title: vehicle rep 2

city: Montreal

first: William

last: Muller

state: Quebec

address: 1160 Avenue des Pins

country: Canada

institute: McGill University

description: GCRC 1991 + Captisol (vehicle) sample 2

data_processing:
Raw read of fastq format were obtained after adapter removal in BaseSpace. Index of the mm10 mouse or hg38 human genome was built using hisat2-v2.0.4.
Paired-end clean reads were aligned to the reference genome using hisat2-v2.0.4. Annotations for repeat elements were obtained from RepeatMasker (open-4.0.5).
The pysam python module was used to compute number of reads mapping to repeat elements (in gtf format); reads mapping to features were then RPKM normalized.
Genome_build: hg38
Supplementary_files_format_and_content: gtf files for repeat element features, along with two additional columns 1) number of reads mapping to feature using pysam and 2) rpkm

source_name: Human tissue grown in immunocompromised mouse

growth_protocol: Patient-derived xenografts (PDX) were implanted into female NOD/SCID/gamma (NSG) immunocompromised mice (Charles River Laboratories).

extract_protocol:
RNA from 4 mice per condition were isolated using the RNeasy kit (Qiagen), and pooled for sequencing.
250~300 bp insert strand specific library with rRNA removal (Ribo-ZeroTM Magnetic Kit)
RNA-Seq, 100 M reads, ribo depleted library, paired-end sequencing (NovoGene Lnc-RNA sequencing service)

treatment_protocol: Mice were randomly assigned to treatment groups and monitored for tumor growth by twice-weekly palpation. Treatments began once tumors had reached a size of 5 mm x 5 mm (approximately 65 mm3). GSK126 (custom synthesis by MercaChem) in 20% Sulfobutylether-β-cyclodextrin (Captisol - Medchem Express) was administered at 300 mg/kg three times per week by intraperitoneal injection.

value: HER2+ PDX (patient derived xenograft)

tag: tissue type

value: Breast tumour biopsy

tag: treatment

value: Vehicle control


title: ET15 [methylation]

status: Public on Aug 26 2019

type: genomic

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Human Tumor

label_protocol: standard Illumina protocol

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out using a Qiagen Blood & Cell Culture DNA Midi Kit (Qiagen, Hilden, Germany) after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany).

tag: subject status

value: Embryonal Tumor/Multilayered Rosettes (ETMR) patient

tag: subset

value: C19MC amplified

tag: sample type

value: FFPE


title: ET27 [methylation]


title: 04T098

type: SRA

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

library_source: transcriptomic

data_processing:
Read files were quality-checked with FastQC.
Adapter sequences were removed with cutadapt v1.11 and only those reads longer than 15bp and shorter than 35bp were kept for further analysis.
Reads were aligned to the human genome (GRCh37/hg19) with Bowtie 1.0.0 and Samtools 0.1.18 allowing no mismatches and a maximum of 1 alignment per read.
Raw counts for miRNAs were obtained with HTSeq v0.5.3p9, using the miRBase v20 annotation for hg19
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Raw read counts obtained with HTSeq

molecule: total RNA

source_name: Anaplastic thyroid carcinoma

extract_protocol:
Tissues were fresh frozen in OCT. RNA was harvested using Trizol reagent.
2µg of total RNA samples were used and  were processed with kit "NEXTflex Illumina Small RNA Sequencing Kit v3" (Bioo Scientific catalog# 5132) by following manufacturer instructions. Briefly, samples were sequentially ligated to randomized 3' and 5' adapters, with a truncated form of T4 RNA Ligase 2 and the T4 RNA ligase 1, respectively. Reverse transcription with a MMuLV Reverse Transcriptase yielded cDNA adapter-ligated libraries that were amplified by 14 cycles of PCR. Amplified products were either purified by double-sided SPRI selection of by PAGE extraction, according to their BioAnalyzer size profile. Pooled purified fractions were applied to an Illumina flow cell for cluster generation, and sequenced on an Illumina HiSeq2000 by following manufacturer's protocols. Sequencing read ends contain a variable length of the 3' adapter, whose sequence is nnnnTGGAATTCTCGGGTGCCAAGG. As a consequence of the use of adapters with random tetramers, both the first four bases of the read and the four bases at the beginning of the 3' adapter are noninformative. Following 3' adapter trimming, those first and last four bases of the read were trimmed too.

tag: tissue

value: Primary tumor

tag: disease

value: Anaplastic thyroid carcinoma


title: ET14 [methylation]


title: ET13 [methylation]


title: ET13_R1 [methylation]


title: vehicle rep 1

description: GCRC 1991 + Captisol (vehicle) sample 1


title: 04T097


title: drug treated rep 2

description: GCRC 1991 + GSK126 sample 2

value: Drug treated


title: ET12 [methylation]

value: Frozen


title: ET10 [methylation]


title: Vehicle-treated rep3

city: Bethesda

first: Clifton

middle: Lee

last: Dalgard

state: Maryland

address: 4301 Jones Bridge Road B2038

department: Anatomy Physiology & Genetics

country: USA

institute: Uniformed Services University

data_processing:
FASTQ data were generated using CASAVA
Raw reads were analyzed and groomed using FASTQC and FASTQ Groomer
RPKM values for transcriptome expression levels were generated using Bowtie 2, TopHat 2 and Cufflinks 2.
RPKM values were used for Comparative Marker Selection and differential gene analysis by Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample profiled.

