title: ATAC-seq on CRISPR mESC R1 cells, Oct4-Sox2 at Btbd11 enhancer mutated, replicate 2

description: Library name: mesc_Btbd11_scenario_WT_coop_mut_B_atac_2

value: CRISPR Oct4-Sox2 mutation at Btbd11 enhancer


title: ATAC-seq on CRISPR mESC R1 cells, Sox2 at Btbd11 enhancer mutated, replicate 2

status: Public on Oct 31 2025

type: SRA

city: Kansas City

first: Melanie

last: Weilert

state: MO

country: USA

institute: Stowers Institute for Medical Research

description: Library name: mesc_Btbd11_scenario_WT_coop_mut_A_atac_2

library_source: genomic

data_processing:
Reads were pre-trimmed for adapters using Cutadapt (v.4.2) and aligned to the mouse genome assembly mm10 using bowtie2 (v.2.3.5.1).
Any CRISPR ATAC-seq experiments were aligned to a custom mm10 genome assembly modified to contain the expected CRISPR mutations. Duplicated alignments were marked using Picard (v.2.23.8) (Broad Institute n.d.). Alignments were then deduplicated, filtered for fragment lengths exceeding 600 bp, corrected for dovetailed alignment pairs, and end-adjusted to accommodate the Tn5 enzymatic cut correction of -4/+4.
Normalized read-per-million (RPM) ATAC-seq tracks were generated by scaling the aligned coverage to the weighted total reads.
Cut site ATAC-seq coverage used for training ChromBPNet models were generated by isolating the bases on each end of an aligned fragment, consolidating those “cut events” into coverage tracks. ATAC-seq peaks were mapped using MACS2 (v.2.2.7.1) with default settings.
Assembly: UCSC mm10
Supplementary files format and content: BigWig coverage of ATAC-seq cutsites

molecule: genomic DNA

organism: Mus musculus

growth_protocol: R1 ESCs were cultured on 0.1% gelatin-coated plates without feeder cells in N2B27 medium (DMEM/F12 with 1:1 mix of GlutaMax/N2 and Neurobasal medium/B27, Invitrogen) supplemented with 2 mM L-glutamine (Stemcell Technologies), 1x 2-mercaptoethanol (Millipore), 1x NEAA (Stemcell Technologies), 3 µM CHIR99021 (Stemcell Technologies), 1 µM PD0325901 (Stemcell Technologies), 0.033% BSA solution (Invitrogen) and 107 U/mL LIF (Millipore).

extract_protocol:
For each ATAC-seq experiment, 100,000 R1 wildtype or CRISPR-edited mouse embryonic stem cells were used. Cells were washed once in cold PBS, with centrifugation at 500 x g and 4 °C for 5 minutes. The cell pellets were then resuspended in 50 µL of cold ATAC Resuspension Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) supplemented with 0.1% IGEPAL CA-630, 0.1% Tween-20, and 0.01% Digitonin (Promega, G9441). After a 3 minute incubation on ice, 1 mL of cold ATAC Resuspension Buffer supplemented with 0.1% Tween-20 was added and the samples were centrifuged at 500 x g and 4°C for 10 minutes. Tagmentation was performed at 1000 rpm and 37 °C for 30 minutes in a 50 μL reaction volume containing 10 μL of 5x Tagment DNA Buffer (50 mM Tris-HCl pH 7.4, 25 mM MgCl2, 50% DMF), 0.5 μL 10% Tween-20, 0.5 μL 1% Digitonin,1 µL of 20 µM Tn5 transposase loaded with oligonucleotides, and 38 µL water. For all experiments, the Tn5 used was purified in-house using pETM11-Sumo3-Tn5 and His6-tagged SenP2 protease plasmids.
DNA fragments were purified using the Monarch PCR & DNA Cleanup Kit (NEB, #T1030) and used as input for library preparation using Illumina Nextera Dual Indexing. During library preparation, qPCR was performed to prevent over-amplification, and libraries were purified using a 2% agarose gel and the Monarch DNA Gel Extraction kit (NEB, #T1020). Paired-end sequencing was performed on an Illumina NextSeq 500 and 2000 instruments (2 x 75 bp cycles).

treatment_protocol: For each of the five candidate mutations across two genomic loci  (Akr1cl and Btbd11 enhancers), crRNA target sites were designed using the IDT target predictor tool by evaluating the predicted on-target efficiency score and off-target potential. Alt-R CRISPR-Cas9 crRNA was designed to contain ∼40 bases of homology from the targeted cut site. Equimolar amounts (stock of 100 μm) of Alt-R crRNA and tracrRNA-ATTO550 were mixed to form gRNA at a final concentration of 50 μM. The mixture was heated at 95°C for 5 min and cooled at RT. The single-stranded donor oligonucleotides (ssODN) were designed to contain ∼40 bases of homology from the targeted cut site (crRNA and ssODN sequences were designed using the IDT software tool). A ribonucleoprotein (RNP) complex was formed by combining 150 pmol of gRNA (crRNA+tracrRNA) and 125 pmol of Cas9 HiFi v3 protein (IDT) with hybridization for 20 min at RT. The RNP was combined with 100 pmol of ssODN donor and 100 pmol of electroporation enhancer v2 and delivered to 1.5e5 cells by Neon electroporation (1,400 V, 10 m, 3 pulses; Neon Transfection System, MPK5000, Life Technologies). Immediately after electroporation, cells were cultured in 0.5 μM Alt-R HDR enhancer V2 of 0.69 mM. After 24 h, cells were washed with PBS before FACS sorting on S6 FACSymphony. Single cells were directly sorted into 96-well plates. Cells were screened for the expected mutations through paired-end sequencing on an Illumina MiSeq instrument (250 cycles).

tag: cell line

tag: genotype

value: CRISPR Sox2 mutation at Btbd11 enhancer


title: control, RV, replicate3

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

library_source: transcriptomic single cell

data_processing:
All datasets were processed using Cellranger 2.0.2.
FASTQ files were generated using the mkfastq function
Reads were aligned to a custom mm9 reference containing tdTomato and ZsGreen reporter genes.
Cellranger aggr was used to aggregate individual libraries after read depth normalization.
Data was analyzed using Seurat v3
Assembly: mm9
Supplementary files format and content: Seurat object

molecule: total RNA

source_name: mouse embryonic heart

extract_protocol:
Embryonic hearts were dissected from pregnant dams at E13.5 in 1% FBS in PBS. Yolk sacs were used for genotyping. Hearts were then microdissected to obtain the interventricular septum (IVS), left ventricular (LV) and right ventricular (RV) tissue. Tissues were singularized with TryplE at 37C, quenched with 1% FBS in PBS, filtered and centrifuged at 300g for 5 minutes. The resulting pellet was resuspended in 1% FBS in PBS and counted using an automated cell counter. A 30μL aliquot of the cell suspension was used for library generation.
Single cell droplet libraries were generated with the Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1, accoring to manufacturer's instructions.

tag: tissue

value: mouse embryonic heart

tag: developmental stage

value: control


title: K4me3_CCRCC1570

city: Boston

first: Karl

last: Semaan

state: MA

address: Brookline Ave 450

institute: Dana-Farber Cancer Institute

data_processing:
ChIP-seq and MeDIP-seq reads were aligned to the hg19 human genome build using Burrows–Wheeler Aligner version 0.7.1740. Non-uniquely mapping and redundant reads were discarded. MACS version 2.1.1.2014061641 was used for ChIP-seq peak calling with a q value (false discovery rate (FDR)) threshold of 0.01. Fragment locations were converted to BED files using BEDTools (version 2.29.2) bamtobed with the -bedpe flag set. For analyses involving overlap with genomic regions, fragments were imported as GRanges objects and collapsed to 1 bp at the center of the fragment location to ensure that a fragment can map to only one site. LPWGS data were used to estimate ctDNA using ichorCNA with default settings.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

organism: Homo sapiens

source_name: Plasma

extract_protocol:
MeDIP was performed using the MagMeDIP kit from Diagenode.Samples were purified using the iPure Kit v2 from Diagenode
ChIP-seq libraries were generated from purified input and IP sample DNA using the ThruPLEX DNA-seq Kit from TakaraBio. Libraries were sequenced using 150-base paired-end reads on an Illumina platform. MeDIP-Seq libraries were generated using the KAPA HyperPrep Kit, complemented by end-repair, A-tailing, and ligation of NEBNext adaptors. 10 ng of DNA was used as starting material.Libraries were sequenced using 150-base paired-end reads on an Illumina platform.

value: Plasma

tag: experiment type

value: H3K4me3 ChIP-seq

tag: genome build


title: ATAC-seq on CRISPR mESC R1 cells, Sox2 at Btbd11 enhancer mutated, replicate 1

description: Library name: mesc_Btbd11_scenario_WT_coop_mut_A_atac_1


title: mutant, IVS, replicate1, techrep3

value: mutant


title: normal diet 20 weeks, No.3

city: DAEGU

first: Soyoung

last: Kwak

address: Myeongdeok-ro 16-gil

department: Nuclear Medicine

country: South Korea

institute: Keimyung University Dongsan Hospital

description: Library name: B1_con3

library_source: transcriptomic

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012).
Bowtie2  indices were either generated from genome assembly sequence or the representative transcript  sequences for aligning to the genome and transcriptome.
The alignment file was used for assembling transcripts, estimating their abundances and detecting differential expression of genes.  Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010).
The RC (Read Count) data were processed based on TMM+CPM normalization method using EdgeR within R (R development Core Team, 2020)  using Bioconductor (Gentleman et al.,2004).
Gene classification was based on searches done by DAVID (http://david.abcc.ncifcrf.gov/) and Medline databases (http://www.ncbi.nlm.nih.gov/).
Assembly: mm10
Supplementary files format and content: FASTQC files include raw counts for each sample

source_name: epididymal white adipose tissue

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed by Agilent 2100 bioanalyzer using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using ND-2000 Spectrophotometer (Thermo Inc., DE, USA).
For control and test RNAs, the construction of library was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions. In brief, each 500ng total RNA were prepared and an oligo-dT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to the RNA and reverse transcription was performed. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. The double-stranded library was purified by using magnetic beads to remove all reaction components.

