title: replicate 1 oxycodone therapeutic exposed (0-24hpf) total RNA at 48 hpf

description: Library name: R1OT

value: 35.14ng/mL oxycodone


title: LNWT_CON_1

status: Public on Jun 04 2025

type: SRA

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

country: USA

institute: UT Health Science Center at San Antonio

library_source: transcriptomic

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat2 aligner.
gene count measurements were obtained using HTSeq using refseq annotation. LNCaP_KO_1 was not used in the differential expression analysis.
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

molecule: total RNA

organism: Homo sapiens

source_name: LNCaP treated with DMSO, rep 1

growth_protocol: LNCaP, LNCaP RPS6KB1 KO and LNCaP RPS6KB1 OE cells were cultured using RPMI 1640 medium supplemented with 10% FBS, antibiotic/anti-mycotic agent (Corning and is cat# 30-004-CI). Media for LNCaP OE cells was also supplemented with 20 microg/ml puromycin.

extract_protocol:
Total RNA was extracted using TRIzol reagent and Zymo Research Total RNA extraction kit  and quantified using nanodrop and Agilent bioanalyzer.
Total RNA samples were used for sequencing library preparation with KAPA RNA HyperPrep kit with RiboErase (HMR) following KAPA RNA library preparation protocol. Each library was bar-coded and then pooled for sequencing run paired-end sequencing protocol.

treatment_protocol: Cells were treated with Berberine prepared as 10mg/ml stock (Sigma B3251) in 100% methanol (Sigma 179337) and filtered using a 0.20μm filter (Corning 431222). For RPS6KB1 KO and OE cells: freshly procured LNCaP cells were used to generate stable RPS6KB1 knockout (KO) cells using CRISPR/Cas9 system by Applied StemCell Inc (Milpitas, CA). Two gRNAs targeting exon 4 of RPS6KB1 locus produced double strand breaks, generating a 56 base pair deletion.  RPS6KB1 KO cells were maintained in complete RPMI medium.

tag: cell lines

value: LNCaP Prostate cancer cell line

tag: rps6kb1 status

value: LNCaP WT

tag: treatment

value: Vehicle


title: M20 corticosterone 14 days

city: Magdalenka

first: Grzegorz

middle: Roman

last: juszczak

address: Jastrzebiec, ul Postepu 36A

country: Poland

institute: Institute of Genetics and Animal Biotechnology

description:
enrichment of polyadenylated RNA
stranded library

data_processing:
Initial data analysis included quality validation of raw and trimmed data in fastq format using MultiQC and FastQC tools, trimming of adapters using Trim Galore, alignment of reads to mouse GRCm39 genome assembly using hisat2, quality validation of the aligned data using MultiQC / BamQC and feature counting with featureCounts. The count files were analyzed with edgeR package. The data derived from all 48 samples were filtered by filterByExpr function. The data were normalized with the normLibSizes function using default TMM method. Differences between groups were tested with the edgeR exactTest while Bonferroni-Hochberg method was used to calculate adjusted p-values.
Assembly: mouse GRCm39 genome assembly
Supplementary files format and content: Excel file containing CPM values for each sample and results of statistical comparisons between groups.

organism: Mus musculus

source_name: hippocampus

extract_protocol:
RNA was extracted from the individual hippocampal samples using the GeneMATRIX Universal RNA Purification Kit (Eurx) according to the manufacturer-supplied protocol. Obtained RNA samples were additionally purified with the DNase Max kit (Qiagen) to remove remnants of DNA.
Library construction protocol included mRNA enrichment with Oligo dT, RNA fragmentation and reverse transcription (second-strand cDNA synthesis with dUTP instead of dTTP for preparation of stranded specific mRNA libraries), end repair, A-tailing, adaptor ligation, PCR amplification, single strand separation and cyclization and DNA nanoball synthesis preceinding  sequencing on DNBseq platform.

treatment_protocol: The mice were assigned to three corticosterone-treated groups that received the glucocorticoid dissolved in drinking water (100 g/mL) for 5, 14 or 28 nights and to three control groups that were euthanized at the same time as corticosterone treated animals. Bottles with drinking water were changed every evening at the end of the light phase. Sample collection was performed during the first hour of the light phase following the last night of treatment.

tag: tissue

value: hippocampus

tag: developmental stage

value: adult

tag: Sex

value: male

tag: strain

value: Swiss-Webster

value: corticosterone

tag: time

value: 14 days


title: replicate 3 fentanyl therapeutic exposed (0-24hpf) total RNA at 48hpf

city: Bozeman

first: Christa

last: Merzdorf

state: Montana

address: 109 Lewis Hall

department: MCB

institute: Montana State University

description: Library name: R4FT

data_processing:
Sequenced by NovaGene via Novaseq X Plus Platform paired end reads
Raw reads are available as the fq.gz files
Trimmed via trimmomatic, and ran through rCorrector, then mapped to GRCz11 (ensemble) constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files
Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files
Supplementary files format and content: txt files of aggregated count matrixes, see above
Supplementary files format and content: the counts derived from Salmon

organism: Danio rerio

source_name: Total embryo (50 embryo homogenate)

growth_protocol: zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C

extract_protocol:
Trizol Chloroform extraction of total RNA followed by Dnase I treatment, and Monarch RNA cleanup kit (T2030L). All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100
Zymo-Seq RiboFree Total RNA library Kit (R30003)

treatment_protocol: one of the following conditions: fentanyl effluent (FE; 0.629 pg/mL), fentanyl therapeutic (FT; 3.14 ng/mL), oxycodone effluent (OE; 10.6 pg/mL), oxycodone therapeutic (OT; 35.14 ng/mL), Control. Opioid exposed embryos were exposed from 0 to 24 hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.

value: Total embryo (50 embryo homogenate)

tag: genotype

value: WT

value: 3.14 ng/mL fentanyl

tag: batch


title: Sample_15

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

description: Library name: Sample_15

data_processing:
First, using trimmomatic (v 0.39), we removed adapters from the sequences, retaining only sequences that had > 100 nucleotides in length and an average quality> 30. We aligned the reads to the chicken genome (galgal1) using Hisat2 . Next, we used Samtools (v 1.10) to retain the reads with one match to the genome, followed with removing duplicates using bammarkduplicates from biobambam2 (v 2.0.95). Samples with or more than 90% of correct alignment were used for counting.
Assembly: galgal1
Supplementary files format and content: read counts in a tab delimited text file

organism: Gallus gallus

source_name: PVN

growth_protocol: Fertilized Hubbard x Cobb-500 eggs (Gallus gallus) were obtained from a nearby commercial hatchery (same source and flock breeder age as our previous studies. Upon arrival, eggs were kept at 26.6ºC for 12 hours and then were randomly divided into a control and embryonic heat conditioning (EHC) group. These groups were separated into two incubators (Rite Farm Products Pro-1056) and labeled control and EHC, respectively. Both groups from embryonic day (ED) 0-7 were incubated at 37.5ºC and 80% relative humidity. The eggs in the control group continued to be incubated at 37.5ºC until hatch at ED 21. The EHC group was separated from the control group at ED 7 and introduced to an increase in temperature to 39.5ºC and 80% relative humidity for 12 hours per day (07:30–19:30), and 37.5ºC for the remainder of the 24 hours until ED 16. The EHC group then spent the remaining 5 days at 37.5ºC until hatch. After ED 18.5, all eggs were subjected to candling. Infertile eggs and dead embryos were removed from the study. Eggs with viable embryos were transferred to a common hatching incubator (Rite Farm Products Pro-264) and maintained within their separate groups (separate enclosed trays to prevent mixing of treatments) at 36.9ºC and 50% relative humidity for 18 hours. The temperature was gradually decreased to 35ºC until the hatch was collected. Hatched chicks were arbitrarily divided into group cages based on treatment in preparation for the acute day 4 post-hatch heat challenge. The holding room temperature was set at 30ºC, with ad libitum access to food and water, and 24 hr continuous light exposure, similar to our previous studies

extract_protocol:
Total RNA was isolated using the Total RNA purification Micro Kit (Norgen Biotek, Thorold, ON, Canada) according to the manufacturer’s instructions. Samples were thawed to room temperature (3 minutes) and vortexed for 30 seconds. 100 µl of 70% molecular-biology grade ethanol was added to the lysate and then steps were performed according to the kit’s instructions
Illumina’s Stranded Total RNA Prep, Ligation with Ribo Zero Plus Sample Prep Kit

treatment_protocol: On day 4 post-hatch, Control and EHC groups were subjected to an acute heat challenge at 36ºC. Samples were collected at three timepoints: 0 (before heat challenge; baseline), 2 hours, and 12 hours from the start of the increased temperature. Within these three time points, 10 birds were collected and euthanized from control and EHC groups, with 20 birds total for each time point. Chicks were weighed individually, euthanized by decapitation, and sexed via gonad identification.

value: PVN

tag: time point

tag: biological replicate

value: Male

value: C


title: replicate 5 fentanyl therapeutic exposed (0-24hpf) total RNA at 48hpf

description: Library name: R6FT


title: LNWT_BER_3

source_name: LNCaP treated with Berberine, rep 3

value: Berberine, 24h treatment with 5 microg/ml


title: Sample_60

description: Library name: Sample_60


title: M43 control 5 days

value: vehicle

value: 5 days


title: LNWT_BER_2

source_name: LNCaP treated with Berberine, rep 2

value: LNCaP Prostate cancer cell line

value: LNCaP WT


title: M39 control 5 days

value: hippocampus


title: Sample_11

description: Library name: Sample_11

source_name: nCPa

value: nCPa

value: Female

value: EHC


title: Sample_29

description: Library name: Sample_29


title: replicate 1 fentanyl therapeutic exposed (0-24hpf) total RNA at 48hpf

description: Library name: R1FT


title: M37 control 5 days

value: adult

value: male

value: Swiss-Webster


title: Sample_26

description: Library name: Sample_26


title: M24 corticosterone 14 days

value: corticosterone

value: 14 days


title: LNWT_BER_1

source_name: LNCaP treated with Berberine, rep 1


title: LNCaP_KO_3

source_name: LNCaP  with RPS6KB1 KO, rep 3

value: LNCaP KO


title: M35 control 5 days


title: replicate 5 fentanyl effluent exposed (0-24hpf) total RNA at 48hpf

description: Library name: R7FE

value: Total embryo (50 embryo homogenate)

value: WT

value: 0.629pg/mL fentanyl


title: Sample_28

description: Library name: Sample_28

source_name: POAH

value: POAH


title: LNCaP_KO_2

source_name: LNCaP  with RPS6KB1 KO, rep 2


title: replicate 4 fentanyl effluent exposed (0-24hpf) total RNA at 48hpf

description: Library name: R6FE


title: M33 control 5 days

value: vehicle

value: 5 days


title: Sample_10

description: Library name: Sample_10


title: replicate 4 fentanyl therapeutic exposed (0-24hpf) total RNA at 48hpf

description: Library name: R5FT

value: 3.14 ng/mL fentanyl


title: Sample_40

description: Library name: Sample_40

value: C


title: M17 control 5 days

value: hippocampus


title: LNCaP_WT_3

source_name: LNCaP  WT, rep 3

value: LNCaP Prostate cancer cell line

value: LNCaP WT


title: LNCaP_KO_1

source_name: LNCaP  with RPS6KB1 KO, rep 1


title: M15 control 5 days

value: adult


title: replicate 2 fentanyl effluent exposed (0-24hpf) total RNA at 48hpf

description: Library name: R2FE


title: Sample_43

description: Library name: Sample_43

value: Male

value: EHC


title: Sample_30

description: Library name: Sample_30

value: PVN

value: Female


title: replicate 1 fentanyl effluent exposed (0-24hpf) total RNA at 48hpf

description: Library name: R1FE


title: M13 control 5 days

value: male

value: Swiss-Webster


title: LNCaP_WT_2

source_name: LNCaP  WT, rep 2


title: LNCaP_WT_1

source_name: LNCaP  WT, rep 1


title: M46 corticosterone 5 days

value: corticosterone


title: replicate 8 control WT zebrafish 48hpf total RNA

description: Library name: R04Control

value: Total embryo (50 embryo homogenate)

