title: SET2_WT_nutrient-rich_R2

value: WT


title: 3d_iii

status: Public on May 30 2019

type: SRA

city: Singapore

first: Cheryl

last: Lee

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: Treated with 200nM ZSTK474 for 3days

library_source: transcriptomic

data_processing:
Trimmed by Trim Galore!
Aligned to GRCm38 using Hisat2
Reads were quantitated using the RNA-seq quantitation pipeline in Seqmonk
Genome_build: GRCm38
Supplementary_files_format_and_content: Reads were quantitated using the RNA-seq quantitation pipeline in Seqmonk

molecule: total RNA

organism: Mus musculus

source_name: Trophoblast stem cells

growth_protocol: TSCs were maintained in TSC media (70% fibroblast conditioned media (FCM), 30% base media, 25 ng/mL FGF4 and 1 µg/mL heparin).

extract_protocol:
RNA was isolated using PureLink™ RNA Micro Scale kit (Invitrogen 12183016).
Library prep was prepared using ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre SSV21124), together with Dynabeads mRNA Purification Kit (Life Technologies 61006) to enrich for mRNA

tag: tissue

value: Extraembryonic

tag: strain

value: ICR

tag: agent

value: 200nM ZSTK474

tag: time point


title: SET2_WT_nutrient-rich_R1

city: Seoul

first: Kyung-Tae

address: Yonsei-ro 50, Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

data_processing:
Illumina Casava1.7 software used for basecalling.
and the sequenced reads were trimmed to remove the adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic v0.32 with ‘adapter seq’ of TruSeq3-PE.fa and MINLEN:36.
The reads were aligned to the Cryptococcus neoformans var. grubii H99 (from Broad Institute) using Tophat v2.0.13 with the Bowtie v2.2.3 algorithm.
Tophat was performed with “-G” option and other parameters were default. Transcript assembly and abundance estimation was performed by Cufflinks v2.2.1. To correct the sequence expression count bias, we used ‘--max-bundle-frags 50000000’ option. The isoform transcripts were also calculated, and the relative transcript abundances were displayed via FPKM (Fragments Per Kilobase of exon per Million fragments mapped).
Genome_build: Cryptococcus neoformans var. grubii H99 (from Broad Institute)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM and expected counts for each Sample.

molecule: polyA RNA

organism: Cryptococcus neoformans H99

source_name: H99_total RNA

growth_protocol: Cryptococcus neoformans WT and deletion mutant strains were inoculated into 50 ml of YPD medium liquid medium and cultured overnight at 30°C in a shaking incubator. Cells were subinnoculated in fresh YPD medium until OD600 indicated 0.6 to 0.8.

extract_protocol:
Incubated cells were spun down, frozen in liquid nitrogen and lyophilized overnight. Total RNA was isolated by trizol extraction method using Easy-blue (iNtRON). The prepared total RNAs were purified with RNeasy Mini Kit (QIAGEN). The concentration was measured by Quant-IT RiboGreen (Invitrogen).
The quality of the RNA was verified by the TapeStation RNA screentape (Agilent) and the RNA Integrity Number (RIN) greater than 7.0 was used to construct the cDNA library (TruSeq mRNA Sample Prep kit, Illumina).

treatment_protocol: For the nutrient-starvation, the subinoculated cells were washed three times with phosphate-buffered saline, and resuspended in liquid YNB medium containing ammonium sulfate without glucose. After resuspension, cells were further incubated at 30°C in shaking incubator for 2 h.

value: H99 total RNA

tag: genotype/variation

tag: growth medium

value: YPD medium


title: 3d_ii

description: Treated with 200nM ZSTK474 for 3days


title: Kidney, tumor, pool#3 (n=3 donors)_total RNA

city: Québec

first: Chantal

last: Guillemette

state: Québec

address: 2705 blvd Laurier

department: Faculty of Pharmacy

country: Canada

institute: Laval University

description: Tissue biopsy

data_processing:
Illumina CASAVA software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to Hg19 whole genome and UGT reference transcriptome (Tourancheau, The Pharmacogenomics Journal, 2016; 16:60-70)  using tophat v2.0.13 (parameters: --no-novel-juncs) and bowtie v1.0.0-1 (Trapnell, Nat Biotechnol. 2013;31:46-53)
The aligned reads were assembled by Cufflinks program to produce transcripts annotated to the same reference genome.
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks output

organism: Homo sapiens

source_name: Kidney, tumor, pool#3 (n=3 donors)

extract_protocol:
RNA was extracted from 1 ug of each tissue using TriReagent followed by RNA cleanup using QIAGEN RNeasy Mini Kit with DNAse I. Equal amount of RNA from 3 tissue samples (or 5 tissue samples for normal intestine/colon) were pooled and External RNA Controls Consortium (ERCC) standards RNA Spike-In Mix 1 (ThermoFisher Scientific) were spiked into pooled RNA samples. 1 ug total RNA from each pool was used to prepare sequencing librairies with Illumina TruSeq RNA Sample Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: pooled male and female

value: kidney


title: Intestine and colon, normal, pool#1 (n=5 donors)_total RNA

description: Tissue biopsy

value: Intestine and colon


title: D6 Physics

type: RNA

city: Incheon Metropolitan City

first: Yong Seung

address: SimGokro 100gil 25

department: College of Medicine

institute: Catholic Kwandong University

description: gene expression from cultured HDF cells with ESC culture media for 6 day after ultrasound stimulus.

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the GeneChip® PrimeView™ Human Gene Expression Arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained using SAPE (Streptavidin Phycoerythrin) and washed in a Genechip Fluidics Station 450 (Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix). the image data was extracted through Affymetrix Commnad Console software1.1.

data_processing: The raw .cel file generated through above procedure meant expression intensity data and was used for the next step. Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, PLIER algorithm implemented in Affymetrix Expression Console software was used.

source_name: HDF cells were cultured with hESC medium for 6 days after ultrasound stimulus

label_protocol: Per RNA sample, 300 ng were used as input into the Affymetrix procedure as recommended by protocol (http://www.affymetrix.com). Briefly, 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA (cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: Physics cells were cultured suspension with ultrasound-treated ESC culture media ( 5.0 W/cm2, for 10 min) on a 35-mm bacterial petri dish at 37 oC in an atmosphere of 5% CO2. The ultrasound-treated ESC culture media was replaced every two days.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, USA). RNA quality was assessed by Agilent 2100 bioanalyser (Agilent Technologies, USA), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, USA).

treatment_protocol: To generate Physics, 1 x 106 HDF cells were directly exposed to ultrasound (20 KHz, 1.0 W/cm2) for 5 sec. And then, 2 x 105 treated cells were cultured with ultrasound-treated ESC culture media ( 5.0 W/cm2, for 10 min) on a 35-mm bacterial petri dish  for 6 or 40 days.

value: dermal fibroblasts isolated from adult skin


title: SET1_bzp4_nutrient-starved_R3

value: bzp4 mutant

value: YNB medium containing AS without glucose


title: 3d_i

description: Treated with 200nM ZSTK474 for 3days


title: D40 Physics

description: gene expression from cultured HDF cells with ESC culture media for 40 day after ultrasound stimulus.

source_name: HDF cells were cultured with hESC medium for 40 days after ultrasound stimulus


title: Six2b

city: Parkville

first: Belinda

last: Phipson

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

data_processing:
The 10x Genomics Cell Ranger pipeline (v1.3.1) was used to align, filter and de-duplicate reads before counting those overlapping genes to produce count matrices for each sample.
Count matrics for Six2a, Six2b, and Six2c were combined using cellranger aggr with no normalisation. The resulting dataset consisst of a matrix file (matrix.mtx) containing the UMI count values, barcode file (matrix.tsv) containing the detected cell barcodes and gene file (genes.tsv) containing the ENSEMBL ids of the detected genes. The dense matrix of the full dataset is provided in CSV format (counts.csv).
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files and CSV file containing count matrix.

source_name: mouse kidney

growth_protocol: Kidneys from multiple litters of Six2GFP+ mouse embryos at E14.5 were pooled into three replicate tubes.

extract_protocol:
Chromium Single Cell Library kit V2
Illumina HiSeq HT chemistry- 100bp paired end sequencing

treatment_protocol: Six2GFP+ cells were isolated using gates for Six2GFP fluorescence, propidium iodide to exclude dead cells, and size to exclude cell debris and doublets. Isolated Six2GFP+ cells were collected and stored on ice in 50% PBS, 50% DMEM with 5% FCS, then run in parallel on a 10x chip.

tag: cell type

value: nephron progenitor

tag: age


title: Kidney, tumor, pool#2 (n=3 donors)_total RNA

description: Tissue biopsy

source_name: Kidney, tumor, pool#2 (n=3 donors)


title: healthy control01

city: Nanjing

first: Xiaojun

last: LI

state: China

address: 305 East  Zhongshan Road，Xuanwu Distriction

department: Institute of Clinical Laboratory Science,

country: China

institute: Jinling Hospital, Nanjing University School of Medicine

description: circRNA expression data of colon tissue from HC

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 4 out of 12 samples have flags in P or M (“All Targets Value”) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.

source_name: healthy controls

label_protocol: Total RNAs were digested with RNAse R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit, Arraystar).

extract_protocol: Total RNAs were isolated from pinch tissues using TRIzol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the standard protocol. The yield and purity were quantified with a NanoDrop ND-1000 (Agilent, Santa Clara, CA, USA) and the integrity of the RNAs was assessed by 1% formaldehyde denaturing agarose gel electrophoresis.

treatment_protocol: The pinch tissues were immediately submerged in RNAlater(Sigma) at 2-8℃ overnight, then transferred to –80℃.

value: Female


title: 6h_iii

description: Treated with 200nM ZSTK474 for 6h


title: 6h_ii

description: Treated with 200nM ZSTK474 for 6h


title: SET1_bzp4_nutrient-starved_R2


title: Kidney, tumor, pool#1 (n=3 donors)_total RNA

description: Tissue biopsy

source_name: Kidney, tumor, pool#1 (n=3 donors)


title: SET1_bzp4_nutrient-starved_R1


title: healthy control03

value: Male


title: healthy control02


title: healthy control04


title: 6h_i

description: Treated with 200nM ZSTK474 for 6h


title: SET1_bzp4_nutrient-rich_R3


title: Kidney, normal, pool#2 (n=3 donors)_total RNA

description: Tissue biopsy

source_name: Kidney, normal, pool#2 (n=3 donors)


title: 1h_iii

description: Treated with 200nM ZSTK474 for 1h


title: Kidney, normal, pool#1 (n=3 donors)_total RNA

description: Tissue biopsy

source_name: Kidney, normal, pool#1 (n=3 donors)


title: SET1_bzp4_nutrient-rich_R1


title: 1h_ii

description: Treated with 200nM ZSTK474 for 1h


title: Patient 7 Crohn’s Disease03

description: circRNA expression data of colon tissue from CD patients

source_name: Crohn’s Disease


title: Patient 6 Crohn’s Disease02


title: Liver, normal, pool#3 (n=3 donors)_total RNA

description: Tissue biopsy

source_name: Liver, normal, pool#3 (n=3 donors)

value: liver


title: 1h_i

description: Treated with 200nM ZSTK474 for 1h


title: Patient 5 Crohn’s Disease01


title: Patient 8 Crohn’s Disease04


title: 0h_iii

description: Not treated with ZSTK474


title: Liver, normal, pool#2 (n=3 donors)_total RNA

description: Tissue biopsy

source_name: Liver, normal, pool#2 (n=3 donors)


title: Kidney, normal, pool#3 (n=3 donors)_total RNA

description: Tissue biopsy

source_name: Kidney, normal, pool#3 (n=3 donors)