organism: Rattus norvegicus

source_name: PAIII tumor

extract_protocol:
Samples of grossly dissected, frozen primary tumors were mounted on a cryostat chuck. Serial thick sections (300 micron) were then cut and mounted on cold slides. Ten random samples were micro-dissected from viable regions of the tumor in 300 micron thick sections with a 1 mm diameter micropunch device. The tumor samples were then soaked in RNA Later at four degrees Celsius overnight before isolation of total RNA.
One microgram of total RNA was input for library preparation using the TruSeq RNA Sample Prep Kit v2

value: vehicle


title: ET9 [methylation]


title: ET22 [methylation]


title: Vehicle-treated rep1


title: ET193 [methylation]

hyb_protocol: Illumina

label_protocol: Illumina

tag: material


title: Vehicle-treated rep2


title: ET8 [methylation]


title: ET3_R1 [methylation]


title: ET7 [methylation]


title: ET5 [methylation]


title: Digitoxin-treated rep2

value: digitoxin


title: Digitoxin-treated rep3


title: ET1 [methylation]


title: ET6 [methylation]


title: ET186 [methylation]


title: ET191 [methylation]

value: C19MC balanced


title: ET3 [methylation]


title: ET4 [methylation]


title: ET1_R2 [methylation]


title: ET190 [methylation]


title: ET1_R1 [methylation]


title: ET176 [methylation]


title: HEPG2_D8.2_Control

type: RNA

city: Rockville

first: Jeffrey

last: Robinson

state: United States

address: 9630 Gudelsky Dr

department: Translational Life Sciences Technology

institute: UMBC

description:
lab ID:
ST, 20180726, 07/19 seeded, low density

hyb_protocol: Nanostring GX protocol

scan_protocol: Nanostring nCounter platform

data_processing: nSolver 4.0 software

source_name: in vitro  cell culture, adherent

label_protocol: Nanostring GX protocol

growth_protocol: Adherent cell cultures grown on permeable membrane inserts or cell-culture treated polystyrene (full details in pub methods section)

extract_protocol: Qiagen RNeasy - total RNA

treatment_protocol: Cells were variously treated with 10uM Dexamethasone or transient MiR-mimic miRNA lipofection

tag: experimental treatment

value: Control

tag: biological replicate.plate replicate

tag: timecourse day number

tag: cell line


title: HEPG2_D7.2_Control

description:
lab ID:
ST, 20180726, 07/20 seeded


title: HEPG2_D7.1_Control

description:
lab ID:
ST, 20180726, 07/20 seeded


title: HEPG2_D8.1_Control


title: ET2 [methylation]


title: drug treated rep 1

description: GCRC 1991 + GSK126 sample 1


title: ET192 [methylation]


title: Digitoxin-treated rep1


title: ET174_R2 [methylation]


title: ET175 [methylation]


title: HEPG2_D4.2_Control

description:
lab ID:
ST, 20180723, 07/20 seeded


title: ET161 [methylation]


title: ET174 [methylation]


title: ET174_R1 [methylation]


title: ET90 [methylation]


title: HEPG2_D4.1_Control

description:
lab ID:
ST, 20180723, 07/20 seeded


title: HEPG2_D5.2_Control

description:
lab ID:
ST, 20180723, 07/19 seeded, low density


title: ET82_R1 [methylation]


title: HEPG2_D5.1_Control


title: HT29_D7.2_Control

description:
lab ID:
ST, 20180726, 07/20 seeded


title: HT29_D7.1_Control

description:
lab ID:
ST, 20180726, 07/20 seeded


title: ET11 [methylation]


title: HT29_D8.4_Control


title: P28 WT Astrocyte rep 5

city: Blacksburg

first: Michelle

middle: L.

last: Olsen

state: VA

address: 970 Washington Street SW

department: School of Neuroscience

institute: Virginia Polytechnic and State University

data_processing:
Raw RNA-Seq reads were concatenated (per R1 and R2 fastq read, respectively) and quality trimmed using Trim Galore! Version 0.4.3 . Sequence quality of trimmed reads was inspected using FastQC (version 0.11.15) .
The STAR aligner  (version 2.5.2) was used in the basic two-pass mode to align the trimmed reads to the iGenomes UCSC mm10 mouse genome . BAM files were sorted by coordinate, and indexed using SAMtools  (version 1.3.1).
STAR-aligned BAM files were processed in the University of Alabama at Birmingham Galaxy  platform using Stringtie  (Galaxy tool version 1.3.3.1) as described in the recommended workflow , with minor modifications: 1) the reverse strand option was selected and 2) the iGenomes UCSC mm10 genome was used as the reference guide assembly data set for the first Stringtie run.
Genome_build: mm10
Supplementary_files_format_and_content: Tabular file containing StringTie output assembled transcript expression

organism: Mus musculus

source_name: Acutely isolated cortical astrocytes

extract_protocol:
Astrocytes were acutely isolated as previously described (Holt and Olsen, 2016; Kahanovitch et al., 2018; Stoica et al., 2017). Following dissociation, microglia and myelin were first removed from the cell suspension. Cells were incubated for 15 minutes at 4°C with 15µL of Miltenyi Biotec’s Myelin Removal Kit and Cd11b+ MicroBeads. The suspension was then applied to a prepped LS column, washed three times, and the flow-through collected. This flow through was subsequently used to isolate astrocytes utilizing Miltenyi Biotec’s ACSA-2+ MicroBead kit. The cell suspension (in 150uL 0.5% fatty-acid free BSA in PBS) was incubated at 4°C for 15 minutes with 15-20µL FcR blocker, followed by a 15 minute incubation with 15-20µL ACSA-2 microbeads.  Cells were applied to a prepped LS column. Astrocytes were eluted from the LS column after three washes, with 5mL buffer and the supplied plunger. Total RNA was isolated using Ambion’s PureLink RNA Mini Isolation kit according to the manufacturer’s instructions. RNA samples designated for RNA Sequencing were eluted in 30 µL filtered, autoclaved Mill-Q water. RNA samples were tested for quality on the Agilent Tapestation 2200 (Agilent Technologies, Santa Clara, CA).
The NEB Next rRNA Depletion Kit (NEB #E6310X) was used to process 250 ng of total RNA. RNA-Seq libraries (400 bp) were created using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760L). Samples were individually indexed using the NEBNext Multiplex Oligos for Illumina (NEB #E6609S). Adapter ligated DNA was amplified in 13 cycles of PCR enrichment. Libraries were quantified with the Quanti-iT dsDNA HS Kit (Invitrogen) and qPCR. Library validation was performed on the Agilent 2200 Tapestation. Independently indexed stranded cDNA libraries were pooled and sequenced for 150 cycles with the Illumina NovaSeq 6000 S2 Kit. All samples were sequenced at 85-90 million read depth, paired-end 2 x 150 bp, and in reverse-stranded orientation.

