title: Wild type K12MG1655_1

description:
WT_S1
processed data file: Raw_counts.txt

value: WT


title: P2775_268

status: Public on Dec 31 2021

type: SRA

city: Badalona

first: Elisabetta

last: Mereu

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

description:
full-lenght RNA-seq
P2775.tsv

library_source: transcriptomic

data_processing:
Reads were then demultiplexed according to the cell barcodes
Sequenced reads were filtered for low-complexity or low-quality sequence.
High quality reads were mapped according to the GEM pipeline
Genome_build: Mouse: Gencode release 21, assembly GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing gene expression values as read counts

molecule: polyA RNA

organism: Mus musculus

source_name: S94F1_P3 Core

extract_protocol:
Cells were sorted into 96-well plates containing the lysis buffer. Reverse transcription was performed using SuperScrpit II (Invitrogen) in the presence of oligo-dT30VN, template-switching oligonucleotides and betaine. The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kappa Biosystems), ISPCR primer and 22 cycles of amplification. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitvity DNA Kit (Agilent Technologies). 140 pg of the amplified cDNA were fragmented using Nextera® XT (Illumina) and amplified with indexed Nextera® PCR primers. Products were purified twice with Agencourt Ampure XP beads and quantified again using a Bioanalyzer High Sensitvity DNA Kit. Sequencing of Nextera® libraries from 384 cells was carried out in one lane on a Illumina HiSeq2500 v4.
Full-length single-cell RNA sequencing libraries were prepared using the Smart-seq2 protocol
single cell RNA-seq (scRNA-seq)

tag: protocol

tag: cell type

value: Glioblastoma

tag: treatment

value: EGFR


title: P2775_267

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_265

description:
full-lenght RNA-seq
P2775.tsv


title: ref6 28 rep1

city: Beijing

first: Xiaofeng

last: Cao

state: Beijing

address: No.1 West Beichen Road, Chaoyang District

department: National Key Lab of Plant Genomics

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Bases calling was performed with RTA (Real Time Analysis) software version 1.18.64.
Paired-end sequencing reads were mapped to the Arabidopsis thaliana TAIR10 reference genome using Bowtie2 (version 2.2.8) in local alignment mode. Multiple mapping reads, unmated reads, and mated reads that mapped too far apart (> 4 X fragment length) for paired-end reads were excluded for downstream analysis. In order to avoid double counting in overlapping regions for paired-end data, the first read mate was used to calculate normalized genome coverage tracks by deepTools2 after extending ChIP-seq reads to the average estimated fragment length, disregarding the second read mate.
For RNA-seq, all reads were mapped to TAIR10 reference genome using HISAT2 (version 2.0.5) with default parameters. To count the uniquely mapped reads, featureCounts (version 1.6.2) was used to calculate the read count per gene and RPKM value. Then the differentially expressed genes were identified by DESeq2 (version 1.20.0) with this criteria (q-value < 0.05, log2(Fold change) > 2).
ChIP-seq peaks were called using MACS2 (v 2.1.1) with the “--gsize 1.19e8 --keep-dup 1” option. Peaks were annotated to the gene with the closest TSS by ChIPseeker.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: All Arabidopsis materials were grown on half-strength Murashige and Skoog (MS) medium with 1% sucrose at 22°C and 28°C under long day conditions (LD, 16 hours light, 8 hours dark), and 10-day-old seedlings were used for ChIP-Seq experiments.

extract_protocol:
Chromatin Immunoprecipitation (ChIP) assays were performed using 3 g 10-day-old seedlings as previously described with minor modifications (Cui, X. et al., 2016, Nat Genet 48, 694-9). Antibody used in ChIP was anti-REF6 antibody. 1-2 ng DNA was used for ChIP-seq.
Libraries were constructed with the NEXTflex Rapid DNA-seq Prep Kit for Illumina Sequencing (BIOO Scientific, #5144-03) according to the manufacturer's protocol.

tag: ecotype

value: Columbia

tag: genotype

value: ref6 knockout


title: ref6 28 rep3


title: P2775_266

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_264

description:
full-lenght RNA-seq
P2775.tsv

source_name: S94F1_P3 Inv


title: col 28 rep1

value: wild type


title: ref6 22 rep2


title: P2775_260

description:
full-lenght RNA-seq
P2775.tsv


title: ref6 22 rep3


title: P2775_257

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_258

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_263

description:
full-lenght RNA-seq
P2775.tsv


title: ref6 22 rep1


title: col 22 rep2


title: P2775_261

description:
full-lenght RNA-seq
P2775.tsv


title: col 22 rep1


title: col 22 rep3


title: P2775_262

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_259

description:
full-lenght RNA-seq
P2775.tsv


title: Wild type K12MG1655_2

city: Uppsala

first: Ankita

last: Pal

address: Husargatan 3

department: Medical Biochemistry and Microbiology

country: Sweden

institute: Uppsala University

description:
WT_S2
processed data file: Raw_counts.txt

data_processing:
Illumina Hi-seq 2500 used for sequencing.
CUTADAPT used for removing adapter sequence and low-quality reads (q >= 20).
BWA used for read mapping and alignment to reference genome (GenBank accession no. NC_000913.3).
Samtools used for compressing alignment files and sorting.
FeatureCounts used for assigning counts at gene level.
EdgeR used for differential gene expression analysis.
Genome_build: Reference genome used: E.coli K12 MG1655, accession number : NC_000913.3
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited .txt file containing raw reads count.

molecule: total RNA

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Bacteria grown in M9+ glucose + 40 mM MOPS

growth_protocol: Escherichia coli cells grown in a bioreactor under aerobic conditions with M9+glucose+ 40mM MOPS at 37 degree Celsius and 700 rpm till exponential phase.

extract_protocol:
Total RNA extracted at exponential phase.
Total RNA extraction was done using the TRIzol-chloroform method. DNase treatment was done to remove any DNA contamination after which enrichment for mRNA was done using the MicrobExpress Kit.
Single-end, strand specific libraries for RNA sequencing were prepared using NEBNext Ultra II Directional RNA library kit. The sequencing was carried out on HiSeq 2500 Rapid Run Mode using 1x50 bp single-end reads.

tag: media

value: Glucose minimal media

tag: growth phase

value: Exponential


title: REF6 ChIP 28 rep1

library_source: genomic

molecule: genomic DNA

tag: antibody


title: REF6 ChIP 28 rep2


title: ref6 28 rep2


title: P2775_256

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_255

description:
full-lenght RNA-seq
P2775.tsv


title: col 28 rep3


title: col 28 rep2


title: REF6 ChIP 22 rep2


title: P2775_254

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_253

description:
full-lenght RNA-seq
P2775.tsv


title: H3K27me3 ref6 28 rep2


title: P2775_252

description:
full-lenght RNA-seq
P2775.tsv


title: REF6 ChIP 22 rep1


title: H3K27me3 ref6 28 rep1


title: H3K27me3 col 28 rep2


title: P2775_251

description:
full-lenght RNA-seq
P2775.tsv


title: H3K27me3 col 22 rep2


title: H3K27me3 ref6 22 rep2


title: P2775_248

description:
full-lenght RNA-seq
P2775.tsv


title: H3K27me3 col 28 rep1


title: P2775_247

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_249

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_246

description:
full-lenght RNA-seq
P2775.tsv


title: H3K27me3 ref6 22 rep1


title: P2775_243

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_242

description:
full-lenght RNA-seq
P2775.tsv


title: Control-D2R3 [RNA-seq]

city: West Lafayette

first: Vikki

middle: M

last: Weake

state: Indiana

address: 175 S University St

department: Biochemistry

country: USA

institute: Purdue University

data_processing:
Sanger/Illumina 1.9 used for base calling.
Raw reads were trimmed to discard adapter reads and low quality reads (Q<30) using Trimmomatic settings: HEADCROP:8 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:30 MINLEN:75.  Cleaned reads were mapped to Drosophila melanogaster genome version dm6 using STAR producing BAM files that are sorted by coordinate and gene counts
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files.
Differential gene expression analysis was performed with DESeq2 using STAR-produced counts as input.
Genome_build: UCSC Aug. 2014 - BDGP Release 6 + ISO1 MT/dm6
Supplementary_files_format_and_content: Processed file is a text file that has STAR-produced raw counts for each sample

organism: Drosophila melanogaster

source_name: Retina

growth_protocol: Flies (genotype: w;;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506];UAS-ClkDN or UAS-LacZ) were raised at 12:12 light:dark cycle at 25 degrees C on standard fly food. Following eclosion (day 1), they were aged for 1 or 10 days (D1 or D10) and transfered to new food every other day.  Flies were collected at relative Zeitgeber Time ZT9

extract_protocol:
Male flies were harvested at indicated time point and heads were removed by freezing the flies in liquid nitrogen followed by five rounds of vortexing and freezing. RNA was extracted with Direct-Zol microprep kit (ZymoResearch) and quantified with Qubit HS RNA (ThermoFisher)
nuclear RNA-seq: Rnaseq libraries were constructed with Ovation® SoLo RNA-Seq Library Preparation Kit (Nugen-Tecan) using 10 ng of RNA as starting material

tag: cell-type

value: Photoreceptor neuron

tag: genotype/variation

value: LacZ overexpression


title: H3K27me3 col 22 rep1


title: P2775_244

description:
full-lenght RNA-seq
P2775.tsv


title: Control-D10R2 [RNA-seq]


title: Control-D10R1 [RNA-seq]


title: P2775_245

description:
full-lenght RNA-seq
P2775.tsv


title: Control-D10R3 [RNA-seq]


title: P2775_240

description:
full-lenght RNA-seq
P2775.tsv


title: Control-D2R2 [RNA-seq]


title: P2775_239

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_238

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_241

description:
full-lenght RNA-seq
P2775.tsv


title: ClockDN-D10R2 [RNA-seq]

value: ClkDN overexpression


title: ClockDN-D10R3 [RNA-seq]


title: RSV2

city: Kongens Lyngby

first: Xiao

last: Wang

address: Bagsværdvej 103, ST

country: Denmark

institute: Konge Larsen Aps

data_processing:
raw reads containing ploy N (Percentage of uncertain N ≥ 10%) A/T/G/C, with 5’ adapter contaminants, without 3’ adapters or insert tags and low-quality reads (Percentage of Qphred less than 20 ≥ 50%)
The miRNA tags were mapped to the reference genome of Bos taurus (UMD_3.1.1/bosTau8) by Bowtie software (version 0.12.9)
The mapped miRNA tags were used to seek the known miRNAs using miRBase20.0 as the reference, so the potential miRNA and the secondary structures were obtained by mirdeep2 software
Genome_build: UMD_3.1.1/bosTau8
Supplementary_files_format_and_content: Tab-delimited text files include DE genes

organism: Bos taurus

source_name: Case group

growth_protocol: Following the RSV formulating method in the previous study (Li et al., 2015), 105 μM mother solution was formulated by using 22.8 mg RSV (Molar mass = 228) (Sangon Biotech, Shanghai, China) dissolved into 1 mL Dimethyl sulfoxide (DMSO; Sangon Biotech , Shanghai, China). Afterwards, 1 uL mother solution and 1 uL pure DMSO diluted into 5 mL DM.

extract_protocol: Libraries were prepared according to Illumina's instructions

treatment_protocol: One group of cells was treated with constant doses of 20 μM RSV in DM (i.e., 1uL mother solution added in 5 mL DM), which is the case group. Another group of cells was treated with 1 uL DMSO as the control group.