value: epididymal white adipose tissue

value: Wild type

tag: treatment

value: normal diet

tag: batch


title: ATAC-seq on wildtype mESC R1 cells, CRISPR side-by-side control, replicate 2

description: Library name: mesc_Btbd11_scenario_WT_coop_WT_atac_2

value: WT


title: K4me3_CCRCC2973


title: K4me3_CCRCC2970


title: control, RV, replicate2


title: control, RV, replicate1


title: ATAC-seq on CRISPR mESC R1 cells, distal Sox2 at Akr1cl enhancer mutated, replicate 1

description: Library name: mesc_Akr1cl_scenario_context_mut_A_atac_1

value: CRISPR distal Sox2 mutation at Akr1cl enhancer


title: ATAC-seq on native mESC R1 cells, replicate 2

description: Library name: mesc_native_atac_2


title: K27ac_TRCC_27

value: H3K27ac ChIP-seq


title: ATAC-seq on wildtype mESC R1 cells, CRISPR side-by-side control, replicate 1

description: Library name: mesc_Btbd11_scenario_WT_coop_WT_atac_1


title: control, LV, replicate4


title: K27ac_TRCC_26


title: ATAC-seq on native mESC R1 cells, replicate 1

description: Library name: mesc_native_atac_1


title: control, LV, replicate3


title: K27ac_TRCC_5


title: K27ac_TRCC_25


title: ChIP-nexus on CRISPR mESC R1 cells, proximal Sox2 at Akr1cl enhancer mutated, replicate 3

description: Library name: mesc_Akr1cl_scenario_context_mut_B_sox2_nexus_3_r1.fastq.gz

data_processing:
Reads were preprocessed by trimming off fixed and random barcode components from the sequenced reads, reassigning barcode information as read names for downstream processing.
Reads were pre-trimmed for adapters using Cutadapt (v.4.2) and aligned to the mouse genome assembly mm10 using bowtie2 (v.2.3.5.1). Any CRISPR ChIP-nexus experiments were aligned to a custom mm10 genome assembly modified to contain the expected CRISPR mutations. Alignments were then deduplicated from aligned coordinates and their corresponding barcodes. Coverage was generated pooling the first “stop” base of each deduplicated read, separated into two tracks by read orientation.
Normalized read-per-million (RPM) ChIP-nexus tracks were generated by scaling the aligned coverage to the weighted total reads.
ChIP-nexus peaks were mapped using MACS2 (v.2.2.7.1) with parameters designed to resimulate the full fragment length coverage rather than the single stop base coverage (--keep-dup=all -f=BAM --shift=-75 --extsize=150).
Assembly: UCSC mm10
Supplementary files format and content: BigWig coverage of ChIP-nexus data, separated by positive and negative strands

extract_protocol:
ChIP-nexus experiments were performed using 10 million cells per ChIP. The cells were first washed once with PBS, crosslinked using 1% formaldehyde, and quenched after 10 minutes using 125 mM glycine. Fixed cells were then washed twice more with ice cold PBS and resuspended in chilled lysis buffer (15 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.5% N-lauroylsarcosine, 0.1% sodium deoxycholate and 0.1% SDS). After a 10 minute incubation on ice, a Bioruptor Pico (Diagenode) was used to sonicate the chromatin with five or six cycles, 30 seconds on/off. The commercially available Sox2 (Active Motif, 39843) antibody was used for these experiments. For each ChIP, 10 µg of antibody was conjugated to 50 µL of Protein A or G dynabeads (Invitrogen).
Following the ChIP, ChIP-nexus library preparation was performed including end repair, dA-tailing, adapter ligation, barcode extension, and lambda exonuclease digestion. Addition of the ChIP-nexus adapter mix containing four fixed barcodes and PCR library amplification was performed directly after circularization of the purified DNA fragments (without addition of the oligo and BamHI digestion).

value: CRISPR proximal Sox2 mutation at Akr1cl enhancer


title: K27ac_TRCC_8


title: ATAC-seq on CRISPR mESC R1 cells, Oct4-Sox2 at Btbd11 enhancer mutated, replicate 1

description: Library name: mesc_Btbd11_scenario_WT_coop_mut_B_atac_1


title: K27ac_TRCC_24


title: control, LV, replicate2


title: ChIP-nexus on CRISPR mESC R1 cells, distal Sox2 at Akr1cl enhancer mutated, replicate 3

description: Library name: mesc_Akr1cl_scenario_context_mut_A_sox2_nexus_3_r1.fastq.gz


title: ChIP-nexus on CRISPR mESC R1 cells, distal Sox2 at Akr1cl enhancer mutated, replicate 1

description: Library name: mesc_Akr1cl_scenario_context_mut_A_sox2_nexus_1_r1.fastq.gz


title: ATAC-seq on native mESC R1 cells, replicate 3

description: Library name: mesc_native_atac_3


title: K27ac_TRCC_22


title: ChIP-nexus on wildtype mESC R1 cells, CRISPR side-by-side control, replicate 2

description: Library name: mesc_R1_sox2_nexus_crisprctl_2


title: K27ac_TRCC_13_6


title: control, LV, replicate1, techrep1


title: control, IVS, replicate4, techrep2


title: Tumor microenvironment cells, HiPt

city: Birmingham

first: Runhua

last: Liu

state: AL

address: 1720 2nd Avenue South

institute: University of Alabama at Birmingham

description:
Library name: Sample 12
Gene_Counts All samples.txt

data_processing:
The final sequenced data will be processed by 10xGenomics Cell Ranger pipeline and then visualized by Loupe browser or Partek software, or by “R” Seurat package. RNA-seq data was analyzed with Partek software.
Assembly: Mus_musculus (mm10)

source_name: Prostate

extract_protocol:
For RNA-seq, epithelial cells were stained with EPCAM, viability dye, and 7-AAD, and viable cells were sorted from the digested prostate and further extracted with QIAGEN Rneasy RNA Micro Kit. 150 ng RNA was used for the construction of a sequencing library. For scRNA-seq, the whole prostate was digested by collagenase/hyaluronidase (Cat# 07912) StemCell) for 1-2 h. Viable cells were sorted from whole digested prostate, 10,000 cells were collected for further sequencing library.
Sorted viable single cells will loaded into 10xcontroller and individual cells will be captured into oil droplets to form Gel Bead-In-EMulsions (GEMs). The single cell cDNA libraries will be constructed by following 10xGenomics Chromium GEM-X Single Cell 3' v4 Gene Expression User Guide, and then sequenced by illumina Nextseq500 or Novaseq 6000 machine, with targeting minimum 20,000 reads/cell.

value: Prostate

tag: cell type

value: Tumor microenvironment cells

value: Hi-Myc/Ptenf/f


title: Tumor microenvironment cells, Pten KO

description:
Library name: Sample 11
Gene_Counts All samples.txt

value: Ptenf/f


title: K27ac_TRCC_13_5


title: Tumor microenvironment cells, Scr

description:
Library name: Sample 9
Gene_Counts All samples.txt


title: control, IVS, replicate4, techrep1


title: ChIP-nexus on CRISPR mESC R1 cells, proximal Sox2 at Akr1cl enhancer mutated, replicate 2

description: Library name: mesc_Akr1cl_scenario_context_mut_B_sox2_nexus_2_r1.fastq.gz


title: control, IVS, replicate3


title: wild type age 3 weeks wt43

city: Jerusalem

first: Eithan

last: Galun

address: Hadassah Ein Kerem

country: Israel

institute: Hadassah Medical Organization

data_processing:
Fastq files were quality tested with fastqc V0.12.1, trimmed and filtered with trim_galore V0.6.1.
Filtered sequencing reads were mapped directly to the transcriptome with salmon quant utility V1.10.0. For this analysis --gcBias and --validateMappings were set.
Counts were aggregated for a raw count matrix.
Assembly: mm10
Supplementary files format and content: Tab delimited text file includes raw counts for each sample.

source_name: Liver

growth_protocol: miR-122 knockout (KO) mice (C57BL/6miR-122em2Hhtg) were generated in collaboration with Prof. Dr. Nicola Gagliani and Prof. Samuel Huber at the University Medical Center Hamburg-Eppendorf, Hamburg, Germany. The genomic region of miR-122 (chr18:65,381,932-65,381,997) was targeted with 2 sgRNA guide sequences (sgRNA1:AACAGACGTCAAGTCACGCGTGG, sgRNA2:AGTGTGATAATGGCGTTTGATGG) generating a 60bp deletion. All mice were screened by genotyping the miR-122 genomic region by PCR analysis (for primer sequences, see table S1). Two separate colonies generated by separate founders were maintained for experimentation. Male mice were used in all the experiments. Mice were maintained under specific pathogen-free (SPF) conditions in an animal facility with a temperature of approximately 23°C in a 12-hour light-dark cycle and received sterile commercial rodent chow and water ad libitum unless otherwise indicated. Maintenance of mice and all experimental procedures were performed by the Institutional Animal Care and Use Committee approved animal treatment protocols (license number OPRR-A01– 5011). All animal experiments were performed after a stringent ethical consideration and approval by the Hebrew University Of Jerusalem, Israel. The experiments were regulated by veterinarian specialists.

extract_protocol:
RNA was extracted using MaXtract High Density (QIAGEN, Redwood City, CA) according to the manufacturer's instructions. Integrity of the RNA was analyzed by a ND-1000 V3.7.1, according to the manufacturer’s instructions. Only samples with an RNA integrity number (RIN) of 9 or greater were sequenced.
RNA samples contained 1000-2000 ng in 50 ul of RNAse/DNAse free water were used for the library construction according to manufacture recommendations; RNAseq libraries were eluted in 30 μl of elution buffer. Then they were adjusted to 10 nM pool, the adjusted pool was loaded into Nextseq 500 machine (Illumina), as 76 bp single end read using the NextSeq 500/550 High-Output v2.5 Kit (75 cycles).  Binary Base Call (BCL) output files from a NoveSeq machine were converted to FASTQ format, using BCL to FASTQ (bcl2fastq v2.20.0.422 Copyright (c) 2007–2017 Illumina, Inc.)

treatment_protocol: Liver specimens were snap-frozen in liquid nitrogen for further analysis.

value: Liver

tag: strain

tag: Sex

value: male

tag: age

value: 3 weeks


title: ChIP-nexus on CRISPR mESC R1 cells, proximal Sox2 at Akr1cl enhancer mutated, replicate 1

description: Library name: mesc_Akr1cl_scenario_context_mut_B_sox2_nexus_1_r1.fastq.gz


title: wild type age 3 weeks wt42


title: K27ac_TRCC_13_3

value: Plasma


title: miR-122 KO age 3 weeks b252

value: miR-122 KO


title: K27ac_TRCC_13_2


title: control, LV, replicate1, techrep2

value: mouse embryonic heart

value: control


title: miR-122 KO age 3 weeks b249


title: miR-122 KO age 3 weeks b324


title: control, IVS, replicate1, techrep2


title: ChIP-nexus on CRISPR mESC R1 cells, distal Sox2 at Akr1cl enhancer mutated, replicate 2

description: Library name: mesc_Akr1cl_scenario_context_mut_A_sox2_nexus_2_r1.fastq.gz


title: ChIP-nexus on wildtype mESC R1 cells, CRISPR side-by-side control, replicate 1

description: Library name: mesc_R1_sox2_nexus_crisprctl_1


title: K27ac_TRCC_13_1


title: control, IVS, replicate1, techrep1


title: RRSV 14dpi, scRNAseq

city: Fuzhou

first: Lu

last: Wang

state: Fujian

address: No.15 Shangxiadian road

department: College of Plant protection

country: China

institute: Fujian Agriculture and Forestry University

description:
The base of the stem of rice
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: IRGSP-1.0, RRSV_genomes(GCA_000852965.1), Rice_grassy_stunt_tenuivirus_isolate_FZ0403
Supplementary files format and content: Tab-separated values files and matrix files

