title: Liver_CVC_rep3

city: chengdu

first: chong

last: zhao

address: NO.1,4th Keyuan Road

institute: Lab of Gastroenterology and Hepatology

description:
V4
Prevention of CCl4-induced liver fibrosis

data_processing:
Raw data were firstly processed through custom perl and python scripts, and were then filtered by Q20, Q30 and GC contents.
The acquired clean data were mapped to the mouse reference genome (mm10) using HISAT2 (v2.2.1).
For each sample, read counts for each gene were obtained with featureCounts (v1.5.0-p3) and were standardized as fragments per kilobase million (FPKM).
Assembly: mm10
Supplementary files format and content: CVC_gene_fpkm.txt: Matrix table with mRNA FPKM for each sample.

source_name: Liver

extract_protocol:
Total RNA was extracted from liver samples using TRIzol reagent (Thermo Fisher Scientific, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Liver

value: Wild type

value: 6-week CCl4 and CVC i.p.


title: com124, EO, 6cm

status: Public on Aug 31 2023

type: SRA

city: Potsdam

first: Feng

last: Cheng

address: Meistersingerstr., 5

country: Germany

institute: University of Potsdam

library_source: transcriptomic

data_processing:
We trimmed the adapter sequences and low quality reads using a 4 bp sliding window with a mean quality threshold of 25, and a minimum read length of 36 bp by Trimmomatic v0.39
The quality-filtered reads were mapped to the C. compressirostris genome using RSEM for gene level-quantification estimation. The estimated counts were imported into R/Bioconductor with the tximport package, which produced count matrices from gene-level quantification by taking the effective gene length into account
Supplementary files format and content: Tab-delimited text file includes length, effective_length, expected_count, TPM and FPKM on gene level

molecule: total RNA

organism: Campylomormyrus compressirostris

source_name: electric organ

extract_protocol:
The RNA isolation was performed in all the electric organ samples using QIAGEN RNeasy Fibrous Tissue Mini Kit.
mRNA enrichment was performed by poly (A) capture from isolated RNA using NEXTflex Poly (A) Beads. Strand-specific transcriptomic libraries were built using NEXTflex Rapid Directional RNA-Seq Kit (Bioo Scientific, USA) based on the manufacturer’s instructions.

tag: tissue

value: electric organ


title: Liver_CVC_rep1

country: China

description:
V1
Prevention of CCl4-induced liver fibrosis

organism: Mus musculus

tag: genotype

tag: treatment


title: safb1/2 dko clone 13 + rescue FL safb1 plasmid

city: Chapel Hill

first: Joseph

middle: Mauro

last: Calabrese

state: North Carolina

address: 120 Mason Farm Road

department: Pharmacology

country: USA

institute: University of North Carolina at Chapel Hill

description: final_30998_ucsc_safb_peaks_20220512.txt

data_processing:
aligned to mm10 genome with STAR.
filtered for sq30
called peaks using MACS
used subread featureCounts to align reads to called peaks
normalized in R for signle of WT/DKO and rescue over eGFP
Assembly: mm10
Supplementary files format and content: wiggle tracks
Supplementary files format and content: excel file of processed data

source_name: FLAG, Sigma F1804

growth_protocol: RMCE embryonic Stem Cells were maintained in DMEM supplemented with 15% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: KAPA RNA Hyperprep Kit with RiboErase, 9uL of purified pulldown RNA + 1uL ERCC Spike in RNA

value: FLAG, Sigma F1804

tag: strain

value: CAST/B6 Male Rosa26-RMCE

tag: cell type

value: embryonic stem cells

value: WT

value: 3 Days Doxycycline induction


title: Liver_CVC_rep2

description:
V2
Prevention of CCl4-induced liver fibrosis


title: safb1/2 dko clone 13 + egfp plasmid, rescue negative control

value: safb1/2 dko


title: safb1/2 dko clone 13, safb1 IP, dko bio rep #2

description:
dko_saf_pos_scaled.wig
dko_saf_neg_scaled.wig
final_30998_ucsc_safb_peaks_20220512.txt

source_name: SAFB1, Bethyl #A300-812A

value: SAFB1, Bethyl #A300-812A


title: com123, EO, 6cm


title: Liver_CCl4_rep3

description:
S1862
CCl4-induced liver fibrosis

value: 6-week CCl4 i.p.


title: com104, EO, 6cm


title: Liver_CCl4_rep2

description:
C2
CCl4-induced liver fibrosis


title: safb1/2 dko clone 4, safb1 IP, dko bio rep #1


title: com121, EO, 6cm


title: CUTO17 PozR

city: London

first: Simon

last: Vyse

state: United Kingdom

address: 237 Fulham Rd

department: Molecular Pathology

country: United Kingdom

institute: Institute of Cancer Research

data_processing:
The quality of raw reads was first assessed using Novogene in-house script. Clean reads were obtained for further analysis after removing reads with low quality, adapter sequences and poly-Ns.
Reads were aligned to the Human genome (Homo sapiens, GRCh38) with HISAT2 (V2.0.5). The read numbers mapped to each gene was quantified with HTSeq (v0.6.1).
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) of each gene was calculated based on gene length and mapped read counts.
For differential gene expression analysis, read counts for each sequenced library were firstly adjusted by edgeR program through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGseq R package (v1.34.1). The P values were adjusted using the Benjamini and Hochberg methods. Adjusted pvalue of 0.005 and |log2(Fold Change)| of 1 were set as the threshold for significantly differential expression.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes mean normalised FPKM values for each sample

organism: Homo sapiens

source_name: CUTO17 PozR

growth_protocol: CUTO17 cells are cultured in RPMI medium supplemented with 10% foetal bovine serum and 100 units/ml pencillin and 100 mg/ml streptomycin. To generate CUTO17 PozR cells, CUTO17 cells were routinely cultured with 500 nM poziotinib in growth medium for 3 months.

extract_protocol:
Total RNA was extracted from CUTO17 and CUTO17 PozR cell lines using RNeasy Mini kit (QIAgen) according to manufacturer’s instructions.
A total amount of 400 ng RNA per sample was used as input. 250~300 bp insert cDNA library was prepared using NEB Next® Ultra™ RNA Library Prep Kit (NEB) following manufacturer’s protocol.

treatment_protocol: 1 million CUTO17 and CUTO17 PozR cells were seeded in T25 flasks for 24 h before harvesting.

value: Non-small cell lung adenocarcinoma

tag: cell line

value: EGFR N771_H773dupNPH

tag: phenotype

value: with acquired drug resistance to the EGFR inhibitor poziotinib


title: Liver_CCl4_rep1

description:
C1
CCl4-induced liver fibrosis


title: CUTO17

value: parental line, sensitive to poziotinib


title: com14, SM, adult

source_name: skeletal muscle

extract_protocol:
The RNA isolation was performed in all the electric organ and skeletal muscle samples using QIAGEN RNeasy Fibrous Tissue Mini Kit.
mRNA enrichment was performed by poly (A) capture from isolated RNA using NEXTflex Poly (A) Beads. Strand-specific transcriptomic libraries were built using NEXTflex Rapid Directional RNA-Seq Kit (Bioo Scientific, USA) based on the manufacturer’s instructions.

value: skeletal muscle


title: wt clone 20, safb1 IP,  wt bio rep #2

description:
wt_saf_pos_scaled.wig
wt_saf_neg_scaled.wig
final_30998_ucsc_safb_peaks_20220512.txt


title: Liver_Oil_rep2

description:
N2
Control

value: Liver

value: 6-week oil i.p.


title: Liver_Oil_rep3

description:
N4
Control

value: Wild type


title: com13, SM, adult


title: wt clone 20, IgG IP, negative control #2

description:
igg_pos_scaled.wig
igg_neg_scaled.wig
final_30998_ucsc_safb_peaks_20220512.txt

source_name: IgG, Invitrogen #026502

value: IgG, Invitrogen #026502


title: Liver_Oil_rep1

description:
N1
Control


title: com15, SM, adult


title: com12, SM, adult


title: parent wt, IgG IP, negative control #1


title: com103, EO, adult

value: electric organ


title: The musk gland -Single-Nucleus RNA-seq_4

city: Yangling District，Xianyang City

first: Zhanjun

last: Ren

state: Shaanxi Province

institute: Northwest A&F University

description:
Musk gland, musk secretory period, 3-year-old
nuclear RNA
snRNA-seq

library_source: transcriptomic single cell

data_processing:
The raw data were quality controlled using 10×Genomics analysis software Cell Ranger ARC (version 1.0).
For snRNA-seq data, Cell Ranger ARC first pruned the reads to remove the TSO sequence at the 5’ end and the polyA sequence at the 3’ end. Then, Spliced Transcripts Alignment to a Reference (STAR) alignment software was called to align Read2 to the reference genome (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA317652/). If the read was considered to be uniquely mapped to the transcriptome, it was used for UMI counting.
For snATAC-seq data, Cell Ranger ARC first pruned the reads to remove the adaptor sequence and primer sequence. Then, BWA-MEM was called to align the read pairs to the reference genome, and the insertion fragment was constructed according to the position of the read pairs to the reference genome. Reads with unique alignment and MAPQ>30 were determined using duplication analysis for subsequent analysis.
Next, Cell Ranger ARC was used to filter and correct UMIs, and the number of unique UMIs was calculated as the expression level of the gene in the cell. Cell Ranger ARC was used to identify peaks, and peaks with a distance of less than 500bp between two peaks were merged into one peak.
Barcode filtering combined snRNA-seq and snATAC-seq data to form the final identified effective cell population.
Assembly: Moschus berezovskii NCBI genome PRJNA317652
Supplementary files format and content: Matrix table with gene counts for every cell and every sample.
Supplementary files format and content: Matrix table with peak counts for every cell and every sample.

organism: Moschus berezovskii

source_name: the musk gland

extract_protocol:
After washing musk gland tissues with PBS buffer to remove blood and dirt, put it in a culture dish. About 90% of each musk gland was divided into smaller portions (1mm3 each) using scissors and directly transferred into clean RNase-free Eppendorf tubes, immediately frozen in liquid nitrogen, and stored at -80℃ until single nucleus suspension was prepared. In short, the musk gland tissues were lysed with 500μl of precooled lysis buffer in a Dounce homogenizer, and the tissues were pressed with a grinding rod to make the tissues become homogenate. Later, 700μl of nuclear cleaning buffer was added, and the tissue homogenate was filtered into a 50ml centrifuge tube with a 70μm cell strainer to obtain about 1ml of filtrate. Then, 1ml of 50% iodixanol was added to the filtrate. Next, 1ml of 33% iodixanol and 2ml of 30% iodixanol were prepared into gradient solution in a 15ml centrifuge tube, and then 2ml of iodixanol solution containing nuclei was added. After centrifugation for 20min, a white nuclear layer appeared at the interface between 33% iodixanol and 30% iodixanol solution. The nucleus layer was transferred to a new 15ml centrifuge tube with a wide orifice pipette tip, and the nucleus cleaning buffer was repeatedly added to resuspend the nuclei. Finally, the nucleus suspension was obtained by filtering with a 40μm filter. After centrifugation for 5min, the nucleus resuspension was added to resuspend nucleus precipitation, and trypan blue staining was used to count nuclei.
According to the manufacturer’s instructions, the single nucleus suspension and transposase mixture were mixed and incubated. After transposase entered the nucleus, it preferentially fragmented the DNA in the open region of chromatin, and added sequencing primer to the end of the DNA fragment. Based on the 10×Genomics single-nucleus capturing system, single-nucleus RNA sequencing+single-nucleus ATAC sequencing was performed on the collected nucleus suspension. It partitioned thousands of nuclei into nanoliter-scale Gel Bead-In-Emulsions (GEMs) with a common 10×Barcode. After GEMs were collected, the Gel Beads were dissolved to release the capture sequences, and the nuclei were lysed to release DNA fragments, pre-mRNA and mature mRNA, and labeled the ends of the fragments. There are two kinds of capture sequences on the Gel Beads, corresponding to snRNA-seq library and snATAC-seq library respectively. The sequencing libraries were prepared according to the manufacturer's instructions, using 7 cycles of cDNA/dsDNA preamplification, followed by an addition of 35μl of purified preamplification product for RNA library construction using 8 cycles, followed by an addition of 40μl of purified preamplification product for ATAC library construction using 8 cycles. P5, P7, sample index and sequencing primers were included during RNA library construction through fragmentation, end repair, A-tail addition, ligation and PCR to obtain the standard sequencing library. The final library containing P5 and P7 primers was used for Illumina bridge amplification. P7 and sample index were added during ATAC library construction through PCR to construct the standard sequencing library. In the same way, snATAC-seq library also contained P5 and P7 primers for Illumina bridge amplification. Finally, the constructed snRNA-seq library and snATAC-seq library were high-throughput sequencing using the double-ended sequencing mode of Illumina Novaseq 6000, and the double-ended 150bp and 50bp readings were respectively generated for downstream analysis.