title: SET1_WT_nutrient-starved_R2


title: 0h_ii

description: Not treated with ZSTK474


title: Patient 4 ulcerative colitis04

description: circRNA expression data of colon tissue from UC patients

source_name: ulcerative colitis


title: Liver, normal, pool#1 (n=3 donors)_total RNA

description: Tissue biopsy

source_name: Liver, normal, pool#1 (n=3 donors)


title: Patient 3 ulcerative colitis03


title: Biopsy 467

city: Indianapolis

first: Brad

last: Griesenauer

state: Indiana

address: 635 Barnhill Dr, MS 420

department: Microbiology and Immunology

country: USA

institute: Indiana University School of Medicine

description:
Sample 4
H_ducreyi_Raw_Read_Counts.txt
Human_Raw_Read_Counts.txt

data_processing:
For the human samples, the sequence data were mapped to the human reference genome hg19 with STAR-2.5.2b
For the bacterial samples, the sequence data were mapped to the regerene genome Haemophilu ducreyi 35000hp ASM794v1  with bowtie 2 (version 2.3.2)
featureCounts (subread-1.6.0) was used to quantify gene expression (parameters applied: "“-s 2 –p –Q 10")
Differential expression analysis was performed using edgeR
Genome_build: Haemophilu ducreyi 35000hp reference genome  ASM794v1 and human reference genome hg19
Supplementary_files_format_and_content: Two files (one for H. ducreyi and one for human) containing raw counts of sequencing reads

organism:
[Haemophilus] ducreyi
Homo sapiens

source_name: H. ducreyi-infected pustules from humans

growth_protocol: For samples 1-4, RNA was directly extracted from H. ducreyi-infected pustules on human volunteers. For samples 5-8, RNA was directly extracted from human wound-control sites. For samples 9-12, H. ducreyi was grown under GMP conditions to mid-log phase in a proteose peptone broth-based medium with 1% IsoVitaleX, 5% heat-inactivated fetal calf serum, and 50 ug/ml hemin and grown at 33°C for 5-6 hours.

extract_protocol:
Biopsy samples immediately after collection and the extra inocula immediately after inoculation were placed in 2 mL RNAlater, incubated for 30 minutes at room temperature, and stored in RNAlater for one day at -80°C. Using a mini-Beadbeater (Biospec Products), we next homogenized the samples and extracted total RNA using a RNeasy Fibrous Tissue Mini kit according to manufacturer’s instructions along with addition of lysozyme (20 ug/mL) added at the proteinase K step. The RNA was treated twice with TURBO DNA-free DNase (Ambion) following manufacturer’s instructions. RNA concentrations and integrities were measured using a NanoPhotometer P330 (Implen). RNA samples were stored at -80°C until all samples were ready for sequencing. We removed 23S, 16S, and 5S rRNA before RNA-seq using the Ribo-Zero Gold rRNA Removal Kit (Epidemiology) (Epicentre Biotechnologies) following manufacturer’s instructions and confirmed their removal using the Agilent 2100 Bioanalyzer.
Twelve libraries (four mid-log phase growth H. ducreyi cultures, four infected sites, and four wounded sites) were constructed using the TruSeq Stranded Total RNA Library kit (Illumina) following manufacturer’s instructions.

tag: time

value: 6-8 days post-infection

value: 6 mm skin


title: 0h_i

description: Not treated with ZSTK474

source_name: Trophoblast stem cells

value: Extraembryonic


title: Inoculum 466

description:
Sample 11
H_ducreyi_Raw_Read_Counts.txt

organism: [Haemophilus] ducreyi

source_name: Mid-log phase growth H. ducreyi

value: Day of infection


title: Inoculum 467

description:
Sample 12
H_ducreyi_Raw_Read_Counts.txt


title: SET1_WT_nutrient-rich_R3

source_name: H99_total RNA

value: WT


title: SET1_bzp4_nutrient-rich_R2

value: H99 total RNA


title: MKN-45_circAGO2

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

description: Gene expression after stable transfection of circAGO2

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 containing adapter, reads containing 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: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

growth_protocol: Human gastric cancer cell line MKN-45 was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

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

treatment_protocol: The circAGO2 expression or empty vectors were transfected into tumor cells, and stable cell lines were screened by administration of puromycin.

tag: treatment

value: stably transfected with circAGO2

value: gastric cancer cell line

tag: cell line

tag: passages


title: SET1_WT_nutrient-rich_R2

value: YPD medium


title: Patient 2 ulcerative colitis02


title: Inoculum 465

description:
Sample 10
H_ducreyi_Raw_Read_Counts.txt


title: Patient 1 ulcerative colitis01


title: Biopsy 466

description:
Sample 3
H_ducreyi_Raw_Read_Counts.txt
Human_Raw_Read_Counts.txt


title: MKN-45_mock

description: Gene expression after stable transfection of empty vector

value: stably transfected with empty vector


title: SET1_WT_nutrient-starved_R3


title: Inoculum 462

description:
Sample 9
H_ducreyi_Raw_Read_Counts.txt


title: SET1_WT_nutrient-rich_R1


title: Biopsy 465

description:
Sample 2
H_ducreyi_Raw_Read_Counts.txt
Human_Raw_Read_Counts.txt


title: SET1_WT_nutrient-starved_R1


title: Control choroid

status: Public on May 29 2019

city: Takayama-cho Ikoma-shi, Nara

first: Yasuhisa

last: Tanaka

state: Japan

country: Japan

institute: Santen Pharmaceutical CO., LTD

hyb_protocol: Cy3-labelled RNA were hybridized Expression Hybridization kit (Agilent) for 22 hour at 55℃ following the manufacturers instructions.

scan_protocol: After washed, the microarray were scanned by DNA Microarray Scanner (Agilent)

data_processing: The scanning data was digitized using Feature Extraction ver 10.7.1.1 software (Agilent).

source_name: Control

label_protocol: Cy3 labeled RNA was prepared from 100 ng RNA using the miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA extraction was performed using the miRNeasy Micro kit (QIAGEN) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-ND1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent).

value: Choroid


title: Lens-induced sclera

source_name: Lens-indiced

value: Sclera


title: Lens-induced SCN

value: SCN


title: Lens-induced LGN

value: LGN


title: Control retina

value: Retina


title: Control sclera


title: Lens-induced iris

value: Iris


title: Lens-induced lens

value: Lens


title: 0D LGN

source_name: 0D lens


title: Control lens


title: Control SCN


title: 0D SCN


title: GC23 WT_Female_E2_2

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: danRer7
Supplementary_files_format_and_content: excel files include RPKM values for each Sample

organism: Danio rerio

source_name: liver, β-Estradiol

growth_protocol: All zebrafish was maintained according to the standard Institutional Animal Care and Use Committee guidelines (IACUC). At 3 months post fertilization, a selected group of wild-type male and female zebrafish were seperated into individual tanks to control food consumption.

extract_protocol:
Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol (Life Technologies), isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA-free kit (Life Technologies) and RNA quality and quantity were determined using Qubit (Thermo Fisher) and bioanalyzer (Agilent).
For library construction, NEBNext Directional RNA Library Prep Kit for Illumina (#E7420L) was used according to the company's protocol

treatment_protocol: Zebrafish were raised until at 3 months post fertilization. Fish were then treated daily with DMSO or β-Estradiol for a period of 6 weeks.

value: liver

tag: developmental stage

value: adult

tag: genotype

value: Wild-type


title: GC21 WT_Male_E2_3


title: 0D choroid


title: Lens-induced choroid


title: Control iris


title: 0D retina


title: 0D lens


title: GC22 WT_Female_E2_1


title: Control LGN


title: Control cornea

value: Cornea


title: 0D cornea


title: 0D iris


title: Lens-induced cornea


title: Lens-induced retina


title: 0D sclera


title: Biopsy 462

description:
Sample 1
H_ducreyi_Raw_Read_Counts.txt
Human_Raw_Read_Counts.txt

value: 6-8 days post-infection

value: 6 mm skin


title: GC19 WT_Male_E2_1


title: GC12 WT_Female_3

source_name: liver, DMSO


title: GC11 WT_Female_2


title: 48h_2mg_N_Tri1_Rep1_Batch2

city: Adelaide

first: Thazin

middle: Nwe

last: Aung

state: South Australia

address: Frome

institute: University of Adelaide

description:
strand-specific RNA-seq
S48h_Tri1
Sample 52(Batch2)

data_processing:
FastQC (v0.11.4, Babraham Bioinformatics) was used to check the quality of raw reads before proceeding with downstream analysis. Trim_galore (v0.3.7, Babraham Bioinformatics) with the parameters: --stringency 5 --paired --fastqc_args was used to trim adaptors and low-quality sequences.
STAR (v2.5.3a) was then applied to align the trimmed reads to the reference genome (hg19, UCSC) with the parameters: --outSAMstrandField intronMotif --outSAMattributes All --outFilterMismatchNmax 10 --seedSearchStartLmax 30 --outSAMtype BAM SortedByCoordinate
Subread (v1.5.2) was used to generate read counts data with the following parameters featureCounts -p -t exon -g gene_id
Differentially expressed genes between treatments were analysed and selected using edgeR (v3.22.3) with false discovery rate (FDR) < 0.05
Removal of unwanted variance (RUVs) package in R was applied to two different batches of transcriptome datasets to eliminate batch variance
Genome_build: hg19, UCSC
Supplementary_files_format_and_content: Tab delimited matrix showing raw counts of refGenes from two batches of raw sequencing samples. Comma separated values containing the combined processed data file generated using RUVs package in R.

source_name: total RNAs, cell line

growth_protocol: MDA-MB-231 cells were purchased from the American Type Culture Collection (ATCC, VA, USA). HEK-293 and HFF were kindly provided by Prof. Andrea Yool (Medical School, University of Adelaide). Cells were cultured in Dulbecco's Modified Eagle's Medium (Thermo Fisher Scientific) with 10 % Fetal bovine serum (Thermo Fisher Scientific) at 370C with 5 % CO2.

extract_protocol:
Total RNA was isolated by using an RNA extraction kit (Thermo Fisher Scientific) according to the manufacturer’s instructions and RNA samples were quantified and quality determined using a Bioanalyzer at the Cancer Genome Facility of the Australian Cancer Research Foundatin (Australia).
RNA samples with RNA integrity number (RINs) > 7.0 were sent to be sequenced at Novogene (China). Briefly, after QC procedures were performed, mRNA was isolated using oligo(dT) beads and randomly fragmented by adding fragmentation buffer, followed by cDNA synthesis primed with random hexamers. Next, a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added for second-strand synthesis. After end repair, barcode ligation and sequencing adaptor ligation, the double-stranded cDNA library was size selected and PCR amplified. Sequencing was carried out on an Illumina HiSeq platform PE150 with paired-end 150 bp reads.