organism: Oryza sativa

source_name: stem base 1.5cm-2.5cm above node

extract_protocol:
Rice seedlings tested to be infected with the virus were taken out, the stem bases were cut 1.5cm (7dpi), 2.0cm (14dpi), and 2.5cm (21dpi), then chopped and soaked in mannitol. The stems segments were enzymatically (1.5% Cellulose RS, 0.75% Macerozyme R-10, 10mM MES (pH 5.7 with KOH), 0.4M Mannitol) hydrolyzed for 4 hours. Next, the hydrolysate is filtered through a cellular filter with a diameter of 40 microns, the filtered liquid was centrifuged at 100g for 5min at 4℃, supernatant was removed, and the precipitation was cleaned twice with W5 solution(2mM MES pH5.7 with KOH, 154mM NaCl, 125mM CaCl2, 5mMKCl). The collected protoplasts were finally re-suspended with a 5%PBS buffer and adjusted to a concentration of 500 to 1000 cells/μL. The protoplasts are kept on ice for later use.
The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits (10X Genomics, Pleasanton, CA). Briefly, cells were concentrated to approximately 1000 cells/uL and loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs). After the RT step, GEMs were broken and barcoded-cDNA was purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors and index PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). All libraries were sequenced by illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

value: Mixed cells

value: stem base 1.5cm-2.5cm above node

value: 14dpi, 21 days old


title: K27ac_TRCC_12_9


title: RRSV 21dpi, scRNAseq

value: 21dpi, 28 days old


title: wild type age 2 weeks wt100

value: WT

value: 2 weeks


title: wild type age 2 weeks wt99


title: Tumor microenvironment cells, Hi-Myc

description:
Library name: Sample 10
Gene_Counts All samples.txt

value: Prostate

value: Hi-Myc


title: K27ac_TRCC_13_4

value: H3K27ac ChIP-seq


title: K27ac_TRCC_12_8


title: RRSV 7dpi, scRNAseq

value: 7dpi, 14 days old


title: wild type age 3 weeks wt44

value: Liver


title: EV5_4

city: Beijing

first: wanjun

last: Peng

address: No.5, Panjiayuan Nanli,Chaoyang District, Beijing

institute: Institute of Laboratory Animal Science

data_processing:
lllumina Casava2.19 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Reasearch, 2009.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

molecule: polyA RNA

source_name: muscle

extract_protocol:
Tissues were removed, flsah frozen on dry ice, and RNA was harvested using Trizol reagent. Lllumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction
RNA libraries were prepared for sequencing using standard lllumina protocols

value: muscle

value: EV_A71 infection


title: wild type age 2 weeks wt59

value: male


title: EV5_3


title: K27ac_TRCC_12_7

value: Plasma


title: RGSV 21dpi, scRNAseq


title: miR-122 KO age 2 weeks b327

value: miR-122 KO


title: control, IVS, replicate2

value: mouse embryonic heart

value: control


title: K27ac_TRCC_12_6


title: EV5_1


title: K27ac_TRCC_12_5


title: miR-122 KO age 2 weeks b326


title: EV2_5


title: K27ac_TRCC_12_4


title: RGSV 7dpi, scRNAseq

value: Mixed cells

value: stem base 1.5cm-2.5cm above node


title: EV2_4


title: wild type age 6 weeks wt20

value: 6 weeks


title: EV5_5

value: WT


title: Mock 21dpi, scRNAseq

value: 21dpi, 28 days old


title: wild type age 6 weeks wt19


title: EV2_3


title: K27ac_TRCC_12_13


title: wild type age 6 weeks wt18


title: Mock 14dpi, scRNAseq

value: 14dpi, 21 days old


title: K27ac_TRCC_12_12


title: miR-122 KO age 6 weeks b315


title: miR-122 KO age 6 weeks b316


title: K27ac_TRCC_12_10


title: EV2_2


title: K27ac_TRCC_12_3


title: RGSV 14dpi, scRNAseq


title: NC5_5

value: Negative control


title: NC5_3


title: miR-122 KO age 2 weeks b294

value: 2 weeks


title: NC5_1


title: miR-122 KO age 6 weeks b314


title: Human control, rep 56

city: ראשון לציון

first: Iddo

last: Magen

state: Not in US

address: בן אליעזר 32, 17

institute: Weizmann Institute

description: Library name: CTRL_rep21

library_source: other

data_processing:
Read alignment using CLC genomic workbench (Qiagen)
low-abudnant sample filtering
data imputation, batch correction and normalization by DESeq2 algorithm.
Assembly: GRCm38 for small RNA
Supplementary files format and content: tab-delimited text files include raw counts and corrected counts  for each sample

molecule: other

source_name: blood plasma

extract_protocol:
RNA extraction RNA was extracted from plasma of ALS patients by adding 5 volumes of Qiazol to one volume of plasma, followed by miRNeasy micro kit (Qiagen) according to manufacturer’s protocols and RNA yield was quantified using Qubit fluorometer Qubit fluorometer (RNA broad range assay kit; ThermoFisher Scientific).
small RNA libraries were constructed using the QIAseq miRNA library kit following manufacturer's instructions.

value: blood plasma


title: K27ac_TRCC_10_3

value: H3K27ac ChIP-seq


title: K27ac_TRCC_10_4


title: Mock 7dpi, scRNAseq

value: 7dpi, 14 days old


title: K27ac_TRCC_12_11


title: NC2_5

value: muscle


title: NC2_3


title: Human control, rep 55

address: בן אליעזר 32, 17

description: Library name: CTRL_rep20


title: Treatment-3

type: RNA

city: shihezi

first: runhui

last: qiu

state: xinjiang

address: No. 221 bei Si Lu

institute: shihezi university

description: Brucella

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction software (version 10.7.1.1, Agilent Technologies) was used to process the original image to extract the original data. Quantile standardization is then performed on the raw data. The normalized data were filtered, with at least one set of 100% Detected probes left for follow-up analysis in each set of samples for comparison. The P value and fold change value of t-test were used to screen differential genes. The screening criteria were up-regulated or down-regulated fold change value > = 2.0 and p value < = 0.05. At the same time, scatter plot was used to screen the difference results of each group, volcano maps (for groups with biological duplications) and clustering maps. Next, target gene prediction was performed on the differential mirnas, and the predicted target genes were subjected to GO and KEGG enrichment analysis to determine the biological functions or pathways that the differential mirnas might affect

source_name: cell sample, Brucella treatment, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: THP1 In a six-well plate, the assay was performed after growth for 24, after the cells had grown through the monolayer.

extract_protocol: RNA was prepared using the Versagene  RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Brucella was infected at 1 MOI and cell samples were collected twelve hours later.

value: macrophage


title: K27ac_TRCC_10_2

value: Plasma


title: NC5_4


title: Treatment-1

description: Brucella

source_name: cell sample, Brucella treatment, replicate 1


title: K27ac_CCRCC2999


title: SGSS05-NS replicate 1

city: Rome

first: Veronica

last: Veschi

address: Viale Regina Elena, 291

country: Italy

institute: “La Sapienza” University of Rome

data_processing:
Illumina RTA 1.18.64 software used for basecalling.
Sequenced reads were trimmed with Trimmomatic (version 0.30), then mapped to hg19 using STAR (version 2.4.2a) with the quantMode option
The gene reads count data from STAR for SGSS05-NS samples were analyzed separately with R Package edgeR (version 3.10.5).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include reads count for each sample

source_name: Neuroblastoma

extract_protocol:
SY5Y cells 12 hours after treatment with 3μM SGSS05-NS were harvested and cell pellets were collected. From these pellets total RNA extraction was carried out using an RNeasy Plus Kit. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neuroblastoma

value: MYCN wild type


title: SGSS05-NS replicate 2


title: Treatment-2

description: Brucella

source_name: cell sample, Brucella treatment, replicate 2


title: Human control, rep 54

address: בן אליעזר 32, 17

description: Library name: CTRL_rep19


title: Con-1

description: control

source_name: cell sample, control, replicate 1


title: Con-3

description: control

source_name: cell sample, control, replicate 3


title: NC0_5


title: K27ac_CCRCC2975


title: NC2_2


title: Human control, rep 50

address: בן אליעזר 32, 17

description: Library name: CTRL_rep15


title: NC2_1


title: NC0_4


title: DMSO replicate 1

value: DMSO


title: K27ac_CCRCC2974


title: Human control, rep 53

address: בן אליעזר 32, 17

description: Library name: CTRL_rep18


title: Con-2

description: control

source_name: cell sample, control, replicate 2


title: Human control, rep 52

address: בן אליעזר 32, 17

description: Library name: CTRL_rep17


title: M/E siHIPK3 TamRes_3

city: Leiden

first: Bob

last: van de Water

state: Leiden

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

data_processing:
Allignment to the human GRCh38 reference genome was performed using STAR (version 2.4.2a) and duplicate marking, sorting and indexing was performed using sambaba.
Gene expression was quantified using HTseq.
Differential gene expression analysis was performed using DESeq2.
Assembly: Grch38 (release 84)
Supplementary files format and content: tab-delimited text files including raw counts for each sample

growth_protocol: MCF7/EGFR cells were maintained in RPMI-1640 medium with L-glutamine and 25 mM HEPES, supplemented with 10% FBS and penicillin/streptomycin. Cells were plated at 300,000 cells/well in 12-wells plate 1 day prior to siRNA transfection.

extract_protocol:
RNA was isolated with the RNeasy Plus Mini Kit (Qiagen) following manufacturer's instructions.
DNA libraries were prepared using the TruSeq Stranded mRNA library Prep kit following manufacturer's instructions.

treatment_protocol: Knockdown of HIPK3 or control siRNA was performed in in phenol-red free RPMI-1640 medium supplemented with 5% charchoal dextran treated FBS and penicillin/streptomycin. Cells were refreshed 24 hours after transfection with the same medium. 48 hours thereafter, cells were treated with control (DMSO), EGF (100 ng/mL), or EGF (100ng/mL), 4-hydroxytamoxifen (0.1 uM) and E2 (0.1 nM) for 6 hours prior to lysis and collection of RNA.

value: EGFR overexpression

value: breast cancer cell line

value: EGF 100 ng/mL, 0.1 nM estradiol, 0.1 uM 4-hydroxytamoxifen

tag: sirna


title: Human control, rep 51

address: בן אליעזר 32, 17

description: Library name: CTRL_rep16


title: DMSO replicate 2


title: NC0_2

value: WT


title: K27ac_CCRCC2997


title: NC0_1


title: Human control, rep 48

address: בן אליעזר 32, 17

description: Library name: CTRL_rep13


title: K27ac_CCRCC2971


title: Human control, rep 47

address: בן אליעזר 32, 17

description: Library name: CTRL_rep12


title: K27ac_TRCC_10_1


title: M/E siHIPK3 TamRes_1


title: M/E siHIPK3 TamRes_2


title: Cortex13_MW

city: Amsterdam

first: Aldo

last: Jongejan

address: Meibergdreef 9

department: Epidemiology & Data Science

institute: Amsterdam University Medical Centers

data_processing:
Trimmed using Trimmomatic v0.36 for adapter sequences.
Aligned using HISAT2 (v2.1.0) (default parameters; -p 4 --dta-cufflinks --rna-strandness RF)
Gene level counts were obtained using HTSeq (v0.11) with default parameters except "-stranded = reverse" and the mouse GTF from Ensembl (release 93)
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited file contains raw count data as obtained using HTSeq; rownames contain the Ensemble gene identifier; one column per sample.

