trimmed from FASTQ files containing raw, paired-end reads using Fastp 0.20 with “--detect_adapter_for_pe” option.
Adapter-trimmed reads were aligned to the Mus musculus mm10 genome assembly using BWA-MEM 0.7.17 with 8 threads and default parameters.
Reads that did not map, had an unmapped mate, were not a primary alignment, failed platform quality control checks, and/or were PCR or optical duplicates were filtered from BAM files using the “samtools view” subcommand with  “-F 1804” option from Samtools 1.9.
Reads aligning to mitochondrial genes were also removed. Duplicate reads were removed from BAM files using the “sambamba markdup” subcommand with “-r” option from Sambamba 0.6.8. Reads intersecting ENCODE blacklist regions were removed using the “bedtools intersect” subcommand with “-v” option from Bedtools 2.30.
Peaks were called on filtered BAM files using the “macs2 callpeak” subcommand with “--broad --format BAMPE --gsize mm” options from MACS2 2.2.7.1.
Counts-per-milion (CPM) normalized bigWig coverage tracks were generated from filtered BAM files using bamCoverage from Deeptools version 3.5 with parameters “--binSize 10 --smoothLength 50 --normalizeUsing CPM”.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak

molecule: genomic DNA

organism: Mus musculus

growth_protocol: These cells are maintained in RPMI (11875119, Gibco) supplemented with 10% heat inactivated fetal bovine serum (FBS, HyClone), 2mM GlutaMAX (35050061, Gibco), 100units/mL Penicillin and 100 ug/mL Streptomycin (15140122, Gibco), 2% SCF from CHO,  conditioned media, and 0.6µM of Estrogen (E-2758, Sigma), cultured at 5% CO2 and 37°C.

extract_protocol:
Clean and Concentrator-5 Kit (D4003, Zymo)
As described in Buenrostro et al., 2015, Curr Protoc Mol Bio

treatment_protocol: Estrogen removal for 48h

value: Bone marrow immortelized

value: sgRNA Asxl1 B2/pMICH-CSF3R-T618I


title: CKO_11-week-old_2

city: Suzhou

first: Changshun

last: Shao

state: Jiangsu

address: No.199 Renai Road

department: Institute for Translational Medicine

institute: Soochow University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver

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.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

tag: tissue

value: liver

tag: age

tag: strain


title: Healthy donor 1, 28zeta CAR, un-stimulated

value: T cells expressing 28zeta CAR


title: WT_11-week-old_2

value: WT


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 0130

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

description:
cell-free DNA 5hmC
PLCO-104

data_processing:
Adapter sequences were removed from raw sequencing reads using Trimmomatic
Low quality bases at the 5’ and 3’ were trimmed based on phred score to a minimum length of 30 bp
The sequencing reads were then aligned to the human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode
Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length
Alignments with Mapping Quality Score ≥ 10 were counted based on the GENCODE gene body annotations using featureCounts without strand information
The raw read counts were then normalized using DESeq2, which performs an internal normalization that corrects for library size.
Assembly: hg19
Supplementary files format and content: Text file with normalized reads counts for all samples.
Library strategy: 5hmC-Seal sequencing

source_name: peripheral plasma

growth_protocol: Not applicable

extract_protocol:
Cell-free DNA was extracted using the QIAmp Circulating cfDNA Extraction Kit (Qiagen)
3-8 ng cfDNA was used in the 5hmC-Seal assay (see Li W, Zhang X, Lu X, You L, Song Y, Luo Z, et al. 5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers. Cell Res 2017;27:1243-57). Libraries were constructed on-bead using the KAPA HyperPlus kit (Roche).

treatment_protocol: Not applicable

value: peripheral plasma

tag: dna source

value: cell-free DNA


title: sgB2/Empty_3

value: sgRNA Asxl1 B2/pMICH-Empty


title: CKO_11-week-old_1


title: WT_11-week-old_1


title: TRM_113_LIL, scTCRseq

city: Gangnam-gu

first: Hong-Hee

last: Won

address: 81, Irwon-ro

country: South Korea

institute: SungKyunKwan University

description: 10x Genomics v7.0.0

data_processing:
The scTCR-seq data were assembled using the Cell Ranger VDJ pipeline (10x Genomics).
For demultiplexing for HCC_M1_LIL sample, we used Demuxlet software in scRNA-seq data.
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
Supplementary files format and content: Comma-separated matrix files
Library strategy: TCR-Seq

source_name: adjacent normal liver from tumor

extract_protocol:
The library preparation was performed using either the Chromium Next GEM Single cell 5’kit v2 (10x Genomics) with a cell recovery target of 5,000 per patient, following the manufacturer’s instruction.
The libraries were processed according to manufacturer’s recommendation (10x Genomics), and sequenced on a HiSeq 2500, MGI seq, and Novaseq systems.

treatment_protocol: Tissues were minced and mechanically dissociated using gentleMACS (Miltenyi biotec), and then enzymatically dissociated using a tumor dissociation kit (Miltenyi biotec, 130-095-929) at 37°C for 20 minutes.

value: adjacent normal liver from tumor

value: T cell receptors


title: CKO-3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38
Supplementary files format and content: FPKM, count values for each Sample

tag: strain background


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 2346

description:
cell-free DNA 5hmC
PLCO-098


title: TRM_261_TIL, scRNAseq

description: 10x Genomics v7.0.0

library_source: transcriptomic single cell

data_processing:
The scRNA-seq reads were preprocessed with CellRanger (10x Genomics)..
For demultiplexing for HCC_M1_LIL sample, we used Demuxlet software.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: Tab-separated features files, space-separated matrix files, and barcodes file

source_name: liver tumor

extract_protocol:
The library preparation was performed using either the Chromium Next GEM Single cell 5’kit v2 (10x Genomics) with a cell recovery target of 5,000 per patient, following the manufacturer’s instruction.
The libraries were processed according to manufacturer’s recommendation (10x Genomics), and sequenced on a HiSeq 2500 system using 100 bp paired-end sequencing. The raw sequencing reads were processed using CellRanger (version 4.0.0/5.0.1) (10x Genomics) with default parameter values using the human reference sequence (version GRCh38) and annotation (version GENCODE v32) of which pre-built reference packages were provided from 10x Genomics (version 2020-A).

value: liver tumor

value: Immune cells


title: sgB2/Empty_2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 8458

description:
cell-free DNA 5hmC
PLCO-097


title: TRM_113_TIL, scTCRseq

description: 10x Genomics v7.0.0


title: sgNT/Empty_2

value: sgRNA non targetting/pMICH-Empty


title: TRM_233_TIL, scRNAseq

description: 10x Genomics v7.0.0


title: CKO-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 6658

description:
cell-free DNA 5hmC
PLCO-099


title: CKO-1


title: WT-3


title: TRM_184_TIL, scRNAseq

description: 10x Genomics v7.0.0


title: TRM_113_TIL, scRNAseq

description: 10x Genomics v7.0.0


title: sgNT/Empty_3


title: sgNT/Empty_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LT 3784

description:
cell-free DNA 5hmC
PLCO-096


title: Capture Hi-C WT rep2

city: Baltimore

first: Xiang

last: Qiu

address: 251 Bayview Blvd.

institute: National Institutes of Health

description:
Capture Hi-C
Capture Hi-C WT Merged.hic

data_processing:
Capture Hi-C and Hi-ChIP reads were aligned to the mm10 genome and processed using the Juicer1 pipeline to generate .hic files. Juicer was run with the flags “-g mm10 -s Arima”. To compare experiments, capture Hi-C and Hi-ChIP data were normalized in two ways: 1) by down-sampling each experiment to the same number of total reads and 2) by down-sampling each experiment to the same number of reads within the IgH locus.
Capture Hi-C reads were processed using Juicer version 1.6 (parameters -g mm10 -s Arima) to generate hic files
Assembly: mm10
Supplementary files format and content: hic

source_name: Pro-B cell line

growth_protocol: Pro-B cell lines were grown with complete 1640 RPMI medium (10% fetal bovine serum and 0.05mM 2-Mercaptoethanol)

extract_protocol:
The capture Hi-C was carried out as previously described (Qiu et al., 2020). Hi-C was performed using the Arima Hi-C Kit (Arima Genetics Inc. Cat#A510008), and for each sample, 1×10^6 cells were used.
Capture Hi-C libraries were prepared for sequencing using standard Illumina protocols. Libraries were sequenced on a Nova Seq SP, pair ends (2X150bp)
Capture Hi-C

treatment_protocol: No treatment.

value: Pro-B cell line

value: Bone marrow


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 9287

description:
cell-free DNA 5hmC
PLCO-094


title: sgB2/Empty_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 3216

description:
cell-free DNA 5hmC
PLCO-093


title: TRM_113_LIL, scRNAseq

description: 10x Genomics v7.0.0


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UY 6894

description:
cell-free DNA 5hmC
PLCO-095


title: Capture Hi-C WT rep1

description:
Capture Hi-C
Capture Hi-C WT Merged.hic


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 3908

description:
cell-free DNA 5hmC
PLCO-092


title: Healthy donor 2, 28zeta CAR, stimulated with target cells

value: T cell

value: Primary human T cells

value: stimulated with target cells


title: HCC_M1_LIL, scRNAseq

description: 10x Genomics v7.0.0


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 5986

description:
cell-free DNA 5hmC
PLCO-090


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 1594

description:
cell-free DNA 5hmC
PLCO-091


title: Capture Hi-C Eu-- #1 rep1

description:
Capture Hi-C
Capture Hi-C Eu-- 1 Merged.hic


title: CTCF Hi-ChIP 3'CBEs-- rep1

data_processing:
Hi-ChIP reads were aligned to the mm10 genome and processed using the Juicer1 pipeline to generate .hic files. Juicer was run with the flags “-g mm10 -s Arima”. To compare experiments, capture Hi-C and Hi-ChIP data were normalized in two ways: 1) by down-sampling each experiment to the same number of total reads and 2) by down-sampling each experiment to the same number of reads within the IgH locus.
Hi-ChIP reads were processed using Juicer version 1.6 (parameters -g mm10 -s Arima) to generate hic files
Assembly: mm10
Supplementary files format and content: Hi-C
Library strategy: Hi-ChIP

source_name: Bone marrow

growth_protocol: RPMI medium with 10% fetal bovine serum (FBS), 1X MEM non-essential amino acids solution, and 1X 2-Mercaptoethanol at 37 ºC in a 5% CO2 humidified atmosphere

extract_protocol:
5×106 cells were used. Resuspended crosslinked cells (method described as above) in 20 μL of Lysis Buffer in a tube
HiChIP was performed using the Arima Hi-C+ Kit (Arima Genetics Inc. Cat# A101020) precisely following the manufacturer’s protocols (Arima-HiC+ documents A160168 v00 (HiChIP) and A160169 v00 (library preparation)).