treatment_protocol: Drug treatments were as follows: CKI (2.0 mg/m) or fractionated and reconstituted mixtures (2 mg/ml equivalent) for 24 and 48 hours

tag: tumor type

value: breast cancer


title: GC24 WT_Female_E2_3


title: 48h_2mg_N_Tri3_Rep3_Batch2

description:
strand-specific RNA-seq
S48h_Tri3
Sample 54(Batch2)


title: 48h_2mg_N_Tri2_Rep2_Batch2

description:
strand-specific RNA-seq
S48h_Tri2
Sample 53(Batch2)


title: GC10 WT_Female_1


title: GC8 WT_Male_2


title: 48h_2mg_N_Omt3_Rep3_Batch2

description:
strand-specific RNA-seq
S48h_OMT3
Sample 51(Batch2)


title: 48h_2mg_N_Omt2_Rep2_Batch2

description:
strand-specific RNA-seq
S48h_OMT2
Sample 50(Batch2)


title: 48h_2mg_N_Nme2_Rep2_Batch2

description:
strand-specific RNA-seq
S48h_Nme2
Sample 47(Batch2)


title: 48h_2mg_N_Omt1_Rep1_Batch2

description:
strand-specific RNA-seq
S48h_OMT1
Sample 49(Batch2)


title: 48h_2mg_N_Nme3_Rep3_Batch2

description:
strand-specific RNA-seq
S48h_Nme3
Sample 48(Batch2)


title: 48h_2mg_CKI3_Rep3_Batch2

description:
strand-specific RNA-seq
S48h_CKI3
Sample 42(Batch2)

value: CKI


title: 48h_2mg_N_Mac1_Rep1_Batch2

description:
strand-specific RNA-seq
S48h_Mac1
Sample 43(Batch2)


title: 48h_2mg_N_Mac3_Rep3_Batch2

description:
strand-specific RNA-seq
S48h_Mac3
Sample 45(Batch2)


title: 48h_2mg_CKI2_Rep2_Batch2

description:
strand-specific RNA-seq
S48h_CKI2
Sample 41(Batch2)


title: 48h_UT2_Rep2_Batch2

description:
strand-specific RNA-seq
S48h_UT2
Sample 38(Batch2)

value: UT


title: 48h_2mg_CKI1_Rep1_Batch2

description:
strand-specific RNA-seq
S48h_CKI1
Sample 40(Batch2)


title: 48h_2mg_MOO_2_Rep2_Batch1

description:
strand-specific RNA-seq
MOO_2_48h
Sample 35(Batch1)

value: MOO


title: 48h_2mg_MOO_3_Rep3_Batch1

description:
strand-specific RNA-seq
MOO_3_48h
Sample 36(Batch1)


title: 48h_2mg_MOO_1_Rep1_Batch1

description:
strand-specific RNA-seq
MOO_1_48h
Sample 34(Batch1)


title: GC7 WT_Male_1


title: 48h_UT3_Rep3_Batch2

description:
strand-specific RNA-seq
S48h_UT3
Sample 39(Batch2)


title: 48h_2mg_OO_3_Rep3_Batch1

description:
strand-specific RNA-seq
OO_3_48h
Sample 33(Batch1)

value: OO


title: 48h_2mg_N_Mac2_Rep2_Batch2

description:
strand-specific RNA-seq
S48h_Mac2
Sample 44(Batch2)


title: 48h_2mg_N_3_3_Rep3_Batch1

description:
strand-specific RNA-seq
N_3_3_48h
Sample 30(Batch1)


title: 48h_2mg_OO_1_Rep1_Batch1

description:
strand-specific RNA-seq
OO_1_48h
Sample 31(Batch1)


title: 48h_2mg_N_3_2_Rep2_Batch1

description:
strand-specific RNA-seq
N_3_2_48h
Sample 29(Batch1)


title: 48h_2mg_CKI1_Rep1_Batch1

description:
strand-specific RNA-seq
CKI1_48h
Sample 22(Batch1)


title: 48h_2mg_N_2_3_Rep3_Batch1

description:
strand-specific RNA-seq
N_2_3_48h
Sample 27(Batch1)


title: 48h_2mg_N_2_1_Rep1_Batch1

description:
strand-specific RNA-seq
N_2_1_48h
Sample 25(Batch1)


title: 48h_UT3_Rep3_Batch1

description:
strand-specific RNA-seq
UT3_48h
Sample 21(Batch1)


title: 48h_2mg_CKI3_Rep3_Batch1

description:
strand-specific RNA-seq
CKI3_48h
Sample 24(Batch1)


title: 24h_2mg_MOO_1_Rep1_Batch1

description:
strand-specific RNA-seq
MOO_1_24h
Sample 16(Batch1)


title: 24h_2mg_MOO_2_Rep2_Batch1

description:
strand-specific RNA-seq
MOO_2_24h
Sample 17(Batch1)


title: 48h_2mg_N_2_2_Rep2_Batch1

description:
strand-specific RNA-seq
N_2_2_48h
Sample 26(Batch1)


title: 24h_2mg_OO_1_Rep1_Batch1

description:
strand-specific RNA-seq
OO_1_24h
Sample 13(Batch1)


title: 48h_2mg_CKI2_Rep2_Batch1

description:
strand-specific RNA-seq
CKI2_48h
Sample 23(Batch1)


title: 24h_2mg_MOO_3_Rep3_Batch1

description:
strand-specific RNA-seq
MOO_3_24h
Sample 18(Batch1)


title: 24h_2mg_N_3_3_Rep3_Batch1

description:
strand-specific RNA-seq
N_3_3_24h
Sample 12(Batch1)


title: 24h_2mg_OO_Rep2_Batch1

description:
strand-specific RNA-seq
OO_24h
Sample 14(Batch1)


title: 24h_2mg_N_3_1_Rep1_Batch1

description:
strand-specific RNA-seq
N_3_1_24h
Sample 10(Batch1)


title: 24h_2mg_N_2_3_Rep3_Batch1

description:
strand-specific RNA-seq
N_2_3_24h
Sample 9(Batch1)


title: 24h_2mg_N_2_1_Rep1_Batch1

description:
strand-specific RNA-seq
N_2_1_24h
Sample 7(Batch1)


title: 24h_2mg_CKI3_Rep3_Batch1

description:
strand-specific RNA-seq
CKI3_24h
Sample 6(Batch1)


title: 48h_UT2_Rep2_Batch1

description:
strand-specific RNA-seq
UT2_48h
Sample 20(Batch1)


title: 48h_UT1_Rep1_Batch1

description:
strand-specific RNA-seq
UT1_48h
Sample 19(Batch1)


title: 24h_2mg_CKI_Rep1_Batch1

description:
strand-specific RNA-seq
CKI_24h
Sample 4(Batch1)


title: 24h_UT3_Rep3_Batch1

description:
strand-specific RNA-seq
UT3_24h
Sample 3(Batch1)


title: 24h_UT1_Rep1_Batch1

description:
strand-specific RNA-seq
UT1_24h
Sample 1(Batch1)


title: RS-CC: pooled control crown for 2 samples

city: Birmingham

first: Sarah

middle: B

last: Peters

state: AL

address: 1918 University Blvd, MCLM 643

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

data_processing:
Illumina bcl2fastq  software version 1.8.4 used for basecalling.
Raw sequence fastq files were trimmed using TrimGalore! version 0.4.1 with parameters --paired --trim1
STAR version 2.5.1b was used to align the trimmed fastq files to the UCSC mm10 reference genome using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Cufflinks version 2.2.1 was used to estimate transcript abundances using parameters -g -L
Genome_build: mm10
Supplementary_files_format_and_content: Excel file (tab-delimited) containing gene symbols and FPKM values for each sample

source_name: Control crown dental pulp

extract_protocol:
Teeth were dissected divided into roots and crowns.  Dental pulp tissue was removed and immersed in Lysis Buffer (Quiagen #1015762).  Samples were pestled to break up tissue and RNA was isolated with RNA Sample Prep Tool (Zymo Research #R2072).
RNA libraries were prepared using the Agilent SureSelect Strand-Specific mRNA protocol for Illiumina sequencing as per the manufacturer's instructions.

value: postnatal dental pulp cells

value: postnatal day 7


title: GC20 WT_Male_E2_2


title: 24h_2mg_N_3_Rep2_Batch1

description:
strand-specific RNA-seq
N_3_24h
Sample 11(Batch1)


title: 24h_2mg_CKI1_Rep2_Batch1

description:
strand-specific RNA-seq
CKI1_24h
Sample 5(Batch1)


title: RS-RC: pooled control root for 2 samples

source_name: Control root dental pulp


title: WTRC12BAT

city: Bethesda

first: LEI

last: WANG

state: MD

address: Building 8A, Room B1A05 8 Center Dr , MD 20814

institute: NIH

data_processing:
Reads were trimmed for adapter sequences using cutadapt v1.16.
Trimmed reads were then aligned to the mouse mm9 genome using hisat v2.1.0
Expression data were analyzed by genomatix genome analyzer.
Genome_build: mm9
Supplementary_files_format_and_content: tsv files include RPKM values for each Sample ...

source_name: BAT tissue

extract_protocol:
Adipose tissue (iWAT and eWAT) of 16-week-old C57BL/6J mice (males) was digested with KRH buffer (2% FFA-free BSA) containing 3.3mg/ml collagenase I via incubation at 37 ℃ for 30-45 min. When the tissue was fully digested, 10 ml of KRH buffer was added to terminate collagenase activity. Cells were then filtered through a 250 μm cell strainer. After 10 min, the floating top layer containing mature adipocytes was collected. Mature adipocytes were washed twice with KRH buffer containing 5 mM EDTA and then used for RNA-seq analysis. Brown adipose tissues (BAT) were isolated and quickly freezed in liquied nitrogen.
Total RNA extracted from mature adipocytes (iWAT and eWAT) and BAT tissue. RNAs with RIN >8 (assessed by the Agilent 2100 Bioanalyzer system) were used to prepare transcriptome libraries using the NEBNext Ultra RNA library prep kit (New England Biolabs).

treatment_protocol: Fed with regular chow

value: BAT adipocytes

value: wild type


title: WTRC13IWAT

source_name: iWAT adipocytes

value: iWAT adipocytes


title: WTRC7EWAT

source_name: eWAT adipocytes

value: eWAT adipocytes


title: WTRC12IWAT


title: WTRC6BAT


title: WTRC8BAT


title: WTRC7BAT


title: WTRC13EWAT


title: WTRC15EWAT


title: WTRC11BAT


title: WTRC11EWAT


title: WTRC13BAT


title: WTRC8EWAT


title: WTRC14IWAT


title: WTRC11IWAT


title: liver.Se2.25.rep2

first: Sun Hee

last: Yim

address: 77 Ave Louis Pasteur, RM435

department: Medicine

institute: BWH/Harvard Medical School

data_processing:
Samples were pooled and sequenced on one HiSeq run using Illumina TruSeq Stranded Total RNA Kit RS-122-2201.
Basecalling was performed by RTA (version 1.18.64).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Reads were filtered with a base call quality >94% of bases with Q30 and and above.
Trimming of adapters and low-quality bases was performed using Trimmomatic (version 0.33).
First pass alignment of reads to the mm10 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMtype BAM Unsorted
Second pass alignment of reads to the mm10 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMunmapped Within --outWigType None --outWigStrand Stranded --sjdbFileChrStartEnd /path/to/sjdbFile.txt --sjdbGTFfile /path/to/annotations.gtf --limitSjdbInsertNsj 4000000 --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate
Gene-level expression quantificiation and library size normalization in counts-per-million was performed using RSEM (version 1.3.0).
Quantile-normalization and differential expression was performed using limma-voom (version 3.34.5).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files are limma-voom normalized differential expression output.