source_name: cortex

growth_protocol: 12 week old mice were used

extract_protocol:
Total RNA was extracted from Cortex of 12 mice using TriReagent (Sigma) and the ISOLATE II RNA Mini Kit (BIOLINE). (sixTbl1xr1Y446C/Y446Cmice and six wild-type mice; three males and three females of each genotype).
In order to create cDNA libraries, samples were prepared using the Kapa mRNA Hyperprep kit (Roche, Basel, Switserland). Concentration of the library samples was measured using the Quant-it DNA HS assay (Thermo Fisher Scientific, Waltham, MA, USA). Libraries were equimolar pooled and the pool was checked on Tapestation using DNA1000 ScreenTape (Agilent Technologies, Santa Clara, CA, USA). The libraries were sequenced on the NovaSeq6000 PE150 sequencer (Illumina, San Diego, CA, USA), producing at least 40M 150-bp paired-end reads per library.

treatment_protocol: Male and female mice at the age of 12 weeks were killed by exsanguination.Cortex was removed, immediately frozen on dry ice and stored at -80 °C until further processing

value: cortex

value: wild type

tag: gender

value: Male

value: 12 weeks


title: Cortex27_MH


title: K27ac_CCRCC2970


title: M/E siHIPK3 EGF_3

value: EGF 100 ng/mL


title: M/E siHIPK3 EGF_2


title: Cortex12_MW


title: K27ac_CCRCC1730

value: H3K27ac ChIP-seq


title: Human control, rep 45

address: בן אליעזר 32, 17

description: Library name: CTRL_rep10

value: blood plasma


title: K27ac_CCRCC2973


title: Cortex10_MH


title: M/E siHIPK3 n.s._3


title: Human control, rep 46

address: בן אליעזר 32, 17

description: Library name: CTRL_rep11


title: K27ac_CCRCC170


title: mTRCC_8

value: MeDIP-seq


title: Cortex8_MW


title: M/E siHIPK3 EGF_1


title: mTRCC_5


title: M/E siHIPK3 n.s._2


title: Cortex7_MH


title: Human control, rep 43

address: בן אליעזר 32, 17

description: Library name: CTRL_rep8


title: Human control, rep 42

address: בן אליעזר 32, 17

description: Library name: CTRL_rep7


title: Human control, rep 44

address: בן אליעזר 32, 17

description: Library name: CTRL_rep9


title: M/E siHIPK3 n.s._1


title: Cortex6_FH

value: Female


title: Human control, rep 41

address: בן אליעזר 32, 17

description: Library name: CTRL_rep6


title: mTRCC_26

value: Plasma


title: Cortex5_FW


title: M/E siCtrl1/2 TamRes_3


title: Human control, rep 40

address: בן אליעזר 32, 17

description: Library name: CTRL_rep5


title: mTRCC_25


title: mTRCC_27


title: M/E siCtrl1/2 TamRes_2


title: Cortex3_FH


title: M/E siCtrl1/2 TamRes_1


title: Cortex4_FW


title: Human control, rep 39

address: בן אליעזר 32, 17

description: Library name: CTRL_rep4


title: mTRCC_24


title: M/E siCtrl1/2 EGF_3


title: Human control, rep 38

address: בן אליעזר 32, 17

description: Library name: CTRL_rep3


title: Cortex1_FH


title: mTRCC_22


title: M/E siCtrl1/2 EGF_2


title: Human control, rep 37

address: בן אליעזר 32, 17

description: Library name: CTRL_rep2


title: Human control, rep 36

address: בן אליעזר 32, 17

description: Library name: CTRL_rep1


title: Cortex2_FW


title: mTRCC_13_6


title: mTRCC_13_5


title: M/E siCtrl1/2 EGF_1


title: Human control, rep 35

address: בן אליעזר 32, 17

description: Library name: NEWCTRL35


title: hippocampus received 400 mGy X-ray irradiation from 17-month-old 3xTg-AD mice, rep 4

city: Hong Kong

first: MA

last: Chi Him Eddie

address: Tat Chee Avenue, Kowloon, Hong Kong

department: Department of Neuroscience

country: Hong Kong

institute: City University of Hong Kong

data_processing:
RNA-seq raw reads were mapped to the UCSC human reference genome (GRCh38) and calculation of gene counts using STAR (version 2.7.8a) with default parameters.
The multi-mapped reads were filtered out and only the uniquely mapped reads were retained.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts and TPM values for each sample

source_name: hippocampus

growth_protocol: hippocampus from 17-month-old female WT or 3xTg-AD mice treated with or without 400 mGy X-ray irradiation

extract_protocol:
hippocampus were dissected out from  17-month-old female WT or 3xTg-AD mice treated with or without 400 mGy X-ray irradiation, and total RNA was extracted using Trizol reagent. A total of 100ng of total RNA was used as input RNA for each sample.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra II Directional RNA Library Prep Kit following the manufacturer's protocols.

value: hippocampus

value: X-ray irradiation


title: mTRCC_13_4


title: M/E siCtrl1/2 n.s._3

value: DMSO


title: Human control, rep 34

address: בן אליעזר 32, 17

description: Library name: NEWCTRL34


title: mTRCC_13_3


title: hippocampus received 400 mGy X-ray irradiation from 17-month-old 3xTg-AD mice, rep 3

treatment_protocol: 17-month-old female WT or 3xTg-AD mice treated with or without 400 mGy X-ray irradiation


title: M/E siCtrl1/2 n.s._2

value: EGFR overexpression


title: hippocampus received 400 mGy X-ray irradiation from 17-month-old 3xTg-AD mice, rep 2


title: mTRCC_13_2


title: M/E siCtrl1/2 n.s._1

value: breast cancer cell line


title: Human control, rep 33

address: בן אליעזר 32, 17

description: Library name: NEWCTRL33


title: hippocampus received 400 mGy X-ray irradiation from 17-month-old 3xTg-AD mice, rep 1


title: Sham irradiated hippocampus from  17-month-old 3xTg-AD mice, rep 3

value: control


title: Human control, rep 32

address: בן אליעזר 32, 17

description: Library name: NEWCTRL32


title: mTRCC_13_1


title: Ovary, PT91_4

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

description: Library name: Sample 16

data_processing:
Total RNA was used for mRNA isolation using the NEBNext Ploy(A) mRNA Magnetic Isolation module (New England Biolabs, catalog # E7490). RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 (Illumina Inc., CA, U.S.A). Sequencing was performed by Novogene.
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Paired-end clean reads were mapped to the reference genome using HISAT2 v2.0.5. software. We selected Hisat2 as the mapping tool because it can generate a database of splice junctions based on the gene model annotation file and generate a better mapping result than other non-splice mapping tools.
Featurecounts v1.5.0-p3 was used to count the read numbers mapped of each gene, including known and novel genes. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: DESeq2 was used for differential expression analysis between the control and treatments and performed using the DESeq2R package (1.20.0).
Supplementary files format and content: ensembl_danio_rerio_grcz11_gca_000002035_4
Supplementary files format and content: Excel file containing read count, fpkm, log2 fold change, p-value

organism: Danio rerio

source_name: Ovary

extract_protocol:
Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer (ThermoFisher/Invitrogen, Grand Island, NY), and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.). RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

value: Ovary

value: female


title: Human control, rep 31

address: בן אליעזר 32, 17

description: Library name: NEWCTRL31


title: mTRCC_12_9

source_name: Plasma


title: Ovary, PT91_3

description: Library name: Sample 15


title: Ovary, PT91_2

description: Library name: Sample 14


title: Human control, rep 29

address: בן אליעזר 32, 17

description: Library name: NEWCTRL29


title: Ovary, PT91_1

description: Library name: Sample 13


title: Sham irradiated hippocampus from  17-month-old 3xTg-AD mice, rep 1


title: Human control, rep 30

address: בן אליעזר 32, 17

description: Library name: NEWCTRL30


title: mTRCC_12_8


title: hippocampus received 400 mGy X-ray irradiation from 17-month-old WT mice, rep 5

value: WT


title: Human control, rep 28

address: בן אליעזר 32, 17

description: Library name: NEWCTRL28


title: mTRCC_12_7


title: Ovary, PNX_4

description: Library name: Sample 12

value: PNX


title: Ovary, PNX_3

description: Library name: Sample 11


title: mTRCC_12_5


title: hippocampus received 400 mGy X-ray irradiation from 17-month-old WT mice, rep 4


title: Human control, rep 27

address: בן אליעזר 32, 17

description: Library name: NEWCTRL27


title: mTRCC_12_6


title: Human control, rep 26

address: בן אליעזר 32, 17

description: Library name: NEWCTRL26


title: mTRCC_12_4


title: Ovary, PNX_2

description: Library name: Sample 10


title: hippocampus received 400 mGy X-ray irradiation from 17-month-old WT mice, rep 3


title: Human control, rep 25

address: בן אליעזר 32, 17

description: Library name: NEWCTRL25


title: Sham irradiated hippocampus from  17-month-old 3xTg-AD mice, rep 2


title: hippocampus received 400 mGy X-ray irradiation from 17-month-old WT mice, rep 2


title: Human control, rep 24

address: בן אליעזר 32, 17

description: Library name: NEWCTRL24


title: hippocampus received 400 mGy X-ray irradiation from 17-month-old WT mice, rep 1


title: mTRCC_12_3


title: Ovary, PNX_1

description: Library name: Sample 9


title: mTRCC_12_2


title: Sham irradiated hippocampus from 17-month-old WT mice, rep 5


title: Ovary, A8535_3

description: Library name: Sample 7


title: mTRCC_12_13


title: Ovary, A8535_2

description: Library name: Sample 6


title: Human control, rep 22

address: בן אליעזר 32, 17

description: Library name: NEWCTRL22


title: mTRCC_12_11


title: Sham irradiated hippocampus from 17-month-old WT mice, rep 6


title: Sham irradiated hippocampus from 17-month-old WT mice, rep 4


title: Human control, rep 23

address: בן אליעזר 32, 17

description: Library name: NEWCTRL23


title: Sham irradiated hippocampus from 17-month-old WT mice, rep 3


title: mTRCC_12_10


title: mTRCC_12_12


title: Ovary, A8535_1

description: Library name: Sample 5


title: Human control, rep 20

address: בן אליעזר 32, 17

description: Library name: NEWCTRL20


title: Ovary, Cntl_4

description: Library name: Sample 4

value: Control


title: Sham irradiated hippocampus from 17-month-old WT mice, rep 2


title: Human control, rep 19

address: בן אליעזר 32, 17

description: Library name: NEWCTRL19


title: Ovary, A8535_4

description: Library name: Sample 8


title: mTRCC_12_1


title: Ovary, Cntl_3

description: Library name: Sample 3


title: Ovary, Cntl_2

description: Library name: Sample 2


title: Human control, rep 17

address: בן אליעזר 32, 17

description: Library name: NEWCTRL17


title: Human control, rep 18

address: בן אליעזר 32, 17

description: Library name: NEWCTRL18


title: Sham irradiated hippocampus from 17-month-old WT mice, rep 1


title: mTRCC_10_3


title: Ovary, Cntl_1

description: Library name: Sample 1


title: Human control, rep 21

address: בן אליעזר 32, 17

description: Library name: NEWCTRL21


title: hippocampus received 400 mGy X-ray irradiation from 9-month-old 3xTg-AD mice, rep 3

growth_protocol: hippocampus from 9-month-old female WT or 3xTg-AD mice treated with or without 400 mGy X-ray irradiation

extract_protocol:
hippocampus were dissected out from  9-month-old female WT or 3xTg-AD mice treated with or without 400 mGy X-ray irradiation, and total RNA was extracted using Trizol reagent. A total of 100ng of total RNA was used as input RNA for each sample.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra II Directional RNA Library Prep Kit following the manufacturer's protocols.