value: Primary myoblasts

tag: tissue

value: fetal beef longissimus dorsi muscle

value: 20 μM resveratrol


title: P2775_250

description:
full-lenght RNA-seq
P2775.tsv


title: ClockDN-D10R1 [RNA-seq]


title: P2775_235

description:
full-lenght RNA-seq
P2775.tsv


title: ClockDN-D2R2 [RNA-seq]


title: ClockDN-D2R3 [RNA-seq]


title: ClockDN-D2R1  [RNA-seq]


title: P2775_234

description:
full-lenght RNA-seq
P2775.tsv


title: Control-D2R1 [RNA-seq]


title: P2775_236

description:
full-lenght RNA-seq
P2775.tsv


title: D101_DD_2

description: processed data file: D20_LD-DD_counts.txt

growth_protocol: Flies (genotype: w;;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]) were raised at 12:12 light:dark cycle at 25 degrees C on standard fly food. Following eclosion (day 1), they were aged for 20, 30, 40, 50 and 60 with transfer to new food every other day.  Flies were collected at ZT 6

tag: Sex

value: male


title: D101_DD_1


title: D101_LD_1


title: D101_LD_2


title: D20R3

tag: age (days)


title: P2775_228

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_227

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_230

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_237

description:
full-lenght RNA-seq
P2775.tsv


title: D20R2


title: P2775_226

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_231

description:
full-lenght RNA-seq
P2775.tsv


title: D20R1


title: P2775_225

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_224

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_223

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_233

description:
full-lenght RNA-seq
P2775.tsv


title: D601

description: Accessible chromatin

data_processing:
Sanger/Illumina 1.9 used for base calling.
Raw reads were trimmed to discard adapter reads and low quality reads (Q<30) using Trimmomatic settings: HEADCROP:15 CROP:35. Cleaned reads were mapped to Drosophila melanogaster genome version dm6 using Bowtie2 producing SAM files.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files.
BAM files are normalized to GC content using deepTools computeGCBias and correctGCBias packages, then bigwig files are obtained using bamCoverage package
Genome_build: UCSC Aug. 2014 - BDGP Release 6 + ISO1 MT/dm6
Supplementary_files_format_and_content: Processed file is a bigwig file for each sample

growth_protocol: Flies (genotype: w;;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]) were raised at 12:12 light:dark cycle at 25 degrees C on standard fly food. Following eclosion (day 1), they were aged for 30, 40, 50 and 60 with transfer to new food every other day.  Flies were collected at ZT 6

extract_protocol:
Male flies were harvested at indicated time point and heads were removed by freezing the flies in liquid nitrogen followed by five rounds of vortexing and freezing. Purified nuclei were obtained using an immunoenrichment protocol (Jauregui-Lozano, 2021)
Omni-ATAC libraries were made with Illumina Tagment DNA TDE1 Enzyme and Buffer kit and "IDT for Illumina" Nextera DNA UD Indexes Set A

value: Retina

tag: time point

value: day 60 after eclosion


title: D603

description: Accessible chromatin


title: D503

description: Accessible chromatin

value: day 50 after eclosion


title: P2775_221

description:
full-lenght RNA-seq
P2775.tsv

value: Glioblastoma


title: P2775_222

description:
full-lenght RNA-seq
P2775.tsv

value: EGFR


title: P2775_232

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_219

description:
full-lenght RNA-seq
P2775.tsv


title: D403

description: Accessible chromatin

value: day 40 after eclosion


title: D402

description: Accessible chromatin


title: D501

description: Accessible chromatin


title: P2775_229

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_220

description:
full-lenght RNA-seq
P2775.tsv


title: D401

description: Accessible chromatin


title: D303

description: Accessible chromatin

value: day 30 after eclosion


title: D602

description: Accessible chromatin


title: P2775_216

description:
full-lenght RNA-seq
P2775.tsv


title: D502

description: Accessible chromatin


title: P2775_217

description:
full-lenght RNA-seq
P2775.tsv


title: D302

description: Accessible chromatin


title: P2775_215

description:
full-lenght RNA-seq
P2775.tsv


title: D301

description: Accessible chromatin


title: D203

description: Accessible chromatin

value: day 20 after eclosion


title: D202

description: Accessible chromatin


title: P2775_212

description:
full-lenght RNA-seq
P2775.tsv


title: D201

description: Accessible chromatin


title: P2775_211

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_210

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_209

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_208

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_218

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_207

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_205

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_206

description:
full-lenght RNA-seq
P2775.tsv


title: Control-D2R2

description: Accessible chromatin

value: day 2


title: Control-D10R3

description: Accessible chromatin

value: day 10


title: Control-D10R2

description: Accessible chromatin

value: Photoreceptor neuron


title: ClockDN-D10R3

description: Accessible chromatin


title: Control-D2R3

description: Accessible chromatin

value: LacZ overexpression


title: P2775_214

description:
full-lenght RNA-seq
P2775.tsv


title: Control-D2R1

description: Accessible chromatin


title: P2775_213

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_202

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_204

description:
full-lenght RNA-seq
P2775.tsv


title: ClockDN-D2R3

description: Accessible chromatin

value: ClkDN overexpression


title: P2775_200

description:
full-lenght RNA-seq
P2775.tsv


title: ClockDN-D10R2

description: Accessible chromatin


title: ClockDN-D2R2

description: Accessible chromatin


title: P2775_203

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_198

description:
full-lenght RNA-seq
P2775.tsv


title: ClockDN-D2R1

description: Accessible chromatin


title: P2775_201

description:
full-lenght RNA-seq
P2775.tsv


title: D60R2

extract_protocol:
Male flies were harvested at indicated time point and heads were removed by freezing the flies in liquid nitrogen followed by five rounds of vortexing and freezing. RNA was extracted with Direct-Zol microprep kit (ZymoResearch) and quantified with Qubit HS RNA (ThermoFisher)
Rnaseq libraries were constructed with Ovation® SoLo RNA-Seq Library Preparation Kit (Nugen-Tecan) using 10 ng of RNA as starting material

tag: molecule subtype

value: nuclear RNA


title: D60R3


title: P2775_199

description:
full-lenght RNA-seq
P2775.tsv


title: Control-D10R1

description: Accessible chromatin


title: P2775_197

description:
full-lenght RNA-seq
P2775.tsv


title: ClockDN-D10R1

description: Accessible chromatin


title: D60R1


title: D50R3


title: P2775_195

description:
full-lenght RNA-seq
P2775.tsv


title: D50R2


title: P2774_192

description:
full-lenght RNA-seq
P2774.tsv

source_name: S94F1_P2 Inv


title: P2775_193

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_194

description:
full-lenght RNA-seq
P2775.tsv


title: D40R3


title: D30R2


title: P2774_191

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_189

description:
full-lenght RNA-seq
P2774.tsv


title: D40R1


title: P2774_190

description:
full-lenght RNA-seq
P2774.tsv


title: D30R3


title: D50R1


title: P2774_188

description:
full-lenght RNA-seq
P2774.tsv


title: D30R1


title: Top3D30R2

first: Hana

last: Hall

address: 175 S University St, Biochemistry Builiding, room 320

growth_protocol: Flies (genotype: P{w[+mC]=UAS-Dcr-2.D}1, w[1118];P{y[+t7.7] v[+t1.8]=TRiP.JF01282}attP2;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]) or P{w[+mC]=UAS-Dcr-2.D}1, w[1118];P{w[v+]=[UAS-mCherry-RNAi]}attP2;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]) were raised at 12:12 light:dark cycle at 25 degrees C on standard fly food. Following eclosion (day 1), they were aged for 30 days with transfer to new food every other day.  Flies were collected at ZT 6

value: siRNA against Top3beta


title: P2774_186

description:
full-lenght RNA-seq
P2774.tsv

source_name: empty


title: D40R2


title: P2774_187

description:
full-lenght RNA-seq
P2774.tsv


title: day 6 post amputation control

city: Lexington

first: Jeramiah

middle: James

last: Smith

state: KY

address: 101 Morgan Building

department: Biology

institute: University of Kentucky

data_processing:
Assignment of barcodes to cells and transcript quantification and clustering were performed using cellranger-6.0.0.
Genome_build: GSE136546_transcriptome.fa.gz
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx
Supplementary_files_format_and_content: Merged_filtered_feature_bc_matrix.h5

organism: Ambystoma mexicanum

source_name: day 6 post amputation control

extract_protocol:
Single nuclei.
Single-nuclei RNA library using 10X Genomics platform, v3 chemistry.

value: Tail amputation stump

tag: developmental stage

value: stage 42

value: control

tag: timepoint

value: day 6 post amputation


title: P2775_196

description:
full-lenght RNA-seq
P2775.tsv

tag: protocol


title: Top3D30R1

tag: cell type


title: BJ1

city: Harbin

first: Jian

address: 600 Changjiang Road

institute: Northeast Agricultural University

data_processing:
BGI500 own software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni .
Genome_build: GCF_000188115.4_SL3.0
Supplementary_files_format_and_content: FPKM values for each Sample

organism: Solanum lycopersicum

source_name: Tomato_Compound raceme

growth_protocol: Tomatoes grow naturally in the greenhouse.All tomato tissues were collected and used to RNA sequencing.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI500 protocols

tag: cultivar

value: Compound raceme

value: Axillary bud


title: BJ3


title: day 6 post amputation 10 uM romidepsin

source_name: day 6 post amputation 10 uM romidepsin

tag: treatment

value: romidepsin


title: P2774_185

description:
full-lenght RNA-seq
P2774.tsv

source_name: S94F1_P2 Core

value: Glioblastoma

value: EGFR


title: BJ2


title: mChD30R2

value: siRNA against mCherry (control)


title: P2774_184

description:
full-lenght RNA-seq
P2774.tsv


title: WT3

value: monomaker


title: mChD30R1


title: P2774_183

description:
full-lenght RNA-seq
P2774.tsv


title: WT1


title: MapR_D50_R3

data_processing:
Library strategy: MapR
Sanger/Illumina 1.9 used for base calling.
Raw reads were trimmed to discard adapter reads and low quality reads (Q<30) using Trimmomatic settings: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:23 MINLEN:75.  Cleaned reads were mapped to Drosophila melanogaster genome version dm6 using Bowtie2 with settings: --sensitive.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files.
Bigwig files were generated using deepTools subpackage bamCoverage, and bigwig files were analyzed using multiBigwigSummary, computeMatrix, plotCorrelation, plotProfile and plotHeatmap. Dm6 refGene GTF file was used for all analysis, available at UCSC.
Genome_build: UCSC Aug. 2014 - BDGP Release 6 + ISO1 MT/dm6
Supplementary_files_format_and_content: All processed files are bigwig files containing CPM-normalized tracks

growth_protocol: Flies (genotype: w;;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]) were raised at 12:12 light:dark cycle at 25 degrees C on standard fly food. Following eclosion (day 1), they were aged for 10, 30 and 50 days with transfer to new food every other day.

extract_protocol:
Male flies were harvested at indicated time point and heads were removed by freezing the flies in liquid nitrogen followed by five rounds of vortexing and freezing. MapR was performed following Yan, 2020.
MapR libraries were made with Nugen Ovation Ultralow V2 using 2 ng of DNA as starting material.