tag: strain

tag: cell type

value: Astrocyte

tag: age

value: Postnatal days 25-31

tag: genotype

value: WT

tag: Sex

value: Male


title: ET164 [methylation]


title: P28 WT Astrocyte rep 4


title: HT29_D8.2_Control


title: HT29_D8.3_Control


title: HT29_D8.1_Control


title: ET163 [methylation]


title: P28 WT Astrocyte rep 3


title: ET162 [methylation]


title: wt_BAT_cold_1

city: Neuherberg

first: Stephan

last: Herzig

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

description:
mice were exposed to 5°C for one week
G200_A05_Exp4_BAT_WT1.CEL (WT)

hyb_protocol: Hybridization, washing, and scanning were carried out on an Affymetrix GeneTitan platform.

data_processing: Scans of the Affymetrix arrays were processed using packages from the  Bioconductor project. Arrays were normalized using the Robust Multi-array Average method  (Bolstad et al., 2003; Irizarry et al., 2003). Probe sets were defined by assigning probes to  unique gene identifiers, e.g. Entrez ID (Dai et al., 2005), which total 20985 on the Gene 1.0  ST arrays. Changes in gene expression were calculated as signal log ratios between treatment  and control. These ratios were used to create heatmaps within Excel.

label: biotin

molecule: polyA RNA

source_name: brown adipose tissue,wild type, cold exposure

label_protocol: RNA was labelled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Thermo Fisher) according to the manufacturer's protocol.

growth_protocol: Mice were 16-20 weeks old at the start of the cold treatment.

extract_protocol: RNA was isolated from mouse peritoneal macrophages using RNeasy mini columns (Qiagen)

treatment_protocol: Mice were exposed to 5°C for one week.

value: wild type

tag: stress

value: cold exposure

value: brown adipose tissue (BAT)


title: KO_BAT_cold_4

description:
mice were exposed to 5°C for one week
G200_D07_Exp4_BAT_KO4.CEL (KO)

scan_protocol: Hybridization, washing, and scanning were carried out on an Affymetrix GeneTitan platform.

source_name: brown adipose tissue, GRBATKO, cold exposure

value: GRBATKO


title: KO_BAT_cold_1

description:
mice were exposed to 5°C for one week
G200_C05_Exp4_BAT_KO1.CEL (KO)


title: Scr-t96-C

data_processing:
RNA-seq processing:
101 bp pair-end reads were analyzed with the nextpresso pipeline (http://http://bioinfo.cnio.es/nextpresso/) as follows: sequencing quality was checked with FastQC v0.11.0(2). Reads were align with FastQC v0.11.0. Reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 using Bowtie 1.0.0 and SAMtools 0.1.19, allowing 2 mismatches and 20 multihits. Differential expression was tested with Cufflinks and also with HTSeq using the human GRCh37/hg19 transcript annotations from from https://ccb.jhu.edu/software/tophat/igenomes.shtml. For the detection of differential Alternative Splicing events analysis, first, reads were aligned to the human genome (hg19) using STAR 2.5 and SAMtools 1.3.1. Then, the rMATS statistical software was used to evaluate the presence of differential Alternative Splicing events from replicate RNA-Seq data.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tabulated text file with gene FPKM values

source_name: CAL62 cell line

growth_protocol: Cells were maintained at 37°C and 5% CO2 in humidified atmosphere and grown in RPMI-1640 growth medium (SIGMA) supplemented with 10% (v/v) Fetal Bovine Serum (SIGMA).

extract_protocol:
Total RNA was extracted with Trizol
One µg of total RNA from each sample was used. Average sample RNA Integrity Number was 9.8 (range 9.6-10) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB, Cat. No. E7760) as recommended by the manufacturer. This kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced. Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument HiSeq2500 by following manufacturer's protocols.

treatment_protocol: Isogenic cell lines were doxycycline un-treated or treated (1ug/ml) for 96h

value: Thyroid anaplastic carcinoma

tag: treatment

value: Doxycycline (1ug/ml), 96 hours

tag: expressing

value: Scrambled control

tag: time

value: 96 hours


title: KO_BAT_cold_2

description:
mice were exposed to 5°C for one week
G200_C07_Exp4_BAT_KO2.CEL (KO)


title: wt_BAT_cold_3

description:
mice were exposed to 5°C for one week
G200_B05_Exp4_BAT_WT3.CEL (WT)


title: Fibro_D8.2_Control

description:
lab ID:
ST, 20180726, 07/19 seeded

value: CCD18Co (fibroblast)


title: P28 WT Astrocyte rep 2


title: wt_BAT_cold_4

description:
mice were exposed to 5°C for one week
G200_B07_Exp4_BAT_WT4_4.CEL (WT)


title: ET160 [methylation]

tag: subject status

value: Embryonal Tumor/Multilayered Rosettes (ETMR) patient

tag: subset

tag: sample type

value: Frozen


title: P28 WT Astrocyte rep 1


title: EC TGFbR1/2 ApoE HFD

city: New Haven

first: Michael

last: Simons

state: CT

address: 3oo George St, Suite 773

department: Department: Internal Medicine Cardiology

institute: Yale University

description: EC TGFbR1/2 KO Apoe mice feed with HFD

data_processing:
UMI-tools is used for the end to end processing of scRNA-Seq data
Identified cell barcodes and UMI in the read sequence, which are then extracted from Read 1 and added to Read 2 read name. STAR,was used to map extracted reads from Read 2 to the reference mouse genome build 38 (GRCm38), followed by assigning reads to genes using featureCounts tool from the subread package (version 1.6.0). Quantification was performed using UMI-tools count function to find the number of unique UMIs mapping to each gene (GENCODE mouse annotation, release M15).
Count data was filtered by: removing cells for which UMI count was less than 3,000 or total number of detected genes was less than 1,500; removing genes that were not expressed in less than or equal to 5% of the remaining cells in at least one sample
ApoE and TGFβR2 UMI counts were removed from the processed data matrix
Genome_build: GRCm38, version M15 (Ensembl 90)
Supplementary_files_format_and_content: CSV files include raw and TMM values for all samples