title: hippocampus received 400 mGy X-ray irradiation from 9-month-old 3xTg-AD mice, rep 2

treatment_protocol: 9-month-old female WT or 3xTg-AD mice treated with or without 400 mGy X-ray irradiation


title: mTRCC_10_2


title: Human control, rep 15

address: בן אליעזר 32, 17

description: Library name: NEWCTRL15


title: mTRCC_10_1


title: GC-Con2, mRNA-Seq

city: Nanjing

first: Han

last: Chen

state: Jiangsu

address: #300 Guzhou Road, Gulou District

institute: Nanjing Medical University

description:
Library name: Sample11
27-2

data_processing:
GLC genomics Workbench
Assembly: hg38
Supplementary files format and content: CSV files

extract_protocol:
RNA was harvested using Rensay mini plus kit. total  TNA was used for the construction of sequenceing library
RNA library for RNA-seq was prepared using SMARTER mRNA-seq Library Prep kit following manufacturer‘s protocols.’

value: Gastric cancer


title: Sham irradiated hippocampus from 9-month-old 3xTg-AD mice, rep 3


title: GC-Con3, mRNA-Seq

description:
Library name: Sample12
27-3


title: mCCRCC2975


title: Sham irradiated hippocampus from 9-month-old 3xTg-AD mice, rep 2


title: GC-Hp3, mRNA-Seq

description:
Library name: Sample9
27L-3

value: H. pylori LPS


title: GC-Con1, mRNA-Seq

description:
Library name: Sample10
27-1


title: Sham irradiated hippocampus from 9-month-old 3xTg-AD mice, rep 1


title: mCCRCC2974


title: Human control, rep 12

address: בן אליעזר 32, 17

description: Library name: NEWCTRL12

value: blood plasma


title: Human control, rep 13

address: בן אליעזר 32, 17

description: Library name: NEWCTRL13


title: Human control, rep 14

address: בן אליעזר 32, 17

description: Library name: NEWCTRL14


title: mCCRCC2973

value: MeDIP-seq


title: mTRCC_10_4


title: Human control, rep 11

address: בן אליעזר 32, 17

description: Library name: NEWCTRL11


title: GC-Hp2, mRNA-Seq

description:
Library name: Sample8
27L-2


title: GC-Hp1, mRNA-Seq

description:
Library name: Sample7
27L-1


title: mCCRCC2971


title: hippocampus received 400 mGy X-ray irradiation from 9-month-old WT mice, rep 2


title: Human control, rep 10

address: בן אליעזר 32, 17

description: Library name: NEWCTRL10


title: Human control, rep 16

address: בן אליעזר 32, 17

description: Library name: NEWCTRL16


title: mCCRCC2970


title: hippocampus received 400 mGy X-ray irradiation from 9-month-old 3xTg-AD mice, rep 1


title: hippocampus received 400 mGy X-ray irradiation from 9-month-old WT mice, rep 1


title: Human control, rep 9

address: בן אליעזר 32, 17

description: Library name: NEWCTRL9


title: mCCRCC1570


title: GC-Con2, PANDORA-Seq

description:
Library name: Sample5
27-2


title: S_2_SZ3

city: Pittsburgh

first: Shivendra

middle: V.

last: Singh

state: PA

address: 5117 Centre Avenue, UPMC HCC Research Pavilion Suite 2.32A

institute: University of Pittsburgh

data_processing:
HISAT2 software was used for alignment for RNA-seq sequencing data analysis. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) was used to estimate gene expression levels.
genome build Homo Sapiens(GRCh37/hg19)
Supplementary files format and content: Summary of gene expression level with annotation information

source_name: breast cancer cells

growth_protocol: The MDA-MB-231 cells were plated in 6-cm dish at a density of 5×105 cells/dish in triplicate and incubated overnight for attachment.

extract_protocol:
The cells were harvested by trypsin treatment and total RNA was extracted using the RNeasy mini kit (Qiagen, Germantown, MD).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The cells were treated with vecicle consisting of DMSO (final concentration - 0.01%) and water (final concentration - 0.05%) or 1 µM of SFN and/or 0.5 µM of ZA for 48 hours prior to RNA isolation and RNA-Seq analysis.

tag: cell line name

value: Cells were treated with 1 µM of SFN and 0.5 µM of ZA for 48 hours.


title: GC-Con3, PANDORA-Seq

description:
Library name: Sample6
27-3


title: Sham irradiated hippocampus from 9-month-old WT mice, rep 1


title: S_2_SZ2


title: GC-Hp3, PANDORA-Seq

description:
Library name: Sample3
27L-3


title: Human control, rep 8

address: בן אליעזר 32, 17

description: Library name: NEWCTRL8


title: Human control, rep 6

address: בן אליעזר 32, 17

description: Library name: NEWCTRL6


title: Human control, rep 7

address: בן אליעזר 32, 17

description: Library name: NEWCTRL7


title: hippocampus received 400 mGy X-ray irradiation from 9-month-old WT mice, rep 3


title: S_2_SZ1


title: S_2_Z3

value: Cells were treated with 0.5 µM of ZA for 48 hours.


title: Human control, rep 5

address: בן אליעזר 32, 17

description: Library name: NEWCTRL5


title: GC-Hp2, PANDORA-Seq

description:
Library name: Sample2
27L-2


title: GC-Hp1, PANDORA-Seq

description:
Library name: Sample1
27L-1


title: R11419 ITB Infected T48

city: New Delhi

first: Dhiraj

last: Kumar

address: Aruna Asaf Ali Marg

country: India

institute: International Centre for Genetic Engineering and Biotechnology

description: 2 X 151bp

data_processing:
Reads mapped using STAR aligner against human genome GRCh38
Used featureCounts to obtain counts for genes based on GENCODE v31 annotation
Read count normalisation done using DESeq2
Assembly: Human genome GRCh38
Supplementary files format and content: tab-delimited text files include raw values for each Sample

source_name: Monocytes derived Macrophages

extract_protocol:
Total RNA was extracted from MDMs following the double extraction protocol:  RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol, Thermo Fisher Scientific, Waltham, MA, USA) followed by a Qiagen RNeasy Micro clean-up procedure (Qiagen, Hilden, Germany).
cDNA libraries were prepared using 2 ng of total RNA using the SMARTSeq v2 protocol with the following modifications: 1. Addition of 20 µM TSO; 2. Use of 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA).

tag: subject

value: Monocytes derived Macrophages

value: ITB

value: Infected

tag: time


title: E16.5-scRNA-Library

city: Stanford

first: Francisco

middle: Xavier

last: Galdos

address: 265 Campus Dr.

department: Cardiovascular Institute

institute: Stanford University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, accessible peak calculation, and aggregation were conducted using CellRanger-ARC-1.0.1 software (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
Assembly: mm10
Supplementary files format and content: Tab separated value  and matrix files
Supplementary files format and content: BED format ATAC peak files

molecule: nuclear RNA

source_name: Heart

extract_protocol:
Freshly harvest mouse embryonic hearts were digested into single cells using 1 mL of 0.25% trypsin-EDTA at 37 degrees Celsius for 5 minutes with gentle trituration using a 1000 uL pipette. Equal volume of collagenase mixture (collagenase A and B) dissolved in HBSS without calcium and 40% FBS was then added to the trypsin mixture for an additional 20 minutes. Cells were triturated using a 1000 uL pipette throughout incubation period and were then pelleted by centrifugation for 5 minutes at 200g at 4 degrees Celsius. Cells were then washed and resuspended in cold PBS + 0.04% BSA. Nuclei were extracted from cell suspensions by following protocol CG000366 Rev D provided by 10X Genomics. Cells were centrifuged at 500 rcf for 5 minutes at 4°C and incubated in a diluted (0.1X) lysis buffer on ice for 5 minutes. They were subsequently washed twice in wash buffer and nuclei were centrifuged again at 500 rcf for 5 minutes. Nuclei pellets were then resuspended in a diluted nuclei buffer and subsequent steps for scRNA-seq and scATAC-seq capture were conducted using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (CG000338 Rev F) protocol.
Input nuclei concentration was adjusted to achieve an input nuclei number of 10,000 cells per timepoint according to the manufacturer’s protocol. Samples were incubated with transposition mix containing ATAC enzyme and buffer for 60 minutes at 37°C as specified by the protocol. GEMs were generated using three separate gel bead tubes, one per sample. Post-GEM incubation cleanup was performed per the manufacturer’s protocol. Following pre-amplification PCR, 40 µl of pre-amplified sample was used to generate the ATAC library, while 35 µl sample was used to construct the cDNA and gene expression libraries. Library quality and average fragment size were assessed using a Bioanalyzer (Agilent, G2939A) High Sensitivity DNA chip (Agilent, 5067-4626). Libraries were sequenced with Illumina NovaSeq 6000 at 20,000 read pairs per nuclei for the gene expression library and 25,000 read pairs per nuclei for the ATAC library.

value: Heart

value: Mixed Embryonic Celltypes

value: Wildtype


title: Human control, rep 4

address: בן אליעזר 32, 17

description: Library name: NEWCTRL4


title: E10.5-scRNA-Library

description: 10X Genomics


title: E10.5-scATAC-Library

description: 10X Genomics

library_source: genomic single cell


title: GC-Con1, PANDORA-Seq

description:
Library name: Sample4
27-1

tag: cell line


title: S_2_Z1


title: Human control, rep 3

address: בן אליעזר 32, 17

description: Library name: NEWCTRL3


title: R11418 ITB Uninfected T0

description: 2 X 151bp

tag: genotype

value: Uninfected


title: R11417 ITB Infected T48

description: 2 X 151bp


title: Sham irradiated hippocampus from 9-month-old WT mice, rep 3

tag: tissue

value: hippocampus

value: control


title: Human control, rep 2

address: בן אליעזר 32, 17

description: Library name: NEWCTRL2


title: E8.5-scATAC-Library

description: 10X Genomics


title: S_2_S2

value: Cells were treated with 1 µM of SFN for 48 hours.


