title: AI001_34_post

value: surgical specimen


title: H1299 cells, siCLOCK, rep1

status: Public on Feb 19 2022

type: SRA

city: Wuhan

first: Yixian

last: Fan

state: Hubei

address: Hangkong Road 13, Wuhan

country: China

institute: Huazhong University of Science and Technology

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke.
Trimmed reads were then mapped to human genome (GRCh38) using STAR aligner (v2.7.9a) with standard ENCODE RNA-seq pipeline options, and gene level counts were obtained by setting --quantMode parameter to “GeneCounts”.
Read counts for annotated genes were subsequently normalized to transcripts per million (TPM).
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen).
Double stranded PCR products were heated denatured and circularized by the splint oligo sequence to get the library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on BGIseq500 platform.

tag: cell line

tag: treatment

value: siCLOCK


title: E14Tg2a_ctcfAIDplusIAA_mit_rep2

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

data_processing:
Gencode (vM12) gtf was used after adding a pre-mRNA isoform for each annotated gene, spanning the longest isoform of all available mRNA isoforms
Reads were aligned using STAR
Quantifications were made by RSEM and counts transformed into Transcripts per Million
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

organism: Mus musculus

source_name: Embryonic Stem cells

growth_protocol: ES cells were cultured on standard serum and LIF conditions and passaged 1:10 every 2-3 days. To obtain mitotic ES cells a double synchronisation method (4h in the presence of 10 μM of RO-3306 (Sigma, SML0569), followed by 4h with 50 ng/ml nocodazole (Sigma, M1404), and shake-off.

extract_protocol:
RNA was extracted with 500 μl TRIzol (ThermoFisher, 15596026), according to the manufacturer’s protocol, and treated with DNAse I (Qiagen,) for 20min at 37°C. Following phenol:chloroform purification, RNAs were resuspended in Ultrapure DNAse/RNase Free Distilled Water (Thermo, 10977035)
Ribo-depleted, stranded and paired-end RNA-seq libraries were prepared and sequenced by Novogene Co Ltd

treatment_protocol: CTCF depletion in CTCF-AID cells was achieved with 0.5 mM auxin (IAA Sigma, I5148) for 2h, starting after 2h of nocodazole treatment. IAA was maintained throughout the whole release procedure.

tag: cell type

value: E14Tg2a cells engineered for auxin-induced degradation of CTCF

tag: strain

tag: time point

value: nocodazole-arrested and shake-off

value: IAA (auxin)


title: AI001_33_post

city: Chicago

first: Seema

middle: Ahsan

last: Khan

state: IL

address: 303 E. Superior Street, 4-111

country: USA

institute: Northwestern University

description: Generating RNA-seq data from primary tumors.

data_processing:
RNA sequencing data analysis was performed using Artificial Intelligene’s (AI, www.artificialintelligene.com) RNAseq analysis platform. Briefly, short reads were aligned to the hg19 human genome using STAR. Subsequently cufflinks packages were used to perform transcript assemblies. Downstream differential gene expression calling on the reference and experimental groups of interest was performed using DESeq2. To perform clustering analyses on a group of samples, a union of all the genes and their expression RPKM values within that group was generated to build a read count matrix for the group of interest. Various unsupervised and other machine learning techniques were applied to this composite read count matrix of interest. The sample-sample correlation heatmaps represent the correlation observed between any two samples. The sample-feature heatmaps represent the signal intensity of a feature for any given sample. ggplot2, heatmap.2 and Pheatmap packages in R were used to build various heatmaps. Functional analysis was performed using gene set enrichment analyses.
Genome_build: HG19
Supplementary_files_format_and_content: AI001_ReadCounts.csv

source_name: breast

extract_protocol:
Roche high pure FFPET kit (Cat # 0665077500)
RNA libraries were prepared using TruSeq RNA Access Library Prep Guide, RS-301-9001DOC, Part# 15049525 Rev. B (Illumina, Inc.)
paired end RNA-seq

tag: tissue

value: tumor containing tissue

tag: specimen type

tag: age at diagnois

tag: characteristics

value: menopausal status:premenopausal

tag: tumor type

value: IDC

tag: er status

value: high positive

tag: pr status

tag: treatment group

value: placebo

tag: ki67 response

value: No


title: H_1_PB_pos_1

city: Heidelberg

first: Ricardo

last: Grieshaber-Bouyer

address: Im Neuenheimer Feld 410

department: Division of Rheumatology

country: Germany

institute: Heidelberg University Hospital

data_processing:
Short sequence reads were aligned to the reference genome (GRCh38) and Ensembl transcriptome using STAR aligner.
The uniquely aligned reads were used to quantify gene expression levels for all Ensembl genes.
Genes with low expression (less than 10 reads in at least three samples in at least one group) were removed.
Data was analyzed in limma using voom normalization and the expression of each gene was modeled as a combination of donor- and group-specific effects.
Genome_build: GRCh38
Supplementary_files_format_and_content: Two data files are presented and contain log2 normalized, library size normalized counts per million. First, CD177neg and CD177pos neutrophils separately and second CD177neg and CD177pos data averaged for each individual donor/patient.

source_name: blood

extract_protocol:
RNA was extracted from lysed neutrophils using the Qiagen RNeasy micro kit following manufacturer instructions. RNA sequencing was performed at the Broad Institute under the Smartseq2 protocol. Samples were sequenced on an Illumina NextSeq500 with 25bp paired-end reads and an average sequencing depth of 6 x 106 reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: healthy

value: pos


title: E14Tg2a_ctcfAIDplusIAA_mit_rep1


title: H1299 cells, control, rep3

value: serum free medium


title: E14Tg2a_ctcfAIDminusIAA_asy_rep3

value: asynchronous

value: untreated


title: H_1_PB_neg_1

value: neg


title: AI001_33_pre

value: core needle biospy


title: A_6_SF_pos

source_name: synovial fluid

value: arthritis


title: H1299 cells, control, rep2


title: E14Tg2a_ctcfAIDminusIAA_asy_rep2

value: E14Tg2a cells engineered for auxin-induced degradation of CTCF


title: A_6_SF_neg


title: H1299 cells, control, rep1


title: E14Tg2a_ctcfAIDplusIAA_mit_rep3

value: nocodazole-arrested and shake-off


title: E14Tg2a_ctcfAIDminusIAA_asy_rep1


title: glh-1(red117)

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

description: all_gene_rpkm_siRNAsuppression_revised.csv

data_processing:
Genomic alignment was performed by using Bowtie 1.2.3
siRNA RPKM values were calculated for all protein coding genes.
Genome_build: WS190(ce6)
Supplementary_files_format_and_content: tab-delimited text file, rows are different genes, columns are different libraries.

organism: Caenorhabditis elegans

source_name: young adults

extract_protocol: RNA-seq libraries were prepared by Novogene using NEB Next Multiplex Small RNA Library Prep Set for Illumina

tag: genotype

value: glh-1(red117) I

tag: fragment inserted in cer3

tag: strain name

tag: rna-seq method

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs

tag: 5’ barcodes for srna or rna-seq

value: mixture of AGCG, CGTC, GTTA, TATG


title: E14Tg2a_ctcfAIDminusIAA_120m_rep2

tag: cell type

tag: strain

value: 120min post-release

tag: treatment


title: E14Tg2a_ctcfAIDminusIAA_120m_rep1

tag: time point


title: AI001_28_post

tag: tissue

value: tumor containing tissue

tag: specimen type

value: surgical specimen

tag: age at diagnois

value: menopausal status:postmenopausal

value: IDC

value: high positive

value: TPA


title: A_6_PB_neg


title: AI001_28_pre

tag: characteristics

tag: tumor type

tag: er status

value: No


title: E14Tg2a_ctcfAIDminusIAA_90m_rep3

value: 90min post-release

value: untreated


title: AI001_27_post

value: menopausal status:premenopausal

tag: pr status

tag: treatment group

value: placebo

tag: ki67 response


title: AI001_32_pre

value: core needle biospy

value: negative

value: Yes


title: A_5_SF_neg

tag: group

value: arthritis

value: neg


title: Cer3::oma-1(red118) with oma-1 piRNAi sRNA-seq

tag: genotype

value: Cer3(red118) IV;kstEx4 (21ur-199 anti-oma-1+Pmyo-2::mCherry+Prps-17::hygromycinR)]

tag: fragment inserted in cer3

tag: strain name

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs

value: mixture of AGCG, CGTC, GTTA, TATG


title: Cer3::oma-1(red118)

value: Cer3(red118) IV

tag: rna-seq method

tag: 5’ barcodes for srna or rna-seq


title: E14Tg2a_ctcfAIDminusIAA_90m_rep1

tag: cell type

value: E14Tg2a cells engineered for auxin-induced degradation of CTCF

tag: strain

tag: treatment


title: A_5_SF_pos

value: pos


title: A_5_PB_pos


title: AI001_27_pre

tag: tissue

value: tumor containing tissue

tag: specimen type

value: IDC

value: high positive


title: E14Tg2a_ctcfAIDminusIAA_60m_rep2

tag: time point

value: 60min post-release

value: untreated


title: AI001_32_post

value: surgical specimen

tag: age at diagnois

tag: characteristics

value: menopausal status:premenopausal

tag: tumor type

value: TPA


title: A_5_PB_neg


title: Cer3::oma-1(red20), control (L4440) RNAi,  sRNA-seq

value: Cer3(red20) IV


title: A_6_PB_pos

value: arthritis


title: Cer8::oma-1(red20) rep 2 sRNA-seq

value: mixture of CTGG, ACTG, GAAG, TGCC


title: AI001_26_pre

value: core needle biospy

tag: er status

tag: pr status

tag: treatment group

value: No


title: pgl-1(red116)

