title: Kasumi-1 IL10 REP1 (K_IL10_1)

city: Tianjin

first: Yingxi

last: Xu

address: 288 Nanjing Road

department: State Key Laboratory of Experimental Hematology

institute: Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: GRCh38(hg38)
Supplementary_files_format_and_content: tab-delimited tex files include FPKM values for each samples

source_name: AML cell line

growth_protocol: Kaumi-1 cells were cultured in RPMI1640 medium with 20% FBS.

extract_protocol:
Kasumi-1 cells were spined down, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Kasumi-1 cells were treated with 0.5%BSA(Ctrl) or 10ng/ml rhIL10(IL10) for 72h.

tag: cell type

value: AML

value: 10ng/ml rhIL10

tag: cell line


title: THP-1 without infection rep2

status: Public on Sep 30 2021

type: SRA

city: ChangSha

first: Yongwei

last: Zhu

state: Hunan

address: No.87,  Xiangya Street

country: China

institute: CSU Xiangya hospital

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using bowtie2 v2.3.5 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using a protocol from Trapnell C et al., Nat Biotechnol, 2010.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TMP values for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: THP-1 human monocyte macrophages were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum, and HEK293T cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, which were both cultured at 37°C with 5% CO2. H37Rv and H37Rv△1759c were cultured in Middlebrook 7H9 medium (Becton Dickinson, Difco, 271310) supplemented with 10% oleic acid, albumin, dextrose (OADC) (Becton Dickinson, Difco, 212352), 0.5% (v/v) glycerol (Sigma Aldrich, G5516), and 0.05% (v/v) Tween 80 (Sigma Aldrich, P8074).

extract_protocol:
Total miRNA of the 9 samples was isolated by using an RNeasy minikit (Qiagen, 217004) .
RNA libraries were prepared for sequencing using standard Illumina protocols
Hiseq Single-End RNA-Seq

treatment_protocol: THP-1 cells were differentiated with 100 ng/mL phorbol myristate acetate (PMA) for 48 h and incubated with 1640 medium for another 8 h. Cells were infected with H37Rv or  H37Rv△1759c  at an MOI of 1 . At 4 h postinfection (4 hpi), cells were washed three times with phosphate-buffered saline (PBS) and incubated at 37°C with fresh medium. Cells were collected with TRIzol reagent  at  24 h postinfection ( 24 hpi).

tag: treatment

value: negative control


title: NC40: pre-infection

city: Covington

first: Joseph

middle: C

last: Mudd

state: LA

address: 18703 Three Rivers rd

country: USA

institute: Tulane University

data_processing:
Sequencing reads were demultiplexed and adapter-trimmed with Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).  The –hardtrim  option was used to clip the first 6 basepairs of mate R2 that exhibited low quality scores.  Because reads were derived from 2 separate species with different genomes and different genome annotations, these were treated as different datasets from alignment to gene correlation steps.  In brief, lanes were concatenated and mapped with STAR aligner to their respective species genomes, Mmul_10 (GCF_003339764.) for RM and ChlSabl.1 (GCF_000409795.2) for AGM (49).  Parameters were modified from the default run option that gave the highest percentage of uniquely mapped reads:  --outFilterScoreMinOverLread 0   --outFilterMatchNmin 0   --outFilterMatchNminOverLread 0   --outFilterMismatchNmax 2.  Counts were generated by the STAR option –quantMode geneCounts and an n  n matrix was prepared as input for the R package DESeq2 (50).  Data was fitted to a generalized linear model in accordance with the DEseqdataset function.  Samples that received an RNA concentration step during the isolation process were found to strongly influence fitted values of the model.  Thus a revised analysis was performed incorporating the effect of RNA clean-up into the generalized linear model.  Hidden variables were further incorporated with the R package SVA and the object was post-filtered to remove genes with at least 4 samples having normalized counts < 10.
Genome_build: Mmul_8.0.1 (for rhesus samples), ChlSabl.1 (for AGM samples
Supplementary_files_format_and_content: tab delimited text files correspond to transcript read counts calculated by Htseq-count

organism: Chlorocebus sabaeus

source_name: PAXgene

extract_protocol:
collection protocol: Whole venous blood was collected from nonhuman primates using a BD Vacutainer Safety-Lok Blood Collection Set (BD catg#367281) and BD Vacutainer one use needle holder (BD catg# 364815). Blood was added to the PAXgene Blood RNA reagent tube (PreAnalytiX catg#762165) in the same ratio as the manufacturer’s guidelines. Post collection, PAXgene blood tubes were stored upright for a minimum of two hours and then placed into the -20C freezer until further processing.
Samples were processed in accordance with the PreAnalytiX PAXgene Blood RNA Kit (PreAnalytiX catg#762165). The RNA Clean & Concentrator-5 kit (Zymo, Catg#R1015) was used to purify and increase RNA samples with low yields. Procedures were followed per manufacturer’s guidelines. For AGM NC33, Paxgene tubes were not collected at 1 and 3 dpi due to blood being prioritized for other assays.
Total RNA samples were quantitated using Qubit RNA HS Assay kit (Invitrogen Q32855). A RIN for each sample was determined by running 1ul on an Agilent 4150 TapeStation using RNA Screen Tapes (Agilent 5067-5576). 1-2 ug of each sample were treated with Baseline Zero DNase (Epicentre, DB0711K) for 30 minutes at 37°C. DNase was inactivated by adding 2ul 10X Stop solution and following a 10 minute incubation at 65°C. The Total RNAs were then purified using Agencourt RNAClean XP magnetic beads by following the manufactory recommendation (Beckman Coulter Life Sciences). 10 ng of each sample were used to make SMART-Seq libraries following the SMART-Seq Stranded Kit User Manual (Takara Bio). Briefly, cDNAs were first generated from all total RNA fragments after RNA fragmentation. Addition of Illumina adapters and indexes and then library purification were followed. Final library amplification and purification were performed after enzymatically removing ribosomal fragments originating from rRNA molecules by using probes specific to mammalian rRNA.
Libraries were quantitated using Qubit DNA HS Assay kit (Molecular Probes Life Technologies, Q32854). Average size of each library was determined by running each sample on Agilent 4150 TapeStation using D1000 Screen Tapes. (Agilent 5067-5582). Each library was diluted to 4nM in DNase RNase free ultrapure water (Invitrogen 10977-015). All libraries were pooled at a concentration of 4nM before denaturing with 0.2 N NaOH for 5 min at RT. The libraries were neutralized using 0.2 N Tris-HCl, pH 7 before being diluted to 20pM in HT1 buffer (Illumina).
Finally, denatured libraries were loaded into an Illumina NextSeq 550 v2 High-Output reagent cartridge at a final concentration of 1.2pM in HT1 buffer. Denatured PhiX control library was also included at 1% concentration. Dual indexes and paired end 75bp sequencing was performed on a High-Output flow cell yielding about 18M read pairs per sample.

value: uninfected

tag: tissue

value: Blood

tag: time

value: PRE


title: NC34: 1 dpi SARS-CoV-2


title: DNA_oncoscan_prostatecancer_15-008/032

type: genomic

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

description: OncoScan CNV for prostate cancer sample from patient 15-008/032

hyb_protocol: Labeled libraries were hybridized to Affymetrix OncoScan CNV arrays according to the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner according to the manufacturer's instructions.

data_processing:
CEL files were processed with the Affymetrix OncoScan console to generate OSCHP files. OSCHP files were processed with Biodiscovery Nexus Copy Number software using default settings for the OSCHP-TuScan algorithm.
Regions of LOH and/or copy number change were reported for each genomic interval, with a listing of gene symbols in each interval.

label: biotin

molecule: genomic DNA

source_name: prostate cancer tissue

label_protocol: Libraries were labeled with biotin according to the manufacturer's instructions.

extract_protocol: Genomic DNA was purifed from ribbons of FFPE tissues using the QIAamp DNA FFPE Tissue Kit according to the manufacturer's instructions.

treatment_protocol: Patients with prostate cancer underwent radical prostatectomy with no prior therapy. Prostate tissues were grossed, accessioned, fixed in formalin, and embedded in paraffin.

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

value: prostate cancer tissue


title: Kasumi-1 IL10 REP3 (K_IL10_3)


title: DNA_oncoscan_prostatecancer_15-008/026

description: OncoScan CNV for prostate cancer sample from patient 15-008/026


title: hDMCs-BMP4 Dorsomorphin rep3

city: FuZhou

first: XIAOXIAO

last: HU

address: Qishan Branch

institute: Fujian Normal University

description: Normalized_counts_file_BMP4 Dorsomorphin.txt

data_processing:
Illumilla HiSeq X Ten was used to perform sequencing
Reads were mapped to genome with HISAT2
counted in genomic features with featureCounts software
DEseq2 was used to differ differential expressions
Genome_build: hg38
Supplementary_files_format_and_content: TXT

source_name: human dental mesenchymal cells

extract_protocol:
Total RNA of cultured hDMCs was extracted using RNeasy Mini Kit (Qiagen, 74104).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMP4 protein (R&D Systems, 314-BP-050) was added to the medium at the final concentration of 100ng/ml. For small molecule inhibition experiments, dorsomorphin (Sigma, P5499), SB203580 (CST, 5633), U0126 (CST, 9903), and SP600125 (Abcam, ab120065) were added into the medium at the final concentration of 20uM. DMSO (Sigma, 76314) was used as negative control.

value: molar tooth germ

value: BMP4 Dorsomorphin


title: S1067__00054

type: RNA

city: Belfast

first: Stuart

last: McIntosh

address: 97 Lisburn Road

country: United Kingdom

institute: Queen's University Belfast

description:
Baseline diagnostic core biopsy
Gene expression data from breast cancer pre-treatment
Baseline tumour core biopsies were taken from breast cancers under ultrasound guidance

hyb_protocol: Following fragmentation, RNA was hybridised onto Affymetrix GeneChip arrays. GeneChips were washed and stained in the Affymetrix GeneChips fluidics stating 450

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000

data_processing: Microarray data was processed using the Robust Multi-array average method.