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 2305

description:
cell-free DNA 5hmC
PLCO-089


title: Capture Hi-C Eu-- #2 rep2

description:
Capture Hi-C
Capture Hi-C Eu-- 2 Merged.hic


title: Normal_3

city: Shanghai

first: Jingyan

last: Huang

state: China

address: 639 Zhizaoju Road

institute: Shanghai Jiaotong University

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: mm 10
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

source_name: skin

extract_protocol:
RNA was harvested using Trizol (Invitrogen) and total RNA was used to construct sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: skin


title: K562, RNA, rep1

city: Pullman

first: Sascha

last: Duttke

state: Washington

address: BLS 147, 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

description:
Library name: homo_sapiens_K562_RNA-r1
SRR9916722 downsampled to one million reads

data_processing:
K562 raw reads from GSE135498 were downsampled to one million reads using SeqKit's sample and then trimmed of their adapter sequences using HOMER.
Trimmed reads were aligned to the hg38 genome using the STAR index provided in supplementary files. Alignment files were then used to create tag directories using HOMER makeTagDirectory and bedGraphs with makeUCSCfile. Peaks representing Transcription Start Regions (TSRs) for csRNA-seq and expressed small RNAs for sRNA-seq, were defined using HOMER’s findcsRNATSS.pl and a minimum read count of 7 per 10 million was required for regions to be considered.
Assembly: hg38
Supplementary files format and content: Files ending in -combo.tar.gz are compressed tag directories used to generate the provided bedGraphs and peak files (.tss.txt). The STAR index (hg38), built for aligning the reads, is also included as a gzipped tar file.

extract_protocol:
Refer to GSE135498
Refer to GSE135498


title: Rad21 Hi-ChIP WT rep1


title: Capture Hi-C Eu-- #2 rep1


title: Rad21 Hi-ChIP WT rep2


title: WT-2

value: liver


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 6990

description:
cell-free DNA 5hmC
PLCO-088


title: CTCF Hi-ChIP WT rep2


title: Capture Hi-C EF1a For #2 rep2

description:
Capture Hi-C
Capture Hi-C EF1a For 2 Merged.hic

value: forward EF1a promoter replacement


title: Normal_2


title: WT-1

value: WT


title: CTCF Hi-ChIP WT rep1


title: Normal_1


title: Capture Hi-C EF1a For #2 rep1


title: Keloid_3


title: CTCF Hi-ChIP 3'CBEs-- rep2


title: TRM_132_LIL, scRNAseq

description: 10x Genomics v7.0.0


title: Capture Hi-C EF1a Rev #2 rep2

description:
Capture Hi-C
Capture Hi-C EF1a Rev 2 Merged.hic

value: reverse EF1a promoter replacement


title: CTCF Hi-ChIP 3'CBEs Inv #2 rep2

value: 3'CBEs inversion


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 6680

description:
cell-free DNA 5hmC
PLCO-084

value: peripheral plasma

value: cell-free DNA


title: Capture Hi-C Eu-- #1 rep2


title: Keloid_2


title: CTCF Hi-ChIP 3'CBEs Inv #2 rep1


title: Capture Hi-C EF1a Rev #2 rep1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 6925

description:
cell-free DNA 5hmC
PLCO-083


title: Keloid_1


title: Capture Hi-C EF1a Rev #1 rep2

description:
Capture Hi-C
Capture Hi-C EF1a Rev 1 Merged.hic


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UM 0491

description:
cell-free DNA 5hmC
PLCO-082


title: WT14 iMg, Mock + Veh

city: Philadelphia

first: Kelly

last: Jordan-Sciutto

state: PA

address: 240 S. 40th St, Levy Building, Room 312

department: Oral Medicine

institute: University of Pennsylvania, School of Dental Medicine

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: The trimmed reads were mapped to the Homo sapiens GRCh38 with ERCC genes reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Supplementary files format and content: Tab-delimited text files with raw counts for each sample

molecule: polyA RNA

growth_protocol: Primary human monocytes isolated from healthy volunteers using magnetic bead-based separation were obtained by the Penn Human Immunology Cor. These cells were plated at 2.4x105 cells/mL and differentiated in DMEM containing 10% human serum and 20 ng/mL M-CSF for seven days. iMg were generated from 9 day old human iPSC-derived common myeloid progenitors purchased the CHOP Stem Cell Core and differentiated into iMg over 11 days in RPMI (HyClone) containing 10% FBS, 25 ng/mL M-CSF, 100 ng/mL IL-34, and 50 ng/mL TGF-β.

extract_protocol:
Following supernatant collection on DPI 9, MDMs and iMg were lysed in wells using Buffer RLT (Qiagen RNeasy Mini Kit 74104), and pooled RNA was isolated using manufacturer protocols. RNA purity and concentration were confirmed using Nanodrop, and Zymo RNA Clean & Concentrator-25 was used on any samples that did not pass initial quality control (260/280 absorbance > 2, 260/230 absorbance > 1.8, minimum concentration 50 ng/µL).
Libraries prepared via Illumina-compatible kit by Azenta/Genewiz using PolyA selection

treatment_protocol: Fully differentiated MDMs and iMg were treated with HIVADA at a concentration of 1 ng/mL HIV p24 on day post-infection 0 (DPI 0). After 24 hours (DPI 1), HIV-containing medium was removed and cannabinoid treatments were added. JWH-133 (Axon 1418) was reconstituted in dimethyl sulfoxide (DMSO, Veh) and serially diluted to ensure a uniform final volume of vehicle across treatment groups. Every 48 hours until DPI 9, 100% of culture medium was replaced and cannabinoid treatments were added.

value: iPSC-Derived Microlgia

value: Mock + DMSO


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LS 1569

description:
cell-free DNA 5hmC
PLCO-081


title: Rad21 Hi-ChIP IGCR1-- rep2


title: WT14 iMg, HIV + Veh

value: HIV + DMSO


title: CTCF Hi-ChIP IGCR1-- rep2


title: Capture Hi-C EF1a Rev #1 rep1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 0588

description:
cell-free DNA 5hmC
PLCO-080


title: Capture Hi-C EF1a For #1 rep2

description:
Capture Hi-C
Capture Hi-C EF1a For 1 Merged.hic


title: WT14 iMg, HIV + JWH-133 1 uM

value: HIV + JWH-133 1uM


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 7097

description:
cell-free DNA 5hmC
PLCO-087


title: Capture Hi-C EF1a For #1 rep1

value: Pro-B cell line


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 5680

description:
cell-free DNA 5hmC
PLCO-079


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 3967

description:
cell-free DNA 5hmC
PLCO-085


title: CTCF Hi-ChIP IGCR1-- rep1

value: Bone marrow


title: CTCF Hi-ChIP 3'CBEs Inv #1 rep2


title: WT10 iMg, Mock + Veh


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IM 4221

description:
cell-free DNA 5hmC
PLCO-078


title: CTCF Hi-ChIP 3'CBEs Inv #1 rep1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 9293

description:
cell-free DNA 5hmC
PLCO-077


title: WT10 iMg, HIV + Veh


title: WT10 iMg, HIV + JWH-133 1 uM


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 2216

description:
cell-free DNA 5hmC
PLCO-075


title: ICC_p53LKO, 3977 T5

type: RNA

city: Ulm

first: André

last: Lechel

address: Albert-Einstein-Allee 23

department: Department of Internal Medicine I

country: Germany

institute: University hospital Ulm

description: intrahepatic cholangiocarcinoma

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s protocol. On completion of the fragmentation reaction, 25 µl of 2x Agilent HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 8x60K Microarrays (G4852A) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C prewarmed GE Wash buffer 2 (Agilent) and 30 seconds with Acetonitril.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray Scanner G2505B (3micron) with the the Agilent Scan Control Version A.8.5.1 .