value: the musk gland

tag: age

value: 3 years old

tag: gender

value: male

tag: condition

value: musk secretory period


title: Olive_oil

description:
O4
Control
One sample from murine liver tissue.

data_processing:
The Cell Ranger software pipeline provided by 10× Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell (barcodes.tsv: gene file; features.tsv: cell barcode file; matrix.mtx: gene-barcode counts).

molecule: polyA RNA

source_name: murine liver tissue

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, and index adaptor ligated and library amplification.
RNA libraries were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.


title: parent wt, safb IP, wt bio rep #1

value: CAST/B6 Male Rosa26-RMCE

value: embryonic stem cells

value: WT

value: 3 Days Doxycycline induction


title: The musk gland -Single-Nucleus RNA-seq_3

description:
Musk gland, musk secretory period, 11-month-old
nuclear RNA
snRNA-seq

value: 11 months old


title: com102, EO, adult


title: The musk gland -Single-Nucleus RNA-seq_2

data_processing:
10×Genomics Cell Ranger ARC software (version 1.0) was used to perform data quality statistics on the raw data.
STAR was used to align Read 2 with the reference genome.
BWA-MEM was used to align read pairs with the reference genome, and construct the insertion fragment according to the reads alignment to the genome position.
Cell Ranger ARC called SAMtools to determine the forward strand end position +4bp and the reverse strand end position -5bp of fragments as the action sites of Tn5 transposase.
For each base, a 401bp moving window was established, and a smooth signal window was generated using a ZINBA-like mixture model. We set a signal threshold based on an odds-ratio of 1/5 to determine whether a region is a peak signal.
Assembly: Moschus berezovskii NCBI genome PRJNA317652
Supplementary files format and content: Matrix table with gene counts for every cell in FMD2
Supplementary files format and content: Matrix table with peak counts for every cell in FMD2

source_name: The musk gland

extract_protocol:
The musk gland samples were quickly put on ice and cut into pieces of 1-mm3 with scissors. Then they were placed into clean RNase-free Eppendorf tubes, immediately frozen in liquid nitrogen, and stored at -80℃. The frozen tissues were transferred to a 1.5 ml microcentrifuge tube with tweezers, then 500 µl frozen 0.1×lysis buffer was added, and then homogenized 15 times with a particle pestle immediately, and incubated on ice for 5 min. The pipette was mixed with the tip of the large-bore pipette for 10 times and incubated on ice for 10 min. Added 500 µl of freezing wash buffer to the lysed cells. The suspension was passed through a 70 µm filter into a 2 ml test tube, centrifuged at 500 rcf at 4℃ for 5 min, and the supernatant was removed without destroying the nucleus precipitation. Then added 1ml of freezing wash buffer, mixed 5 times with a pipette, centrifuged at 500 rcf at 4℃ for 5 min, and the supernatant was removed without destroying the nucleus precipitation. Finally, the nucleus were resuspended in the cooled diluted nucleus buffer and counted by trypan blue staining.
For sNucRNA-seq library, pre-mRNA and mature mRNA were captured using poly (dT) sequence. Subsequently, the GEM structure was broken, all the cDNA were mixed, and PCR amplification was performed to obtain enough cDNA to construct the library. The cDNA were digested into fragments of about 200-300 bp, and then the standard sequencing library was obtained by PCR amplification after conventional next-generation sequencing library construction steps such as end repair, adding A-tailing, sequencing adapters P5, P7 and sample index. High-throughput sequencing was performed on the constructed library using the paired-end sequencing mode of Illumina sequencing platform. In Read 1, a 16 bp Barcode sequence and a 10 bp UMI sequence were included for cell determination and expression quantification; in Read 2, cDNA fragments were included for reference genome alignment to determine the genes corresponding to mRNA.   For sNucATAC-seq library, tagged DNA fragments were captured using spacer sequence. Subsequently, the GEM structure was broken, all the dsDNA were mixed, and PCR amplification was performed to obtain enough DNA to construct the library. Sequencing adapter P7 and sample index were added to DNA fragments by PCR amplification to construct a standard sequencing library. High-throughput sequencing was performed on the constructed library using the paired-end sequencing mode of Illumina sequencing platform. In Read 1, a 16 bp Barcode sequence was included. After excluding the i5 and i7 sample index of 10bp, the remaining sequence information of Read1 and Read2 was used to identify the information of the inserted fragment.

value: 6 years old


title: The musk gland -Single-Nucleus ATAC-Seq_3

description:
Musk gland, musk secretory period, 11-month-old
nuclear DNA
snATAC-seq

library_source: genomic single cell

molecule: genomic DNA


title: com101, EO, adult


title: CVC

description:
V
Treatment of CCl4-induced liver fibrosis
One sample from murine liver tissue.

value: 3-week CCl4 i.p., then 3-week CCl4 and CVC i.p.


title: safb1/2 dko clone 13, embryonic stem cell, dko rep #2

data_processing:
reads were aligned to genome using star/2.5.4b
filtered for reads that passed quality score q30
used subread featureCounts with gencode.vM25.basic.annotation.gtf to assign sequence reads to features
deseq2
Assembly: mm10
Supplementary files format and content: wig
Supplementary files format and content: excel file of processed data

source_name: Embryonic Stem Cells

extract_protocol:
50uL of sonicated cell lysate was prepared with Zymo Clean and Concentrator
KAPA RNA Hyperprep Kit with RiboErase, 100ng of input sequenced

value: Embryonic Stem Cells

value: SAFB1/2 DKO clone 13


title: safb1/2 dko clone 4, embryonic stem cell, dko rep #1


title: com100, EO, adult


title: The musk gland -Single-Nucleus ATAC-Seq_2

library_source: genomic


title: wt clone 44, embryonic stem cell, wt bio rep #3


title: The musk gland -Single-Nucleus ATAC-Seq_4

description:
Musk gland, musk secretory period, 3-year-old
nuclear DNA
snATAC-seq


title: wt clone 44, safb1 IP, wt bio rep #3

value: SAFB1, Bethyl #A300-812A


title: KrasG12D colonic organoid + TNF, rep5

city: Chuo-ku

first: Haruna

last: Takeda

state: Tokyo

address: 5-1-1 Tsukiji,

country: Japan

institute: National Cancer Center Japan

data_processing:
Reference sequences for mapping were prepared using rsem-prepare-reference of RSEM version 1.3.1 and STAR version 2.7.7a.
Reads were trimmed using trim_galore of Trim Galore version 0.6.7 and Cutadapt version 3.5.
The processed reads were mapped to the reference sequences and TPM (Transcripts Per Million) were calculated using rsem-calculate-expression of RSEM version 1.3.1 and STAR version 2.7.10a.
Gene and isoform TPM values were extracted from TPM columns of RSEM result files.
Assembly: GRCm39
Supplementary files format and content: tab-deliminted text file includes TPM values for each sample.

source_name: colon

extract_protocol:
Organoids embedded in Matrigel were dissolved in ISOGEN, and RNA was extracted following the protocol.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (Cat No. 7770)  following manufacturer's protocols.

treatment_protocol: wt colonic organoids an KrasG12D colonic organoids were treated with TNFa (40 ng/ml) for 3 wks.

value: colon

value: organoid

value: epithelial cells

value: TNFa


title: KrasG12D colonic organoid + TNF, rep4


title: KrasG12D colonic organoid + TNF, rep3


title: wt clone 20, embryonic stem cell, wt bio rep #2


title: CCl4

description:
C1
CCl4-induced liver fibrosis
One sample from murine liver tissue.

value: Liver

value: Wild type

value: 6-week CCl4 i.p.


title: com97, EO, adult

value: electric organ


title: parent wt, embryonic stem cell, wt bio rep #1

value: CAST/B6 Male Rosa26-RMCE

value: embryonic stem cells


title: The musk gland -Single-Nucleus ATAC-Seq

data_processing:
10×Genomics Cell Ranger ARC software (version 1.0) was used to perform data quality statistics on the raw data.
STAR was used to align Read 2 with the reference genome.
BWA-MEM was used to align read pairs with the reference genome, and construct the insertion fragment according to the reads alignment to the genome position.
Cell Ranger ARC called SAMtools to determine the forward strand end position +4bp and the reverse strand end position -5bp of fragments as the action sites of Tn5 transposase.
For each base, a 401bp moving window was established, and a smooth signal window was generated using a ZINBA-like mixture model. We set a signal threshold based on an odds-ratio of 1/5 to determine whether a region is a peak signal.
Genome_build: Moschus berezovskii NCBI genome PRJNA317652
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cluster
Supplementary_files_format_and_content: AllGene average expression text files
Supplementary_files_format_and_content: DePeak text files

extract_protocol:
The musk gland sample was quickly put on ice and cut into pieces of about 1-mm3 with scissors. Then it was placed into clean RNase-free Eppendorf tubes, immediately frozen in liquid nitrogen, and stored at -80℃. The frozen tissue was transferred to a 1.5 ml microcentrifuge tube with tweezers, then 500 µl frozen 0.1×lysis buffer was added, and then homogenized 15 times with a particle pestle immediately, and incubated on ice for 5 min. The pipette was mixed with the tip of the large-bore pipette for 10 times and incubated on ice for 10 min. Added 500 µl of freezing wash buffer to the lysed cells. The suspension was passed through a 70 µm filter into a 2 ml test tube, centrifuged at 500 rcf at 4℃ for 5 min, and the supernatant was removed without destroying the nucleus precipitation. Then added 1ml of freezing wash buffer, mixed 5 times with a pipette, centrifuged at 500 rcf at 4℃ for 5 min, and the supernatant was removed without destroying the nucleus precipitation. Finally, the nucleus were resuspended in the cooled diluted nucleus buffer and counted by trypan blue staining.
For sNucRNA-seq library, pre-mRNA and mature mRNA were captured using poly (dT) sequence. Subsequently, the GEM structure was broken, all the cDNA were mixed, and PCR amplification was performed to obtain enough cDNA to construct the library. The cDNA were digested into fragments of about 200-300 bp, and then the standard sequencing library was obtained by PCR amplification after conventional next-generation sequencing library construction steps such as end repair, adding A-tailing, sequencing adapters P5, P7 and sample index. High-throughput sequencing was performed on the constructed library using the paired-end sequencing mode of Illumina sequencing platform. In Read 1, a 16 bp Barcode sequence and a 10 bp UMI sequence were included for cell determination and expression quantification; in Read 2, cDNA fragments were included for reference genome alignment to determine the genes corresponding to mRNA.   For sNucATAC-seq library, tagged DNA fragments were captured using spacer sequence. Subsequently, the GEM structure was broken, all the dsDNA were mixed, and PCR amplification was performed to obtain enough DNA to construct the library. Sequencing adapter P7 and sample index were added to DNA fragments by PCR amplification to construct a standard sequencing library. High-throughput sequencing was performed on the constructed library using the paired-end sequencing mode of Illumina sequencing platform. In Read 1, a 16 bp Barcode sequence was included. After excluding the i5 and i7 sample index of 10bp, the remaining sequence information of Read1 and Read2 was used to identify the information of the inserted fragment.
sNucRNA-seq and sNucATAC-seq