title: S_2_S3


title: Human control, rep 1

address: בן אליעזר 32, 17

description: Library name: NEWCTRL1


title: Sham irradiated hippocampus from 9-month-old WT mice, rep 2

value: WT


title: A549 cells, IL1B+Bud, 24h, rep4

city: Calgary

first: Alex

last: Gao

state: Alberta

address: 3330 Hospital Dr NW

department: Physiology and Pharmacology

country: Canada

institute: University of Calgary

description: Library name: Sample 78

data_processing:
Good-quality reads were mapped to GRCh38/hg38 reference human transcriptome using kallisto with 100 bootstraps per sample.
Normalization and differential expression analysis was performed using the R package, sleuth. Genes with low abundance (<5 estimated counts in at least 90% of all samples) were filtered out before subsequent analysis. The Wald test was used to determine fold change (b value) and false-discovery rate (FDR) for each treatment when compared to NS control at each time point separately. Differentially expressed genes (DEGs) were taken as showing FDR ≤0.05 and log2(fold) ≥1 or ≤-1.
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains TPM values for each sample
Supplementary files format and content: tab-delimited text file contains fold change and FDR values for each sample

growth_protocol: The human pulmonary type II cell line, A549, was grown under standard culture condition using Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 2mM L-glutamine. Cells were incubated at 37°C in 5% CO2 and were grown to confluence either in 100mm, or 6/12/24-well plates, as appropriate. Prior to experiments, cells were incubated overnight in basal media that was serum- and additive-free.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA Extraction kit (MN-740955, Macherey-Nagel) and cDNA prepared from 0.5μg of RNA.
RNA sequencing libraries, from 4 independent experiments, were prepared using Illumina TruSeq Stranded mRNA Library Prep kits with the poly(A) mRNA magnetic isolation module as described by the manufacturer. Libraries were validated by D1000 Screen Tape assay on an Agilent 2200 TapeStation system and quantified using Kapa qPCR Library Quantification kits.

treatment_protocol: Budesonide was dissolved in DMSO as a 10mM stock. Unless specifically indicated, budesonide was used at 300nM on cells, representing a concentration that was maximally effective/near maximal on a 2×GRE reporter and gene expression in A549 cells. Final DMSO concentrations on cells were ≤ 0.1%. Recombinant human IL1B was dissolved in phosphate-buffered saline (PBS) containing 0.1% bovine serum albumin (BSA). IL1B was previously found to be maximally or near maximally effective on NF-κB reporters and gene expression at 1ng/ml and this concentration was used in all experiments unless specifically indicated. Following overnight incubation in serum free medium, cells were changed to fresh serum free medium and either not stimulated (NS) or treated with, IL1B, budesonide or IL1B plus budesonide for the indicated times prior to harvesting for RNA extraction. Data are from four independent experiments with the exception of the 12 h time point which was from three independent experiments.

value: lung carcinoma epithelial cells

value: IL1B + Budesonide


title: R11415 ITB Infected T48

description: 2 X 151bp


title: R11416 ITB Uninfected T0

description: 2 X 151bp


title: E16.5-scATAC-Library

description: 10X Genomics


title: S_2_S1


title: 06 Naringin3

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

country: Japan

institute: Graduate School of Medical Sciences, Kumamoto University

data_processing:
illumina Local Run Manager v2.4.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence/poly A/T tail/short sequence length reads using Trimmomatic v0.39 and PRINSEQ-lite v0.20.4
Trimmed sequence reads were mapped to UCSC mm39 using STAR v2.7.9a
Read count extraction using featureCount function from the Subread v1.6.0
Read count normalized using edgeR v3.40.0
Assembly: mm39
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: Lymph node

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Lymph node

value: Administration of Naringin


title: Human control, rep 49

address: בן אליעזר 32, 17

description: Library name: CTRL_rep14

value: blood plasma


title: S_2_C3

value: Cells were treated with vehicle for 48 hours.


title: S_2_Z2

value: Cells were treated with 0.5 µM of ZA for 48 hours.


title: 05 Naringin2


title: R11413 ITB Infected T48

description: 2 X 151bp

value: Monocytes derived Macrophages

value: ITB


title: S_2_C2


title: A549 cells, IL1B+Bud, 2h, rep4

description: Library name: Sample 75


title: Sp2

city: Chongqing

first: Liu

last: Xiang

address: Tiansheng Street

institute: Southwest University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
clean data were mapped to the reference genome of Homo sapiens from GRCh38 using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and logfold-change cutoff of 1 were used to judge the statistical significance of gene expression differences.
Assembly: GRCh38
Supplementary files format and content: tab-delimited excel file includes raw counts for each Sample

growth_protocol: SU-DHL-2 cells were maintained in 1640 supplemented with 15% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNAs were extracted  using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).2 μg total RNAs were used for stranded RNA sequencing library
RNA libraries for RNA-seg were prepared using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme Biotech, NR612-02)  following manufacturer's protocols.

treatment_protocol: SU-DHL-2 cells were treated with Spautin-1(10 μM) or solvent and continue to cultivate in 1640 supplemented with 15% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

value: DLBCL cell line

value: Human B-cell lymphoma cell

value: Spautin-1(10 μM, 36 h)


title: 03 Control3

value: Control


title: R11409 ITB Infected T48

description: 2 X 151bp

value: Infected


title: R11412 ITB Uninfected T0

description: 2 X 151bp

value: Uninfected


title: 02 Control2


title: A549 cells, Bud, 24h, rep4

description: Library name: Sample 73

value: Budesonide


title: E8.5-scRNA-Library

description: 10X Genomics

value: Heart

value: Mixed Embryonic Celltypes

value: Wildtype


title: S_2_C1


title: R11408 ITB Uninfected T0

description: 2 X 151bp


title: A549 cells, IL1B+Bud, 12h, rep4

description: Library name: Sample 77

value: lung carcinoma epithelial cells

value: WT

value: IL1B + Budesonide


title: 01 Control1

value: Lymph node


title: A549 cells, Bud, 12h, rep4

description: Library name: Sample 72


title: R11407 control Infected T48

description: 2 X 151bp

value: control


title: Control2

value: vehicle control


title: R11414 ITB Uninfected T0

description: 2 X 151bp

value: Monocytes derived Macrophages

value: ITB


title: R11406 control Uninfected T0

description: 2 X 151bp


title: Sp1

value: DLBCL cell line

value: Human B-cell lymphoma cell


title: A549 cells, IL1B+Bud, 6h, rep4

description: Library name: Sample 76


title: SKM-1 cells, shNUDT21-3

city: Taiyuan

first: Shuo

last: Li

state: Shanxi Province

address: No.382, Wuyi Road, Taiyuan, Shanxi Province, China

department: Second Clinical Medical College

institute: Shanxi Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: marrow

growth_protocol: All cells used for the experiments were cultured in 1640 supplemented with 10% fetal bovine serum and 1% antibiotics and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol (Takara, Japan),1 μg of total RNA was used to construct the sequencing library
Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: marrow

value: Human myelodysplastic syndrome cells


title: R11405 control Infected T48

description: 2 X 151bp

value: Infected


title: A549 cells, Bud, 2h, rep4

description: Library name: Sample 70

value: Budesonide


title: A549 cells, Bud, 6h, rep4

description: Library name: Sample 71


title: 04 Naringin1

value: Administration of Naringin


title: SKM-1 cells, shNUDT21-2


title: A549 cells, IL1B+Bud, 1h, rep4

description: Library name: Sample 74


title: SKM-1 cells, shNUDT21-1


title: A549 cells, IL1B, 24h, rep4

description: Library name: Sample 68


title: R 60

city: Tianjin

first: Quan

last: Gu

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, Tianjin, China

description: 5x106 BM nucleated cells (BMNCs) from B6.SJL mice (CD45.1+) were intravenously injected into female CB6F1 recipients (CD45.2+) 4 hours after sub-lethal- irradiation (4.0 Gy, twice) to establish the BMT model. Additional spleen cells (6x107) from female C57BL/6 mice were injected into the BMT mice to establish the aGVHD model. Mice were orally administrated with 30 mg/kg ruxolitinib and followed up to 60 days.

data_processing:
FastQC0.11.3 to perform basic statistics on the quality of the raw reads
celltanger3.1.0 count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline  using default parameters
All downstream single-cell analyses were performed using Cell Ranger and Seurat ( (Macosko et al., 2015; Satija et al., 2015) unless mentioned specifically
Subsequent analysis of cellranger reanalyze and Seurat were all performed basing on this output gene expression matrix
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and sample

source_name: bone marrow

extract_protocol:
We isolated stromal cells from mice by fluorescence activated cell sorting (FACS) after labeling CD45, lineage mix, and CD71 to deplete hematopoietic cells, and Calcein AM and DAPI to eliminate the dead cells
The cell suspension and gel beads contained Barcode sequencing generated single-cell gel bead-in emulsions (GEMs) for reverse transcription and library preparation using a Chromium Single Cell 30 v2 Reagent Kit (10x Genomics).
10x Genomics

value: bone marrow


title: SKM-1 cells, sh control-3


title: A549 cells, IL1B, 12h, rep4

description: Library name: Sample 67


title: Control1


title: SKM-1 cells, sh control-2


title: R11401 control Infected T48

description: 2 X 151bp


title: SKM-1 cells, sh control-1


title: A549 cells, IL1B, 6h, rep4

description: Library name: Sample 66


title: R11400 control Uninfected T0

description: 2 X 151bp

value: Uninfected


title: A549 cells, IL1B, 2h, rep4

description: Library name: Sample 65

value: lung carcinoma epithelial cells


title: R11399 control Infected T48

description: 2 X 151bp


title: A549 cells, IL1B, 1h, rep4

description: Library name: Sample 64

value: WT


title: A549 cells, Bud, 1h, rep4

description: Library name: Sample 69


title: A549 cells, NS, 24h, rep4

description: Library name: Sample 63

value: NS


title: R11404 control Uninfected T0

description: 2 X 151bp


title: R11398 control Uninfected T0

description: 2 X 151bp


title: MUTZ-1 cells, shNUDT21-2


title: R11403 control Infected T48

description: 2 X 151bp


title: hskm_miR-136_6

city: Stockholm

first: Mutsumi

last: Katayama

address: Solnavägen 9

country: Sweden

institute: Karolinska Institutet

hyb_protocol: 3ug of biotin labeld final target was hybidized  to Human Gene 2.0 ST Arrays in Affymetrix GeneChip Hybridization Oven 645

scan_protocol: The arrays were scanned in Affymetrix Gene Chip Scanner 3000

data_processing: RMA processing in Affymetrix Comand Console

label: biotin

source_name: primary human skeletal muscle cell (Subject 1), miRNA-negative control transfected

label_protocol: 150ng total RNA was used to prepare final targets using Affymetrix User manual for GeneChip  WT Plus Kit.

extract_protocol: Extraction of total RNA was performed with miRNeasy kit (QIAGEN) according to the manufacturer's instructions.