label: Biotin

source_name: Breast cancer pre-treatment biopsy

label_protocol: 3.5 µg biotinylated RNA was prepared using the NuGEN Encore Biotin Module

extract_protocol: Extraction of total RNA was carried out in accordance with standard SOPs

treatment_protocol: All baseline samples were taken prior to any anti-cancer treatment

value: Breast cancer


title: DNA_oncoscan_prostatecancer_15-008/028

description: OncoScan CNV for prostate cancer sample from patient 15-008/028

value: unknown


title: THP-1 whith H37RV infection rep1

value: positive control


title: Kasumi-1 Ctrl REP3 (K_C_3)


title: S1067__00055


title: hDMCs-BMP4 DMSO rep3

description: Normalized_counts_file_BMP4 DMSO.txt

value: BMP4 DMSO


title: DNA_oncoscan_prostatecancer_15-008/033

description: OncoScan CNV for prostate cancer sample from patient 15-008/033


title: hDMCs-BMP4 DMSO rep2

description: Normalized_counts_file_BMP4 DMSO.txt


title: Kasumi-1 IL10 REP2 (K_IL10_2)


title: Kasumi-1 Ctrl REP1 (K_C_1)


title: DNA_oncoscan_prostatecancer_15-008/029

description: OncoScan CNV for prostate cancer sample from patient 15-008/029


title: DNA_oncoscan_prostatecancer_15-008/023

description: OncoScan CNV for prostate cancer sample from patient 15-008/023


title: DNA_oncoscan_prostatecancer_15-008/025

description: OncoScan CNV for prostate cancer sample from patient 15-008/025


title: Kasumi-1 Ctrl REP2 (K_C_2)


title: hDMCs-BMP4 DMSO rep1

description: Normalized_counts_file_BMP4 DMSO.txt


title: S1067__00052_F1


title: BAGBra_8

city: Juiz de Fora

first: Ana Luisa

middle: Sousa

last: Azevedo

state: Minas Gerais

address: Rua Eugenio do Nascimento, 610

country: Brazil

institute: Empresa Brasileira de Pesquisa Agropecuaria

data_processing:
The sequenced RNA quality control was evaluated using FastQC software v 0.11.8 (Babraham Bioinformatics, Babraham, England).
A transcriptome assembly was built by two approaches: through Trinity v 2.8.4 (Grabherr et al., 2011), and Stringtie v 2.0.4 software (Pertea et al., 2015), using Urochloa ruziziensis as reference genome. Then, the final transcriptome was assembled using those two de novo assembles by PASA v 2.2 (Haas et al., 2003).
Salmon v 0.7.2 software (Patro et al., 2017) was used to quantify the sequenced reads.
The quantification files were used for differential expressed genes analysis.
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

organism: Urochloa humidicola

source_name: Young leaves

value: Young leaves

value: Low Lignin


title: DNA_oncoscan_prostatecancer_15-008/021

description: OncoScan CNV for prostate cancer sample from patient 15-008/021


title: S1067__00051_F1


title: DNA_oncoscan_prostatecancer_15-008/020

description: OncoScan CNV for prostate cancer sample from patient 15-008/020


title: hDMCs-BMP4 SMAD4 siRNA rep3

description: Normalized_counts_file_BMP4 SMAD4 siRNA.txt

value: BMP4 SMAD4 siRNA


title: hDMCs-BMP4 Dorsomorphin rep1


title: BAGBra_7


title: S1067__00048_A1


title: S1067__00058


title: BAGBra_6


title: hDMCs-BMP4 SMAD4 siRNA rep2


title: S1067__00053_F1


title: BAGBra_4

value: High Lignin


title: DNA_oncoscan_prostatecancer_15-008/019

description: OncoScan CNV for prostate cancer sample from patient 15-008/019


title: BAGBra_5


title: hDMCs-BMP4 control siRNA rep3

description: Normalized_counts_file_BMP4 control siRNA.txt

value: BMP4 control siRNA


title: DNA_oncoscan_prostatecancer_15-008/018

description: OncoScan CNV for prostate cancer sample from patient 15-008/018


title: S1067__00056


title: BAGBra_3


title: BAGBra_2


title: S1067__00047_A1


title: DNA_oncoscan_prostatecancer_15-008/017

description: OncoScan CNV for prostate cancer sample from patient 15-008/017


title: DNA_oncoscan_prostatecancer_15-008/015

description: OncoScan CNV for prostate cancer sample from patient 15-008/015

value: recurrence


title: BAGBra_1


title: hDMCs-BMP4 control siRNA rep2


title: DNA_oncoscan_prostatecancer_15-008/013

description: OncoScan CNV for prostate cancer sample from patient 15-008/013


title: hDMCs-BMP4 control siRNA rep1


title: S1067__00045


title: DNA_oncoscan_prostatecancer_15-008/014

description: OncoScan CNV for prostate cancer sample from patient 15-008/014


title: S1067__00057


title: hDMCs-BMP4 SMAD4 siRNA rep1


title: hDMCs-BSA control siRNA rep3

description: Normalized_counts_file_BSA control siRNA.txt

value: BSA control siRNA


title: DNA_oncoscan_prostatecancer_15-008/010

description: OncoScan CNV for prostate cancer sample from patient 15-008/010

value: male


title: hDMCs-BSA control siRNA rep1


title: S1067__00046

description:
Baseline diagnostic core biopsy
Gene expression data from breast cancer pre-treatment
Baseline tumour core biopsies were taken from breast cancers under ultrasound guidance


title: WT_Periphilin2

city: Cambridge

first: Sergio

last: Martínez Cuesta

address: 1 Francis Crick Avenue

department: Data Sciences and Quantitative Biology, Discovery Sciences

institute: AstraZeneca

description:
PPHLN RIPseq
WTHA.dedup.bw
WTHA.v2.bed
ripseq_genes.txt

data_processing:
The data was processed as described in the methods section of the associated manuscript. Details about the analysis are available in https://github.com/semacu/hush
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files contain quantification of signal in genes of interest, bed files contain peaks calculated with a tailored peak calling strategy and bigwig capture genomic signal. Data was processed jointly with RNA-seq and ChIP-seq data available in GSE95374

molecule: nuclear RNA

source_name: HEK293T cells

growth_protocol: HEK293T were obtained from ATCC and HeLa were obtained from ECACC. All cell lines were cultured at 37°C and 5% CO2 in Iscove's Modified Dulbecco's Medium (IMDM, Sigma-Aldrich) supplemented with 10% fetal calf serum (FCS, Gibco), 1x GlutaMAX (Gibco), and 100 U/mL penicillin/streptomycin (Gibco).

extract_protocol:
RIPseq:  Lysates from UV-treated cells were clarified from sonicated nuclei and RNA-protein complexes were isolated with anti-HA magnetic beads. ChIPseq: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K9me3 antibody.
RIPseq: Immunoprecipitated RNA was subjected to DNA library preparation using SMARTer Stranded Total RNA-Seq Kit V3 – Pico Input Mammalian (Takara Bio, USA) kit according to the manufacturer’s instructions and following conditions: initial fragmentation at 94°C for 3-4 min, ribosomal RNA depletion step included, 5 PCR cycles for PCR adding adapters and indexes and 12 for final library amplification). The library quality was determined using Bioanalyzer, and sequenced using Illumina MiniSeq System with the following specifications: 32 bp (R1) and 43 bp (R2), paired-end reads were sequenced using MiniSeq High-Output 75 cycles kit. ChIPseq: ChIP DNA and input DNA were subjected to library preparation with NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer's instructions. Libraries were purified, quantified, multiplexed (with NEBNext Multiplex Oligos for Illumina) and sequenced with 2× 50-bp pair-end reads on Illumina Novaseq platform (Genomics Core, Cancer Research UK Cambridge Institute).

tag: genotype

value: PPHLN1 HA knock-in


title: hDMCs-BSA control siRNA rep2


title: S1067__00040_F1


title: DNA_oncoscan_prostatecancer_15-008/012

description: OncoScan CNV for prostate cancer sample from patient 15-008/012

value: remission


title: DNA_oncoscan_prostatecancer_15-008/009

description: OncoScan CNV for prostate cancer sample from patient 15-008/009

value: white

value: prostate cancer tissue


title: S1067__00044_F1


title: Caffeine 24h_BrdUIP_LateS

city: Tsu

first: Takuya

last: Hayakawa

state: Mie

address: 1577 Kuriyamachiya

department: Bioresources

country: Japan

institute: Mie University

library_source: genomic

data_processing:
Library strategy: E/LRepli-seq
The raw Fastq files were trimmed to remove adapter sequences using the cutadapt program before mapping. We performed two-step adapter trimming, first removing the Illumina adapter according to the index of each NGS library and then removing the SEQXE adapter. hg19 reference genome (chr1–22, chrX, chrY) assemblies were used. Mapping to the hg19 reference genome used the Picard tool to remove duplicated reads and defining MAPQ>10 as uniquely mapped reads. We also filtered out the reads that overlapped with the hg19 blacklists. After blacklist filtering, we counted the reads from the early- and late-S-phase BrdU-IP samples in sliding windows of 300 kb at 40-kb intervals, and performed reads per million (rpm) normalization. The ratio of early-S-phase to late-S-phase read counts log2 ((early-S reads)/ (late-S reads)) was calculated for each bin. The average RT profiles were obtained by calculating log2 ((averaged early-S)/(averaged late-S)).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_fmt.txt: Tab-delimited text files

source_name: RPE cells

growth_protocol: Human retinal pigment epithelium (RPE) cells were grown in MEMα (Wako, Osaka, Japan) supplemented with 10% FBS at 37℃ with 5% CO2.

extract_protocol:
Cells were washed twice with ice-cold PBS, trypsinized, and fixed in 75% ethanol. Fixed cells were resuspended in PBS contained 1% FBS, stained with propidium iodide (50 µg/ml) for 15 min in the presence of RNase A (100 µg/ml). These cells were sorted into early and late S phase fractions by SH800 flow cytometer (SONY). After phenol-chloroform extraction of DNA from 10,000 cells, sonication was performed to cut the DNA into an average size of about 100-700 bp. Then, immunoprecipitation with anti-BrdU mouse monoclonal antibody (BD Biosciences, #555627) was performed in each fraction to enrich BrdU-substituted replicating DNA. Isolated early and late replicating DNA was amplified individually by WGA (Sigma. SEQXE).
NGS libraries were constructed from early- and late-replicating DNA after WGA with a TruSeq DNA PCR-Free High Throughput Library Prep Kit (Illumina, San Diego, CA, USA) and NEXTflex® DNA-Seq Kit, both according to the manufacturers’ instructions.

treatment_protocol: DNA replication stress was induced by exposure to 1 µM camptothecin (CPT; TopoGEN, Buena Vista, VA, USA) with or without 1 mM caffeine (Nacalai Tesque, Kyoto, Japan).

value: RPE

value: caffeine for 24 h

tag: cell phase

value: Late S

tag: ip

value: BrdU-IP


title: Caffeine 7h_BrdUIP_LateS

value: caffeine for 7 h


title: DNA_oncoscan_prostatecancer_15-008/007

description: OncoScan CNV for prostate cancer sample from patient 15-008/007


title: S1067__00038

value: Breast cancer


title: mito low

city: Indianapolis

first: Bin

last: Guo

state: Indiana

address: 950 W. Walnut Street

department: Microbiology & Immunology

institute: Indiana University

description: Mito SOX staining low (15%)

data_processing:
fastq files were aligned to version 3.0.0 cellranger GRCh38 human reference and obtained feature counts by cellranger count tool
Genome_build: version 3.0.0 cellranger GRCh38 human reference
Supplementary_files_format_and_content: Feature count results from cellranger: Filtered feature-barcode matrices containing only cellular barcodes in MEX format. (In Targeted Gene Expression samples, the non-targeted genes are not present.)

molecule: polyA RNA

source_name: Mito SOX staining low (15%)

growth_protocol: Stemlin II medium with human SCF, TPO and Flt3L (100ng/mL)

extract_protocol:
Mononuclear cells (MNCs) from normal human cord blood (CB) were isolated by density gradient centrifugation with Ficoll-Paque Plus (GE Healthcare, Piscataway, NJ, USA). CD34+ cells were enriched using an immunomagnetic selection kit (Miltenyi Biotec, Auburn, CA, USA). MNCs were resuspended in MACS buffer (0.5% BSA, 2mM EDTA in PBS, pH7.2). FcR blocking reagent (Miltenyi Biotec, #130-046-702) and CD34 microbeads (Miltenyi Biotec, #130-046-702) were added sequentially, and then the cells were incubated for 30 min at 4℃. The cells were washed with MACS buffer and centrifuged at 300 g for 10 min. The supernatant was aspirated and the cells were resuspended in 1 mL MACS buffer. Magnetic separation was performed with an appropriate MACS column (Miltenyi Biotec, #130-042-401).
For single cell RNA-seq, the libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits (10X Genomics, Pleasanton, CA). mitoROS low and mitoROS high CB CD34+ cells were concentrated to 1000 cells/uL and approximately 10,000 cells were loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs), which results into expected mRNA barcoding of 8,000 single-cells for each sample. After the reverse transcription, 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 HiSeq Xten (Illumina, San Diego, CA) on a 150 bp paired-end run.