value: the musk gland

value: 6 months old

value: male


title: KrasG12D colonic organoid + TNF, rep2


title: mouse ESC, total H3, safb 1/2 dko rep 2

description:
dnh3_b6_q30.bam
total_h3_b6_scaled.wig
h3_reps_fc_R

data_processing:
aligned to mm10 b6 and cast genomes using bowtie2
filtered for reads that passed q30 quality filter
peaks were called using macs2 callPeak
used bedtools intersect to find peak overlaps
used subread featureCounts to assign sequencing reads to called peaks
Assembly: mm10
Supplementary files format and content: wig
Supplementary files format and content: excel file of processed data
Supplementary files format and content: bed files of processed data

source_name: embryonic stem cells

extract_protocol:
Cells were fixed with 0.6% formaldehyde
NEB End Repair, purified with AMPure XP Beads, A-Tailing with Klenow Fragment, Ligated 1uM TruSeq Adapters

tag: antibody

value: H3, Proteintech #17168-1-AP

value: safb1/2 double ko, clone 13

value: 3 Days Doxycycline induction


title: KrasG12D colonic organoid + TNF, rep1


title: KrasG12D colonic organoid, rep5

value: cont


title: mouse ESC, total H3, safb 1/2 dko rep 1

description:
doh3_b6_q30.bam
total_h3_b6_scaled.wig
h3_reps_fc_R


title: The musk gland -Single-Nucleus RNA-seq


title: KrasG12D colonic organoid, rep2

value: colon


title: KrasG12D colonic organoid, rep3

value: organoid


title: KrasG12D colonic organoid, rep4

value: epithelial cells


title: mouse ESC, H3K27me3, safb 1/2 dko rep 3

description:
dko13Old_k27_b6_q30.bam
total_dko_k27_b6_scaled.wig
dko_k27_reps_fc_R
k27_promoters_reps_fc

value: H3K27me3, Abcam, ab6002


title: mouse ESC, H3K27me3, safb 1/2 dko rep 4

description:
dko13New_k27_b6_q30.bam
total_dko_k27_b6_scaled.wig
dko_k27_reps_fc_R
k27_promoters_reps_fc


title: mouse ESC, total H3, wt rep 2

description:
rnh3_b6_q30.bam
total_h3_b6_scaled.wig
h3_reps_fc_R

value: WT


title: KrasG12D colonic organoid, rep1


title: mouse ESC, H3K27me3, wt rep 5

description:
rmceNew_k27_b6_q30.bam
total_wt_k27_b6_scaled.wig
wt_k27_reps_fc_R
k27_promoters_reps_fc


title: K562 T1, biological rep2

type: RNA

city: Murcia

first: Lola

last: Rodríguez Ruiz

address: C/Campus universitario, 5

country: Spain

institute: University of Murcia

hyb_protocol: Following fragmentation and labeling, 2,3 ug of ss-cDNA were hybridized for 16 hr at 45C on Clariom S Array human. Cartridges were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the Affymetrix Scanner 3000.

data_processing:
Default analysis settings and global scaling as normalization method were analyzed with Robust Multiarray Analysis (RMA) using Affymetrix Expression Comand Console default analysis settings and global scaling as normalization method. Statistical analysis was done using Partek Genomic Suite (Partek Incorporated).
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: K562 hemin differentiation 24h

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT Plus Reagent Kit, Affymetrix).

growth_protocol: K562 cells (CRL-3343; American Type Culture Collection) were maintained in RPMI culture medium supplemented with 10% fetal calf serum (FCS), 2 mM Glutamine,   439 and 1% penicillin-streptomycin. 37°C and 5% CO2 with saturating humidity.

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

treatment_protocol: K562 were treated with 50 µM hemin (Sigma-Aldrich) for 24 h.

value: Human chronic myeloid leukemia

value: 24h hemin treatment


title: mouse ESC, total H3, wt rep 1

description:
roh3_b6_q30.bam
total_h3_b6_scaled.wig
h3_reps_fc_R


title: Cheek skin-acne, A6

city: Nanjing

first: meng

last: zhou

address: Jiangwangmiao Street

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description: Gene expression in acne patient

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses. When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes 1.5 and p-values  0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.

source_name: Cheek skin-acne

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from the lesions of patients with severe acne and healthy  control using a miRNeasy Mini kit (Qiagen) according to the manufacturer’s protocol. The RNA quantity and quality were measured by NanoDrop ND-1000 (NanoDrop products, Wilmington, DE, USA). The RNA integrity was assessed by electrophoresis on a denaturing agarose gel.

value: acne lesions

tag: tissue location

value: Cheek

tag: Sex

value: Male


title: wt colonic organoid +TNF, rep5

value: TNFa


title: K562 T1, biological rep1


title: K562 T0, biological rep1

source_name: K562 without differentiation

value: 0h hemin treatment


title: K562 T0, biological rep2


title: mouse ESC, H3K27me3, wt rep 4

description:
rmceOld_k27_b6_q30.bam
total_wt_k27_b6_scaled.wig
wt_k27_reps_fc_R
k27_promoters_reps_fc

value: CAST/B6 Male Rosa26-RMCE

value: embryonic stem cells


title: wt colonic organoid +TNF, rep4


title: iPast_201B7_rep3

city: Tokyo

first: Hirotaka

last: Watanabe

state: Other

address: 35 Shinanomachi, Shinjuku-ku

department: Physiology

institute: Keio University School of Medicine

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45°C on GeneChip Clariom S Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were normalized using Robust Multichip Analysis (RMA) algorithm.

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip WT PLUS Reagent Kit User Manual ,  Affymetrix).Biotinylated ss-cDNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

growth_protocol: Human astrocytes were derived from isogenic iPSC carrying APOE3 or APOE4, and the terminal differentiated iPSC-derived astrocytes were cultured in medium devoid of serum.

extract_protocol: Total RNA was extracted with an RNeasy Kit (Qiagen, Hilden, Germany), and RNA was quantified using a NanoDrop-2000c spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: iPSC-derived astrocytes


title: Cheek skin-acne, A4

description: Gene expression in acne patient


title: Forehead skin-acne, A5

description: Gene expression in acne patient

source_name: Forehead skin-acne

value: Forehead


title: iPast_201B7_rep2


title: Chin skin-normal, N6

description: Gene expression in healthy skin

source_name: Chin skin-nomal

value: healthy skin

value: Chin


title: iPast_#89-8_rep1


title: iPast_#87-8_rep1


title: iPast_#89-1_rep1


title: Cheek skin-acne, A3

description: Gene expression in acne patient


title: Cheek skin-acne, A2

description: Gene expression in acne patient


title: wt colonic organoid +TNF, rep3

value: colon

value: organoid


title: mouse ESC, H3K27me3, safb 1/2 dko rep 2

description:
dko13_k27_b6_q30.bam
total_dko_k27_b6_scaled.wig
dko_k27_reps_fc_R
k27_promoters_reps_fc

value: H3K27me3, Abcam, ab6002

value: safb1/2 double ko, clone 13

value: 3 Days Doxycycline induction


title: wt colonic organoid +TNF, rep2

value: epithelial cells

value: WT


title: mouse ESC, H3K27me3, safb 1/2 dko rep 1

description:
dko4_k27_b6_q30.bam
total_dko_k27_b6_scaled.wig
dko_k27_reps_fc_R
k27_promoters_reps_fc

value: safb1/2 double ko, clone 4


title: mouse ESC, H3K27me3, wt rep 3

description:
wt44_k27_b6_q30.bam
total_wt_k27_b6_scaled.wig
wt_k27_reps_fc_R
k27_promoters_reps_fc


title: Whole intestine epithelial cells, KAT2A/KAT2B DKO replicate 3

city: Piscataway

first: Michael

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, The State University of New Jersey

data_processing:
Alignment: Reads from fastq files were aligned using Kallisto (v0.46.1) to the mm9 genome with 100 bootstraps.
Read normalization: Transcript abundance HDF5 binary files were imported with tximport. FPKM normalization calculation and differential expression analysis were conducted with DESeq2 (v1.32).
Bigwig coverage: Bam files were generated by TopHat (v2.1.1), which were then used by bamCoverage from deepTools (v3.5.1) to produce bigwig files.
Assembly: mm9
Supplementary files format and content: bigwig, FPKM, and DESeq2 output files for each sample
Supplementary files format and content: FPKM table and differential enrichment analysis were generated as a TXT file by DESeq2.

source_name: whole intestinal epithelial cells

extract_protocol: Primary whole epithelial cells were isolated from the proximal half of the small intestine of adult mice (5 weeks old) after incubation in EDTA for 40 minutes total at 4 C in tubes coated with 0.1% BSA in PBS. RNA extraction was performed using Trizol and chloroform-based methodology. Approximately 10-15 ug of RNA was submitted to BGI for library prep and sequencing.

treatment_protocol: KAT2A/KAT2B DKO was induced with 100 mg/kg tamoxifen in 10% ethanol and 90% corn oil via intraperitoneal injections for 3 days daily. Controls received vehicle injections of 10% ethanol and 90% corn oil without tamoxifen.