value: primary human skeletal muscle cells


title: hskm_nc_6


title: hskm_siScr_6


title: A549 cells, NS, 12h, rep4

description: Library name: Sample 62


title: R11402 control Uninfected T0

description: 2 X 151bp

value: control


title: hskm_miR-136_5


title: hskm_nc_5


title: hskm_siNRDC_6


title: MUTZ-1 cells, shNUDT21-1


title: A549 cells, NS, 6h, rep4

description: Library name: Sample 61


title: hskm_miR-136_4


title: hskm_siNRDC_5


title: R11410 CD Uninfected T0

description: 2 X 151bp

value: CD


title: MUTZ-1 cells, shNUDT21-3


title: R11411 CD Infected T48

description: 2 X 151bp

value: Monocytes derived Macrophages


title: A549 cells, NS, 1h, rep4

description: Library name: Sample 59


title: R11394 CD Uninfected T0

description: 2 X 151bp


title: hskm_siScr_5


title: A549 cells, IL1B+Bud, 24h, rep3

description: Library name: Sample 58

value: IL1B + Budesonide


title: R11395 CD Infected T48

description: 2 X 151bp


title: ovRAGE_AGEanchored

city: Seoul

first: Minjeong

last: Jang

state: Asia/Oceania

address: 75, Nowon-ro, Nowon-gu, Seoul, Republic of Korea

institute: Korea Institute of Radiological and Medical Sciences (KIRAMS)

data_processing:
the libraries were evaluated using the TapeStation HS D1000 Screen Tape (Agilent Technologies, Santa Clara, CA, USA) to determine the mean fragment size. Quantification was performed using a library quantification kit and StepOne Real-Time PCR System (Life Technologies, Carlsbad, CA, USA). High-throughput sequencing was performed via paired-end 100 sequencing using NovaSeq 6000 (Illumina, San Diego, CA, USA).
Assembly: hg18
Supplementary files format and content: tab-delimited text file included raw counts for each Samples

source_name: ReN

extract_protocol:
Total RNA was isolated using the QIAzol lysis reagent (79306, Qiagen, Germantown, MD, USA). RNA quality was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using an NanoDrop-2000 spectrophotometer (ND-2000, Thermo Fisher Scientific).
Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA-Seq Kit (New England BioLabs, Hitchin, UK). mRNA isolation was performed using a Poly(A) RNA Selection Kit (LEXOGEN, Wein, Austria). The isolated mRNAs were used for cDNA synthesis and shearing by following the manufacturer’s instructions. Indexing was performed using Illumina indexes 1–12.

value: ReN

value: ovRAGE

value: AGEanchored


title: MUTZ-1 cells, sh control-3

value: marrow

value: Human myelodysplastic syndrome cells


title: A549 cells, NS, 2h, rep4

description: Library name: Sample 60


title: MUTZ -1cells, sh control-2


title: hskm_nc_4


title: R11393 CD Infected T48

description: 2 X 151bp

value: Infected


title: hskm_siScr_4


title: MUTZ -1cells, sh control-1


title: shRAGE_AGEanchored

value: shRAGE


title: R11391 CD Infected T48

description: 2 X 151bp


title: A549 cells, IL1B+Bud, 2h, rep3

description: Library name: Sample 56


title: hskm_miR-136_3


title: hskm_siNRDC_4


title: shRAGE_control


title: A549 cells, IL1B+Bud, 6h, rep3

description: Library name: Sample 57


title: R11385 CD Infected T48

description: 2 X 151bp


title: R11392 CD Uninfected T0

description: 2 X 151bp


title: ovRAGE_control


title: A549 cells, IL1B+Bud, 1h, rep3

description: Library name: Sample 55


title: WT_AGEanchored


title: A549 cells, Bud, 24h, rep3

description: Library name: Sample 54

value: Budesonide


title: R11384 CD Uninfected T0

description: 2 X 151bp

value: Uninfected


title: WT_solubleAGE

value: solubleAGE


title: hskm_nc_3


title: A549 cells, Bud, 12h, rep3

description: Library name: Sample 53

value: lung carcinoma epithelial cells

value: WT


title: R11390 CD Uninfected T0

description: 2 X 151bp


title: hskm_siNRDC_3

value: primary human skeletal muscle cells


title: A549 cells, Bud, 2h, rep3

description: Library name: Sample 51


title: hskm_siScr_3


title: WT_control

value: control


title: R11383 CD Infected T48

description: 2 X 151bp

value: CD


title: hskm_miR-136_2


title: Tonsil, pediatric, oSDB, ID57, EBV-,  CPAP-

city: Aurora

first: Regie Lyn

last: Santos-Cortez

state: CO

department: Otolaryngology-Head and Neck Surgery

institute: University of Colorado Anschutz Medical Campus, School of Medicine

data_processing:
Salmon, BBDuk
Assembly: GRCh38.p13
Supplementary files format and content: raw and normalized counts

source_name: Tonsil

extract_protocol:
Qiagen AllPrep DNA/RNA Micro Kit
Illumina Poly A Selected Total RNA Library
bulk mRNA-Seq

value: Tonsil

tag: status

value: EBV-, CPAP-

value: Tonsillectomy


title: A549 cells, Bud, 1h, rep3

description: Library name: Sample 50


title: hskm_nc_2


title: Tonsil, pediatric, oSDB, ID35, EBV+, CPAP-

value: EBV+, CPAP-


title: R11382 CD Uninfected T0

description: 2 X 151bp

value: Monocytes derived Macrophages


title: A549 cells, Bud, 6h, rep3

description: Library name: Sample 52


title: Tonsil, pediatric, oSDB, ID32, EBV+, CPAP+

value: EBV+, CPAP+


title: A549 cells, IL1B, 2h, rep3

description: Library name: Sample 46


title: MS645_EGR1_IP

city: 长春市

last: Liu

state: 吉林省

address: 东民主大街519转化医学院

institute: 1st hospital

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

source_name: breast

growth_protocol: HCC1806 cells were cultured in RPMI-1640 contained 10% fetal calf serum , 100 units of penicillin  and 100 µg/ml streptomycin.

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

treatment_protocol: HCC1806 cells were treated with DMSO, MS645 and ARV771 for 8 hours

value: breast

value: triple-negative breast cancer

value: wt

value: HCC1806 cells treated with MS645


title: Tonsil, pediatric, oSDB, ID29, EBV-, CPAP-


title: hskm_miR-136_1


title: seedling_phyA_FR_input_2

city: Chicago

first: Shun

state: IL

address: 929 E. 57th. Street

department: Chemistry

institute: University of Chicago

data_processing:
Base mutations of each A site from each sample were called by pileup2var. Mutation counts from two replicates were merged and sites with coverage less than 5 were discarded. m6A site detection and quantification was calculated according to the spike-in data. Firstly, the overall mutation rate background (MRB) of each genotype group was determined by merging 0% A-modified spike-in data from all treated replicates of the corresponding group. Then MRB normalization factor for each group was defined as MRB of that group divided by median MRB. MRB of each motif (NNANN) was calculated from 0% A-modified spike-in data from all merged treated samples and was scaled by the MRB normalization factor of each group to represent the final MRB of each motif in the corresponding group. Secondly, each group’s overall conversion efficiency (CR) of mutation rates into m6A fractions was determined by merging 100% A-modified spike-in data from all treated replicates of the corresponding group. Then CR normalization factor for each group was defined as CR of that group divided by median CR. CR of each motif (NNANN) was defined as the coefficient of a linear function (if r2 > 0.9) or mutation rate of 100% A-modified spike-in of that motif (if r2 ≤ 0.9) and was scaled by the CR normalization factor of each group to represent the final CR of each motif in the corresponding group. Finally, high confidence m6A sites were identified according to the following criteria: (1) mutation rates of input samples < 5% or the number of mutations < 2; (2) mutation rates of treated samples > mutation rates of input samples x 3; (3) mutation rates of treated samples > 2% and the number of mutations ≥ 2; (4) m6A fractions converted from mutation rates using the final CR of individual motif ≥ 10%; (5) p-values of fisher’s exact test between treated and input samples < 0.1; (6) adjusted p-values of binomial test in the treated samples using the final MRB of individual motif < 0.05.
Assembly: TAIR10
Supplementary files format and content: m6A sites with fractions in BED format
Library strategy: m6A-Sac-seq

organism: Arabidopsis thaliana

growth_protocol: WT and mutant seedlings grown in the dark, far-red light (5 μmol m−2 s−1) or red light (25 μmol  m−2 s−1) for 6 days were used.

extract_protocol:
Total RNA was isolated using Direct-zol RNA Miniprep Kits (Zymo, Cat. # R2052). Polyadenylated RNA was purified from total RNA with two rounds of polyA-tail purification using the Dynabeads® mRNA DIRECT™ kit (Thermo Scientific, Cat. # 61012).
All the libraries were constructed by the m6A-Sac-seq protocol{Ge, 2023 #34}. The resulting library was purified by AMPure XP beads (Beckman Coulter) following the manufacturer’s directions and subjected to next-generation sequencing.