value: WT


title: PT649_Tumor [TCR-Seq]

city: St Louis

first: Jichang

last: Han

state: MO

address: 4905 Children's PI

institute: Washington University in St Louis

data_processing:
Library strategy: TCR-Seq
Illumina base call (BCL) files converted to FASTQ using "cellranger mkfastq"
Expression data processed with "cellranger count" using a custom reference package of 30,727 genes from RefSeq gene models
TCR data processed with "cellranger vdj" and the custom reference package
Genome_build: GRCh38
Cellranger version 3.0
Supplementary_files_format_and_content: mtx
Supplementary_files_format_and_content: filtered_contig_annotations

molecule: polyA RNA

source_name: T cells

extract_protocol:
Skin biopsies (each a 3-cm ellipse) were taken from areas of depigmented borders. Metastatic melanoma tumors were biopsied in clinic or taken from clinically indicated operative specimens (1-cm2). 50-70ml blood was collected into sodium heparin tubes on same day as tissue biopsy. Skin and tumor were digested using 1 mg/mL collagenase type II and 2 mg/mL of DNase I at 37 degrees for 1 hour. A fresh surgical lymph node tumor specimen was minced and digested in 5 mg/mL of collagenase type II and 10 mg/mL of DNaseI in RPMI-1640 at 37 °C for 1 hour. Cold PBS+0.2% BSA was added to stop the digest. The sample was blocked with TruStain FcX 198 (Biolegend) and stained with BV711-conjugated anti-human CD45 (HI30;), PE-Dazzle 594-conjugated anti-human CD8 (SK1), and DAPI viability stain, followed by sorting to isolate live CD8+CD45+ T cells on a SONY SH800 Cell Sorter. The entire sorted volume was loaded onto a Single Cell A chip and processed on a Chromium instrument (10X Genomics). The RNA-seq library and V(D)J library for TCR-seq were generated and data were processed as described above for mouse scRNAseq above, however the human reference genome GRCh38 was used to generate gene expression matrices.
10X Genomics Chromium Single Cell 5' Library and Gel Bead Kit
PolyA priming for single-cell RNA-seq.  TCR enrichment using the Chromium Single Cell V(D)J Enrichment Kit, Human T cell

tag: patient

value: Tumor

tag: disease state

value: Partial response

tag: disease

value: Long-term melanoma


title: PT649_LN [TCR-Seq]

value: Lymph Node


title: replicate 9 control WT zebrafish 48hpf total RNA

description: Library name: R05Control


title: M44 corticosterone 5 days

value: hippocampus

value: 5 days


title: Sample_27

description: Library name: Sample_27


title: Hepatocyte-like cells, Etoposide, Day5

city: Sao Paulo

first: Kayque

last: Alves Telles Silva

address: 106 Matao St.

country: Brazil

institute: University of Sao Paulo

description: Library name: Sample 2

library_source: genomic

data_processing:
According to NovoGene's in-house protocols, Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ ≥ 13), non mitochondrial chromosome, and properly paired reads (longer than 18 nt).
Assembly: hg38
Supplementary files format and content: Processes data include peak files for each sample.

molecule: genomic DNA

source_name: WTCII

extract_protocol:
According to NovoGene's in-house protocols, nuclei was extracted from samples. The nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min.
According to NovoGene's in-house protocols, equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit.

tag: cell line

value: WTCII

tag: cell type

value: Hepatocyte-like cells


title: replicate 3 fentanyl effluent exposed (0-24hpf) total RNA at 48hpf

description: Library name: R4FE

value: 0.629pg/mL fentanyl


title: replicate 2 fentanyl therapeutic exposed (0-24hpf) total RNA at 48hpf

description: Library name: R2FT

value: 3.14 ng/mL fentanyl


title: Sample_25

description: Library name: Sample_25

value: POAH

value: Male

value: EHC


title: replicate 6 control WT zebrafish 48hpf total RNA

description: Library name: R02Control


title: M38 corticosterone 5 days

value: adult

value: male

value: Swiss-Webster


title: M42 corticosterone 5 days

value: corticosterone


title: replicate 7 control WT zebrafish 48hpf total RNA

description: Library name: R03Control

value: Total embryo (50 embryo homogenate)

value: WT


title: Sample_12

description: Library name: Sample_12

value: PVN

value: Female


title: M34 corticosterone 5 days

value: hippocampus


title: Hepatocyte-like cells, Control, Day5

description: Library name: Sample 1


title: replicate 5 control WT zebrafish 48hpf total RNA

description: Library name: R01Control


title: replicate 4 control WT zebrafish 48hpf total RNA

description: Library name: R8Control


title: Escherichia coli, M9 glucose, plasmid-free control, replicate 2

city: Kgs. Lyngby

first: Christoffer

last: Rode

address: Søltofts Plads, Building 220

country: Denmark

institute: Technical University of Denmark

description:
Library name: ecoli_CR_00088
12

data_processing:
Mapping and logtpm determined using the iModulonMiner workflow, https://doi.org/10.1371/journal.pcbi.1012546
Assembly: Genome assembly ASM584v2
Supplementary files format and content: tab-delimited text files includes feature counts for each Sample
Supplementary files format and content: csv file includes log-TPM values for each sample

organism: Escherichia coli

growth_protocol: Cells were grown in minimal M9 growth medium with either 0.2% glucose or 0.2% glycerol carbon source in 250 mL shake flasks at 40 mL working volume, shaking at 37C and at 225 RPM. Cells were grown to OD600 = 2.00, then sampled for total RNA extraction.

extract_protocol:
Total RNA was extracted from cultures following the protocol in the RNAprotect Bacteria Reagent Handbook (Qiagen). Once main cultures reached OD600 = 2, 2.5 mL culture was added to 5 mL RNAprotect Bacteria Reagent (Qiagen), vortexed, and incubated at room temperature for 5 minutes. Sample pellets were resuspended in 400 L elution buffer and split into two aliquots which were stored at -80C. Total RNA was then extracted and purified from thawed pellets on a QIAcube Connect Instrument (Qiagen) using the RNeasy Protect Bacteria Mini Kit (Qiagen). Lysozyme was used for enzymatic lysis of cells together with Proteinase K for degrading protein and SUPERaseIn RNAse inhibitor (Thermo Fisher) for protecting RNA. A DNase treatment step was added to the protocol to remove DNA contamination. Total RNA was eluted in 30 L RNase-free water, then stored at -80 C. The extracted RNA was shipped to sequencing at Azenta Life Sciences.
Enrichment, cDNA synthesis, and adapter ligation

value: Plasmid-free

value: Glucose

value: Replicate 2


title: replicate 3 control WT zebrafish 48hpf total RNA

description: Library name: R5Control


title: PT649_Tumor [RNA-Seq]

data_processing:
Illumina base call (BCL) files converted to FASTQ using "cellranger mkfastq"
Expression data processed with "cellranger count" using a custom reference package of 30,727 genes from RefSeq gene models
TCR data processed with "cellranger vdj" and the custom reference package
Genome_build: GRCh38
Cellranger version 3.0
Supplementary_files_format_and_content: mtx
Supplementary_files_format_and_content: filtered_contig_annotations

value: Tumor

value: Partial response

value: Long-term melanoma


title: PT649_Blood [TCR-Seq]

value: Blood


title: M18 corticosterone 5 days

value: 5 days


title: PT649_Skin [TCR-Seq]

value: Skin


title: M16 corticosterone 5 days

value: adult

value: male


title: Escherichia coli, M9 glycerol, plasmid-free control, replicate 2

description:
Library name: ecoli_CR_00070
18

value: Glycerol


title: PT649_Skin [RNA-Seq]


title: Escherichia coli, M9 glycerol, plasmid-free control, replicate 1

description:
Library name: ecoli_CR_00069
17

value: Replicate 1


title: PT649_Blood [RNA-Seq]


title: replicate 1 control WT zebrafish 48hpf total RNA

description: Library name: R2Control

value: Total embryo (50 embryo homogenate)

value: WT


title: RNPC3_4_ONT

status: Public on Jun 03 2025

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description: rRNA-depleted total RNA

data_processing:
Illumina: Quality assessment of the FASTQ files was conducted with FastQC  (version 0.11.8) and  MultiQC (version 1.10.1). ONT: Reads were basecalled in super-accuracy mode (dna_r9.4.1_450bps_sup_prom) with demultiplexing, using Guppy (version 6.0.6) and default parameters.
Illumina: Sequenced reads were mapped to the hg38 human reference genome using the align function in the Rsubread package (version 2.4.3). ONT: Sequenced reads were mapped to the CHM13v2 human reference genome with minimap2 (version 2.24).
Gene-level counts were summarised using the featureCounts function of Rsubread (version 2.10.2).
ONT: Transcript-level counts were generated using bambu (version 1.0.3).
ONT: Gene counts were filtered by expression level using edgeR (version 3.38.1).
Illumina: Gene counts were normalised using the trimmed mean of M-values (TMM) methods in edgeR (version 3.32.1). ONT: Gene counts were normalised using the trimmed mean of M-values (TMM) methods in edgeR (version 3.38.1).
Illumina: Differential expression analysis was conducted using limma (version 3.46.0). ONT: Differential expression analysis was conducted using edgeR's quasi-likelihood method.
Assembly: hg38 (Illumina), CHM13v2 (ONT)
Supplementary files format and content: Tab-delimited text files with columns representing gene IDs, gene length, and the number of reads mapping to that gene.

source_name: Human lung cancer cell line A549

growth_protocol: A549 cells were cultured in RPMI medium supplemented with 1X GlutaMAX (Gibco, Cat#35050061) and 5% FBS.

extract_protocol:
Total RNA was extracted using TRIsure™ reagent (Bioline, Cat#38033).
Illumina: Stranded Total RNA with Ribo-Zero for Illumina NovaSeq.   ONT: Long-read transcriptome libraries were prepared from 200 ng total RNA with the Oxford Nanopore Technologies PCR-cDNA (SQK-PCB109) kit, without poly(A) selection and according to the manufacturer’s instructions. 14 cycles of PCR were performed with an elongation time of 2 minutes and 30 seconds.  The pool of 8 indexed libraries was sequenced on 3 PromethION R9.4.1 flow cells (FLO-PRO002) on a PromethION 24 instrument running MinKNOW (version 22.03.2), refuelling the flow cells with Flush Buffer anytime the sequencing speed dropped below 300 bases per second.

treatment_protocol: Transfected with either human ON-TARGETplus siRNAs to RNPC3 (Dharmacon Inc., Cat#J-021646-18-0050) or Non-targeted (NT) siRNA (Dharmacon Inc., Cat#D-001810-01-05) using DharmaFECT 1 (Dharmacon  Inc.,  Cat#T-2001-03 according to the manufacturer’s protocol. Treatment was continued for 72h.