tag: genotype

value: pgl-1(red116) IV

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs

value: mixture of AGCG, CGTC, GTTA, TATG


title: A_4_SF_pos

tag: group

value: pos


title: A_4_SF_neg

value: neg


title: E14Tg2a_ctcfAIDminusIAA_50m_rep3

value: E14Tg2a cells engineered for auxin-induced degradation of CTCF

value: 50min post-release


title: E14Tg2a_ctcfAIDminusIAA_60m_rep1

value: 60min post-release


title: Cer3::oma-1(red20), oma-1 RNAi,  sRNA-seq

tag: fragment inserted in cer3

tag: strain name


title: E14Tg2a_ctcfAIDminusIAA_50m_rep1

value: untreated


title: Cer8::oma-1(red20) rep 1 sRNA-seq

tag: rna-seq method

tag: 5’ barcodes for srna or rna-seq


title: A_4_PB_pos


title: E14Tg2a_ctcfAIDminusIAA_40m_rep2

tag: cell type

tag: strain

value: 40min post-release


title: AI001_25_pre

tag: tissue

value: tumor containing tissue

value: menopausal status:postmenopausal

value: IDC

value: high positive

value: placebo

tag: ki67 response


title: fem-1(hc17) 25C sRNA-seq


title: A_4_PB_neg

value: arthritis


title: glp-1(e2141), 25C sRNA-seq


title: E14Tg2a_ctcfAIDminusIAA_40m_rep1

tag: time point

tag: treatment


title: AI001_24_post

tag: specimen type

value: surgical specimen

tag: age at diagnois

tag: characteristics

value: TPA

value: Yes


title: Cer3::oma-1(red20);deps-1(-) sRNA-seq

value: deps-1 (bn124) I;Cer3(red20) IV

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs

value: mixture of CTGG, ACTG, GAAG, TGCC


title: AI001_24_pre

value: core needle biospy

tag: tumor type

tag: er status

tag: pr status


title: E14Tg2a_ctcfAIDminusIAA_20m_rep2

value: E14Tg2a cells engineered for auxin-induced degradation of CTCF

value: 20min post-release


title: AI001_26_post

value: menopausal status:premenopausal

tag: treatment group

value: No


title: AI001_23_post

value: tumor containing tissue


title: A_3_SF_neg

tag: group

value: neg


title: E14Tg2a_ctcfAIDminusIAA_mit_rep2

value: nocodazole-arrested and shake-off

value: untreated


title: A_3_PB_pos

value: pos


title: E14Tg2a_ctcfAIDminusIAA_mit_rep1


title: AI001_25_post

value: menopausal status:postmenopausal

value: IDC

value: high positive

value: placebo


title: Cer3::oma-1(red20);pgl-1(-) rep 1 sRNA-seq

tag: genotype

value: Cer3(red20) pgl-1(red116) IV

tag: fragment inserted in cer3

tag: strain name

value: mixture of AGCG, CGTC, GTTA, TATG


title: Cer3::oma-1(red20);glh-1(-) sRNA-seq

value: glh-1(red117) I; Cer3(red20) IV

tag: rna-seq method

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs

tag: 5’ barcodes for srna or rna-seq


title: E14Tg2a_ctcfAIDminusIAA_20m_rep1

tag: cell type

value: E14Tg2a cells engineered for auxin-induced degradation of CTCF

tag: strain


title: Cer3::oma-1(red20);pgl-1(-) rep 2 sRNA-seq


title: Cer3::oma-1(red20);prde-1(-) sRNA-seq

value: Cer3(red20) IV; prde-1(red139) V


title: AI001_22_post

tag: tissue

value: surgical specimen

value: menopausal status:premenopausal

tag: ki67 response


title: AI001_23_pre

value: tumor containing tissue

tag: specimen type

value: core needle biospy

value: No


title: AI001_21_post

tag: age at diagnois


title: E14Tg2a_ctcfAIDminusIAA_mit_rep3

tag: time point

value: nocodazole-arrested and shake-off

tag: treatment

value: untreated


title: A_2_PB_pos

value: arthritis

value: pos


title: AI001_22_pre

tag: characteristics

tag: tumor type

value: IDC

tag: er status

value: high positive


title: E14Tg2a_ccnaTg2a_asy_rep3

value: E14Tg2a cells expressing a CCNA-GFP cell cycle reporter

value: asynchronous


title: A_3_PB_neg

tag: group

value: neg


title: A_2_SF_neg


title: A_2_PB_neg


title: A_2_SF_pos


title: E14Tg2a_ccnaTg2a_asy_rep1


title: AI001_20_post

value: negative

tag: pr status

tag: treatment group

value: TPA


title: E14Tg2a_ccnaTg2a_asy_rep2


title: A_3_SF_pos


title: AI001_21_pre

value: placebo


title: oma-1::Cer3 sRNA-seq

tag: genotype

tag: fragment inserted in cer3

tag: strain name

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs

value: mixture of CTGG, ACTG, GAAG, TGCC


title: AI001_20_pre

value: tumor containing tissue

value: menopausal status:premenopausal


title: A_1_SF_pos


title: Cer3::oma-1(red20);prg-1(-) sRNA-seq

value: Cer3(red20) IV; prg-1(red115) I

tag: rna-seq method

tag: 5’ barcodes for srna or rna-seq

value: mixture of AGCG, CGTC, GTTA, TATG


title: Cer3::oma-1(red20); CSR-1-AID auxin (-) rep2 sRNA-seq

value: Cer3(red20) ieSi38 [sun-1p::TIR1::mRuby::sun-1 3'UTR + Cbr-unc-119(+)] csr-1(red121) IV


title: E14Tg2a_ccnaTg2a_120m_rep2

tag: cell type

tag: strain

value: 120min post-release

value: untreated


title: A_1_SF_neg

value: arthritis


title: AI001_19_post

tag: tissue

tag: specimen type

value: surgical specimen

value: IDC

value: high positive

tag: ki67 response

value: Yes


title: A_1_PB_neg

value: neg


title: Cer3::oma-1(red20); CSR-1-AID auxin (+) rep1 sRNA-seq


title: E14Tg2a_ccnaTg2a_90m_rep1

value: E14Tg2a cells expressing a CCNA-GFP cell cycle reporter

tag: time point

value: 90min post-release

tag: treatment


title: E14Tg2a_ccnaTg2a_90m_rep3


title: AI001_19_pre

value: core needle biospy

tag: age at diagnois

tag: characteristics

tag: tumor type

value: placebo


title: Cer3::oma-1(red20); hrde-1(tm1200) rep 2 sRNA-seq

value: cer3(red20) IV;hrde-1(tm1200) III

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs

value: mixture of CTGG, ACTG, GAAG, TGCC


title: E14Tg2a_ccnaTg2a_120m_rep1


title: Cer3::oma-1(red20); CSR-1-AID auxin (+) rep2 sRNA-seq

value: mixture of AGCG, CGTC, GTTA, TATG


title: Cer3::oma-1(red20); CSR-1-AID auxin (-) rep1 sRNA-seq

value: Cer3(red20) ieSi38 [sun-1p::TIR1::mRuby::sun-1 3'UTR + Cbr-unc-119(+)] csr-1(red121) IV


title: Cer3::oma-1(red20); hrde-1(tm1200) rep 1 sRNA-seq


title: AI001_17_pre

value: tumor containing tissue

value: menopausal status:postmenopausal

tag: er status

value: negative

tag: pr status

value: No


title: AI001_17_post

value: surgical specimen

value: IDC

tag: treatment group


title: AI001_18_pre

value: high positive

value: TPA


title: E14Tg2a_ccnaTg2a_60m_rep2

value: E14Tg2a cells expressing a CCNA-GFP cell cycle reporter

value: 60min post-release

value: untreated


title: E14Tg2a_ccnaTg2a_60m_rep1


title: AI001_18_post


title: E14Tg2a_ccnaTg2a_50m_rep3

value: 50min post-release


title: Cer3::oma-1(red20); oma-1 piRNAi sRNA-seq

tag: genotype

value: Cer3(red20) IV;kstEx4 (21ur-199 anti-oma-1+Pmyo-2::mCherry+Prps-17::hygromycinR)]

tag: fragment inserted in cer3


title: MuZ2

city: Shenyang

first: Xiaoxue

last: Wang

state: Liaoning

address: 120 Dongling Road, Shenhe District

department: Rice Research Institute

institute: Shenyang Agricultural University

description: MuZ2 is the mutant rep 2.

data_processing:
The clustering of the index-coded samples is 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 are sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads are generated.
Raw data (raw reads) of fastq format are firstly processed through in-house perl scripts.
Index of the reference genome is built using Bowtie v2.2.3 and paired-end clean reads are aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 is used to count the reads numbers mapped to each gene.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: fpkm, read counts

organism: Oryza sativa

source_name: 7-day-old seedlings

growth_protocol: 7-day-old seedlings of WT and mutant  grown under 14 h light and 10 h dark are sequenced.

extract_protocol:
Total RNA is extracted with Takara RNAiso Plus (Takara, Cat# 9108)
Sequencing libraries are generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes are added to attribute sequences to each sample. The library quality is assessed on the Agilent Bioanalyzer 2100 system.

tag: replication

tag: genotype/variation

value: MuZ1 mutant

tag: cultivar

value: L. japonica


title: WTZ2

description: WTZ2 is wild type rep 2.

tag: strain

value: wild type


title: MuZ1

description: MuZ1 is the mutant rep 1.


title: AI001_15_post

tag: tissue

value: placebo

value: Yes


title: A_1_PB_pos

tag: group

value: arthritis

value: pos


title: Cer3::oma-1(red40) (reverse complementary) sRNA-seq

value: Cer3(red40) IV

value: oma-1 (reverse complementary)

tag: strain name

tag: rna-seq method

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs

tag: 5’ barcodes for srna or rna-seq

value: mixture of AGCG, CGTC, GTTA, TATG


title: E14Tg2a_ccnaTg2a_40m_rep2

tag: cell type

tag: time point

value: 40min post-release

tag: treatment


title: AI001_15_pre

value: tumor containing tissue

tag: specimen type

value: core needle biospy

tag: age at diagnois

tag: characteristics

value: menopausal status:postmenopausal

tag: tumor type

value: IDC

tag: er status

value: high positive

tag: ki67 response


title: Cer3::oma-1(red20);oma-1 deletion (red110) sRNA-seq

tag: genotype

value: Cer3(red20) oma-1(red110) IV

tag: fragment inserted in cer3


title: WTZ1

description: WTZ1 is wild type rep 1.

tag: replication

tag: strain

tag: genotype/variation

tag: cultivar

value: L. japonica


title: E14Tg2a_ccnaTg2a_40m_rep1

value: E14Tg2a cells expressing a CCNA-GFP cell cycle reporter

value: untreated


title: Cer3::oma-1(red20); unc-119 piRNAi  sRNA-seq

value: Cer3(red20) IV;kstEx7[21ur-199 anti unc-119+Pmyo-2::mCherry+Prps-27::hygromycinR]

tag: strain name

tag: rna-seq method


title: E14Tg2a_ccnaTg2a_30m_rep1

tag: cell type

value: 30min post-release


title: AI001_14_pre

tag: tissue

value: menopausal status:premenopausal

tag: pr status

tag: treatment group

value: TPA

value: No


title: E14Tg2a_ccnaTg2a_30m_rep3

tag: time point

tag: treatment


title: AI001_13_post

tag: specimen type

value: surgical specimen

tag: age at diagnois

tag: characteristics

tag: tumor type

value: placebo


title: Cer3::gfp; oma-1::gfp sRNA-seq

tag: genotype

value: Cer3(red52) oma-1(red44) IV

tag: fragment inserted in cer3

value: gfp

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs

tag: 5’ barcodes for srna or rna-seq

value: mixture of CTGG, ACTG, GAAG, TGCC


title: Cer3::meg-2 sRNA-seq

value: Cer3(red130) IV

value: mixture of AGCG, CGTC, GTTA, TATG


title: Cer3::gfp; Pmex-5::gfp sRNA-seq

value: Cer3 (red52) IV; Pmex-5::gfp (single copy MosSCI at ttTi5605) II


title: E14Tg2a_ccnaTg2a_20m_rep1

tag: strain

value: 20min post-release


title: AI001_13_pre

value: tumor containing tissue

value: core needle biospy

value: menopausal status:postmenopausal

value: IDC

tag: er status

value: high positive

tag: ki67 response


title: Sma Total -TEX

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
FastQ quality trimming using FastX (version 0.0.13)  and a cut-off value of 20
Fastq to fasta conversion using FastX  FastX (version 0.0.13)
PolyA removal and sitze filtering by READemption 0.2.6
Read alignment using READemption 0.2.6 and segemehl 0.1.7
Coverage calculation using READemption 0.2.6
Genome_build: HG326223.1
Supplementary_files_format_and_content: Wiggle files containing strand specific coverages normalized by total number of aligned read multiplied by 1 M (Counts per Million)

organism: Serratia marcescens

source_name: total bacterial cell lysate

growth_protocol: Growth in liquid LB media (10 g/l tryptone, 5 g/l yeast extract, 5 g/l NaCl) with good aeration at 30°C for to mid log phase (5 h)

extract_protocol:
RNA extracted by hot phenol method and treated with DNase
cDNA libraries for the Illumina sequencing platform were constructed by vertis Biotechnology AG, Germany, as described previously (Berezikov et al.,2006), without the RNA size-fractionation step prior to cDNA synthesis. Briefly, RNA samples were polyA-tailed using polyA polymerase. Then, the 5'-PPP termini were converted to 5'-P using tobacco acid pyrophosphatase (TAP) to allow for the ligation of the 5’ end RNA adapter. First-strand cDNA was synthesized by an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. In a PCR-based amplification step using a high fidelity DNA polymerase the cDNA concentration was increased to 20-30 ng/µl. A library-specific barcode for multiplex sequencing was part of a 3'-sequencing adapter.