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). Further processing (background correction, percentile shift normalization, summarization, log2 transformation, median shift) was done in Rstudio following Agilent's standardized method.

source_name: tumor, 16 weeks CCl4 treatment

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoPhotometer

growth_protocol: mice were kept in a pathogen-free environment

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA was quantified using a NanoPhotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: mice were treated with 0.5µl CCl4/g bodyweight, diluted 1:3 with olive oil every three days (i.p.)

value: ICC tumor


title: Rad21 Hi-ChIP IGCR1-- rep1


title: WT6 iMg, Mock + Veh


title: ICC_p53LKO, 5283 T20

description: intrahepatic cholangiocarcinoma


title: H3K27ac ChIP-Seq WT rep2

description: ChIP-Seq

data_processing:
ChIP-seq reads were aligned to the mm10 genome using bwa-mem26. Aligned reads were converted to bigWig format using deepTools7 bamCoverage with the flags “—normalizeUsing CPM –ignoreDuplicates –minMappingQuality 30 –binSize 1”.
ChIP-seq reads were aligned to mm10 using bwa-mem2 version 2.2.1
Aligned reads were processed using bamCoverage from deepTools version 3.5.1 (parameters --normalizeUsing CPM --ignoreDuplicates --minMappingQuality 30 --binSize 1) to generate bigWig files
Assembly: mm10
Supplementary files format and content: bw

extract_protocol:
Prepared 1X10^6 cells in 1ml in 1.5 mL tubes, fix cells in 1% FA at RT for 10 min. (37% FA: 27μl/ml). Added 50 μl 2.5 M Glycine in PBS (final 125 mM) and rotate at RT for 5 min.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols. Libraries were sequenced on a Nova Seq SP, Single or pair ends


title: H3K27ac ChIP-Seq WT rep1

description: ChIP-Seq


title: ICC_p53LKO, 3976 T8

description: intrahepatic cholangiocarcinoma


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 9706

description:
cell-free DNA 5hmC
PLCO-073


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 9530

description:
cell-free DNA 5hmC
PLCO-074


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 3170

description:
cell-free DNA 5hmC
PLCO-072


title: H3K4me3 ChIP-Seq WT rep1

description: ChIP-Seq


title: ND607 MDM, Mock + Veh

value: Monocyte-Derived Macrophage


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UJ 1007

description:
cell-free DNA 5hmC
PLCO-071


title: H3K4me3 ChIP-Seq WT rep2

description: ChIP-Seq


title: Rad21 ChIP-Seq Eu-- rep1

description: ChIP-Seq


title: HCC_p53LKO, 3975 T4

description: hepatocellular carcinoma

value: HCC tumor


title: ND607 MDM, HIV + JWH-133 1 uM


title: ND607 MDM, HIV + Veh


title: HCC_p53LKO, 3733 T1

description: hepatocellular carcinoma


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 4016

description:
cell-free DNA 5hmC
PLCO-070


title: H3K27ac ChIP-Seq Eu-- rep1

description: ChIP-Seq


title: ICC_p53LKO, 3731 T3

description: intrahepatic cholangiocarcinoma


title: H3K27ac ChIP-Seq Eu-- rep2

description: ChIP-Seq


title: HCC_p53LKO, 3731 T2

description: hepatocellular carcinoma


title: ND410 MDM, Mock + Veh


title: H3K4me3 ChIP-Seq Eu-- rep2

description: ChIP-Seq


title: WT6 iMg, HIV + Veh


title: ND410 MDM, HIV + Veh


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 2995

description:
cell-free DNA 5hmC
PLCO-067


title: ND410 MDM, HIV + JWH-133 1 uM


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 2281

description:
cell-free DNA 5hmC
PLCO-066


title: HCC_p53f/f, 3717 T2

description: hepatocellular carcinoma


title: H3K4me3 ChIP-Seq Eu-- rep1

description: ChIP-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 9816

description:
cell-free DNA 5hmC
PLCO-068


title: HCC_p53LKO, 5283 T7

description: hepatocellular carcinoma


title: CTCF ChIP-Seq Eu-- rep1

description: ChIP-Seq


title: CTCF ChIP-Seq Eu-- rep2

description: ChIP-Seq


title: ND224 MDM, HIV + Veh


title: ICC_p53LKO, 3733 T3

description: intrahepatic cholangiocarcinoma


title: HCC_p53LKO, 3976 T1

description: hepatocellular carcinoma


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 1318

description:
cell-free DNA 5hmC
PLCO-065


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UR 0921

description:
cell-free DNA 5hmC
PLCO-069


title: RfxCas13d-2C-NLS mRNA + gpri-miR430, rep3

city: Kansas City

first: Gabriel

last: da Silva Pescador

state: MO

institute: Stowers Institute for Medical Research

description: instrument model: G4

data_processing:
sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.
Assembly: danrer11
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Total RNA then was extracted using standard TRIzol protocol as described in the manufacturer’s instructions (ThermoFisher Scientific).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Cat. No. E7760L), at a 1/10th reaction volume.

value: whole embryo

value: 6 hpf

value: Optimized nuclear RfxCas13d


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UY 3491

description:
cell-free DNA 5hmC
PLCO-064


title: HCC_p53f/f, 3716 T1

description: hepatocellular carcinoma


title: Rad21 ChIP-Seq EF1a For #1 rep2

description: ChIP-Seq

value: forward EF1a promoter replacement


title: RfxCas13d-2C-NLS mRNA + gpri-miR430, rep2

description: instrument model: G4


title: Rad21 ChIP-Seq Eu-- rep2

description: ChIP-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 1450

description:
cell-free DNA 5hmC
PLCO-063


title: HCC_p53f/f, 3681 T1

description: hepatocellular carcinoma


title: ND224 MDM, Mock + Veh

value: WT


title: RfxCas13d-2C-NLS mRNA + gpri-miR430, rep1

description: instrument model: G4


title: HCC_p53f/f, 3715 T2

description: hepatocellular carcinoma


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID KF 5420

description:
cell-free DNA 5hmC
PLCO-062


title: Rad21 ChIP-Seq EF1a For #1 rep1

description: ChIP-Seq


title: N3_sim_1

city: Bangkok

first: Paak

last: Rewthamrongsris

state: Patumwan

address: 34 Henri-Dunant Road, Wangmai

department: Department of Anatomy

country: Thailand

institute: Faculty of Dentistry, Chulalongkorn University

description: Library name: sample6

data_processing:
Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Clean data were aligned to reference genome via software Hisat2 (v2.2.1).
HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package
Assembly: Reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Subsequently, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Supplementary files format and content: Microsoft excel 16.75

source_name: Apical Papilla

growth_protocol: Apical papilla tissues were collected for cell explantation. Cells were cultured in Dulbecco-modified Eagle medium (DMEM, Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS, Gibco), 2 mM L-glutamine (GlutaMAXTM, Gibco), 100 μg/mL streptomycin, and 100 U/ml penicillin (Sigma-Aldrich, USA) at 37 ° C in a humidified atmosphere with 5% CO2.

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

treatment_protocol: Cells were treated with simvastatin (cat. No. 000008154, Sigma-Aldrich) at a concentration range from 100 nM to 1000 nM.

value: Apical Papilla

value: SCAPs

value: simvastatin


title: HCC_p53f/f, 3717 T1

description: hepatocellular carcinoma


title: RfxCas13d-NLS mRNA + gpri-miR430, rep3

description: instrument model: G4

value: Nuclear RfxCas13d


title: RfxCas13d-NLS mRNA + gpri-miR430, rep2

description: instrument model: G4


title: N2_sim_1

description: Library name: sample5


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 7187

description:
cell-free DNA 5hmC
PLCO-061

value: peripheral plasma

value: cell-free DNA


title: H3K27ac ChIP-Seq EF1a For #1 rep1

description: ChIP-Seq


title: N1_sim_1

description: Library name: sample4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 2125

description:
cell-free DNA 5hmC
PLCO-060


title: RfxCas13d-NLS mRNA + gpri-miR430, rep1

description: instrument model: G4


title: RfxCas13d mRNA + gpri-miR430, rep3

description: instrument model: G4

value: Cytosolic RfxCas13d


title: H3K4me3 ChIP-Seq EF1a For #1 rep2

description: ChIP-Seq

value: Pro-B cell line


title: N3_control_1

description: Library name: sample3

value: Control


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IX 0090

description:
cell-free DNA 5hmC
PLCO-058


title: H3K4me3 ChIP-Seq EF1a For #1 rep1

description: ChIP-Seq

value: Bone marrow


title: N1_control_1

description: Library name: sample1


title: N2_control_1

description: Library name: sample2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 6707

description:
cell-free DNA 5hmC
PLCO-057


title: CTCF ChIP-Seq EF1a For #1 rep2

description: ChIP-Seq


title: CTCF ChIP-Seq EF1a For #1 rep1

description: ChIP-Seq


title: RfxCas13d mRNA + gpri-miR430, rep1

description: instrument model: G4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 3303

description:
cell-free DNA 5hmC
PLCO-056


title: RfxCas13d mRNA + gpri-miR430, rep2

description: instrument model: G4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 7459

description:
cell-free DNA 5hmC
PLCO-055


title: H3K27ac ChIP-Seq EF1a For #1 rep2

description: ChIP-Seq


title: bone 9

city: Jerusalem

first: Liran

last: Carmel

address: The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description: Bisulfite-seq

data_processing:
Modern specimen: sequence quality was evaluated using FastQC (v0.11.9) and then trimmed with Trim-Galore (v0.6.7) with parameters: --quality 30 --phred33 --fastqc --gzip --clip_R1 5 --clip_R2 10 --length 70 --paired
The samples were aligned to hg19 genome assembly using Bismark v0.23.0 with the following parameters: --bowtie2 --non_bs_mm -p 4 --multicore 4.
We then used deduplicate_bismark to remove PCR duplications and bismark_methylation_extractor to extract methylation calls with the following parameters: -p --parallel 4 --bedGraph.
Assembly: hg19 (GRCh37)
Supplementary files format and content: BISMARK cov.gz files: tab-deleimited with columns <chromosome> <start position> <end position> <methylation percentage> <count methylated reads> <count unmethylated reads>
Supplementary files format and content: Ancient Reconstructed methylation bed file: <chromosome> <start position (0-based)> <end position> <methylation percentage>

source_name: present-day human

extract_protocol:
DNA was extracted from bones using QIAamp® DNA Investigator kit (56504, Qiagen). Bones were cut to thin slices (0.2-0.5 mm) and then thoroughly washed (X5) with PBS, to clean samples from blood. Bones were crushed with mortar and pestle in liquid nitrogen, and 100 mg bone powder was taken to extract DNA according to the protocol Isolation of Total DNA from Bones and Teeth of the DNA Investigator kit.
Illumina TruSeq Sample Preparation kit

value: bone (femur)

tag: gender

value: female


title: Non inyected, rep3

description: instrument model: G4

value: whole embryo


title: Rad21 ChIP-Seq EF1a For #2 rep2

description: ChIP-Seq


title: bone 8

description: Bisulfite-seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 2838

description:
cell-free DNA 5hmC
PLCO-054


title: H3K27ac ChIP-Seq EF1a For #2 rep2

description: ChIP-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IU 0439

description:
cell-free DNA 5hmC
PLCO-053


title: bone 7

description: Bisulfite-seq


title: Rad21 ChIP-Seq EF1a For #2 rep1

description: ChIP-Seq


title: Non inyected, rep1

description: instrument model: G4

value: 6 hpf


title: bone 6

description: Bisulfite-seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 6973

description:
cell-free DNA 5hmC
PLCO-052


title: H3K27ac ChIP-Seq EF1a For #2 rep1

description: ChIP-Seq


title: Cas7-11 knockdown, 50pg GFP, rep3

description: instrument model: G4

extract_protocol:
Total RNA then was extracted using standard TRIzol protocol as described in the manufacturer’s instructions (ThermoFisher Scientific).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Cat. No. E7760L).