source_name: whole aorta

extract_protocol:
Digest the mice whole aorta and sort GFP positive cells (endothelial cells)
Libraries were prepared for sequencing at Yale using Chromium™ system (10x Genomics)

treatment_protocol: mice were fed with HFD for 4 months

tag: tissue

value: whole aorta

value: endothelial cells

tag: genotype/variation

value: TGF<beta>RiEC-Apoe

tag: diet

value: high fat diet


title: wt_BAT_cold_2

description:
mice were exposed to 5°C for one week
G200_A07_Exp4_BAT_WT2.CEL (WT)


title: KO_BAT_cold_3

description:
mice were exposed to 5°C for one week
G200_D05_Exp4_BAT_KO3.CEL (KO)


title: Scr-t96-B


title: ET159 [methylation]

value: C19MC amplified


title: EC TGFbR1/2 ApoE ND

description: EC TGFbR1/2 KO Apoe mice feed with ND

value: normal diet


title: Scr-t96-A


title: ET158 [methylation]

value: FFPE


title: Fibro_D8.1_Control

description:
lab ID:
ST, 20180726, 0719 seeded

tag: experimental treatment

value: Control

tag: biological replicate.plate replicate

tag: timecourse day number


title: Caco2_D8.4_Control

description:
lab ID:
ST, 20180622, 06/15 seeded

tag: cell line


title: Caco2_D8.3_Control

description:
lab ID:
ST, 20180622, 06/15 seeded


title: ET157 [methylation]


title: Scr-t0-C

tag: cell type

value: control

value: 0 hours


title: ApoE HFD

description: ApoE mice feed with HFD

value: Apoe-/-


title: Caco2_D8.2_Control

description:
lab ID:
ST, 20180622, 06/15 seeded


title: ApoE ND

description: ApoE mice feed with ND


title: ET156 [methylation]


title: Caco2_D8.1_Control

description:
lab ID:
ST, 20180622, 06/15 seeded


title: ET155 [methylation]


title: light blastocyst 29 embryo

city: SHANG HAI

first: Zhigang

last: Xue

address: Siping Road

country: China

institute: Tongji University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT2.1.0 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using htseq-count (v0.9.1) with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: pre-implantaion embryo

tag: group

value: light

tag: Stage

value: blastocyst

tag: strain


title: Scr-t0-A

value: Thyroid anaplastic carcinoma

tag: treatment

value: Scrambled control


title: Scr-t0-B

tag: expressing


title: HT29_D4.2_Control

description:
lab ID:
ST, 20180723, 07/20 seeded


title: light blastocyst 23 embryo


title: ET154 [methylation]

value: Embryonal Tumor/Multilayered Rosettes (ETMR) patient


title: mir139-t96-C

value: Doxycycline (1ug/ml), 96 hours

value: mature hsa-miR-139-5p

tag: time

value: 96 hours


title: HT29_D5.4_Control


title: light blastocyst 24 embryo


title: ET153 [methylation]

tag: subject status


title: HT29_D4.1_Control

description:
lab ID:
ST, 20180723, 07/20 seeded


title: mir139-t96-B


title: ET152 [methylation]

tag: subset

value: C19MC balanced


title: mir139-t96-A


title: light blastocyst 15 embryo


title: mir139-t0-C


title: ET151 [methylation]

tag: sample type


title: HT29_D5.2_Control


title: HT29_D5.3_Control


title: mir139-t0-B


title: Fibro_D5.2_Control

description:
lab ID:
ST, 20180723, 07/19 seeded

value: CCD18Co (fibroblast)


title: light morula 9 embryo

value: morula


title: HT29_D5.1_Control


title: light blastocyst 13 embryo


title: light blastocyst 26 embryo


title: ET149 [methylation]

value: C19MC amplified


title: light morula 6 embryo


title: ET148 [methylation]

value: FFPE


title: light morula 5 embryo


title: ET86_R2 [methylation]

value: Frozen


title: ET86_R1 [methylation]


title: light morula 3 embryo


title: light morula 1 embryo


title: ET85_R1 [methylation]


title: Fibro_D5.1_Control

description:
lab ID:
ST, 20180723, 07/19 seeded

value: Control


title: ET84_R1 [methylation]


title: light 8-cell 9 embryo


title: ET84 [methylation]


title: ET150 [methylation]


title: Caco2_D5.4_Control

description:
lab ID:
ST, 20180619, 06/15 seeded


title: Caco2_D5.3_Control

description:
lab ID:
ST, 20180619, 06/15 seeded


title: light morula 12 embryo


title: light 8-cell 8 embryo


title: Caco2_D5.2_Control

description:
lab ID:
ST, 20180619, 06/15 seeded


title: mir139-t0-A

value: control

value: 0 hours


title: ET83_R1 [methylation]


title: ET82 [methylation]


title: light 8-cell 7 embryo

value: light


title: CRL1790_miR18b.3

description:
lab ID:
SA_62, 20150428

value: CCD841CoN (CRL1790)


title: light 8-cell 6 embryo


title: CRL1790_miR890.6

description:
lab ID:
SA_63, 20150428


title: CRL1790_miR155.4

description:
lab ID:
SA_61, 20150428


title: ET81_R1 [methylation]


title: ET81 [methylation]


title: light 8-cell 5 embryo


title: CRL1790_Control.5

description:
lab ID:
SA_57, 20150428


title: ET80 [methylation]


title: ET78 [methylation]


title: light 8-cell 12 embryo


title: light 8-cell 10 embryo


title: CRL1790_miR890.5

description:
lab ID:
SA_51b, 20150423


title: light 8-cell 11 embryo


title: CRL1790_miR142.5

description:
lab ID:
SA_49a, 20150423


title: light 4-cell 7 embryo


title: Caco2_D5.1_Control

description:
lab ID:
ST, 20180619, 06/15 seeded


title: light 4-cell 9 embryo


title: CRL1790_miR142.4

description:
lab ID:
SA_40, 20150416


title: light 4-cell 6 embryo


title: CRL1790_cel67.4

description:
lab ID:
SA_48b, 20150423


title: light 4-cell 5 embryo


title: CRL1790_cel67.3

description:
lab ID:
SA_38, 20150416


title: CRL1790_cel67.5

description:
lab ID:
SA_59, 20150428


title: CRL1790_miR890.4

description:
lab ID:
SA_44, 20150416


title: CRL1790_miR890.3

description:
lab ID:
SA_63, 20150428


title: CRL1790_Control,4

description:
lab ID:
SA_36, 20150416


title: light 4-cell 14 embryo


title: CRL1790_miR18b.2

description:
lab ID:
SA_62, 20150428


title: ET16 [methylation]