value: human cord blood

value: CD34+ cells

value: Stemline II medium with human SCF, TPO, Flt3L (100 ng/mL)


title: WT_empty1

description:
control RIPseq
WTempty.dedup.bw
WTHA.v2.bed
ripseq_genes.txt

value: wild type


title: DNA_oncoscan_prostatecancer_15-008/008

description: OncoScan CNV for prostate cancer sample from patient 15-008/008


title: mito high

description: Mito SOX staining high (15%)

source_name: Mito SOX staining high (15%)

treatment_protocol: Stemlin II medium with human SCF, TPO and Flt3L (100ng/mL)


title: S1067__00041_F1


title: S1067__00042_F1


title: WT_Periphilin1


title: Caffeine 24h_BrdUIP_EarlyS

value: Early S


title: WT_empty2


title: DNA_oncoscan_prostatecancer_15-008/005

description: OncoScan CNV for prostate cancer sample from patient 15-008/005


title: S1067__00034


title: S1067__00037


title: DNA_oncoscan_prostatecancer_15-008/006

description: OncoScan CNV for prostate cancer sample from patient 15-008/006

value: recurrence


title: SETDB1KO_empty3

description:
control RIPseq in SETDB1 KO
empty.SKOempty.dedup.bw
HA.SKOHA.v2.bed
ripseq_genes.txt

value: SETDB1 KO pool


title: SETDB1KO_Periphilin rep 4

description:
PPHLN RIPseq in SETDB1 KO
HA.SKOHA.dedup.bw
HA.SKOHA.v2.bed
ripseq_genes.txt

value: PPHLN HA knock in; SETDB1 KO pool

tag: antibody

value: anti-HA


title: DNA_oncoscan_prostatecancer_15-008/003

description: OncoScan CNV for prostate cancer sample from patient 15-008/003

value: male

value: white

value: remission


title: S1067__00035_H


title: CPT+Caffeine 7h_BrdUIP_LateS_replicate 2

tag: cell type

value: RPE

value: camptothecin and caffeine simultaneously for 7 h


title: S1067__00031


title: DNA_oncoscan_prostatecancer_15-008/001

description: OncoScan CNV for prostate cancer sample from patient 15-008/001

value: prostate cancer tissue


title: S1067__00028_F1


title: CPT 7h_BrdUIP_LateS_replicate 2

value: camptothecin for 7 h

value: Late S

value: BrdU-IP


title: tomato self graft - 5 DAG - Replicate 4

city: Raleigh

first: Lisa

last: Van den Broeck

state: NORTH CAROLINA

address: 112 Derieux Place

department: Plant and Microbial Biology

institute: North Carolina State University

description:
Named TT_5d in processed file
Supplemental_Table1
TT_5d_R4

data_processing:
Gene expression analysis of raw RNA-seq data was performed using the TuxNet interface (Spurney et al, 2019).
TuxNet uses ea-utils fastq-mcf (Aronesty, 2011, Aronesty, 2013) for preprocessing, hisat2 (Kim et al, 2015) for genome alignment, and Cufflinks (Trapnell et al, 2012) for differential expression analysis.

organism: Capsicum annuum

source_name: Graft junction

extract_protocol:
RNA was extracted using TRIzol reagent. The purified RNA was treated with DNAseI.
RNA-seq libraries were constructed using 2.5 µg of total RNA per sample, isolated with the NEBNext® Poly(A) mRNA Magnetic Isolation Module, followed by the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® using NEBNext® Multiplex Oligos for Illumina®.

value: tomato self graft - 5 DAG


title: CPT+Caffeine 7h_BrdUIP_LateS_replicate 1


title: CPT 7h_BrdUIP_EarlyS_replicate 2


title: SETDB1KO_Periphilin rep 1


title: tomato self graft - 5 DAG - Replicate 1

description:
Named TT_5d in processed file
Supplemental_Table1
TT_5d_R1


title: S1067__00026

value: Breast cancer


title: S1067__00027


title: CPT 7h_BrdUIP_EarlyS_replicate 1

description:
CPT_7h_replicate1_300w40s_fmt.txt
CPT_7h_average_300w40s_fmt.txt


title: Caffeine 7h_BrdUIP_EarlyS

value: caffeine for 7 h


title: SETDB1KO_empty4


title: DNA_oncoscan_prostatecancer_15-008/004

description: OncoScan CNV for prostate cancer sample from patient 15-008/004


title: tomato self graft - 3 DAG - Replicate 3

description:
Named TT_3d in processed file
Supplemental_Table1
TT_3d_R3

value: tomato self graft - 3 DAG


title: S1067__00023_F1

description:
Baseline diagnostic core biopsy
Gene expression data from breast cancer pre-treatment
Baseline tumour core biopsies were taken from breast cancers under ultrasound guidance


title: S1067__00039


title: SETDB1KO_Periphilin rep 3


title: ∆rrpAB rep4

city: LONDON

first: Fauzy

last: Nasher

address: Keppel Street,

institute: London School of Hygiene and Tropical Medicine

data_processing:
Raw reads were obtained from an Illumina Miseq paired-end sequencing platform (Illumina).
The paired-end reads were trimmed and filtered using Sickle v1.200  by using a sliding window approach and trimming the reads where the average base quality drops below 20. Only the reads that were above 10 bp length were kept after trimming. Bowtie2 was used to map the reads against the reference sequences; C. jejuni strains 11168H assembly GCA_900117385.1. This generated the mapping in SAM format which were converted to BAM format using Samtools  and were index sorted. We used gffread from cufflinks suite to convert annotations from GFF to GTF format. These were used in Bedtools (with multicov-bams option)with the mapped reads to generate transcript counts per samples. A shell utility by the authorswas then used to collate all these transcripts into a n=20 samples x p=1,628 transcripts for 11168H strain. Statistical analysis was performed in R using the combined data generated from the bioinformatics as well as meta data associated with the study (multifactorial design). We used DESeq DataSet from Matrix()function fromDESeq2  package with the adjusted p-value significance cut-off of 0.05 and log fold change cut-off of 1.5. This function uses negative binomial GLM to obtain maximum likelihood estimates for the transcripts log fold change between the two conditions.
Genome_build: C. jejuni strains 11168H assembly GCA_900117385.1.
Supplementary_files_format_and_content: Excel file include RPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Campylobacter jejuni

source_name: not applicable

growth_protocol: RNA-Seq was used to identify differentially expressed genes between wild type strains, ∆rrpA  and ∆rrpB mutants at mid-log (~6 hrs) of growth. 11168H wild type, 11168H∆rrpA, 11168H∆rrpB and 11168H∆rrpAB were plated out on BA plates and incubated at 37°C under microaerobic conditions for 6 hrs. 11168H is hypermotile variant of strain 11168 which is the background strain for  the samples used in the study.

extract_protocol:
RNA was extracted from the pelleted bacteria cells using PureLink™ RNA Mini Kit (Invitrogen), following manufactures protocol. RNA was isolated from five independent experiments performed on different days Ribosomal RNA was depleted using Ribominus (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: rrpAB double mutant

tag: culture method

value: cell suspension culture (6 hrs growth)


title: Peripheral blood of normal newborn

city: Nanjing

first: Yufei

last: Chen

state: Jiangsu Province

address: 300 Guang Zhou Road

department: Department of Pediatrics

institute: The First Afﬁliated Hospital of Nanjing Medical University

description: Gene expression in peripheral blood of normal newborns

hyb_protocol: Each slide was hybridized with 1.65 μg Cy3-labeled cRNA using a Gene Expression Hybridization Kit (Cat# 5188-5242; Agilent Technologies) in a Hybridization Oven (Cat# G2545A; Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Slides were scanned by an Agilent Microarray Scanner (Cat# G2565CA; Agilent Technologies) with default settings (dye channel: green; scan resolution = 3 µm; PMT: 100%, 20 bit).

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent Technologies). Raw data were normalized by the quantile algorithm of limma package in

source_name: Peripheral blood of normal newborn

label_protocol: RNA was amplified and labeled by a Low Input Quick Amp WT Labeling Kit (Cat# 5190-2943; Agilent Technologies) following the manufacturer’s instructions.

extract_protocol: Total RNA of placenta tissue was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: All specimens were obtained at the time of cesarean section for obstetrical indications. Placental bed biopsy specimens were collected around the umbilical cord, about 1×1×1cm3 size, and preserved in 600μl RNA Stabilization Solution (Cat#AM7020, Ambion, Austin, TX, US)under -20℃.

tag: subject status

value: normal newborn

tag: tissue

value: whole blood


title: Peripheral blood in premature infants with BPD

description: Gene expression in peripheral blood of premature infants with BPD

value: premature infant with BPD

value: male


title: Caffeine 2h_BrdUIP_EarlyS

tag: treatment

value: caffeine for 2 h

value: Early S


title: tomato self graft - 3 DAG - Replicate 2

description:
Named TT_3d in processed file
Supplemental_Table1
TT_3d_R2


title: tomato self graft - 3 DAG - Replicate 1

description:
Named TT_3d in processed file
Supplemental_Table1
TT_3d_R1


title: CPT+Caffeine 7h_BrdUIP_EarlyS_replicate 2

value: RPE

value: camptothecin and caffeine simultaneously for 7 h


title: tomato self graft - 5 DAG - Replicate 2

description:
Named TT_5d in processed file
Supplemental_Table1
TT_5d_R2


title: S1067__00030


title: ∆rrpAB rep2


title: ∆rrpAB rep3


title: CPT+Caffeine 7h_BrdUIP_EarlyS_replicate 1

description:
CPT+caf_7h_replicate1_300w40s_fmt.txt
CPT+caf_7h_average_300w40s_fmt.txt


title: tomato self graft - 5 DAG - Replicate 3

description:
Named TT_5d in processed file
Supplemental_Table1
TT_5d_R3


title: Caffeine 2h_BrdUIP_LateS


title: SETDB1KO_Periphilin rep 2

value: PPHLN HA knock in; SETDB1 KO pool

value: anti-HA


title: SETDB1KO_empty rep 1

description:
control RIPseq in SETDB1 KO
empty.SKOempty.dedup.bw
HA.SKOHA.v2.bed
ripseq_genes.txt

value: SETDB1 KO pool


title: SETDB1KO_empty rep 2


title: S1067__00021_F1


title: CPT+Caffeine_2h_BrdUIP_LateS_replicate 2

value: camptothecin and caffeine simultaneously for 2 h

value: Late S

value: BrdU-IP


title: S1067__00020

value: Breast cancer


title: ∆rrpAB rep1

value: rrpAB double mutant


title: tomato self graft - 1 DAG - Replicate 3

description:
Named TT_1d in processed file
Supplemental_Table1
TT_1d_R3

value: tomato self graft - 1 DAG


title: CPT+Caffeine_2h_BrdUIP_EarlyS_replicate 2


title: S1067__00019


title: ∆rrpB rep4

value: rrpB mutant

value: cell suspension culture (6 hrs growth)


title: S1067__00018


title: CPT 7h_BrdUIP_LateS_replicate 1

value: camptothecin for 7 h


title: ∆rrpAB rep5


title: pepper self graft - 5 DAG - Replicate 4

description:
Named PP_5d in processed file
Supplemental_Table4
PP_5d_R4

value: pepper self graft - 5 DAG


title: tomato self graft - 1 DAG - Replicate 1

description:
Named TT_1d in processed file
Supplemental_Table1
TT_1d_R1


title: S1067__00025_F1


title: CPT 2h_BrdUIP_EarlyS_replicate 2

value: camptothecin for 2 h


title: tomato self graft - 3 DAG - Replicate 4

description:
Named TT_3d in processed file
Supplemental_Table1
TT_3d_R4

value: tomato self graft - 3 DAG


title: S1067__00013


title: ∆rrpA rep5

value: rrpA mutant


title: CPT+Caffeine_2h_BrdUIP_LateS_replicate 1

value: RPE


title: CPT 2h_BrdUIP_LateS_replicate 1


title: S1067__00012


title: S1067__00024_F1


title: ∆rrpA rep4


title: pepper self graft - 5 DAG - Replicate 1

description:
Named PP_5d in processed file
Supplemental_Table4
PP_5d_R1


title: pepper self graft - 3 DAG - Replicate 4

description:
Named PP_3d in processed file
Supplemental_Table4
PP_3d_R4

value: pepper self graft - 3 DAG


title: control_BrdUIP_EarlyS_replicate 2

value: untreated

value: Early S


title: ∆rrpA rep3


title: tomato self graft - 1 DAG - Replicate 4

description:
Named TT_1d in processed file
Supplemental_Table1
TT_1d_R4


title: ∆rrpB rep3


title: ∆rrpB rep5


title: S1067__00016


title: CPT+Caffeine_2h BrdUIP_EarlyS_replicate 1

description:
CPT+caf_2h_replicate1_300w40s_fmt.txt
CPT+caf_2h_average_300w40s_fmt.txt