value: Db10 wild type


title: Sma WT

description: RNA after CoIP

extract_protocol:
Strain SLM17 (encoding Hfq-FLAG) and wild type S. marcescens Db10 (negative control) were grown for 5 hours (mid log) in 500 ml LB medium. Cultures were normalised to an OD600 of 2.0 in a final volume of 50 ml (equivalent to 1x1011 cells) and collected by centrifugation. Cell pellets were washed in 700μl of lysis buffer (20mM Tris pH8.0, 1mM MgCl2, 150mM KCl, 1mM DTT), re-isolated and snap-frozen in liquid nitrogen. Thawed pellets were suspended in 800 μl of lysis buffer with 800 μl of quartz beads (diameter 0.1 mm) and cells broken by vortexing (30 s burst followed by 30 s chill on ice) for 10 min, then centrifuged to remove cells and debris. Supernatants were decanted to fresh tubes and 400 μl of Lysis buffer was added to the pellets, which were vortexed for a further 5 min and supernatant again recovered. The combined supernatants for each sample were centrifuged and transferred to fresh tubes to produce the final cleared cell lysates. Anti-FLAG M2 magnetic beads (Sigma, M8823) were prepared as per the manufacturer’s instructions. 50 μl of beads were added to 800 μl of cleared cell lysate, followed by incubation with agitation for four hours at 4oC. A magnetic stand was used to isolate the beads from solution. The supernatant was removed from each sample and beads were washed a further 3 times with 1 ml of TBS and supernatants pooled for each sample.  Protein/RNA complexes were recovered from the beads by re-suspension in 0.5 ml of lysis buffer followed by phenol:chloroform extraction. RNA was concentrated from the aqueous phase by ethanol precipitation, followed by DNase I treatment using the using the RNase free DNase set (Qiagen). Protein was recovered from the phenol phase by acetone precipitation and resuspended in 100 μl of Laemmli buffer. RNA was quantified using the NanoDrop and protein samples were analysed by SDS-PAGE and anti-FLAG immunoblot to confirm success of the Co-IP.
cDNA libraries for the Illumina sequencing platform were constructed by vertis Biotechnology AG, Germany, as described previously (Berezikov et al.,2006), without the RNA size-fractionation step prior to cDNA synthesis. Briefly, RNA samples were polyA-tailed using polyA polymerase. Then, the 5'-PPP termini were converted to 5'-P using tobacco acid pyrophosphatase (TAP) to allow for the ligation of the 5’ end RNA adapter. First-strand cDNA was synthesized by an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. In a PCR-based amplification step using a high fidelity DNA polymerase the cDNA concentration was increased to 20-30 ng/µl. A library-specific barcode for multiplex sequencing was part of a 3'-sequencing adapter.

tag: rip antibody

value: Monoclonal ANTI-FLAG^® M2 antibody produced in mouse conjugated to magnetic beads, Sigma, M8823, SL6M0090V


title: AI001_14_post

value: surgical specimen

value: menopausal status:premenopausal

value: TPA

value: No


title: Sma Total +TEX

value: TEX


title: CP3

city: Glasgow

first: Miguel

last: Pineda

address: 120 university avenue

country: United Kingdom

institute: University of Glasgow

data_processing:
FastQC was used for initial quality control checks on raw sequence data coming from high throughput sequencing pipelines.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCM38 mouse reference using Hisat2 v2.1.0.
Featurecounts version 1.4.6 was used to quantify reads counts.
Genome_build: GRCM38
Supplementary_files_format_and_content: tab-delimited text files include read counts values for each sample generated with feature counts.

source_name: mouse synovium

extract_protocol:
Mouse SFs were expanded and grown ex vivo were seeded in culture plates, RNA was extracted after treatment.
library preparation using polyA selection (TruSeq stranded mRNA kit)

value: synovium

tag: condition

value: CP treated (experimental)


title: Sma FLAG

description: RNA after CoIP

value: Db10 hfq-3FLAG


title: CP2

tag: tissue


title: Cer3::mex-5 sRNA-seq

value: Cer3(red147a) IV

tag: strain name

tag: rna-seq method

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs

value: mixture of AGCG, CGTC, GTTA, TATG


title: AI001_12_post

value: tumor containing tissue

tag: pr status

value: low positive

tag: treatment group


title: AI001_12_pre

tag: specimen type

value: core needle biospy

value: menopausal status:postmenopausal

value: IDC


title: E14Tg2a_ccnaTg2a_mit_rep3

tag: cell type

value: E14Tg2a cells expressing a CCNA-GFP cell cycle reporter

tag: time point

value: nocodazole-arrested and shake-off

tag: treatment

value: untreated


title: Cer3::him-8 sRNA-seq

tag: genotype

value: Cer3(red146) IV


title: CP1


title: E14Tg2a_ccnaTg2a_mit_rep2


title: AI001_11_post

value: surgical specimen

tag: age at diagnois

tag: characteristics

tag: tumor type

value: high positive

value: TPA

value: No


title: Cer3::oma-1(red20); oma-1 deletion (tm1396) sRNA-seq

tag: fragment inserted in cer3

tag: 5’ barcodes for srna or rna-seq

value: mixture of CTGG, ACTG, GAAG, TGCC, AGCG, CGTC, GTTA, TATG


title: Cer3::him-5 sRNA-seq

value: Cer3(red145) IV


title: E14Tg2a_ccnaTg2a_mit_rep1

tag: strain


title: E14Tg2a_ccnaTg2a_20m_rep2

value: 20min post-release


title: AI001_11_pre

tag: er status

tag: ki67 response


title: Cer3::zim-3 rep2 sRNA-seq

value: Cer3(red47) IV

tag: strain name

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs

value: mixture of AGCG, CGTC, GTTA, TATG,  CTGG, ACTG, GAAG, TGCC


title: NT3

tag: tissue

value: synovium

tag: condition

value: Negative control (control)


title: NT2


title: AI001_10_post

value: tumor containing tissue

value: menopausal status:postmenopausal

value: IDC

tag: pr status

tag: treatment group

value: placebo

value: Yes


title: NT1


title: Cer3::cah-4 sRNA-seq

value: Cer3(red127) IV

tag: rna-seq method

value: mixture of AGCG, CGTC, GTTA, TATG


title: Cer3::zim-3 rep1 sRNA-seq


title: AI001_10_pre

tag: specimen type

value: core needle biospy

value: high positive


title: AP_3

city: Rome

first: Daniela

last: Laricchiuta

state: Rome

address: Via del fosso di fiorano, 64

department: Preclinical neuroscience

country: Italy

institute: IRCCS Fondazione Santa Lucia

data_processing:
For the processing of raw data (format conversion and de-multiplexing), Bcl2Fastq 2.20 version of the Illumina pipeline was used.
GRCm38.p6 genome was used to map the reads, and transcript abundances were estimated using Salmon v1.2
To obtain gene-level count matrices the quantification data were imported using tximport.
From here on, we separated the samples in two tables (one for each comparison, namely BA vs AV and BA vs AP)  due to the following preprocessing strategies being dependent on the design matrix in use.
Differences in RNA composition between samples were corrected by the Trimmed mean of M-values (TMM) normalization (Robinson and Oshlack, 2010), and filtered for low counts based on a count per million reads (CPM) criteria.
Subsequently, ARSyNseq was used to remove the technical batch effect and NOISeqBIO was used to assess differential gene expression (q>0.95, equivalent to FDR-corrected P<0.05)
Genome_build: GRCm38.p6

source_name: Amygdala

extract_protocol:
Amygdalae were punched and manual and enzymatic dissociations were performed using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec, Bergisch Gladbach, Germany). Pyramidal neurons were then sorted by using the MoFlo Astrios EQ (Beckman Coulter, California, USA) into ice-cold lysis buffer (Reliaprep RNA Cell Miniprep System, Promega, Wisconsin, USA) and then stored at -80°C until RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina PE protocols.

tag: cell type

value: Pyramidal neurons

value: B6.Cg-Tg(Thy1-YFP)HJrs/J (Thy1-YFP)

tag: phenotype

value: approaching (AP)


title: AP_2


title: AI001_09_post

value: surgical specimen

tag: age at diagnois

value: menopausal status:premenopausal

value: negative

value: TPA


title: AI001_09_pre

tag: characteristics


title: AP_1


title: Cer3:ida-1 sRNA-seq

tag: genotype

value: Cer3(red125) IV

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs


title: Mutant 110

city: St. Louis

first: Jeannine

middle: M

last: Basta

state: MO

department: Internal Medicine/Nephrology

institute: Washington University in St. Louis

description: ribosomal RNA-depleted RNA

data_processing:
Basecalling was performed by Torrent Suite version 4 and 5 software using the default settings
Alignment to mus musculus genome mm10 sequence was performed using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20 nt
The total sequencing base pair coverage in all exons was summed for all annotated genes in each sample and normalized to total coverage using BEDtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics 11:e1005655.
Normalization factors were calculated by averaging the total exon coverage for all replicates and dividing this average by the total exon coverage for each individual sample. The total coverage for each gene in each replicate was then multiplied by these factors after adding an offset of 1 to each gene to preclude division by 0 in subsequent calculations.
The averages and p values of the coverage values for all genes in the individual groups were calculated using Microsoft Office Excel. The expression values for each gene are the normalized strand-specific total nucleotide coverage for each gene.
Genome_build: mus musculus mm10
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated expressed genes and statistical comparison of expression in wild type kidney to mutant kidney.

source_name: kidney

growth_protocol: In utero mouse kidney growth to E17.5

extract_protocol:
Total RNA was isolated from three E17.5 kidneys for each genotype using an RNeasy Mini Kit (Qiagen 74104) with on the column DNAse I treatment. Ribosomal RNA was depleted from 1 μg of total RNA using Ribominus Eukaryote System v2 (Life Technologies).
Construction of barcoded sequencing libraries was performed using the Ion Total RNA-seq v2 kits (Life Technologies) according to the manufacturer’s instructions.

treatment_protocol: Fresh kidney tissue harvested.

tag: brg1 allele

value: Six2Cre Brg1flx/flx

tag: developmental stage

value: kidney


title: Cer3::ttm-2 sRNA-seq

value: Cer3(red126) IV

tag: fragment inserted in cer3

tag: 5’ barcodes for srna or rna-seq


title: AI001_08_post

value: tumor containing tissue

value: menopausal status:postmenopausal

tag: tumor type

value: ILC

tag: er status

value: placebo

tag: ki67 response

value: No


title: Control 136

description: ribosomal RNA-depleted RNA

value: Brg1 flx/flx

tag: tissue


title: Mutant 131

description: ribosomal RNA-depleted RNA


title: mixed_sample (non-demultiplexed)

city: Boston

first: Vijayashree

last: Sathyanarayana Mysore

state: MA

address: 77 avenue Louis Pasteur

department: Pathology

institute: BWH-Harvard University

data_processing:
We mapped raw sequencing reads to a customized genome, the combination of Mus musculus (GRCm38 assembly), Rattus (Rnor6 assembly) and Red fluorescent protein gene (Genbank accession AF506027) protein, using CellRanger v3.1.0. We quantified gene expression, the number of unique molecular identifiers (UMIs), in all cells, that yielded a gene by cell expression matrix. We then performed all downstream analysis using custom scripts and Seurat v3.1.4 package in R v3.5.1. For quality control, we filtered out cells in which more than 20% of total UMIs were derived from mitochondrial genes. In order to remove potential doublets, we retained those cells which expressed between 1250 to 3000 unique genes. Due to sequence homology between mouse and rat genomes, we retained those cells having at-least 2000 UMIs mapped to mouse genome and not more than 100 UMIs mapped to rat genome. We then normalized each cell to 10,000 reads and log-transformed them. We identified top 2000 highly variable genes based on disspersion. Based on the highly variable genes, we scaled the data matrix to have mean 0 and variance 1. We normalized the expression matrix using L2 norm and calculated cosine distance. For dimensionality reduction, we performed prinicipal component analysis to obtain 50 principal components using Seurat's RunPCA function and used them to project cells onto UMAP space using umap package.
Cell by gene matrix was processed using Seurat v3.2. Genes epxressed in minimum 50 cells were retained. Cells having genes between 1250 and 3000 were retained.
Shared nearest neighbour graphs of cells was construcuted on UMAP embeddedings using Seurat v3.2. Louvian method with multilevel refinement was used with resolution 0.4 to define cell-clusters.
Cell-type markers were calculated with wilcox test withminimum log-fold threshold of log(2) using Seurat v3.2.
Genome_build: the combination of Mus musculus (GRCm38 assembly), Rattus (Rnor6 assembly) and Red fluorescent protein gene (Genbank accession AF506027) protein
Supplementary_files_format_and_content: Cell by gene matrix; Meta data of individual cells

organism:
Mus musculus
Rattus norvegicus

source_name: Bone marrow

extract_protocol: The population was pooled together and were loaded onto 10X.