tag: developmental stage

value: seedling

value: input + far-red light

value: phyA mutant


title: Tonsil, pediatric, oSDB, ID34, EBV+, CPAP-


title: A549 cells, IL1B, 24h, rep3

description: Library name: Sample 49

value: lung carcinoma epithelial cells

value: WT


title: R11381 CD Infected T48

description: 2 X 151bp

value: Infected


title: hskm_siNRDC_2

value: primary human skeletal muscle cells


title: MS645_EGR1_input

address: 东民主大街519转化医学院


title: R11380 CD Uninfected T0

description: 2 X 151bp

value: CD

value: Uninfected


title: A549 cells, IL1B, 12h, rep3

description: Library name: Sample 48


title: hskm_siScr_2


title: Tonsil, pediatric, oSDB, ID28, EBV-, CPAP-

value: Tonsil

value: EBV-, CPAP-

value: Tonsillectomy


title: Tonsil, pediatric, oSDB, ID33, EBV+, CPAP-

value: EBV+, CPAP-


title: seedling_phyA_FR_input_1


title: hskm_nc_1


title: seedling_phyA_FR_2

value: MjDim1 + far-red light


title: A549 cells, IL1B, 6h, rep3

description: Library name: Sample 47


title: R11379 CD Infected T48

description: 2 X 151bp

value: Monocytes derived Macrophages


title: A549 cells, IL1B, 1h, rep3

description: Library name: Sample 45


title: Tonsil, pediatric, oSDB, ID26, EBV+, CPAP-


title: A549 cells, NS, 24h, rep3

description: Library name: Sample 44

value: NS


title: R11378 CD Uninfected T0

description: 2 X 151bp


title: Tonsil, pediatric, oSDB, ID27, EBV-, CPAP-


title: ARV771_EGR1_IP

address: 东民主大街519转化医学院

value: breast

value: triple-negative breast cancer

value: wt

value: HCC1806 cells treated with ARV771


title: ARV771_EGR1_input

address: 东民主大街519转化医学院


title: A549 cells, NS, 12h, rep3

description: Library name: Sample 43

value: lung carcinoma epithelial cells


title: hskm_siNRDC_1


title: A549 cells, NS, 2h, rep3

description: Library name: Sample 42

value: WT


title: DMSO_EGR1_input

address: 东民主大街519转化医学院

value: HCC1806 cells treated with DMSO


title: A549 cells, NS, 1h, rep3

description: Library name: Sample 41


title: DMSO_EGR1_IP

address: 东民主大街519转化医学院

value: HCC1807 cells treated with DMSO


title: Tonsil, pediatric, oSDB, ID24, EBV-, CPAP-


title: seedling_phyA_FR_1

value: seedling

value: phyA mutant


title: hskm_siScr_1

value: primary human skeletal muscle cells


title: seedling_mta_FR_input_2

value: input + far-red light

value: mta mutant


title: Tonsil, pediatric, oSDB, ID20, EBV-, CPAP-

value: Tonsil

value: EBV-, CPAP-

value: Tonsillectomy


title: Tonsil, pediatric, oSDB, ID18, EBV+, CPAP-

value: EBV+, CPAP-


title: A549 cells, IL1B+Bud, 24h, rep2

description: Library name: Sample 40

value: IL1B + Budesonide


title: MS645_BRD4_IP

address: 东民主大街519转化医学院

value: breast

value: triple-negative breast cancer

value: HCC1806 cells treated with MS645


title: seedling_mta_FR_input_1


title: MS645_H3K27ac_IP

address: 东民主大街519转化医学院

value: wt


title: seedling_mta_FR_2

value: MjDim1 + far-red light


title: A549 cells, IL1B+Bud, 12h, rep2

description: Library name: Sample 39

value: lung carcinoma epithelial cells

value: WT


title: MS645_input

address: 东民主大街519转化医学院


title: seedling_mta_FR_1

value: seedling


title: Tonsil, pediatric, oSDB, ID8, EBV-, CPAP-


title: seedling_fio1_FR_input_2

value: fio1 mutant


title: A549 cells, IL1B+Bud, 6h, rep2

description: Library name: Sample 38


title: Tonsil, pediatric, oSDB, ID5, EBV-, CPAP+

value: EBV-, CPAP+


title: ARV771_H3K27ac_IP

address: 东民主大街519转化医学院

value: HCC1806 cells treated with ARV771


title: A549 cells, IL1B+Bud, 2h, rep2

description: Library name: Sample 37


title: A549 cells, IL1B+Bud, 1h, rep2

description: Library name: Sample 36


title: Tonsil, pediatric, oSDB, ID9, EBV-, CPAP+


title: seedling_fio1_FR_input_1

value: input + far-red light


title: ARV771_BRD4_IP

address: 东民主大街519转化医学院


title: Tonsil, pediatric, oSDB, ID2, EBV+, CPAP-

value: Tonsil


title: A549 cells, Bud, 24h, rep2

description: Library name: Sample 35

value: Budesonide


title: seedling_fio1_FR_1


title: ARV771_input

address: 东民主大街519转化医学院


title: A549 cells, Bud, 12h, rep2

description: Library name: Sample 34


title: DMSO_H3K27ac_IP

address: 东民主大街519转化医学院

value: HCC1808 cells treated with DMSO


title: S03_TREG

city: London

first: Cristiano

last: Scotta

address: Kingston Lane

department: Life Science

country: United Kingdom

institute: Brunel University

data_processing:
25 million reads (paired end) were sequenced for each sample on the NovaSeq 6000 following the manufacturer's protocols.
Fastq files were trimmed and aligned using kallisto, and differential gene expression performed using DESeq2.
Assembly: hg38
Supplementary files format and content: treg_mac_counts is a tab-delimited text file which includes raw counts for each sample.
Supplementary files format and content: mac_treg_comparison_annotated is a tab-delimited text file of defferentially expressed gene profile of macrophages cultured alone against macrophages  cultured in the presence of regulatory T cells. The file includes ensembl_gene_id, baseMean, log2FoldChange, lfcSE, pvalue, padj, hgnc_symbol and gene_biotype for each gene.

source_name: Blood (PBMC)

growth_protocol: Human monocytes isolated from healthy donors were differentiated into monocyte-derived macrophages with M-CSF and polarized with IL-4 for 48h

extract_protocol:
To extract RNA, cells were harvested, washed with PBS and FACS sorted to have highly pure macrophage population. Then, cells were lysed in TRIzolTM land RNA extracted using Rneasy® Mini Kit (Qiagen), according to the manufacturers’ protocol. Extracted RNA samples were quantified by NanoDrop™ 8000 Spectrophotometer (Thermo Fisher Scientific) and quality tested on TapeStation 4200 (Agilent).
For sequencing library preparation, 100ng of total RNA was used as input for a poly-A selection. Libraries were prepared according to NovaSeq 6000 Sequencing System.

treatment_protocol: Differentiated macrophages were cultured alone or in the presence of autologous regulatory T cells at a ratio of 1:1 in serum free RPMI for 24h.

value: Blood (PBMC)

value: Monocyte-derived macrophages


title: seedling_fio1_FR_2


title: seedling_Col_R_input_2

value: input + red light

value: wild type


title: DMSO_BRD4_IP

address: 东民主大街519转化医学院

value: breast

value: triple-negative breast cancer

value: HCC1807 cells treated with DMSO


title: A04_TREG


title: DMSO_input

address: 东民主大街519转化医学院

value: wt

value: HCC1806 cells treated with DMSO


title: seedling_Col_R_2

value: seedling

value: MjDim1 + red light


title: seedling_Col_R_input_1


title: A549 cells, Bud, 6h, rep2

description: Library name: Sample 33

value: lung carcinoma epithelial cells

value: WT


title: A04_M2


title: MS645_3

address: 东民主大街519转化医学院

data_processing:
The raw data was filtered with SOAPnuke (v1.5.2) by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 50%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the reference genome by HISAT (v2.1.0)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5) .The expression level of genes was calculated by RSEM (v1.2.8)
Annotating assembled Unigene with seven major functional databases (KEGG, GO, NR, NT, SwissProt, Pfam, and KOG), and predicting the transcription factors.
Time Series analysis was performed by Mfuzz (v2.34.0), and gene co-expression network analysis was performed by WGCNA (v1.48). Within-group differential gene analysis was performed using DESeq  under the conditions of Fold Change >=2 and Adjusted P value <= 0.001. PossionDis was performed between-group differential gene analysis under the conditions of Fold Change>= 2 and FDR <=0.001. Using the pheatmap function on the differential gene set to draw a heatmap of differential gene clusters. According to the GO and KEGG annotation results and classifications, the differentially expressed genes were functionally classified, the phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) in R software was used for KEGG enrichment analysis, and the TermFinder package was used for GO Enrichment analysis (https://metacpan.org/pod/GO::TermFinder). With a Q value of ≤ 0.05 as the threshold, candidate genes that met this condition were defined as significantly enriched.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts values for each Sample

extract_protocol:
Cells were lysed in Trizol reagent (GE healthcare), and total RNA were isolated according to standard protocal.Three biological replicates were prepared for each treatment.
Briefly,  mRNA is enriched by oligo (dT) -attached magnetic beads and fragmented. Reaction systems are prepared to synthesize the double-stranded cDNA. Double-stranded cDNA fragments are subjected to end-repair,  a single ‘A’ nucleotide attachment and adaptor ligation. The PCR reaction system and program are configured and set up to amplify the product. Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated.

value: triple negative breast cancer cell


title: S03_M2


title: A03_TREG


title: MS645_2

address: 东民主大街519转化医学院


title: A549 cells, Bud, 1h, rep2

description: Library name: Sample 31


title: A03_M2


title: RNA_14_HiPSC-derived Podocytes INF2 mutation

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

country: Germany

institute: RWTH Aachen University Medical School

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the GRCh38 genome using STAR version 2.6.1c.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: HiPSC from FSGS patient (INF2 mutation) differentiated into podocytes

growth_protocol: CiPodocytes were cultured in RPMI medium containing 10% fetal calf serum, 1% Insulin-Transferrin-Selenium,1% penicillin-streptomycin at 33°C for proliferation and at 37°C for differentiation for 10 days. HiPSCs were cultured in mTeSR1 medium (Stem Cell Technologies) containing 1% penicillin-streptomycin. Nephron progenitor cells were generated by differentiation of hiPSCs for 2 days in DMEM/F12 containing 1x B27 supplement, 1% penicillin-streptomycin, 3 μM CHIR99021, 50 ng/mL activin A and 10 μM ROCK inhibitor Y27632 with additional culture for 14 days in DMEM/F12 containing 1x B27 supplement, 1% penicillin-streptomycin, 3 μM CHIR99021, 50 ng/mL activin A, and 50 ng/mL BMP7. HiPSC-derived podocytes were generated by further differentiation of nephron progenitor cells for additional 5 days in DMEM/F12 medium containing containing 1x B27 supplement, 1% penicillin-streptomycin, 3 μM CHIR99021, 50 ng/mL activin A, 50 ng/mL BMP7, 25 ng/μL VEGF, and 0.5 μM all-trans retinoic acid.

extract_protocol:
RNA was isolated using the ReliaPrep™ RNA Miniprep Systems (Promega, Walldorf, Germany) according to the manufacturer´s protocol.
Novogene NGS DNA Library Prep Set (Cat No.PT004). Libraries were sequenced on IlluminaNovaseq 6000  (Illumina).

value: Podocyte

value: INF2 mutation

value: untreated


title: MS645_1

address: 东民主大街519转化医学院


title: A549 cells, IL1B, 12h, rep2

description: Library name: Sample 29


title: seedling_Col_FR_input_2

value: input + far-red light


title: A549 cells, IL1B, 24h, rep2

description: Library name: Sample 30


title: seedling_Col_FR_input_1


title: RNA_13_HiPSC-derived Podocytes INF2 mutation

value: HiPSC from FSGS patient (INF2 mutation) differentiated into podocytes


title: seedling_Col_FR_2

value: MjDim1 + far-red light


title: A549 cells, IL1B, 6h, rep2

description: Library name: Sample 28


title: A549 cells, IL1B, 2h, rep2

description: Library name: Sample 27


title: DMSO_3

address: 东民主大街519转化医学院

value: DMSO


title: DMSO_2

address: 东民主大街519转化医学院

value: breast


title: RNA_12_Nephron progenitor cells INF2 mutation

source_name: HiPSC from FSGS patient (INF2 mutation) differentiated into nephron progenitor cells

value: Nephron progenitor cells


title: seedling_Col_FR_1

value: wild type


title: RNA_11_Nephron progenitor cells INF2 mutation

value: HiPSC from FSGS patient (INF2 mutation) differentiated into nephron progenitor cells


title: A549 cells, IL1B, 1h, rep2

description: Library name: Sample 26


title: DMSO_1

address: 东民主大街519转化医学院

value: wt


title: RNA_10_HiPSC INF2 mutation

source_name: HiPSC from FSGS patient (INF2 mutation) generated from dermal fibroblasts

value: HiPSC


title: seedling_Col_D_input_2

value: seedling

value: input + dark


title: A549 cells, NS, 24h, rep2

description: Library name: Sample 25

value: lung carcinoma epithelial cells

value: WT

value: NS


title: ARV771_3

address: 东民主大街519转化医学院

value: triple negative breast cancer cell


title: seedling_Col_D_input_1


title: RNA_9_HiPSC INF2 mutation

value: HiPSC from FSGS patient (INF2 mutation) generated from dermal fibroblasts

value: INF2 mutation

value: untreated


title: A549 cells, Bud, 2h, rep2

description: Library name: Sample 32

value: Budesonide


title: ARV771_2

address: 东民主大街519转化医学院


title: ARV771_1

address: 东民主大街519转化医学院


title: A549 cells, NS, 6h, rep2

description: Library name: Sample 23


title: RNA_8_HiPSC-derived Podocytes wildtype

source_name: HiPSC from healthy donor terminally differentiated into podocytes

value: Podocyte

value: Wildtype


title: seedling_Col_D_2

value: MjDim1 + dark


title: A549 cells, NS, 12h, rep2

description: Library name: Sample 24


title: seedling_Col_D_1

value: wild type