value: Cas7-11 knockdown


title: hk_ef_3

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adapter contaminations were removed using cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38.99 mouse transcriptome, with RSEM v1.3.1, to obtain expression estimates at gene level.
Expected expression counts were then processed with an analysis pipeline that used Bioconductor package Limma for normalization, considering only those genes for which expression was at least 1 count per million (CPM) in at least 3 samples.
Assembly: GRCm38.99
Supplementary files format and content: Normalized counts (CPM) for genes with expression level of at least 1 count per million (CPM) in at least 3 samples.

extract_protocol:
BM cells were isolated as described above. Lineage negative (Lin-) cells were enriched by staining with a panel of biotinylated antibodies against lineage committed cells (CD3, CD45R, CD11b (1:100) Ter-119, Gr-1 (1:20), all from BD Pharmigen). After washing, cells were incubated with streptavidin magnetic beads (Miltenyi) and passed through LS columns (Miltenyi), the negative fraction was collected for further staining with Sca-1 (APC), c-kit (CD117; PE), CD48 (APCCy7), CD150 (BV650), Streptavidin (BV421) (1:200) antibodies and with the viability marker Hoechst 33258 prior to sorting by FACS Aria II. GMPs were identified as Lin-c-kit+ sca-11- CD48+ CD150- cells. Total RNA was isolated from GMP (miRNeasy Micro Kit)
Libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s instructions. All libraries were sequenced in a Nextseq 2000 (Illumina)

treatment_protocol: Mice treated with DSS 3%, 5 days. After 5 days resting, mice were sack and GMP isolated. Mice treated with HK-EF i.v, after 10 days mice were sack and GMP isolated

value: Granulocyte/monocyte progenitor

value: HK-EF


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 2335

description:
cell-free DNA 5hmC
PLCO-051


title: hk_ef_2

value: WT


title: H3K4me3 ChIP-Seq EF1a For #2 rep2

description: ChIP-Seq

value: forward EF1a promoter replacement


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LS 1396

description:
cell-free DNA 5hmC
PLCO-050


title: Cas7-11 knockdown, 50pg GFP, rep2

description: instrument model: G4


title: Cas7-11 knockdown, 50pg GFP, rep1

description: instrument model: G4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UQ 4947

description:
cell-free DNA 5hmC
PLCO-049


title: hk_ef_1


title: dss_3

value: DSS


title: H3K4me3 ChIP-Seq EF1a For #2 rep1

description: ChIP-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 0045

description:
cell-free DNA 5hmC
PLCO-048


title: Cas7-11 control, 50pg GFP, rep3

description: instrument model: G4

value: Cas7-11 control


title: Cas7-11 control, 50pg GFP, rep2

description: instrument model: G4


title: dss_2


title: CTCF ChIP-Seq EF1a For #2 rep2

description: ChIP-Seq


title: Non inyected, rep2

description: instrument model: G4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 2261

description:
cell-free DNA 5hmC
PLCO-046

value: peripheral plasma


title: CTCF ChIP-Seq EF1a For #2 rep1

description: ChIP-Seq


title: dss_1


title: Cas7-11 control, 50pg GFP, rep1

description: instrument model: G4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 6723

description:
cell-free DNA 5hmC
PLCO-045

value: cell-free DNA


title: Ctr3

value: excipient


title: Cas7-11 knockdown, 10pg GFP, rep4

description: instrument model: G4


title: H3K27ac ChIP-Seq EF1a Rev #2 rep1

description: ChIP-Seq

value: Pro-B cell line

value: reverse EF1a promoter replacement


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 8952

description:
cell-free DNA 5hmC
PLCO-044


title: Cas7-11 knockdown, 10pg GFP, rep3

description: instrument model: G4


title: Ctr2

value: Bone marrow


title: H3K4me3 ChIP-Seq EF1a Rev #2 rep2

description: ChIP-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UJ 8792

description:
cell-free DNA 5hmC
PLCO-043


title: Ctr1


title: H3K4me3 ChIP-Seq EF1a Rev #2 rep1

description: ChIP-Seq


title: CTCF ChIP-Seq EF1a Rev #2 rep2

description: ChIP-Seq


title: bqv_3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UY 4031

description:
cell-free DNA 5hmC
PLCO-041


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 9440

description:
cell-free DNA 5hmC
PLCO-042


title: Cas7-11 knockdown, 10pg GFP, rep1

description: instrument model: G4


title: Cas7-11 control, 10pg GFP, rep4

description: instrument model: G4


title: CTCF ChIP-Seq EF1a Rev #2 rep1

description: ChIP-Seq


title: Rad21ChIP-Seq  EF1a Rev #1 rep2

description: ChIP-Seq


title: Cas7-11 control, 10pg GFP, rep3

description: instrument model: G4


title: bqv_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 6119

description:
cell-free DNA 5hmC
PLCO-040


title: Rad21 ChIP-Seq  EF1a Rev #1 rep1

description: ChIP-Seq


title: H3K27ac ChIP-Seq EF1a Rev #2 rep2

description: ChIP-Seq


title: bqv_2


title: b_hk_ef_3


title: Cas7-11 control, 10pg GFP, rep2

description: instrument model: G4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 8376

description:
cell-free DNA 5hmC
PLCO-039


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 1112

description:
cell-free DNA 5hmC
PLCO-038


title: H3K27ac ChIP-Seq  EF1a Rev #1 rep2

description: ChIP-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 7865

description:
cell-free DNA 5hmC
PLCO-037


title: H3K27ac ChIP-Seq  EF1a Rev #1 rep1

description: ChIP-Seq


title: DjCas13d knockdown, 50pg GFP, rep3

description: instrument model: G4

value: DjCas13d knockdown


title: Cas7-11 knockdown, 10pg GFP, rep2

description: instrument model: G4


title: b_hk_ef_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 6673

description:
cell-free DNA 5hmC
PLCO-036


title: DjCas13d knockdown, 50pg GFP, rep2

description: instrument model: G4


title: H3K4me3 ChIP-Seq  EF1a Rev #1 rep2

description: ChIP-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 2161

description:
cell-free DNA 5hmC
PLCO-035


title: b_dss_3


title: b_dss_2


title: DjCas13d knockdown, 50pg GFP, rep1

description: instrument model: G4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 3007

description:
cell-free DNA 5hmC
PLCO-034


title: H3K4me3 ChIP-Seq  EF1a Rev #1 rep1

description: ChIP-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 9270

description:
cell-free DNA 5hmC
PLCO-033


title: b_dss_1


title: DjCas13d control, 50pg GFP, rep2

description: instrument model: G4

value: DjCas13d control


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 6904

description:
cell-free DNA 5hmC
PLCO-032


title: s9_DSS_IP3

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adapter contaminations were removed using cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned with bowtie2 against autosomes and chrX of the mm10 mouse genomic reference, with parameters “bowtie2 –local -I 10 -X 700 --no-mixed --no-discordant --very-sensitive”
Duplicated reads were marked with Piccad. Alignments were filtered with samtools to keep only paired and properly mapped reads, with parameters “samtools view -b -h -q 30 -f 2 -F 780”.
Peaks were called with macs3, using parameters “macs3 callpeaks -t alignment_file -g mm -B –SPMR -f BAMPE -q 0.01 –keep-dup auto”.
Assembly: mm10
Supplementary files format and content: Genomic intervals in narrowPeak format, generated by macs3
Library strategy: CUT&Tag

extract_protocol:
BM cells were isolated as described above. Lineage negative (Lin-) cells were enriched by staining with a panel of biotinylated antibodies against lineage committed cells (CD3, CD45R, CD11b (1:100) Ter-119, Gr-1 (1:20), all from BD Pharmigen). After washing, cells were incubated with streptavidin magnetic beads (Miltenyi) and passed through LS columns (Miltenyi), the negative fraction was collected for further staining with Sca-1 (APC), c-kit (CD117; PE), CD48 (APCCy7), CD150 (BV650), Streptavidin (BV421) (1:200) antibodies and with the viability marker Hoechst 33258 prior to sorting by FACS Aria II. GMPs were identified as Lin-c-kit+ sca-11- CD48+ CD150- cells
Cut&Tag libraries were purified using a PCR purification MinElute kit Libraries size and quality were assessed using a 2100 Bioanalyzer instrument (Agilent).