title: light 4-cell 11 embryo


title: light 4-cell 13 embryo


title: light 2-cell 9 embryo


title: light 2-cell 16 embryo


title: CRL1790_miR142.3

description:
lab ID:
SA_60, 20150428


title: light 4-cell 1 embryo


title: light 2-cell 15 embryo


title: HUVEC 24hr IL1B Stimulation+ 24hr cytokine withdraw, Replicate 3

city: Toronto

first: Jason

last: Fish

state: ON

address: 101 College Street

institute: University Health Network

description: lncRNA and mRNA expression

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: The slides were scanned using the Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).
After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs were defined as having a fold change >2 and p<0.05.

source_name: HUVEC

label_protocol: First, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Afterwards, the mRNA was amplified, and the Agilent Quick Amp Labeling Kit was used to generate Cy3 fluorescent labeled cRNA.

growth_protocol: HUVECs were cultured in Endothelial Cell Medium (ECM) with 5% FBS and Endothelial Cell Growth Supplement (ScienCell). Passages 3-6 were used for experiments.

extract_protocol: RNA was extracted using TRIzol as per manufacturer's instructions. Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: HUVECs were either left unstimulated or were stimulated with IL-1β (10ng/ml) for 4 hours or 24 hours or were stimulated for 24 hours and had a 24 hour cytokine withdraw period.

value: human umbilical vein endothelial cells


title: HUVEC 24hr IL1B Stimulation, Replicate 2

description: lncRNA and mRNA expression


title: light 2-cell 14 embryo


title: CRL1790_miR155.2

description:
lab ID:
SA_54b, 20150423


title: HUVEC 24hr IL1B Stimulation+ 24hr cytokine withdraw, Replicate 2

description: lncRNA and mRNA expression


title: HUVEC 24hr IL1B Stimulation, Replicate 3

description: lncRNA and mRNA expression


title: HUVEC 24hr IL1B Stimulation, Replicate 1

description: lncRNA and mRNA expression


title: CRL1790_miR155.1

description:
lab ID:
SA_54a, 20150423


title: light 2-cell 12 embryo


title: HUVEC 4hr IL1B Stimulation, Replicate 2

description: lncRNA and mRNA expression


title: CRL1790_miR18b.1

description:
lab ID:
SA_50b, 20150423


title: HUVEC Unstimulated, Replicate 3

description: lncRNA and mRNA expression


title: 20-K

city: Milwaukee

first: Justine

middle: M

last: Abais-Battad

state: Wisconsin

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description:
K_CRLLS_CRLHS_10W.csv
K_MCWHS_CRLHS_10W.csv
BvsK_CRLHS_10W.csv

data_processing:
The adapter sequences were removed from the output reads by the tool cutadapt (http://code.google.com/p/cutadapt/).
Sequences with low quality (base quality < 13) at both ends of reads were further trimmed, and trimmed reads with < 25 bp were removed using Trim_galore 0.2.5 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
The remaining reads were aligned with the rat genome (rn5) using TopHat2 (v2.1.1) with mammalian default parameters (http://tophat.cbcb.umd.edu/).
A parsimonious set of transcripts was constructed from alignments using Cufflinks (v2.2.1) (http://cufflinks.cbcb.umd.edu/).
Transcript abundance was quantified as fragments per kilobase of exon per million fragments mapped (FPKM).
Genome_build: rn5
Supplementary_files_format_and_content: processed files are the output of cuffdiff's differential expression output (gene_exp.diff) with default columns. Each csv file is named based on the comparison within. Comparisons are made between blood and kidney in files starting with "BvsK_" within same group, and across different groups either in blood in the files starting with "B_" or in the kidney in the files starting with "K_". each value uses the 4 samples in the group

source_name: Kidney T-cells

extract_protocol:
RNA was extracted from isolated T-cells using TRIzol method. cDNA libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: rat type