tag: age

value: 50 days


title: P2774_181

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_182

description:
full-lenght RNA-seq
P2774.tsv


title: STAT5BKO_LSK

city: Vienna

first: Veronika

last: Sexl

address: Veterinaerplatz 1

department: Pharmacology / Toxikology

country: Austria

institute: University of Veterinary Medicine Vienna

description: 10X Genomics scRNA-seq

data_processing:
The official 10x Genomics Cell Ranger pipeline 3.0.2 was used for Sample demultiplexing, barcode processing and UMI counting.
Reads were aligned to the mouse reference genome (version mm10).
Each library was processed separately using the cellranger count tool to generate gene-barcode matrices.
Gene-barcode matrices were imported into Seurat and normalized and scaled with default settings.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: RData file containing raw barcode/gene matrices, normalized, and integrated data; metadata containing barcode to cluster matrices;

source_name: FACS-sorted LSK cells of 3 pooled Stat5b-/- mice (1x male, 2x female)

growth_protocol: FACS-sorted bone marrow LSK cells

extract_protocol: 10X Genomics scRNA-seq

treatment_protocol: no treatment was applied

tag: genotype

tag: age of mice

value: 8 weeks

value: bone marrow

value: FACS-sorted bone marrow LSK cells


title: control-1

city: Chongqing

first: Xue

last: Gong

address: Changjiang branch Road

institute: Army Medical University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Tophat  against the GRCm38/mm10 mouse reference genome and unmapped reads were mapped to Tophat-Fusion.
Identification and annotation of circRNA was performed by distinguishing the “GT/AG” splicing site using Python.
Reads Per Million-mapped reads (RPM) were calculated using HTseq.
Genome_build: mm10
Supplementary_files_format_and_content: xls files include RPM values and junction counts for detected circRNA candidates in each sample.

source_name: Aorta

extract_protocol:
Aortae were removed, washed in cold PBS and flash frozen in liquid nitrogen before sending to Ribobio (Guangzhou, China) for sequencing.
1 ug of total RNA was prepared for the construction of sequencing libraries using  NEBNext® Ultra™ RNA Library Prep Kit for Illumina (Cat# E7530S).

treatment_protocol: 3-month-old ApoE-/- mice were fed a high-fat diet for 3 months (AS group) and C57BL/6J and ApoE-/- (control) mice were fed a chow diet.

tag: strain

value: Aorta

value: ApoE-/-


title: day 0 post amputation control

source_name: day 0 post amputation control

value: Tail amputation stump

value: day 0 post amputation


title: P2774_180

description:
full-lenght RNA-seq
P2774.tsv


title: SRC-3 KO_RNA-Seq_ZT20

city: Houston

first: Huan

last: Meng

state: Texas

address: One Baylor Plaza BCM 130

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

data_processing:
Fastq files containing raw RNA-seq reads were aligned to the mouse genome (mm10/NCBI38) using HISAT2. RNA-seq quantification was performed with htseq-count (default parameters). Protein-coding genes were quantified by iGenome annotation. Quantification values were normalized with DESeq2, followed by filtering out of zero expression genes in each replicate or time point.
Genome_build: mm10

source_name: LIVER

extract_protocol: These RNA samples (500ng of total RNA for each timepoint) were converted into strand-specific total mRNA-seq libraries with the TruSeq Stranded Total RNA (Illumina) per the manufacturer’s protocol. The size selected libraries were analyzed for quality control with High Sensitivity DNA chip on a Bioanalyzer 2100 (Agilent), and the pooled libraries were sequenced with the HiSeq 3000 (Illumina) using a 75-bp paired-end for an average of 40 million paired-end reads per sample at the MD Anderson Cancer Center

treatment_protocol: RNA samples were isolated from two biological replicates of mouse liver tissues from zeitgeber time 0 (ZT0) every 4 hours for 24 hours with the miRNeasy Mini Kit (Qiagen) per the manufacturer’s instructions. The two replicates from each timepoint were combined before library preparation.

tag: gender

value: Male

value: 12-16 weeks of age

value: SRC-3 -/- KO mice

value: Liver


title: STAT5AKO_LSK

description: 10X Genomics scRNA-seq

source_name: FACS-sorted LSK cells of 3 pooled Stat5a-/- mice (2x male, 1x female)


title: MapR_D30_R3

value: Photoreceptor neuron

value: 30 days


title: MapR_D50_R1


title: control-2


title: P2774_179

description:
full-lenght RNA-seq
P2774.tsv

value: Glioblastoma

value: EGFR


title: P2774_177

description:
full-lenght RNA-seq
P2774.tsv


title: MapR_D30_R2


title: SRC-3 KO_RNA-Seq_ZT08


title: P2774_178

description:
full-lenght RNA-seq
P2774.tsv


title: MapR_D30_R1


title: SRC-3 KO_RNA-Seq_ZT04


title: WT2

value: monomaker

value: Axillary bud


title: SRC-3 KO_RNA-Seq_ZT12


title: SRC-3 WT_RNA-Seq_ZT20

value: SRC-3 +/+ WT mice


title: MapR_RNaseH_plus

value: 10 days


title: MapR_D50_R2

value: 50 days


title: P2774_176

description:
full-lenght RNA-seq
P2774.tsv


title: SRC-3 WT_RNA-Seq_ZT16


title: SRC-3 KO_RNA-Seq_ZT16


title: STAT5WT_LSK

description: 10X Genomics scRNA-seq

source_name: FACS-sorted LSK cells of 3 pooled wt mice (2x male, 1x female)

value: WT

value: 8 weeks

value: bone marrow

value: FACS-sorted bone marrow LSK cells


title: SRC-3 WT_RNA-Seq_ZT04

value: Male


title: P2774_175

description:
full-lenght RNA-seq
P2774.tsv


title: MapR_D10_R2


title: SRC-3 WT_RNA-Seq_ZT08

value: 12-16 weeks of age


title: P2774_174

description:
full-lenght RNA-seq
P2774.tsv


title: SRC-3 WT_RNA-Seq_ZT00


title: P2774_173

description:
full-lenght RNA-seq
P2774.tsv


title: MapR_D10_R1


title: SRC-3 KO_RNA-Seq_ZT00

value: SRC-3 -/- KO mice


title: SRC-3_WT_ChIP_CHOW_ZT8

data_processing:
ChIP-seq sequencing reads were mapped to the mouse genome (mm10/NCBI38) with BOWTIE2. The mapping allowed a maximum of two mismatches and removed duplicated reads to ensure only “unique” reads were allowed for output to the bam file. Unique reads with mapping scores higher than 15 were kept for subsequent ChIP-seq analysis. MACS2 version 2.1.1.20160309 was used to perform the peak calling. Duplicates at each time point were pooled, and heatmap and enrichment plotting were carried out. In all the sequencing analysis, the differential sequencing reads were “down-sampled” to the lowest number of uniquely mapped reads for the normalization of sequencing depth.
Genome_build: mm10

extract_protocol: The DNA libraries were prepared at the MD Anderson Cancer Center, which generated ~40 million 75 bp single-end reads (for the timecourse samples) or paired-end reads per samples (for the comprehensive three timepoints samples). DNA libraries generated from  10ng input DNA  were prepared with KAPA Hyper Prep Kit (KAPABIOSYSTEMS). The size selection was performed using SPRIselect beads (Beckman Coulter), followed by quality control analyzed using the High Sensitivity DNA chip on Bioanalyzer 2100 (Agilent). The DNA libraries were pooled and sequenced using HiSeq 3000 (Illumina).

treatment_protocol: Mouse liver chromatin was prepared with the ChIP-IT Kit (Active Motif) per the manufacturer’s instruction with the following modifications. Briefly, mouse liver samples were dissected into small pieces in PBS containing 1% formaldehyde and incubated for 15 min at room temperature, followed by the addition of 0.125 M glycine to stop the reaction. The formaldehyde-fixed samples were then washed in PBS, followed by homogenization in lysis buffer. The released nuclei were pelleted and resuspended in digestion buffer for 5 minutes at 37°C. An appropriate amount of Micrococcal nuclease (MNase) (NEB) was then added to enzymatically digest the chromatin. The optimal amount of incubation time was pre-determined to shear the chromatin into a 150-1000bp banded pattern, and the reaction was stopped by 0.5 M EDTA, followed by chilling on ice for 10 minutes. Following chromatin quantification, an aliquot of 100 microgram of mouse liver chromatin and 10 microgram of anti-SRC-3 antibody (Cell signaling 5E11) or 10 microgram of anti-XBP1s antibody (Biolegend Poly6195) was used The co-immunoprecipitated complexes were then washed and eluted with elution buffer. The genomic DNA input and ChIP DNA fragments were reverse crosslinked at 65°C overnight, and treated with RNaseA and proteinase K, and then purified by phenol-chloroform extraction and ethanol precipitation.

tag: antibody

value: anti-SRC-3 (Cell Signaling 5E11)

value: Liver

tag: diet

value: CHOW


title: P2774_172

description:
full-lenght RNA-seq
P2774.tsv

value: Glioblastoma


title: SRC-3_KO_ChIP_CHOW_ZT8

tag: tissue


title: SRC-3_WT_ChIP_CHOW_CT24


title: P2774_171

description:
full-lenght RNA-seq
P2774.tsv

value: EGFR


title: XBP1s_LKO_ChIP_CHOW_CT24

value: C57BJ/L6 background

value: AlbCre;Xbp1 flx/flx (LKO, liver-specific knockout) mice

value: anti-XBP1s (Biolegend Poly6195)


title: SRC-3_KO_ChIP_CHOW_CT24


title: P2774_170

description:
full-lenght RNA-seq
P2774.tsv


title: XBP1s_ChIP_FASTING_ZT20

value: C57BJ/L6 WT mice

value: FASTING


title: MapR_D10_R3

value: Photoreceptor neuron

value: 10 days


title: SRC-3 WT_RNA-Seq_ZT12

value: SRC-3 +/+ WT mice


title: XBP1s_ChIP_FASTING_ZT16


title: XBP1s_ChIP_FASTING_ZT12


title: SRC-3_WT_ChIP_CHOW_ZT0


title: XBP1s_ChIP_FASTING_ZT08


title: P2774_169

description:
full-lenght RNA-seq
P2774.tsv


title: XBP1s_ChIP_FASTING_ZT04


title: P2774_168

description:
full-lenght RNA-seq
P2774.tsv


title: XBP1s_WT_ChIP_CHOW_CT24

value: Xbp1 flx/flx (WT, wild-type) mice


title: P2774_167

description:
full-lenght RNA-seq
P2774.tsv


title: XBP1s_ChIP_FASTING_ZT00

value: Male


title: e3.P013_16_Pl_III_Fibr_co-cult

type: RNA

city: München

first: Michael

last: Quante

address: Ismaninger Str 22

department: II Medizinische Klinik

country: Germany

institute: Technische Universität München

hyb_protocol: 60 ul (25 ng/ul) of fragemented and labeled cDNA was hybridized to Mouse Genome 2.1ST GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the RMA algorithm as implemented in Bioconductor/R.

label: biotin

source_name: Small intestinal epithelial myofibroblast organoids from mouse Pl_III indirectly co-cultured with epithelial cells

label_protocol: 150 ng RNA was amplified, biotin labeled and fragmented using the Ambion WT Expression kit and GeneChip WT Terminal Labeling and Controls kit.