title: CTCF ChIP-Seq  EF1a Rev #1 rep1

description: ChIP-Seq


title: DjCas13d control, 50pg GFP, rep1

description: instrument model: G4

value: whole embryo


title: Cas7-11 control, 10pg GFP, rep1

description: instrument model: G4

value: 6 hpf


title: b_hk_ef_2


title: s8_DSS_IP2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LR 1253

description:
cell-free DNA 5hmC
PLCO-031


title: Rad21 ChIP-Seq  EF1a Rev #2 rep2

description: ChIP-Seq


title: DjCas13d knockdown, 10pg GFP, rep3

description: instrument model: G4


title: Rad21 ChIP-Seq  EF1a Rev #2 rep1

description: ChIP-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 7569

description:
cell-free DNA 5hmC
PLCO-030


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID II 1143

description:
cell-free DNA 5hmC
PLCO-029


title: s5_Control_IP3

value: Excipient


title: DjCas13d knockdown, 10pg GFP, rep2

description: instrument model: G4


title: Rad21 ChIP-Seq WT rep2

description: ChIP-Seq


title: CTCF ChIP-Seq WT rep2

description: ChIP-Seq


title: DjCas13d control, 50pg GFP, rep3

description: instrument model: G4


title: DjCas13d knockdown, 10pg GFP, rep1

description: instrument model: G4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IQ 7967

description:
cell-free DNA 5hmC
PLCO-028


title: s4_Control_IP2

value: Granulocyte/monocyte progenitor


title: CTCF ChIP-Seq  EF1a Rev #1 rep2

description: ChIP-Seq


title: DjCas13d control, 10pg GFP, rep3

description: instrument model: G4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IH 9931

description:
cell-free DNA 5hmC
PLCO-027


title: DjCas13d control, 10pg GFP, rep2

description: instrument model: G4


title: s25_HK_PNK_IP3

value: HK-EF


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 5201

description:
cell-free DNA 5hmC
PLCO-026


title: Directional RNA-Seq 3'CBEs Inv #2 rep2

description: Directional RNA-Seq

data_processing:
RNA-seq reads were aligned to the mm10 genome using STAR8. Aligned reads were converted to bigwig format and filtered by strand orientation using deepTools7 bamCoverage with the flags “—normalizeUsing CPM —filterRNAstrand forward” or “—normalizeUsing CPM –filterRNAstrand reverse”.
RNA-seq reads were aligned to mm10 using STAR version 2.7.10b
Aligned reads were processed using bamCoverage from deepTools version 3.5.1 (parameters --normalizeUsing CPM --filterRNAstrand forward or reverse) to generate bigWig files
Assembly: mm10
Supplementary files format and content: bw

extract_protocol:
Directional RNA-Seq experiments were performed with two steps: rRNA depletion (PerkinElmer, Cat# NOVA-512961) and rapid directional RNA-Seq (PerkinElmer, Cat# NOVA-5198-01) according to manufacturer protocol.
Directional RNA-Seq libraries were prepared for sequencing using standard Illumina protocols. Libraries were sequenced on a Nova Seq SP, pair ends (2X150bp)
Directional RNA-Seq

value: 3'CBEs inversion


title: s24_HK_PNK_IP2


title: Directional RNA-Seq 3'CBEs Inv #2 rep1

description: Directional RNA-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UY 3881

description:
cell-free DNA 5hmC
PLCO-025

data_processing:
Adapter sequences were removed from raw sequencing reads using Trimmomatic
Low quality bases at the 5’ and 3’ were trimmed based on phred score to a minimum length of 30 bp
The sequencing reads were then aligned to the human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode
Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length
Alignments with Mapping Quality Score ≥ 10 were counted based on the GENCODE gene body annotations using featureCounts without strand information
The raw read counts were then normalized using DESeq2, which performs an internal normalization that corrects for library size.
Assembly: hg19
Supplementary files format and content: Text file with normalized reads counts for all samples.
Library strategy: 5hmC-Seal sequencing

extract_protocol:
Cell-free DNA was extracted using the QIAmp Circulating cfDNA Extraction Kit (Qiagen)
3-8 ng cfDNA was used in the 5hmC-Seal assay (see Li W, Zhang X, Lu X, You L, Song Y, Luo Z, et al. 5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers. Cell Res 2017;27:1243-57). Libraries were constructed on-bead using the KAPA HyperPlus kit (Roche).


title: RfxCas13d knockdown, 50pg GFP, rep3

description: instrument model: G4

value: RfxCas13d knockdown


title: s7_DSS_IP1

value: WT

value: DSS


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 2359

description:
cell-free DNA 5hmC
PLCO-024

value: peripheral plasma


title: s23_HK_PNK_IP1


title: RfxCas13d knockdown, 50pg GFP, rep2

description: instrument model: G4


title: Directional RNA-Seq 3'CBEs Inv #1 rep2

description: Directional RNA-Seq


title: Directional RNA-Seq 3'CBEs Inv #1 rep1

description: Directional RNA-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IX 1287

description:
cell-free DNA 5hmC
PLCO-022

value: cell-free DNA


title: RfxCas13d knockdown, 50pg GFP, rep1

description: instrument model: G4


title: Rad21 ChIP-Seq WT rep1

description: ChIP-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UV 6345

description:
cell-free DNA 5hmC
PLCO-020


title: RfxCas13d control, 50pg GFP, rep3

description: instrument model: G4

value: RfxCas13d control


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 4825

description:
cell-free DNA 5hmC
PLCO-021


title: s3_Control_IP1


title: s20_HK_IP2


title: Directional RNA-Seq 3'CBEs-- rep2

description: Directional RNA-Seq

value: Pro-B cell line


title: Directional RNA-Seq WT rep1

description: Directional RNA-Seq


title: RfxCas13d control, 50pg GFP, rep2

description: instrument model: G4


title: DjCas13d control, 10pg GFP, rep1

description: instrument model: G4


title: s17_MK_DSS_IP3


title: CTCF ChIP-Seq WT rep1

description: ChIP-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 6027

description:
cell-free DNA 5hmC
PLCO-019


title: Directional RNA-Seq 3'CBEs-- rep1

description: Directional RNA-Seq


title: s16_MK_DSS_IP2


title: s19_HK_IP1


title: RfxCas13d knockdown, 10pg GFP, rep2

description: instrument model: G4


title: s15_MK_DSS_IP1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 2976

description:
cell-free DNA 5hmC
PLCO-017


title: s21_HK_IP3


title: Directional RNA-Seq EF1a Rev #1 rep2

description: Directional RNA-Seq

value: reverse EF1a promoter replacement


title: RfxCas13d control, 50pg GFP, rep1

description: instrument model: G4


title: RfxCas13d knockdown, 10pg GFP, rep1

description: instrument model: G4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 7698

description:
cell-free DNA 5hmC
PLCO-016


title: s13_MK_IP3

value: Bone marrow


title: Directional RNA-Seq WT rep2

description: Directional RNA-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 7899

description:
cell-free DNA 5hmC
PLCO-018


title: Directional RNA-Seq EF1a Rev #1 rep1

description: Directional RNA-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 6708

description:
cell-free DNA 5hmC
PLCO-015


title: s11_MK_IP1


title: Directional RNA-Seq EF1a For #1 rep2

description: Directional RNA-Seq

value: forward EF1a promoter replacement


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 3857

description:
cell-free DNA 5hmC
PLCO-014


title: RfxCas13d control, 10pg GFP, rep1

description: instrument model: G4


title: MEFs, sheIF2B5_sheIF4E_Total_rep4

city: Stockholm

first: Krzysztof

middle: Jan

last: Szkop

state: Solna

address: SciLifeLab, Tomtebodavägen 23

department: Department of Oncology and Pathology

country: Sweden

institute: Karolinska Institutet

data_processing:
BBmap (v. 36.59)(parameters: k = 13, ktrim=n, useshortkmers=t, mink = 5, qtrim=t, trimq = 10, minlength = 25) was used to trim reads for adapter sequences and low-quality base calls. The resulting reads were aligned to the mm10 genome assembly using HISAT2 (v.2.0.4) (parameters: -no-mixed and -no-discordant). The aligned reads were summarized using the htseq-count (mm10 GTF annotation from the UCSC database).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw gene counts for every gene and every sample

source_name: MEFs

extract_protocol:
Mouse Embryonic fibroblast (MEF) was used in the Lentivirus shRNA gene knockdown experiments. Lentiviral shRNAs targeted to eIF2B-epsilon, eIF4E were generated by HEK293 cell, then infected MEF for two days. The infected MEFs were selected by puromycin before RNA purification. RNA was purified by Trizol-LS according to manufactorary instruction before RNA-seq library generation.
TruSeq Stranded Total RNA protocol
RNA-seq of polysomal and total RNA samples

value: MEFs

value: sheIF2B-epsilon + sheIF4E

tag: fraction

value: total mRNA


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UM 0504

description:
cell-free DNA 5hmC
PLCO-013


title: Directional RNA-Seq EF1a For #1 rep1

description: Directional RNA-Seq


title: RfxCas13d control, 10pg GFP, rep2

description: instrument model: G4

value: whole embryo

value: 6 hpf


title: MEFs, sheIF2B5_sheIF4E_Total_rep3


title: rat lung, DA, rep6

city: Jinan

first: Xu

last: Zhou

address: No. 42, Wenhua West Road, Jinan 250011, Shandong, China

institute: Affiliated Hospital of Shandong University of Traditional Chinese Medicine

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQ format, which contains sequence information and corresponding sequencing quality information.
Fastp (version 0.23.1) was used to perform basic statistics on the quality of the raw reads.
HISAT2 (v2.2.1) was used as a comparison tool.
HTSeq (v2.0.2) was used as quantitative software for transcriptome analysis.
Assembly: mRatBN7.2
Supplementary files format and content: read count, fpkm

organism: Rattus norvegicus

source_name: lung

extract_protocol:
RNA was harvested using Trizol (Ambion/Invitrogen, USA). 200 ng of total RNA was used for the construction of sequencing libraries.
After isolating, and passing integrity and total quantity testing, mRNA was used to synthesize complementary DNA (cDNA). Amplification was carried out via polymerase chain reaction (PCR), followed by purification using AMPure XP Beads. Library quality was detected using an Agilent 2100 system and the NovaSeq 6000 Illumina high-throughput sequencing platform was used to sequence the library.