value: SS/CRL

tag: chow

value: HS, 3 weeks

tag: age

value: 10 weeks


title: light 2-cell 10 embryo


title: HUVEC 24hr IL1B Stimulation+ 24hr cytokine withdraw, Replicate 1

description: lncRNA and mRNA expression


title: CRL1790_cel67.2

description:
lab ID:
SA_48b, 20150423

tag: experimental treatment


title: HUVEC Unstimulated, Replicate 2

description: lncRNA and mRNA expression


title: CRL1790_miR155.3

description:
lab ID:
SA_61, 20150428

tag: biological replicate.plate replicate


title: CRL1790_Control.3

description:
lab ID:
SA_57, 20150428

tag: timecourse day number


title: HUVEC 4hr IL1B Stimulation, Replicate 1

description: lncRNA and mRNA expression


title: 18-K


title: HUVEC 4hr IL1B Stimulation, Replicate 3

description: lncRNA and mRNA expression


title: 17-K


title: 16-K

description:
K_CRLLS_CRLHS_10W.csv
K_MCWLS_CRLLS_10W.csv
BvsK_CRLLS_10W.csv

value: LS


title: CRL1790_miR890.1

description:
lab ID:
SA_44, 20150416

tag: cell line


title: control blastocyst 1 embryo

value: blastocyst


title: Caco2_D30.1_DEX100

description:
lab ID:
JR, 20170330, 03/01 seeded


title: control morula 6 embryo


title: control morula 9 embryo


title: 14-K


title: Caco2_D30.2_DEX

description:
lab ID:
JR, 20170330, 03/01 seeded

value: DEX


title: 15-K


title: control blastocyst 2 embryo


title: 19-K


title: control morula 26 embryo


title: 12-K

description:
K_MCWLS_7W_10W.csv
BvsK_MCWLS_7W.csv

value: SS/MCW

value: 7 weeks


title: control morula 2 embryo

value: morula


title: 13-K


title: Caco2_D30.3_Control

description:
lab ID:
JR, 20170330, 03/01 seeded


title: control blastocyst 3 embryo


title: Caco2_D30.2_Control

description:
lab ID:
JR, 20170330, 03/01 seeded


title: Caco2_D23.1_DEX100

description:
lab ID:
JR, 20170323, 03/01 seeded


title: HUVEC Unstimulated, Replicate 1

description: lncRNA and mRNA expression

tag: cell type


title: 11-K

description:
K_MCWLS_7W_10W.csv
BvsK_MCWLS_7W.csv


title: Caco2_D30.1_DEX

description:
lab ID:
JR, 20170330, 03/01 seeded


title: control morula 23 embryo

tag: group


title: control morula 21 embryo

tag: Stage


title: Caco2_D23.1_DEX

description:
lab ID:
JR, 20170323, 03/01 seeded


title: 10-K

description:
K_MCWLS_7W_10W.csv
BvsK_MCWLS_7W.csv


title: Clonorchis sinensis adult 3

city: Seoul

first: Sung-Jong

last: Hong

address: Heukseok-ro

department: Dept. of Medical Environmental Biology

country: South Korea

institute: Chung-Ang University

description: Synthetic cDNAs were spotted on 326 spots for positive control. Nothing was spotted on 453 spots with the aim of negative control, such as 136 plants, 299 phages and 18 bacteria. Therefore, a total of 779 spot data were already eliminated from the whole 12396 spot data on the custom-fabricated 12K oligonucleotide array, remaining 11617 C. sinensis genes.

hyb_protocol: For the detailed information, see Combimatrix 100 μl cap protocol.

scan_protocol: After removing the PBS wash buffer, the hybridization chamber console was disassembled. The microarray surface was immediately covered with imaging solution and a LifterSlipTM coverslip. Using a lint-free tissue, any excess imaging solution was removed from the edge of the LifterSlipTM coverslip. The processed microarray was scanned using a Genepix 4000B scanner (Axon, Foster, CA, USA).

data_processing: To improve the reliability of the data, the signals were filtered with the following criteria: 1) factory-built controls and control probes were excluded, 2) only positive value signals were analyzed, 3) saturated signals displaying values more than 60,000 were excluded, and 4) 5% low-ranking signals were excluded. For backgournd normalization, the background signal value obtained from factory-built control probes was subtracted from the signal of each spot. Then, for global normalization, systematic variation affecting the measured gene expression levels was removed (Kakuda et al., 1998). These methods assume that the control sample and experimental sample intensities are related by a constant factor, i.e., R = kG, and the center of the distribution of log ratios is shifted to zero.

organism: Clonorchis sinensis

source_name: adult whole body

label_protocol: In a tube, 20 μl of double-stranded cDNA (dsDNA) and 20 μl of IVT master mix (12 μl of Biotin-NTP Mix, 4 μl of 10× T7 Reaction Buffer, and 4 μl of T7 Enzyme Mix) were mixed thoroughly by pipetting and centrifuged briefly. To synthesize biotin-labeled antisense RNA (aRNA), the mixture was incubated for 14 hr at 37°C, and the reaction was stopped by adding 60 μl of nuclease-free water. To the aRNA sample was added 350 μl of aRNA binding buffer and 250 μl of 100% ethanol, and the sample was mixed well by pipetting. The mixture was passed through the aRNA filter cartridge to purify biotin-labeled aRNA. After washing with 650 μl of wash buffer, aRNA was eluted with 100 μl of 50 - 60°C nuclease-free water. The aRNA was stored at -80°C until use.

extract_protocol: For the detailed information, see the reference: Reference genes for quantitative analysis on Clonorchis sinensis gene expression by real-time PCR. Parasitol Res. 2009 Jan;104(2):321-8. doi: 10.1007/s00436-008-1195-x. PMID: 18815810

tag: tissue

value: whole body

tag: status after 5 years

value: Dead

value: adult worm


title: Clonorchis sinensis adult 2


title: 8-K

description:
K_MCWHS_CRLHS_10W.csv
K_MCWLS_MCWHS_10W.csv
BvsK_MCWHS_10W.csv


title: 9-K

description:
K_MCWLS_7W_10W.csv
BvsK_MCWLS_7W.csv


title: Caco2_D15.3_DEX

description:
lab ID:
JR, 20170315, 03/01 seeded


title: newly excysted juvenile worm whole body 4

source_name: newly excysted juvenile worm whole body

value: newly excysted juvenile worm


title: Caco2_D23.1_Control

description:
lab ID:
JR, 20170323, 03/01 seeded

value: Control


title: control morula 14 embryo

value: control

tag: strain


title: 5-K


title: control morula 1 embryo


title: Clonorchis sinensis adult 1


title: CRL1790_miR142.2

description:
lab ID:
SA_40, 20150416

value: CCD841CoN (CRL1790)


title: Caco2_D25.2_Control

description:
lab ID:
JR, 20170323, 02/28 seeded


title: control morula 18 embryo


title: Caco2_D30.1_Control

description:
lab ID:
JR, 20170328, 02/28 seeded


title: newly excysted juvenile worm whole body 2


title: Caco2_D15.3_Control

description:
lab ID:
JR, 20170315, 03/01 seeded


title: control morula 10 embryo


title: 7-K


title: newly excysted juvenile worm whole body 1


title: control morula 16 embryo


title: 3-K

description:
K_MCWLS_7W_10W.csv
K_MCWLS_CRLLS_10W.csv
K_MCWLS_MCWHS_10W.csv
BvsK_MCWLS_10W.csv