source_name: Mouse fed with 2.25ppm dietary Se for 5 weeks

growth_protocol: Normal chow until the Se diet was fed

extract_protocol:
TRIzol® Reagent (Thermo Fisher Scientific)
TruSeq Stranded Total RNA Kit (Illumina; RS-122-2201)

treatment_protocol: Eight-weeks old C57BL/6J male mice were fed with diet supplemented with either 0, 0.1, 0.4 or 2.25 ppm for five weeks

tag: gender

value: male

tag: pathology

value: No gross pathology observed

value: Mouse whole liver


title: liver.Se2.25.rep1

tag: strain

tag: tissue


title: 48h_2mg_N_Nme1_Rep1_Batch2

description:
strand-specific RNA-seq
S48h_Nme1
Sample 46(Batch2)


title: liver.Se0.4.rep3

source_name: Mouse fed with 0.4ppm dietary Se for 5 weeks


title: WTRC15IWAT


title: liver.Se0.4.rep2


title: 48h_2mg_OO_2_Rep2_Batch1

description:
strand-specific RNA-seq
OO_2_48h
Sample 32(Batch1)


title: liver.Se0.1.rep1

source_name: Mouse fed with 0.1 ppm dietary Se for 5 weeks


title: brain.Se0.4.rep1

value: Mouse whole brain


title: liver.Se0.0.rep3

source_name: Mouse fed with 0 ppm dietary Se for 5 weeks


title: brain.Se2.25.rep3


title: brain.Se0.4.rep3


title: brain.Se2.25.rep2


title: WTRC7IWAT


title: liver.Se0.1.rep3


title: liver.Se0.1.rep2


title: 48h_2mg_N_3_1_Rep1_Batch1

description:
strand-specific RNA-seq
N_3_1_48h
Sample 28(Batch1)


title: liver.Se0.0.rep1


title: brain.Se2.25.rep1


title: 24h_2mg_OO_3_Rep3_Batch1

description:
strand-specific RNA-seq
OO_3_24h
Sample 15(Batch1)


title: liver.Se0.0.rep2


title: liver.Se0.4.rep1


title: brain.Se0.4.rep2


title: brain.Se0.1.rep2


title: 24h_UT2_Rep2_Batch1

description:
strand-specific RNA-seq
UT2_24h
Sample 2(Batch1)


title: brain.Se0.1.rep1


title: brain.Se0.0.rep2


title: brain.Se0.0.rep3


title: brain.Se0.0.rep1


title: brain.Se0.1.rep3


title: 24h_2mg_N_2_2_Rep2_Batch1

description:
strand-specific RNA-seq
N_2_2_24h
Sample 8(Batch1)


title: pa5dy-4

city: Chicago

first: Xiaofeng

last: Zhou

state: Illinois

address: 801 S Paulina Street

institute: University of Illinois at Chicago

data_processing:
Raw sequencing reads (50 nt) were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70).
Single end sequencing reads were cleaned with quality filter, adapter cutter, and length filter, using ACGT101_miR_v4.2g from LC Sciences.
The cleaned reads were mapped to miRBase (miRBase v21) using Bowtie v1.1.1.
The un-mapped reads were mapped to multiple databases including mRNA (NCBI M_musculus/RNA build 01/12/2015), Rfam11, and genomic DNA (UCSC mm10), using Bowtie v1.1.1.
Novel miRNA candidates were identified from genome mapped reads based on the propensity of hairpin formation in corresponding genome positions, using ACGT101_miR_v4.2g from LC Sciences.
Data were normalized by dividing sequence counts of individual samples by corresponding normalization factors which are the median values of the ratios between specific sample counts and geometric mean counts of all samples.
Genome_build: mm10, mirbase v21.0
Supplementary_files_format_and_content: seq read count

source_name: 5 days post wounding_oral mucosa

extract_protocol:
Total RNA (including small RNA) was isolated from normal and wound tissue samples stored in RNALater using a miRNeasy Mini Kit (QIAGEN, Hilden, Germany).
small RNA libraries were generated using the Illumina Truseq Small RNA Preparation kit (San Diego, CA)

treatment_protocol: Full thickness incisional wounds were made on the dorsal skin and the anterior of the hard palate of the mice. The wound tissue specimens were harvested at 6h, 24h and 5 days post-wounding.

value: Balb/c

tag: treatment/timepoint

value: 5 days post wounding

value: oral mucosa


title: pa5dy-2


title: pa24h-4

source_name: 24 hr post wounding_oral mucosa

value: 24 hr post wounding


title: pa6hr-3

source_name: 6 hr post wounding_oral mucosa

value: 6 hr post wounding


title: sk5dy-3

source_name: 5 days post wounding_skin

value: skin


title: pa0hr-1

source_name: unwounded (0 hr)_oral mucosa

value: unwounded (0 hr)


title: pa6hr-2


title: pa24h-3


title: dme-7/+ pollen RNA-seq rep2

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

data_processing:
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases, 100 base reads and 150 base reads were divided in half. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
RNA-Seq: TE transcript annotation was created using four biological replicates of pollen RNA-seq data. Tophat2, Hisat, and STAR were used to align the RNA-seq reads to the TAIR10 genome
Transcripts were assembled using CLASS2, StringTie, and Cufflinks, respectively.
Assembled transcripts were selected by Mikado using default options except the BLAST and Transdecoder steps were disabled. As a result, 21381 transcripts (called superloci) were identified and included in the output file called mikado-permissive.superloci.gff.
The list of superloci was refined by selecting those overlapping with TAIR10 TE annotation.
TE-like genes were eliminated from the refined list if their CG methylation is less than 0.7 in rosette leaves. This gave rise to an annotation of TE transcripts.
The annotation of TE transcripts was combined with TAIR10 gene annotation for Kallisto analysis which gives rise to the output files named abundance.tsv.
Genome_build: TAIR10
Supplementary_files_format_and_content: rpkm.log2.gff and abundance.tsv

organism: Arabidopsis thaliana

source_name: dme-7/+ pollen

growth_protocol: plants were grown in LD condition (16h lights/8h darkness) at 22-24 degrees

extract_protocol:
follow the instruciton of RNeasy plant micro kit
follow the instructions of Ovation RNA-Seq Systems

value: whole pollen


title: pa24h-2


title: liver.Se2.25.rep3


title: GC9 WT_Male_3

source_name: liver, DMSO

value: liver

value: adult

value: Wild-type


title: pa6hr-1


title: sk5dy-4


title: sk5dy-2


title: 48h_UT1_Rep1_Batch2

description:
strand-specific RNA-seq
S48h_UT1
Sample 37(Batch2)

source_name: total RNAs, cell line

value: breast cancer

value: UT


title: dme-7/+ pollen RNA-seq rep1


title: sk24h-3

source_name: 24 hr post wounding_skin


title: WTRC14EWAT

value: eWAT adipocytes

value: wild type


title: dme-7/+ pollen RNA-seq rep3


title: sk24h-1


title: WT pollen RNA-seq rep6

description:
mikado-permissive.superloci.gff
TAIR10_gene_plus_mikado_TE_transcripts.gff
This sample was used only for TE transcript identification and not the RPKM calculations.

data_processing:
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases, 100 base reads and 150 base reads were divided in half. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
RNA-Seq: TE transcript annotation was created using four biological replicates of pollen RNA-seq data. Tophat2, Hisat, and STAR were used to align the RNA-seq reads to the TAIR10 genome
Transcripts were assembled using CLASS2, StringTie, and Cufflinks, respectively.
Assembled transcripts were selected by Mikado using default options except the BLAST and Transdecoder steps were disabled. As a result, 21381 transcripts (called superloci) were identified and included in the output file called mikado-permissive.superloci.gff.
The list of superloci was refined by selecting those overlapping with TAIR10 TE annotation.
TE-like genes were eliminated from the refined list if their CG methylation is less than 0.7 in rosette leaves. This gave rise to an annotation of TE transcripts.
The annotation of TE transcripts was combined with TAIR10 gene annotation for Kallisto analysis which gives rise to the output files named abundance.tsv.
Genome_build: TAIR10
Supplementary_files_format_and_content: All files are in GFF format. Files contain fractional methylation data either for individual cytosines (single-c) or in 50 bp windows.

source_name: WT pollen

extract_protocol:
follow the instruction of Mirvana miRNA isolation kit
follow the instructions of Ovation RNA-Seq Systems 1–16 for Model  Organisms kit

value: WT


title: sk24h-2


title: sk6hr-3

source_name: 6 hr post wounding_skin


title: pa5dy-1


title: sk6hr-2


title: WT VN BS-seq

library_source: genomic

molecule: genomic DNA

source_name: WT vegetative nuclei

extract_protocol:
follow the instruciton of ChargeSwitch gDNA plant kit
follow the instructions of Ovation Ultralow Methyl-Seq Library Systems and Epitect conversion kit

value: vegetative cell of pollen


title: pVC::H1 VN BS-seq

source_name: pVC::H1.1-mRFP vegetative nuclei


title: pa0hr-3

value: Balb/c


title: sk6hr-1


title: cry1cry2-UV0-R2

city: Örebro

first: Luis

last: Morales

address: Fakultetsgatan 1

department: School of Science and Technology

country: Sweden

institute: Örebro University

data_processing:
The quality of raw reads was first inspected in Chipster using FastQC.
Removal of adapter sequences and trimming and cropping of the reads was done using Trimmomatic-0.33 (Bolgert et al., 2014) in single-end mode. The bases with a quality score less than 20 were trimmed from the beginning and the end of the sequences, and the reads shorter than 30 bases were removed from the analysis (-phred33, LEADING:20, TRAILING:20 and MINLEN:30).
Filtered reads were mapped to the Arabidopsis transcript reference database AtRTD2 (Zhang et al., 2017) using Kallisto V-0.43.0 (CMD:quant) (Bary et al., 2016) with 4000 bootstrap sets. The final count table for each biological replicate was obtained as the mean of the bootstrap runs.
Genome_build: Arabidopsis transcript reference database AtRTD2
Supplementary_files_format_and_content: Matrix-table including gene counts for each sample

source_name: whole rosette

growth_protocol: Seeds of Arabidopsis wild-type Ler and the photoreceptor mutants uvr8-2 (Brown et al., 2005) and cry1cry2 (Neff and Chory, 1998) were sown in plastic pots (8 × 8 cm) containing a 1:1 mixture of peat and vermiculite and kept in darkness at 4°C for 3 days. Thereafter the pots were transferred to environmentally controlled growth rooms at 23°C/19°C (day/night) and 70%/90% relative humidity under 12 h photoperiod with 280 µmol m−2 s−1 PAR irradiance from white fluorescent lamps. One seedling was transplanted into a new plastic pot (5 × 5 cm) using the same substrate type. After transplanting, plants were kept for 14 days in growth rooms. Rosco filter E-color 226 was used to avoid plants receiving the small amount of UV-A radiation emitted by lamps. Thereafter, five plants/pots from each genotype were randomly assigned to individual plastic trays which were moved outdoors to the filtered sunlight treatments.

extract_protocol:
Each biological sample collected consisted of five pooled rosettes frozen in liquid nitrogen and stored at –80°C. The rosette leaves from each pooled sample were ground with mortar and pestle in liquid nitrogen. An aliquote from the powdered sample was separated for gene expression (RNA-seq and qPCR). RNA was extracted with with GeneJet Plant RNA purification Mini Kit (Thermo Scientific). RNA quality and concentration were measured using Agilent 2100 Bioanalyzer and NanoDrop.
RNA-seq library preparation and sequencing was performed at the Institute of Biotechnology, University of Helsinki using two pooled biological replicates. Each replicate consisted of RNA from two different experimental blocks in the field. Libraries were prepared using 1µg total RNA following instructions from Illumina TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Outdoors, five filtered sunlight treatments (UVA+B, UVA350, UVA, UV0 and blue0) were created by using different plastic sheets and films as wavelength-selective long-pass optical filters. These treatments were randomly assigned within four blocks or biological replicates. Plants were moved outdoors under filters on 21.08.2014 at sunrise (07:30 to 08:15). Samples from the different filter frames were collected for RNA-seq analysis after 6h of radiation treatment, at solar noon (13:30 to 14:15). The samples were harvested sequentially by block with treatments and genotypes in random order within each block.