value: camptothecin and caffeine simultaneously for 2 h


title: pepper self graft - 3 DAG - Replicate 3

description:
Named PP_3d in processed file
Supplemental_Table4
PP_3d_R3


title: ∆rrpA rep1


title: tomato self graft - 1 DAG - Replicate 2

description:
Named TT_1d in processed file
Supplemental_Table1
TT_1d_R2


title: S1067__00015

description:
Baseline diagnostic core biopsy
Gene expression data from breast cancer pre-treatment
Baseline tumour core biopsies were taken from breast cancers under ultrasound guidance


title: ∆rrpB rep2


title: ∆rrpB rep1


title: CPT 2h_BrdUIP_LateS_replicate 2

value: Late S


title: control_BrdUIP_LateS_replicate 2

value: BrdU-IP


title: pepper self graft - 5 DAG - Replicate 3

description:
Named PP_5d in processed file
Supplemental_Table4
PP_5d_R3


title: pepper self graft - 3 DAG - Replicate 2

description:
Named PP_3d in processed file
Supplemental_Table4
PP_3d_R2


title: CPT 2h_BrdUIP_EarlyS_replicate 1

description:
CPT_2h_replicate1_300w40s_fmt.txt
CPT_2h_average_300w40s_fmt.txt


title: S1067__00011

value: Breast cancer


title: S1067__00008


title: WT rep5

value: wild type


title: S1067__00010_F1


title: control_BrdUIP_LateS_replicate 1


title: pepper self graft - 1 DAG - Replicate 4

description:
Named PP_1d in processed file
Supplemental_Table4
PP_1d_R4

value: pepper self graft - 1 DAG


title: pepper self graft - 5 DAG - Replicate 2

description:
Named PP_5d in processed file
Supplemental_Table4
PP_5d_R2


title: S1067__00006


title: S1067__00007


title: pepper self graft - 3 DAG - Replicate 1

description:
Named PP_3d in processed file
Supplemental_Table4
PP_3d_R1


title: control_BrdUIP_EarlyS_replicate 1

description:
Control_replicate1_300w40s_fmt.txt
Control_average_300w40s_fmt.txt


title: pepper self graft - 1 DAG - Replicate 2

description:
Named PP_1d in processed file
Supplemental_Table4
PP_1d_R2


title: WT rep2


title: ∆rrpA rep2


title: S1067__00005


title: pepper self graft - 1 DAG - Replicate 3

description:
Named PP_1d in processed file
Supplemental_Table4
PP_1d_R3


title: S1067__00001


title: S1067__00004


title: S1067__00002


title: pepper self graft - 1 DAG - Replicate 1

description:
Named PP_1d in processed file
Supplemental_Table4
PP_1d_R1


title: WT rep3


title: WT rep1


title: WT rep4


title: 7JJ: Jejunum_Low-FCR (L2, 41220)

status: Public on Sep 29 2021

city: Mueang Nakhon Ratchasima

first: Panpradub

last: Sinpru

state: Nakhon Ratchasima

address: Maha Witthayalai Rd

department: School of Animal Technology and Innovation

country: Thailand

institute: Suranaree University of Technology

data_processing:
HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) used for basecalling.
Low-quality reads and those containing adapter contamination were removed by Cutadapt (v1.9.1). The reads were mapped to GRCg6a (Ensembl) using Hisat2 (v2.0.1).
Cufflinks (v2.2.1) was used for the assembly of the mapped reads.
Alternative splicing were extracted, quantified and compared using ASprofile (v1.0). Gene-level reads counts were enumerated using HTSeq (v0.6.1).
Differential gene expression analysis between high- and low-FCR samples was performed using DESeq2 R package [32].
Genome_build: GRCg6a
Supplementary_files_format_and_content: Column 1, gene_id: gene ID; Column 2, Exonic.gene.sizes: exon length; Column 3,5,7,9,11,13, Sample count: count of each gene for each sample; Column 4,6,8,10,12,14, Sample_FPKM: FPKM of each gene for each sample; Column 15-18, Chr，Start，End，Strand: gene location, including chromosome, start position, end position and strand; Column 19, GeneSymbol: gene symbol; Column 20, Description: gene description

organism: Gallus gallus

source_name: Jejunum

growth_protocol: The chickens were fed ad libitum with a starter diet (21% protein), a grower diet (19% protein), and a finisher diet (17% protein) at 0-3, 4-6, and 7-10 weeks of age, respectively. The automatic nipple watering system was installed individually in each cage, and water was freely available for chickens.

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent.One μg of total RNA with RIN value above 7.5 was used for the following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s instruction (Illumina, San Diego, CA, USA).

tag: genetic line

value: Korat chicken

value: 10 weeks

value: jejunum


title: 2JJ: Jejunum_Low-FCR (L1, 41204)


title: 23JJ: Jejunum_High-FCR (H1, 41217)


title: 28JJ: Jejunum_Low-FCR (L3, 41233)


title: 39JJ: Jejunum_High-FCR (H2, 0998)


title: 75JJ: Jejunum_Low-FCR (H3, 1057)


title: Human SSC line_rep1

city: shanghai

first: wenhui

last: zhang

address: jiuzun road 115

institute: shanghai jiaotong  University

description: primary human SSCs  by stably expressing human SV40 large T antigen, we named this cell as SSC in rep_1

hyb_protocol: The pre-hybridization of HOA v7.1 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on HOA v7.1 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm PMT 10 ; 532nm PMT 10) and quantify the fluoresence intensity.

data_processing: The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.

source_name: primary human SSCs expressing human SV40 large T antigen

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

value: primary human SSCs

tag: genotype/variation


title: Transfected cells_rep2

description: human Sertoli cells overexpressing  DAZL, DAZ2, and BOULE ,we named this cell as S71 in rep_2

source_name: Overexpression of DAZL, DAZ2, and BOULEin human Sertoli cells

value: human Sertoli cells

value: overexpression  DAZL, DAZ2, and BOULE


title: Transfected cells_rep1

description: human Sertoli cells overexpressing  DAZL, DAZ2, and BOULE ,we named this cell as R7 in rep_1


title: Human SSC line_rep2

description: primary human SSCs  by stably expressing human SV40 large T antigen, we named this cell as SV40 in rep_2


title: AT-LPS-5 [Sup]

city: Beijing

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL 10´ Blocking Agent and 1 μL of 25´ Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2´ Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-mRNA&lncRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing:
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 5 out of 10 samples were retained as “All Targets Value” for further “m6A methylation level” and “m6A quantity” analyses.
“m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed using the R software. GO analysis was performed using topGO package in R environment for statistical computing and graphics, and Pathway analysis was calculated by fisher's exact test.

organism: Rattus norvegicus

source_name: aortic tissue, LPS

label_protocol: The “IP” RNA and “Sup” RNAs were added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labeling Kit. The synthesized cRNAs were purified by RNeasy Mini Kit. The concentration and specific activity (pmol dye/μg cRNA) were measured with NanoDrop ND-1000.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.

value: Wistar

value: aortic tissue

tag: gender

value: male

value: 8 weeks

value: LPS


title: AT-Ctrl-18 [Sup]

source_name: aortic tissue, Ctrl

value: Control


title: AT-Ctrl-15 [Sup]


title: AT-Ctrl-15 [IP]


title: D_F1

city: Shijiazhuang

first: Desmond

middle: Onyeka

last: Agwunobi

address: No. 20 Road East 2nd Ring South Yuhua District

institute: Hebei Normal University

description: miRNA

data_processing:
Base calling was done using Illumina Cassava 1.8
After the quality control, the clean reads were clustered based on sequence similarity and dominant reads were analyzed by bowtie (version 2.3.4)(Langmead and Salzberg, 2012)
The reads were aligned and compared with those of Genbank and Rfam
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text or .xls files including total reads, unique reads, Readcout TPM, and TPM interval values for each Sample

organism: Dermacentor silvarum

source_name: DS

extract_protocol:
Total RNA was isolated from the whole body of H. longicornis tick samples from each group by TRIzolTM Reagent. RNA sequencing libraries were generated from each sample and the sequencing was performed by Biomarker according to the manual of the NEB Next® UltraTM RNA Library Prep Kit (NEB, Ipswich, MA) in Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Adult ticks

tag: physiological state

value: Unfed ticks


title: AT-LPS-6 [Sup]

tag: age


title: AT-LPS-1 [Sup]


title: AT-Ctrl-20 [Sup]


title: AT-Ctrl-17 [Sup]


title: AT-LPS-3 [Sup]


title: AT-LPS-3 [IP]


title: AT-Ctrl-20 [IP]


title: D_F2

description: miRNA


title: D_E2

description: miRNA

value: 0 ℃


title: AT-Ctrl-18 [IP]


title: D_F3

description: miRNA


title: D_E3

description: miRNA


title: D_E1

description: miRNA


title: AT-Ctrl-17 [IP]


title: D_B3

description: miRNA

value: 4 ℃


title: AT-LPS-5 [IP]


title: D_B2

description: miRNA


title: D_C1

description: miRNA


title: D_C3

description: miRNA


title: D_C2

description: miRNA


title: D_B1

description: miRNA


title: D_A2

description: miRNA

value: 8 ℃


title: D_A1

description: miRNA


title: AT-LPS-6 [IP]


title: D_A3

description: miRNA


title: AT-LPS-1 [IP]


title: OsERF106OE_Salt_002

city: Taipei

first: MenChi

last: Chang

state: Taiwan (R.O.C.)

address: No. 1, Sec. 4, Roosevelt Rd.

department: Agronomy

country: Taiwan

institute: National Taiwan University

hyb_protocol: 1.65 μg of Cy3-labled cRNA was fragmented at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Rice 4*44K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying steps. The microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: The array image was analyzed by the Feature Extraction software version 10.7.1.1 using the default setting.

organism: Oryza sativa

source_name: OsERF106, salt, 8-day-old, replicate2

label_protocol: 200 ng of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: (optional)

extract_protocol: Total RNA was extracted from plant tissue using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. To avoid genomic DNA contamination, total RNA was treated with Turbo DNA-freeTM DNase (Ambion) following the manufacturer’s instructions.

treatment_protocol: 7-day-old rice seedling of OsERF106 and TNG67 treated with or without 150mM NaCl for 1 day.