title: control 8-cell 4 embryo


title: 6-K


title: 2-K


title: Caco2_D25.4_DEX

description:
lab ID:
JR, 20170330, 03/05 seeded


title: control morula 12 embryo


title: control morula 20 embryo


title: T4-Punch3

city: Worcester

first: Paul

last: Yan

state: MA

address: 368 Plantation Street

department: RNA Therapeutics Institute

institute: University of Massachusetts Medical School

data_processing:
Reads aligned using STAR/2.5.3a.
Mapped exon reads were counted with HTSeq/0.10.0.
Genome_build: macaca_fascicularis_5.0 (GCA_000364345.1)
Supplementary_files_format_and_content: count

organism: Macaca fascicularis

source_name: Brain punch

extract_protocol:
Brain punches were flash frozen in liquid nitrogen at time of collection. RNA was isolated using Monarch® Total RNA Miniprep Kit (NEB, T2010S) following manufacturer protocol. Briefly, DNA/RNA protection solution was added to frozen tissue and allowed to thaw at room temperature. Tissue in solution was homogenized by passing through 27G needle and inubated for 30 minutes at 55C with proteinase K. Lysate was then passed through gDNA removal column, bound to RNA column, subjected to on-column DNase treatment, and eluted with nuclease free water.
Library preparation was performed using TruSeq® Stranded mRNA Library Prep (Illumina, 20020594) following manufacturer protocol. Briefly, mRNA was pulled isolated from total RNA via poly-A selection beads. cDNA synthesis was performed using ProtoScript® II Reverse Transcriptase (NEB, M0368L) followed by second strand synthesis. 3' ends were adenylated and indexed adaptors ligated. Size selection was done using Ampure XP beads (Beckman Coulter, A63881).

tag: animal

tag: punch

tag: sirna treatment

value: Treated


title: T3-Punch3


title: 4-K


title: newly excysted juvenile worm whole body 3


title: Caco2_D15.2_Control

description:
lab ID:
JR, 20170313, 02/28 seeded


title: Caco2_D15.1_Control

description:
lab ID:
JR, 20170313, 02/28 seeded


title: control 4-cell 6 embryo


title: 19-B

description:
B_CRLLS_CRLHS_10W.csv
B_MCWHS_CRLHS_10W.csv
BvsK_CRLHS_10W.csv

source_name: Circulating T-cells

value: SS/CRL


title: T4-Punch2


title: T4-Punch1


title: 1-K


title: control 8-cell 3 embryo


title: Caco2_D25.3_DEX

description:
lab ID:
JR, 20170330, 03/05 seeded


title: control 4-cell 5 embryo


title: control 8-cell 1 embryo


title: Caco2_D25.1_DEX

description:
lab ID:
JR, 20170330, 03/05 seeded


title: T3-Punch2


title: T3-Punch1


title: T2-Punch2


title: 20-B

value: HS, 3 weeks


title: Caco2_D25.3_Control

description:
lab ID:
JR, 20170323, 02/28 seeded


title: Caco2_D25.2_DEX

description:
lab ID:
JR, 20170330, 03/05 seeded


title: 18-B

value: 10 weeks


title: T2-Punch1


title: control 4-cell 4 embryo


title: 17-B


title: 15-B

description:
B_CRLLS_CRLHS_10W.csv
B_MCWLS_CRLLS_10W.csv
BvsK_CRLLS_10W.csv

value: LS


title: Caco2_D15.2_DEX

description:
lab ID:
JR, 20170320, 03/05 seeded


title: Caco2_D15.1_DEX

description:
lab ID:
JR, 20170320, 03/05 seeded


title: T1-Punch2


title: 16-B


title: control 8-cell 2 embryo


title: control 4-cell 3 embryo


title: 14-B


title: control 4-cell 2 embryo


title: Caco2_D7.3_Control

description:
lab ID:
JR, 20170305, 0227 seeded


title: T2-Punch3


title: T1-Punch3


title: 13-B


title: N4-Punch3

value: Non-treated


title: Caco2_D7.2_Control

description:
lab ID:
JR, 20170305, 0227 seeded


title: control 2-cell 8 embryo


title: control 2-cell 9 embryo


title: control 2-cell 24 embryo


title: N4-Punch1


title: Caco2_D4.1_Control

description:
lab ID:
JR, 20170302, 0227 seeded


title: N4-Punch2


title: 11-B

description:
B_MCWLS_7W_10W.csv
BvsK_MCWLS_7W.csv


title: 10-B

description:
B_MCWLS_7W_10W.csv
BvsK_MCWLS_7W.csv


title: Caco2_D1.2_Control

description:
lab ID:
JR, 20170301, 0301 seeded


title: T1-Punch1


title: 9-B

description:
B_MCWLS_7W_10W.csv
BvsK_MCWLS_7W.csv


title: control 4-cell 1 embryo


title: control 2-cell 12 embryo


title: N3-Punch2


title: Caco2_D10.1_Control

description:
lab ID:
JR, 20160928, 0919 seeded


title: control 2-cell 11 embryo


title: 8-B

description:
B_MCWHS_CRLHS_10W.csv
B_MCWLS_MCWHS_10W.csv
BvsK_MCWHS_10W.csv


title: N3-Punch1


title: 12-B

description:
B_MCWLS_7W_10W.csv
BvsK_MCWLS_7W.csv


title: Caco2_D4.2_Control

description:
lab ID:
JR, 20170302, 0227 seeded


title: Caco2_D7.1_Control

description:
lab ID:
JR, 20160925, 0919 seeded


title: N2-Punch3


title: control 2-cell 10 embryo


title: 6-B


title: Caco2_D1.3_Control

description:
lab ID:
JR, 20170305, 0305 seeded


title: N2-Punch2


title: 5-B


title: control 2-cell 17 embryo


title: CRL1790_miR142.1

description:
lab ID:
SA_40, 20160416


title: Caco2_D1.1_Control

description:
lab ID:
JR, 20160919, 0919 seeded


title: Granulosa cells Old

city: Québec City

first: Marc-André

last: Sirard

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

description:
mitochondrial genomic DNA
single replicate

library_source: genomic

data_processing:
Adapters were removed and low-quality reads were trimmed using trimmomatic version 0.36
Methylation calls were then produced for the bovine mitochondrial genome, refseq sequence   NC_006853.1, using BISMARK version 0.18.2
Genome_build: NC_006853.1
Supplementary_files_format_and_content: tab-delimited text files include methylation abundance measurements