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

extract_protocol: RNA was isolated using RNeasy mini Qiagen kit according to the manufacturer’s guidelines.

treatment_protocol: SI crypts were isolated from wt C57BL/6 mice and cultured in a 3D culture system. For an indirect co-culture SI MFs were seeded on the insert (Transwell, 24 mm diameter insert, 0.4 µm pore size, tissue culture treated polyester membrane, Corning) that was placed in a 6-well plate. Cells were cultured overnight in a medium composed of RPMI, 10% FBS and 1% penicillin/ streptomycin. Then, SI organoids were mixed with Matrigel and seeded in the 6-well plate, below the insert. Cells were cultured for 24 h in the Basal Medium. After that, organoids were harvested for RNA isolation.

tag: genotype/variation

value: wildtype

value: male

value: Small Intestine


title: SRC-3_ChIP_FASTING_ZT12

value: 12-16 weeks of age

value: anti-SRC-3 (Cell Signaling 5E11)

value: Liver


title: e2.P013_14_Pl_II_Fibr_co-cult

source_name: Small intestinal epithelial myofibroblast organoids from mouse Pl_II indirectly co-cultured with epithelial cells


title: P2774_166

description:
full-lenght RNA-seq
P2774.tsv

value: Glioblastoma

value: EGFR


title: SRC-3_ChIP_FASTING_ZT16

value: C57BJ/L6 background


title: d3.P013_15_Pl_III_Fibr_monoc

source_name: Small intestinal epithelial myofibroblast organoids from mouse Pl_II monocultured


title: e1.P013_12_Pl_I_Fibr_co-cult

source_name: Small intestinal epithelial myofibroblast organoids from mouse Pl_I indirectly co-cultured with epithelial cells

treatment_protocol:
SI crypts were isolated from wt C57BL/6 mice and cultured in a 3D culture system
For an indirect co-culture SI MFs were seeded on the insert (Transwell, 24 mm diameter
nsert, 0.4 µm pore size, tissue culture treated polyester membrane, Corning) that was
placed in a 6-well plate. Cells were cultured overnight in a medium composed of RPMI, 10%
FBS and 1% penicillin/ streptomycin. Then, SI organoids were mixed with Matrigel and
seeded in the 6-well plate, below the insert. Cells were cultured for 24 h in the Basal
Medium. After that, organoids were harvested for RNA isolation,


title: SRC-3_ChIP_FASTING_ZT20


title: c4.P013_09_Tum_Apc_cr_P36

source_name: Apc+/1638N small intestinal adenoma  cells  (n=3) from mouse P36


title: d2.P013_13_Pl_II_Fibr_monoc_2


title: P2774_163

description:
full-lenght RNA-seq
P2774.tsv

source_name: S94F1_P2 Inv


title: P2774_164

description:
full-lenght RNA-seq
P2774.tsv


title: SRC-3_ChIP_FASTING_ZT04


title: XBP1s_ChIP_CHOW_ZT08

value: anti-XBP1s (Biolegend Poly6195)

value: CHOW


title: P2774_162

description:
full-lenght RNA-seq
P2774.tsv


title: XBP1s_ChIP_CHOW_ZT20

value: C57BJ/L6 WT mice


title: XBP1s_ChIP_CHOW_ZT16


title: SRC-3_ChIP_FASTING_ZT08

value: FASTING


title: XBP1s_ChIP_CHOW_ZT12


title: XBP1s_ChIP_CHOW_ZT00


title: P2774_160

description:
full-lenght RNA-seq
P2774.tsv


title: SRC-3_ChIP_FASTING_ZT00


title: SRC-3_ChIP_CHOW_ZT16


title: XBP1s_ChIP_CHOW_ZT04


title: SRC-3_ChIP_CHOW_ZT00


title: SRC-3_ChIP_CHOW_ZT12


title: SRC-3_ChIP_CHOW_ZT08


title: SRC-3_ChIP_CHOW_ZT04


title: P2774_161

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_159

description:
full-lenght RNA-seq
P2774.tsv


title: SRC-3_ChIP_CHOW_ZT20


title: P2774_165

description:
full-lenght RNA-seq
P2774.tsv


title: c2.P013_10_Tum_Apc_cr_T2_P23_2

source_name: Apc+/1638N small intestinal adenoma  cells  (n=3) from mouse P23


title: c3b.P013_08_Tum_Apc_cr_P34_b

source_name: Apc+/1638N small intestinal adenoma  cells  (n=3) from mouse P34 Technical replicate of d1a


title: VSMCs, si-circ-2

data_processing:
Hiseq control software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic, and masked for low-complexity or low-quality sequence, then mapped to the GRCm38/mm10 mouse reference genome using hisat2 and mapped to gene using bowie2.
Gene expression was caculated based on FPKM (Fragments per Kilobase of exon model per Million mapped fragments) using FeatureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: csv files include FPKM values for each sample

source_name: mouse vascular smooth muscle cells (VSMCs)

growth_protocol: Mouse vascular smooth muscle cells (VSMCs) were transfected with scramble siRNA (scr) and circEsyt2 siRNA (si-circ) for 48 hours, respectivly.

extract_protocol:
VSMCs were washed twice in cold PBS and lysed in RNAiso (Takara, Cat# 108-95-2) before sent to BioWavelet (Chongqing, China) for sequencing. The first-strand of cDNA was synthesized using SuperScript III reverse transcriptase (Invitrogen, Cat# 18080-085) followed by the second-strand synthesis using synthesis enzyme mix (Biowavelet, Cat# BWR001) according to guidelines.
RNA libraries were prepared using TruePrep DNA Library Prep Kit for Illumina (Vazyme, Cat# TD503) according to the standard protocol.

tag: passage

value: circEsyt2 siRNA (si-circ)


title: c1a.P013_05_Tum_Apc_cr_T2_P21

source_name: Apc+/1638N small intestinal adenoma  cells  (n=3) from mouse P21 Technical replicate of c1b


title: P2774_158

description:
full-lenght RNA-seq
P2774.tsv

source_name: S94F1_P2 Core


title: IR4_IR

city: Kunming

first: Jinqiao

last: Qian

address: #295 Xichang Road

department: Anesthesiology

institute: the First Affiliated Hospital of Kunming Medical University

description: Rats were male and commercially-available SD rats (HSLAC, Changsha, China).

hyb_protocol: The Hy3™-labeled samples were hybridized on the miRCURY™ LNA Array (v.18.0) (Exiqon) according to array manual.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering.

organism: Rattus norvegicus

source_name: myocardium

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling.

growth_protocol: All rats were raised in Pathogen-free room and the room was maintained at a constant temperature of 23±1℃ with a 12 h light/dark cycle. Food and water were available ad libitum in the home cages.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: SD rats were randomizedly were randomly divided into three groups as following, control(Con), ischemia-reperfusion (IR), and dexmedetomidine preconditioning (DP) groups. At the end of observation, rats were deeply anesthetized and then hearts were rapidly harveste.

value: 8 weeks old

tag: Sex

value: myocardium


title: P2774_157

description:
full-lenght RNA-seq
P2774.tsv

extract_protocol:
Cells were sorted into 96-well plates containing the lysis buffer. Reverse transcription was performed using SuperScrpit II (Invitrogen) in the presence of oligo-dT30VN, template-switching oligonucleotides and betaine. The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kappa Biosystems), ISPCR primer and 22 cycles of amplification. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitvity DNA Kit (Agilent Technologies). 140 pg of the amplified cDNA were fragmented using Nextera® XT (Illumina) and amplified with indexed Nextera® PCR primers. Products were purified twice with Agencourt Ampure XP beads and quantified again using a Bioanalyzer High Sensitvity DNA Kit. Sequencing of Nextera® libraries from 384 cells was carried out in one lane on a Illumina HiSeq2500 v4.
Full-length single-cell RNA sequencing libraries were prepared using the Smart-seq2 protocol
single cell RNA-seq (scRNA-seq)


title: c3a.P013_07_Tum_Apc_cr_P34

source_name: Apc+/1638N small intestinal adenoma  cells  (n=3) from mouse P34 Technical replicate of d1b


title: VSMCs, si-circ-1

value: mouse vascular smooth muscle cells (VSMCs)


title: VSMCs, scr-1

value: control


title: VSMCs, scr-2


title: d1.P013_11_Pl_I_Fibr_monoc

source_name: Small intestinal epithelial myofibroblast organoids from mouse Pl_I monocultured

value: wildtype

value: male


title: PrES-B7_S115_002

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Base calling was performed using Off-line Basecaller (OLB) v1.9.4 provided by Illumina.
Sequences were filtered and trimmed using trim_galore version 0.6.4_ev.
Sequences were aligned and counted on mouse genome using Kallisto version 0.46.2 with mRNA database generated using RefSeq database and default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: plain text

source_name: PrES

growth_protocol: C57B6N × 129X1 F1 (#1M, #6M) ESCs were cultured in serum-free ES medium (ESM): Neurobasal:DMEMF12(1:1), 0.5 × N2 supplement (Thermo Fisher Scientific), 0.5 × B27 supplement (Thermo Fisher Scientific), 0.15 mM 1-thioglycerol (Sigma), 0.05% bovine serum albumin (BSA, Sigma), 1 × glutamine-penicillin-streptomycin (Thermo Fisher Scientific), 3μM CHIR99021, 1μM PD0325901, 103U/ml ESGRO LIF on a gelatin-coated dish or in serum ESM (2iL): Knockout DMEM (Thermo Fisher Scientific) , 20% FBS, 1xNEAA, 0.1mM β-mercaptoethanol, 1 × penicillin-streptomycin, 3μM CHIR99021, 1μM PD0325901, and 103U/ml ESGRO LIF on mouse embryonic fibroblasts (MEF) feeder dish. CD1 TSCs (#1-4M, #2-2M, #8M, #1F, #2-3F, #2-4F) were derived in serum-free TS medium: Neurobasal: DMEMF12(1:1), 0.5 × N2 supplement (Thermo Fisher Scientific), 0.5 × B27 supplement (Thermo Fisher Scientific), 0.15mM 1-thioglycerol (Sigma), 0.05% bovine serum albumin (BSA, Sigma), 1 × glutamine-penicillin-streptomycin (Thermo Fisher Scientific), 50ng/ml human FGF4, 10μg/ml heparin, 20ng/ml human Activin A, 10μM XAV939, 10μM Y27632 on MEF feeder dish. CD1 (Clea) or PWK (BRC, RIKEN) × C57BL6N (Charles River) F1 blastocysts were collected at E3.5. CD1-Tg(CAG-EGFP) mice were kindly gifted from Prof. T. Wakayama (Yamanashi university). Culture conditions used in this study is summarized in Supplementary Table 1. Each blastocyst was transferred to one well of a 48-well MEF feeder plate in +C10F4HPDGF medium (Suppl table 1): StemFit® Basic02, 1xpenicillin-streptomycin (Thermo Fisher Scientific), 10μM CHIR99021 (Reprocell), 50ng/ml human FGF4 (Sigma), 1ng/ml heparin (Sigma), 25ng/ml human PDGF-AA (R&D). Embryos were cultured in +C10F4HPDGF medium for at least 5 days until they formed outgrowths. The outgrowth was dissociated with 1xTrypLE™ Select (Thermo Fisher Scientific) and transferred into a new 48-well MEF feeder plate. After 5-7 days, PrES cell colonies reached 50-80% confluence and the cells were passaged into a 12-well MEF feeder plate. PrES cells were frozen in Cellbanker® 1plus (Zenoaq). XEN cells were derived according to a standard protocol (1) with minor modifications. CD1 blastocysts were collected at E3.5. Each blastocyst was transferred to one well of a 48-well MEF feeder plate in serum-containing ES medium: RPMI1640 (Thermo Fisher Scientific), 20% fetal bovine serum (FBS, Biosera), 1 × penicillin-streptomycin (Thermo Fisher Scientific), 1 × non-essential amino acids (NEAA, Thermo Fisher Scientific), 0.1mM β-mercaptoethanol (β-ME, Sigma), 103U/ml ESGRO LIF on a MEF feeder plate. Embryos were cultured for at least 7 days until they formed outgrowths. The outgrowth was removed by pipetting and the remaining adherent cells were continuously cultured for another 7 days. The proliferated cells were dissociated with 0.05% trypsin-EDTA (Thermo Fisher Scientific) and transferred into a new 48-well MEF feeder plate, then expanded into a 6-well plate. XEN cells were frozen in Cellbanker® 1plus (Zenoaq) and stored in a -150°C freezer (Panasonic). Removal of the primary outgrowth was not necessary when CHIR99021 (3μM) was added.