treatment_protocol: Wild type and Ccr2 knock out monocytes were co-cultured with Rat fat pad endothelial cells or monocytes left on plastic were harvested and subjected to 10X. Sample populations were atined with Total-Seq A hashtag antibodies #1-#10.

value: Murine monocytes w/ or w/x Rat endothelial cells

value: Wild type or Ccr2 Knock out

tag: cell line

value: Rat Fat pad endothelial cells

tag: hashing


title: Cer3:unc-22 sRNA-seq

value: Cer3(red124) IV

tag: strain name

tag: rna-seq method

value: mixture of AGCG, CGTC, GTTA, TATG


title: AV_3

tag: cell type

value: Pyramidal neurons

tag: strain

value: B6.Cg-Tg(Thy1-YFP)HJrs/J (Thy1-YFP)

value: avoiding (AV)


title: Control 109

description: ribosomal RNA-depleted RNA


title: AI001_08_pre

tag: specimen type

value: core needle biospy

tag: age at diagnois

value: high positive

tag: pr status

tag: treatment group


title: Cer3::rpl-1 sRNA-seq

tag: genotype

value: Cer3(red123) IV

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs


title: AV_2

tag: phenotype


title: Control 106

description: ribosomal RNA-depleted RNA

tag: brg1 allele

tag: developmental stage

value: kidney


title: AI001_07_post

value: tumor containing tissue

value: surgical specimen

tag: characteristics

value: menopausal status:postmenopausal

tag: tumor type

value: ILC

tag: er status

value: TPA

value: Yes


title: AV_1


title: Cer3::gfp sRNA-seq

value: Cer3(red52) IV

tag: fragment inserted in cer3

value: gfp

tag: 5’ barcodes for srna or rna-seq


title: AI001_07_pre

tag: tissue

tag: ki67 response


title: Input rep 2

library_source: genomic

data_processing:
Basecalling was performed by Torrent Suite version 4 and 5 software using the default settings
Reads were aligned to the mm10 mouse genome using the TMAP aligner map4 algorithm without soft clipping (-g 3 option).
Genome at each base pair for Input and each ChIP sample was calculated using BEDtools genomecoveragebed (-d option).
Enrichment in ChIP sample coverage relative to Input coverage in sliding 250 bp windows with 50 bp steps was calculated using custom R scripts as described in Dorsett and Misulovin, Methods Mol Biol. 2017; 1515:125-139. Coverage in each window was normalized to total genome coverage prior to normalization to Input.
ChIP enrichment was averaged for all replicates to generate final processed data files.
Final sgr files were converted to BigWig files using the UCSC bedGraphToBigWig utility.
Genome_build: mus musculus mm10
Supplementary_files_format_and_content: BigWig files for each antibody (Brg1, Sall1, H3K4me1, H3K27ac, and RNAPol2S2) of enrichment over Input.

molecule: genomic DNA

growth_protocol: In utero mouse kidney growth to E16.5

extract_protocol:
E16.5 kidney chromatin was extracted from isolated nuclei and sheared to 100-1000bp. Primary antibody was incubated overnight for ChIP reactions. Crosslinks were reversed by adding NaCl and heating at 65 °C for 15 h, RNase A was added and incubated for 2 h at 37 °C, and Proteinase K added and incubated 2 h at 63 °C. DNA was isolated using the MinElute PCR Purification Kit (Qiagen 28004). 2 ng DNA was sheared to 100–300 bp.
Libraries were constructed using the Ion Plus Fragment Library Kit (Thermofisher Scientific 4471269) according to (Dorsett and Misulovin, Methods Mol Biol. 2017; 1515:125-139).

treatment_protocol: E16.5 kidneys were isolated in PBS + Ca and Mg on ice and crosslinked, washed, and homogenized in lysis buffer.

value: wildtype

tag: chip antibody

tag: chip antibody vendor/cagalog number


title: BA_3

tag: cell type

value: Pyramidal neurons

tag: strain

value: balancing (BA)


title: BA_2

value: B6.Cg-Tg(Thy1-YFP)HJrs/J (Thy1-YFP)


title: Mutant 111

description: ribosomal RNA-depleted RNA

value: Six2Cre Brg1flx/flx


title: RNAPol2Ser2

value: RNA Pol2 Ser2

value: Cell Signaling/ E1Z3G- 13499


title: Input rep 1


title: WT rep 2 sRNA-seq

tag: strain name

tag: rna-seq method

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs

value: mixture of AGCG, CGTC, GTTA, TATG


title: Cer3::oma-1(red20)  sRNA-seq

tag: genotype

value: Cer3(red20) IV

value: mixture of CTGG, ACTG, GAAG, TGCC


title: BA_1

tag: phenotype


title: AI001_04_pre

value: tumor containing tissue

tag: specimen type

value: core needle biospy

tag: age at diagnois

value: menopausal status:premenopausal

value: IDC

value: high positive

tag: pr status

value: low positive

tag: treatment group


title: AI001_05_post

value: surgical specimen

tag: characteristics

tag: tumor type

tag: er status

value: placebo

value: No


title: H3K4me1

tag: tissue

value: kidney

tag: developmental stage

value: wildtype

value: Abcam/ ab8895


title: H3K27ac

tag: chip antibody

value: Cell Signaling/ 8173


title: AI001_05_pre

tag: ki67 response


title: AI001_04_post

value: TPA

value: Yes


title: Mperf15ko_cut1h_R3

city: Zwijnaarde

first: Lieven

last: De Veylder

address: Technologiepark 71

country: Belgium

institute: VIB-UGent Center for Plant Systems Biology

data_processing:
Illumina CASAVA software used for basecalling.
Single-end reads were trimmed for adaptor sequences and aligned to the  MpTak1v5.1 exome using Salmon v0.7.2.
Transcript quantification was also performed by Salmon v0.7.2.
Genome_build: MpTak1v5.1 exome
Supplementary_files_format_and_content: tab-delimited text files generated from Salmon quantification, contain length of transcript in nucleotides, computed effective length, transcripts per million (TPM) and number of reads.

organism: Marchantia polymorpha

source_name: Mperf15ko 14-day-old thalli

growth_protocol: For each sample, approximately 40 Tak-1 or Mperf15ko gemmae were plated on half-strength Gamborg’s B5 medium with 1% plant agar. Every independent biological replicate contained 12 plants.

extract_protocol:
Thalli samples were isolated and frozen in liquid nitrogen. RNA was extracted using QIAGEN Rneasy Mini kit.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq® Stranded mRNA Sample Prep Kit.

treatment_protocol: 14-day-old Tak-1 or Mperf15ko thalli grown in 1/2 B5 1% agar were collected pre (control samples) or post blades wounded after 1 hours (wounded samples).

value: thalli

tag: strain/line

tag: treatment

value: 1h cut


title: Mperf15ko_cut1h_R2


title: Sall1 rep 3

tag: chip antibody vendor/cagalog number

value: Abcam / ab31526


title: RNA-seq AGM-EC-Cre  (Tet1/2/3 triple deleted EC Replicate #2)

city: New York

first: Meelad

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
For RNA-seq, Trim Galore (Version 0.3.7) was used to trim the low-quality bases and the adapters. Clean reads were mapped to the mouse genome mm10 using TopHat2 (Version 2.0.13) (Kim et al., 2013). HTseq (Version 0.11.0) (Anders et al., 2015) was used to calculated read counts mapped to genes. Cufflinks(Version 2.2.1) (Trapnell et al., 2012) was used to calculate Fragments Per Kilobase of transcript per Million (FPKMs). Differential expression was identified using R package DESeq2 (Love et al., 2014). Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files were generated using bamCoverage from deepTools (Version 3.1.0) (Ramirez et al., 2016).
For WGBS, Trim Galore (Version 0.3.7) was used to trim the first 4 unsteady bases from 5' of both strands. And low-quality reads were trimmed by default parameter “-q 20”. For adapter trimming, sequence “GATCGGAAGAGC” was used instead of the Illumina default adapters ('AGATCGGAAGAGC') according to the Kit instruction. Besides, the methylation conversion rate decreases after 50 bp according to the Kit property, so all sequences longer than 50bp were cropped to 50bp by Trimmomatic (Version 0.36). Then the filtered reads were mapped to mm10 genome by Bismark (0.18.1) (Krueger and Andrews, 2011) with option “--non_directional”. Duplicated sequences were removed by deduplicate_bismark. Methylpy (Version 1.4.0) (Schultz et al., 2015) was used to call methylation state for all Cs over the genome and convert the methylation level to bigwig files.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Endothelial cell

growth_protocol: Male Tet1/2/3F/F R26-CreER mice were crossed with female Tet1/2/3F/F +/+ mice and tamoxifen was intraperitoneally injected at E7.5.

extract_protocol:
RNA and DNA were extracted from EC or HSPC at the same time using QIAGEN All Prep DNA/RNA Micro Kit (QIAGEN, cat. no. 80284).
RNA-seq libraries were prepared using the Nextera XT Index Kit (15055293, illumina).  RNA-seq libraries were then subjected to 75 bp paired-end sequencing (Illumina NextSeq 500 platform) at the Einstein Epigenomics core. WGBS library construction was done using Pico Methyl-Seq TM Library Prep Kit (ZYMO research, cat. no.D5455 for IIIumina-based Sequencing). Then the libraries  were sequenced with Illumina HiSeq 4000. 150 bp paired-end reads were sequenced.

tag: cell type

value: Endothelial cell

tag: strain

value: mixed 129/C57BL/6

tag: isolation tissue

value: E11.5 embryo AGM

tag: cell markers

value: Tet1/2/3F/F +/Rosa26-CreER

value: Tamoxifen at E7.5


title: AI001_02_post

value: tumor containing tissue

tag: specimen type

value: surgical specimen

tag: age at diagnois

value: menopausal status:postmenopausal

value: IDC

value: high positive

value: negative


title: RNA-seq AGM-EC-Cre  (Tet1/2/3 triple deleted EC Replicate #3)

tag: genotype


title: Mperf15ko_cut1h_R1


title: AI001_02_pre

value: core needle biospy

tag: characteristics

tag: pr status

tag: treatment group

value: placebo


title: Sall1 rep 2

tag: tissue

value: kidney

value: wildtype


title: RNA-seq AGM-EC-Cre (Tet1/2/3 triple deleted EC Replicate #1)


title: Tak-1_cut1h_R3

source_name: Tak-1 14-day-old thalli

value: thalli

value: 1h cut


title: RNA-seq AGM-EC-WT (wild type EC Replicate #3)

value: Endothelial cell


title: Sall1 rep 1

tag: developmental stage

value: Abcam / ab31526


title: Tak-1_cut1h_R2


title: WT rep 1 sRNA-seq

tag: fragment inserted in cer3

tag: strain name

tag: rna-seq method

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs

tag: 5’ barcodes for srna or rna-seq

value: mixture of AGCG, CGTC, GTTA, TATG


title: RNA-seq AGM-EC-WT (wild type EC Replicate #2)

value: mixed 129/C57BL/6

value: E11.5 embryo AGM

tag: treatment

value: Tamoxifen at E7.5


title: Brg1 rep 2

tag: chip antibody

tag: chip antibody vendor/cagalog number

value: Abcam/ ab110641


title: Tak-1_cut1h_R1

tag: strain/line


title: AI001_01_pre

value: tumor containing tissue

value: menopausal status:postmenopausal

tag: tumor type

value: IDC

tag: er status

tag: ki67 response

value: No


title: WGBS AGM-HSPC-Cre (Tet1/2/3 triple deleted HSPC)

source_name: Hematopoietic stem and progenitor cell

tag: cell type

value: Hematopoietic stem and progenitor cell

tag: strain

tag: isolation tissue

tag: cell markers

tag: genotype

value: Tet1/2/3F/F +/Rosa26-CreER


title: RNA-seq AGM-EC-WT (wild type EC Replicate #1)


title: Brg1 rep 1

tag: tissue

value: kidney

tag: developmental stage

value: wildtype


title: Mperf15ko_control_R3

value: thalli

value: control


title: WGBS AGM-HSPC-WT (wild type HSPC)