value: 5 weeks

value: Female

value: whole intestinal epithelial cells

value: KAT2A/KAT2B DKO

value: Tamoxifen injections IP


title: Whole intestine epithelial cells, KAT2A/KAT2B DKO replicate 4


title: mouse ESC, H3K27me3, wt rep 2

description:
wt20_k27_b6_q30.bam
total_wt_k27_b6_scaled.wig
wt_k27_reps_fc_R
k27_promoters_reps_fc

value: CAST/B6 Male Rosa26-RMCE

value: embryonic stem cells


title: wt colonic organoid, rep5

value: cont


title: Whole intestine epithelial cells, KAT2A/KAT2B DKO replicate 2

value: Male


title: Whole intestine epithelial cells, KAT2A/KAT2B DKO replicate 1


title: mouse ESC, H3K27me3, wt rep 1

description:
rmce_k27_b6_q30.bam
total_wt_k27_b6_scaled.wig
wt_k27_reps_fc_R
k27_promoters_reps_fc


title: Whole intestine epithelial cells, control replicate 4

value: Control

value: Vehicle injections IP


title: iPast_#87-5_rep1

value: iPSC-derived astrocytes


title: wt colonic organoid, rep2

value: colon

value: organoid


title: iPast_201B7_rep1


title: Living_body_peripheral_blood_CON_D6 [miRNA]

city: Shanghai

first: Xiaoqiang

last: Chai

state: Shanghai

address: No.130 Dongan Road

department: Institutes of Biomedical Sciences

institute: Fudan University

description:
Gene expression in whole blood from healthy controls
CON_D6

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
With a total of 37 samples, the raw data from all of the 37 samples was handled within the R statistical computing framework version 3.0.2 (http://www.R-project.org) to obtain the processed data. As for miRNA raw data, R package AgiMicroRna providing useful functionality for the following processing, quality assessment for Agilent microRNA array data was employed used. In AgiMicroRna, the processed microRNA signal can be obtained using total Gene Signal (TGS) computed by the AFE and RMA algorithm. There were altogether 499 probes with corresponding miRNA in subsequent analysis after the normalization. As well as for mRNA, R package Agi4x44PreProcess was used for background correction, normalization and filtering probes according to different quality flags during the microarray standardization in our study. Ultimately, total 28155 probes mapping 14507 genes denoted by ENTREZ ID were obtained between arrays.

source_name: peripheral blood, CON, D6

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

treatment_protocol: Morning fasting venous blood samples from donors were collected for RNA extraction. Peripheral blood mononuclear cells (PBMCs) were isolated from the blood by Ficoll gradient separation. In order to achieve lysis and inactivate endogenous, RNAses Cells were mixed with mirVana RNA lysis buffer (Ambion, Austin, Texas, USA). Then the lysates were frozen at -80°C until RNA purification.

tag: individual

value: healthy control

tag: disease state

value: control

value: whole blood

value: female


title: Cheek skin-normal, N5

description: Gene expression in healthy skin

source_name: Cheek skin,nomal

value: healthy skin

value: Cheek


title: Whole intestine epithelial cells, control replicate 3

value: 5 weeks

value: Female

value: whole intestinal epithelial cells


title: Cheek skin-normal, N3

description: Gene expression in healthy skin


title: wt colonic organoid +TNF, rep1

value: epithelial cells

value: WT

value: TNFa


title: Cheek skin-normal, N1

description: Gene expression in healthy skin

value: Male


title: wt colonic organoid, rep1

value: cont


title: Forehead skin-normal, N2

description: Gene expression in healthy skin

source_name: Forehead skin,nomal

value: Forehead


title: Forehead skin-acne, A1

description: Gene expression in acne patient

value: acne lesions


title: Whole intestine epithelial cells, control replicate 2

value: Control

value: Vehicle injections IP


title: Living_body_peripheral_blood_CON_D4 [miRNA]

description:
Gene expression in whole blood from healthy controls
CON_D4

source_name: peripheral blood, CON, D4

value: healthy control

value: control

value: male


title: Cheek skin-normal, N4

description: Gene expression in healthy skin

value: healthy skin


title: wt DSS colonic organoid, rep3

treatment_protocol: 2.5% Dextran Sodium Sulfate (DSS) dissolved in drinking water were administrated to mice for 5 days at the age of 10 weeks, then after an interval of 2 weeks, another 2.5% DSS were administrated for 5 days.

value: colon

value: organoid

value: wt

value: DSS (5 days x2)


title: Living_body_peripheral_blood_CON_D3 [miRNA]

description:
Gene expression in whole blood from healthy controls
CON_D3

source_name: peripheral blood, CON, D3

value: whole blood

value: female


title: Living_body_peripheral_blood_CON_D2 [miRNA]

description:
Gene expression in whole blood from healthy controls
CON_D2

source_name: peripheral blood, CON, D2


title: wt colonic organoid, rep3

value: epithelial cells

value: WT


title: wt DSS colonic organoid, rep1


title: DRG, Infant, SNI, rep3

first: Atsushi

last: Sakai

address: 1-1-5 Sendagi, Bunkyo-ku

institute: Nippon Medical School

data_processing:
Raw read data were filtered using Cutadapt and the filtered read data were aligned to the rat genome (Rnor_6.0) using Hisat2 with default parameters.
Gene differential analysis was performed using DESeq2.
Assembly: rn6
Supplementary files format and content: comma-delimited csv file includes FPKM, FC, and padj values for each condition

organism: Rattus norvegicus

source_name: DRG

extract_protocol:
Total RNA was extracted using RNAiso Plus following the manufacturer’s instruction (Takara Bio, Shiga, Japan).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA kit following manufacturer's protocols.

value: DRG

value: Sprague Dawley

value: SNI surgery

tag: time

value: Day 14


title: Living_body_peripheral_blood_CON_D7 [miRNA]

description:
Gene expression in whole blood from healthy controls
CON_D7

source_name: peripheral blood, CON, D7


title: DRG, Infant, SNI, rep4


title: wt control colonic organoid, rep3

value: cont


title: Living_body_peripheral_blood_CON_D5 [miRNA]

description:
Gene expression in whole blood from healthy controls
CON_D5

source_name: peripheral blood, CON, D5

value: healthy control


title: DRG, Infant, SNI, rep2


title: DRG, Infant, SNI, rep1


title: wt control colonic organoid, rep2

source_name: colon


title: Whole intestine epithelial cells, control replicate 1

value: 5 weeks

value: Male

value: whole intestinal epithelial cells

value: Control

value: Vehicle injections IP


title: DRG, Infant, sham, rep4

value: male

value: sham surgery


title: wt DSS colonic organoid, rep2

value: colon

value: organoid

value: wt

value: DSS (5 days x2)


title: DRG, Infant, sham, rep3

value: DRG


title: Living_body_peripheral_blood_LVL_B11 [miRNA]

description:
Gene expression in whole blood from patient B11 with low viral load
LVL_B11

source_name: peripheral blood, LVL, B11

value: patient B11

value: low viral load

value: whole blood

value: female


title: EC.WT.2

city: Singapore

first: Jessica

middle: R

last: Gaunt

address: 11 Mandalay Road

department: LKC Medicine

country: Singapore

institute: Nanyang Technological University

description:
nuclear RNA
10x Genomics

data_processing:
SnRNAseq data was aligned to the mm10 pre-mRNA reference genome using CellRanger (v3.1.0) with an expected cells value of 10,000. Downstream processing was performed using Seurat (v3.2). First, all samples were processed individually. Barcodes with >5% mitochondrial RNA were removed. UMIs were normalised by library size, multiplied by a scale factor of 10,000 and log-transformed. Highly variable genes (N=5000) were identified using the variance-stabilising transformation (VST) method. A shared nearest neighbour graph was constructed and clustering was performed using the Louvain algorithm, followed by uniform manifold approximation and projection (UMAP). We used N=45 principal components (PCs) for DCN and N=60 PCs for EC with clustering resolution 0.7. Clusters of droplets with very low counts and numbers of features as well as high % of mitochondrial RNA, representing low quality cells and/or ambient RNA, were removed. DoubletFinder (v2.0.3) was used to label droplets that may contain multiplets (parameters: 45 PCs, sct=false, GT=false, pN=0.25).
SCTransform (v2) was applied to each sample, followed by SCT integraton (50 PCs, 3000 features). Dimensionality reduction was performed on the integrated dataset as described above at low (res.=0.3, PCs=30), medium (res.=0.7, PCs=50) and high (res.=1.0, PCs=70) resolutions and cluster labels were determined by marker gene expression. Individual cell-types (astrocytes, neurons, microglia, oligodendrocytes, OPCs and vascular cells) were then analysed using Monocle3 to classify cell subtypes. During these steps, further filtering was performed using marker genes and DoubletFinder to identify clusters of multiplets and low quality cells. Final cell-type labels were adjusted according to results of subcluster analyses.
Assembly: mm10 pre-mRNA
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Entorhinal cortex

extract_protocol:
Mice were anaesthetized with isoflurane before decapitation. Brains were dissected on ice and rested in pre-bubbled slurry cutting solution [250 mM sucrose, 26 mM NaHCO3, 10 mM [D+] glucose, 3 mM myo-inositol, 2.5 mM KCl, 2 mM sodium pyruvate, 1.25 mM NaH2PO4·2H2O, 0.5 mM ascorbic acid, 1 mM kynurenic acid, 0.1 mM CaCl2 and 4 mM MgCl2] for 1 min. A downward cut across the midbrain was made to separate the cerebellum from the frontal cortex. To dissect DCN, the cerebellum was first sectioned at 300µm in cold cutting solution using a vibratome [Leica VT-1200]. Approximately 4-5 sections were used to microdissect the DCN in chilled pre-bubbled artificial cerebrospinal fluid [ACSF: 10 mM [D+] glucose, 126 mM NaCl, 24 mM NaHCO3, 1 mM NaH2PO4·2H2O, 2.5mM KCl, 0.4mM ascorbic acid, 2 mM CaCl2 and 2 mM MgCl2] under a light microscope. For EC dissection, a longitudinal cut was made to separate the two hemispheres. With the medial surface of the hemispheres facing up, the thalamic and hypothalamic region were scooped outpeeled back and removed, exposing the hippocampal formation. The hippocampus region was further rolled out, with the hippocampus remaining attached to the EC via the subiculum. The entorhinal cortex was then dissected by making four cuts: one vertical cut was made parallel to the join between the hpc and EC, roughly one hippocampus width away; then horizontal cuts were made at the top and bottom of the join, and finally a vertical cut was made to sever the EC and hippocampus. Dissected tissues were transferred to chilled homogenisation buffer [0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine, pH 7.8] in a Dounce homogeniser and homogenised with 10 strokes of the pestle. To lyse the samples, NP-40 detergent was added to obtain a final concentration of 0.3% and samples were dounced with 5 additional strokes. Lysates were filtered using 40um FlowMi tip strainers to remove debris and clumped nuclei. Each 2ml sample was gently mixed with 4.6ml 1.8M sucrose cushion buffer [1.8M sucrose, 10mM Tris-HCl, 1.5 mM MgCl2, pH 6.9] and layered over a 3ml sucrose cushion. Samples were spun in an ultracentrifuge at 30,000 x g for 45 mins at 4°C. The supernatant was then removed and pellets were resuspended in 90ul nuclei resuspension buffer [10mM Tris-HCl, 0.25 M Sucrose, 25 mM KCl, 1.5 mM MgCl2, 1.5 mM CaCl2, pH 6.9]. Nuclei were inspected and counted under a microscope using a hemocytometer and Trypan blue dye.
cDNA libraries were generated according to manufacturer’s protocol (10x Genomics, Inc.). In brief, approximately 10, 000 nuclei per sample were processed using the Chromiium Single Cell 3’ v3 Gene Expression kit. The libraries were subsequently sequenced using NovaSeq6000 (NovogeneAIT Genomics).