value: 3 weeks old plants

tag: solar treatment

value: whole rosette


title: sk0hr-2

source_name: unwounded (0 hr)_skin


title: cry1cry2-UVA350-R2


title: pa0hr-2

value: oral mucosa


title: cry1cry2-UVA-R2

value: UVA


title: sk0hr-1

value: skin


title: cry1cry2-UV-A-B-R2

value: UVA+B


title: HB9_3dpc_1

city: Miami

first: Kyung (Kevin)

last: Park

state: FL

address: 1095 NW 14th Terrace, Miami Project to Cure Paralysis, LPLC room 4-20

department: Neurological Surgery

institute: University of Miami

description:
SL142662
pre-amplified mRNA, tRNA depleted

data_processing:
Reads were aligned using TopHat v2.0.11 to the mm10 Bowtie genome index.
Reads were counted using the Bioconductor package easyRNASeq v1.6.0.
edgeR v3.14.0 was used to calculate differential gene expression.
Genes were included if they were expressed at ≥ 1 count per million in at least 3 of the 12 samples. Genes were considered differentially expressed if log2FC ≥ 1 and the FDR adjusted p-value ≤ 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including annotations and RPKM values for each Sample

source_name: Retina

extract_protocol:
Tissue Preparation: Opn4CreERT/+;R26-tdTomatof/f (Opn4) and HB9:GFP (HB9) mice were used for the RNA sequencing experiment. HB9:GFP mice were also injected with tamoxifen. Tamoxifen was injected I.P. (0.124mg/g body weight) for 5 consecutive days starting at P21. At P42 animals underwent optic nerve crush (Crush) or sham surgery 3 days prior to tissue collection. Adult mouse RGCs were dissociated. The retina was removed in HBSS (ThermoFisher, 14170161) and transferred to DMEM (ThermoFisher, 11995065) and 17U/ml papain (Worthington Biochem, PAPL). The retina was enzymatically dissociated for 30 minutes at 37°C in a water bath. Following incubation with papain, the retina was washed 5 times with DMEM. The retina was then triturated in FluoroBrite DMEM (ThermoFisher, A1896701) with B27 supplement and 20mM HEPES (ThermoFisher, 15630080). The cells were briefly spun down, resuspended in FluoroBrite DMEM + B27 + HEPES, and passed through a 100μm filter. Cells were plated at low density and allowed to settle. Under epifluorescent illumination tdTomato+ or GFP+, RGCs were located. Phase contrast was used to visualize that the cell was isolated from other cells. Pipettes were pulled with a Sutter Instrument puller. Tips were trimmed to the desired size. A Sutter Instrument micromanipulator was loaded with a pipette with an opening slightly larger than the cell to be captured. Care was taken to prevent excess media from entering the pipette as it was positioned in the media. A cell was only collected if it could be picked up without any additional contaminating cells. The collected cell was promptly lysed in RNA lysis buffer. Cells were only collected for up to 2 hours after the animal was euthanized. 10 cells were collected from each animal. 3 pools of 10 cells were combined to make 1 biological sample.
RNA-purification for sequencing: The Absolutely RNA Nanoprep kit (Agilent, 400753) was used to purify RNA. RNA was purified according to the manufacturer’s protocol. 70% ethanol was substituted for 80% sulfolane. RNA was eluted in 11μl of 1:1 elution buffer:water. RNA was reverse transcribed and pre-amplified for 11 cycles with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, 634888) according to the manufacturer’s protocol. An aliquot of the pre-amplified product was reserved for quality control qPCR.
Ocean Ridge Biosciences (Deerfield Beach, FL) sequenced the RNA. Briefly, cDNA was assessed for quality by capillary electrophoresis on Agilent 2100 Bioanalyzer High Sensitivity DNA chips (Agilent Technologies, Santa Clara, CA). 100 pg of pre-amplified cDNA was used for library preparation. The Nextera XT DNA Library Preparation Kit (Illumina Inc., San Diego, CA) was used to prepare cDNA libraries for sequencing. The libraries were pooled at equimolar concentrations and sequenced on an Illumina HiSeq Flow Cell v4 with 50-bp paired-end reads. All samples had a minimum of 30 million passed-filter 50nt paired-end reads.

value: retina

value: retinal ganglion cell


title: HB9_3dpc_3

description:
SL142664
pre-amplified mRNA, tRNA depleted


title: sk0hr-3

value: unwounded (0 hr)


title: uvr8-2-UVA350-R2


title: HB9_Sham_2

description:
SL142660
pre-amplified mRNA, tRNA depleted


title: uvr8-2-UVA-R2


title: HB9_Sham_1

description:
SL142659
pre-amplified mRNA, tRNA depleted


title: HB9_Sham_3

description:
SL142661
pre-amplified mRNA, tRNA depleted


title: Opn4_3dpc_3

description:
SL142658
pre-amplified mRNA, tRNA depleted


title: Ler-blue0-R2

value: Ler


title: uvr8-2-blue0-R2


title: uvr8-2-UV0-R2


title: cry1cry2-blue0-R2


title: uvr8-2-UV-A-B-R2


title: Opn4_Sham_3

description:
SL142655
pre-amplified mRNA, tRNA depleted


title: Opn4_3dpc_1

description:
SL142656
pre-amplified mRNA, tRNA depleted


title: Opn4_3dpc_2

description:
SL142657
pre-amplified mRNA, tRNA depleted


title: Ler-UV-A-B-R2


title: Ler-UVA-R2


title: Ler-UVA350-R2


title: Opn4_Sham_2

description:
SL142654
pre-amplified mRNA, tRNA depleted


title: HB9_3dpc_2

description:
SL142663
pre-amplified mRNA, tRNA depleted


title: Opn4_Sham_1

description:
SL142653
pre-amplified mRNA, tRNA depleted


title: cry1cry2-UV0-R1


title: AR-48568

city: Heidelberg

first: Axel

last: Roers

address: Im Neuenheimer Feld 305

department: Institute of Immunology

country: Germany

institute: Heidelberg University Hospital

data_processing:
[Alignment] Alignment of the samples with GSNAP to the mm10 reference, and using Ensembl 75 for the support of splicesite detection
[Gene counting] Featurecounts was used to assign the reads to genes with the help of Ensembl 75 annotation
Genome_build: mm10
Supplementary_files_format_and_content: 13samples_featureCounts.mm10.E75.csv This is a ";" separated text file, containing the following files: GeneID, Strand, Length, Chromosome, Start, End position, followed by the 13 samples

source_name: purified CD45+ CD49f- epidermal cells

extract_protocol:
epidermal cells were isolated accoring  to Jensen et al., Nat Protoc. 2010 May;5(5):898-911. doi: 10.1038/nprot.2010.39.
Samples were prepared according to the SMARTer® Ultra® Low Input RNA for Illumina® Sequencing - Clontech (version 2)

value: purified CD45+ CD49f- epidermal cells

tag: rnaseh2b genotype

value: flox/flox

tag: cre-genotpye


title: cry1cry2-UVA350-R1


title: cry1cry2-blue0-R1


title: AR-48566

tag: cell type


title: cry1cry2-UVA-R1


title: cry1cry2-UV-A-B-R1


title: AR-51736


title: AR-51724


title: AR-51727


title: Ler-UV0-R2


title: uvr8-2-UV0-R1


title: uvr8-2-UV-A-B-R1


title: uvr8-2-UVA-R1


title: uvr8-2-UVA350-R1


title: AR-48560


title: AR-48565


title: Ler-blue0-R1


title: AR-48567


title: AR-48559


title: AR-51737


title: Ler-UVA350-R1


title: Ler-UV0-R1


title: AR-51730


title: AR-51728


title: Ler-UVA-R1


title: Ler-UV-A-B-R1


title: L6380_7

data_processing:
[Alignment] Alignment of the samples with GSNAP to the mm10 reference, and using Ensembl 75 for the support of splicesite detection
[Gene counting] Featurecounts was used to assign the reads to genes with the help of Ensembl 75 annotation
Genome_build: mm10
Supplementary_files_format_and_content: 6samples_featureCounts.mm10.E75.csv This is a ";" separated text file, containing the following files: GeneID, Strand, Length, Chromosome, Start, End position, followed by the six samples

source_name: purified CD49f+ epidermal cells

extract_protocol:
epidermal cells were isolated accoring  to Jensen et al., Nat Protoc. 2010 May;5(5):898-911. doi: 10.1038/nprot.2010.39.
Samples were prepared according to the NEBNext I Ultra Direction RNA KIT manual

value: purified CD49f+ epidermal cells


title: L6381_8


title: L6382_9


title: L6379_6


title: uvr8-2-blue0-R1


title: L6377_3


title: L6378_4


title: AR-51723


title: Nfkbiz KO keratinocyte v-rasHa transduced, biological rep 1

first: Christophe

last: Cataisson

state: Maryland

address: 37 Covent drive

institute: National Cancer Institute

hyb_protocol: procedure performed by Genomics Laboratory  Cancer Research Technology Program  Frederick National Laboratory for Cancer Research  http://atp.ncifcrf.gov

data_processing: Raw gene expression data (.CEL files) were processed using Qlucore Omics Explorer (QOE) software (version 3; Qlucore AB, Lund, Sweden).

label: biotin

source_name: KO RAS

growth_protocol: Keratinocyte grown in regular media (no starvation)

extract_protocol: Trizol + Qiagen column purification

treatment_protocol: v-rasHa transduction for 3 days

tag: genoptype

value: Nfkbiz KO v-rasHa transduced

value: keratinocyte


title: Nfkbiz KO keratinocyte v-rasHa transduced, biological rep 2

scan_protocol: procedure performed by Genomics Laboratory  Cancer Research Technology Program  Frederick National Laboratory for Cancer Research  http://atp.ncifcrf.gov


title: 1.5yr.mTEC

first: Yongge

last: Zhao

address: 9000 Rockville Pike

institute: NCI

data_processing:
Reads were trimmed to remove adapters, sequencing primers or any such unwanted sequences. Trimmed reads were aligned to mm10 blacklisted regions and only reads not aligning to the blacklisted regions were included for further analysis.
Reads were aligned to mm10 genome using bowtie2 aligner to generate a BAM alignment file.
Duplicates arising due to PCR artifacts were marked and removed using Picardtools package from the Broad Institute
Custom R scripts were run to correct for differences in sequencing depths across samples applying Cyclic Loess normalization.
Resulting normalized bed files were used to call peaks using macs2 with ENCODE recommended parameters for ATAC-Seq data.
Genome_build: mm10

source_name: mTEC

growth_protocol: samples were isolated by cell sorting from thymus single cell suspensions

extract_protocol:
DNA was extracted by incubating the cells in 50ul of cold lysis buffer (10 mM TRIS-HCl, pH 7.4, 10mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630) for 15 min while centrifuging (500 x g, 4°C)
Pelleted nuclei were resuspended in transposition reaction mix with Tn5 Transposase (Illumina FC-121-1030) and incubated 45 min with gentle shaking at 37°C. Tagmented DNA was purified using SPRIselect beads (Beckman Coulter B23317) and amplified by PCR. Resulting libraries were size-selected and purified again by SPRIselect beads

value: WT

value: Thymus

tag: sorting profile

value: DAPI- EpCAM+ CD45- Ly51- UEA-1+

value: mTEC


title: 5wk.keratinocytes.rep1

source_name: kreatinocyte

value: Skin

value: DAPI- EpCAM+ CD45- Sca-1-

value: kreatinocyte


title: 3wk.keratinocytes.rep2


title: 3wk.keratinocytes.rep1


title: 5wk.keratinocytes.rep2


title: wildtype keratinocyte v-rasHa transduced, biological rep 2

source_name: WT RAS

label_protocol: procedure performed by Genomics Laboratory  Cancer Research Technology Program  Frederick National Laboratory for Cancer Research  http://atp.ncifcrf.gov

value: wildtype v-rasHa transduced


title: Nfkbiz KO keratinocyte v-rasHa transduced, biological rep 3


title: wildtype keratinocyte v-rasHa transduced, biological rep 4


title: wildtype keratinocyte v-rasHa transduced, biological rep 3


title: Nfkbiz KO keratinocyte v-rasHa transduced, biological rep 4


title: wildtype keratinocyte v-rasHa transduced, biological rep 1


title: ECO_RAVI_8W_2

city: Seoul

first: Suji

last: Kim

state: Gwanak-gu

address: 1, Gwanak-ro

department: Veterinary Medicine

institute: Seoul National University

description: gene expression of porcine whole blood raised in the RAVI system for 8 weeks

hyb_protocol: 1650ng of each labeled cRNA was fragmented by adding 11 µl 10x blocking agent and 2.2 µl of 25 x fragmentation buffer, and then heated at 60℃ for 30 min. Finally, 55 ul 2 x GE hybridization buffer was added to dilute the labeled cRNA. 100 µl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint HD Porcine GE 4X44K Microarrays (Agilent®). The slides were incubated for 17 h at 65 ℃ in an Agilent hybridization oven. Then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

data_processing: Microarray results were extracted using Agilent Feature Extraction software v11.0 (Agilent Technologies). Array probes that have Flag A in samples were filtered out.