value: RNPC3 siRNA


title: RNPC3_3_ONT

description: rRNA-depleted total RNA


title: NT_3_ONT

description: rRNA-depleted total RNA

value: Non-targeted (NT) siRNA


title: RNPC3_2_ONT

description: rRNA-depleted total RNA


title: RNPC3_1_ONT

description: rRNA-depleted total RNA


title: Orangutan_iPSC, Control3

city: Dallas

first: Leijie

last: Li

address: 5323 Harry Hines Blvd.

department: Molecular Biology

institute: UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER

description:
Ocontrol_3
Ocontrol_count.txt

data_processing:
Hisat2 v 2.1.0 and Stringtie v 2.1.7 pipeline
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore v 0.6.10
Trimmed sequence reads were mapped to GRCh38/GRCm39 genomics by using Hisat2 v 2.1.0
Read count extraction using StringTie v 2.1.7
Assembly: GRCh38 for human;  Pan_tro 3.0 for chimpanzee; Susie_PAB v2 for orangutan
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Pongo abelii

source_name: Orangutan iPSCs

growth_protocol: All parental (contributor) and composite PSC lines were cultured in mTeSR Plus on Matrigel in a humidified atmosphere with 5% CO2 at 37*C.

extract_protocol:
RNA was harvested using the RNeasy Mini Plus Kit (Qiagen).
RNA libraries for RNA-seq were prepared using the SMARTer mRNA-Seq Library Prep Kit following the manufacturer's protocols.

treatment_protocol: Contributor and composite PSC lines were collected at ~70% confluency for lysis and RNA extraction.

value: Orangutan iPSCs

value: pluripotent stem cells


title: NT_2_ONT

description: rRNA-depleted total RNA


title: Orangutan_iPSC, Control2

description:
Ocontrol_2
Ocontrol_count.txt


title: NT_1_ONT

description: rRNA-depleted total RNA


title: Escherichia coli, M9 glucose, plasmid-free control, replicate 1

description:
Library name: ecoli_CR_00077
1

value: Plasmid-free

value: Glucose


title: PT649_LN [RNA-Seq]

value: Lymph Node

value: Partial response


title: Orangutan_iPSC, Control1

description:
Ocontrol_1
Ocontrol_count.txt


title: LSKs isolated from mice fed HFD

city: New York

first: Timothy

middle: Craigin

last: Wang

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University Irving Medical Center

description: 10x Genomics Single Cell 3' v3

library_source: transcriptomic single cell

data_processing:
Data was processed using Cell Ranger software v.6.2.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
Total BM cells were isolated from mice by crushing the femur, tibiae, and pelvic bones in staining medium composed of Hank’s buffered saline solution (HBSS) containing 3% heat-inactivated fetal bovine serum (FBS). Single-cell suspensions were purified on a Ficoll gradient, and then red blood cells were. Total BM cell counts were obtained using an automated cell counter. BM cells were lineage depleted using lineage microbeads and a MACS separator. Lineage-depleted BM cells were then blocked using purified rat IgG diluted 1:100 in staining buffer. Cells were then incubated with the following lineage antibodies conjugated to PE-Cy5: Gr1 (1:800), CD11b (1:800), CD3 (1:400), TER119 (1:400), CD5 (1:800), B220 (1:800), CD4 (1:800), CD19 (1:800), CD8a (1:800), in addition to the following antibodies staining for HSPC markers: c-Kit-APC-Cy7 (1:800) and Sca1-BV421 (1:400). LSK cells were sorted into HBSS + 3% FBS, allowed to rest on ice for 30 minutes, then were sequenced.
Library was performed according to the Single Cell 3' v3 protocol (10x Genomics).

value: Bone marrow

value: lineage- Sca-1+ c-Kit+

value: 24 weeks HFD


title: Human_Orangutan hybrid with orangutan mitochondria, Tetraploid3

description:
HOo3
HO_human_count.txt
HO_orangutan_count.txt

organism:
Pongo abelii
Homo sapiens

source_name: Tetraploid

value: Tetraploid

value: Hybrid tetraploid


title: PIF3:OE SD-27°C, biol rep 3

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

data_processing:
The high-quality sequence data set is mapped to the reference Arabidopsis genome using the HISAT2 package.
Mapped sequences were then converted from SAM file format to BAM file format and sorted using the SAMTOOLS package.
FPKM value were calculated using the StringTie package.
Differential expression analysis between the groups was performed using the DESeq2 package.
Assembly: TAIR 10
Supplementary files format and content: tab-delimited text files includes FPKM values for each sample.

organism: Arabidopsis thaliana

source_name: six-day-old seedlings

growth_protocol: Seeds were plated on MS-media supplemented with 0.8 % agar.

extract_protocol:
RNA was extracted using RNeasy Plant Mini Kit for RNA Extraction (Qiagen).
RNA libraries for RNA-sequencing were prepared using KAPA mRNA HyperPrep Kit following manufacturer's protocol.

treatment_protocol: Seeds were stratified in dark for 3 days at 4°C before transfering to light at 22°C-long days condition for germination (2-days). After which plates were shifted to either 22°C or 27°C short condition.

value: six-day-old seedlings

value: PIF3 overexpression line


title: sheepRV_shunt_3

city: San Francisco

first: Michael

middle: A

last: Smith

state: CA

address: 550 16th St, 5th Floor

department: Pediatrics

institute: UC San Francisco

description: Library name: 31127-011

data_processing:
The CLC Genomics Workbench was used for data processing. Reads were trimmed and ribosomal RNA reads were removed. All remaining reads were then mapped to the Sheep (Texel) genome Ovis Aries (Ovar v3.1) with ENSEMBL version 103 annotation.
Assembly: Ovar v3.1
Supplementary files format and content: Excel file containing matrix of raw counts for all genes/samples

organism: Ovis aries

source_name: Right ventricle

extract_protocol:
RNA was isolated using the RNeasy Plus Universal Mini (QIAGEN) according to manufacturer’s instructions
Library preparation was done using the QIAseq Stranded mRNA Kit (QIAGEN). After quality control, sequencing was performed on a NextSeq instrument (2x75bp reads) according to the manufacturer instructions (Illumina Inc.).

value: Right ventricle

value: shunt


title: replicate 2 control WT zebrafish 48hpf total RNA

description: Library name: R4Control

source_name: Total embryo (50 embryo homogenate)

value: Total embryo (50 embryo homogenate)

value: WT


title: Human_Orangutan hybrid with orangutan mitochondria, Tetraploid2

description:
HOo2
HO_human_count.txt
HO_orangutan_count.txt


title: sheepRV_shunt_4

description: Library name: 31127-012


title: PIF3:OE SD-27°C, biol rep 2


title: sheepRV_shunt_2

description: Library name: 31127-010


title: sheepRV_shunt_1

description: Library name: 31127-009


title: Human_Orangutan hybrid with orangutan mitochondria, Tetraploid1

description:
HOo1
HO_human_count.txt
HO_orangutan_count.txt


title: sheepRV_control_4

description: Library name: 31127-008

value: control


title: PIF3:OE SD-27°C, biol rep 1


title: sheepRV_control_3

description: Library name: 31127-007


title: NT_4_ONT

description: rRNA-depleted total RNA

value: Non-targeted (NT) siRNA


title: PIF3:OE SD-22°C, biol rep 3


title: sheepRV_control_2

description: Library name: 31127-006


title: sheepRV_control_1

description: Library name: 31127-005


title: Human_Orangutan hybrid with human mitochondria, Tetraploid3

description:
HOh3
HO_human_count.txt
HO_orangutan_count.txt


title: Human_Orangutan hybrid with human mitochondria, Tetraploid2

description:
HOh2
HO_human_count.txt
HO_orangutan_count.txt


title: sheepRV_fetal_4

description: Library name: 31127-004

value: fetal


title: LSKs isolated from mice fed LFD

description: 10x Genomics Single Cell 3' v3

value: 24 weeks LFD

value: male


title: PIF3:OE SD-22°C, biol rep 2


title: sheepRV_fetal_2

description: Library name: 31127-002


title: sheepRV_fetal_3

description: Library name: 31127-003


title: Human_Orangutan hybrid with human mitochondria, Tetraploid1

description:
HOh1
HO_human_count.txt
HO_orangutan_count.txt


title: sheepRV_fetal_1

description: Library name: 31127-001


title: old-3, 21M

city: Nanjing

first: Shi

last: Runqing

state: Jiangsu

address: Department of Gerontology 300 Guangzhou Road

country: China

institute: The First Affiliated Hospital of Nanjing Medical University

data_processing:
Data filtering raw data obtained from sequencing was filtered using soapnuke (v1.5.6) [1], and 1) reads containing the linker (linker contamination) were filtered out; 2) Reads with unknown base N content greater than 5%; 3) Low quality reads (reads with a quality value lower than 15 Accounting for more than 20% of the total base number of the reads are low-quality reads) to obtain clean data. Later, Dr Tom multi omics data mining system（ https://biosys.bgi.com ）Carry out data analysis, mapping and mining.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Gastrocnemius muscle

extract_protocol:
RNA was harvested using traditional TRIzol methods.
After sample quality inspection, take a certain amount of RNA sample, denature at appropriate temperature to open its secondary structure, and use oligo (DT) magnetic beads to enrich mRNA. Add interrupting reagent to the mRNA obtained in the previous step, react at an appropriate temperature for a certain time, and fragment the mRNA. Prepare one strand synthesis reaction system and set the reaction procedure to synthesize one strand cDNA; The second strand synthesis reaction system was prepared, and the reaction procedure was set to synthesize the second strand cDNA. The reaction system was prepared by end repair, adding "a" and linker connection, and the reaction procedure was set to repair the ends of double stranded cDNA, and adding a base at the 3 'end; The linker ligation reaction system was prepared, and the reaction procedure was set to connect the linker with cDNA. The PCR reaction system was prepared, and the reaction procedure was set to amplify the product. After the quality inspection of the library, the PCR product was denatured into a single strand, the cyclization reaction system was prepared, and the reaction procedure was set to obtain a single stranded circular product, which digested the linear DNA molecules that were not cyclized. Single stranded circular DNA molecules replicate through rolling rings to form a DNA nanosphere (DNB) containing multiple copies. The obtained DNBS were added into the mesh pores on the chip using high-density DNA nano chip technology, and sequenced by combined probe anchor polymerization (CPAs).

value: Gastrocnemius muscle


title: old-1, 21M


title: old-2, 21M


title: mid-3, 15M


title: pif3-1, SD-27°C, biol rep 3

value: pif3-1 homozygous mutant of T-DNA insertion in Col-0 background


title: PIF3:OE SD-22°C, biol rep 1


title: pif3-1, SD-27°C, biol rep 2


title: mid-2, 15M


title: pif3-1, SD-27°C, biol rep 1


title: mid-1, 15M


title: youth-2, 6M


title: 906739N

type: RNA

city: Shanghai

first: Wentao

last: Zhang

address: Rd Yanchang

institute: Shanghai tenth people‘s hospital

description: piRNA expression

hyb_protocol: Hybridization was performed at 65°C for 17 hours in Agilent’s SureHyb Hybridization Chambers. After being washed in an ozone-free environment, the slides were fixed and scanned with using the Agilent DNA Microarray Scanner

scan_protocol: The Arraystar HG19 piRNA array is designed for profiling of piRNAs in human germ cells. Human piRNAs are downloaded from NCBI database, and mapped to the HG19 genome sequence using UCSC Blat. piRNAs with good match are selected and on this array probes of about 23000 piRNAs are designed successfully using a duplex method. Most of the probes are replicated twice and the rest probes are printed once.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, piRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Significant differentially expressed genes between two samples were identified through Fold Change filtering. Significant differentially expressed genes between two groups were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the R software (version 3.1.2).