value: lung

tag: Sex

value: Male

value: Sprague Dawley

value: 2,3-butanedione (also known as diacetyl, DA)


title: rat lung, DA, rep5


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 2407

description:
cell-free DNA 5hmC
PLCO-012


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LR 1452

description:
cell-free DNA 5hmC
PLCO-011


title: rat lung, DA, rep4


title: MEFs, sheIF2B5_sheIF4E_Poly_rep4

data_processing:
BBmap (v. 36.59)(parameters: k = 13, ktrim=n, useshortkmers=t, mink = 5, qtrim=t, trimq = 10, minlength = 25) was used to trim reads for adapter sequences and low-quality base calls. The resulting reads were aligned to the mm10 genome assembly using HISAT2 (v.2.0.4) (parameters: -no-mixed and -no-discordant). The aligned reads were summarized using the htseq-count (mm10 GTF annotation from the UCSC database).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw gene counts for every gene and every sample
Library strategy: Polysome-seq

value: polysome associated mRNA


title: MEFs, sheIF2B5_sheIF4E_Total_rep1


title: Directional RNA-Seq EF1a Rev #2 rep2

description: Directional RNA-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 5767

description:
cell-free DNA 5hmC
PLCO-008

value: peripheral plasma


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UQ 5192

description:
cell-free DNA 5hmC
PLCO-010

value: cell-free DNA


title: RfxCas13d control, 10pg GFP, rep3

description: instrument model: G4

value: RfxCas13d control


title: Directional RNA-Seq EF1a Rev #2 rep1

description: Directional RNA-Seq

value: Pro-B cell line


title: s12_MK_IP2

value: Granulocyte/monocyte progenitor

value: Excipient


title: rat lung, DA, rep3


title: rat lung, DA, rep2


title: Directional RNA-Seq Eu-- #1 rep2

description: Directional RNA-Seq

value: Bone marrow


title: MEFs, sheIF2B5_sheIF4E_Poly_rep3

value: MEFs


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UU 8701

description:
cell-free DNA 5hmC
PLCO-007


title: rat lung, DA, rep1


title: MEFs, sheIF2B5_sheIF4E_Poly_rep2

value: sheIF2B-epsilon + sheIF4E


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 7266

description:
cell-free DNA 5hmC
PLCO-006


title: rat lung, control, rep6

value: aseptic distilled water


title: Directional RNA-Seq Eu-- #2 rep2

description: Directional RNA-Seq


title: Directional RNA-Seq EF1a For #2 rep2

description: Directional RNA-Seq

value: forward EF1a promoter replacement


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IS 3602

description:
cell-free DNA 5hmC
PLCO-004


title: MEFs, sheIF2B5_sheIF4E_Total_rep2

value: total mRNA


title: rat lung, control, rep5

value: lung


title: Directional RNA-Seq EF1a For #2 rep1

description: Directional RNA-Seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IQ 7631

description:
cell-free DNA 5hmC
PLCO-003


title: MEFs, sheIF2B5_Total_rep4


title: Directional RNA-Seq Eu-- #2 rep1

description: Directional RNA-Seq


title: Directional RNA-Seq Eu-- #1 rep1

description: Directional RNA-Seq


title: rat lung, control, rep4

value: Male


title: rat lung, control, rep3

value: Sprague Dawley


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 0934

description:
cell-free DNA 5hmC
PLCO-002


title: MEFs, sheIF2B5_Total_rep2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID KD 7452

description:
cell-free DNA 5hmC
PLCO-001


title: 10: Ethylene Rep 1

city: Knoxville

first: Brad

middle: M

last: Binder

state: Tennessee

address: 309 Ken and Blaire Mossman Bldg.

department: Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee

data_processing:
Sequence quality evaluated
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
Trimmed reads were then mapped to the Azospirillum_brasilense reference genome available on ENSEMBL using the Bowtie2 aligner v.2.2.6.
BAM files were generated.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
From this differential expression was determined using DESeq2.
Genome_build: GCA_001315015.1
Supplementary_files_format_and_content: Text files contain abundance data for each sample. Excel spreadsheet contains comparison of transcript levels in air versus ethylene.

organism: Azospirillum brasilense

source_name: Azospirillum cells

growth_protocol: Cells were grown in liquid minimal media for A. brasilense (MMAB) with sodium nitrate for 12h at 28C prior to experimental treatments.

extract_protocol:
RNA extracted using Trizol.
According to Illumina protocols.

treatment_protocol: Samples were treated with ethylene-free air or 0.1 ppm ethylene for 4h prior to extraction of RNA.

value: Ethylene treated

value: Azospirillum cells


title: 11: Ethylene Rep 2


title: 12: Ethylene Rep 3


title: rat lung, control, rep2


title: MPN136

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

institute: Catholic University of Korea

description: TRANSCRIPTOMIC SINGLE CELL

data_processing:
The sequenced data were processed into expression matrices with the CellRanger v3.1.0 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: HDF5 format

source_name: bone marrow aspirates

extract_protocol:
Individual cells in BM aspirates were isolated by density gradient centrifugation using Ficoll-Paque Plus medium (GE Healthcare). After removing red blood cells using RBC lysis buffer (Miltenyi Biotec), the cells were counted and stored at −80°C until use
The scRNA-seq library was prepared using the Chromium instrument system with Single Cell 3’ v3 Reagent kit (10x Genomics) according to the manufacturer’s protocol. scRNA-seq libraries were sequenced on Illumina NovaSeq platform.

value: bone marrow aspirates

tag: group

value: Overt PMF

tag: disease

value: PMF


title: MEFs, sheIF2B5_sheIF4E_Poly_rep1

value: polysome associated mRNA


title: rat lung, control, rep1


title: MEFs, sheIF2B5_Poly_rep4


title: MPN104

description: TRANSCRIPTOMIC SINGLE CELL


title: MEFs, sheIF2B5_Poly_rep3


title: 8: Air Rep 2

value: Air control


title: RVM SYNs, Neonatal saline exposures postnatal days P12-P16 and reexposure on P29, S16

city: Wauwatosa

first: Banani

last: Banerjee

state: WI

address: 8701 Watertown Plank Road

department: Medicine

institute: Medical College of Wisconsin

data_processing:
The raw reads corresponding to the Illumina RNA-Seq FASTQ files were aligned in Strand NGS software v4.0 against the rat reference genome (Build rn6, Refseq). Quantification was done to obtain the read densities by Strand NGS software. Differential expression analysis of mRNA from 2 different group was performed using the DESeq in Strand NGS software.
Assembly: Rat reference genome (Build rn6, Refseq)
Supplementary files format and content: Excel files with gene expression profiles and fold changes in all the replicate samples

source_name: RVM brainstem

extract_protocol:
RVM tissues were removed on P30 from rats and immediately processed for synaptoneurosomes (SYNs) isolation. Total RNA was extracted from RVM SYNs preparation using Qiagen miRNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturers’ instruction.
The library was prepared for sequencing from 300 ng RNA of each sample using the Illumina standard total RNA prep ligation with ribo-zero plus library preparation kit (Illumina, San Diego, CA, USA). The quality and quantity of amplified libraries were evaluated using Qubit (Invitrogen, Carlsbad, CA, USA) and Agilent TapeStation high sensitivity D1000 Screen Tape. The average fragment length of the cDNA libraries was 330 bp. RNA-seq libraries were sequenced using paired-end and SP flow cell on Illumina NovaSeq 6000 instruments following the manufacturer’s protocol.

treatment_protocol: Two treatment protocols defined as non-rechallenge (NRC protocol) and rechallenge (RC protocol) were used in this study.  In all treatment protocols, rats were anesthetized with isoflurane (1.5% induction and 1.0% maintenance with flow rate 1 L/min). In RC protocol, female pups received transurethral injections of protamine sulfate (1% in saline, 0.1 ml) followed by transurethral zymosan (1% in saline, 0.1 ml) exposures from postnatal day 12 through 16 (P12 to P16).  The protamine solution was left inside the bladder for 20 min after each injection before instillation of zymosan into the bladder.  The control group pups received two doses of intravesical saline (0.1 mL) at similar intervals as described for the experimental group.  On postnatal day 29 (P29), the experimental group received an acute rechallenge of protamine sulfate (1% in saline, 0.1 ml) followed by zymosan (1% in saline, 0.1 ml) as described above, whereas the control group received two doses of saline (0.1 mL) at similar intervals.  In NRC protocol, both experimental and control groups received similar neonatal treatment as described for RC protocol, however, the rats did not receive any rechallenge on P29.  Brainstem RVM tissues were collected from both RC and NRC groups on P30.

value: RVM brainstem

value: SD, Female

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and reexposure on P29, RVM tissues collected on P37


title: RVM SYNs, Neonatal saline exposures postnatal days P12-P16 and reexposure on P29, S15

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and reexposure on P29, RVM tissues collected on P36


title: MEFs, sheIF2B5_Poly_rep2

value: MEFs


title: 7: Air Rep 1


title: MPN101

description: TRANSCRIPTOMIC SINGLE CELL


title: MPN098

description: TRANSCRIPTOMIC SINGLE CELL


title: MEFs, sheIF2B5_Poly_rep1


title: GDPH_3

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

data_processing:
Read alignment was carried out with STAR (2.7.9a) and gene expression levels was determined using RSEM (1.3.3).
TPM normalization of raw data was performed.
Assembly: PN40024.v4
Supplementary files format and content: Tab-separated value (tsv) file includes raw counts for each samples.
Supplementary files format and content: Tab-seprated value (tsv) file includes TPM normalized counts for each sample.

organism: Vitis vinifera

source_name: Deseeded berries

growth_protocol: The trial took place in 2022 in Southern Italy on twelve-years-old vines of Vitis vinifera L. cv. Black Magic grafted on 1103P. Vines were planted at 2 x 2.5 m between vines and rows, respectively, using a tendone training system. The vineyard was covered with a plastic film, positioned before budburst, and removed at harvest to anticipate further the ripening of this early variety.

extract_protocol:
Total RNA was extracted from 100 mg of the berry samples using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich).
Libraries were prepared using the Stranded mRNA prep kit (Illumina).