value: 150mM NaCl for 1 day


title: OsERF106OE_Control_003

source_name: OsERF106, CK, 8-day-old, replicate3

value: control


title: OsERF106OE_Control_002


title: OsERF106OE_Control_001


title: OsERF106OE_Salt_001

source_name: OsERF106, salt, 8-day-old, replicate1


title: TNG67_Salt_003

source_name: TNG67, salt, 8-day-old, replicate3


title: OsERF106OE_Salt_003

source_name: OsERF106, salt, 8-day-old, replicate3


title: TNG67_Salt_001

source_name: TNG67, salt, 8-day-old, replicate1


title: TNG67_Salt_002

source_name: TNG67, salt, 8-day-old, replicate2


title: TNG67_Control_003

source_name: TNG67, CK, 8-day-old, replicate3


title: TNG67_Control_002

source_name: TNG67, CK, 8-day-old, replicate2


title: TNG67_Control_001

source_name: TNG67, CK, 8-day-old, replicate1


title: T_081 [Methylation]

city: Washington

first: Rency

middle: S

last: Varghese

state: District of Columbia

address: 4000 Reservoir Rd NW, Building D

department: Oncology

institute: Georgetown University

hyb_protocol: Bisulfite-converted DNAs were whole-genome-amplified and enzymatically fragmented prior to hybridization to the array.

scan_protocol: Genome-wide DNA methylation analysis was performed using the Infinium HumanMethylationEPIC BeadChip (Illumina)

data_processing: Raw signal intensity data were imported from idat files into the ChAMP package in R/Bioconductor for processing.

source_name: Liver

label_protocol: Standard Illumina Protocol

extract_protocol: DNA from fresh-frozen tissue samples was extracted using the QIAamp DNA mini kit (QIAGEN) and bisulfite converted using the EZ DNA Methylation-Gold Kit (Zymo Research).

tag: disease status

value: Norm

tag: race

value: AA


title: F_0.5_ETOH_t_4.5hr

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

description:
0.5% ETOH for 2hrs; t=4.5hr after wash
The 0.5% ETOH treatment group was not included in downstream analysis

data_processing:
Single cell scale RNA-seq libraries were sequenced using on an Illumina HiSeq 4000
Raw sequencing data (Illumina sequencer’s base call files (BCLs) was converted to fastq files using the Illumina bcl2fastq program
Reads were mapped to the genome using the Xenopus laevis 9.1 genome with STAR alignment and a modified BLAST and FASTQC in the NGS pipeline
Count data is rlog transformed (package DESeq2), batch corrected (COMBAT algorithm), expression filtered, quantile normalisation, filtered for significance and annotated with gene names.
The 0.5% ETOH treatments were not included in the downstream analysis
Genome_build: Xenopus laevis 9.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Xenopus laevis

source_name: whole embryo

extract_protocol:
For each sample, 5-10 staged embryos were collected and stored at -80°C. RNA purification was performed using the Bio-Rad Aurum Total RNA Mini Kit (according to the manufacturer's instructions). RNA samples were used for cDNA synthesis using the Bio-Rad iScriptTM Reverse Transcription Supermix for RT-qPCR kit (according to the manufacturer's instructions).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wildtype

tag: isolate

value: female F

tag: Sex

value: not determined

value: whole embryo


title: T_067 [Methylation]


title: T_066 [Methylation]

value: HCC


title: F_control_t_4.5hr

description: control for 2hrs; t=4.5hr after wash

value: control t=4.5hr


title: F_10nM_RA_t_4.5hr

description: 10nM RA for 2hrs; t=4.5hr after wash

value: 10nM RA t=4.5hr


title: T_064 [Methylation]

value: EA


title: T_080 [Methylation]


title: T_049 [Methylation]


title: T_074 [Methylation]


title: T_061 [Methylation]


title: F_50uM_DEAB_t_3hr

description: 50µM DEAB for 2hrs; t=3hr after wash

value: 50µM DEAB t=3hr


title: T_063 [Methylation]


title: T_054 [Methylation]


title: T_051 [Methylation]


title: T_045 [Methylation]


title: F_10nM_RA_t_3hr

description: 10nM RA for 2hrs; t=3hr after wash

value: 10nM RA t=3hr


title: T_057 [Methylation]


title: T_056 [Methylation]


title: T_075 [Methylation]


title: T_062 [Methylation]


title: F_50uM_DEAB_t_4.5hr

description: 50µM DEAB for 2hrs; t=4.5hr after wash

value: 50µM DEAB t=4.5hr


title: T_048 [Methylation]


title: F_0.5_ETOH_t_1.5hr

description:
0.5% ETOH for 2hrs; t=1.5hr after wash
The 0.5% ETOH treatment group was not included in downstream analysis


title: F_50uM_DEAB_t_1.5hr

description: 50µM DEAB for 2hrs; t=1.5hr after wash

value: 50µM DEAB t=1.5hr


title: F_0.5_ETOH_t_0hr

description:
0.5% ETOH for 2hrs; t=0hr after wash
The 0.5% ETOH treatment group was not included in downstream analysis

value: 0.5% ETOH t=0hr


title: T_043 [Methylation]


title: T_046 [Methylation]


title: F_control_t_3hr

description: control for 2hrs; t=3hr after wash

value: control t=3hr


title: F_control_t_1.5hr

description: control for 2hrs; t=1.5hr after wash

value: control t=1.5hr


title: T_053 [Methylation]


title: F_50uM_DEAB_t_0hr

description: 50µM DEAB for 2hrs; t=0hr after wash

value: 50µM DEAB t=0hr


title: T_052 [Methylation]

value: Norm

value: AA


title: F_10nM_RA_t_0hr

description: 10nM RA for 2hrs; t=0hr after wash

value: wildtype

value: female F

value: 10nM RA t=0hr


title: GBA-carrier_4

city: Gatchina

first: Katerina

last: Basharova

address: 1, mkr. Orlova roshcha

country: Russia

institute: NRC "Kurchatov Institute" - PNPI

data_processing:
The RNA molecules were sequenced on the Illumina HiSeq1500 platform.
Quality control for each sample was performed by FastQC (v0.11.9) and RSeQC (v4.0.0)). In this step, clean data (clean reads) were obtained by removing low-quality reads, reads containing adapters, and reads containing ploy-N from raw data. Removal adapter was done with Cutadapt.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: fastq files for each sample
Supplementary_files_format_and_content: Matrix table of raw counts

source_name: monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from 24 mL peripheral blood of participants by the density gradient centrifugation (Ficoll-Paque PLUS, GE Healthcare, USA). PBMCs were differentiated by macrophage colony-stimulating factor (M-CSF) (10ng/ml) (Sigma-Aldrich, USA) in RPMI1640 medium (Gibco, USA) supplemented with 10% FCS (Gibco, USA) with harvesting after 5 days. Phenotypical maturation of mono-cyte-derived macrophages was confirmed by light microscopy and flow cytometry with specific antibodies to CD14+ and CD68+ (eBioscience, USA)

extract_protocol:
RNA was isolated from monocyte-derived macrophages and amplified following the user manual of the SMART-Seq™ v4 Ultra™ Low Input RNA Kit for sequencing.
Sequencing libraries were generated using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA), following the manufacturer’s recommendations.

value: male

tag: status

value: GBAcarriers

tag: mutation

tag: zygosity

value: heterozygous


title: Control_4

treatment_protocol: PBMCs were differentiated by macrophage colony-stimulating factor (M-CSF) (10ng/ml) (Sigma-Aldrich, USA) in RPMI1640 medium (Gibco, USA) supplemented with 10% FCS (Gibco, USA) with harvesting after 5 days.

value: female

value: Controls


title: E_control_t_4.5hr

description: control for 2hrs; t=4.5hr after wash

tag: strain

value: female E

value: not determined

value: whole embryo

value: control t=4.5hr


title: T_042 [Methylation]

value: HCC


title: F_0.5_ETOH_t_3hr

description:
0.5% ETOH for 2hrs; t=3hr after wash
The 0.5% ETOH treatment group was not included in downstream analysis

value: 0.5% ETOH t=3hr


title: F_control_t_0hr

description: control for 2hrs; t=0hr after wash

value: control t=0hr


title: E_0.5_ETOH_t_4.5hr


title: E_50uM_DEAB_t_4.5hr

description: 50µM DEAB for 2hrs; t=4.5hr after wash

value: 50µM DEAB t=4.5hr


title: E_50uM_DEAB_t_3hr

description: 50µM DEAB for 2hrs; t=3hr after wash

value: 50µM DEAB t=3hr


title: E_0.5_ETOH_t_3hr

value: wildtype


title: T_032 [Methylation]

value: Norm

value: EA


title: T_031 [Methylation]


title: E_10nM_RA_t_3hr

description: 10nM RA for 2hrs; t=3hr after wash

value: 10nM RA t=3hr


title: GBA-PD_5

value: male

value: GBAPD


title: GBA_PD_4

value: female

value: heterozygous


title: GBA-carrier_3

value: GBAcarriers


title: Control_3

value: Controls


title: E_control_t_3hr

description: control for 2hrs; t=3hr after wash

value: female E

value: not determined

value: whole embryo

value: control t=3hr


title: E_10nM_RA_t_4.5hr

description: 10nM RA for 2hrs; t=4.5hr after wash

value: 10nM RA t=4.5hr


title: GBA-PD_3


title: E_0.5_ETOH_t_1.5hr


title: T_038 [Methylation]

value: HCC


title: GBA-carrier_2


title: E_50uM_DEAB_t_1.5hr

description: 50µM DEAB for 2hrs; t=1.5hr after wash

value: 50µM DEAB t=1.5hr


title: E_10nM_RA_t_1.5hr

description: 10nM RA for 2hrs; t=1.5hr after wash

value: wildtype

value: 10nM RA t=1.5hr


title: GBA-PD_2


title: T_018 [Methylation]

value: AA


title: Control_2


title: E_control_t_1.5hr

description: control for 2hrs; t=1.5hr after wash

value: control t=1.5hr


title: E_0.5_ETOH_t_0hr

value: 0.5% ETOH t=0hr


title: Mock_PG1F_2_II

city: New

first: Sean

last: Houghton

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
STAR alignment (v 2.6.1)
Salmon quantification (0.11.2)
Genome_build: Mesocricetus_auratus (ensembl MesAur1)
Supplementary_files_format_and_content: Gene count matrix

organism: Mesocricetus auratus

growth_protocol: Standard Golden Syrian Hamsters

extract_protocol:
Fat tissue was harvested and lysed in TRIZOL and subjected to RNA extraction using Trizol extraction protocol
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Mock infected or SARS-CoV-2 treated hamsters

tag: organ

value: Fat

value: Mock PG1F

tag: infection

value: Mock


title: Mock_SCF_2_I

value: Mock SCF


title: Mock_PG1F_3_II


title: Mock_PG1F_1_II


title: T4 genomic DNA from adipose/connective tissue

city: Shanghai

first: Lian-Qun

last: Wu

address: 83 Fenyang Road

institute: Fudan University

description:
thyroid-associated ophthalmopathy
T4

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human  MethylationEPIC(850K) BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
methylated signal intensities provided in the non-normalized Matrix

label: Cy5 and Cy3

source_name: adipose/connective tissue  4

extract_protocol: genomic DNA was extracted and purified from  samples using Qiagen DNeasy Kit according to standard instructions

tag: disease

value: thyroid-associated ophthalmopathy


title: Cov2_PG1F_6

value: Cov2 PG1F


title: T_004 [Methylation]

value: EA


title: E_50uM_DEAB_t_0hr

description: 50µM DEAB for 2hrs; t=0hr after wash

value: female E

value: not determined

tag: tissue

value: whole embryo

tag: treatment

value: 50µM DEAB t=0hr


title: T3 genomic DNA from adipose/connective tissue

description:
thyroid-associated ophthalmopathy
T3

source_name: adipose/connective tissue  3


title: C1 genomic DNA from adipose/connective tissue

description:
normal
C1

source_name: adipose/connective tissue  5

value: normal


title: Cov2_PG1F_5


title: Cov2_PG1F_4


title: GBA-carrier_1

tag: gender

value: male

value: GBAcarriers

value: heterozygous


title: E_control_t_0hr

description: control for 2hrs; t=0hr after wash

value: wildtype

value: control t=0hr


title: Cov2_SAT_1

value: Fat

value: Cov2 SAT


title: Cov2_SAT_2


title: Low_nutrition_fetal_LT_muscle

city: Tsukuba

first: Susumu

last: Muroya

state: Ibaraki

address: Ikenodai 2

department: Animal Products Research Division

institute: NARO Institute of Livestock and Grassland Science

description: SkM-L

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263.