extract_protocol:
mRNA were extracted following Illumina's instructions.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combi

value: not treated

value: single cell PrES


title: IR1_IR


title: PrES-B7_S115_001


title: PrES-B6_S114_002


title: IR2_IR


title: DP4_DP


title: c1b.P013_06_Tum_Apc_cr_T2_P21_b

source_name: Apc+/1638N small intestinal adenoma  cells  (n=3) from mouse P21 Technical replicate of c1a

value: Small Intestine


title: b1,P013_02_Cr_Co-cult_P28

source_name: Small intestinal epithelial organoids indirectly co-cultured with myofibroblasts from mouse P28


title: b2.P013_04_Cr_Co-cult_P30

source_name: Small intestinal epithelial organoids indirectly co-cultured with myofibroblasts from mouse P30


title: C57BL/6J-1

source_name: Aorta

value: Aorta

value: wild type


title: a2.P013_03_Cr_Monoc_P30

source_name: Small intestinal epithelial monocultured  organoids from mouse P30


title: C57BL/6J-2


title: AS-1

value: ApoE-/-


title: PrES-B6_S114_001


title: AS-2


title: DP3_DP


title: a1.P013_01_Cr_Monoc_P28

source_name: Small intestinal epithelial monocultured  organoids from mouse P28


title: PrES-B5_S113_002


title: C3_Con


title: DP2_DP


title: PrES-B5_S113_001


title: PrES-B4_S112_002


title: C1_Con


title: C2_Con


title: PrES-B4_S112_001


title: PrES-B3_S111_002


title: PrES-B3_S111_001


title: HDAC4_knockdown_subject2

city: Daegu

first: Ji Hwan

last: Park

state: Gyeongbuk

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Newbiology

country: South Korea

institute: DGIST

description: Gene expression in HDAC4 siRNA transfected Primary human skin fibroblasts [ subject2 ]

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
The adaptor sequences were trimmed by the cutadapt (v1.4.2) and then aligned to the reference mouse genome (GRCh38) using the STAR aligner(ver 2.6.1).
gene feature (GRCh38.104.gtf) quantification to fragments per kilobase of transcript per million fragments (FPKM) using Cufflinks (Sample_*.zip)
Genome_build: GRCh38

organism: Homo sapiens

source_name: Primary human skin fibroblasts, HDAC4 siRNA transfected, subject2

growth_protocol: Primary human skin fibroblasts were obtained from healthy donors. Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Welgene, Daegu, South Korea) containing 10 % fetal bovine serum (FBS, Gibco, Rockvile, MD), 1 % penicillin (Gibco) at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated from the primary human dermal fibroblasts (HDFs) transfected with HDAC4 siRNA or HDAC4 overexpression vector and their controls (control siRNA and control pcDNA vector) using Trizol (Invitrogen, USA).
Isolated RNA was fragmented using TruSeq Stranded Total RNA Sample Prep Kit (Illumina, San Diego, USA) according to the manufacturer’s protocol, and libraries for sequencing were then generated based on reverse transcription of the fragmented RNA using Superscript II reverse transcriptase (Invitrogen, USA). After adaptor ligation, libraries were sequenced using HiSeq 2500 system.

treatment_protocol: Negative control siRNA (AccuTargetTM Negative control siRNA), and siRNAs targeting HDAC4 were purchased from Bioneer (Daejeon, Republic of Korea). Skin fibroblasts were transfected with control scrambled siRNA or siRNAs targeting HDAC4 using jetPRIME® (Polyplus-transfection® S, IIIkirch, France), as recommended by the manufacturer. The mammalian expression plasmid for HDAC4 (plasmid #30485) was purchased from Addgene (Cambridge, MA, USA) The plasmid was transiently transfected into human dermal fibroblasts using jetPRIME® (Polyplus-transfection® S, IIIkirch, France) following the manufacturer's instructions. HDAC4 lentiviral particles were produced according to the manufacturer’s protocol (System Biosciences, Mountain View, CA, USA) using pCDH-CMV-MCS-EF1-Puro plasmid or pCDH-CMV-HDAC4-EF1-Puro plasmid. pCDH-CMV-HDAC4-EF1-Puro plasmid made by amplifying the HDAC4 cDNA from pcDNA3.1-HDAC4 plasmid using PCR and subcloning it into pCDH-CMV-MCS-EF1-Puro plasmid. Briefly, HEK-293TN cells were transfected with each plasmid with pGag-pol and pVSV-G using Lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA). Viral supernatant was collected and transduced into human dermal fibroblasts. Infected cells were selected by 5μg/ml of puromycin (SNUH-IBC-1903-007-004).

value: Primary human skin fibroblasts

value: HDAC4 siRNA transfected


title: HDAC4_knockdown_subject1

description: Gene expression in HDAC4 siRNA transfected Primary human skin fibroblasts [ subject1 ]

source_name: Primary human skin fibroblasts, HDAC4 siRNA transfected, subject1


title: HDAC4_knockdown_subject3

description: Gene expression in HDAC4 siRNA transfected Primary human skin fibroblasts [ subject3 ]

source_name: Primary human skin fibroblasts, HDAC4 siRNA transfected, subject3


title: HDAC4_dummay-siRNA_subject3

description: Gene expression in control scrambled siRNA transfected Primary human skin fibroblasts [ subject3 ]

source_name: Primary human skin fibroblasts, control scrambled siRNA transfected, subject3

value: control scrambled siRNA transfected


title: PrES-B1_S109_002


title: PrES-B2_S110_002


title: HDAC4_dummay-siRNA_subject2

description: Gene expression in control scrambled siRNA transfected Primary human skin fibroblasts [ subject2 ]

source_name: Primary human skin fibroblasts, control scrambled siRNA transfected, subject2


title: PrES-B1_S109_001


title: PrES-B12_S120_002


title: HDAC4_dummay-siRNA_subject1

description: Gene expression in control scrambled siRNA transfected Primary human skin fibroblasts [ subject1 ]

source_name: Primary human skin fibroblasts, control scrambled siRNA transfected, subject1


title: HDAC4_overexpression_subject3

description: Gene expression in HDAC4 overexpression vector transfected Primary human skin fibroblasts [ subject3 ]

source_name: Primary human skin fibroblasts, HDAC4 overexpression vector transfected, subject3

value: HDAC4 overexpression vector transfected


title: PrES-B12_S120_001


title: PrES-B2_S110_001


title: HDAC4_overexpression_subject2

description: Gene expression in HDAC4 overexpression vector transfected Primary human skin fibroblasts [ subject2 ]

source_name: Primary human skin fibroblasts, HDAC4 overexpression vector transfected, subject2


title: SF8386

type: genomic

city: Lebanon

first: Lucas

last: Salas

state: NH

address: 1 Medical Center Dr, DHMC

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software

label: Cy5 and Cy3

source_name: FFPE GBM Recurrent tumor sample, Trial arm: Control

label_protocol: Standard Illumina Protocol

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

value: glioblastoma tumor

tag: subject

value: Recurrent

tag: slide

tag: array

tag: ChIP

tag: age (years)

value: M

tag: vital status

value: Dead

tag: overall survival (days)

tag: treatment time (days)

tag: trial arm

value: Control

tag: estimated sample purity

tag: fresh frozen (ff) or ffpe

value: FFPE


title: PrES-B11_S119_002

tag: strain

tag: treatment

tag: cell type


title: Autopsy 5 ant

source_name: FF GBM Recurrent tumor sample, Trial arm: Treatment

tag: tissue

value: F

value: Treatment

value: FF


title: SF8847


title: Patient 1 Autopsy 23


title: VU 10390

source_name: FF GBM Primary tumor sample, Trial arm: Control

value: Primary


title: VU 10900

source_name: FF GBM Recurrent tumor sample, Trial arm: Control


title: Biopsy 1

source_name: FFPE GBM Primary tumor sample, Trial arm: Treatment


title: HDAC4_overexpression_subject1

description: Gene expression in HDAC4 overexpression vector transfected Primary human skin fibroblasts [ subject1 ]

source_name: Primary human skin fibroblasts, HDAC4 overexpression vector transfected, subject1


title: Patient 5 Autopsy Post


title: VU 11162


title: Biopsy 6


title: Patient 1 Autopsy 22


title: SF9400

source_name: FFPE GBM Primary tumor sample, Trial arm: Control


title: Autopsy Tumor 4 B


title: VU 11141


title: Biopsy 2


title: 3 Autopsy Tumor 2

source_name: FFPE GBM Recurrent tumor sample, Trial arm: Treatment


title: Autopsy 5 mid


title: Autopsy Tumor 4 C


title: Patient 1 Autopsy 21


title: Sorghum leaves-heat small RNA library

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

data_processing:
Remove low quality reads with nucleotides of scores lower than 30 in the first 25 nucleotides
Keep the sequences whose lengths are greater than or equal to 18 bp (the 3' adapter sequences of reads had been removed by the sequencing facility)
Sort and remove repetitive sequences
Calculate the counts of unique sequences
The unique sequences were aligned to genome sequence of Sorghum bicolor
Genome_build: JGI S.bicolor v1.0
Supplementary_files_format_and_content: sequences and count values

organism: Sorghum bicolor

source_name: Sorghum leaves

growth_protocol: Sorghum (Sorghum bicolor (L.) Moench) seeds were sown in pots (0.2 m diameter × 0.45 m tall) filled with pure, fine sand soil and grown in growth chambers (Conviron Ltd., Winnipeg, Canada) at 28°/20°C (day/night) with a photoperiod of 14 h/10 h (day/night). After germination, sorghum seedlings were thinned to one plant per pot.

extract_protocol:
Total RNA was extracted from leaves of control, drought or heat, drought and heat-exposed sorghum using the Trizol reagent
Small RNA libraries were constructed using Illumina TruSeq small RNA protocol.

treatment_protocol: To impose heat stress,  30 days after sowing, sorghum seedlings grown at 28°/20°C (day/night) were transferred to another growth chamber maintained at 38°/30°C (day/night) for 50 days. Drought stress was imposed by withholding irrigation for one week on 73-day-old (after sowing) plants grown at 28°/20°C (day/night).  Drought and heat combination was imposed by withholding irrigation for one week on 73-day-old (after sowing) plants grown at 38°/30°C (day/night). At the end of stress treatment, leaf samples from control, drought or heat, drought and heat-stressed plants were harvested

value: leaves

value: heat


title: Sorghum leaves-drought small RNA library

value: drought


title: VU 10852


title: VU 11014


title: PrES-A9_S105_002

source_name: PrES

value: not treated

value: single cell PrES


title: HDAC4_pcDNA_subject1

description: Gene expression in pcDNA transfected Primary human skin fibroblasts [ subject1 ]

source_name: Primary human skin fibroblasts, pcDNA transfected, subject1

value: Primary human skin fibroblasts

value: pcDNA transfected


title: VU 10292

value: glioblastoma tumor


title: CRC liver metastatic tissue 3

city: Guangzhou

first: Beiping

last: Zhong

address: Erheng Road, Yuancun, Tianhe District, Guangzhou City

department: Department of Colorectal Surgery

institute: The Sixth Affiliated Hospital of Sun Yat-sen University

data_processing:
reads were filtered by fastp (version 0.18.0)
paired-end clean reads were mapped to the reference genome using HISAT2.2.4 with “-rna-strandness RF” and other parameters set as a default.
count were quantified from BAM files using featureCounts(v2.0.2)
Genome_build: hg38
Supplementary_files_format_and_content: gene count in csv format

source_name: human CRC tissue

extract_protocol: CRC patients' tissue were collected from the Sixth Affiliated Hospital of Sun Yat-sen Universitye. Total RNA was isolated and purified with the RNeasy Mini Kit (Qiagen, USA). The RNA samples were sent to Gene Denovo Biotechnology Company (Guangzhou, China) for sequencing and mRNA library generation.