organism: Sus scrofa

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5 2010). Briefly, 100ng of total RNA form each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/ug cRNA) were measured by NanoDrop ND-1000 (NanoDrop, Wilmington, USA).

growth_protocol: Twenty of six-week-old waened pigs were raised in two rooms, each equipped with a gasoline heater and a mineral heat ware for 8 weeks.

extract_protocol: Tota RNA was isolated form the experimental porcine using PAXgene Blood RNA Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol.

treatment_protocol: Two weeks after the stocking, the porcine atropic thinitis vaccine was administered pigs at 2 weeks, 4 weeks, and 8 weeks post vaccination.

value: whole blood


title: ECO_CONTROL_8W_1

description: gene expression of porcine whole blood raised in the gasoline heater system for 8 weeks


title: ECO_RAVI_8W_1


title: ECO_CONTROL_4W_2

description: gene expression of porcine whole blood raised in the gasoline heater system for 4 weeks


title: ECO_RAVI_4W_2

description: gene expression of porcine whole blood raised in the RAVI system for 4 weeks


title: SAMPLE 48: GBM16-79-2

first: Junseong

address: 222 Banpo-daero, Seocho-gu

department: Cancer Evolution Research Center

institute: The Catholic University of Korea

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were variance stabilizing transformed and quantile normalized using the R/Bioconductor lumi package

label: Biotin

source_name: Glioblastoma

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA was extracted from the tumor mass using a Qiagen RNeasy Plus Mini kit.

value: Brain

tag: Sex

value: Male

tag: age

value: Glioblastoma

tag: genotype/variation

value: IDH1 wildtype


title: SAMPLE 46: GBM16-23

value: Female


title: SAMPLE 50: GBM16-117


title: ECO_CONTROL_8W_2


title: ECO_CONTROL_4W_1


title: ECO_RAVI_4W_1


title: SAMPLE 52: GBM16-139


title: ECO_RAVI_2W_2

description: gene expression of porcine whole blood raised in the RAVI system for 2 weeks


title: ECO_RAVI_2W_1


title: SAMPLE 49: GBM16-104


title: SAMPLE 47: GBM16-27


title: SAMPLE 51: GBM16-137-2


title: 4wk.mTEC


title: E17.5.mTEC


title: WT pollen RNA-seq rep5

description:
mikado-permissive.superloci.gff
TAIR10_gene_plus_mikado_TE_transcripts.gff
This sample was used only for TE transcript identification and not the RPKM calculations.

extract_protocol:
follow the instruction of Mirvana miRNA isolation kit
follow the instructions of ScriptSeq v2 RNA-seq lib prep kit

value: whole pollen


title: E17.5.cTEC

source_name: cTEC

value: DAPI- EpCAM+ CD45- Ly51+ UEA-1-

value: cTEC


title: WT pollen RNA-seq rep4

value: WT


title: E15.5.mTEC

description:
e15.5_mTEC_1_S3
e15.5_mTEC_2_S4

value: Thymus


title: E15.5.cTEC

description:
e15.5_cTEC_1_S1
e15.5_cTEC_1_S2


title: PKCζ-KO_P.berghei sporozoite_rep1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description:
PKCζ-KO Huh7 cells at 6 h post P. berghei sporozoites infection
H7_KS

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values

source_name: PKCζ-KO Huh7 cells infected with P. berghei sporozoites

extract_protocol:
Total RNA was extracted from whole cells using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: To identify PKCζ-dependent HGF-inducible or P. berghei sporozoite-inducible genes, 2.5×105 WT or PKCζ-KO Huh7 cells were infected or not with 5×105 P. berghei sporozoites, treated or not with HGF. Salivary glands that were isolated from uninfected 50 mosquitoes, washed in PBS and homogenized in 700 μl of Ca2+ DMEM are defined as “mosquito debris”. Huh7 cells treated with 100 μl mosquito debris were used for further RNA extraction.

value: Huh7 cells

value: PKC zeta KO


title: PKCζ-KO_Medium_rep1

description:
PKCζ-KO Huh7 cells at 6 h post RPMI treatment
H7_KM

source_name: PKCζ-KO Huh7 cells uninfected with PRMI


title: WT_HGF_rep2

description:
WT Huh7 cells at 6 h post HGF (50 ng/ml) treatment
H7_WH

source_name: wild type Huh7 cells uninfected with HGF

value: wild type


title: SAMPLE 44: GBM15-88


title: PKCζ-KO_HGF_rep1

description:
PKCζ-KO Huh7 cells at 6 h post HGF (50 ng/ml) treatment
H7_KH

source_name: PKCζ-KO Huh7 cells uninfected with HGF


title: SAMPLE 42: GBM15-51


title: SAMPLE 43: GBM15-87


title: WT_P.berghei sporozoite_rep2

description:
WT Huh7 cells at 6 h post P. berghei sporozoites infection
H7_WS

source_name: wild type Huh7 cells infected with P. berghei sporozoites


title: ECO_CONTROL_2W_1

description: gene expression of porcine whole blood raised in the gasoline heater system for 2 weeks


title: ECO_CONTROL_2W_2


title: SAMPLE 41: GBM15-47


title: SAMPLE 39: GBM15-11


title: SAMPLE 37: GBM14-67


title: SAMPLE 34: GBM14-46


title: SAMPLE 33: GBM14-39


title: pVC::H1 pollen RNA-seq rep2

source_name: pVC::H1.1-mRFP pollen

extract_protocol:
follow the instruciton of RNeasy plant micro kit
follow the instructions of Ovation RNA-Seq Systems 1–16 for Model  Organisms kit


title: SAMPLE 36: GBM14-56


title: WT_Medium_rep2

description:
WT Huh7 cells at 6 h post RPMI treatment
H7_WM

source_name: wild type Huh7 cells uninfected with PRMI


title: pVC::H1 pollen RNA-seq rep3


title: SAMPLE 35: GBM14-48


title: SAMPLE 40: GBM15-15


title: SAMPLE 29: GBM14-15


title: SAMPLE 31: GBM14-27

value: IDH1 mutation


title: SAMPLE 45: GBM16-21


title: SAMPLE 28: GBM14-14


title: SAMPLE 30: GBM14-25


title: SAMPLE 32: GBM14-30


title: pVC::H1 pollen RNA-seq rep1


title: SAMPLE 25: GBM14-08


title: WT_mosquito debris_1

description:
WT Huh7 cells at 6 h post mosquito debris treatment
WT_Dub1

source_name: wild type Huh7 cells uninfected with mosquito debris


title: WT_HGF_rep1

description:
WT Huh7 cells at 6 h post HGF (50 ng/ml) treatment
WT_HGF

source_name: wild type Huh7 cells uninfected with P. berghei sporozoites


title: WT pollen RNA-seq rep2

source_name: WT pollen


title: WT pollen RNA-seq rep3


title: SAMPLE 20: GBM13-79


title: SAMPLE 22: GBM14-01


title: WT_P.berghei sporozoite_rep1

description:
WT Huh7 cells at 6 h post P. berghei sporozoites infection
WT_Spo


title: SAMPLE 24: GBM14-06


title: WT pollen RNA-seq rep1


title: SAMPLE 27: GBM14-12


title: WT_mosquito debris_2

description:
WT Huh7 cells at 6 h post mosquito debris treatment
WT_Dub2


title: WT_Medium_rep1

description:
WT Huh7 cells at 6 h post RPMI treatment
WT_med


title: SAMPLE 23: GBM14-05


title: SAMPLE 21: GBM13-87


title: SAMPLE 26: GBM14-11-2


title: WT SN BS-seq

source_name: WT sperm nuclei

value: sperm cell of pollen


title: SAMPLE 19: GBM13-71


title: SAMPLE 38: GBM14-73


title: 5H_MV_rep1

city: London

last: Aref

address: 72 Huntley St, Fitzrovia,

department: Haematology department

institute: UCL Cancer Institute

data_processing:
1) Pre-process (adaptor removal, low quality bases removed, reads labelled with UMI) fastp
2) Aligment to genome RNA-STAR
3) Removal of PCR duplicates using mapping co-ordinate & UMI JE-Suite
4) Read-per-transcript count using iGenome annotation FeatureCounts
Differentially expressed genes were identified by DESeq2
Genome_build: UCSC hg38
Run data were demultiplexed and converted to fastq files using Illumina’s bcl2fastq Conversion Software v2.19.
Fastq files were then aligned to the human genome UCSC hg38 using RNA-STAR 2.5.2b then UMI deduplicated using Je-suite (1.2.1).
Reads per transcript were counted using FeatureCounts and differential expression was estimated using the BioConductor package SARTools, a DESeq2 wrapper.
All annotation and sequences were obtained from Illumina iGenomes (http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html)

source_name: bone marrow-derived mesenchymal stromal cells

growth_protocol: 3x10^5 cells were plated in 6-well tissue culture treated plates and placed in an incubator (5%CO2 and 37C) for 16 hours prior to mock-infection or MV infection

extract_protocol:
RNA was isolated using the TriZol reagent method according to manufacturer's protocol.
Libraries were prepared by UCL Genomics using the KAPA mRNA HyperPrep Kit (p/n KK8580) according to manufacturer's instructions
Briefly, mRNA was isolated from total RNA using Oligo dT beads to pull down poly-adenylated transcripts.
The purified mRNA was fragmented using chemical hydrolysis (heat and divalent metal cation) and primed with random hexamers.
Strand-specific first strand cDNA was generated using Reverse Transcriptase in the presence of Actinomycin D. This allows for RNA dependent synthesis while preventing spurious DNA-dependent synthesis.
The second cDNA strand was synthesised using dUTP in place of dTTP, to mark the second strand. The resultant cDNA is then "A-tailed" at the 3' end to prevent self-ligation and adapter dimerisation.
Full length xGen adaptors (IDT), containing two unique 8bp sample specific indexes, a unique molecular identifier (N8) and a T overhang are ligated to the A-Tailed cDNA.
Successfully ligated cDNA molecules were then enriched with limited cycle PCR (14 cycles – the actual number is dependent on the amount of input RNA)
The high fidelity polymerase employed in the PCR is unable to extend through uracil. This means only the first strand cDNA is amplified for sequencing, making the library strand specific (first-strand)

treatment_protocol: hTERT and 5H cells were either mock-infected or infected with MV at a multiplicity of infection (MOI of 1.0) and total RNA was extracted at 24 hours post infection.