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1. The raw data for same gene was then summarized automatically in Agilent feature extraction protocol providing expression data for each gene probed on the array. Array probes that have Flag A in samples were filtered out and the remaining gProcessedSignal value was transformed by logarithm. Then, quantile normalization of log2(probes) values using library(preprocessCore) in R was performed.

organism: Bos taurus

source_name: Longissimus muscle, low nutriion, 8.5-mo fetus, mixture (n=4)

label_protocol: Cyanine-3 (Cy3) labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit.

growth_protocol: According to the JFSC, the recommended contents of dry matter (DM), neutral detergent fiber, acidic detergent fiber, ash, crude protein (CP), Ca, and P in diet are 68.0, 56.1, 36.0, 11.1, 8.0, 0.6, and 0.3%, respectively (all values are expressed as a percentage of DM) . The cows randomly assigned to the LN (n = 5) and HN (n = 6) diet groups were fed the respective diet during gestation including prepregnant period. Metabolizable energy of the mixture feed for 100% requirement was estimated as 8.56 MJ/kg DM.

extract_protocol: Total RNA was extracted from the LT muscle using the mirVanaTM microRNA isolation kit (Thermo Fisher Scientific), following the manufacturer’s instructions. The quantity and quality of the RNA were determined using an Agilent Bioanalyzer 2100 with an RNA 6000 Pico kit (Agilent Technologies)

treatment_protocol: The fetuses were euthanized by exsanguination at day 260 ± 8.3 of gestation after injecting 200 mg of lidocaine (AstraZeneca, Osaka, Japan) into the jugular vein. The longissimus thoracis (LT) muscle was collected from the right side of the fetal carcass, frozen with liquid nitrogen or soaked in RNAlater (Thermo Fisher Scientific).

tag: breed

value: Japanese Black cattle

value: Low nutrition

value: Longissimus muscle tissue


title: T_005 [Methylation]

value: Norm


title: Cov2_SAT_3


title: F_10nM_RA_t_1.5hr

description: 10nM RA for 2hrs; t=1.5hr after wash

value: female F

value: 10nM RA t=1.5hr


title: D_50uM_DEAB_t_4.5hr

description: 50µM DEAB for 2hrs; t=4.5hr after wash

value: female D

value: not determined

value: 50µM DEAB t=4.5hr


title: T_039 [Methylation]

value: EA


title: T_010 [Methylation]

value: HCC


title: T_019 [Methylation]

value: AA


title: T_011 [Methylation]


title: High_nutrition_fetal_LT_muscle

description: SkM-H

source_name: Longissimus muscle, high nutriion, 8.5-mo fetus, mixture (n=4)

value: High nutrition


title: C4 genomic DNA from adipose/connective tissue

description:
normal
C4

source_name: adipose/connective tissue  8

value: normal


title: Mock_SCF_2

value: Mock SCF

value: Mock


title: Cov2_SCF_3

value: Fat

value: Cov2 SCF


title: Mock_SCF_3


title: Cov2_SCF_1


title: T1 genomic DNA from adipose/connective tissue

description:
thyroid-associated ophthalmopathy
T1

source_name: adipose/connective tissue  1

value: thyroid-associated ophthalmopathy


title: Cov2_SCF_2


title: D_control_t_4.5hr

description: control for 2hrs; t=4.5hr after wash

value: wildtype

value: whole embryo

value: control t=4.5hr


title: Mouse PMN

city: Montréal

first: Tarik

last: Moroy

address: 110 Pine Ave W, Montreal

country: Canada

institute: IRCM

description: Polymorphonuclear leukocytes were isolated from blood collected from healthy 12 to 15-week-old wild-type mice, and pooled.

data_processing:
Adaptor were trimmed using Cutadapt V1.7.1
Quality Control was performed with fastqc V0.11.3
Identical sequences were collapsed into a single fasta sequence and were filtered to keep only those detected at least twice using a custom script
Genome_build: NA
Supplementary_files_format_and_content: Fasta files containing the aligned sequences that were detected at least twice in the dataset, separated in 2 groups based on the size (8-15nt and 16-30nt)

organism: Mus musculus

source_name: Polymorphonuclear leukocytes isolated from mouse blood

growth_protocol: Please refer to the Samples section above

extract_protocol:
Total RNA samples were prepared using TRIzol® reagent or TRIzol LS® reagent for liquid samples (Invitrogen Life Technologies, Carlsbad, CA, USA) following the manufacturer’s recommendations. Contaminating DNA was degraded by DNase I (M0303S, New England Biolabs, MA, USA) treatment following manufacturer’s instructions. Total RNA was shipped on dry ice and analyzed by Arraystar Inc. RNA sequencing service (Rockville, MD).
The purity, quality, and concentration of total RNA samples were determined with NanoDrop ND-1000 (Thermo Fisher Scientific) and 2100 Bioanalyzer (Agilent, Santa Clara, CA). Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: (1) 3′-adapter ligation, (2) 5′-adapter ligation, (3) cDNA synthesis, (4) PCR amplification, and (5) size selection of approximately 120 to 150 bp of PCR-amplified fragments (corresponding to approximately 8 to 30 nt of small RNA). The complete libraries were quantified by Agilent 2100 Bioanalyser. Samples were diluted to a final concentration of 8 pM, denatured as single-stranded DNA, and cluster generation was performed on the Illumina cBot using TruSeq Rapid SR cluster kit (GD-402-4001, Illumina, San Diego, USA). Afterward, the clusters were sequenced for 51 cycles on Illumina HiSeq 2000 using TruSeq Rapid SBS Kits (FC-402-4002, Illumina, San Diego, USA), as per the manufacturer's instructions.

tag: genotype

value: wild-type

value: healthy 12 to 15-week-old mice

tag: sample type

value: Mouse PMN


title: Mouse N2a cells

description: Cells were maintained in Eagle's Minimum Essential Medium, supplemented with 10% (v/v) fetal bovine serum (FBS), 1 mM sodium pyruvate, 100 units/ml penicillin, 100 μg/ml streptomycin, and 2 mM L-glutamine in a humidified incubator under 5% CO2 at 37˚C.

source_name: Neuronal N2a cells from mouse brain

value: Mouse N2a cells


title: Mouse NIH/3T3 cells

description: Cells were maintained in Dulbecco's Modified Eagle's Medium, supplemented with 10% (v/v) fetal bovine serum (FBS), 1 mM sodium pyruvate, 100 units/ml penicillin, 100 μg/ml streptomycin, and 2 mM L-glutamine in a humidified incubator under 5% CO2 at 37˚C.

source_name: NIH/3T3: NIH Swiss mouse embryonic fibroblast cells

value: NIH/Swiss

value: Mouse NIH/3T3 cells


title: Mock_PG1F_2

tag: disease status

value: Mock PG1F


title: D_10nM_RA_t_4.5hr

description: 10nM RA for 2hrs; t=4.5hr after wash

value: female D

value: not determined

value: 10nM RA t=4.5hr


title: C3 genomic DNA from adipose/connective tissue

description:
normal
C3

source_name: adipose/connective tissue  7

value: normal


title: D_50uM_DEAB_t_3hr

description: 50µM DEAB for 2hrs; t=3hr after wash

value: 50µM DEAB t=3hr


title: Mock_PG1F_1

value: Fat

value: Mock


title: Mock_SCF_1

value: Mock SCF


title: TrkA suture rxn 3 [C1]

city: Dallas

first: Robert

middle: J

last: Tower

address: 5323 Harry Hines Blvd

institute: UTSW

data_processing:
SpaceRanger
Seurat
Genome_build: mm10
Supplementary_files_format_and_content: spatial folder, matrix.h5 files and text file for suture coordinates and genotype

source_name: TrkAF592A mutant and control P0 sagittal suture

growth_protocol: Mothers treated with 1NMPP1 from conception until birth

extract_protocol:
enzymatic permeabilization (manufacturer's protocol)
10X Visium Spatial Gene Expression (manufacturer's protocol)

treatment_protocol: 200uM 1NMPP1 supplied in the drinking water

tag: developmental stage

tag: genotype/variation

value: TrkAF592A mutant and control

value: Sagittal suture


title: E_10nM_RA_t_0hr

description: 10nM RA for 2hrs; t=0hr after wash

value: wildtype

tag: isolate

value: female E

tag: Sex

value: whole embryo

value: 10nM RA t=0hr


title: Mouse Cerebellum

description: Brain cortex tissue was collected, after PBS washing, from exsanguinated 24-month-old C57BL/6 mice and flash frozen in liquid nitrogen before storage at -80°C.

source_name: Brain cerebellum tissue sampled from old mice

value: wild-type

tag: age

value: Mouse Cerebellum


title: D_0.5_ETOH_t_3hr

value: 0.5% ETOH t=3hr


title: Cov2_PG1F_1

value: Cov2 PG1F


title: Mock_PG1F_3

value: Mock PG1F


title: T_081 [miRNA-Seq]

data_processing:
The miRNA-seq data were analyzed using the QIAseq miRNA quantification data analysis software.
First, we calculated the unique molecular index (UMI) counts and primary miRNA mapping.
Then, the UMI counts were analyzed to calculate the changes in miRNA expression.
Finally, the quantified data were normalized using the trimmed mean of M-values (TMM) method before statistical analysis was performed.
Supplementary_files_format_and_content: UMI counts

extract_protocol:
RNA samples from the 32 fresh-frozen samples (16 HCC and 16 adjacent normal) were isolated using the RNeasy Plus Universal Mini Kit (Qiagen) with on-column RNase-free DNase treatment. The RNA quality and quantity were estimated based on ultraviolet-visible (UV-VIS) spectrophotometry using the NanoDrop ND-1000 spectrophotometer. The RNA integrity was assessed using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer.
Aliquots of the RNA samples (16 HCC and 16 adjacent normal)  were analyzed using the Qiagen’s QIAseq miRNA library kit for library preparation prior to sequencing by Illumina NextSeq 550 (se,75bp)

value: Adjacent Normal

tag: race

value: AA


title: T_080 [miRNA-Seq]

value: HCC


title: TrkA suture rxn 4 [D1]


title: Cov2_PG1F_2

value: Fat


title: D_10nM_RA_t_3hr

description: 10nM RA for 2hrs; t=3hr after wash

tag: strain

value: female D

value: not determined

value: 10nM RA t=3hr


title: GBA-PD_1

value: male

tag: status

value: GBAPD

tag: mutation

tag: zygosity

value: heterozygous


title: C2 genomic DNA from adipose/connective tissue

description:
normal
C2

source_name: adipose/connective tissue  6

tag: disease

value: normal


title: T_066 [miRNA-Seq]

source_name: Liver


title: D_50uM_DEAB_t_1.5hr

description: 50µM DEAB for 2hrs; t=1.5hr after wash

source_name: whole embryo

value: wildtype

tag: tissue

value: whole embryo

tag: treatment

value: 50µM DEAB t=1.5hr


title: T_062 [miRNA-Seq]

value: EA


title: D_0.5_ETOH_t_1.5hr


title: Lung hCD147-5

city: Xi'an

first: Jiejie

last: Geng

state: Shanxi

address: Changle West road

department: Cell biology department

institute: The Fourth Military Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: raw counts

source_name: Lung hCD147

extract_protocol:
Lung tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 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: infection with SARS-CoV-2

tag: time point

value: 2 dpi

value: lung


title: T_061 [miRNA-Seq]


title: TrkA suture rxn 2 [B1]