title: Mperf15ko_control_R2


title: Taro_apex_leaf_4

city: Urbana

first: Dessiree

middle: Patricia

last: Zerpa Catanho

state: Illinois

address: 1201 W. Gregory Dr, 279 ERML

institute: University of Illinois at Urbana-Champaign

description: Apex leaf from replicate 4

data_processing:
FastQC (Version v.0.11.9) for raw read quality evaluation
Trimmomatic-0.36 (Version 3, 29 June 2007) for adapters and low-quality reads removal (ILLUMINACLIP:Adapters.fa:2:30:10 HEADCROP:10 LEADING:28 TRAILING:28 MINLEN:30)
Hisat2 (Version 2.0.5) for alignment
SAM files to BAM files converted with Samtools (Tools for alignments in the SAM format) Version: 1.9 (using htslib 1.9)
Aligned reads were counted using featureCounts (Version 2.0.0) and summarized per gene ID
Genome_build: Taro_Lachesis_assembly_Chr.fa (obtained from Yin et al., 2020)
Supplementary_files_format_and_content: Processed data files (Text document) contain raw read counts (not normalized) for each "Geneid". Processed FASTA file contains the sequences for each "Geneid" identifier used in the processed data files (Text document)

organism: Colocasia esculenta

source_name: Apex leaf

growth_protocol: The upper corm and leaves of ‘Bin Liang’ taro were harvested, the leaves and petioles were removed, and the apical meristems with the very young leaves and leaf primordia were excised. The tissue was frozen in liquid nitrogen and ground into powder. Total RNA was extracted with TRIzol (Invitrogen, Carlsbad, California), treated with DNAse, and purified with the TruSeq stranded mRNA Sample Prep Kit, followed by standard Illumina single-end sequencing. Illumina recommended protocols for sample purification, library preparation of cDNAs, fragmentation, adapter ligation, PCR amplification and size selection were used. Sequencing was performed at the Roy J. Carver Biotechnology Center at the University of Illinois Urbana-Champaign on a HiSeq2000 platform and using a TruSeq SBS sequencing kit (version 3).

extract_protocol:
TRIzol Reagent (Ambion USA)
TruSeq® Stranded mRNA LT kit (Illumina USA) was follow to build the libraries

value: Apex leaf

tag: cultivar

value: Bing Liang


title: RNA-seq AGM-HSPC-Cre (Tet1/2/3 triple deleted HSPC Replicate #2)


title: Taro_apex_leaf_3

description: Apex leaf from replicate 3


title: Mperf15ko_control_R1


title: RNA-seq AGM-HSPC-Cre (Tet1/2/3 triple deleted HSPC Replicate #1)


title: WGBS AGM-EC-WT (wild type EC)

value: Endothelial cell


title: Taro_apex_leaf_2

description: Apex leaf from replicate 2


title: Tak-1_control_R3


title: AI001_01_post

tag: specimen type

value: surgical specimen

tag: age at diagnois

tag: characteristics

value: high positive

tag: pr status

tag: treatment group

value: placebo


title: Tak-1_control_R2

tag: strain/line

tag: treatment


title: RNA-seq AGM-HSPC-WT (wild type HSPC Replicate #2)

value: mixed 129/C57BL/6

value: E11.5 embryo AGM

value: Tamoxifen at E7.5


title: SW480 5-Fu resistant Rep2

city: Duarte

first: Yate-Ching

last: Yuan

state: CA

address: 1500 East Duarte

institute: City of Hope

data_processing:
Base calling was performed with the Illumina Real-Time Analysis software (RTA3, v3.4.4) and the FASTQ files were generated with bcl2fastq (version 2.20.0.422).
Partek Flow v10.0.22.0121 used to process bulk RNA-sequencing data.
Multiplexed sequencing raw reads were trimmed to remove low-quality reads from both ends based on Phred quality scores lower than 35 before alignment.
Sequence reads mapped to the human genome GRCh38 by STAR 2.7.8a (Dobin et al., 2013) with default parameters.
After alignment the final BAM files were quantified using Partek E/M (Xing et al., 2016) algorithm and annotated using Ensembl Transcripts release 102 to generate gene counts.
The gene counts were normalized and differential gene analyzed by DESeq2 (Love et al., 2014) between 5FUR resistant and parental CRC cells.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Raw counts

source_name: human colon cancer cells SW480 5-FU

growth_protocol: DMEM with 10% Fetal bovine serum (FBS).

extract_protocol:
Total RNA extraction was performed by using QIAZOL reagent.
SureSelect XT HS2 mRNA Library Preparation Kit.

treatment_protocol: 5FU resistant (5FUR) cell lines (HCT116 5FUR and SW480 5FUR) were established by continuous culturing of cells with increasing dose of 5FU for more than 9 months.

tag: cell line

value: Colorectal cancer cells

tag: phenotype

value: 5-FU resistant


title: SG3

city: tianjin

first: xiao

last: shan

address: No. 22, Meteorological Station Road, Heping District

institute: tian jin medical university

data_processing:
Basecalls performed using MGISEQ-2000.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to GCF_000001635.26_GRCm38.p6 whole genome using BWA.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample ...

source_name: bone marrow derived macrophage

extract_protocol:
BMDMs were washed with cold PBS for twice, then collected to extract total RNA using Trizol reagent.
RNA libraries were prepared for sequencing using  oligo -dT beads

treatment_protocol: The control group used normal medium, NSG group compared with the control group without serine, glycine

value: bone marrow derived macrophage (BMDM)

value: untreated


title: Tak-1_control_R1


title: SG4


title: RNA-seq AGM-HSPC-WT (wild type HSPC Replicate #1)

tag: cell type

value: Hematopoietic stem and progenitor cell


title: RNA-seq AGM-HSPC-Cre (Tet1/2/3 triple deleted HSPC Replicate #3)

tag: strain

value: Tet1/2/3F/F +/Rosa26-CreER


title: SG2


title: NK cells - EP3F/F

city: Tianjin

first: Yujun

last: Shen

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

data_processing:
The raw sequencing data of gene expression were aligned with the GRCm39 mouse reference genome using the STAR algorithm in CellRanger software (version 3.0.0). Cells with genes with expression values outside the limit of mean value ± 2 fold of standard deviation and > 10% mitochondrial gene mapped reads were filtered from downstream analyses. Library size normalization was performed in Seurat on the filtered matrix to obtain the normalized count.
The top variable genes across single cells were identified using a previously described method . The most variable genes were selected using the FindVariableGenes function in Seurat .
Graph-based clustering was performed to cluster cells according to their gene expression profiles using the FindClusters function in Seurat.
We used the FindAllMarkers function in Seurat to identify the marker genes of each cluster.
A total of 289 differentially expressed genes (DEGs) were identified using the FindMarkers function (test.use = MAST) in Seurat(Table S3). A P value < 0.05, and |log2foldchange| > 0.58 was set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of upregulated genes were performed by Metascape and Database for Annotation, Visualization, and Integrated Discovery (DAVID) Bioinformatics Resources 6.8 . Gene set enrichment analysis (GSEA) was used to complete GO and KEGG term enrichment analysis with the Molecular Signatures Database (MSigDB) C5 GO gene sets and C2 KEGG gene sets (Version 7.2)
The single-cell regulatory network inference and clustering (SCENIC) analysis was run using the motifs database for RcisTarget and GRNboost (SCENIC version 1.1.2.2, which corresponds to RcisTarget 1.2.1 and AUCell 1.4.1) with the default parameters
Genome_build: GRCm39 mouse reference genome
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: spleen

extract_protocol:
Flow sorted splenic CD27+CD11b+ NK cells from two mice from each group (EP3F/F and NKp46CreEP3F/F) were pooled for droplet-based single-cell RNA-seq (10x Genomics platform)
Library preparation was performed using the Single Cell 3 v2 kit (10X Genomics) according to the manufacturer’s protocol
single-cell RNA-seq

value: spleen

value: splenic CD27+CD11b+ NK cells


title: NSI2

city: harbin

first: jingxue

last: sun

state: heilongjiang

address: 246 xuefu road

institute: The Second Affiliated Hospital of Harbin Medical University

data_processing:
The fastx toolkit software was used（ http://hannonlab.cshl.edu/fastx_toolkit/ ）to performing quality filtering
BLAST comparison(http://blast.ncbi.nlm.nih.gov/)  quality controled sequences with mature miRNA sequences of corresponding species in miRBase database(http://www.mirbase.org/).
All sequences for each sample and unique sequences after dereplication, respectively, were compared with the rfam database（ http://rfam.xfam.org/ ). Statistical annotation to different types of small RNAs
Compared small RNA sequences from each sample with miRNA precursors and maturases from their corresponding species in the miRBase database. And aligned the known miRNAs and their secondary structures in close relatives by combining the sequences of their cognate miRNAs from each species, and counted the expression of the known miRNAs in each sample.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include miRNA expression levels for each sample

source_name: exosomes

extract_protocol:
Plasma exosomes were extracted, and RNA was harvested using Trizol reagent. Illumina TruSeq smallRNA sample Preparation kit  was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tisssue

value: Plasma derived exosomes

tag: disease

value: Graves ophthalpathy

tag: disease stage

value: moderate-to-severe and active

tag: treament

value: intravenous glucocorticoid therapy

tag: glucocorticoid sensitivity

value: insensitive

tag: age

tag: molecule subtype

value: microRNA


title: NSI3


title: WGBS AGM-EC-Cre (Tet1/2/3 triple deleted EC)

value: Endothelial cell

value: mixed 129/C57BL/6

tag: isolation tissue

tag: cell markers

tag: genotype


title: NSG3

tag: tissue

value: serine deficiency


title: RNA-seq AGM-HSPC-WT (wild type HSPC Replicate #3)

value: E11.5 embryo AGM

value: Tamoxifen at E7.5


title: Taro_apex_leaf_1

description: Apex leaf from replicate 1

value: Apex leaf

tag: cultivar

value: Bing Liang


title: NSI1


title: HCT116 5-Fu resistant Rep1

source_name: human colon cancer cells HCT116 5-FU

value: Colorectal cancer cells

value: 5-FU resistant


title: SI3

value: sensitive


title: Vehicle_rep 1

first: Abderhman

last: Abuhashem

state: NY

address: Rockefeller Research Labs, 430 E 67th St

department: Developmental Biology Program

institute: Sloan-Kettering Institute for Cancer Research

data_processing:
bcl2fastq used to generate FASTQ files
Reads are aligned to mm10 using rnaStar aligner (Dobin 2012). Two pass mapping method is used (Engstrom 2013)
The output SAM file was processed using PICARD tools to produce BAMs
Generate expression count matrix using Htseq
Raw count matrix analyzed using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: Scaled counts/gene for each sample and log2 fold change of treated/vehicle. Both are DEseq output matrixes

molecule: polyA RNA

source_name: Three 2-cell embryos

growth_protocol: Culture in KSOM at 37C and 5% CO2

extract_protocol:
SMART-seq v4 Ultra Low Input kit (Clonetech)
nonstranded, generated using the SMART-seq v4 Ultra Low Input kit

treatment_protocol: DMSO or dTAG-13 mixed with the culture medium

tag: treatment

value: Outbred/ICR

value: Nelfb dTAG/dTAG


title: Vehicle_rep 2


title: dTAG-13 rep 2

value: 500nM dTAG-13


title: NSG2

value: bone marrow derived macrophage (BMDM)


title: SI2

value: Plasma derived exosomes

value: Graves ophthalpathy

value: moderate-to-severe and active

value: intravenous glucocorticoid therapy


title: HCT116 Parental Rep2

source_name: human colon cancer cells HCT116

tag: cell line

value: Parental


title: dTAG-13_rep 1


title: NSG1

value: serine deficiency


title: SI1

value: microRNA


title: SW480 5-Fu resistant Rep1

tag: phenotype


title: SW480 Parental Rep2

source_name: human colon cancer cells SW480

tag: cell type


title: NK cells - NKp46CreEP3F/F

tag: strain

value: spleen

value: splenic CD27+CD11b+ NK cells


title: SG1

value: untreated


title: NSG4


title: SW480 Parental Rep1

value: Colorectal cancer cells


title: HCT116 5-Fu resistant Rep2

value: 5-FU resistant


title: myc-h3x2-wt-HU70-x35

status: Public on Feb 18 2022

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64 with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-200 bp)
genome coverage with bedtools (-pc -d)
Genome_build: GCA_000146045.2, for samples ending with X39, S43, S44 and S47c ombined S. cerevisiae (GCA_000146045.2) and C. glabrata (GCF_000002545.3_ASM254v2) genome
Supplementary_files_format_and_content: *.out.txt file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (CHr 1-16+mitochondria); or 24,495,413 bases in the combined genome (first S.cerevisae then C. glabrata). The chromosomes are included sequentially in the outfile. If the C. glabrata genome was included it also goes sequentially after the S.cerevisae genome.