tag: cell line

value: MV-susceptible MSC cell line (5H)

tag: infection

value: infected with MV


title: 5H_Uninfected_rep3

value: uninfected


title: 5H_MV_rep3


title: 5H_Uninfected_rep1


title: hTERT_MV_rep3

value: MV-resistant MSC cell line (hTERT)


title: SAMPLE 17: GBM13-64

value: Brain

value: Glioblastoma


title: SAMPLE 15: GBM13-53

value: Female

value: IDH1 wildtype


title: SAMPLE 18: GBM13-68


title: SAMPLE 16: GBM13-61

value: Male


title: D-11c

first: Stefania

last: Senger

address: 114, 16th st. Charlestown, Navy Yard

department: Pediatrics

institute: Massachusetts General Hospital

data_processing:
STAR was used to map sequencing reads to human reference genome (Ensembl annotation of hg19 assembly).
Read counts over transcripts were calculated using HTSeq v.0.6.0 based on Ensembl annotation of hg19 genome.
Differential expression analysis was performed using EdgeR.
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: Tab-delimited table of RPKM values

source_name: Duodenal organoids

growth_protocol: Duodenal biopsies from non-celiac and celiac patients were collected by upper endoscopic The isolation of intestinal epithelial cells was performed as previously described (Jung et al., 2011; VanDussen KL, 2015; Senger et al., 2018). Crypts were plated in matrigel and grown in L-WRN/ISC medium, at 37oC in humid atmosphere with 5% CO2. The duodenal epithelial spheroids culture was passaged every 7-9 days using a standard trypsin-based cell dissociation protocol. About 2x106cells/mL singles were re-plated in matrigel supported by L-WRN/ISC medium.

extract_protocol:
RNA extraction from organoids from NC and CeD donors was carried out in TRIzol reagent (#15596018, ThermoFischer Scientific, MA) accordingly to manufacturer’s directions and flash frozen at -80oC for further RNA purification. Total RNA was purified using Zymo-Spin column (#R2050, Zymo Research, Tustin, CA), accordingly to manufacturer’s protocol.
Total RNA was subjected to polyA selection, followed by library construction using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA)

value: Duodenal organoids

tag: diagnosis

value: non-celiac

tag: passage

tag: primary cell from

value: epithelium small intestine


title: D-64

value: Celiac disease


title: D-15c


title: 5H_Uninfected_rep2


title: 5H_MV_rep2


title: SAMPLE 14: GBM13-41


title: SAMPLE 12: GBM13-20


title: SAMPLE 13: GBM13-30


title: SAMPLE 9: GBM13-15


title: SAMPLE 10: GBM13-17


title: SAMPLE 11: GBM13-18


title: D-10


title: SAMPLE 8: GBM13-14


title: SAMPLE 7: GBM13-03


title: SAMPLE 2: GBM11-11


title: hTERT_MV_rep2


title: SAMPLE 5: GBM11-21


title: D-14c


title: SAMPLE 3: GBM11-12


title: hTERT_MV_rep1


title: hTERT_Uninfected_rep3


title: hTERT_Uninfected_rep2


title: hTERT_Uninfected_rep1


title: BI-2


title: AF22-LacZ-CTR

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

institute: Lund University

data_processing:
Alignment: For all RNAseq data sets, the sequencing reads were mapped to the human reference genome (hg38) using STAR aligner v2.5.0a (Dobin et al., 2013)
Align for coding gene analysis: For quantification of NCBI genes (O'Leary et al., 2016) entries, reads mapping to 10 or less positions were kept and the primary alignments were used for quantification. Mapping was performed with splice junction overhang of minimum one base, assisted by Gencode v25 annotation.
Align for retroelement analysis: The analysis of retrotransposons only included uniquely mapped reads (-- outFilterMultimapNmax 1). A maximum of 0.03 mismatches per base were allowed (--outFilterMismatchNoverLmax 0.03).
Genes and TEs were quantified using the Subread package FeatureCounts (Liao et al., 2014).
RepeatMasker annotation for hg38 was downloaded from the UCSC table browser (Karolchik et al., 2004).
Genome_build: hg38
Supplementary_files_format_and_content: DNMT1KO_AF22.hg38.NCBI.genesBestRefSeq.exon.primary.txt: Abundance measurement of NCBI genes for CTR (839) and DNMT1-KO (840) in AF22 cells. Also contains ID, genomic position, length and strand orientation of transcript.
Supplementary_files_format_and_content: DNMT1KO_AF22.hg38.uniqueMapping.RepeatMasker.notInNCBIexon.txt.filtered.txt: Abundance measurement of LINE,SINE,LTR and SVA elements for CTR (839) and DNMT1-KO (840) in AF22 cells. Also contains ID, genomic position, length and strand orientation of transcript.
Supplementary_files_format_and_content: DNMT1KO.hg38.NCBI.genesBestRefSeq.exon.primary.txt: Abundance measurement of NCBI genes for CTR and DNMT1-KO in Sai cells. Also contains ID, genomic position, length and strand orientation of transcript.
Supplementary_files_format_and_content: DNMT1KO.hg38.uniqueMapping.RepeatMasker.notInNCBIexon.txt.filtered.txt: Abundance measurement of LINE,SINE,LTR and SVA elements for CTR and DNMT1-KO in Sai cells. Also contains ID, genomic position, length and strand orientation of transcript.

source_name: AF22 cells

growth_protocol: The DNMT1-KO and subsequent analysis was performed on the embryo-derived human neural epithelial-like stem cell line, Sai2 (Tailor et al., 2013), and was maintained as previously described (Falk et al., 2012).

extract_protocol:
Total RNA from hNPCs was isolated using the RNeasy Mini Kit (Qiagen)
Libraries from DNMT1-KO and control hNPCs were generated using Illumina TruSeq Stranded mRNA library prep kit (poly-A selection) and sequenced on a HiSeq2500 (PE 2x125bp)

treatment_protocol: LV.gRNA.CAS9GFP vectors (Liao et al., 2015) were used to target DNMT1 (DNMT1-KO) or LacZ (control). Lentiviral vectors were produced as previously described (Zufferey et al., 1997) and were of titers 109 TU/ml which was determined using qRT-PCR (Georgievska et al., 2004). hNPCs were transduced with an MOI 10-15 and allowed to expand 10 days prior to FACS (FACSAria, BD sciences). Cells were detached and resuspended in basic culture media with Rock inhibitor (10µM, Miltenyi) and propidium iodide (BD Bioscience), and strained (70µm, BD Bioscience). GFP positive cells were spun down (400g, 7min) and snap frozen on dry ice. Cell pellets were kept at -80°C until RNA was isolated. All groups were performed in biological triplicates

value: iPS-derived neural progenitor cells

tag: vector

tag: grna target

value: LacZ


title: DNMT1-KO-2

source_name: Sai cells

value: fetal-derived neural progenitor cells


title: SAMPLE 6: GBM12-44

source_name: Glioblastoma

tag: tissue


title: DNMT1-KO-3


title: SAMPLE 4: GBM11-20


title: ChIP-seq_H3K27me3_DNMT1ko_2

description: ChIP-sequencing

data_processing:
ChIP-seq: The raw 50bp fastq files where trimmed and filtered with trimmomatic, and quality was assessed with fastqc. The reads were then mapped to hg38 with bowtie2 with –sensitive-local mapping parameters. We next filtered out multi-mapping reads but removing all reads with MAPQ<10 using Samtools (Li et al., 2009) (REF), keeping only reads has one unique best alignment. Bam files were converted to bedGraph and bigwig using UCSC tools.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig (of uniquely mapping reads).

source_name: fetal-derived neural progenitor cells (sai)

extract_protocol: Nextera DNA Library Prep Kit

tag: viral vector

value: DNMT1 exon 32

tag: chip-antibody

value: H3K27me3 Anti-trimethyl-Histone H3 (Lys27) Ab Millipore 07-449


title: ChIP-seq_H3K27me3_DNMT1ko_1

description: ChIP-sequencing

value: fetal-derived neural progenitor cells (sai)


title: ChIP-seq_pol-II_DNMT1ko_2

description: ChIP-sequencing

value: Pol II:RPB2 , N-term cat# GTX102535-S


title: DNMT1-KO-1


title: SAMPLE 1: GBM09-13


title: ChIP-seq_pol-II_DNMT1ko_1

description: ChIP-sequencing


title: LacZ-CTR-2


title: LacZ-CTR-3


title: ChIP-seq_H3K27ac_DNMT1ko_2

description: ChIP-sequencing

value: H3K27Ac Diagenode #C15410196


title: ChIP-seq_H3K27me3_CTR_2

description: ChIP-sequencing


title: AF22-DNMT1-KO


title: ChIP-seq_H3K27ac_DNMT1ko_1

description: ChIP-sequencing


title: KO_48hr_10

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

data_processing:
BCL files were converted to fastq using bcl2fastq (v2.20.0.422).
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36).
Transcript quantification was performed by salmon (v0.8.2) using arguments '-l IU --gcBias' and tximport (v1.8.0) using the UCSC mm10 known gene transcript assembly (v9).
DESeq2 (v1.14.1) was used to calculate differential expression.
Supplementary_files_format_and_content: Text files are raw counts (1 count = 1 read pair) as quantified by salmon (v0.8.2) and imported by tximport (v1.8.0). Also provided are transcript IDs, gene name, and gene descriptions.

source_name: splenic B cells

extract_protocol:
RNA was isolated using TRIzol (Invitrogen) and RNeasy Mini Kit (QIAGEN catalog # 74104) according to instructions provided by the manufacturer.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2 ng total RNA with RNA integrity numbers ranging from 8.1 to 9.6 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech catalog # 63488), with 12 cycles of amplification. Subsequently, 10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 56.8 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 58% to 75%.

tag: genotype

value: KO

tag: replicate

tag: condition


title: KO_48hr_11


title: WT_48hr_9

value: WT


title: ChIP-seq_H3K27ac_CTR_2

description: ChIP-sequencing

tag: cell type


title: ChIP-seq_pol-II_CTR_2

description: ChIP-sequencing


title: WT_48hr_8


title: ChIP-seq_pol-II_CTR_1

description: ChIP-sequencing


title: WT_48hr_7


title: KO_0hr_6


title: RH4 Entinostat 6 hour

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

description: Paired-end

data_processing:
RNA-seq reads were aligned to the hg19 reference genome using STAR.
Gene expression values were calculated as Transcripts per Million (TPM) using STAR and the UCSC reference at the gene level.
Differential gene expression was determined using EdgeR.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: TPM files are provided in txt format at the gene-level.

source_name: FP-RMS cell line, PAX3-FOXO1

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.

extract_protocol:
RNA was extracted from FP-RMS cell lines using the RNeasy mini kit (Qiagen).
Standard Illumina barcodes were introduced during library preparation.

treatment_protocol: Drug was dissolved in DMSO to a stock concentration of 10 mM, and additionally diluted in DMEM to a final concentration of 0.5, 1, 5, or 10 µM (or DMSO of equivalent final volume), exposing cells for 1, 6 or 24 hours before extracting RNA.

value: FP-RMS cell line

tag: treatment time

value: 6 hours

tag: treatment

value: Entinostat 1 uM

tag: drug target


title: RH4 Entinostat 1 hour

description: Paired-end

tag: cell line

value: 1 hours


title: KO_0hr_5


title: WT_0hr_3


title: RH4 DMSO 24 hours

description: Paired-end

value: 24 hours

value: DMSO 0.1%

value: control


title: LacZ-CTR-1


title: KO_0hr_4


title: WT_0hr_2


title: RH4 DMSO 6 hours

description: Paired-end


title: RH4 Entinostat 24 hour

description: Paired-end


title: ChIP-seq_H3K27me3_CTR_1

description: ChIP-sequencing


title: WT_0hr_1


title: KO_48hr_12


title: RH41 WT161 low

description: Paired-end

value: WT161 1 uM


title: RH41 WT161 high

description: Paired-end


title: ets-4/daf-16 24h4C rep2

city: Oslo

first: Rafal

last: Ciosk

state: Oslo

address: Blindernveien 31

department: Department of Biosciences

country: Norway

institute: University of Oslo

description:
ets-4/daf-16 double mutant grow at 20oC with 24 hours 4oC treatment
name in processed data file:
1473F23