value: TrkAF592A mutant and control

value: Sagittal suture


title: T_057 [miRNA-Seq]

value: Adjacent Normal

value: AA


title: D_10nM_RA_t_1.5hr

description: 10nM RA for 2hrs; t=1.5hr after wash

value: female D

value: not determined

value: 10nM RA t=1.5hr


title: T_074 [miRNA-Seq]

value: HCC


title: Lung hCD147-3

tag: genotype


title: TrkA suture rxn 1 [A1]


title: T_063 [miRNA-Seq]


title: T_054 [miRNA-Seq]


title: D_0.5_ETOH_t_4.5hr


title: Control_1

source_name: monocyte-derived macrophages

tag: gender

value: male

value: Controls


title: T_064 [miRNA-Seq]

tag: disease status


title: Lung hACE2-2

source_name: Lung hACE2

tag: strain background

value: infected with SARS-CoV-2


title: Lung hCD147-2


title: D_control_t_3hr

description: control for 2hrs; t=3hr after wash

value: wildtype

value: whole embryo

value: control t=3hr


title: D_control_t_1.5hr

description: control for 2hrs; t=1.5hr after wash

value: control t=1.5hr


title: T_056 [miRNA-Seq]


title: D_50uM_DEAB_t_0hr

description: 50µM DEAB for 2hrs; t=0hr after wash

value: 50µM DEAB t=0hr


title: T_067 [miRNA-Seq]


title: T_075 [miRNA-Seq]


title: Lung Con-3

source_name: Lung Con

value: wild type

value: infection with SARS-CoV-2

value: 2 dpi

value: lung


title: Lung Con-2


title: D_10nM_RA_t_0hr

description: 10nM RA for 2hrs; t=0hr after wash

value: 10nM RA t=0hr


title: T_046 [miRNA-Seq]

value: Adjacent Normal

value: AA


title: D_control_t_0hr

description: control for 2hrs; t=0hr after wash

value: female D

value: not determined

value: control t=0hr


title: T_052 [miRNA-Seq]


title: T_039 [miRNA-Seq]

value: EA


title: T2 genomic DNA from adipose/connective tissue

description:
thyroid-associated ophthalmopathy
T2

source_name: adipose/connective tissue  2

value: thyroid-associated ophthalmopathy


title: T_053 [miRNA-Seq]

value: HCC


title: Lung hACE2-1

value: infected with SARS-CoV-2


title: KO_WSN_3

first: Biao

address: NO. 1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Science

data_processing:
Quality control:Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean  data with high quality.
Reads mapping to the reference genome:featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then  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.
Differential expression analysis:Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq2  R package (1.20.0). DESeq2 provide statistical routinesfor determining differential expression  in digital gene expression data using a model based on the negative binomial distribution. The  resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling  the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were  assigned as differentially expressed.
GO and KEGG enrichment analysis of differentially expressed genes:Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented  by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with  corrected Pvalue less than 0.05 were considered significantly enriched by differential  expressed genes. KEGG is a database resource for understanding high-level functions and  utilities of the biological system, such as the cell, the organism and the ecosystem, from  molecular-level information, especially large-scale molecular datasets generated by genome  sequencing and other high-through put experimental technologies  (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical  enrichment of differential expression genes in KEGG pathways.
Genome_build: mm10

source_name: lung

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

tag: tisssue

value: WSN-infected for 48 hours

value: Eif4b CKO


title: D_0.5_ETOH_t_0hr

value: wildtype

tag: isolate

value: whole embryo

value: 0.5% ETOH t=0hr


title: T_045 [miRNA-Seq]


title: T_042 [miRNA-Seq]


title: KO_PBS_3

value: WSN-uninfected for 48 hours


title: C_0.5_ETOH_t_3hr

value: female C

tag: Sex

value: 0.5% ETOH t=3hr


title: C_50uM_DEAB_t_4.5hr

description: 50µM DEAB for 2hrs; t=4.5hr after wash

value: 50µM DEAB t=4.5hr


title: T_043 [miRNA-Seq]

value: Adjacent Normal

value: AA


title: T_048 [miRNA-Seq]


title: KO_WSN_2

value: lung

tag: age


title: KO_PBS_2


title: T_019 [miRNA-Seq]

tag: race


title: C_10nM_RA_t_4.5hr

description: 10nM RA for 2hrs; t=4.5hr after wash

tag: strain

value: not determined

value: 10nM RA t=4.5hr


title: T_051 [miRNA-Seq]


title: T_010 [miRNA-Seq]

value: EA


title: T_032 [miRNA-Seq]


title: KO_PBS_1


title: Lung Con-1

value: wild type

value: infection with SARS-CoV-2

value: 2 dpi


title: T_031 [miRNA-Seq]

value: HCC


title: T_049 [miRNA-Seq]


title: C_0.5_ETOH_t_4.5hr

value: wildtype


title: T_004 [miRNA-Seq]


title: KO_WSN_1

value: WSN-infected for 48 hours

value: Eif4b CKO


title: T_038 [miRNA-Seq]


title: C_50uM_DEAB_t_3hr

description: 50µM DEAB for 2hrs; t=3hr after wash

value: whole embryo

value: 50µM DEAB t=3hr


title: C_control_t_4.5hr

description: control for 2hrs; t=4.5hr after wash

value: female C

value: control t=4.5hr


title: T_005 [miRNA-Seq]

value: Adjacent Normal


title: WT_WSN_2

value: wilde type


title: C_control_t_3hr

description: control for 2hrs; t=3hr after wash

value: control t=3hr


title: T_018 [miRNA-Seq]

value: AA


title: TT-seq_DMSO-3h_SPT5-dTAG-DLD1_rep3

first: Linna

last: Peng

address: Dong'an Road

data_processing:
Library strategy: TT-seq
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter “-q 25” .
The remaining reads were aligned to human hg19 and mouse mm10 assemblies using STAR v2.7.5c with parameters “-outFilterMultimapNmax 1 -alignSJoverhangMin 8 -alignSJDBoverhangMin 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.02 -alignIntronMin 20 -alignIntronMax 1000000 -alignMatesGapMax 1000000 -outSAMtype BAM SortedByCoordinate” (Dobin et al., 2013).
SAMtools v1.9 (Li et al., 2009) was used to quality filter SAM files with “-q 7 -f 2” and duplicated reads were removed using Picard v2.23.3 (https://broadinstitute.github.io/picard/).
The counts of spike-in mm10 reads were used to generate normalization factors for coverage profiles.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files

source_name: SPT5-dTAG DLD1

growth_protocol: Colorectal adenocarcinoma cell line DLD1 cells were cultured in DMEM (Dulbecco’s Modified Eagle’s medium, Hyclone) supplemented with 10% fetal bovine serum (FBS, Biowest), nonessential amino acids (Gibco) at 37 °C and 5% CO2.

extract_protocol:
RNA was isolated with TRIzol.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme NR603-02). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: Cells were treated with DMSO or dTAG-13 for 3h. Add 4SU directly to the tissue culture medium to a final concentration of 500 μm. Incubate the cells with 4SU for 15 min.

tag: cell line

tag: cell type

value: colorectal adenocarcinoma cells

value: untreated

value: SPT5 knock-in of a dTAG tag


title: C_50uM_DEAB_t_1.5hr

description: 50µM DEAB for 2hrs; t=1.5hr after wash

value: not determined

value: 50µM DEAB t=1.5hr


title: C_10nM_RA_t_3hr

description: 10nM RA for 2hrs; t=3hr after wash

value: 10nM RA t=3hr


title: TT-seq_dTAG-3h_SPT5-dTAG-DLD1_rep3

value: treated with dTAG13 for 3 hours


title: TT-seq_DMSO-3h_SPT5-dTAG-DLD1_rep2


title: PIGS-HRD1-DKO

city: Wuxi

first: Yi-Shi

last: Liu

state: Jiangsu

address: No.1800, Lihu road

department: School of Biotechnology

institute: Jiangnan University

data_processing:
The raw reads containing adaptors and the low-quality reads from the raw data were removed using Trimmomatic to obtain clean reads.
The clean reads were mapped to the hg38 reference genome using hisat2 (version 2.1.0).
The output BAM files were converted to SAM files using SAMtools 1.9. The final TPM values were obtained using Stringtie 1.3.5.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HEK293 cells

extract_protocol:
Total RNA was extracted from whole cells with the mirVana miRNA Isolation Kit according to the manufacturer’s protocol. RNA quality and integrity were evaluated with an Agilent 2100 Bioanalyzer. Samples with an RNA integrity number (RIN) ≥ 7 were considered to be of high quality and were processed further and subjected to subsequent analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human Embryonic Kidney 293

value: PIGS and HRD1-/-


title: WT_WSN_3

last: Chen

value: lung

value: WSN-infected for 48 hours


title: WT_PBS_3

value: WSN-uninfected for 48 hours


title: PIGS-HRD1-CD55-TKO

value: PIGS, CD55, and HRD1-/-


title: TT-seq_dTAG-3h_SPT5-dTAG-DLD1_rep2


title: PIGS-HRD1-CD55-TKO+HA-CD55


title: T_011 [miRNA-Seq]

value: Adjacent Normal

value: EA


title: WT_PBS_1

value: wilde type


title: PRO_dTAG-3h_SPT5-dTAG-Vector_DLD1_rep2

data_processing:
Library strategy: PRO-Seq
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter “-q 25 --length 15” .
Ribosomal RNA reads were removed using Bowtie v2.3.5.1 with “--un-conc-gz” (Langmead and Salzberg, 2012)
The remaining reads were aligned to hg19 or mm10 genome using Bowtie v2.3.5.1 with “--local --sensitive-local” (Langmead and Salzberg, 2012).
Removal of low mapping quality reads and duplicated reads and calculation of normalization factor were performed with SAMtools v1.9 (Li et al., 2009) and Picard v2.23.3 (https://broadinstitute.github.io/picard/).
Strand-specific PRO-seq signal normalized by spike-in reads was generated by deeptools v3.5.0 (Ramirez et al., 2016) with "--Offset 1" for single-base files and "--Offset None" for full-length files.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: SPT5-dTAG-Vector DLD1

extract_protocol:
RNA was isolated with TRIzol.
Enriched RNA was ligated with RNA adapters. Reverse transcription (RT) was performed using the Superscript III enzyme (Invitrogen). The reverse transcription products were proceeded to library amplification by using the Q5 enzyme mix.  Libraries were sequenced on the Illumina HiSeq X Ten following the manufacturer's protocols.

treatment_protocol: Cells were treated with DMSO or dTAG 13 for 3h.

value: SPT5 knock-in of a dTAG tag, then ectopic vector-only expression


title: PRO_dTAG-3h_SPT5-dTAG-Vector_DLD1_rep1

value: colorectal adenocarcinoma cells


title: PRO_dTAG-3h_SPT5-dTAG-SPT5-WT_DLD1

source_name: SPT5-dTAG-SPT5-WT DLD1

value: SPT5 knock-in of a dTAG tag, then ectopic SPT5-WT expression


title: C_10nM_RA_t_1.5hr

description: 10nM RA for 2hrs; t=1.5hr after wash

value: wildtype

value: female C

value: whole embryo

value: 10nM RA t=1.5hr


title: PRO_dTAG-3h_SPT5-dTAG-SPT5-CTR-T4A_DLD1

source_name: SPT5-dTAG-SPT5-CTR-T4A DLD1

value: treated with dTAG13 for 3 hours

value: SPT5 knock-in of a dTAG tag, then ectopic SPT5-CTR-T4A expression


title: GATA-1 V205M

city: Hershey

first: Bowen

last: Yan

address: HERSHEY MED CTR 500 UNIVERSITY DRIVE 500 UNIVERSITY DRIVE

institute: PENNSYLVANIA STATE UNIV

data_processing:
Sequenced reads were trimmed for adaptor sequence
Reads were aligned to the mouse mm10 genome using Tophat
deepTools was used to generate the bigwig file
Differential expressions between wild type and mutation cells were determined with the Cuffdiff tool from Cufflinks, To prevent false positives, only genes with 50 or more reads in one of the conditions were included in the analysis. Genes were considered to be differentially regulated if the fold change was greater than two for upregulation or less than 0.5 for downregulation.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, fold-change

source_name: G1E cells

extract_protocol:
Total RNA was isolated and DNAse I treated using RNA purification kit (Genesee Scientific, San Diego).
RNA libraries were prepared using the TruSeq RNA sample prep kit (Illumina, San Diego) and sequenced on the Illumina HiSeq 2000 according to the manufacturer's instructions.