source_name: 906739N,adjacent tissue,renal cancer

label_protocol: Sample labeling was performed using a RNA ligase method. Briefly, One microgram of each sample was 3'-end-labeled with Cy3 fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Cy3), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C. After stopping the labeling procedure, the Cy3-labeled samples were hybridized on the Arraystar Human piRNA Array.

extract_protocol: RNA quantity and quality were measured NanoDrop ND-1000. RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: Radical Nephrectomy

value: renal cancer

value: adjacent tissue


title: pif3-1, SD-22°C, biol rep 3


title: youth-3, 6M


title: pif3-1, SD-22°C, biol rep 2


title: youth-1, 6M


title: pif3-1, SD-22°C, biol rep 1


title: Control, D4, F+

city: Minneapolis

first: Daniel

last: Garry

state: Minnesota

address: 2231 6th Street SE, Suite 4-156

department: Lillehei Heart Institute

institute: University of Minnesota

description:
Library name: Garry_102_Lane5_FL_S16
10X Genomics

data_processing:
Single cell RNA-seq expression was quantified using unique molecular identifiers (UMIs) by 10x Genomics’ “Cell Ranger” software.
Assembly: Mus musculus reference genome mm10 (GRCm38)
Supplementary files format and content: The processed data file is in HDF5 format and was generated using the Cell Ranger pipeline (10x Genomics). It contains filtered gene expression matrices for high-quality nuclei, including cell barcodes, gene annotations, and UMI count matrices in sparse format. Only nuclei that passed quality control filtering are included.

source_name: Embryoid bodies

extract_protocol:
Single cells from differentiated iHA-Etv2 embryoid bodies (EBs) at days 2, 3, and 4 (with and without doxycycline treatment) were isolated by FACS based on FLK1 and PDGFRα expression. Flow cytometry staining was performed using fluorophore-conjugated antibodies: FLK1-APC and PDGFRα-PE. Propidium iodide (PI) was used to exclude non-viable cells. A minimum of 10,000 viable cells were collected per condition for single-cell RNA sequencing.
Single-cell RNA-seq was performed using the 10x Genomics Chromium Single Cell platform. Cell barcoding and cDNA library preparation were carried out following the manufacturer's protocol at the University of Minnesota Genomics Center (UMGC). Library quality was assessed using an Agilent Bioanalyzer High Sensitivity DNA chip. Sequencing was performed on an Illumina NovaSeq S4 platform with 2 × 150 bp reads, targeting approximately 50,000 reads per cell.

value: Embryoid bodies

value: iHA-Etv2 (inducible HA-tagged Etv2) ESCs

value: Embryonic stem cell-Embryoid body (ES-EB)

value: Control


title: Control, D2, -/-

description:
Library name: Garry_103_2_FL_S3
10X Genomics


title: Control, D4, +/+

description:
Library name: Garry_102_Lane6_FL_S17
10X Genomics


title: Control, D4, -/-

description:
Library name: Garry_102_Lane4_FL_S15
10X Genomics


title: LNWT_TRT_2

source_name: LNCaP  with radiation treatment, rep 2

tag: cell lines

value: LNCaP Prostate cancer cell line

value: LNCaP WT

value: Radiation (2Gy)


title: DER120_NL (non-lesional vitiligo)

city: New York City

first: Agata

last: Kurowski

address: 1180 5th Avenue

department: Department of Dermatology

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: DER120_NL
10X Genomics

data_processing:
cellranger-7.2.0
Assembly: GRCh38-2020-A
Supplementary files format and content: tsv, mtx
Supplementary files format and content: Patient privacy concerns regarding public access to the raw data.

source_name: Skin

extract_protocol:
Miltenyi Biotec Whole Skin Dissociation Kit
Chromium Next GEM Single Cell 5' (Dual index)

value: Skin


title: lrb123, SD-27°C, biol rep 2

value: six-day-old seedlings

value: lrb123, triple homozygous mutant of T-DNA insertion mutants- lrb1-1, lrb2-1, lrb3-1 in Col-0 background


title: biofilm, 30-hour, rep2

city: Hanover

first: Charles

last: Puerner

state: NH

address: 1 Rope Ferry Rd

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth College

description:
Library name: BF30_2
column name in biofilmTL_ALLcounts.txt is BF30_2

data_processing:
trimming was performed with cutadapt v 2.4: nextseq-trim=20, minumum length = 1, quality cutoff = 20
Read mapping was performed with STAR v 2.7.2b: output type = BAM SortedByCoordinate, outFilterType = BySJout, genome = A1163 (v  FungiDB-52), gff file = A1163 (v FungiDB-52)
Read counting was performed with htseq-count v 0.11.2: format = BAM, stranded = no, order = pos
Assembly: FungiDB-52_AfumigatusA1163_Genome.fasta
Supplementary files format and content: tab-delimited text file included raw counts for each sample

organism: Aspergillus fumigatus

source_name: Mycelium (submerged Biofilm)

growth_protocol: 37C, 5% CO2, Glucose Minimal Media

extract_protocol:
Tissue was harvested in TRI reagent with bead beating, RNA was purified from the aqueous phase with Qiagen RNAeasy Plus Mini kit. DNA contamination was removed with the TURBO DNA-free kit (Ambion). 200ng of RNA was used for library construction.
RNA libraries for RNAseq were prepared using the mRNA HyperPrep kit (Kapa Bioscience) following manufacturer’s instructions.

value: Mycelium (submerged Biofilm)


title: biofilm, 30-hour, rep3

description:
Library name: BF30_3
column name in biofilmTL_ALLcounts.txt is BF30_3


title: lrb123, SD-27°C, biol rep 3


title: 902827N

description: piRNA expression

source_name: 902827N,adjacent tissue,renal cancer


title: DER120_LS (lesional vitiligo)

description:
Library name: DER120_LS
10X Genomics


title: 906739T

description: piRNA expression

source_name: 906739T,cancer tissue,renal cancer

value: cancer tissue


title: 871367T

description: piRNA expression

source_name: 871367T,cancer tissue,renal cancer


title: OE, D4, F+

description:
Library name: Garry_102_Lane1_FL_S12
10X Genomics

value: OE

value: Doxycycline


title: biofilm, 24-hour, rep3

description:
Library name: BF24_3
column name in biofilmTL_ALLcounts.txt is BF24_3


title: DER119_NL (non-lesional vitiligo)

description:
Library name: DER119_NL
10X Genomics


title: lrb123, SD-22°C, biol rep 3


title: Control, D3, +/+

description:
Library name: Garry_101_pluspluscontrol_FL_S7
10X Genomics


title: 902827T

description: piRNA expression

source_name: 902827T,cancer tissue,renal cancer


title: LNWT_TRTBER_2

city: San Antonio

first: Yidong

last: Chen

address: 8403 Floyd Curl Drive, MSC 7784

institute: UT Health Science Center at San Antonio

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat2 aligner.
gene count measurements were obtained using HTSeq using refseq annotation. LNCaP_KO_1 was not used in the differential expression analysis.
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: LNCaP with Berberine and radiation traetment, rep 2

extract_protocol:
Total RNA was extracted using TRIzol reagent and Zymo Research Total RNA extraction kit  and quantified using nanodrop and Agilent bioanalyzer.
Total RNA samples were used for sequencing library preparation with KAPA RNA HyperPrep kit with RiboErase (HMR) following KAPA RNA library preparation protocol. Each library was bar-coded and then pooled for sequencing run paired-end sequencing protocol.

tag: rps6kb1 status

value: Berberine+Radiation


title: biofilm, 24-hour, rep2

description:
Library name: BF24_2
column name in biofilmTL_ALLcounts.txt is BF24_2


title: Control, D4, P+

description:
Library name: Garry_102_Lane3_FL_S14
10X Genomics

tag: treatment


title: DER119_LS (lesional vitiligo)

description:
Library name: DER119_LS
10X Genomics

tag: tissue


title: lrb123, SD-22°C, biol rep 2


title: lrb123, SD-22°C, biol rep 1


title: DER115_NL (non-lesional vitiligo)

description:
Library name: DER115_NL
10X Genomics


title: Control, D3, -/-

description:
Library name: Garry_101_negnegcontrol_FL_S8
10X Genomics


title: biofilm, 30-hour, rep1

description:
Library name: BF30_1
column name in biofilmTL_ALLcounts.txt is BF30_1


title: biofilm, 24-hour, rep1

description:
Library name: BF24_1
column name in biofilmTL_ALLcounts.txt is BF24_1


title: Control, D3, P+

description:
Library name: Garry_101_PDpluscontrol_FL_S9
10X Genomics


title: pif4-101, SD-27°C, biol rep 3

value: pif4-101, T-DNA insertion mutant in Col-0 background


title: OE, D3, -/-

description:
Library name: Garry_101_OEnegneg_FL_S4
10X Genomics


title: biofilm, 18-hour, rep2

description:
Library name: BF18_2
column name in biofilmTL_ALLcounts.txt is BF18_2


title: DER114_NL (non-lesional vitiligo)

description:
Library name: DER114_NL
10X Genomics


title: 871367N

description: piRNA expression

source_name: 871367N,adjacent tissue,renal cancer

value: renal cancer

value: adjacent tissue


title: lrb123, SD-27°C, biol rep 1


title: pif4-101, SD-27°C, biol rep 2


title: OE, D3, F+

description:
Library name: Garry_101_FIk1plusOE_FL_S5
10X Genomics

value: Embryoid bodies

value: iHA-Etv2 (inducible HA-tagged Etv2) ESCs


title: biofilm, 18-hour, rep1

description:
Library name: BF18_1
column name in biofilmTL_ALLcounts.txt is BF18_1


title: DER114_LS (lesional vitiligo)

description:
Library name: DER114_LS
10X Genomics


title: pif4-101, SD-27°C, biol rep 1


title: Control, D3, F+

description:
Library name: Garry_101_FIK1pluscontrol_FL_S6
10X Genomics

value: Embryonic stem cell-Embryoid body (ES-EB)

value: Control


title: biofilm, 12-hour, rep3

description:
Library name: BF12_3
column name in biofilmTL_ALLcounts.txt is BF12_3


title: CON194 (healthy skin)

description:
Library name: CON194
10X Genomics


title: OE_3KR_3_input

city: Hangzhou

first: Putao

last: Yuan

address: No. 3, Qingchun Road East

department: Department of Orthopaedic Surgery

institute: Sir Run Run Shaw Hospital, Zhejiang University School of Medicine

description:
Library name: SAMPLES9
OE_3KR_3_input

data_processing:
Base calling software: BCL convert
Assembly: eg GRCH38
Supplementary files format and content: fpkm.xlsx

source_name: BMSCs primary cells

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification.
m6A-seq

value: BMSCs primary cells

value: Mesenchymal stem cells


title: biofilm, 12-hour, rep2

description:
Library name: BF12_2
column name in biofilmTL_ALLcounts.txt is BF12_2