organism: Saccharomyces cerevisiae

source_name: Sensor-carrying cells

growth_protocol: yeast cells were grown to saturation overnight in YPD and then dilute in fresh,pre-warmed YPD and incubated for at least 6 hours at 30deg before G1 arrest (alpha factor). After 3 hours in alpha factor, cells were released into HU and samples for ChIP taken in 10-20 minute intervals. The number after 'HU' in the sample title indicates the minutes after release into HU.

extract_protocol:
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Cell pellets (each from 50 ml of cultures at OD600 0.4, 20 ODs total) were thawed on ice and washed in 10 ml 1M sorbitol. After complete liquid removal, pellets were resuspended in 600 ul RIPA buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail) and transferred to chilled LoBind Eppendorf microcentrifuge tubes containing ~500 ul of 0.5 mm zirconium oxide beads (Next Advance, ZrOB05). Cells were processed for 3 cycles in a Bullet Blender 24 (Next Advance) at level 8 for 1 min, with 1 minute on ice between cycles. Debris and lysate were transferred by piercing a hole in the bottom of the tube, placing a clean chilled tube under and centrifuging at 600xg for 5 seconds at 4C. The upper tube with the Zirconium beads was discarded and the lysate was hard spun at 17,000xg for 10 minutes at 4C. The supernatant containing cleaved solubilized 8xmyc tags was discarded, and the pellet was thoroughly resuspended in 100 ul NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail), and SLIM-ChIP protocol was carried continued as in Gutin et al.  SLIM-Chip, as per Gutin et al, Cell Reports 2019
SLIM-Chip, as per Gutin et al, Cell Reports 2019

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

tag: sensor

tag: antibody

value: myc

tag: growth condition

value: wt


title: myc-h3x2-wt-HU130-x35


title: myc-h3x2-wt-HU90-x35


title: myc-h3x2-wt-HU180-x35


title: myc-h3x2-wt-HU110-x35


title: myc-h3x2-wt-HU60-x35


title: myc-h3x2-wt-HU150-x35


title: myc-h3x2-wt-HU30-x35


title: myc-h3x2b-wt-alpha-x35

value: alpha


title: myc-h3x2a-wt-alpha-x35


title: myc-h3x2-wt-async-x35

value: async


title: myc-h3x2-wt-HU40-x35


title: myc-h3x2-wt-HU15-x35


title: myc-h3x2-rtt-HU180-x36

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, rtt109::NAT

value: rtt


title: myc-h3x2-rtt-HU130-x36


title: myc-h3x2-rtt-HU110-x36


title: myc-h3x2-rtt-HU150-x36


title: HCT116 Parental Rep1


title: myc-h3x2-rtt-HU90-x36


title: myc-h3x2-rtt-HU50-x36


title: myc-h3x2-rtt-HU70-x36


title: myc-h3x2-rtt-HU40-x36


title: myc-h3x2-rtt-HU30-x36


title: myc-h3x2-rtt-HU15-x36


title: myc-h3x2-rtt-alpha-x36


title: myc-h3x2-rtt-async-x36


title: myc-h3x2-rtt-HU180-x35


title: myc-h3x2-wt-HU50-x35


title: myc-h3x2-rtt-HU70-x35


title: myc-h3x2-rtt-HU130-x35


title: myc-h3x2-rtt-HU150-x35


title: myc-h3x2-rtt-HU60-x35


title: myc-h3x2-rtt-HU110-x35


title: myc-h3x2b-rtt-async-x35


title: myc-h3x2a-rtt-async-x35


title: myc-h3x2b-rtt-alpha-x35


title: myc-h3x2-rtt-HU30-x35


title: myc-h3x2-rtt-HU15-x35


title: ha-h3x2-wt-HU180-x35

value: ha


title: myc-h3x2-rtt-HU50-x35


title: ha-h3x2-wt-HU110-x35


title: ha-h3x2-wt-HU130-x35


title: ha-h3x2-wt-HU90-x35


title: ha-h3x2-wt-HU70-x35


title: ha-h3x2-wt-HU50-x35


title: ha-h3x2-wt-HU60-x35


title: ha-h3x2-wt-HU40-x35


title: myc-h3x2-rtt-HU40-x35


title: ha-h3x2-wt-HU150-x35


title: ha-h3x2b-wt-alpha-x35


title: ha-h3x2-wt-HU30-x35


title: ha-h3x2-wt-HU15-x35


title: ha-h3x2a-wt-alpha-x35


title: myc-h3x2-rtt-HU60-x36


title: ha-h3x2-wt-async-x35


title: myc-h3x2a-rtt-alpha-x35


title: ha-h3x2-rtt-HU150-x36


title: ha-h3x2-rtt-HU90-x36


title: ha-h3x2-rtt-HU180-x36


title: ha-h3x2-rtt-HU70-x36


title: ha-h3x2-rtt-HU130-x36


title: ha-h3x2-rtt-HU110-x36


title: myc-h3x2-rtt-HU90-x35


title: ha-h3x2-rtt-HU30-x36


title: ha-h3x2-rtt-HU60-x36


title: ha-h3x2-rtt-HU15-x36


title: ha-h3x2-rtt-HU50-x36


title: ha-h3x2-rtt-async-x36


title: ha-h3x2-rtt-HU180-x35


title: ha-h3x2-rtt-alpha-x36


title: ha-h3x2-rtt-HU150-x35


title: ha-h3x2-rtt-HU110-x35


title: ha-h3x2-rtt-HU50-x35


title: ha-h3x2-rtt-HU130-x35


title: ha-h3x2-rtt-HU60-x35


title: ha-h3x2-rtt-HU90-x35


title: ha-h3x2-rtt-HU30-x35


title: ha-h3x2a-rtt-alpha-x35


title: ha-h3x2b-rtt-alpha-x35


title: ha-h3x2-rtt-HU40-x35


title: ha-h3x2b-rtt-async-x35


title: ha-h3x2-rtt-HU70-x35


title: ha-h3x2a-rtt-async-x35


title: ha-h3x2-rtt-HU15-x35


title: ha-h3x2-rtt-HU40-x36


title: Vibrio vulnificus RtxA1 deficient mutant strain infection_Blood_12hpi_rep1 [CKS_61]

type: RNA

city: Burjassot

first: Carmen

last: Amaro

state: Valencia

address: Dr. Moliner, 50

department: Microbiology and Ecology

country: Spain

institute: University of Valencia

description: Gene expression after 12hr in V.vulnificus RtxA1 deficient mutant strain (strain R99) infected peripheral blood.

hyb_protocol: 1.65 μg of cDNA-labbled of each sample was used for the hybridization to custom european eel array during 17h at 65ºC following the instructions of Agilent’s GE Hybridization Kit.

scan_protocol: Microarrays slides were scanned with Agilent Technologies Scanner model G2505B. Spot intensities and other quality control features were extracted with Agilent’s Feature Extraction software version 10.4.0.0. Txt files generated were imported into the Gene GeneSpring software GX 12.5.

data_processing: Percentile shift normalization was made to adjust all spot intensities in an array. This normalization takes each column in an experiment independently, and computes the median expression values for this array, across all spots. It then subtracts this value from the expression value of each entity (Bolstad et al, 2003). After Percentile normalization, all data were filtered by comparison of the standard deviation expression among groups (filter by expression). The entities that had values lesser or greater than the standard deviation value were retained. This filter procedure allowed selected genes that have outlier samples, and filter out genes that have a low variation in expression values across all samples.

organism: Anguilla anguilla

source_name: Peripheral Blood,V.vulnificus RtxA1 deficient mutant strain infected, 12hpi, rep1

label_protocol: RNA samples were labelled with a single dye, Cy3. Denatured samples of RNA were reversed transcribed and indirectly labelled with Cy3. RNA labelling were performed according to agilent Quick Amp Labelling kit instructions.

growth_protocol: Adult European eels (Anguilla anguilla) of around 100 g of body weight were purchased from a local eel-farm that does not vaccinate against V. vulnificus. Eel maintenance and all the experiments described above were performed at 28°C in 180-liter tanks containing either 60 (infection experiments) or 120 L (the rest of experiments and animal maintenance) of saline water (SW, 1.5% NaCl, pH 7) with a system of aeration and filtration in the facilities of the Central Service for Experimental Research (SCSIE) of the University of Valencia (Spain).

extract_protocol: Total RNA (from eels B, RBCs, and WBCs obtained at 0, 3, and 12 hpi) was extracted with NucleoZOL (Macherey-Nagel) following the manufacturer’s instructions. Possible contaminating DNA was eliminated using TURBOTM DNase (Ambion) and then RNA was cleaned with RNA Cleanup and Concentration Micro Kit RNA (Thermo Scientific) according to the manufacturer’s instructions.

treatment_protocol: For transcriptomic experiments, eels of 100 g were distributed into two groups, the tested (n= 24 individuals) and the control group (n= 6 individuals). Individuals were then immersed either in an infective bath containing 2x106 CFU of the strain R99 (the previously estimated LD50) (tested group) or in sterilized SW (control group). After 1 h of immersion, fish were transferred separately into new tanks and kept under constant conditions until sampling.

value: Whole blood

value: Peripheral Blood


title: Vibrio vulnificus WT strain infection_WBC_3hpi_rep2 [CKS_50]

description: Gene expression after 3hr in V.vulnificus WT strain (strain R99) infected isolated white blood cells.

source_name: Isolated white blood cells,V.vulnificus WT strain infected, 3hpi, rep2

value: Isolated white blood cells

value: V.vulnificus WT strain infected, 3hpi


title: Vibrio vulnificus RtxA1 deficient mutant strain infection_Blood_0hpi_rep1 [CKS_55]

description: Gene expression after 0hr in V.vulnificus RtxA1 deficient mutant strain (strain R99) infected peripheral blood.

source_name: Peripheral Blood,V.vulnificus RtxA1 deficient mutant strain infected, 0hpi, rep1


title: Vibrio vulnificus RtxA1 deficient mutant strain infection_Blood_3hpi_rep3 [CKS_60]

description: Gene expression after 3hr in V.vulnificus RtxA1 deficient mutant strain (strain R99) infected peripheral blood.

source_name: Peripheral Blood,V.vulnificus RtxA1 deficient mutant strain infected, 3hpi, rep3


title: Vibrio vulnificus RtxA1 deficient mutant strain infection_Blood_0hpi_rep2 [CKS_56]

source_name: Peripheral Blood,V.vulnificus RtxA1 deficient mutant strain infected, 0hpi, rep2


title: Vibrio vulnificus WT strain infection_WBC_0hpi_rep1 [CKS_46]

description: Gene expression after 0hr in V.vulnificus WT strain (strain R99) infected isolated white blood cells.

source_name: Isolated white blood cells,V.vulnificus WT strain infected, 0hpi, rep1

value: V.vulnificus WT strain infected, 0hpi


title: Vibrio vulnificus RtxA1 deficient mutant strain infection_Blood_0hpi_rep3 [CKS_57]

source_name: Peripheral Blood,V.vulnificus RtxA1 deficient mutant strain infected, 0hpi, rep3


title: Vibrio vulnificus WT strain infection_WBC_0hpi_rep3 [CKS_48]

source_name: Isolated white blood cells,V.vulnificus WT strain infected, 0hpi, rep3


title: Vibrio vulnificus WT strain infection_WBC_12hpi_rep3 [CKS_54]

description: Gene expression after 12hr in V.vulnificus WT strain (strain R99) infected isolated white blood cells.