value: GATA-1 V205M

value: β-estrodiol induction


title: WT_WSN_1

value: lung

value: WSN-infected for 48 hours


title: WT_PBS_2

value: WSN-uninfected for 48 hours


title: TT-seq_DMSO-3h_SPT5-dTAG-DLD1_rep1

value: untreated

value: SPT5 knock-in of a dTAG tag


title: PRO_dTAG-3h_SPT5-dTAG-SPT5-666A_DLD1

source_name: SPT5-dTAG-SPT5-666A DLD1

value: SPT5 knock-in of a dTAG tag, then ectopic SPT5-S666A expression


title: PIGS-KO

value: Human Embryonic Kidney 293

value: PIGS-/-


title: C_0.5_ETOH_t_0hr

value: not determined

value: 0.5% ETOH t=0hr


title: C_10nM_RA_t_0hr

description: 10nM RA for 2hrs; t=0hr after wash

value: wildtype

value: female C

value: 10nM RA t=0hr


title: PRO_dTAG-3h_INTS8-SPT5-dTAG-vector_DLD1_rep2

source_name: INTS8-SPT5-dTAG-vector DLD1

value: colorectal adenocarcinoma cells

value: treated with dTAG13 for 3 hours

value: INTS8 and SPT5 double knock-in of a dTAG tag, then ectopic vector-only expression


title: C_0.5_ETOH_t_1.5hr

value: whole embryo


title: GATA-1 2RA

value: GATA-1 2RA

value: β-estrodiol induction


title: PRO_dTAG-3h_INTS8-SPT5-dTAG-SPT5-WT_DLD1

source_name: INTS8-SPT5-dTAG-SPT5-WT DLD1

value: INTS8 and SPT5 double knock-in of a dTAG tag, then ectopic SPT5-WT expression


title: C_control_t_1.5hr

description: control for 2hrs; t=1.5hr after wash

value: control t=1.5hr


title: Cov2_PG1F_3

tag: organ

value: Fat

value: Cov2 PG1F

tag: infection


title: PRO_dTAG-3h_INTS8-SPT5-dTAG-SPT5-666A_DLD1

source_name: INTS8-SPT5-dTAG-SPT5-666A DLD1

value: INTS8 and SPT5 double knock-in of a dTAG tag, then ectopic SPT5-S666A expression


title: PRO_dTAG-3h_INTS8-dTAG_DLD1_rep2

source_name: INTS8-dTAG DLD1

value: INTS8 knock-in of a dTAG tag


title: PRO_dTAG-3h_INTS8-SPT5-dTAG-vector_DLD1_rep1


title: PRO_dTAG-3h_SPT5-dTAG_DLD1_rep2

value: SPT5 knock-in of a dTAG tag


title: L_10nM_RA_t_3hr

data_processing: Relative gene expression was determined by the ΔΔCt method. Gapdh was used as a housekeeping gene for normalization of the data.

label: Eva Green

source_name: whole embryo

label_protocol: not provided

growth_protocol: Embryos were obtained by in vitro fertilization, incubated in 0.1% MBSH and staged according to Nieuwkoop and Faber(Nieuwkoop and Faber, 1967).

extract_protocol: For each sample, 5-10 staged embryos were collected and stored at -80°C. RNA purification was performed using the Bio-Rad Aurum Total RNA Mini Kit (according to the manufacturer's instructions). RNA samples were used for cDNA synthesis using the Bio-Rad iScriptTM Reverse Transcription Supermix for RT-qPCR kit (according to the manufacturer's instructions).

treatment_protocol: The experimental design involves treating embryos for 2 hours from late blastula (st. 9.5) to early gastrula (st. 10.25) and collecting samples every 1.5 hours after terminating and washing the treatment. Embryos were treated with RA (10 nM) or DEAB (50 µM). For each biological repeat, all treatments, controls, and time points were collected from a single fertilization, from the eggs (clutch) of a single female.

tag: treatment group

value: 10nM RA for 2hrs , t=3hr after wash


title: L_10nM_RA_t_4.5hr

value: wildtype

value: 10nM RA for 2hrs , t=4.5hr after wash


title: C_50uM_DEAB_t_0hr

description: 50µM DEAB for 2hrs; t=0hr after wash

value: female C

value: not determined

tag: tissue

tag: treatment

value: 50µM DEAB t=0hr


title: L_10nM_RA_t_1.5hr

tag: genotype

value: 10nM RA for 2hrs , t=1.5hr after wash


title: B_0.5_ETOH_t_4.5hr

value: female B

value: whole embryo


title: TT-seq_dTAG-3h_SPT5-dTAG-DLD1_rep1

value: colorectal adenocarcinoma cells

value: treated with dTAG13 for 3 hours


title: C_control_t_0hr

description: control for 2hrs; t=0hr after wash

value: control t=0hr


title: GATA-1 WT

value: GATA-1 WT

value: β-estrodiol induction


title: B_control_t_4.5hr

description: control for 2hrs; t=4.5hr after wash

value: control t=4.5hr


title: G1E

value: control


title: L_10nM_RA_t_0hr

value: 10nM RA for 2hrs , t=0hr after wash


title: PRO_DMSO-3h_SPT5-dTAG_DLD1_rep1

value: untreated

value: SPT5 knock-in of a dTAG tag


title: B_50uM_DEAB_t_4.5hr

description: 50µM DEAB for 2hrs; t=4.5hr after wash

value: wildtype

value: 50µM DEAB t=4.5hr


title: PRO_DMSO-3h_INTS8-SPT5-dTAG-vector_DLD1_rep1

value: INTS8 and SPT5 double knock-in of a dTAG tag, then ectopic vector-only expression


title: L_50uM_DEAB_t_4.5hr

value: 50µM DEAB for 2hrs , t=4.5hr after wash


title: B_0.5_ETOH_t_3hr

value: not determined

value: 0.5% ETOH t=3hr


title: B_50uM_DEAB_t_3hr

description: 50µM DEAB for 2hrs; t=3hr after wash

value: female B

value: whole embryo

value: 50µM DEAB t=3hr


title: PRO_dTAG-3h_INTS8-SPT5-dTAG-SPT5-CTR-T4A_DLD1

source_name: INTS8-SPT5-dTAG-SPT5-CTR-T4A DLD1

value: colorectal adenocarcinoma cells

value: treated with dTAG13 for 3 hours

value: INTS8 and SPT5 double knock-in of a dTAG tag, then ectopic SPT5-CTR-T4A expression


title: B_10nM_RA_t_4.5hr

description: 10nM RA for 2hrs; t=4.5hr after wash

value: 10nM RA t=4.5hr


title: PRO_dTAG-3h_INTS8-dTAG_DLD1_rep1

value: INTS8 knock-in of a dTAG tag


title: PRO_dTAG-3h_SPT5-dTAG_DLD1_rep1


title: PRO_DMSO-3h_INTS8-SPT5-dTAG-vector_DLD1_rep2


title: PRO_DMSO-3h_SPT5-dTAG-Vector_DLD1_rep1

value: SPT5 knock-in of a dTAG tag, then ectopic vector-only expression


title: PRO_DMSO-3h_INTS8-SPT5-dTAG-SPT5-CTR-T4A_DLD1

value: untreated


title: L_50uM_DEAB_t_1.5hr

value: 50µM DEAB for 2hrs , t=1.5hr after wash


title: L_50uM_DEAB_t_3hr

value: wildtype

value: 50µM DEAB for 2hrs , t=3hr after wash


title: L_50uM_DEAB_t_0hr

value: 50µM DEAB for 2hrs , t=0hr after wash


title: PRO_DMSO-3h_INTS8-dTAG_DLD1_rep2


title: PRO_DMSO-3h_SPT5-dTAG-Vector_DLD1_rep2


title: PRO_DMSO-3h_SPT5-dTAG_DLD1_rep2

value: SPT5 knock-in of a dTAG tag


title: B_control_t_3hr

description: control for 2hrs; t=3hr after wash

value: not determined

value: control t=3hr


title: ATAC_Spt5_Control_rep1_DLD1

data_processing:
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter “-q 25” .
The remaining reads were aligned to human (hg19) genome assembly using Bowtie 2 v2.3.5.1 with parameters “-N 1 -L 25 -X 2000 --no-mixed --no-discordant” (Langmead and Salzberg, 2012).
All unmapped reads, low mapping quality reads (MAPQ < 30) and PCR duplicates were removed using SAMtools v1.9(Li et al., 2009) and Picard v2.23.3 (https://broadinstitute.github.io/picard/).
Reads counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) with deeptools v3.5.0 and peaks were called using macs2 v2.2.6 (Ramirez et al., 2016; Zhang et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files include FPKM values for each Sample

extract_protocol:
DNA was isolated with PCR clear-up.
Libraries were prepared according to Vazyme's instructions accompanying the TruePrep DNA Library Prep Kit V2 (Vazyme TD501-02). Libraries were sequenced on the Illumina HiSeq X Ten following the manufacturer's protocols.

treatment_protocol: One replicate was DMSO or dTAG-13 treated for 3 hours.

value: colorectal adenocarcinoma cell lines


title: PRO_DMSO-3h_INTS8-SPT5-dTAG-SPT5-666A_DLD1

value: INTS8 and SPT5 double knock-in of a dTAG tag, then ectopic SPT5-S666A expression


title: RNA-seq_dTAG-24h_SPT5-fkbp-DLD1_rep2

data_processing:
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter "-q 25".
The remaining reads were aligned to human hg19 and mouse mm10 assemblies using STAR v2.7.5c with parameter "--outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMismatchNmax 2 --outSJfilterReads Unique".
PCR duplicates were removed using Picard v2.23.3 (https://broadinstitute.github.io/picard/).
The number of spike-in mm10 reads was counted with SAMtools v1.9 and normalization factor alpha = 1e6/mm10_count was calculated (Li et al., 2009).
Strand-specific RNA-seq signal normalized by spike-in reads was generated by deeptools v3.5.0 (Ramirez et al., 2016).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files

extract_protocol:
RNA was isolated with TRIzol.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme NR603-02). Libraries were sequenced on the Illumina HiSeq X Ten following the manufacturer's protocols.

treatment_protocol: Cells were treated with DMSO or dTAG-13 for 12h, or 24h.

value: treated with dTAG13 for 24 hours


title: RNA-seq_dTAG-12h_SPT5-fkbp-DLD1_rep2

data_processing:
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter "-q 25" .
The remaining reads were aligned to human hg19 and mouse mm10 assemblies using STAR v2.7.5c with parameter "--outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMismatchNmax 2 --outSJfilterReads Unique"
PCR duplicates were removed using Picard v2.23.3 (https://broadinstitute.github.io/picard/).
The number of spike-in mm10 reads was counted with SAMtools v1.9 and normalization factor alpha = 1e6/mm10_count was calculated (Li et al., 2009).
Strand-specific RNA-seq signal normalized by spike-in reads was generated by deeptools v3.5.0 (Ramirez et al., 2016).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files

value: treated with dTAG13 for 12 hours