title: pif4-101, SD-22°C, biol rep 3


title: CON171 (healthy skin)

description:
Library name: CON171
10X Genomics

value: Skin


title: OE_3KR_2_input

description:
Library name: SAMPLES8
OE_3KR_2_input


title: pif4-101, SD-22°C, biol rep 2

value: six-day-old seedlings


title: biofilm, 18-hour, rep3

description:
Library name: BF18_3
column name in biofilmTL_ALLcounts.txt is BF18_3


title: DER115_LS (lesional vitiligo)

description:
Library name: DER115_LS
10X Genomics


title: CON161 (healthy skin)

description:
Library name: CON161
10X Genomics


title: pif4-101, SD-22°C, biol rep 1


title: OE_3KR_1_input

description:
Library name: SAMPLES7
OE_3KR_1_input


title: BIO023_LS (lesional vitiligo)

description:
Library name: BIO023_LS
10X Genomics


title: CB-ECFC cells, Healthy6

city: Belfast

first: Karla

middle: M

last: O'Neill

address: 97 Lisburn Rd

department: Wellcome Wolfson institute for Experimental Medicine

country: United Kingdom

institute: Queens University Belfast

description: Library name: sample11

data_processing:
Quality control was performed using FastQC v0.11.8.
Alignment was done using STAR v2.7.3a against the GRCh38 human reference genome (Gencode v33 annotation).
Read counting was carried out using HTSeq v0.11.3.
SAM/BAM file handling was managed with SAMtools v1.17 and Picard v3.0.0. Mapping quality and coverage statistics were generated using Qualimap v2.3.0
MultiQC v1.14 was used to aggregate and summarize QC metrics across samples
Assembly: GRCh38 (Gencode v33)
Supplementary files format and content: raw count files for each sample in tab delimited text file format

source_name: cord-blood

growth_protocol: cells were cultured in Endothelial Growth Basal Medium-2 (EGM2, supplemented with BulletKit, Lonza) and 12% Foetal Bovine Serum (FBS) at 37°C with 5% CO2, in collagen coated flasks.

extract_protocol:
RNA was extracted from all samples using High Pure RNA isolation kit (Roche, 11828665001)
Libraries were prepared using KAPA HyperPrep with RiboErase kit as per manufacturer instructions

value: cord-blood

value: Progenitor Endothelial cells


title: Col-0, SD-27°C, biol rep 2

source_name: six-day-old seedlings

value: Wild-type, Columbia-0


title: CB-ECFC cells, Diabetic6

description: Library name: sample12


title: OE_WT_3_input

description:
Library name: SAMPLES3
OE_WT_3_input

value: WT


title: Col-0, SD-27°C, biol rep 1


title: OE_WT_2_input

description:
Library name: SAMPLES2
OE_WT_2_input


title: Col-0, SD-27°C, biol rep 3


title: CB-ECFC cells, Diabetic5

description: Library name: sample10


title: 632 (healthy skin)

description:
Library name: 632
10X Genomics


title: OE_WT_1_input

description:
Library name: SAMPLES1
OE_WT_1_input


title: CB-ECFC cells, Healthy5

description: Library name: sample9


title: Col-0, SD-22°C, biol rep 3


title: POD14-Exo_2

city: shanghai

first: Jing

state: Shanghai

address: No. 389 Xincun Road, Shanghai

institute: tongji university

description:
Library name: sample 6
3' mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMl: read2 contains transcript seguence

data_processing:
1) Assessment of the quality of raw data.
2) Quantitative quality control of the Cell Ranger gene.
3) Post-quantitative quality control: Filtering low-quality cells, filtering low-abundance genes (depending on the specific circumstances of the project), etc.
4) Standardized processing of gene expression.
5) Cellular heterogeneity analysis: dimensionality reduction clustering, Marker gene identification, cell type identification, cell subsets, and other downstream personalized analyses.
6) Gene expression analysis: Differential gene analysis, differential gene enrichment analysis, and other downstream personalized analyses.
Assembly: GRCm39
Supplementary files format and content: Cell Ranger software output files

source_name: skin

extract_protocol:
GEM Generation & Barcoding；Post GEM–RTCleanup & cDNAAmplification； 3ʹ Gene Expression Library Construction；Post Library Construction QC；
The FASTQ files were processed and aligned to mm10 mouse  human reference genome using Cell Ranger software (version 7.0.1) from 10x Genomics, with unique molecular identifier (UMI) counts summarized for each barcode. The UMI count matrix was then analyzed using Seurat[1] (version 4.0.0) R package. To remove low-quality cells and likely multiplet captures, a set of criteria were conducted: Cells were filtered by (1) gene numbers (gene numbers < 200), (2) UMI (UMI < 0.7), (4) percentage of mitochondrial RNA UMIs (proportion of UMIs mapped to mitochondrial genes > 10%) and (5) percentage of hemoglobin RNA UMIs (proportion of UMIs mapped to hemoglobin genes > 5%). Subsequently, the DoubletFinder[2] package (version 2.0.3) was used to identify potential doublets. To obtain the normalized gene expression data, library size normalization was processed using the NormalizeData function. Specifically, the global-scaling normalization method “LogNormalize” normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), and log-transformed the results.

value: skin


title: 486_NL (non-lesional vitiligo)

description:
Library name: 486_NL
10X Genomics


title: biofilm, 12-hour, rep1

description:
Library name: BF12_1
column name in biofilmTL_ALLcounts.txt is BF12_1

value: Mycelium (submerged Biofilm)


title: Col-0, SD-22°C, biol rep 2


title: CB-ECFC cells, Diabetic3

description: Library name: sample6


title: CB-ECFC cells, Healthy4

description: Library name: sample7


title: POD14-Exo_1

description:
Library name: sample 5
3' mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMl: read2 contains transcript seguence


title: Col-0, SD-22°C, biol rep 1


title: POD14_2

description:
Library name: sample 4
3' mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMl: read2 contains transcript seguence


title: 465 (healthy skin)

description:
Library name: 465
10X Genomics


title: 658 (healthy skin)

description:
Library name: 658
10X Genomics


title: ChIP_SKMEL5_OE2_V5

first: Miranda

last: Hunter

address: 418 E 68th St

institute: Memorial Sloan Kettering Cancer Center

description: Library name: ChIP_SKMEL5_OE2_V5

data_processing:
ChIP sequencing reads were trimmed and filtered for quality and library adapters using version 0.4.5 of TrimGalore with a quality setting of 15, and running cutadapt96 (v1.15) and FastQC (v0.11.5). Reads were aligned to human assembly hg38 with version 2.3.4.1 of bowtie297 and were deduplicated using MarkDuplicates in version 2.16.0 of Picard Tools. To ascertain enriched regions, MACS298 was used with a p-value setting of 0.001 and run against a matched control for each condition. A peak atlas was created by combining the superset of all peaks using the ‘merge’ function in the BEDTools suite v2.29.2. Read density profiles were created using deepTools 'bamCoverage’ v3.3.0, normalized to 10 million uniquely mapped reads and with read pileups extended to 200 bp. Version 1.6.1 of featureCounts was used to build a raw counts matrix and DESeq2 was used to calculate differential enrichment for all pairwise contrasts for experiments with replicates. For single sample data, MACS2 was run by swapping bams of different conditions to find differential regions. Peak-gene associations were created by assigning all intragenic peaks to that gene, while intergenic peaks were assigned using linear genomic distance to transcription start site. Gene set enrichment analysis91 was performed with the pre-ranked option and default parameters, where each gene was assigned the single peak with the largest (in magnitude) log2 fold change associated with it. Composite and tornado plots were created using deepTools100 (v3.3.0) by running computeMatrix and plotHeatmap on normalized bigwigs with average signal sampled in 25 bp windows and flanking region defined by the surrounding 2 kb. Motif signatures were obtained using HOMER101 (v4.5).
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Tumor

extract_protocol:
For profiling of HMGB2 binding in A375 and SKMEL5 cells, freshly harvested cells (~20 million cells/replicate/condition) were cross-linked first with 1.5 mM EGS (Thermo Fisher 21565) for 20 min at room temperature, and subsequently with 1% formaldehyde (Thermo Fisher 28906) for 40 min at 4°C. The reaction was quenched by the addition of glycine to the final concentration of 0.125 M. Fixed cells were washed twice with PBS and resuspended in SDS buffer (100 mM NaCl, 50 mM Tris-HCl pH 8.0, 5 mM EDTA, 0.5% SDS, 1x protease inhibitor cocktail, Roche). The resulting nuclei were spun down, resuspended in the immunoprecipitation buffer (100 mM NaCl, 100 mM TrisHCl pH 8.0, 5 mM EDTA, 5% Triton X-100) at 1 mL per 0.5 million cells mixed in 2:1 ratio, with the addition of 1x protease inhibitor cocktail (Millipore Sigma 11836170001). Nuclei were processed on a Covaris E220 Focused-ultrasonicator to achieve an average fragment length of 200-300 bp with the following parameters: PIP=140, Duty Factor=5, CBP/Burst per sec=200, Time = 20 min (for A375 cells) or 45 min (for SKMEL5 cells). Chromatin concentrations were estimated using the Pierce™ BCA Protein Assay Kit (Thermo Fisher 23227) according to the manufacturer’s instructions. The immunoprecipitation reactions were set up in 500 µL of the immunoprecipitation buffer in Protein LoBind tubes (Eppendorf 22431081) and pre-cleared with 50 µL of Protein G Dynabeads (Thermo Fisher 10004D) for two hours at 4°C. After pre-clearing, the samples were transferred into new Protein LoBind tubes and incubated overnight at 4°C with 5 µg of HMGB2 (abcam ab67282), V5 (abcam ab9116, used for SKMEL5 ChIP only) and H3K4me3 (Epicypher 13-0041) antibodies. For normalization purposes, 5 µL of Drosophila spike-in chromatin (Active Motif 53083) and 2 µL of spike-in antibody (Active Motif 61686) were added to each reaction.
The next day, 50 µL of BSA-blocked Protein G Dynabeads were added to each reaction and incubated for 2 hours at 4°C. The beads were then washed two times with low-salt washing buffer (150mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), two times with high-salt washing buffer (500 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), two times with LiCL wash buffer (250 mM LiCl, 10 mM TrisHCl pH8.0, 1 mM EDTA, 1% Na-deoxycholate, 1% IGEPAL CA-630) and one time with TE buffer (10 mM TrisHCl pH 8.0, 1 mM EDTA). The samples were then reverse-crosslinked overnight in the elution buffer (1% SDS, 0.1 M NaHCO3) and purified using the ChIP DNA Clean & Concentrator kit (Zymo Research D5205) following the manufacturer’s instructions. After quantification of the recovered DNA fragments, libraries were prepared using the ThruPLEX®DNA-Seq kit (Takara R400676) following the manufacturer’s instructions, purified with SPRIselect magnetic beads (Beckman Coulter B23318), and quantified using a Qubit Flex fluorometer (Thermo Fisher) and profiled by TapeStation (Agilent). The libraries were sent to MSKCC Integrated Genomics Operation core facility for sequencing on an Illumina NovaSeq 6000 (~30-40 million 100 bp paired-end reads per library).