value: Entorhinal cortex

value: Wild-type

value: 7 months


title: DRG, Infant, sham, rep1

value: Sprague Dawley

value: Day 14


title: Living_body_peripheral_blood_LVL_B10 [miRNA]

description:
Gene expression in whole blood from patient B10 with low viral load
LVL_B10

source_name: peripheral blood, LVL, B10

value: patient B10


title: Living_body_peripheral_blood_LVL_B13 [miRNA]

description:
Gene expression in whole blood from patient B13 with low viral load
LVL_B13

source_name: peripheral blood, LVL, B13

value: patient B13


title: Living_body_peripheral_blood_CON_D1 [miRNA]

description:
Gene expression in whole blood from healthy controls
CON_D1

source_name: peripheral blood, CON, D1

value: healthy control

value: control

value: male


title: Living_body_peripheral_blood_LVL_B9 [miRNA]

description:
Gene expression in whole blood from patient B9 with low viral load
LVL_B9

source_name: peripheral blood, LVL, B9

value: patient B9


title: wt control colonic organoid, rep1

value: colon

value: organoid

value: epithelial cells

value: wt

value: cont


title: Living_body_peripheral_blood_LVL_B12 [miRNA]

description:
Gene expression in whole blood from patient B12 with low viral load
LVL_B12

source_name: peripheral blood, LVL, B12

value: patient B12

value: low viral load

value: whole blood


title: DRG, Adult, SNI, rep3

value: DRG

value: SNI surgery


title: DRG, Adult, SNI, rep4

value: Sprague Dawley

value: Day 14


title: Living_body_peripheral_blood_LVL_B14 [miRNA]

description:
Gene expression in whole blood from patient B14 with low viral load
LVL_B14

source_name: peripheral blood, LVL, B14

value: patient B14

value: female


title: EC.APP.1

description:
nuclear RNA
10x Genomics

value: Entorhinal cortex

value: Male

value: AppNL-G-F/NL-G-F

value: 7 months


title: Living_body_peripheral_blood_LVL_B6 [miRNA]

description:
Gene expression in whole blood from patient B6 with low viral load
LVL_B6

source_name: peripheral blood, LVL, B6

value: patient B6


title: EC.WT.1

description:
nuclear RNA
10x Genomics

value: Wild-type


title: DRG, Adult, SNI, rep2

value: male


title: Living_body_peripheral_blood_LVL_B7 [miRNA]

description:
Gene expression in whole blood from patient B7 with low viral load
LVL_B7

source_name: peripheral blood, LVL, B7

value: patient B7


title: Living_body_peripheral_blood_LVL_B8 [miRNA]

description:
Gene expression in whole blood from patient B8 with low viral load
LVL_B8

source_name: peripheral blood, LVL, B8

value: patient B8


title: EC.APP.2

description:
nuclear RNA
10x Genomics


title: DRG, Adult, SNI, rep1


title: DRG, Infant, sham, rep2

value: sham surgery


title: DCN.WT.1

description:
nuclear RNA
10x Genomics

source_name: Deep cerebellar nuclei

value: Deep cerebellar nuclei


title: DRG, Adult, sham, rep4

value: DRG


title: Living_body_peripheral_blood_LVL_B4 [miRNA]

description:
Gene expression in whole blood from patient B4 with low viral load
LVL_B4

source_name: peripheral blood, LVL, B4

value: patient B4

value: low viral load

value: whole blood


title: DCN.APP.2

description:
nuclear RNA
10x Genomics


title: Living_body_peripheral_blood_LVL_B5 [miRNA]

description:
Gene expression in whole blood from patient B5 with low viral load
LVL_B5

source_name: peripheral blood, LVL, B5

value: patient B5


title: DRG, Adult, sham, rep3

source_name: DRG

value: Sprague Dawley

value: Day 14


title: DCN.WT.2

description:
nuclear RNA
10x Genomics

value: Male


title: Living_body_peripheral_blood_LVL_B3 [miRNA]

description:
Gene expression in whole blood from patient B3 with low viral load
LVL_B3

source_name: peripheral blood, LVL, B3

value: patient B3

value: female


title: DRG, Adult, sham, rep1


title: S-shNPAS4

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

description:
10X single-nuclei RNA-seq
10x Genomics
Protocol 1

data_processing:
Raw sequencing data were processed with Cell Ranger (v6.1.2). Cellranger mkfastq command was used to demultiplex the different samples and cellranger count command was used to generate gene – cell expression matrices. Ambient RNA contamination was inferred and removed using CellBender (v0.232) with standard parameters. Mouse genome mm10 was used for the alignment and genecode vM25 was used for gene annotation and coordinates. We used the R package Seurat (v4.1.0) and customized R scripts for data analyses Data from different samples (SalineCPP, CocaineCPP, SalineNPAS4, CocaineNPAS4) were merged into a unique single cell object. Nuclei with > 250 genes, < 10000 UMIs, and < 5% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) for a resultant expression matrix with 21,516 genes and 52,743 cells. The SCTransform workflow was used for count normalization and data integration using 30 principal components and resolution of 0.5 for Louvain clustering and UMAP. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. After removing 4 clusters showing high expression of glutamatergic neuronal markers and subsequent re-clustering, we identified 20 final distinct clusters. Cell annotation was performed using two different approaches: 1) markers enrichment using a Nucleus Accumbens independent data by Fisher’s exact test and 2) a predictive machine learning model based on a Nucleus Accumbens atlas reference data using the R package scPred. Cell annotation then was manually curated to reflect both analyses. To identify differentially expressed genes between conditions (SalCPP vs CocCPP, CocCPP vs CocNPAS4) in each defined cell types, the R package LIBRA with option MAST was used to perform zero-inflated regression analysis. Genes were defined as significantly differentially expressed at Benjamini–Hochberg correction FDR < 0.05 and abs(log2(Fold Change)) > 0.2. We further confirmed these results using a Wilcoxon’s rank sum test.
Assembly: Mus musculus mm10
Supplementary files format and content: HDF5 Feature-Barcode Matrix

molecule: nuclear RNA

source_name: nucleus accumbens

extract_protocol:
Wild-type C57BL/6J mice received bilateral NAc infusion of AAV-NPAS4 shRNA-GFP or scrambled-GFP control and underwent conditioned place preference for cocaine or saline (total of 4 groups with 4 animals/group). Mice were then rapidly decapitated at 12 weeks of age, and the brains extracted into 4˚C Hibernate A medium with the GlutaMAX, B27 supplement, and NxGen RNase inhibitor (0.2U/uL; Lucigen). NAc tissues were dissected rapidly, flash frozen, and stored at -80˚C until the day of dissociation. These specific steps were modified from Savell et al., 2020 by Hughes, B.W. The following day (when all samples were prepped), frozen tissues were slowly thawed on ice, then chopped with a razor blade ~75-100 times in 2 orthogonal directions. Chopped NAc tissue was lysed with hypotonic lysis buffer (10mM Tris-HCL, 10mM NaCl, 3mM MgCl2, 0.1% (v/v) IGEPAL), then supplemented Hibernate-A medium was added, tissue triturated 15-20 times/sample using 3 glass capillaries with decreasing diameters, then 40-micron filtered. Nuclei were isolated by 500xg centrifugation, washed with 1X PBS + 1% BSA and 0.2U/uL RNase inhibitor. Nuclei were then incubated in 7AAD and underwent FACS to remove clumps and whole cells. Samples were then counted and diluted to 1500 nuclei/ul before immediate processing using the 10x Genomics Single-Cell Protocol by the MUSC Translation Science Lab. Libraries were constructed using the Chromium Single Cell 3’ Library Construction Kit (10x Genomics, v3.1), sequenced at Vanderbilt’s Next Gen Sequencing Core (Illumina NovaSeq 6000).
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v3.1 according to the manufacturer’s protocol. Libraries and sequencing were performed at the Translational Sequencing Core at MUSC.

value: nucleus accumbens

tag: knockdown

value: saline

value: 12 weeks old


title: C-shScram

tag: tissue

value: scScram

value: cocaine


title: C-shNPAS4


title: Living_body_peripheral_blood_LVL_B2 [miRNA]

description:
Gene expression in whole blood from patient B2 with low viral load
LVL_B2

source_name: peripheral blood, LVL, B2

value: patient B2

value: male


title: Living_body_peripheral_blood_LVL_B1 [miRNA]

description:
Gene expression in whole blood from patient B1 with low viral load
LVL_B1

source_name: peripheral blood, LVL, B1

value: patient B1


title: S-shScram


title: CHA52, RBCs, Day33, Fe treatment and untreated

city: Cheongju-si

first: JONG HEE

last: LEE

state: Chungbuk

address: 30, Yeongudanji-ro, Ochang-eup, Cheongwon-gu

department: National Primate Research Center

country: South Korea

institute: Korea Research Institute of Bioscience & Biotechnology

data_processing:
BD Rhapsody WTA Analysis Pipeline Version 1.10.1 was utilized for annotating reads and molecules, determining putative cells, identifying the sample of origin (demultiplexing), and generating expression matrices.
Assembly: GRCh38
Supplementary files format and content: Comma-Separated Values expression data tables

growth_protocol: CHA52 were maintained with mTeSR1. To induce RBCs differentiation, Apel 2 medium containing several cytokines was used

extract_protocol:
Single cell capture was performed using BD Rhapsody Express instrument according to the manufacturer's instrument. cDNA synthesis and Exonuclease I treatment were performed on the mRNA capture beads using BD Rhapsody cDNA kit
scRNA-seq libraries were constructed using BD Rhapsody WTA amplification kit

treatment_protocol: Isolated CD34+ cells from PSC-derived HE was culture in the Apel 2 medifum containing several cytokines with 400 ug/ml of ferric ion

value: embryonic stem cell

tag: genotype

value: WT

value: Red blood cell differentiation


title: NCM460 cells, capTEs, rep3

city: Chengdu

first: keying

last: Lu

state: Sichuan

address: Wuhou

department: State Key Laboratory of Biotherapy

institute: Sichuan university

data_processing:
The electrical data were base-called and processed into FASTQ files using MinKNOW v.20.10.6 integrated with Guppy v4.2.3. Sequencing adapters and barcodes were trimmed from fastq data using Porechop v0.2.4 with the default parameters. The trimmed reads were filtered using NanoFilt v2.8.0 with the commands --quality 7 --length 300. Next, reads were aligned to the reference genome and the reference transcriptome (GRCh38) using minimap2 v2.17 with the parameter -ax splice and -ax map-ont respectively. The resulting SAM file was converted to a BAM file and then sorted and indexed using SAMtools v1.11. The coordinates of TEs were identified by RepeatMasker v4.1.2. The TE and gene expression was quantified using FeatureCounts v2.0.3 with the parameter -f -O --minOverlap 20 -M --fraction -s 0 -L.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each Sample

growth_protocol: All cell lines were grown in 6 cm dishes at 37 °C in a 5% CO2 incubator. The K562, MDA-MB-231 and HCT 116 cell lines were cultured in high-glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin antibiotics (pen-strep). NCM460 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% pen-strep. MCF-10A cells were cultured in DMEM/F12 medium (Ek-Bioscience) containing 5% horse serum, 1% pen-strep, 20 ng/ml EGF, insulin, hydrocortisone and cholera toxin.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions. The RNA concentration was determined using Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Q32852), and the purity and integrity were assessed by a NanoDrop One and Qubit, respectively. The full-length cDNA library was prepared according to the SMART protocol.
To inactivate the 3’-hydroxyl terminus of DNA molecules, a single ddGMP was added to the ends of 2 μg of amplified cDNA in a 50 μL mixture containing 0.1 mM ddGTP (Roche, 03732738001), 0.25 mM CoCl2 (NEB, M0315), 20 U of Terminal Transferase (NEB, M0315) and 1× TdT buffer (NEB, M0315). The reaction was performed at 37 °C for 2 h and stopped by heating for 20 min at 75 °C. After that, the DNA sample was purified using AMPure XP beads and eluted in 24 μL of nuclease-free water. Three microliters of Quick CIP enzyme (NEB, M0525) and 3 μL of 10× Cutsmart buffer (NEB, B7204) were added to the eluate, and the mixture was incubated at 37 °C for 30 min for dephosphorylation. After inactivation of the phosphatase at 80 °C for 5 min, the DNA molecules were cut with 10 pmol of Cas9-gRNA complex (2.5 pmol each) at 37 °C for 15 min. For the removal of Cas9 from cleavage sites, the sample was digested with 1.5 μL protease (Qiagen, 19155) for 10 min at 56 °C, followed by 70 °C for 15 min to inactivate protease. dA-tailing was carried out at 72 °C for 5 min with 1 μL of 10 mM dATP (NEB, N0440) and 5 U of Taq DNA polymerase (Vazyme, P101-d1-AC) added. The product was used directly for adapter ligation by SQK-LSK110 (ONT) or barcoding by NBD114 (ONT).