treatment_protocol: The experimental setup followed a randomized complete block design (RCBD) comprising four plots (biological replicates) per treatment, each containing seven vines. Each plot covered an area of 35 m2 (2.5 m x 14 m). The treatments were carried out applying GDPH SURNAN® (SPAA s.r.l.; Pescara, Italy) and urea (control, 46% N) in a dose of total N (1.25 Kg N ha-1). Both treatments were applied directly on the soil by ferti-irrigation on 30/05/2022 at crop BBCH 79-81. The RNAseq analysis was carried out using berry samples of three out of the four plots (biological replicates). A pool of berries was produced for each biological replicate (plot) to characterize the berry transcriptome 14 days after the treatments. A total of ten berries were sampled from the upper, middle, and basal parts of the first cluster for each of the seven vines of each biological replicate.

value: Deseeded berries

value: Black magic

value: Treatment wit soil application at veraison with a corn gluten-derived protein hydrolysate


title: RVM SYNs, Neonatal saline exposures postnatal days P12-P16 and reexposure on P29, S14

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and reexposure on P29, RVM tissues collected on P35


title: MEFs, sheIF2B5_Total_rep3

value: total mRNA


title: MPN071

description: TRANSCRIPTOMIC SINGLE CELL


title: MEFs, sheIF2B5_Total_rep1


title: MEFs, shControl_Total_rep4

value: shControl


title: MEFs, shControl_Total_rep3


title: RVM SYNs, Neonatal zymosan exposures postnatal days P12-P16 and reexposure on P29, S13

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and reexposure on P29, RVM tissues collected on P34


title: MPN068

description: TRANSCRIPTOMIC SINGLE CELL

value: bone marrow aspirates


title: 9: Air Rep 3

value: Azospirillum cells


title: RVM SYNs, Neonatal zymosan exposures postnatal days P12-P16 and reexposure on P29, S12

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and reexposure on P29, RVM tissues collected on P33


title: MPN063

description: TRANSCRIPTOMIC SINGLE CELL

value: Overt PMF

value: PMF


title: GDPH_1


title: RVM SYNs, Neonatal zymosan exposures postnatal days P12-P16 and reexposure on P29, S11

value: RVM brainstem

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and reexposure on P29, RVM tissues collected on P32


title: Control_3

value: Treatment wit soil application at veraison with urea (control)


title: MEFs, shControl_Total_rep2


title: MPN060

description: TRANSCRIPTOMIC SINGLE CELL


title: RVM SYNs, Neonatal zymosan exposures postnatal days P12-P16 and reexposure on P29, S10

value: SD, Female

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and reexposure on P29, RVM tissues collected on P31


title: Control_2

value: Deseeded berries


title: MEFs, shControl_Total_rep1

value: MEFs


title: MEFs, shControl_Poly_rep4

value: polysome associated mRNA


title: Control_1

value: Black magic


title: RVM SYNs, Neonatal zymosan exposures postnatal days P12-P16 and reexposure on P29, S9

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and reexposure on P29, RVM tissues collected on P30


title: MEFs, shControl_Poly_rep3

value: shControl


title: MPN030

description: TRANSCRIPTOMIC SINGLE CELL


title: Normal 3

city: changsha

first: runlin

last: wen

state: hunan

address: yuelu street

institute: central south university

description:
Isolate 2 mm tissue samples from the same anatomical location in normal spinal cord tissue, including three replicate samples, and perform RNA sequencing.
Control3

data_processing:
Paired-end reads were harvested from sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with hisat2 software (v2.0.4). Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization. Differentially expressed mRNAs were identified by p-value and fold change. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Assembly: GCF_014441545.1
Supplementary files format and content: FASTQ
Supplementary files format and content: BAM

organism: Canis lupus familiaris

source_name: spinal cord

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen, Carlsbad, CA, USA)
the purified mRNA was used for library construction with GenSeq® Directional RNA Library Prep Kit (GenSeq, Inc., Shanghai, China) by following manufacturer’s recommendations. The mRNA was fragmented into ~300 nt in length. The first-strand cDNA was synthesized from the RNA fragments by reverse transcriptase and random hexamer primers, and the second-strand cDNA was synthesized in 2nd Strand Synthesis Buffer with dUTP Mix. Then, the double stranded cDNA fragments were subjected to end-repair and dA-tailing, followed by adapter ligation. The adapter-ligated DNA samples were PCR amplified and purified to obtain sequencing libraries. Finally, the libraries were sequenced with Illumina HiSeq sequencer (Illumina, San Diego, CA, USA) on the paired-end 150 bp mode.

value: spinal cord


title: GDPH_2

value: Treatment wit soil application at veraison with a corn gluten-derived protein hydrolysate


title: MPN016

description: TRANSCRIPTOMIC SINGLE CELL

value: bone marrow aspirates


title: RVM SYNs, Neonatal saline exposures postnatal days P12-P16, S8

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and RVM tissues collected on P37


title: Normal 2

description:
Isolate 2 mm tissue samples from the same anatomical location in normal spinal cord tissue, including three replicate samples, and perform RNA sequencing.
Control2


title: RVM SYNs, Neonatal saline exposures postnatal days P12-P16, S7

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and RVM tissues collected on P36


title: MPN015

description: TRANSCRIPTOMIC SINGLE CELL

value: Overt PMF

value: PMF


title: RVM SYNs, Neonatal saline exposures postnatal days P12-P16, S6

value: RVM brainstem

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and RVM tissues collected on P35


title: Mid nonSR 3

description:
Sixty-five days after spinal cord injury (SCI), isolate tissue samples located 0-2 mm from the injury site, including three replicate samples, and perform RNA sequencing.
Acute3


title: MEFs, shControl_Poly_rep2


title: mESCs, eIF2B-epsilon_Mutant_rep3

source_name: mESCs

extract_protocol:
eIF2B-epsilon R191H mutation was generated in mouse embryonic stem cells (mESC) by using the Crispr/CAS9 genome edition system. RNA was purified by Trizol-LS according to manufactorary instruction before RNA-seq library generation
TruSeq Stranded Total RNA protocol

value: mESCs


title: Mid nonSR 2

description:
Sixty-five days after spinal cord injury (SCI), isolate tissue samples located 0-2 mm from the injury site, including three replicate samples, and perform RNA sequencing.
Acute2


title: MPN035

description: TRANSCRIPTOMIC SINGLE CELL


title: mESCs, eIF2B-epsilon_Mutant_rep2


title: Mid nonSR 1

description:
Sixty-five days after spinal cord injury (SCI), isolate tissue samples located 0-2 mm from the injury site, including three replicate samples, and perform RNA sequencing.
Acute1


title: Normal 1

description:
Isolate 2 mm tissue samples from the same anatomical location in normal spinal cord tissue, including three replicate samples, and perform RNA sequencing.
Control1


title: RVM SYNs, Neonatal zymosan exposures postnatal days P12-P16, S2

value: SD, Female

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and RVM tissues collected on P31


title: MEFs, shControl_Poly_rep1

value: MEFs


title: MPN111

description: TRANSCRIPTOMIC SINGLE CELL

value: prefibrotic

value: Pre-PMF


title: RVM SYNs, Neonatal zymosan exposures postnatal days P12-P16, S5

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and RVM tissues collected on P34


title: RVM SYNs, Neonatal zymosan exposures postnatal days P12-P16, S4

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and RVM tissues collected on P33


title: Mid SR 2-4mm 3

description:
Without adding the modified material, isolate tissue samples located 2-4 mm from the injury site after 5 days, including three replicate samples, and perform RNA sequencing.
Chronicscar2-44

value: spinal cord


title: RVM SYNs, Neonatal zymosan exposures postnatal days P12-P16, S1

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and RVM tissues collected on P30


title: MPN052

description: TRANSCRIPTOMIC SINGLE CELL

value: bone marrow aspirates


title: Mid SR 2-4mm 2

description:
Without adding the modified material, isolate tissue samples located 2-4 mm from the injury site after 5 days, including three replicate samples, and perform RNA sequencing.
Chronicscar2-43


title: MPN019

description: TRANSCRIPTOMIC SINGLE CELL


title: RVM SYNs, Neonatal zymosan exposures postnatal days P12-P16, S3

value: Neonatal zymosan/saline exposures postnatal days P12-P16 and RVM tissues collected on P32


title: mESCs, eIF2B-epsilon_WT_rep2

value: WT


title: MPN069

description: TRANSCRIPTOMIC SINGLE CELL

value: Reactive


title: MPN099

description: TRANSCRIPTOMIC SINGLE CELL

value: PMF


title: MPN014

description: TRANSCRIPTOMIC SINGLE CELL


title: Heart, 1M004

city: Chengdu

first: Yanxia

last: Wu

state: sichuan

address: LinYin street in Wuhou district

institute: Sichuan University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts to remove reads containing adapter, reads containing ploy-N and low quality reads
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)
And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Rattus_norvegicus.mRatBN7.2.110
Supplementary files format and content: Text file includes a matrix table containing gene-counts  for all samples
Supplementary files format and content: Text file includes a matrix table containing gene-FPKM values  for all samples

source_name: Heart

growth_protocol: Male Sprague-Dawley rats were administered a single dose of streptozotocin to induce DCM

extract_protocol:
Total RNA was extracted from the hearts using Trizol
Sequencing libraries were constructed with the NEBNext® UltraTM RNA Library Prep Kit for Illumina®

treatment_protocol: Five months post-diabetes induction, the animals were euthanized humanely, and their hearts were meticulously extracted

value: Heart

tag: disease state

value: DCM

value: STZ


title: mESCs, eIF2B-epsilon_Mutant_rep1

value: mESCs


title: mESCs, ATF4_uORF1mut_rep3

extract_protocol:
ATF4 uORF1 mutation was generated in mouse embryonic stem cells (mESC) by using the Crispr/CAS9 genome edition system. RNA was purified by Trizol-LS according to manufactorary instruction before RNA-seq library generation
TruSeq Stranded Total RNA protocol


title: mESCs, eIF2B-epsilon_WT_rep3


title: Heart, 1M003


title: HEK293T, FLAG-PFN1-CLIP, S, biol rep3

city: RIVERSIDE

first: Yinsheng

last: Wang

state: CA

address: 900 University Ave

department: Chemistry

institute: University of California, Riverside

data_processing:
When obtained the raw fastq file from the sequencers, FastQC was used to perform quality control.
STAR(v2.7.3a) were used to map the sequencing reads to human genome (hg38).
UMI-tools version(version 1.0.1) was used to remove PCR duplications.
Bedgraph files were generated from bedtools v2.29.2 and subsesquently transfromed to bigwig files.
Assembly: hg38
Supplementary files format and content: bigwig files for crosslinking events.