value: Tumor

value: Melanoma


title: POD14_1

description:
Library name: sample 3
3' mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMl: read2 contains transcript seguence


title: adult_2

description:
Library name: sample 2
3' mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMl: read2 contains transcript seguence


title: CB-ECFC cells, Diabetic2

description: Library name: sample4


title: Rat_CTL_2

city: 安徽省合肥市新站区

first: 诗亚

last: 马

address: 安徽省合肥市瑶海区银领时代

institute: Anhui Medical University

description:
Library name: Lib_Rat_CTL_2
Control SD rat

data_processing:
Use FastQC for raw data quality control and remove low-quality reads and adapter sequences. The washed reads were aligned to the rat reference genome (Rattus norvegicus mRatBN7.2) and aligned using STAR software. The gene expression count matrix was calculated using featureCounts software. DESeq2 was used for expression normalization and differential expression analysis. The differential gene selection criterion is |log2FoldChange| > 1 and the adjusted p-value (padj) < 0.05.
Assembly: mRatBN7.2
Supplementary files format and content: The submission file is Expression.xlsx and contains a matrix of gene expression counts, with the gene ID in the row and the sample name in the column. Samples included the acute pancreatitis group (Rat_AP_1, Rat_AP_2, Rat_AP_3) and the control group (Rat_CTL_1, Rat_CTL_2, Rat_CTL_3). Each cell is the count value of the corresponding gene in the sample.

organism: Rattus norvegicus

source_name: pancreas

growth_protocol: Sprague-Dawley (SD) rats, male, 8 weeks old, weighing about 200-250 grams, were purchased from a formal animal testing center. All animals are kept in an environment with a temperature of 22±2°C, a humidity of 55±10%, and a 12-hour light and dark cycle, and eat and drink freely. Acclimatization for one week before the experiment.

extract_protocol:
In this project, Oligo(dT) magnetic beads were used to enrich mRNA with polyA structure in total RNA, and the RNA was interrupted to a fragment of about 300 bp in length by means of ion interruption. The 300 bp length fragment was selected because the adapter sequence length was fixed, and the fragment was too short, which would lead to a high adapter ratio and reduce the proportion of effective data. If the fragment is too long, it is not conducive to the formation of sequencing clusters. The first strand of cDNA was synthesized using a 6-base random primer and reverse transcriptase using RNA as a template, and the second-strand cDNA was synthesized using the first-strand cDNA as a template. Subsequently, PCR amplification was performed to enrich the library fragments, and the library fragments of about 450 bp were selected. The Agilent 2100 Bioanalyzer was used to measure the fragment size, and the total and effective concentrations of the library were determined. After adding different Index sequences according to the sample, the libraries were mixed proportionally, diluted to 2 nM, and alkalinized to form single-stranded libraries, ready for on-machine sequencing.
After RNA extraction, purification, and library construction, the samples were sequenced using next-generation sequencing (NGS) technology and based on the Illumina sequencing platform. The sequencing read length is 150 bp.

treatment_protocol: The acute pancreatitis model was induced by intraperitoneal injection of L-arginine (L-Arg, 5 mg/kg body weight) with a treatment time of 36 hours. The control group was intraperitoneally injected with the same volume of normal saline, and the treatment time was the same. Immediately after the end of treatment, animals are sacrificed and pancreatic tissue is collected for subsequent analysis.

value: pancreas

value: wild type

value: Saline control

tag: group

value: CTL


title: ChIP_SKMEL5_OE1_V5

description: Library name: ChIP_SKMEL5_OE1_V5


title: Rat_CTL_3

address: 安徽省合肥市瑶海区银领时代

description:
Library name: Lib_Rat_CTL_3
Control SD rat


title: CB-ECFC cells, Healthy2

description: Library name: sample3


title: adult_1

description:
Library name: sample 1
3' mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMl: read2 contains transcript seguence


title: Rat_CTL_1

address: 安徽省合肥市瑶海区银领时代

description:
Library name: Lib_Rat_CTL_1
Control SD rat


title: Rat_AP_3

address: 安徽省合肥市瑶海区银领时代

description:
Library name: Lib_Rat_AP_3
Acute pancreatitis model rat

value: L-Arg (5 mg/kg) 36h i.p.

value: AP


title: ChIP_SKMEL5_OE1_HMGB2

description: Library name: ChIP_SKMEL5_OE1_HMGB2


title: CB-ECFC cells, Diabetic1

description: Library name: sample2


title: C57BL6 germ-free mice, Liver, PBS treated M5

city: Camperdown

first: Jian

last: Tan

state: NSW

address: D17 Charles Perkins Centre, The University of Sydney

institute: The University of Sydney

description: Library name: Sample-L17

data_processing:
bcl2fastq 2.17
STAR 2.7.3a
Assembly: GRCm38
Supplementary files format and content: csv containing raw counts for each sample

source_name: Liver

extract_protocol:
RNA was extracted using the Trizol method from whole liver tissue, then RNA purified using the Qiagen RNAeasy MinElute Cleanup Kit
RNA libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina

value: Liver

value: WT, germ-free

value: PBS


title: 486_LS (lesional vitiligo)

description:
Library name: 486_LS
10X Genomics

value: Skin


title: ChIP_SKMEL5_EV2_V5

description: Library name: ChIP_SKMEL5_EV2_V5

value: empty vector


title: Rat_AP_2

address: 安徽省合肥市瑶海区银领时代

description:
Library name: Lib_Rat_AP_2
Acute pancreatitis model rat


title: C57BL6 germ-free mice, Liver, PBS treated M4

description: Library name: Sample-L15


title: M14 corticosterone 5 days

city: Magdalenka

first: Grzegorz

last: juszczak

address: Jastrzebiec, ul Postepu 36A

institute: Institute of Genetics and Animal Biotechnology

description:
enrichment of polyadenylated RNA
stranded library

data_processing:
Initial data analysis included quality validation of raw and trimmed data in fastq format using MultiQC and FastQC tools, trimming of adapters using Trim Galore, alignment of reads to mouse GRCm39 genome assembly using hisat2, quality validation of the aligned data using MultiQC / BamQC and feature counting with featureCounts. The count files were analyzed with edgeR package. The data derived from all 48 samples were filtered by filterByExpr function. The data were normalized with the normLibSizes function using default TMM method. Differences between groups were tested with the edgeR exactTest while Bonferroni-Hochberg method was used to calculate adjusted p-values.
Assembly: mouse GRCm39 genome assembly
Supplementary files format and content: Excel file containing CPM values for each sample and results of statistical comparisons between groups.

source_name: hippocampus

extract_protocol:
RNA was extracted from the individual hippocampal samples using the GeneMATRIX Universal RNA Purification Kit (Eurx) according to the manufacturer-supplied protocol. Obtained RNA samples were additionally purified with the DNase Max kit (Qiagen) to remove remnants of DNA.
Library construction protocol included mRNA enrichment with Oligo dT, RNA fragmentation and reverse transcription (second-strand cDNA synthesis with dUTP instead of dTTP for preparation of stranded specific mRNA libraries), end repair, A-tailing, adaptor ligation, PCR amplification, single strand separation and cyclization and DNA nanoball synthesis preceinding  sequencing on DNBseq platform.

value: hippocampus

tag: developmental stage

value: adult

tag: Sex

value: male

value: Swiss-Webster

value: corticosterone

value: 5 days


title: Chimpanzee_iPSC, Control3

first: Leijie

institute: UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER

description:
Ccontrol_3
Ccontrol_count.txt

data_processing:
Hisat2 v 2.1.0 and Stringtie v 2.1.7 pipeline
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore v 0.6.10
Trimmed sequence reads were mapped to GRCh38/GRCm39 genomics by using Hisat2 v 2.1.0
Read count extraction using StringTie v 2.1.7
Assembly: GRCh38 for human;  Pan_tro 3.0 for chimpanzee; Susie_PAB v2 for orangutan
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Pan troglodytes

source_name: Chimpanzee iPSCs

extract_protocol:
RNA was harvested using the RNeasy Mini Plus Kit (Qiagen).
RNA libraries for RNA-seq were prepared using the SMARTer mRNA-Seq Library Prep Kit following the manufacturer's protocols.

value: Chimpanzee iPSCs

value: pluripotent stem cells

value: WT


title: ChIP_SKMEL5_EV1_V5

description: Library name: ChIP_SKMEL5_EV1_V5

value: Tumor

value: Melanoma


title: Rat_AP_1

address: 安徽省合肥市瑶海区银领时代

description:
Library name: Lib_Rat_AP_1
Acute pancreatitis model rat

value: pancreas

value: wild type

value: L-Arg (5 mg/kg) 36h i.p.

value: AP


title: C57BL6 germ-free mice, Liver, PBS treated M3

description: Library name: Sample-L14

value: Liver

value: WT, germ-free

value: PBS


title: ChIP_SKMEL5_Input

description: Library name: ChIP_SKMEL5_Input

value: empty vector


title: CB-ECFC cells, Healthy3

description: Library name: sample5

value: cord-blood

value: Progenitor Endothelial cells


title: Chimpanzee_iPSC, Control2

description:
Ccontrol_2
Ccontrol_count.txt


title: Sleep deprived pulp

city: BEIJING,CHINA

first: SIQI

last: HUANG

institute: Capital of china medical university

description:
Library name: SD
SD

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: dental pulp tissue

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: dental pulp tissue

value: pulp cell

value: with sleep deprived


title: ChIP_SKMEL5_EV2_HMGB2

description: Library name: ChIP_SKMEL5_EV2_HMGB2


title: C57BL6 germ-free mice, Liver, PBS treated M1

description: Library name: Sample-L11


title: Chimpanzee_iPSC, Control1

city: Dallas

last: Li

description:
Ccontrol_1
Ccontrol_count.txt

value: Chimpanzee iPSCs

value: pluripotent stem cells


title: HK1_BOLF3

city: guangzhou

first: Ning

last: Meng

state: guangdong

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

data_processing:
lllumina casava1.7 software used for basecalling
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38
Fragments Per Kilobase of exon model per Million mapped fragments (TPMs) werw calculated using a protocol from Chepelev et al.
Assembly: hg38
Supplementary files format and content: TPM

extract_protocol:
Cells were lysed in 500 μl Trizol, and then 100 μl chloroform was added. After shaking for 50 seconds, the mixture was left on ice for 10 minutes. The upper aqueous phase was collected by centrifugation at 10,000 rpm for 15 minutes at 4°C. An equal volume of isopropanol was added to the collected aqueous phase and left at -20°C for 1 hour. Finally, RNA was precipitated by centrifugation at 10,000 rpm for 20 minutes at 4°C.
poly-A-tailed mRNA selection (PA)

value: THP1-derived macrophages

value: co-cultured with BOLF1-EVs (100 ng/ml for 48 h)


title: HeLa, MCM2

city: Durham

first: Yiran

last: Guo

state: North Carolina

address: 3 Genome Ct

institute: Duke University

description:
Library name: HeLa_MCM2
anti-MCM2 (Bethyl Laboratories, A300-191A)

data_processing:
Fastq files were mapped to the reference genome (hg19) using bowtie2.3.5
The non-primary alignments, PCR duplicates, or blacklist regions were removed from aligned data by Samtools (v1.9), Picard ‘MarkDuplicates’ function (v2.20.4), and bedtools (v2.28.0), respectively.
Peak calling was conducted by MACS2 (macs2 callpeak -f BAMPE -g hs/mm –keep-dup 1).
Bigwig files, heatmaps and averaged plotting of CUT&RUN signals were generated by deeptools (v3.3.0).
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

source_name: Adenocarcinoma

growth_protocol: HeLa cells were grown in high glucose DMEM plus 10% FBS and 1% antibiotics.