value: normal colon epithelial cell

tag: molecule subtype

value: TE-containing RNA


title: Living_body_peripheral_blood_HVL_A16 [miRNA]

description:
Gene expression in whole blood from patient A16 with high viral load
HVL_A16

source_name: peripheral blood, HVL, A16

value: patient A16

value: high viral load

value: whole blood


title: DCN.APP.1

description:
nuclear RNA
10x Genomics

value: Deep cerebellar nuclei

tag: strain

value: Male

value: AppNL-G-F/NL-G-F

value: 7 months


title: s211217H3

city: CHANG SHA

first: YONG

last: ZHONG

address: XIANGYA ROAD

institute: XIANGYA HOSPITAL

data_processing:
Basecalls performed using bcl2fastq V2.19.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Star 2.5.3a software was used for comparative analysis between sequencing data of single cell RNA and reference genome of Ensembl database
Quantify gene expression using read2 by featureCounts1.6.2 software
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: kidney

extract_protocol:
A moderate amount of renal tissue was taken from the selected patients during renal puncture, and GEXSCOPE ® Single Cell RNA Library Kit Tissue was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: hypertensive nephropathy

value: proteinuria not conform to nephrotic syndrome


title: NCM460 cells, capTEs, rep2

tag: cell line

tag: cell type


title: ShamM20

city: Ottawa

first: Sarah

last: McLaughlin

state: ON

address: 40 Ruskin Street

country: Canada

institute: University of Ottawa Heart Institute

description: NS.1209.001.NEBNext_dual_i7_H4---NEBNext_dual_i5_H4.ShamM20.bam

data_processing:
Base calling completed by Illumina software.
Differential expression analysis was completed by C3G, Canadian Centre for Computational Genomics. The MUGIC pipeline from their Genpipes platform was used.
RNAseq reads were trimmed and adaptors were removed using Trimmomatic and trimmed reads were aligned to the reference genome (Mus musculus assembly GRCm38/mm10) using STAR.
Aligned reads were mapped to transcripts with their abundance measured by fragments per kilobase of exon per million fragments mapped (FPKM) using the Cufflinks program.
Differential expression analysis was completed using edgeR. Briefly, normalization and dispersion factors were calculated, then a generalized linear model (GLM) was fitted for all treatment groups and comparisons were made between PBS vs. rHCI, rHCI vs. sham and PBS vs. sham using the GLM likelihood ratio tests (LRT) function. A Benjamini Hochberg false discovery rate was used to determine significance of differentially expressed genes per treatment group.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix file of read counts for all genes for every sample

source_name: Left ventricle

extract_protocol:
Two days after treatment injection, hearts were harvested, perfused with PBS, and the LV tissue was snap frozen with liquid nitrogen. Frozen LV tissue was ground into a fine powder in liquid nitrogen using a mortar and pestle. From 30 mg of ground LV tissue, RNA was isolated using the RNeasy® mini kit (Qiagen 74004) according to the manufacturer’s instructions.
Next generation RNA sequencing was completed by Genome Quebec. An mRNAseq stranded library was prepared with NEBNext dual adaptor sequences (New England Biolabs) from 500 ng of sample RNA. Libraries were prepared for sequencing using standard Illumina protocols.

value: Left ventricle

tag: model

value: Sham operation

tag: endpoint

value: Age matched timepoint 10 weeks old

tag: treatment

value: No treatment


title: Living_body_peripheral_blood_HVL_A15 [miRNA]

description:
Gene expression in whole blood from patient A15 with high viral load
HVL_A15

source_name: peripheral blood, HVL, A15

value: patient A15

tag: gender

value: female

tag: age


title: s211110H2-2

tag: condition


title: Living_body_peripheral_blood_HVL_A14 [miRNA]

description:
Gene expression in whole blood from patient A14 with high viral load
HVL_A14

source_name: peripheral blood, HVL, A14

tag: individual

value: patient A14


title: ShamM19

description: NS.1226.002.NEBNext_dual_i7_E4---NEBNext_dual_i5_E4.ShamM19.bam


title: ShamM18

description: NS.1209.001.NEBNext_dual_i7_A4---NEBNext_dual_i5_A4.ShamM18.bam


title: HCT 116 cells, capTEs, rep3

source_name: HCT 116

value: HCT 116

value: colorectal carcinoma epithelial cell

value: TE-containing RNA


title: DRG, Adult, sham, rep2

value: DRG

value: Sprague Dawley

tag: Sex

value: male

value: sham surgery

value: Day 14


title: Living_body_peripheral_blood_HVL_A12 [miRNA]

description:
Gene expression in whole blood from patient A12 with high viral load
HVL_A12

source_name: peripheral blood, HVL, A12

value: patient A12

tag: disease state

value: high viral load

value: whole blood


title: Living_body_peripheral_blood_HVL_A13 [miRNA]

description:
Gene expression in whole blood from patient A13 with high viral load
HVL_A13

source_name: peripheral blood, HVL, A13

value: patient A13


title: HCT 116 cells, capTEs, rep2


title: ShamM17

description: NS.1209.001.NEBNext_dual_i7_F3---NEBNext_dual_i5_F3.ShamM17.bam

value: Left ventricle

value: Sham operation

value: Age matched timepoint 10 weeks old


title: NCM460 cells, capTEs, rep1

value: normal colon epithelial cell


title: ShamM16

description: NS.1209.001.NEBNext_dual_i7_B3---NEBNext_dual_i5_B3.ShamM16.bam

value: No treatment


title: Living_body_peripheral_blood_HVL_A11 [miRNA]

description:
Gene expression in whole blood from patient A11 with high viral load
HVL_A11

source_name: peripheral blood, HVL, A11

value: patient A11


title: Living_body_peripheral_blood_HVL_A10 [miRNA]

description:
Gene expression in whole blood from patient A10 with high viral load
HVL_A10

source_name: peripheral blood, HVL, A10

value: patient A10

value: female


title: HCT116oxR_3_miRNA

city: Jinan

first: Xin

last: Zhang

state: Shandong

address: 107 Wenhua Xi Road

institute: Qilu Hospital, Shandong University

description: All.miRNA.Counts.txt

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 17bp c) adaptor sequence.
Utilizing the BWA software, we mapped the clean data to miRBase 21.0 and GRCh38 genome.
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: colorectal cancer cell line

growth_protocol: CRC cell line HCT116 was purchased from ATCC and cultured as recommended.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT116 cells were exposed to an initial oxaliplatin concentration of 0.1 μmol/L in RPMI (Roswell Park Memorial Institute) 1640 (Thermo Fisher Scientific, Wilmington, DE, USA) containing 10% FBS (fetal bovine serum) , 100 U/ml penicillin, and 100 g/ml streptomycin. The surviving population of cells was grown to ~80% confluence and passaged twice to ensure viability. The concentration of oxaliplatin that the surviving population was exposed to was then sequentially increased to 0.5 μmol/L, 1.0 μmol/L, 2 μmol/L and finally to the concentration of 5 μmol/L for 1 year.

tag: phenotype

value: oxaliplatin resistance

value: colorectal cancer cell line


title: HCT116oxR_1_miRNA

description: All.miRNA.Counts.txt


title: rHCIM7

description: NS.1209.001.NEBNext_dual_i7_H3---NEBNext_dual_i5_H3.rHCIM7.bam

tag: tissue

value: Myocardial infarction

value: 2 days after treatment injection

value: Seven days after myocardial infarction received intramyocardial injection of rHCI


title: s210722H1

value: hypertensive nephropathy

value: proteinuria not conform to nephrotic syndrome


title: MCF 10A cells, capTEs, rep2

source_name: MCF 10A

value: MCF 10A

value: normal mammary epithelial cell

value: TE-containing RNA


title: rHCIM3

description: NS.1209.001.NEBNext_dual_i7_E3---NEBNext_dual_i5_E3.rHCIM3.bam

value: Left ventricle


title: HCT116_2_miRNA

description: All.miRNA.Counts.txt

value: parental control


title: rHCIM11

description: NS.1209.001.NEBNext_dual_i7_C4---NEBNext_dual_i5_C4.rHCIM11.bam


title: MDA-MB-231 cells, capTEs, rep3

value: breast cancer epithelial cell


title: MCF 10A cells, capTEs, rep3


title: Living_body_peripheral_blood_HVL_A8 [miRNA]

description:
Gene expression in whole blood from patient A8 with high viral load
HVL_A8

source_name: peripheral blood, HVL, A8

value: patient A8

value: high viral load

value: whole blood


title: HCT116oxR_3_total RNA

description: all.counts.txt

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HiSat2 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: MDA-MB-231 cells, capTEs, rep2


title: HCT116_3_miRNA

description: All.miRNA.Counts.txt


title: rHCIM1

description: NS.1226.002.NEBNext_dual_i7_C3---NEBNext_dual_i5_C3.rHCIM1.bam


title: Living_body_peripheral_blood_HVL_A6 [miRNA]

description:
Gene expression in whole blood from patient A6 with high viral load
HVL_A6

source_name: peripheral blood, HVL, A6

value: patient A6

value: female


title: HCT116oxR_2_total RNA

description: all.counts.txt

value: oxaliplatin resistance

value: colorectal cancer cell line


title: Living_body_peripheral_blood_HVL_A9 [miRNA]

description:
Gene expression in whole blood from patient A9 with high viral load
HVL_A9

source_name: peripheral blood, HVL, A9

value: patient A9

value: male


title: PBSM9

description: NS.1209.001.NEBNext_dual_i7_B4---NEBNext_dual_i5_B4.PBSM9.bam

value: Myocardial infarction

value: 2 days after treatment injection

value: Seven days after myocardial infarction received intramyocardial injection of PBS


title: MDA-MB-231 cells, capTEs, rep1


title: Living_body_peripheral_blood_HVL_A5 [miRNA]

description:
Gene expression in whole blood from patient A5 with high viral load
HVL_A5

source_name: peripheral blood, HVL, A5

value: patient A5


title: MCF 10A cells, capTEs, rep1

value: MCF 10A

value: normal mammary epithelial cell

value: TE-containing RNA


title: PBSM6

description: NS.1211.002.NEBNext_dual_i7_G3---NEBNext_dual_i5_G3.PBSM6.bam

value: Left ventricle


title: HCT116oxR_1_total RNA

description: all.counts.txt


title: rHCIM13

description: NS.1209.001.NEBNext_dual_i7_F4---NEBNext_dual_i5_F4.rHCIM13.bam

value: Seven days after myocardial infarction received intramyocardial injection of rHCI