value: untreated

value: CRC tissue

tag: group

value: metastasis


title: VU 11029

tag: Sex

value: Dead

value: Control


title: 2 Autopsy Tumor

tag: subject

value: Recurrent

value: M

value: FFPE


title: 3 Autopsy Tumor

tag: slide

value: F

value: Treatment


title: 2 Autopsy Tumor 2

tag: array


title: hippocampus of saline-treated rat 2

city: Changsha

first: Jiali

last: Shao

state: Hunan

address: 281 Tongzipo Road, Changsha, Hunan, China

department: Department of Anesthesiology

institute: The affiliated Cancer Hospital of Xiangya School of Medicine, Central South University

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
Sequencing quality are examined by FastQC.
Trimmed reads (pass Illumina quality filter, trimmed 5,3-adaptor bases by cutadapt) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software. The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2.
The abundance of tRF & tiRNA are evaluated using their sequencing counts and is normalized as counts per million of total aligned reads (CPM).
Genome_build: GtRNAdb , tRNAscan-SE
Supplementary_files_format_and_content: The abundance of tRF & tiRNA  is normalized as counts per million of total aligned reads (CPM) in xlsx formats file

source_name: hippocampus

extract_protocol:
The hippocampus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. We use the commercial kit for tRF & tiRNA-seq library preparation, which includes 3-adapter and 5-adapter ligation adaptor ligation, cDNA synthesis and library PCR amplification. The prepared tRF&tiRNA-seq libraries are finally quantified using Agilent BioAnalyzer 2100, then sequenced using Illumina NextSeq 500/550 V2 kit (#FC-4042005, Illumina).
Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~134-160 bp PCR amplified fragments were extracted and purified from the PAGE gel. And finally, the completed libraries were quantified byAgilent 2100 Bioanalyzer.

value: Sprague-Dawley

value: hippocampus

value: saline

tag: age

value: 6-8 weeks


title: PrES-B11_S119_001

value: not treated

value: single cell PrES


title: RNA-seq_PFC ELS Rep5

city: Kensington

first: Irina

last: Voineagu

state: NSW

address: High St

department: Biotechnology and Biomolecular Sciences

country: Australia

institute: The University of New South Wales

data_processing:
Base-calling was peformed using standard Illumina base-calling software
RNA-seq reads were mapped to the rat genome rn6 using the STAR spliced aligner with the following parameters: --outSJfilterOverhangMin 5 5 5 5 --alignSJoverhangMin 5 --alignSJDBoverhangMin 5 --outFilterMultimapNmax 1   --outFilterScoreMin 1   --outFilterMatchNmin 1   --outFilterMismatchNmax 2  --chimSegmentMin 5    --chimScoreMin 15   --chimScoreSeparation 10  --chimJunctionOverhangMin 5.
Data quality was assessed using Qualimap
Gene expression quantification was carried out using the featureCounts function as implementer in STAR using the Ensembl rat genome annotation, release 89.
Genes were filtered to include those expressed at a minimum of 0.5 reads per kilobase per million (rpkm) in a minimum of 2 samples, i.e. 16,041 genes.
Genome_build: rn6
Supplementary_files_format_and_content: Matrix table with rpkm for filtered genes for every sample

source_name: Prefrontal cortex

extract_protocol:
Tissue collection was carried out at post-natal day 91. RNA was extracted from 5 male rat PFC tissue samples per group. RNA was extracted using the Qiagen miRNeasy Mini kit with oncolumn DNase digestion using the QIAGEN RNase-Free DNase kit according to the manufacturers protocol.
Illumina TruSeq Stranded mRNA-seq kit

treatment_protocol: Limited nesting paradigm was performed for ELS rats from post-natal day 2-9

value: prefrontal cortex

value: post natal day 91

tag: condition

value: limited nesting

value: male


title: Autopsy Tumor 6-2

value: glioblastoma tumor

tag: ChIP

tag: age (years)

tag: vital status

value: Dead


title: PrES-B10_S118_002


title: RNA-seq_PFC ELS Rep3


title: Biopsy 3

value: Primary

tag: overall survival (days)

tag: treatment time (days)

tag: trial arm


title: RNA-seq_PFC ELS Rep1

tag: strain


title: PrES-A8_S104_001

tag: treatment


title: RNA-seq_PFC ELS Rep2


title: PrES-A8_S104_002

tag: cell type


title: Sorghum leaves-drought and heat small RNA library

tag: tissue

value: leaves

value: drought


title: Biopsy 4

value: M

tag: estimated sample purity

tag: fresh frozen (ff) or ffpe

value: FFPE


title: Sorghum leaves-control small RNA library

value: control


title: HDAC4_pcDNA_subject3

description: Gene expression in pcDNA transfected Primary human skin fibroblasts [ subject3 ]

source_name: Primary human skin fibroblasts, pcDNA transfected, subject3

value: Primary human skin fibroblasts

value: pcDNA transfected


title: RNA-seq_PFC Con Rep5

value: Sprague-Dawley

tag: Sex


title: HDAC4_pcDNA_subject2

description: Gene expression in pcDNA transfected Primary human skin fibroblasts [ subject2 ]

source_name: Primary human skin fibroblasts, pcDNA transfected, subject2


title: hippocampus of nicotine-treated rat 3

value: hippocampus

value: nicotine

value: 6-8 weeks


title: PrES-B10_S118_001

value: not treated

value: single cell PrES


title: hippocampus of nicotine-treated rat 2


title: hippocampus of nicotine-treated rat 1


title: Autopsy Tumor 6

tag: subject

value: Recurrent

tag: slide

value: Treatment


title: hippocampus of saline-treated rat 3

value: saline

tag: age


title: RNA-seq_PFC Con Rep1

value: prefrontal cortex

value: post natal day 91

tag: condition

value: male


title: PrES-A6_S102_002


title: hippocampus of saline-treated rat 1


title: PrES-A9_S105_001


title: CRC liver metastatic tissue 2

value: untreated

value: CRC tissue

tag: group

value: metastasis


title: CRC liver metastatic tissue 1


title: CRC primary tumor tissue 4

value: without metastasis


title: PrES-A7_S103_002


title: PrES-A5_S101_002


title: RNA-seq_PFC ELS Rep4

value: limited nesting


title: RNA-seq_PFC Con Rep4

value: Sprague-Dawley

value: control


title: CRC primary tumor tissue 3


title: CRC primary tumor tissue 2


title: PrES-A6_S102_001


title: PrES-A7_S103_001


title: RNA-seq_PFC Con Rep3


title: CAF9_2

city: Gangnam-gu

first: Seok-Hyung

last: Kim

state: Seoul

address: 81, Irwon-ro

department: Department of Pathology

institute: Samsung Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimmomatic
trimmed sequenced reads then mapped to hg19 whole genome using STAR
Read count extraction were performed using htseq-count
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes read count values for each Sample

source_name: Human CAF

growth_protocol: All primary human colon CAFs were immortalized with SV40-large T antigen (pHIV7-CNPO-Tag) and hTERT (pHIV7-CNPO-hTERT).  All cells were grown in DMEM medium containing 10% FBS and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml).

extract_protocol:
Total RNA ((including gDNA removal) was extracted using by RNeasy plus mini kit (Cat no.#74134, Qiagen).
Sequencing libraries were prepared using TruSeq RNA Sample Preparation kit v2 (Illumina).  After pooled libraries were denatured, sequencing of each library was carried out using the 100 bp. paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit with HiSeq 2500 (Illumina Technologies., USA).

treatment_protocol: All Human colon CAFs were incubated at 37°C in 5% CO2 and grown to 80-90% confluence.

value: colon cancer associated fibroblasts (CAF)


title: CAF9_3


title: CRC primary tumor tissue 1


title: PrES-A5_S101_001


title: CAF9_1


title: RNA-seq_PFC Con Rep2


title: PrES-A4_S100_002


title: CAF8_3


title: PrES-A4_S100_001


title: CAF8_2


title: CAF8_1


title: PrES-A3_S99_001


title: PrES-A3_S99_002


title: CAF7_2


title: CAF7_3


title: PrES-A2_S98_002


title: PrES-A2_S98_001


title: CAF7_1


title: single intact control blastocyst (after in vivo fertilization and IVC)_KSOM(aa) #10

city: Muenster

first: Michele

last: Boiani

address: Roentgenstrasse 20

institute: Max Planck Institute Muenster

description: Single blastocyst was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit was used, for 16 h (+/- 1h) at 45°C with 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing:
The robust multiarray averaging method was applied for background correction, normalization, and probe summarization using the Affymetrix Expression Console.
#%result_name=Analysis_2_SST_RMA
#%array_type=MTA-1_0
#%annotation=MTA-1_0.na36.mm10.transcript.csv
#%comparison=M vs S

label_protocol: Biotinylated cDNA was prepared using GeneChip WT Pico kit, reverse-transcribing 20 micrograms cRNA and, of these, subjecting 5.5 micrograms to labeling

growth_protocol: Zygotes from B6C3F1 x CD1 mating (stimulated cycle, PMSG + hCG given 48 hours apart) were collected from the oviducts and cultured to the 2-cell stage in KSOM(aa) medium using a 4-well plate under 5% CO2 in air at 37 degrees C. At the 2-cell stage the sister blastomeres were separated from each other and cultured individually in ART medium (GM501 CULT vs SAGE 1-StepTM) in a 96-well plate. Control (zygotic) embryos were cultured individually in KSOM(aa) in 96-well plate, without bisection.

extract_protocol: Individual blastocysts were lysed in in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water according to the manufacturer's instructions.

treatment_protocol: At the 2-cell stage embryos were split, cultured individually to blastocyst stage, and these blastocysts were lysed in Zymo buffer.