extract_protocol:
Cells or nuclei were permeabilized by digtonin and genomic DNA were fragmented by specific antibody recruited MNase. Then fragmented DNA were purified and subjected to library preparation.
Libraries were prepared for sequencing using standard Illumina protocols.

value: Adenocarcinoma

value: HeLa cells

value: epithelial cell


title: Normal pulp

description:
Library name: Con
Con

value: without sleep deprived


title: C57BL6 germ-free mice, Liver, EV treated M4

description: Library name: Sample-L9

value: Liver

value: EV


title: ChIP_SKMEL5_H3K4me3

city: New York

description: Library name: ChIP_SKMEL5_H3K4me3

value: Tumor

value: Melanoma


title: HeLa, PHF8

description:
Library name: HeLa_PHF8
anti-PHF8 (Abcam, ab36068)


title: CB-ECFC cells, Healthy1

description: Library name: sample1

value: cord-blood


title: HeLa, H3K27me3

description:
Library name: HeLa_H3K27me3
anti-H3K27me3 (Cell signaling, 9733)


title: C57BL6 germ-free mice, Liver, EV treated M3

description: Library name: Sample-L8

value: WT, germ-free


title: HK1_BOLF1


title: HeLa, BAHCC1, rep2

description:
Library name: HeLa_BAHCC1_rep2
anti-hBAHCC1(homemade, Fan et al; Nature Genetics, 2020)


title: HK1_3

value: co-cultured with an empty vector control (Vector-EVs)


title: C57BL6 germ-free mice, Liver, PBS treated M2

description: Library name: Sample-L12

value: PBS


title: ChIP_A375_KO1

description: Library name: ChIP_A375_KO1

value: HMGB2 gRNA


title: C57BL6 germ-free mice, Liver, EV treated M2

description: Library name: Sample-L7


title: ChIP_A375_NT_2_HMGB2

description: Library name: ChIP_A375_NT_2_HMGB2

value: Non-targeting gRNA


title: HeLa, BAHCC1, rep1

description:
Library name: HeLa_BAHCC1_rep1
anti-hBAHCC1(homemade, Fan et al; Nature Genetics, 2020)


title: ChIP_A375_Input

description: Library name: ChIP_A375_Input


title: ChIP_SKMEL5_EV1_HMGB2

description: Library name: ChIP_SKMEL5_EV1_HMGB2

value: empty vector


title: PDX333

first: Subhransu

middle: S

last: Sahoo

address: 5323 Harry Hines Blvd

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
bcl files were converted to fastq using bcl2fastq
fastq files were mapped to reference genome using STAR
gene quantification was performed using subread module featurecount using igenomes gtf
Assembly: hg19
Supplementary files format and content: read counts as a text file

source_name: PDX

growth_protocol: The endometrial cancer patient tumor samples were subcutaneously implanted into female NOD scid gamma mice and once the tumors grown the mice were euthanized, and the tumors harvested.

extract_protocol:
Total RNA from PAX2- PDX333 was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) following the manufacturer's instructions.

treatment_protocol: The mice were fed ad libitum on standard chow diet without any treatment.

value: PDX

value: tumor cells (mixed)


title: HK1_BOLF2

value: THP1-derived macrophages

value: co-cultured with BOLF1-EVs (100 ng/ml for 48 h)


title: HK1_2


title: C57BL6 germ-free mice, Liver, EV treated M1

description: Library name: Sample-L6


title: Multiome, EPR Sample 3, GEX

city: Chicago

first: Serdar

middle: E.

last: Bulun

state: IL

address: 303 E Superior Street

department: Obstetrics & Gynecology

institute: Northwestern Feinberg School of Medicine

description: Library name: 1845-EPR_GEX

data_processing:
Multiome files were demultiplexed using Cellranger mkfastq
Demultiplexed data were processed and aligned to the mm10 genome using the CellrangerArc 2.0.2 pipeline
Raw RNA counts were first decontaminated, and then low-quality cells were filtered using both RNA and ATAC QC factors. After filtering, RNA data was log-normalized, and ATAC accessibility values were normalized.
Assembly: mm10
Supplementary files format and content: The processed data from all samples used in this study is stored in a single Seurat object (.rds format).

molecule: nuclear RNA

source_name: Lower abdominal muscle

extract_protocol:
Nuclei isolated from entire LAM utilizing the Chromium Nuclei Isolation Kit with RNase Inhibitor (10X Genomics, #PN-1000494).
Libraries were constructed according to the default manual from 10X Genomics, with further details listed in You et. al. Role of progesterone receptor in inguinal hernia formation via skeletal muscle fibrosis.

treatment_protocol: WT mice 8-10 weeks of age were treated with with placebo/vehicle, E2+P4, or E2+P4+RU486 for 10 weeks before harvesting the LAM.

value: Lower abdominal muscle

tag: strain

value: FVB/N

value: wild-type


title: HK1_1


title: ChIP_A375_NT_1_HMGB2

description: Library name: ChIP_A375_NT_1_HMGB2

tag: genotype


title: C57BL6 germ-free mice, Liver, EV treated M5

description: Library name: Sample-L10

value: Liver

value: EV


title: HeLa_Y1993A_H4K20me2_CUT&Tag

city: Chapel Hill

first: Gang Greg

last: Wang

state: NORTH CAROLINA

address: 405 West Drive

department: UNC Lineberger Comprehensive Cancer Center; Department of Biochemistry and Biophysics

institute: University of North Carolina at chapel hill

data_processing:
Fastq files were mapped to the reference genome (hg19/mm10/dm3) using bowtie2.3.5.
The non-primary alignments, PCR duplicates, or blacklist regions were removed from aligned data by Samtools (v1.9), Picard ‘MarkDuplicates’ function (v2.20.4), and bedtools (v2.28.0), respectively.
Peak calling was conducted by MACS2 (macs2 callpeak -f BAMPE -g hs/mm –keep-dup 1).
Bigwig files, heatmaps and averaged plotting of CUT&RUN and CUT&Tag signals were generated by deeptools (v3.3.0).
Assembly: hg19/dm3/mm10
Supplementary files format and content: bigWig files.
Library strategy: CUT&Tag

organism:
Homo sapiens
Mus musculus

source_name: HeLa cells/MEF cells

growth_protocol: HeLa cells were grown in high glucose DMEM base medium plus 10% FBS and 1% antibiotics.

extract_protocol:
Cells or nuclei were permeabilized by digitonin and genomic DNA were fragmented by specific antibody recruited MNase or Tn5. Then, the fragmented DNA was purified and subjected to multiplexed library preparation.
The multiplexed libraries were prepared for sequencing by using standard Illumina protocols.

treatment_protocol: HeLa cells with the homozygous BAHCC1 TTD-dead mutation (Y1993A) were generated via CRISPR-cas9 based genome editing. HA-tagged MCM3 or HA-tagged ORC1 was introduced into HeLa cells followed by selection for stable expression, which was then doxycycline induced (cells treated with 0.1μg/mL of doxycycline for 24 h).

tag: cell line (human)

value: HeLa

tag: cell line (mouse)

value: MEF

tag: genotype (hela)

value: BAHCC1 TTD-dead mutation Y1993A

tag: antibody

value: anti-H4K20me2 (Invitrogen, MA5-31510)


title: Sample_PAX2- PDX164

state: Texas

data_processing:
bcl files were converted to fastq using bcl2fastq
fastq files were mapped to reference genome using STAR
gene quantification was performed using subread module featurecount using igenomes gtf
differential expression analysis was performed using edgeR
Assembly: hg19
Supplementary files format and content: Normalized TPM counts as a text file

extract_protocol:
Total RNA from PAX2+ PDX and PAX2- PDX were isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) following the manufacturer's instructions.


title: Multiome, EPR Sample 2, GEX

description: Library name: 1693-EPR_GEX


title: HeLa_WT_H4K20me2_CUT&Tag

value: WT


title: Sample_AN3CA_Sh_PAX2_3

description:
S6.TPM
AN3CA.igenomes.genes_normalized.counts.TPM.tab

source_name: Uterus

growth_protocol: AN3CA cells with or without PAX2 were cultured in MEM medium supplemented with 10% FBS and antibiotics (50 U/mL penicillin and 50 mg/L streptomycin) in a humidified atmosphere at 370C containing 5% CO₂.

extract_protocol:
Total RNA from AN3CA cells with or without PAX2 was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) following the manufacturer's instructions.

treatment_protocol: AN3CA cells with or without PAX2 were treated with puromycin to select positively transduced cells.

value: Uterus

value: epithelial cells

value: PAX2 KD


title: Multiome(ATAC)-LSP3_NSCs

city: Bangalore

first: Raghu

last: Padinjat

state: Karnataka

address: Kodigehalli

institute: National Centre for Biological Sciences (NCBS)

description: Library name: LSP3_atac_fragments.tsv.gz

library_source: genomic single cell

data_processing:
Cellranger arc
Assembly: hg38
Supplementary files format and content: Cellranger arc output files: gene expression .h5 files; ATAC .gz.tsv and .gz.tsv.tbi files

source_name: IPSC-derived

extract_protocol:
Nuclei from WT1, LSP NSCs were isolated as per the 10xgenomics protocol for frozen cell lines (CG000365, Rev D).
Libraries for multiome experiment were prepared as per the CG000338 Rev D protocol.

value: IPSC-derived

value: Neural Stem Cells (NSCs)

value: Lowe Syndrome Patient


title: HeLa_KO_H4K20me1_CUT&Tag

value: BAHCC1 KO

value: anti-H4K20me1 (Abcam 9501)


title: Multiome, EPR Sample 2, ATAC

description: Library name: 1693-EPR_ATAC

value: Lower abdominal muscle

value: FVB/N


title: Sample_AN3CA_Sh_PAX2_2

description:
S5.TPM
AN3CA.igenomes.genes_normalized.counts.TPM.tab


title: Multiome(ATAC)-LSP2_NSCs

description: Library name: LSP2_atac_fragments.tsv.gz


title: Multiome, EPR Sample 1, GEX

description: Library name: 1634-EPR_GEX

value: wild-type


title: Multiome(ATAC)-WT1_NSCs

description: Library name: WT1_atac_fragments.tsv.gz

value: Control


title: Sample_AN3CA_Sh_PAX2_1

description:
S4.TPM
AN3CA.igenomes.genes_normalized.counts.TPM.tab


title: Multiome, EPR Sample 3, ATAC

description: Library name: 1845-EPR_ATAC


title: Multiome(GEX)-LSP3_NSCs

description: Library name: LSP3_filtered_feature_bc_matrix.h5


title: Multiome, EPR Sample 1, ATAC

description: Library name: 1634-EPR_ATAC


title: Sample_AN3CA_Sh_EV_3

description:
S3.TPM
AN3CA.igenomes.genes_normalized.counts.TPM.tab


title: ChIP_A375_H3K4me3

description: Library name: ChIP_A375_H3K4me3

value: Tumor

value: Melanoma

value: Non-targeting gRNA


title: Multiome, EP Sample 4, GEX

description: Library name: 1700-EP_GEX


title: HeLa_Y1993A_hBAHCC1_CUT&Tag

value: HeLa

value: MEF

value: BAHCC1 TTD-dead mutation Y1993A

value: anti-hBAHCC1 (homemade; Fan et al., Nature Genetics, 2020)


title: Multiome(GEX)-LSP2_NSCs

description: Library name: LSP2_filtered_feature_bc_matrix.h5


title: HeLa_WT_H4K20me1_CUT&Tag

value: WT


title: Multiome, EP Sample 4, ATAC

description: Library name: 1700-EP_ATAC


title: Sample_AN3CA_Sh_EV_1

description:
S1.TPM
AN3CA.igenomes.genes_normalized.counts.TPM.tab

value: Uterus

value: epithelial cells


title: ChIP_A375_KO2

description: Library name: ChIP_A375_KO2

value: HMGB2 gRNA


title: Multiome(GEX)-WT1_NSCs

description: Library name: WT1_filtered_feature_bc_matrix.h5

value: IPSC-derived

value: Neural Stem Cells (NSCs)


title: HeLa_WT_hBAHCC1_CUT&Tag


title: Multiome, EP Sample 3, GEX

description: Library name: 1696-EP_GEX

value: Lower abdominal muscle


title: Sample_PAX2 re-expressed_P3

growth_protocol: Ishikawa cells with or without PAX2 were cultured in MEM medium supplemented with 5% FBS and antibiotics (50 U/mL penicillin and 50 mg/L streptomycin) in a humidified atmosphere at 370C containing 5% CO₂.