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were mapped to C.elegans genome (Ensembl WBcel235) using STAR with default parameters except: outFilterMismatchNmax 3, outFilterMultimapNmax 1, alignIntronMax 15000, outFilterScoreMinOverL read 0.33, outFilterMatchNminOverLread 0.33. Count matrices were generated for the number of reads overlapping with the exons of protein coding genes using summarizeOverlaps from GenomicFeatures
Genome_build: Ensembl WBcel235
Supplementary_files_format_and_content: csv includes raw read count values from exons of gene for each sample

organism: Caenorhabditis elegans

growth_protocol: All C. elegans strains were maintained at 20°C on nematode growth media (NGM) dishes seeded with the E. coli strain, OP50.

extract_protocol:
1000 animals were collected at day 1 of adulthood and RNA was isolated using Trizol protocol.
Library was prepared using TrueSeq Ilumina mRNA-seq (stranded – high input).

treatment_protocol: At day 1 of adulthood, they are cold adapted at 10°C for 2 hours and then shifted to 4°C for 24 hours.

tag: strain

value: whole worm

tag: age

value: day 1 adult


title: RH41 UNC1999 low

description: Paired-end

value: UNC1999 1 uM


title: ChIP-seq_H3K27ac_CTR_1

description: ChIP-sequencing

value: LacZ


title: ets-4 24h4C rep2

description:
ets-4 mutant grow at 20oC with 24 hours 4oC treatment
name in processed data file:
1473F22

value: ets-4(rrr16) X.


title: RH41 UNC1999 high

description: Paired-end


title: N2 24h4C rep2

description:
Wild type N2 grow at 20oC with 24 hours 4oC treatment
name in processed data file:
1473F21

value: wild type


title: RH41 UNC1215 low

description: Paired-end


title: RH4 DMSO 1 hour

description: Paired-end


title: ets-4/pqm-1 24h4C rep2

description:
ets-4/pqm-1 double mutant grow at 20oC with 24 hours 4oC treatment
name in processed data file:
1473F24


title: ets-4/pqm-1 24h4C rep1

description:
ets-4/pqm-1 double mutant grow at 20oC with 24 hours 4oC treatment
name in processed data file:
1473F20


title: RH41 UNC1215 high

description: Paired-end


title: ets-4/daf-16 24h4C rep1

description:
ets-4/daf-16 double mutant grow at 20oC with 24 hours 4oC treatment
name in processed data file:
1473F19


title: ets-4 24h4C rep1

description:
ets-4 mutant grow at 20oC with 24 hours 4oC treatment
name in processed data file:
1473F18


title: RH41 UNC0638 low

description: Paired-end

value: UNC0638 1 uM


title: RH41 UNC0638 high

description: Paired-end


title: ets-4/pqm-1 20C rep2

description:
ets-4/pqm-1 double mutant grow at 20oC
name in processed data file:
1473F8

source_name: ets-4/pqm-1 double mutant grow at 20oC


title: RH41 Tram low

description: Paired-end

value: Trametinib 1 uM


title: N2 24h4C rep1

description:
Wild type N2 grow at 20oC with 24 hours 4oC treatment
name in processed data file:
1473F17


title: RH41 Tram high

description: Paired-end

value: Trametinib 10 uM


title: ets-4/daf-16 20C rep2

description:
ets-4/daf-16 double mutant grow at 20oC
name in processed data file:
1473F7

source_name: ets-4/daf-16 double mutant grow at 20oC


title: RH41 SGCCBP30 low

description: Paired-end

value: FP-RMS cell line

value: SGC-CBP30 1 uM

value: CREBBP/EP300 bromodomain


title: 201

first: Chung

middle: H

last: Kok

address: North Terrace

institute: South Australia Health and Medical Research Institute

description:
CP-CML
sample_102

hyb_protocol: A total of 12 different labelled samples can be loaded into 12 individual arrays per beadchip.  The chip was then hybridised at 58C for 16 hours in an oven with a rocking platform.  After hybridisation, the chip was washed using the appropriate protocols as outlined in the Illumina manual.  Upon completion of the washing, the chips were then coupled with Cy3.

scan_protocol: scanned in the Illumina iScan Reader. The scanner operating software, GenomeStudio version 1.9.0, converts the signal on the array into a TXT file for analysis.

data_processing: Normalisation was performed using neqc function implemented in limma (Bioconductor) package.

label_protocol: A total of 500ng of total RNA was then prepared for hybridisation to the Ilumina humanHT 12 Expression Beadchip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes GEX-HYB Hybridisation Buffer (supplied with the beadchip). A total hybridisation volume of 15ul was prepared for each sample and 15ul loaded into a single array on the Ilumina humanHT 12 Expression Beadchip.

extract_protocol: RNA was extracted with Trizol reagent, followed by  QIAGEN miRNeasy midi kit in accordance with the prescribed protocol provided with the kit. The quality and quantity of human total RNA was ascertained on the Agilent Bioanalyser 2100 using the NanoChip protocol.

tag: gender

value: Female

tag: disease stage

value: diagnostic chronic phase

tag: bcr-abl1 at 3 month


title: ets-4 20C rep2

description:
ets-4 mutant grow at 20oC
name in processed data file:
1473F6

source_name: ets-4 mutant grow at 20oC


title: 119

description:
CP-CML
sample_112


title: 206

description:
CP-CML
sample_120

value: Male


title: 175

description:
CP-CML
sample_117


title: RH41 SGCCBP30 high

description: Paired-end

value: 6 hours

value: SGC-CBP30 10 uM


title: 167

description:
CP-CML
sample_115


title: 123

description:
CP-CML
sample_113


title: 190

description:
CP-CML
sample_118


title: 113

description:
CP-CML
sample_110


title: 174

description:
CP-CML
sample_116


title: 97

description:
CP-CML
sample_107


title: 116

description:
CP-CML
sample_111


title: 107

description:
CP-CML
sample_109


title: 207

description:
CP-CML
sample_104


title: 61

description:
CP-CML
sample_106


title: 199

description:
CP-CML
sample_119


title: 156

description:
CP-CML
sample_114


title: ets-4/pqm-1 20C rep1

description:
ets-4/pqm-1 double mutant grow at 20oC
name in processed data file:
1473F4

value: whole worm


title: 187

description:
CP-CML
sample_95


title: 202

description:
CP-CML
sample_103


title: 194

description:
CP-CML
sample_99


title: 196

description:
CP-CML
sample_101


title: 193

description:
CP-CML
sample_96


title: N2 20C rep2

description:
Wild type N2 grow at 20oC
name in processed data file:
1473F5

source_name: Wild type N2 grow at 20oC

value: day 1 adult


title: 191

description:
CP-CML
sample_97


title: RH41 SGC0946 high

description: Paired-end


title: RH41 SGC0946 low

description: Paired-end

value: SGC0946 1 uM


title: N2 20C rep1

description:
Wild type N2 grow at 20oC
name in processed data file:
1473F1


title: RH41 PFI3 low

description: Paired-end

value: PFI-3 1 uM


title: ets-4 20C rep1

description:
ets-4 mutant grow at 20oC
name in processed data file:
1473F2

value: ets-4(rrr16) X.


title: RH41 PFI3 high

description: Paired-end

value: PFI-3 10 uM


title: RH41 PFI2 low

description: Paired-end

value: PFI-2 1 uM


title: hsf-1(OE) rep3

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

data_processing:
Basecalling was performed using HiSeq Control Software (Illumina)
Quality control of raw RNA-Seq reads was performed using FastQC
Tuxedo Suite was used for alignment, differential expression analysis and post-analysis diagnostics
RNA-Seq reads were aligned to the C. elegans reference transcriptome (WS220 release) using Bowtie 2
Transcript splicing junctions were mapped using TopHat
FastQC was used for post-alignment quality control to ensure high quality of input data for subsequent analysis steps
Cufflinks was used to assemble the aligned reads, estimate abundance of transcripts and calculate FPKM values
Transcripts that were differentially expressed relative to wild-type were determined using CuffDiff 2 using the following two criteria: false discovery rate (FDR)-adjusted p value < 0.05 and fold-change ≥ 1.5
Genome_build: C. elegans reference transcriptome WS220 release
Supplementary_files_format_and_content: Text file with mapped read counts

source_name: Whole animal

growth_protocol: All strains were maintained at 20˚C on nematode growth medium (NGM) plates seeded with E. coli (OP50 strain). Unhatched eggs were age-synchronized and after 3 days, day 1 adult worms were harvested for RNA extraction.

extract_protocol:
TRIzol reagent (Thermo Fisher) was used to extract total RNA from ~1,000 age-synchronized day 1 adult worms (three biological replicates per genotype). DNase-treatment was performed using TURBO DNA-free kit (Themo Fisher). mRNA was isolated from the DNase-treated total RNA using oligo(dT) and cDNA was synthesized by reverse transcription using TruSeq RNA Library Prep Kit v2 (Illumina).
The samples were end-repaired, poly(A)-tailed, ligated to barcoded oligo adapters (Illumina) and PCR-amplified using Apollo 324 library preparation system (Wafergen Bio-systems) to prepare non-stranded poly(A)-based cDNA libraries with 120 bp insert size.

value: Whole animal

value: Day 1 adult


title: 177

description:
CP-CML
sample_90


title: 179

description:
CP-CML
sample_89


title: ets-4/daf-16 20C rep1

description:
ets-4/daf-16 double mutant grow at 20oC
name in processed data file:
1473F3


title: 178

description:
CP-CML
sample_91


title: hsf-1(OE) rep2


title: RH41 OJI1 low

description: Paired-end

value: FP-RMS cell line

value: OJI-1 1 uM


title: hsf-1(OE) rep1


title: hsb-1(-) rep3

value: hsb-1(cg116) IV


title: RH41 OJI1 high

description: Paired-end

value: OJI-1 10 uM


title: 171

description:
CP-CML
sample_87

value: Female

value: diagnostic chronic phase


title: 165

description:
CP-CML
sample_82

value: Male


title: hsb-1(-) rep2


title: RH41 Merck60 low

description: Paired-end

value: 6 hours

value: Merck60 1 uM


title: hsb-1(-) rep1


title: RH41 Merck60 high

description: Paired-end

value: Merck60 10 uM


title: RH41 MC1568 low

description: Paired-end


title: 169

description:
CP-CML
sample_86


title: 168

description:
CP-CML
sample_84


title: N2 rep3

value: wild-type


title: 153

description:
CP-CML
sample_78


title: 161

description:
CP-CML
sample_80


title: 166

description:
CP-CML
sample_85


title: 152

description:
CP-CML
sample_76


title: N2 rep2


title: RH41 PFI2 high

description: Paired-end

value: PFI-2 10 uM


title: RH41 MC1568 high

description: Paired-end


title: 154

description:
CP-CML
sample_77


title: 146

description:
CP-CML
sample_73


title: 147

description:
CP-CML
sample_72


title: 148

description:
CP-CML
sample_71


title: N2 rep1


title: 149

description:
CP-CML
sample_75


title: 140

description:
CP-CML
sample_69


title: 139

description:
CP-CML
sample_70


title: 142

description:
CP-CML
sample_68


title: 136

description:
CP-CML
sample_66


title: 132

description:
CP-CML
sample_67


title: RH41 LSD690 high

description: Paired-end


title: 131

description:
CP-CML
sample_65


title: 158

description:
CP-CML
sample_81


title: RH41 LSD519 low

description: Paired-end

value: LSD-519 1 uM


title: RH41 LSD519 high

description: Paired-end


title: 127

description:
CP-CML
sample_64


title: RH41 LSD690 low

description: Paired-end

value: LSD-690 1 uM