source_name: Isolated white blood cells,V.vulnificus WT strain infected, 12hpi, rep3

value: V.vulnificus WT strain infected, 12hpi


title: Vibrio vulnificus WT strain infection_Blood_12hpi_rep3 [CKS_36]

description: Gene expression after 12hr in V.vulnificus WT strain (strain R99) infected peripheral blood.

source_name: Peripheral Blood,V.vulnificus WT strain infected, 12hpi, rep3


title: Vibrio vulnificus WT strain infection_RBC_3hpi_rep2 [CKS_41]

description: Gene expression after 3hr in V.vulnificus WT strain (strain R99) infected isolated red blood cells.

source_name: Isolated red blood cells,V.vulnificus WT strain infected, 3hpi, rep2

value: Isolated red blood cells


title: Vibrio vulnificus RtxA1 deficient mutant strain infection_Blood_12hpi_rep3 [CKS_63]

source_name: Peripheral Blood,V.vulnificus RtxA1 deficient mutant strain infected, 12hpi, rep3


title: Vibrio vulnificus RtxA1 deficient mutant strain infection_Blood_12hpi_rep2 [CKS_62]

source_name: Peripheral Blood,V.vulnificus RtxA1 deficient mutant strain infected, 12hpi, rep2


title: Vibrio vulnificus WT strain infection_WBC_12hpi_rep1 [CKS_52]

source_name: Isolated white blood cells,V.vulnificus WT strain infected, 12hpi, rep1


title: Vibrio vulnificus WT strain infection_WBC_0hpi_rep2 [CKS_47]

source_name: Isolated white blood cells,V.vulnificus WT strain infected, 0hpi, rep2


title: Vibrio vulnificus WT strain infection_WBC_3hpi_rep3 [CKS_51]

source_name: Isolated white blood cells,V.vulnificus WT strain infected, 3hpi, rep3


title: Vibrio vulnificus WT strain infection_RBC_0hpi_rep1 [CKS_37]

description: Gene expression after 0hr in V.vulnificus WT strain (strain R99) infected isolated red blood cells.

source_name: Isolated red blood cells,V.vulnificus WT strain infected, 0hpi, rep1


title: Vibrio vulnificus WT strain infection_Blood_12hpi_rep2 [CKS_35]

source_name: Peripheral Blood,V.vulnificus WT strain infected, 12hpi, rep2


title: Vibrio vulnificus RtxA1 deficient mutant strain infection_Blood_3hpi_rep2 [CKS_59]

source_name: Peripheral Blood,V.vulnificus RtxA1 deficient mutant strain infected, 3hpi, rep2


title: Vibrio vulnificus WT strain infection_RBC_3hpi_rep1 [CKS_40]

source_name: Isolated red blood cells,V.vulnificus WT strain infected, 3hpi, rep1


title: Vibrio vulnificus WT strain infection_RBC_12hpi_rep1 [CKS_43]

description: Gene expression after 12hr in V.vulnificus WT strain (strain R99) infected isolated red blood cells.

source_name: Isolated red blood cells,V.vulnificus WT strain infected, 12hpi, rep1


title: Vibrio vulnificus RtxA1 deficient mutant strain infection_Blood_3hpi_rep1 [CKS_58]

source_name: Peripheral Blood,V.vulnificus RtxA1 deficient mutant strain infected, 3hpi, rep1


title: Vibrio vulnificus WT strain infection_WBC_12hpi_rep2 [CKS_53]

source_name: Isolated white blood cells,V.vulnificus WT strain infected, 12hpi, rep2


title: Vibrio vulnificus WT strain infection_RBC_12hpi_rep3 [CKS_45]

source_name: Isolated red blood cells,V.vulnificus WT strain infected, 12hpi, rep3


title: Vibrio vulnificus WT strain infection_Blood_12hpi_rep1 [CKS_34]

source_name: Peripheral Blood,V.vulnificus WT strain infected, 12hpi, rep1


title: Vibrio vulnificus WT strain infection_WBC_3hpi_rep1 [CKS_49]

source_name: Isolated white blood cells,V.vulnificus WT strain infected, 3hpi, rep1


title: Vibrio vulnificus WT strain infection_RBC_3hpi_rep3 [CKS_42]

source_name: Isolated red blood cells,V.vulnificus WT strain infected, 3hpi, rep3


title: Vibrio vulnificus WT strain infection_RBC_0hpi_rep2 [CKS_38]

source_name: Isolated red blood cells,V.vulnificus WT strain infected, 0hpi, rep2


title: Vibrio vulnificus WT strain infection_RBC_12hpi_rep2 [CKS_44]

source_name: Isolated red blood cells,V.vulnificus WT strain infected, 12hpi, rep2


title: Vibrio vulnificus WT strain infection_Blood_3hpi_rep2 [CKS_32]

description: Gene expression after 3hr in V.vulnificus WT strain (strain R99) infected peripheral blood.

source_name: Peripheral Blood,V.vulnificus WT strain infected, 3hpi, rep2


title: Vibrio vulnificus WT strain infection_Blood_0hpi_rep3 [CKS_30]

description: Gene expression after 0hr in V.vulnificus WT strain (strain R99) infected peripheral blood.

source_name: Peripheral Blood,V.vulnificus WT strain infected, 0hpi, rep3


title: Control_WBC_12hpi_rep3 [CKS_27]

description: Gene expression after 12hr in non infected isolated white blood cells.

source_name: Isolated white blood cells,non-infected, 12hpi, rep3

value: non-infected, 12hpi


title: Control_WBC_3hpi_rep1 [CKS_22]

description: Gene expression after 3hr in non infected isolated white blood cells.

source_name: Isolated white blood cells,non-infected, 3hpi, rep1

value: non-infected, 3hpi


title: Control_WBC_12hpi_rep2 [CKS_26]

source_name: Isolated white blood cells,non-infected, 12hpi, rep2


title: Control_RBC_12hpi_rep3 [CKS_18]

description: Gene expression after 12hr in non infected isolated red blood cells.

source_name: Isolated red blood cells,non-infected, 12hpi, rep3


title: Vibrio vulnificus WT strain infection_Blood_3hpi_rep1 [CKS_31]

source_name: Peripheral Blood,V.vulnificus WT strain infected, 3hpi, rep1


title: Control_WBC_0hpi_rep1 [CKS_19]

description: Gene expression after 0hr in non infected isolated white blood cells.

source_name: Isolated white blood cells,non-infected, 0hpi, rep1

value: non-infected, 0hpi


title: Vibrio vulnificus WT strain infection_Blood_0hpi_rep1 [CKS_28]

source_name: Peripheral Blood,V.vulnificus WT strain infected, 0hpi, rep1


title: Control_WBC_0hpi_rep3 [CKS_21]

source_name: Isolated white blood cells,non-infected, 0hpi, rep3


title: Control_WBC_3hpi_rep2 [CKS_23]

source_name: Isolated white blood cells,non-infected, 3hpi, rep2


title: Control_WBC_3hpi_rep3 [CKS_24]

source_name: Isolated white blood cells,non-infected, 3hpi, rep3


title: Control_WBC_12hpi_rep1 [CKS_25]

source_name: Isolated white blood cells,non-infected, 12hpi, rep1


title: Control_RBC_12hpi_rep1 [CKS_16]

source_name: Isolated red blood cells,non-infected, 12hpi, rep1


title: Control_RBC_3hpi_rep1 [CKS_13]

description: Gene expression after 3hr in non infected isolated red blood cells.

source_name: Isolated red blood cells,non-infected, 3hpi, rep1


title: Control_RBC_0hpi_rep3 [CKS_12]

description: Gene expression after 0hr in non infected isolated red blood cells.

source_name: Isolated red blood cells,non-infected, 0hpi, rep3


title: Vibrio vulnificus WT strain infection_Blood_3hpi_rep3 [CKS_33]

source_name: Peripheral Blood,V.vulnificus WT strain infected, 3hpi, rep3


title: Control_Blood_3hpi_rep2 [CKS_5]

description: Gene expression after 3hr in non infected peripheral blood.

source_name: Peripheral Blood,non-infected, 3hpi, rep2


title: Control_Blood_12hpi_rep2 [CKS_8]

description: Gene expression after 12hr in non infected peripheral blood.

source_name: Peripheral Blood,non-infected, 12hpi, rep2


title: Control_Blood_12hpi_rep3 [CKS_9]

source_name: Peripheral Blood,non-infected, 12hpi, rep3


title: Control_RBC_0hpi_rep2 [CKS_11]

source_name: Isolated red blood cells,non-infected, 0hpi, rep2


title: Control_Blood_3hpi_rep3 [CKS_6]

source_name: Peripheral Blood,non-infected, 3hpi, rep3


title: Control_RBC_0hpi_rep1 [CKS_10]

source_name: Isolated red blood cells,non-infected, 0hpi, rep1


title: Control_RBC_3hpi_rep3 [CKS_15]

source_name: Isolated red blood cells,non-infected, 3hpi, rep3


title: Control_RBC_3hpi_rep2 [CKS_14]

source_name: Isolated red blood cells,non-infected, 3hpi, rep2


title: Control_Blood_12hpi_rep1 [CKS_7]

source_name: Peripheral Blood,non-infected, 12hpi, rep1


title: Control_RBC_12hpi_rep2 [CKS_17]

source_name: Isolated red blood cells,non-infected, 12hpi, rep2


title: Control_WBC_0hpi_rep2 [CKS_20]

source_name: Isolated white blood cells,non-infected, 0hpi, rep2


title: Vibrio vulnificus WT strain infection_Blood_0hpi_rep2 [CKS_29]

source_name: Peripheral Blood,V.vulnificus WT strain infected, 0hpi, rep2


title: Control_Blood_3hpi_rep1 [CKS_4]

source_name: Peripheral Blood,non-infected, 3hpi, rep1


title: Control_Blood_0hpi_rep3 [CKS_3]

description: Gene expression after 0hr in non infected peripheral blood.

source_name: Peripheral Blood,non-infected, 0hpi, rep3


title: ELAVTrpA1 1-experimental group

city: Shanghai

first: Yong

last: Ping

state: China

address: 800 Dongchuan Rd. Life Science Buildings #1,RM204

institute: Shanghai Jiao Tong University

description:
trapA1_FPKM
trapA1_GO_stat
trapA1_KEGG_stat

data_processing:
Filter1: trim Smart-seq2 public primer sequence from the Reads
Filter2: Remove the contaminated reads and reads whose N base more than 5% for total bases
Illumina Casava1.7 software used for basecalling.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Genome_build: Ensemble Drosophila melanogaster genes (BDGP6.32)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Abundance measurements).
Supplementary_files_format_and_content: tab-delimited text files include GO and KEGG results (Function Enrichment Analysis ).

organism: Drosophila melanogaster

source_name: 50 brains

growth_protocol: Flies were kept on standard fly food mainly containing cornmeal, yeast, and sucrose and agar at room temperature.

extract_protocol:
Adult brains were dissected in phosphate buffer (0.1 M, pH7.2), and fixed for 20 min in 4% paraformaldehyde.
RNA was extracted using UNlQ-10 Column Trizol Total RNA Isolation Kit (Sangon Biotech) and treated with DNaseI (BBI) to digest DNA. Oligo dT magnetic beads were used to enrich and purify the qualified RNA samples. Purified mRNA was fragmented and used as a template to synthesize the first strand of cDNA with N6 random primer. The second strand of cDNA was synthesized by adding dNTPs, RNaseH and DNA Polymerase I. Eluted and purified double-stranded cDNA was then repaired with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end. Then the target size fragments are recovered by agarose gel electrophoresis and PCR amplification is performed to complete the entire library preparation. Use Qubit3.0 for preliminary quantification, dilute the library to 1ng/ul, and then use Agilent 2100 to detect the insert size of the library. After the insert size meet expectations, performs QPCR to accurately quantify the effective concentration of the library (>10nM). Sequencing was performed on the prepared library with Illumina platform and paired end (PE) strategy.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: brain

tag: Sex

value: male

tag: developmental stage

value: adult

value: post natal day 5-7

tag: group

value: experimental group


title: WTrpA1 1-control group

treatment_protocol: RNA was extracted using UNlQ-10 Column Trizol Total RNA Isolation Kit (Sangon Biotech) and treated with DNaseI (BBI) to digest DNA.