title: HCT116_3_total RNA

description: all.counts.txt

value: parental control


title: HCT116_1_miRNA

description: All.miRNA.Counts.txt


title: PBSM2

description: NS.1209.001.NEBNext_dual_i7_D3---NEBNext_dual_i5_D3.PBSM2.bam


title: Living_body_peripheral_blood_HVL_A3 [miRNA]

description:
Gene expression in whole blood from patient A3 with high viral load
HVL_A3

source_name: peripheral blood, HVL, A3

value: patient A3

value: high viral load

value: whole blood


title: K562 cells, totalRNA-seq, rep2

value: lymphoblast

value: total RNA


title: HCT116_2_total RNA

description: all.counts.txt

value: colorectal cancer cell line


title: Living_body_peripheral_blood_HVL_A7 [miRNA]

description:
Gene expression in whole blood from patient A7 with high viral load
HVL_A7

source_name: peripheral blood, HVL, A7

value: patient A7

value: female


title: Living_body_peripheral_blood_HVL_A2 [miRNA]

description:
Gene expression in whole blood from patient A2 with high viral load
HVL_A2

source_name: peripheral blood, HVL, A2

value: patient A2

value: male


title: PBSM14

description: NS.1209.001.NEBNext_dual_i7_G4---NEBNext_dual_i5_G4.PBSM14.bam

source_name: Left ventricle

value: Myocardial infarction

value: 2 days after treatment injection

value: Seven days after myocardial infarction received intramyocardial injection of PBS


title: K562 cells, totalRNA-seq, rep1


title: HCT116_1_total RNA

description: all.counts.txt


title: PBSM12

description: NS.1209.001.NEBNext_dual_i7_D4---NEBNext_dual_i5_D4.PBSM12.bam


title: K562 cells, capTEs

value: TE-containing RNA


title: HEK293T cells, AA132, 0.1µM

status: Public on Aug 30 2023

city: La Jolla

first: Rockland

middle: Luke

last: Wiseman

state: CA

address: 10550 N Torrey Pines Rd

department: Molecular Medicine

institute: Scripps Research Isntitute

data_processing:
DNAstar Lasergene SeqManPro program was used to process fastq files
Sequences were aligned to the Homo_sapiens-GRCh38.p7
Assembly data were imported into ArrayStar 12.2 with Qseq (DNAStar Inc.)
Assembly: Homo_sapiens-GRCh38.p7
Supplementary files format and content: tab-delimited text files include aligned counts for each sample replicate

growth_protocol: HEK293T cells were maintained in high-glucose DMEM supplemented with 10% fetal bovine serum (FBS), glutamine, and penicilllin/streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were lysed and total RNA was extracted using the Quick-RNA Miniprep kit from Zymo Research (R1055)
Library construction was done by BGI Americas
RNA libraries for RNA-seq were prepared by BGI Americas
RNA-seq on BGI proprietary platform, DNBSEQ

treatment_protocol: HEK293T cells in 10cm plates were treated for 6 h with indicted treatment

value: human embryonic kidney cells

tag: genotype

value: WT

tag: time

value: 6 hours

tag: final concentration


title: HEK293T cells, AA132, 0.3µM


title: HEK293T cells, AA132, 1µM


title: K562 cells, totalRNA-seq, rep3

tag: molecule subtype


title: HEK293T cells, AA132, 6µM

tag: cell line


title: HEK293T cells, AA132, 15µM

tag: cell type


title: HEK293T cells, AA132, 10µM


title: HEK293T cells, AA132, 3µM


title: HEK293T cells, AA147


title: Living_body_peripheral_blood_HVL_A4 [miRNA]

description:
Gene expression in whole blood from patient A4 with high viral load
HVL_A4

source_name: peripheral blood, HVL, A4

value: patient A4


title: HEK293T cells, Tg

value: Thapsigargain


title: HEK293T cells, V

value: Vehicle

value: 0.1% DMSO


title: HeberFERON 72h rep6

city: La Habana

first: Jamilet

last: Miranda

address: Ave. 31 No. 15802 between 158 and 190, Cubanacán, Playa

department: Bioinformatics

country: Cuba

institute: Center for Genetic Engineering and Biotechnology (CIGB)

description:
HeberFERON6_DPA024
Sample name in Raw Data: ag6_DPA024-1

hyb_protocol: HumanHT-12 v4 - Standard Illumina hybridization protocol

scan_protocol: HumanHT-12 v4 - Standard Illumina scanning protocol

data_processing: The Illumina BeadChip was proned to missing intensity values imputed using KNN-imputation. The data were background corrected and normalised using the neqc methodology by Oshlack et al. (2010) PMID: 20929874. Normexp background correction using negative control probes and quantile normalization using negative and positive control probes. Default parameters are used.

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays (HumanHT-12 v4 - Standard Illumina labeling protocol)

growth_protocol: Human glioma cell line U-87MG (ECACC Product number 89081402, Salisbury, Wiltshire, UK) was maintained in complete medium MEM (Sigma, USA), supplemented with 10% Fetal Bovine Serum, 2mM glutamine and 50 µg/ mL de gentamicin (All Gibco) in a humidified atmosphere of 5% CO2 at 37°C. Cells were grown at a cellular density of 35 000 cells/ cm2. After 24 hours, cells were treated with HeberFERON at the IC50 or with equivalent quantities of rIFN-alpha2b and rIFN-gamma using the same culture medium, and incubated for 72h. Untreated cells were included in the experimental setup.

extract_protocol: After 72h of incubation with IFNs medium was discarded and cells washed once with phosphate saline buffer. Cells were pickup in buffer RLT with 143mM β-mercaptoethanol and total RNA purification proceeded following the instructions of RNeasy Plus minikit (Qiagen, USA). Quality control was performed with Agilent Bioanalizer and Nanodrop.

value: HeberFERON

value: glioblastoma-derived cell line U-87MG


title: Living_body_peripheral_blood_HVL_A1 [miRNA]

description:
Gene expression in whole blood from patient A1 with high viral load
HVL_A1

source_name: peripheral blood, HVL, A1

value: patient A1

value: high viral load

value: whole blood


title: HeberFERON 72h rep1

description:
HeberFERON1_DPA019
Sample name in Raw Data: ag1_DPA019-1

treatment_protocol: After 24 hours, cells were treated with HeberFERON at the IC50 or with equivalent quantities of rIFN-alpha2b and rIFN-gamma using the same culture medium, and incubated for 72h. Untreated cells were included in the experimental setup.


title: HeberFERON 72h rep5

description:
HeberFERON5_DPA023
Sample name in Raw Data: ag5_DPA023-1


title: HEK293T cells, AA132, 30µM


title: 190327E-Input

city: Xi'an

first: Feng

address: Changle west Road

department: Department of Pathology

institute: Fourth Military Medical University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using a HiSeq Rapid Duo cBot Sample Loading Kit (Illumina) according to the manufacturer's instructions.
After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500 platform and 50 bp single-end reads were generated.
Chromatin immunoprecipitation (ChIP), sequencing library preparation and data analysis were conducted by LC-Bio( Hangzhou, Zhejiang 310018, China).
Raw sequencing data were cleaned to filter adapters and low quality reads using FASTQC (v0.11.5) and the unique mapped reads were harvested by mapping the cleaned reads to genome with no more than two mismatches by Bowtie 2.
Input, IgG, rabbit anti-H3K27me3 (Millipore, #07-449) ChIP-seq raw reads from wild type and Ezh2-cKO chondrocytes were used to analyzed.
Assembly: MACS2（v2.1.1）was used to call peak, giving a robust and high resolution ChIP-Seq peak predictions.
Supplementary files format and content: Peaks were annotated related genes using Homer (v4.10).
Supplementary files format and content: deepTools (v2.4.1) was used to plot gene coverage of the reads near TSS and TES. ChIPseeker（v1.5.1）was used to depict the reads distribution on chromosomes. Homer（v4.10） was used to search motif and analyze transcription factors.

source_name: cartilage

growth_protocol: DMEM medium containing 10% FBS at 5% CO2 and 37℃

extract_protocol:
Cells was cross-linked with 1% formaldehyde and incubated for 10 min at room temperature. A final concentration of 125 mM of glycine was added to deactivat Formaldehyde. Cells were lysed using 800 μl lysis buffer and sonicated into small chromatin fragments.
Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: cartilage

tag: chip antibody

value: anti-H3K27me3 (Millipore, #07-449)

value: chondrocyte


title: HeberFERON 72h rep3

description:
HeberFERON3_DPA021
Sample name in Raw Data: ag3_DPA021-1


title: IFNalpha2b 72h rep6

description:
IFNa2b6_DPA018
Sample name in Raw Data: a6_DPA018-1


title: wt colonic organoid, rep4

first: Haruna

address: 5-1-1 Tsukiji,

institute: National Cancer Center Japan

data_processing:
Reference sequences for mapping were prepared using rsem-prepare-reference of RSEM version 1.3.1 and STAR version 2.7.7a.
Reads were trimmed using trim_galore of Trim Galore version 0.6.7 and Cutadapt version 3.5.
The processed reads were mapped to the reference sequences and TPM (Transcripts Per Million) were calculated using rsem-calculate-expression of RSEM version 1.3.1 and STAR version 2.7.10a.
Gene and isoform TPM values were extracted from TPM columns of RSEM result files.
Assembly: GRCm39
Supplementary files format and content: tab-deliminted text file includes TPM values for each sample.

source_name: colon

extract_protocol:
Organoids embedded in Matrigel were dissolved in ISOGEN, and RNA was extracted following the protocol.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (Cat No. 7770)  following manufacturer's protocols.

value: colon

value: organoid

value: epithelial cells

tag: strain

value: cont


title: IFNalpha2b 72h rep2

description:
IFNa2b2_DPA014
Sample name in Raw Data: a2_DPA014-1

tag: treatment


title: HeberFERON 72h rep2

description:
HeberFERON2_DPA020
Sample name in Raw Data: ag2_DPA020-1


title: IFNalpha2b 72h rep5

description:
IFNa2b5_DPA017
Sample name in Raw Data: a5_DPA017-1


title: Control untreated rep6

description:
Control_Cell6_DPA006
Sample name in Raw Data: cc6_DPA006-1

value: Control


title: IFNalpha2b 72h rep3

description:
IFNa2b3_DPA015
Sample name in Raw Data: a3_DPA015-1


title: IFNgamma 72h rep6

description:
IFNg6_DPA012
Sample name in Raw Data: g6_DPA012-1

value: IFNgamma


title: IFNgamma 72h rep4

description:
IFNg4_DPA010
Sample name in Raw Data: g4_DPA010-1


title: IFNalpha2b 72h rep1

description:
IFNa2b1_DPA013
Sample name in Raw Data: a1_DPA013-1


title: IFNgamma 72h rep2

description:
IFNg2_DPA008
Sample name in Raw Data: g2_DPA008-1


title: IFNgamma 72h rep5

description:
IFNg5_DPA011
Sample name in Raw Data: g5_DPA011-1


title: Control untreated rep2

description:
Control_Cell2_DPA002
Sample name in Raw Data: cc2_DPA002-1


title: IFNalpha2b 72h rep4

description:
IFNa2b4_DPA016
Sample name in Raw Data: a4_DPA016-1


title: Control untreated rep4

description:
Control_Cell4_DPA004
Sample name in Raw Data: cc4_DPA004-1


title: HeberFERON 72h rep4

description:
HeberFERON4_DPA022
Sample name in Raw Data: ag4_DPA022-1


title: 190327E-ChIP


title: Control untreated rep3

description:
Control_Cell3_DPA003
Sample name in Raw Data: cc3_DPA003-1


title: Control untreated rep5

description:
Control_Cell5_DPA005
Sample name in Raw Data: cc5_DPA005-1


title: 190117JMJD3-Input


title: 190117utx-Input

value: Utx-cKO


title: IFNgamma 72h rep1

description:
IFNg1_DPA007
Sample name in Raw Data: g1_DPA007-1


title: 190117JMJD3-ChIP


title: 190117utx-ChIP


title: 190115WT-Input

value: Wild type


title: 190115WT-ChIP


title: Control untreated rep1

description:
Control_Cell1_DPA001
Sample name in Raw Data: cc1_DPA001-1


title: E0771_BrM_C

city: Madrid

first: Manuel

last: Valiente

address: Melchor Fernández Almagro, 3

institute: CNIO

data_processing:
Read files were quality-checked with FastQC.
Reads were aligned to the mouse genome (GRCm39) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 2.2.1
Assembly: GRCm39/vM26
Supplementary files format and content: tables were generated with Cufflinks 2.2.1 and contain transcripts abundance measured in FPKM values

source_name: E0771 BrM

growth_protocol: Murine B16/F10-BrM (brain metastatic) cells and 482N1 cells were all cultured in DMEM medium supplemented with 10% FBS, 100 IU.ml–1 penicillin/streptomycin, and 1 mg.ml–1 amphotericin B. Murine E0771-BrM cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 100 IU.ml–1 penicillin/streptomycin, 1 mg.ml–1 amphotericin B, and 1% hepes.