extract_protocol:
Total RNA from Ishikawa cells with or without PAX2 was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) following the manufacturer's instructions.

treatment_protocol: Ishikawa cells with or without PAX2 were treated with puromycin to select positively transduced cells. After stable line selection, cells were treated with doxycycline to induce PAX2 expression.

value: Ishikawa

value: PAX2 re-expressed

value: Doxycycline


title: MB468_sgPACT-2_rep3

city: West Lafayette

first: Kyle

last: Cottrell

state: IN

address: 201 S University Street

department: Medicine

institute: Purdue University

description:
Library name: 12-MB468-sgPACT-2
rRNA depleted

data_processing:
Sequence reads were processed using Trimmomatic v.0.36 to remove adapter sequences and poor quality nucleotides. Trimmed reads were aligned to GRCh38 reference genome using STAR aligner v2.5.2b (RRID:SCR_004463). Gene counts were determined using featureCounts from Subread v.1.5.2 (RRID:SCR_009803), only unique exonic reads were counted.
Assembly: GRCh38
Supplementary files format and content: Gene counts from featureCounts, in txt file

source_name: cell line

extract_protocol:
Total RNA was purified using the Nucleospin RNA kit (Macherey-Nagel).
RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). Samples were initially treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA contaminants. The next steps included performing rRNA depletion using QIAseq® FastSelect™−rRNA HMR kit (Qiagen, Germantown, MD, USA ), which was conducted following the manufacturer’s protocol. RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations. Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: cell line

value: TNBC cell line


title: Multiome, EP Sample 3, ATAC

description: Library name: 1696-EP_ATAC

value: FVB/N

value: wild-type


title: Sample_PAX2 re-expressed_P2


title: MB468_sgNTA_rep3

description:
Library name: 11-MB468-sgNTA
rRNA depleted

value: sgNTA


title: HeLa_Y1993A_H4K20me1_CUT&Tag

value: HeLa

value: MEF

value: BAHCC1 TTD-dead mutation Y1993A

value: anti-H4K20me1 (Abcam 9501)


title: Multiome, EP Sample 2, GEX

description: Library name: 1635-EP_GEX


title: MB468_sgPACT-2_rep2

description:
Library name: 10-MB468-sgPACT-2
rRNA depleted


title: Multiome, EP Sample 2, ATAC

description: Library name: 1635-EP_ATAC


title: Sample_PAX2 re-expressed_P1

value: Uterus

value: epithelial cells


title: MB468_sgNTA_rep2

description:
Library name: 9-MB468-sgNTA
rRNA depleted


title: MB468_sgPACT-2_rep1

description:
Library name: 8-MB468-sgPACT-2
rRNA depleted


title: Sample_WT_E3

value: WT


title: Sample_WT_E2


title: OE, D4, -/-

city: Minneapolis

first: Daniel

last: Garry

address: 2231 6th Street SE, Suite 4-156

institute: University of Minnesota

description:
Library name: Garry_102_Lane2_FL_S13
10X Genomics

data_processing:
Single cell RNA-seq expression was quantified using unique molecular identifiers (UMIs) by 10x Genomics’ “Cell Ranger” software.
Assembly: Mus musculus reference genome mm10 (GRCm38)
Supplementary files format and content: The processed data file is in HDF5 format and was generated using the Cell Ranger pipeline (10x Genomics). It contains filtered gene expression matrices for high-quality nuclei, including cell barcodes, gene annotations, and UMI count matrices in sparse format. Only nuclei that passed quality control filtering are included.

source_name: Embryoid bodies

extract_protocol:
Single cells from differentiated iHA-Etv2 embryoid bodies (EBs) at days 2, 3, and 4 (with and without doxycycline treatment) were isolated by FACS based on FLK1 and PDGFRα expression. Flow cytometry staining was performed using fluorophore-conjugated antibodies: FLK1-APC and PDGFRα-PE. Propidium iodide (PI) was used to exclude non-viable cells. A minimum of 10,000 viable cells were collected per condition for single-cell RNA sequencing.
Single-cell RNA-seq was performed using the 10x Genomics Chromium Single Cell platform. Cell barcoding and cDNA library preparation were carried out following the manufacturer's protocol at the University of Minnesota Genomics Center (UMGC). Library quality was assessed using an Agilent Bioanalyzer High Sensitivity DNA chip. Sequencing was performed on an Illumina NovaSeq S4 platform with 2 × 150 bp reads, targeting approximately 50,000 reads per cell.

value: Embryoid bodies

value: iHA-Etv2 (inducible HA-tagged Etv2) ESCs

value: Embryonic stem cell-Embryoid body (ES-EB)

value: OE


title: Multiome, EP Sample 1, GEX

description: Library name: 1583-EP_GEX

value: Lower abdominal muscle


title: Multiome, Veh Sample 3, GEX

description: Library name: 1795-veh_GEX

value: Vehicle


title: MB468_sgNTA_rep1

description:
Library name: 7-MB468-sgNTA
rRNA depleted

value: cell line

value: TNBC cell line


title: HCC1806_sgPACT-2_rep3

description:
Library name: 6-HCC1806-sgPACT-2
rRNA depleted


title: Multiome, Veh Sample 3, ATAC

description: Library name: 1795-veh_ATAC

value: FVB/N

value: wild-type


title: HeLa_WT_HA-ORC1_CUT&RUN

data_processing:
Fastq files were mapped to the reference genome (hg19/mm10/dm3) using bowtie2.3.5.
The non-primary alignments, PCR duplicates, or blacklist regions were removed from aligned data by Samtools (v1.9), Picard ‘MarkDuplicates’ function (v2.20.4), and bedtools (v2.28.0), respectively.
Peak calling was conducted by MACS2 (macs2 callpeak -f BAMPE -g hs/mm –keep-dup 1).
Bigwig files, heatmaps and averaged plotting of CUT&RUN and CUT&Tag signals were generated by deeptools (v3.3.0).
Assembly: hg19/dm3/mm10
Supplementary files format and content: bigWig files.
Library strategy: CUT&RUN

source_name: HeLa cells

value: HeLa

value: WT, HA-ORC1

value: dox_0.1ug/mL for 24h

value: anti-HA (Abcam, ab9110)


title: Multiome, Veh Sample 2, GEX

description: Library name: 1793-veh_GEX


title: HCC1806_sgPACT-2_rep2

description:
Library name: 4-HCC1806-sgPACT-2
rRNA depleted


title: fc2_pub4_24h_rep3

city: Tucson

first: Jesse

middle: Daniel

last: Woodson

state: AZ

address: 1140 E. South Campus Drive, 303 Forbes Hall

department: School of Plant Sciences

institute: University of Arizona

data_processing:
Each sample is represented by two raw files. Concatenation of RAW fastq files was done as: cat file1.fastq file2.fastq > mergedfile.fastq
Data was processed and reads were aligned to the Arabidopsis TAIR10 genome using the CyVerse's Discovery Environment: RMTA (Read Mapping, Transcript Assembly) v.2.6.3 (HISAT2, Stringtie) pipeline with default parameters. Reference: Peri et al., 2020; doi: 10.3389/fgene.2019.01361. PMID: 32038716. HISAT2 (v2.1.0) was used to align sequencing reads. Reads were assembled into transcripts using StringTie (v1.3.4).
The “feature_counts.txt” file obtained from RMTA was used as input for differential gene expression statistical analyses using DESeq2 in R studio (available through CyVerse) with default parameters.
The DESeq2 was performed between samples (i.e., wt vs. mutants in 24h or cycling (16h) light conditions)
Assembly: TAIR10 reference sequence
Supplementary files format and content: feature_counts.txt: tab-delimited text file that includes feature counts of all 18 samples
Supplementary files format and content: deseq2.xlsx: Excel file that includes Gene ID, base mean, Log2Fold Change, fold change, lfcSE, p value, and padj. Each tab is a pairwise comparison between wt and a mutant (fc2 or fc2 pub4) in 24h or 16h (cycling) light conditions.

source_name: total leaf tissue

growth_protocol: Seeds were sterilized and spread on plates containing Linsmaier and Skoog medium pH 5.7 with 0.6% micropropagation type-1 agar powder. Following 3-5 day stratification at 4°C in the dark, seeds were germinated in 24h constant light (permissive) conditions. Seven-day-old plants were then transfered to soil and grown under 120 μmol photons m-2 sec-1 light, at 21°C and 60% humidity.

extract_protocol:
RNA was harvested from total leaf tissue was collected from 19-day-old plants one hour after subjective dawn. Samples were collected in biological triplicates, each replicate consisting of leaves pooled from three plants. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) and residual DNA was removed with the RNase-Free DNase Kit (Qiagen).
A Qubit 2.0 Fluorometer was used to calculate RNA concentration and 4 mg of total RNA was used to prepare libraries with the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, US).

treatment_protocol: Plants were grown under constant (24h) light conditions for 17 days and then shifted to cycling (16h) light conditions (16h light / 8h dark) for 2 days. As a control. A second set of plants reminaed in 24 constant light conditions for the full 19 days.

value: total leaf tissue

value: 19 days constant light

tag: time point

value: harvested 1 hour post subjective dawn on day 19


title: HCC1806_sgC1_rep3

description:
Library name: 5-HCC1806-sgC1
rRNA depleted


title: Multiome, EP Sample 1, ATAC

description: Library name: 1583-EP_ATAC


title: Sample_WT_E1

value: Uterus

value: Ishikawa

value: epithelial cells

value: WT

value: Doxycycline


title: Multiome, Veh Sample 2, ATAC

description: Library name: 1793-veh_ATAC

value: Lower abdominal muscle

value: Vehicle


title: fc2_pub4_24h_rep2


title: HCC1806_sgC1_rep2

description:
Library name: 3-HCC1806-sgC1
rRNA depleted

value: cell line

value: TNBC cell line


title: HeLa_WT_H3K4me1_CST_CUT&Tag

value: anti-H3K4me1 (Cell Signaling Technology, 5326)


title: fc2_pub4_24h_rep1


title: HCC1806_sgPACT-2_rep1

description:
Library name: 2-HCC1806-sgPACT-2
rRNA depleted