tag: age

value: control group


title: ELAVTrpA1 2-experimental group


title: WTrpA1 2-control group


title: Shal495 2-experimental group

description:
Shal495_FPKM
Shal495_GO_stat
Shal495_KEGG_stat


title: WT 1-control group


title: WT 2-control group


title: WAPP1-control group

description:
APP_FPKM
APP_GO_stat
APP_KEGG_stat

value: w;UAS-APP;+


title: ELAVAPP2-experimental group

description:
APP_FPKM
APP_GO_stat
APP_KEGG_stat


title: ELAVAPP1-experimental group

description:
APP_FPKM
APP_GO_stat
APP_KEGG_stat


title: ELAV1-control group

description:
APP_FPKM
APP_GO_stat
APP_KEGG_stat


title: ELAV2-control group

description:
APP_FPKM
APP_GO_stat
APP_KEGG_stat


title: Shal495 1-experimental group


title: Control_Blood_0hpi_rep1 [CKS_1]

source_name: Peripheral Blood,non-infected, 0hpi, rep1

value: Whole blood


title: Control_Blood_0hpi_rep2 [CKS_2]

source_name: Peripheral Blood,non-infected, 0hpi, rep2

value: Peripheral Blood


title: WAPP2-control group

description:
APP_FPKM
APP_GO_stat
APP_KEGG_stat


title: Stress mouse 8

city: Columbus

first: Michael

last: Bailey

state: OH

address: 700 Children's Drive, W410

department: Center for Microbial Pathogenesis

institute: Abigail Wexner Research Institute at Nationwide Children's Hospital

data_processing:
Samples were aligned to the GRCm38.p4 assembly of the mouse reference using RNA-Seq aligner STAR
Feature coverage counts calculated using HTSeq
Raw RNA-Seq expression data was normalized and post-alignment statistics and figures were generated using DESeq2
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: xlsx file of raw counts and normalized data for all samples combined

source_name: colon epithelial cell

extract_protocol:
CD45-EpCAM+ cells were isolated from colon contents using Miltenyi magnetic beads.  Cells were flash frozen, RNA was isolated using Purelink RNA minikit (ThermoFisher).
libraries created using first strand cDNA using ScriptSeq v2 RNA-Seq library prep kit (Epicenter Biotech)

value: stress


title: Control mouse 2

value: control


title: Stress mouse 4


title: Stress mouse 6


title: Control mouse 8


title: Control mouse 10


title: Control mouse 4


title: Stress mouse 2


title: Stress mouse 9


title: Control mouse 1


title: Stress mouse 1


title: Control mouse 3


title: Control mouse 7


title: Control mouse 9


title: Stress mouse 7


title: Stress mouse 3


title: Stress mouse 10


title: BMAL-KO muscle prednisone 1 RNApol-II

city: Cincinnati

first: Mattia

last: Quattrocelli

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

description: RNApol-II ChIP-seq

data_processing:
Reads were aligned to mm10 using bowtie2
Peak analysis was conducted using HOMER software (v4.10) and analyzing peaks in IP samples versus input controls
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph files for all samples and inputs (UCSC genome browser-ready)

source_name: quadriceps muscle

extract_protocol:
Input and IP chromatin was purified using Qiagen MinElute kit.
TrueSeq ChiP-seq library prep (Illumina)

treatment_protocol: Prednisone (Sigma #P6254) was injected  as IP solution of 1mg/kg in 100ul PBS from a 5mg/kg stock solution in DMSO in male BMAL-WT versus BMAL-KO mice (C57BL/6 background; JAX #009100) of approximately 12 weeks of age at ZT0 (lights-on). 4 hours after last injection quadriceps muscles were obtained from each mouse. Chromatin was then fixed, isolated, sonicated and immunoprecipitated.

tag: drug treatment

value: ZT0 prednisone

tag: time of collection

tag: sample type

value: ChIP-seq


title: BMAL-KO muscle prednisone 3 GR

description: GR ChIP-seq


title: BMAL-KO muscle prednisone 2 GR

description: GR ChIP-seq


title: BMAL-KO muscle prednisone 1 GR

description: GR ChIP-seq


title: BMAL-KO muscle prednisone 2 RNApol-II

description: RNApol-II ChIP-seq


title: pooled inputs for BMAL-KO muscle prednisone

description: input DNA


title: Control mouse 5


title: BMAL-KO muscle vehicle 2 RNApol-II

description: RNApol-II ChIP-seq

value: ZT0 vehicle


title: Control mouse 6


title: BMAL-KO muscle vehicle 3 RNApol-II

description: RNApol-II ChIP-seq


title: BMAL-KO muscle prednisone 3 RNApol-II

description: RNApol-II ChIP-seq


title: BMAL-KO muscle vehicle 3 GR

description: GR ChIP-seq


title: BMAL-WT muscle prednisone 3 RNApol-II

description: RNApol-II ChIP-seq


title: BMAL-KO muscle vehicle 1 RNApol-II

description: RNApol-II ChIP-seq


title: BMAL-WT muscle prednisone 2 BMAL1

description: BMAL1 ChIP-seq


title: pooled inputs for BMAL-KO muscle vehicle

description: input DNA


title: BMAL-KO muscle vehicle 1 GR

description: GR ChIP-seq


title: BMAL-WT muscle prednisone 3 GR

description: GR ChIP-seq


title: BMAL-WT muscle prednisone 1 GR

description: GR ChIP-seq


title: BMAL-WT muscle prednisone 2 RNApol-II

description: RNApol-II ChIP-seq


title: BMAL-KO muscle vehicle 2 GR

description: GR ChIP-seq


title: pooled inputs for BMAL-WT muscle prednisone

description: input DNA


title: BMAL-WT muscle prednisone 3 BMAL1

description: BMAL1 ChIP-seq


title: BMAL-WT muscle vehicle 3 RNApol-II

description: RNApol-II ChIP-seq


title: BMAL-WT muscle prednisone 1 RNApol-II

description: RNApol-II ChIP-seq


title: BMAL-WT muscle prednisone 1 BMAL1

description: BMAL1 ChIP-seq


title: BMAL-WT muscle vehicle 2 RNApol-II

description: RNApol-II ChIP-seq


title: BMAL-WT muscle prednisone 2 GR

description: GR ChIP-seq


title: BMAL-WT muscle vehicle 2 BMAL1

description: BMAL1 ChIP-seq


title: BMAL-WT muscle vehicle 1 BMAL1

description: BMAL1 ChIP-seq


title: BMAL-WT muscle vehicle 3 BMAL1

description: BMAL1 ChIP-seq


title: BMAL-WT muscle vehicle 1 RNApol-II

description: RNApol-II ChIP-seq


title: BMAL-WT muscle vehicle 1 GR

description: GR ChIP-seq


title: pooled inputs for BMAL-WT muscle vehicle

description: input DNA


title: BMAL-WT muscle vehicle 2 GR

description: GR ChIP-seq


title: HTG_N_5

city: Changchun

first: Weiwei

last: Cui

state: Jilin

address: Xinmin

institute: Jilin University

data_processing:
Filtration: we removed reads with adapter and N (N means that the nucleobase information cannot be determined) ≥ 0.002, and low-quality reads from raw data.
Comparative analysis: RNA-Seq sequencing data were compared and analyzed using Tophat2, Hisat2, and STAR software.
Transcript splicing: we used Stringtie software to assemble reads into transcripts and quantify them based on the results of the alignment to the genome.
Transcript screening: we used Cuffmerge software to merge the transcripts obtained from each sample splicing.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: blood

extract_protocol:
For each sample, trizol (TAKARA BIO INC., CA, Japan) was added into the whole blood immediately after the blood samples were collected. The ratio of trizol to whole blood is 3:1. And total RNA was isolated and purified using total RNA extraction kit.The chain-specific library was constructed by removing the ribosomal RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: normal blood glucose

tag: bmi


title: HTG_N_6


title: HTG_N_4


title: HTG_P_6

value: prediabetes


title: HTG_N_2


title: HTG_N_3


title: HTG_N_1


title: HTG_P_5


title: BMAL-WT muscle vehicle 3 GR

description: GR ChIP-seq


title: HTG_P_4


title: HTG_D_5

value: diabetes


title: HTG_P_1


title: Stress mouse 5

tag: treatment


title: HTG_P_2


title: 737789N.INPUT

city: ZhenJiang

first: Jiabin

last: Huang

state: JiangSu

address: 8 Dianli Road, Runzhou District

institute: Affiliated People's Hospital of Jiangsu University

data_processing:
The RNA concentration of each sample was measured using NanoDrop ND-1000 instrument (Thermo Fisher Scientific, Waltham, MA, USA).
RNA integrity and gDNA contamination were measured by denatured agarose gel electrophoresis
RNA Quantification and Quality Assurance by Qubit3.
Library quality was measured using Agilent 2100 Bioanalyzer.
MeRIP-Seq was performed by Cloudseq Biotech Inc. (Shanghai, China) according to the published procedure (Meyer et al., 2012) with slight modifications. Briefly, fragmented RNA was incubated with anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer for 2 hours at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) by following the manufacturer’s instruction. Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ RNA Library Prep Kit (NEB). Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer.
Genome_build: HG19
Supplementary_files_format_and_content: excel format

source_name: normal control tissue

extract_protocol:
fragmented RNA was incubated with anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer for 2 hours at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours.
Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer.

value: adenocarcinoma of esophagogastric junction

tag: tumer stage

value: Stage IIIA

value: untreated

tag: tissue

value: normal control tissue


title: 737511N.INPUT

value: Stage IIIB


title: HTG_D_4


title: 739939T.INPUT

source_name: cancer tissue

value: cancer tissue


title: 738156N.INPUT


title: HTG_D_1


title: HTG_D_2


title: HTG_D_3


title: HTG_D_6


title: 738156T.INPUT


title: 737789T.INPUT


title: 739939N.IP


title: 739939N.INPUT


title: 737789N.IP


title: 738156N.IP


title: 737511N.IP


title: Vibrio vulnificus WT strain infection_RBC_0hpi_rep3 [CKS_39]

source_name: Isolated red blood cells,V.vulnificus WT strain infected, 0hpi, rep3

tag: cell type

value: Isolated red blood cells

value: V.vulnificus WT strain infected, 0hpi


title: 737511T.IP


title: FQMR24

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

institute: Aix-Marseille Université - Marseille Medical Genetics

description: mRNA

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
We assessed fastq sequence data quality using FastQC v0.11.5 (Andrews, 2010) and trimmed the reads to remove adapter sequences and low quality bases using DimerRemover.
Single end reads were aligned using STAR v2.5.3a to the GRCh38 human genome release.
BAMS index were generated using Sambamba v0.6.6.
DEGs and abundance measurements were identified using StringTie v1.3.1c and R package DESeq2 v1.18.1 (median of ratio).
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: Tab-delimited text files (.tsv) include RAW count for each Sample and DESeq2 output.

source_name: innervated muscle fiber derivated from hIPS

growth_protocol: The hIPSc were differentiated into functional muscles according to the protocol described in Mazaleyrat et al. (DOI: 10.3390/cells9061531).

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) following manufacturer’s instructions. Quality, quantitation and sizing of total RNA were evaluated using the RNA 6000 Pico assay (Agilent Technologies Ref. 5067-1513) on an Agilent 2100 Bioanalyzer system.
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: disease

value: BAMS


title: FQMR23

description: mRNA

value: innervated muscle fiber derivated from hIPS


title: 738156T.IP


title: FQMR22

description: mRNA


title: 739939T.IP


title: 737789T.IP


title: FQMR21

description: mRNA


title: FQMR20

description: mRNA


title: FQMR13

description: mRNA

value: Control


title: FQMR17

description: mRNA

value: FSHD1 mosaic


title: FQMR27

description: mRNA

value: FSHD1 mosaic isogenic Control


title: FQMR14

description: mRNA