tag: strain background

value: B6C3F1 x CD1

value: Theiler stage 5; 4 dpc (96h IVC)

value: preimplantation mouse embryo

tag: cell numberd

value: approx 80 cells per blastocyst


title: PrES-A1_S97_002

value: not treated

value: single cell PrES


title: CAF6_3


title: single intact control blastocyst (after in vivo fertilization and IVC)_KSOM(aa) #4


title: PrES-A1_S97_001


title: single intact control blastocyst (after in vivo fertilization and IVC)_KSOM(aa) #2


title: blastocyst pair 10 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 10b SAGE 1step

value: approx 40-50 cells per blastocyst


title: CAF6_2


title: single intact control blastocyst (after in vivo fertilization and IVC)_KSOM(aa) #8


title: CAF6_1


title: PrES-A12_S108_002


title: single intact control blastocyst (after in vivo fertilization and IVC)_KSOM(aa) #9


title: single intact control blastocyst (after in vivo fertilization and IVC)_KSOM(aa) #3


title: single intact control blastocyst (after in vivo fertilization and IVC)_KSOM(aa) #7


title: single intact control blastocyst (after in vivo fertilization and IVC)_KSOM(aa) #5


title: single intact control blastocyst (after in vivo fertilization and IVC)_KSOM(aa) #6


title: blastocyst pair 7 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 7a GM501


title: blastocyst pair 9 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 9b SAGE 1step


title: blastocyst pair 10 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 10a GM501


title: single intact control blastocyst (after in vivo fertilization and IVC)_KSOM(aa) #1


title: blastocyst pair 7 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 7b SAGE 1step


title: blastocyst pair 8 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 8b SAGE 1step


title: blastocyst pair 9 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 9a GM501


title: blastocyst pair 5 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 5a GM501


title: PrES-A12_S108_001


title: blastocyst pair 6 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 6a GM501


title: blastocyst pair 4 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 4b SAGE 1step


title: blastocyst pair 4 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 4a GM501


title: CAF5_3


title: CAF5_2


title: PrES-A11_S107_002


title: CAF5_1


title: PrES-A11_S107_001


title: blastocyst pair 6 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 6b SAGE 1step


title: RNA of DATS3

first: Wenru

last: Li

address: No.100, Xianliezhong Road

institute: Institute of Microbiology, Guangdong Academy of Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008).
Genome_build: Pseudomonas aeruginosa PAO1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Pseudomonas aeruginosa PAO1

source_name: Transcriptome of DATS-treated P. aeruginosa PAO1

growth_protocol: Every 50 mL LB medium was inoculated exponential growth phase of P. aeruginosa PAO1, with the bacterial concentration of 1.0E8 CFU/mL.  All the three triplicate experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate at 180 rpm for 5 hours.

extract_protocol:
Cells of P. aeruginosa PAO1 were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
Strand specific library: The construct method of strand specific library is similar to that of NEB library expect that when synthesizing the second strand cDNA, dTTP is replayed by dUTP. After overhangs of the purified double-stranded cDNA are converted into blunt ends, adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization, the second strand cDNA is digested by USER enzyme. The following step is identical with NEB library construction.

treatment_protocol: LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAO1 at a concentration of 1.0E8 CFU/mL. Dially sulfide and diallyl ether were then added at a concentration of either 0 (control) or 0.625 μl/mL, respectively, in triplicate. All nine experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate of 180 rpm for 5 h.

value: DATS-treated sample

tag: growth phase

value: exponential growth phase


title: PrES-A10_S106_002


title: blastocyst pair 8 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 8a GM501


title: blastocyst pair 5 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 5b SAGE 1step


title: CAF4_3


title: RNA of control3 (DATS control)

source_name: Transcriptome of control of P. aeruginosa PAO1

value: native sample


title: PrES-A10_S106_001


title: RNA of DATS1


title: CAF4_2


title: RNA of control2 (DATS control)


title: RNA of DATS2


title: blastocyst pair 3 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 3b SAGE 1step


title: RNA of control1 (DATS control)


title: blastocyst pair 2 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 2a GM501


title: CAF4_1


title: blastocyst pair 1 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 1a GM501


title: ES-H8_S92_001

source_name: ES

value: single cell ES


title: blastocyst pair 3 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 3a GM501


title: blastocyst pair 2 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 2b SAGE 1step


title: Anti.RIP9.cleared.B

city: Los Angeles

middle: Lloyd

last: Hayes

state: CA

address: 5151 State University Dr

department: Chemistry and Biochemistry

institute: California State University Los Angeles

data_processing:
Phred built into Trimmomatic was used for basecalls.
Bad quality reads and adapter sequences were trimmed from the MiSeq libraries using Trimmomatic (Bolger et al., 2014). Next the trimmed datasets were aligned to the maize reference genome B73_RefGen_v4 (Jiao et al., 2017) using bowtie2, tophat2 and cufflink (Langmead and Salzberg, 2012, Trapnell et al., 2012). Resulting files were converted into SAM and BAM format using SAMtools (Li et al., 2009). Performed using a custon script. #java -jar /usr/local/bin/trimmomatic-0.35.jar SE -phred33 mR134-L1-P1-CGATGT CPXRNA.fq ILLUMINACLIP:/usr/local/bin/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36; bowtie2-build [infile fasta] Zea_mays_4_cp; bowtie2 -x Zea_mays_4_cp -U CPXRNA.fq -S CPX.sam; samtools view -S -b CPXRNA.sam > CPXRNA.bam; samtools sort -o CPXRNA.bam CPXRNA.sorted.bam; samtools index CPXRNA.sorted.bam; featureCounts -T 5 -t exon -g gene_id -a ZM_v4.43.gtf -O -o Result.txt CPXRNA sorted.bam#
RPKM was calculated by taking the total number of reads assigned to unique gene features from Zea_mays.B73_RefGen_v4.46.chromosome.Pt.gff3 from Ensembl Genomes and then using the equation [feature reads / (gene length (kb)/ total mapped reads/1,000,000)]
Reads from feature count were exported into a single data sheet using featureCounts.
Redundant reads from FeatureCount that map twice to the inverted repeat were removed to only count single, unique gene features
Genome_build: B73_RefGen_v4
Supplementary_files_format_and_content: BAM files used for genome alignmnets
Supplementary_files_format_and_content: Table including all raw reads and processed RPKM and fold change values

organism: Zea mays

source_name: Chloroplasts

growth_protocol: Zea mays var. Sugar Buns (Johnny’s Selected Seeds, Fair- field, ME, USA) seeds were planted and grown for 14-21 days in a greenhouse.

extract_protocol:
Pre-cleared chloroplast supernatant was placed in the chilled antibody-beads tube, mixed gently by pipetting, and incubated for 20 min at 4°C.
Library construction was performed according to the Illumina TruSeq® Stranded mRNA Sample Preparation Guide with modification.  The input quantity for total RNA was 50 ng and chemically fragmented for three minutes.  First strand synthesis used random primers and reverse transcriptase was used to make cDNA. After second strand synthesis the ds cDNA was cleaned using AMPure XP beads and the cDNA was end repaired and then the 3’ ends were adenylated. Illumina barcoded adapters were ligated on the ends and the adapter ligated fragments were enriched by nine cycles of PCR. The resulting libraries were validated by qPCR and sized by Agilent Bioanalyzer DNA high sensitivity chip. The concentrations for the libraries were normalized and then multiplexed together. The multiplexed libraries were sequenced on the Miseq using version 3 single end 150 cycles chemistry. The version of Miseq control software was MCS v: 2.6.2.1 with real time analysis software, RTA 1.18.54.0.

treatment_protocol: Leaf tissue was homogenized in a blender and intact chloroplasts isolated using a continuous Percol gradient.

value: Chloroplasts from 14-21 day old seedlings

tag: cultivar

value: Sugar Buns

tag: antibody

tag: fraction

value: Supernatent/unbound

value: 14-21 day old seedlings

value: leaf


title: Anti.RIP9.cleared.A


title: CAF3_3

value: colon cancer associated fibroblasts (CAF)


title: blastocyst pair 1 (after in vivo fertilization, 2-cell stage bisection and IVC)_Blastocyst 1b SAGE 1step

value: B6C3F1 x CD1


title: ES-H8_S92_002

tag: strain

tag: treatment


title: ES-H7_S91_002

tag: cell type


title: ZmCpRNA.A

tag: tissue

value: Raw Chloroplast extracts


title: ZmCpRNA.B


title: CAF3_2


title: ES-H7_S91_001


title: CAF3_1


title: Co.IP.Anti.RIP9.B

value: Bound beads


title: Co.IP.Anti.RIP9.A


title: Co.IP.Anti.ORRM1.B


title: Co.IP.Anti.ORRM1.A


title: ES-H6_S90_002


title: CAF2_3


title: Co.IP.AntiOZ1.B


title: Bead.Enriched


title: CAF2_2


title: ES-H5_S89_002


title: Co.IP.AntiOZ1.A


title: ES-H6_S90_001


title: Nr18: kd+G_4-3_dark_4d

city: Würzburg

first: Markus

last: Henninger

address: Julius-von-Sachs Platz 2

institute: University of Würzburg

data_processing:
Sequenced reads were mapped to TAIR10 by STAR for the whole genome using featurecount.
Analysis were performed with DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Seedling

extract_protocol:
Seedlings were harvested, frozen in liquid nitrogen and RNA was harvested using QIAGEN RNEasy Micro-Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 4 days after germination

tag: genotype

tag: light

value: dark

value: Glucose

value: seedling


title: Nr17: kd+G_4-2_dark_4d


title: ES-H5_S89_001

value: not treated


title: CAF1_3


title: Nr12: WT+G_4-3_dark_4d

value: wild type


title: Nr14: kd+G_4-2_4d

value: light


title: Nr11: WT+G_4-2_dark_4d


title: Nr15: kd+G_4-3_4d


title: Nr13: kd+G_4-1_4d


title: CAF1_2


title: ES-H4_S88_002

value: single cell ES


title: ES-H4_S88_001


title: CAF1_1


title: Nr10: WT+G_4-1_dark_4d


title: ES-H3_S87_002


title: Nr09: WT+G_4-3_4d


title: ES-H3_S87_001


title: ES-H2_S86_002


title: Nr08: WT+G_4-2_4d


title: Nr07: WT+G_4-1_4d


title: NS_9

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
Illumina standard primers were trimmed
Paired reads were mapped to the human reference genome (b37) using STAR
Number of reads for each gene was counted using HTSeq
Genome_build: b37
Supplementary_files_format_and_content: raw read count matrix (genes x samples)

source_name: skin

extract_protocol:
Total RNA was isolated with RNeasy Kit (Qiagen) from 5mm skin biopsy that was previously powderized in liquid nitrogen.
Complemetary DNA (cDNA) was prepared using the NuGEN Ovation RNA-Seq System to obtain the strand-specific RNA-seq libraries from 100 ng of total RNA.Ribosomal RNA transcripts were depleted using the Insert Dependent Adaptor Cleavage (InDA-C) technology.. Equimolar pool of the final indexed RNA-Seq libraries were sequenced on an Illumina HiSeq 2500 (paired-end reads 130 bases + 130 bases) to obtain about 50 million paired-end reads per library.