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and  1% (w/v) penicillin/streptomycin. Cells were trypsinized and sub-cultured in humidified atmosphere with 5% CO2 at 37oC

extract_protocol:
After immunoprecipitation and SDS electrophoresis RNA were extracted from a nitrocellulose membrane which contains RNA-protein complex.
Following Buchbender A. et al, 2020, iCLIP libraries were constructed.

treatment_protocol: HEK293T were plated in 100 mm dishes at ~35% confluency a day before transfection. On the next day, the cells were transfected with the FLAG-PFN1 plasmid.

value: Human embryonic kidney

value: FLAG-PFN1 overexpressed


title: Mid SR 2-4mm 1

description:
Without adding the modified material, isolate tissue samples located 2-4 mm from the injury site after 5 days, including three replicate samples, and perform RNA sequencing.
Chronicscar2-42


title: mESCs, eIF2B-epsilon_WT_rep1


title: Acute 2

description:
Five days after spinal cord injury (SCI), isolate tissue samples located 0-2 mm from the injury site, including three replicate samples, and perform RNA sequencing.
Chronic2


title: Acute 3

description:
Five days after spinal cord injury (SCI), isolate tissue samples located 0-2 mm from the injury site, including three replicate samples, and perform RNA sequencing.
Chronic3


title: MPN038

description: TRANSCRIPTOMIC SINGLE CELL

value: prefibrotic


title: Acute 1

description:
Five days after spinal cord injury (SCI), isolate tissue samples located 0-2 mm from the injury site, including three replicate samples, and perform RNA sequencing.
Chronic1


title: mESCs, ATF4_uORF1mut_rep1


title: HEK293T, FLAG-PFN1-CLIP, S, biol rep2


title: Heart, Normal01

value: Normal


title: HEK293T, FLAG-PFN1-CLIP, B, biol rep2


title: Nano-patrol+NIR_rep3

city: Chongqing

first: Wen

last: Zeng

address: Gaotanyan street

department: Department of Cell Biology

institute: Army Medical University

data_processing:
reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Assembly: mRatBN7
Supplementary files format and content: total_count.csv file includes raw counts for each Sample

source_name: brain tissue

extract_protocol:
RNA was harvested using Trizol reagent kit, Total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop 2000; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities.  After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

treatment_protocol: Inject the corresponding drug (saline, rt-PA, Nano-patrol+NIR) 4.5 hours after modeling, and take brain tissue for testing three days later

value: brain tissue

value: Nano-patrol+NIR


title: Mid SR 1

description:
Without adding the modified material, isolate tissue samples located 0-2 mm from the injury site after 5 days, including three replicate samples, and perform RNA sequencing.
Chronicscar1

value: spinal cord


title: Heart, 1M008


title: Heart, Normal03


title: Mid SR 3

description:
Without adding the modified material, isolate tissue samples located 0-2 mm from the injury site after 5 days, including three replicate samples, and perform RNA sequencing.
Chronicscar4


title: Heart, Normal02


title: Mid SR mSC 3

description:
Five days after adding the modified scaffold material to the injury site, isolate tissue samples located 0-2 mm from the injury site, including three replicate samples, and perform RNA sequencing.
Mid4


title: K562, sRNA, rep2

city: Pullman

first: Sascha

last: Duttke

institute: Washington State University

description:
Library name: homo_sapiens_K562_sRNA-r2
SRR9916721 downsampled to one million reads

data_processing:
K562 raw reads from GSE135498 were downsampled to one million reads using SeqKit's sample and then trimmed of their adapter sequences using HOMER.
Trimmed reads were aligned to the hg38 genome using the STAR index provided in supplementary files. Alignment files were then used to create tag directories using HOMER makeTagDirectory and bedGraphs with makeUCSCfile. Peaks representing Transcription Start Regions (TSRs) for csRNA-seq and expressed small RNAs for sRNA-seq, were defined using HOMER’s findcsRNATSS.pl and a minimum read count of 7 per 10 million was required for regions to be considered.
Assembly: hg38
Supplementary files format and content: Files ending in -combo.tar.gz are compressed tag directories used to generate the provided bedGraphs and peak files (.tss.txt). The STAR index (hg38), built for aligning the reads, is also included as a gzipped tar file.

extract_protocol:
Refer to GSE135498
Refer to GSE135498


title: Mid SR 2

description:
Without adding the modified material, isolate tissue samples located 0-2 mm from the injury site after 5 days, including three replicate samples, and perform RNA sequencing.
Chronicscar3


title: mESCs, ATF4_WT_rep3


title: HEK293T, FLAG-PFN1-CLIP, B, biol rep1


title: mESCs, ATF4_uORF1mut_rep2


title: mESCs, ATF4_WT_rep2


title: HEK293T, FLAG-PFN1-CLIP, B, biol rep3


title: K562, sRNA, rep1

description:
Library name: homo_sapiens_K562_sRNA-r1
SRR9916720 downsampled to one million reads


title: Mid SR mSC 1

description:
Five days after adding the modified scaffold material to the injury site, isolate tissue samples located 0-2 mm from the injury site, including three replicate samples, and perform RNA sequencing.
Mid2


title: Nano-patrol+NIR_rep1


title: rt-PA_rep2

value: rt-PA


title: K562, csRNA, rep1

description:
Library name: homo_sapiens_K562_csRNA-r1
library strategy: csRNA-seq. SRR9916716, SRR9916717 downsampled to one million reads


title: Nano-patrol+NIR_rep2


title: scRNA-seq of human brain organoids: day30  in vitro [D30_ASD1_4]

city: Nanjing

first: Yuanlin

last: He

address: 101Longmian Avenue, Jiangning District

institute: Nanjing medical university

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain organoids

extract_protocol:
The organoids were dissociated by trypLE (Life technology) into single cells. The cell debris and other aggregates were removed by an additional low-speed centrifugation. About 12,000 cells were captured and the released RNA were barcoded through reverse transcription in individual GEMs.
scRNA-seq libraries were prepared with the Chromium Single Cell 3′ Library & Gel Bead Kit V3 (10x Genomics, 1000075) and then sequenced on an Illumina NovaSeq6000 with a sequencing depth of at least 50000 reads per cell with a paired-end 150 bp (PE150) reading strategy

value: brain organoids


title: mESCs, ATF4_WT_rep1


title: HEK293T, FLAG-PFN1-CLIP, S, biol rep1


title: Mid SR mSC 2

description:
Five days after adding the modified scaffold material to the injury site, isolate tissue samples located 0-2 mm from the injury site, including three replicate samples, and perform RNA sequencing.
Mid3


title: K562, csRNA, rep2

address: BLS 147, 100 Dairy Road

description:
Library name: homo_sapiens_K562_csRNA-r2
library strategy: csRNA-seq. SRR9916718, SRR9916719 downsampled to one million reads


title: scRNA-seq of human brain organoids: day30  in vitro [D30_NC1B_3]

description: 10x Genomics


title: rt-PA_rep3


title: IP49_692E_input

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

description: HPCs

data_processing:
Sequencing reads were aligned to the hg19 reference genome using bowtie2 following adapter trimming using Cutadapt. Duplicates and reads falling within blacklisted regions (ENCODE) were removed using Picards and bedtools, respectively. For visualization, bigwig files were created using the bamCoverage tool from deepTools, with the options of normalization using Bins Per Million, smoothLength 60, and binSize 20. Peak calling was performed using Homer. All figures were displayed using IGV.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: human iPSC derived CD45+CD34+ hematopoietic progenitor cells (HPCs)

extract_protocol:
ChIP-seq experiments were conducted using feeder-free iPSCs, CD45+CD34+ HPCs, and K562 cells. A Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) was used to eliminate dead cells from feeder-free iPSCs and HPCs. Cells were fixed in PBS with 1% formaldehyde (Thermo Fisher Scientific) with gentle mixing for 10 minutes at room temperature. The reaction was stopped by adding a glycine solution (10x; Cell Signaling Technology) and incubating for 5 minutes at room temperature, followed by two rounds of cold PBS washing. The cells were processed using the SimpleChIP Plus Sonication Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer’s protocol. The chromatin was sonicated with Covaris E220 (Covaris) using a microTUBE AFA Fiber Pre-Slit Crimp-Cap (130 µL). Immunoprecipitation of the cross-linked chromatin was performed using antibodies directed against histone H3 lysine 27 acetylation (H3K27ac) (Cell Signaling Technology).
ChIP-seq libraries were constructed using a ThruPLEX DNA-Seq Kit (Takara) according to the manufacturer’s protocol and sequenced using NextSeq 500 or NovaSeq 6000 (Illumina)

value: Control


title: Asxl1-MT2/T618I_1

city: Portland

first: Julia

last: Maxson

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

data_processing:
Reads were trimmed using Trimmomatic.
Adapter-trimmed reads were aligned to the mm10 genome using STAR.
Protein-coding genes were used to build the feature counts table, and differential expression analysis was performed using DESeq2 with default settings.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNeasy Plus Micro Kit (74004, Qiagen)
Libraries were prepared by BGI

treatment_protocol: Estrogen removal for 24h

value: Bone marrow immortelized


title: scRNA-seq of human brain organoids: day30  in vitro [D30_ASD2_3]

description: 10x Genomics


title: IP80_MDS25J1_IgG

description: iPSC

source_name: iPSC

value: iPSC

value: MDS


title: saline_rep3

value: saline