extract_protocol:
For RNA-seq Total RNA was extracted using the RNeasy kit (Qiagen)
1 µg of total RNA samples was used as provided by the user. Sample RNA Integrity Numbers were in the range 7.6 to 9.4 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (9 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument  by following manufacturer's protocols.

treatment_protocol: No treatment applied

value: E0771 BrM

value: triple negative breast cancer

value: WT

value: No treatment applied


title: B16F10_BrM_B

value: BRAF mutant melanoma


title: 482N1_B

value: lung NSCLC


title: lub001 [HTO]

city: PITTSBURGH

first: runzi

last: sun

state: PA

address: 203 Lothrop st

institute: university of pittsburgh

description: hto hashtag multiplexed T cells from B16 or B16IL33

data_processing:
raw data were processed by cellranger 6.1.1
raw data were processed by CITE-seq COUNT
Genome_build: mm10
Supplementary_files_format_and_content: standard output of 10x cellranger, CITE-seq count, 10x cellranger VDJ

source_name: tumor tissue

growth_protocol: B16 cell lines were grew in RPMI with 10% FBS and 1% P.S.

extract_protocol:
10x single cell chromium
5' GEX along with HTO, TCR libraries

treatment_protocol: no treatment involved

value: tumor

value: T cells

value: mixed with wild type and IL-33 expressing


title: E0771_BrM_A


title: B16F10_BrM_C


title: E0771_BrM_B


title: 482N1_A


title: lub001 [GEX]


title: IFNgamma 72h rep3

description:
IFNg3_DPA009
Sample name in Raw Data: g3_DPA009-1

value: glioblastoma-derived cell line U-87MG


title: 482N1_C


title: genomic DNA from baseline whole blood 987

type: genomic

city: Aurora

middle: J.

last: Borengasser

state: Colorado

address: 12631 E. 17th Ave, Mailstop F-561

department: Pediatrics

institute: University of Colorado - Anschutz Medical Campus

hyb_protocol: Per Illumina protocol

scan_protocol: Per Illumina protocol

data_processing: Array data were pre-processed and normalized using the SeSAMe R package. After removing cross-hybridizing probes, probes overlying SNPs with minor allele frequency >1% in the general population, and probes that failed across multiple samples with an average detection p-value > 0.05, a total of 739,397 cytosine-phosphate-guanine dinucleotide (CpG) probes remained for analysis.

label: Cy5 and Cy3

source_name: baseline whole blood 987

label_protocol: Per Illumina protocol

extract_protocol: Genomic DNA was isolated from whole blood samples using the commercially-available PureLink Genomic DNA Kit (Invitrogen, Carlsbad, CA, USA). Quality was assessed via a NanoDrop 2000/2000c spectrophotometer (ThermoFisher Scientific, Grand Island, NY, USA) and concentrations measured by  Qubit Fluorometer 2.0 (Invitrogen, Carlsbad, CA, USA).

tag: sample id

tag: timepoint

value: baseline

tag: ChIP

tag: array

value: M

tag: race

value: Caucasian

tag: ethnicity

value: Non-hispanic

value: whole blood collected at baseline


title: genomic DNA from baseline whole blood 928

source_name: baseline whole blood 928

tag: age

tag: Sex

value: F

value: Non-Caucasian


title: genomic DNA from baseline whole blood 913

source_name: baseline whole blood 913

tag: tissue


title: genomic DNA from baseline whole blood 957

source_name: baseline whole blood 957


title: genomic DNA from baseline whole blood 918

source_name: baseline whole blood 918


title: genomic DNA from baseline whole blood 907

source_name: baseline whole blood 907


title: genomic DNA from baseline whole blood 905 replicate

source_name: baseline whole blood 905


title: genomic DNA from baseline whole blood 872

source_name: baseline whole blood 872


title: genomic DNA from baseline whole blood 801

source_name: baseline whole blood 801

value: hispanic


title: genomic DNA from baseline whole blood 867

source_name: baseline whole blood 867


title: genomic DNA from baseline whole blood 826

source_name: baseline whole blood 826


title: genomic DNA from baseline whole blood 827

source_name: baseline whole blood 827


title: genomic DNA from baseline whole blood 905


title: genomic DNA from baseline whole blood 833

source_name: baseline whole blood 833


title: genomic DNA from baseline whole blood 771

source_name: baseline whole blood 771


title: genomic DNA from baseline whole blood 770

source_name: baseline whole blood 770


title: genomic DNA from baseline whole blood 732

source_name: baseline whole blood 732


title: genomic DNA from baseline whole blood 726

source_name: baseline whole blood 726


title: genomic DNA from baseline whole blood 713

source_name: baseline whole blood 713


title: genomic DNA from baseline whole blood 669

source_name: baseline whole blood 669


title: genomic DNA from baseline whole blood 684

source_name: baseline whole blood 684


title: genomic DNA from baseline whole blood 712

source_name: baseline whole blood 712


title: genomic DNA from baseline whole blood 681

source_name: baseline whole blood 681


title: genomic DNA from baseline whole blood 607

source_name: baseline whole blood 607


title: HCT116oxR_2_miRNA

description: All.miRNA.Counts.txt

source_name: colorectal cancer cell line

tag: phenotype

value: oxaliplatin resistance

value: colorectal cancer cell line


title: genomic DNA from baseline whole blood 668

source_name: baseline whole blood 668


title: HCT 116 cells, capTEs, rep1

source_name: HCT 116

value: HCT 116

value: colorectal carcinoma epithelial cell

value: TE-containing RNA


title: genomic DNA from baseline whole blood 548

source_name: baseline whole blood 548


title: genomic DNA from baseline whole blood 564

source_name: baseline whole blood 564


title: genomic DNA from baseline whole blood 602

source_name: baseline whole blood 602


title: genomic DNA from baseline whole blood 577

source_name: baseline whole blood 577


title: genomic DNA from baseline whole blood 559

source_name: baseline whole blood 559


title: genomic DNA from baseline whole blood 625

source_name: baseline whole blood 625


title: genomic DNA from baseline whole blood 539

source_name: baseline whole blood 539


title: genomic DNA from baseline whole blood 554

source_name: baseline whole blood 554


title: genomic DNA from baseline whole blood 520

source_name: baseline whole blood 520


title: genomic DNA from baseline whole blood 509

source_name: baseline whole blood 509


title: genomic DNA from baseline whole blood 464

source_name: baseline whole blood 464


title: genomic DNA from baseline whole blood 454

source_name: baseline whole blood 454


title: genomic DNA from baseline whole blood 436

source_name: baseline whole blood 436


title: genomic DNA from baseline whole blood 422

source_name: baseline whole blood 422


title: genomic DNA from baseline whole blood 356

source_name: baseline whole blood 356


title: genomic DNA from baseline whole blood 334

source_name: baseline whole blood 334


title: genomic DNA from baseline whole blood 388

source_name: baseline whole blood 388


title: genomic DNA from baseline whole blood 346

source_name: baseline whole blood 346


title: genomic DNA from baseline whole blood 432

source_name: baseline whole blood 432


title: genomic DNA from baseline whole blood 319 replicate

source_name: baseline whole blood 319


title: genomic DNA from baseline whole blood 319


title: genomic DNA from baseline whole blood 300

source_name: baseline whole blood 300


title: genomic DNA from baseline whole blood 289

source_name: baseline whole blood 289


title: genomic DNA from baseline whole blood 285

source_name: baseline whole blood 285


title: genomic DNA from baseline whole blood 254

source_name: baseline whole blood 254


title: genomic DNA from baseline whole blood 244

source_name: baseline whole blood 244


title: genomic DNA from baseline whole blood 189

source_name: baseline whole blood 189


title: genomic DNA from baseline whole blood 233

source_name: baseline whole blood 233


title: genomic DNA from baseline whole blood 181

source_name: baseline whole blood 181


title: genomic DNA from baseline whole blood 298

source_name: baseline whole blood 298


title: B16F10_BrM_A

value: BRAF mutant melanoma

tag: genotype

value: WT

value: No treatment applied


title: genomic DNA from baseline whole blood 178

source_name: baseline whole blood 178


title: genomic DNA from baseline whole blood 163

source_name: baseline whole blood 163


title: genomic DNA from baseline whole blood 139

source_name: baseline whole blood 139


title: genomic DNA from baseline whole blood 131

source_name: baseline whole blood 131


title: genomic DNA from baseline whole blood 123

source_name: baseline whole blood 123


title: genomic DNA from baseline whole blood 122

source_name: baseline whole blood 122


title: genomic DNA from baseline whole blood 126

source_name: baseline whole blood 126


title: genomic DNA from baseline whole blood 100

source_name: baseline whole blood 100


title: genomic DNA from three month whole blood 987

source_name: three month whole blood 987

value: whole blood collected at 3 months


title: genomic DNA from three month whole blood 957

source_name: three month whole blood 957


title: genomic DNA from three month whole blood 928

source_name: three month whole blood 928


title: genomic DNA from three month whole blood 918

source_name: three month whole blood 918


title: genomic DNA from three month whole blood 913

source_name: three month whole blood 913


title: genomic DNA from three month whole blood 872

source_name: three month whole blood 872


title: genomic DNA from three month whole blood 905

source_name: three month whole blood 905


title: genomic DNA from baseline whole blood 108

source_name: baseline whole blood 108

value: baseline


title: genomic DNA from three month whole blood 907

source_name: three month whole blood 907


title: genomic DNA from three month whole blood 867

source_name: three month whole blood 867


title: genomic DNA from three month whole blood 833

source_name: three month whole blood 833


title: genomic DNA from three month whole blood 827

source_name: three month whole blood 827


title: genomic DNA from three month whole blood 826

source_name: three month whole blood 826


title: genomic DNA from three month whole blood 801

source_name: three month whole blood 801


title: genomic DNA from three month whole blood 771

source_name: three month whole blood 771


title: genomic DNA from three month whole blood 770

source_name: three month whole blood 770