value: skin

tag: disease state

value: lesional

tag: patient name

tag: clinical manifestation

value: NS-ILC


title: Nr05: kd_3-2_dark_3d

tag: age

value: 3 days after germination


title: CAF2_1


title: NS_8


title: Nr04: kd_3-1_dark_3d


title: NS_6


title: Nr06: kd_3-3_dark_3d


title: Nr03: WT_3-3_dark_3d


title: ES-H2_S86_001


title: Nr02: WT_3-2_dark_3d


title: ES-H1_S85_002


title: Nr16: kd+G_4-1_dark_4d


title: NS_67

value: healthy control

value: control


title: ES-H1_S85_001


title: L1701740: kd_5-3_dark_5d

value: 5 days after germination


title: L1701739: kd_5-2_dark_5d


title: ES-G9_S81_002


title: L1701738: kd_5-1_dark_5d


title: L1701737: kd_5-3_light_5d


title: NS_63


title: NS_64


title: L1701736: kd_5-2_light_5d


title: ES-G9_S81_001


title: NS_62


title: L1701735: kd_5-1_light_5d


title: ES-G8_S80_002


title: NS_61


title: L1701734: WT_5-3_dark_5d


title: L1701733: WT_5-2_dark_5d


title: L1701731: WT_5-3_light_5d


title: NS_5


title: ES-G7_S79_002


title: Nr01: WT_3-1_dark_3d


title: L1701730: WT_5-2_light_5d


title: NS_66


title: NS_59


title: NS_58


title: ES-G7_S79_001


title: NS_57


title: L1701726: kd_4-1_dark_4d


title: L1701725: kd_4-3_light_4d


title: ES-G6_S78_001


title: L1701724: kd_4-2_light_4d


title: ES-G6_S78_002


title: NS_56


title: L1701723: kd_4-1_light_4d


title: ES-G8_S80_001


title: NS_54


title: L1701721: WT_4-2_dark_4d


title: L1701722: WT_4-3_dark_4d


title: NS_52


title: ES-G5_S77_001


title: L1701719: WT_4-3_light_4d


title: L1701720: WT_4-1_dark_4d


title: ES-G4_S76_002


title: ES-G5_S77_002


title: L1701717: WT_4-1_light_4d


title: L1701727: kd_4-2_dark_4d


title: L1701729: WT_5-1_light_5d


title: L1701716: kd_3-3_dark_3d


title: NS_49


title: NS_44

value: NS-SE


title: L1701715: kd_3-2_dark_3d


title: ES-G3_S75_002


title: L1701714: kd_3-1_dark_3d


title: L1701713: WT_3-3_dark_3d


title: NS_43


title: L1701712: WT_3-2_dark_3d


title: NS_42


title: L1701711: WT_3-1_dark_3d


title: ES-G2_S74_002


title: HH7_10X_data

city: Oxford

first: Tatjana

last: Sauka-spengler

address: Headley Way, Headington

department: Radcliffe Dept of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Sequenced files were demultiplexed and features counted using CellRanger (v3.0.0)
Seurat (v3.0.1) R package was used for data processing for scRNA samples
Genome_build: galGal6. Custom genomes were build using CellRanger to allow proper mapping of reads/fragments.
Supplementary_files_format_and_content: .tsv.gz containing barcodes, feature counts, and matrix data

organism: Gallus gallus

source_name: HH7 whole epiblast

growth_protocol: ferilized eggs were grown at 37C to the desired stage according Hamburger and Hamilton (1951)

extract_protocol:
embryonic material was dissected and disssociated for FACS using dispase/tyrpsin
As manufacturers protocol, 10X Genomics single-cell RNA-seq Cat. #1000075
3’ Library and Gel Bead Kit v3

treatment_protocol: untreated

value: chick embryonic epiblast

value: untreated


title: NS_41


title: ES-G2_S74_001


title: HH6_10X_data

source_name: HH6 whole epiblast


title: L1701718: WT_4-2_light_4d

value: 4 days after germination


title: NS_40


title: HH5_10X_data

source_name: HH5 NPB dissections


title: ES-G4_S76_001


title: ES-G1_S73_002


title: ES-G1_S73_001


title: NS_3


title: NS_39


title: ES-G12_S84_002


title: ES-G3_S75_001


title: NS_37


title: ES-G12_S84_001


title: ES-G11_S83_002


title: NS_36


title: ES-G11_S83_001


title: NS_35


title: ES-G10_S82_002


title: ES-G10_S82_001


title: Mesenchymal stem cell culture; passage 8

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

institute: University of Nottingham

description:
gene expression data of mesenchymal stem cells (used as control)
MSC_2

hyb_protocol: Following fragmentation and labeling, ss-cDNA were hybridized for 16 hr at 45°C to Human Arrays. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix, P/N 00-0079).

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

data_processing: The raw CEL files were normalized using RMA background correction with quantile normalization, log2 transformation and mean probe-set summarization with adjustment for GC content. Differentially expressed genes were considered significant if p-value with FDR ≤ 0.05 and fold-change of >2 or < -2.

label_protocol: Affymetrix GeneChipTM WT PLUS Reagent Kit

growth_protocol: CPCs were cultured in monolayers in 75 cm2 cell culture flasks until ~80% confluence in GlutaMax DMEM (1.0 g/L glucose) containing 10% FCS and 50 μg/mL gentamycin. MSCs were expanded in monolayers in 75 cm2 cell culture flasks until ~80% confluence in GlutaMax DMEM (4.5 g/L glucose) containing 10% FCS and 1% P/S.

extract_protocol: Total RNA was isolated from cells using the RNeasy kit as per the instructions of the manufacturer, and stored at –80 °C. RNA concentration and purity was determined by a Nanodrop 2000 UV-Vis spectrophotometer.

treatment_protocol: Both CPCs and MSCs were control cultures (did not receive treatment).

value: mesenchymal stem cells

tag: cell culture

value: hTERT immortalized cell line


title: MYb11:none_12h_rep3

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to WS235 whole genome using STAR-2.5.3a
Read counts per gene is extracted via STAR-2.5.3a
Genome_build: WS235
Supplementary_files_format_and_content: tab-delimited text files include Raw reads counts for each Sample

organism: Caenorhabditis elegans

source_name: whole body

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

treatment_protocol: Worms were exposed to OP50, MYb11, MYb115 and BT at the stage L4. The experiments with BT were performed at 20°C.

value: Wild type (N2)

tag: developmental stage

tag: pathogen

tag: timepoint

value: 12 hrs

tag: medium

value: mNGM

tag: temperature


title: NS_34


title: OP50:BT407_24h_rep3

value: 24 hrs


title: OP50:BT247_12h_rep3


title: MYb115:BT407_24h_rep3


title: Mesenchymal stem cell culture; passage 9

description:
gene expression data of mesenchymal stem cells (used as control)
MSC_3


title: OP50:none_24h_rep3


title: NS_33

value: skin


title: Chondrogenic progenitor cell culture; passage 25

description:
gene expression data of chondrogenic progenitor cells
CPC_3

value: chondrogenic progenitor cells


title: Chondrogenic progenitor cell culture; passage 24

description:
gene expression data of chondrogenic progenitor cells
CPC_2


title: NS_38

value: NS-ILC


title: ES-F9_S69_002

value: not treated

value: single cell ES


title: MYb115:BT407_12h_rep3


title: MYb115:none_12h_rep3


title: MYb115:none_12h_rep2


title: ES-F9_S69_001


title: Mesenchymal stem cell culture; passage 7

description:
gene expression data of mesenchymal stem cells (used as control)
MSC_1


title: MYb11:BT247_24h_rep3


title: NS_30

value: healthy control

value: control


title: ES-F8_S68_002


title: Chondrogenic progenitor cell culture; passage 23

description:
gene expression data of chondrogenic progenitor cells
CPC_1


title: OP50:BT247_24h_rep3


title: NS_32

value: lesional


title: ES-F8_S68_001


title: ES-F7_S67_002


title: OP50:none_12h_rep3


title: MYb115:none_24h_rep3


title: MYb11:none_24h_rep3


title: NS_26

value: NS-SE


title: OP50:none_12h_rep2


title: NS_28


title: OP50:none_12h_rep1


title: OP50:BT247_24h_rep2


title: MYb115:BT407_12h_rep2


title: OP50:none_24h_rep2


title: OP50:BT407_24h_rep2


title: NS_31


title: NS_24


title: ES-F6_S66_001


title: ES-F5_S65_001


title: ES-F5_S65_002


title: ES-F7_S67_001


title: NS_21


title: NS_27


title: ES-F6_S66_002


title: NS_20


title: MYb115:none_24h_rep1


title: MYb115:none_24h_rep2


title: MYb11:BT407_24h_rep3


title: NS_19


title: ES-F4_S64_002


title: MYb115:BT407_24h_rep2


title: ES-F4_S64_001


title: MYb115:BT247_12h_rep3


title: OP50:BT407_24h_rep1


title: NS_18


title: MYb115:BT247_12h_rep2


title: ES-F3_S63_002


title: MYb11:BT407_12h_rep3


title: NS_17


title: OP50:none_24h_rep1


title: MYb11:BT407_24h_rep2


title: ES-F3_S63_001


title: ES-F2_S62_002


title: NS_16


title: MYb11:none_24h_rep2


title: MYb11:BT247_12h_rep2


title: NS_15


title: MYb115:BT407_12h_rep1


title: MYb11:BT247_24h_rep2


title: ES-F2_S62_001


title: MYb11:BT407_12h_rep2


title: NS_12


title: MYb11:none_12h_rep2


title: OP50:BT407_12h_rep3


title: ES-F1_S61_002


title: EGFP ChIP-Seq

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

data_processing:
Sequencing reads were aligned to a human reference genome assembly GRCh38.p12 using STAR aligner tuned for ChIP-Seq analysis pipeline (disabled intron detection, 400 bp of maximum gap between read mates, up to 50 reported alignments of multi-mapper reads.
Genome_build: hg38
Supplementary_files_format_and_content: Putative binding sites are provided in a narrowPeak format, as repored by Genrich (https://github.com/jsh58/Genrich).

source_name: Hela cells infected with a modified version of the tetracycline inducible LentiX vector carying EGFP.

growth_protocol: Cells were grown in 10 cm dishes and the expression of RecF8 or EGFP (control) was induced for 24h with 100ng/mL doxycycline.

extract_protocol:
The cell lines were crosslinked with 1% formaldehyde for 10 min at room temperature and further processed following the manufacturer’s protocol for High Cell number using the kit TruChip Chromatin Shearing Kit, Covaris. Chromatin shearing was performed using Covaris M220 sonicator. 1% of the sheared chromatin was separated for qPCR validation (input sample) and the rest was used for immunoprecipitation. Sonicated chromatin was immunoprecipitated using a goat GFP-antibody (MPI-CBG antibody facility) and Protein G sepharose beads (Protein G Sepharose® 4 Fast Flow, GE Healthcare). Eluates were reverse crosslinked followed by RNA and protein digestion.
Sequencing libraries were prepared using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® from 17-75 ng of ChIP DNA with 15 PCR amplification cycle and size selection using AMPure XP beads.

tag: cell line

value: HeLa

tag: chip antibody

value: Anti-GFP antibody, MPI-CBG


title: MYb11:BT247_12h_rep3

tag: strain

tag: treatment


title: OP50:BT247_12h_rep2


title: ES-F1_S61_001

last: Endo

address: 1-7-22 Suehiro, Tsurumi

data_processing:
Base calling was performed using Off-line Basecaller (OLB) v1.9.4 provided by Illumina.
Sequences were filtered and trimmed using trim_galore version 0.6.4_ev.
Sequences were aligned and counted on mouse genome using Kallisto version 0.46.2 with mRNA database generated using RefSeq database and default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: plain text

extract_protocol:
mRNA were extracted following Illumina's instructions.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combi

tag: cell type


title: MYb115:BT247_12h_rep1


title: MYb115:BT407_24h_rep1


title: ES-F12_S72_002


title: MYb115:BT247_24h_rep3


title: RecF8-EGFP ChIP-Seq

data_processing:
Sequencing reads were aligned to a human reference genome assembly GRCh38.p12 using STAR aligner tuned for ChIP-Seq analysis pipeline (disabled intron detection, 400 bp of maximum gap between read mates, up to 50 reported alignments of multi-mapper reads.
Peak calling was performed with Genrich (https://github.com/jsh58/Genrich), using the ENCODE blacklist (https://github.com/Boyle-Lab/Blacklist/raw/master/lists/mm10-blacklist.v2.bed.gz) for filtering out problematic regions and "EGFP ChIP-Seq" sample as a control.
Genome_build: hg38
Supplementary_files_format_and_content: Putative binding sites are provided in a narrowPeak format, as repored by Genrich (https://github.com/jsh58/Genrich).

source_name: Hela cells infected with a modified version of the tetracycline inducible LentiX vector carying RecF8-EGFP fusion.


title: MYb115:BT247_24h_rep2


title: MYb11:none_24h_rep1


title: L1701732: WT_5-1_dark_5d

value: 5 days after germination

tag: genotype

value: wild type

value: dark

tag: tissue

value: seedling