organism: Bos taurus

source_name: Granulosa cells

extract_protocol:
Sample collection: Pools (n = 10) of germinal vesicles (GV) collected at the abattoir (Vigneault et al. 2009), GV collected by OPU (Landry et al. 2016) and 7-day blastocysts produced in vitro (Nivet et al. 2012) starting from abattoir or OPU GV were used in the experiment. Associated granulosa cells were obtained from 113-month-old (aging) or 6-month-old (young) cows (Landry et al. 2016).
The mitochondrial abundancy in oocytes and preimplantation embryos (>200,000 mtDNA copies) does not require mitochondrial enrichment prior to mtDNA purification. For granulosa cells, an enrichment procedure must be use where mitochondria are isolated with hypotonic buffer followed by differential centrifugation.  Briefly cells were suspended in 500 µL of RSB (1X) hypotonic buffer in a 1.0 mL glass homogenizer tube using 10 strokes in a B-pestle, diluted with 350 µL of 2.5X MS buffer and centrifuged at 1,300 x g for 5 min at 4°C. The pellet was resuspended and washed again (1,300 x g for 5 min at 4°C) with 500 µL of 1X MS buffer and the two supernatants were pooled in a clean tube and centrifuged at 16,000 xg for 15 min at 4°C. The pellet was re-suspended in 500 µL of 1X MS buffer and washed (16,000 xg for 15 min at 4°C). Mitochondrial DNA was extracted from the final pellet using ZR Genomic DNA – Tissue MicroPrep (Zymo Research) and suspended in 40 µL of DNA elution buffer, digested with plasmid-safe ATP-dependent DNase (Epicenter) in a final volume of 50 µL for 2 h at 37°C followed by 30 min at 70°C then purified using ZR Genomic DNA – Tissue MicroPrep without proteinase K digestion. The purified DNA was suspended in 10 µL of elution buffer.
Pools of 10 GV or blastocysts were digested with proteinase K for 20 minutes at 50°C in M-digestion buffer (1X) to obtain a final volume of 20 µL. Granulosa cell mtDNA was mixed with 10 µL of 2X M-digestion buffer and brought to a final volume of 20 µL using the reagents from the EZ DNA Methylation-Direct kit (Zymo Research). Since it has been reported that accessibility of human mtDNA to bisulphite varies depending on the tissue of origin (saliva or blood) and can affect methylation pattern analysis (Liu et al., 2016), a restriction enzyme was used (200 U of Sal1 for 4 h at 37°C) to linearize the bovine mtDNA samples prior to treatment with 130 µL of Lightning Conversion Reagent from the Pico Methyl-Seq Library Prep kit (Zymo Research). The WGBS library protocol was followed as recommended by the manufacturer for 10 pg to 1 ng of DNA with 10 cycles for the final two PCR amplification rounds. Purified libraries were suspended in 12 µL of DNA elution buffer.

tag: breed

value: Holstein

value: Granulosa cells

tag: tissue source

value: From 113 month old cow


title: 4-B

description:
B_MCWLS_7W_10W.csv
B_MCWLS_CRLLS_10W.csv
B_MCWLS_MCWHS_10W.csv
BvsK_MCWLS_10W.csv

tag: rat type

value: SS/MCW

tag: chow


title: N3-Punch3


title: N2-Punch1


title: 3-B

tag: age


title: Blastocusts OPU

source_name: 7-Day Blastocysts

value: 7-Day Blastocysts

value: produced in vitro from GV-OPU


title: N1-Punch2


title: Blastocysts abattoir

value: produced in vitro from GV-abattoir


title: CRL1790_Control.2

description:
lab ID:
SA_36, 20160416

tag: experimental treatment

tag: biological replicate.plate replicate


title: Caco2_D3.1_Control

description:
lab ID:
JR, 20160921, 0919 seeded

tag: timecourse day number

tag: cell line


title: CRL1790_Control.1

description:
lab ID:
SA_2b, 20140829


title: 7-B


title: N1-Punch1


title: GV OPU

source_name: Germinal vesicles

tag: cell type

value: Germinal vesicles

value: collected from ovum pic-up


title: N1-Punch3


title: Granulosa cells Young

value: From 6 month old cow


title: 1-B


title: GV abattoir

value: collected at the abattoir


title: Caco2_D25.1_Control

description:
lab ID:
JR, 20160525, 0501 seeded

value: Control


title: trm5-1 mutant Rep 4 (tRNA)

status: Public on Aug 25 2019

city: Adelaide

first: Iain

middle: Robert

last: Searle

state: South Australia

address: North Terrace

department: Molecular and Biomedical Science

country: Australia

institute: The University of Adelaide

data_processing:
Base calling was done using Illumina RTA 1.18.54 for tRNA deep sequencing.
Adapters were trimmed using Trim Galore v0.4.2. RNA-seq reads were aligned to Arabidopsis thaliana TAIR10 genome using STAR v2.5.3 with default parameters;the tRNA reads were aligned to GtRNAdb Arabidopsis thaliana tRNA reference (generated from tRNA-Scan SE based on Arabidopisis thaliana reference genome TAIR10) using segemehl v0.2.0 with default parameters.
SNPs were called using HaplotypeCaller of GATK v.3.7 for tRNA deep sequencing data; differential expression analysis was performed on the RNA-seq data using Deseq2, raw counts were normalised with Sample-wise size factor.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab delimited text files include SNP counts for each sample, raw counts from fetaureCounts and Sample-wide size factor normalised counts with Deseq2.

organism: Arabidopsis thaliana

source_name: 10-day-old whole seedlings

growth_protocol: Arabidopsis thaliana (Columbia accession) wild type and mutant plants were grown in Phoenix Biosystems growth under metal halide lights as previously described in David et al. 2017.

extract_protocol:
Total RNA was isolated from wild type and trm5 10-day-old Arabidopsis seedlings using the Spectrum Plant total RNA kit (SIGMA-ALDRICH) and contaminating DNA removed using DNase I (SIGMA-ALDRICH). To enrich for tRNAs, 10μg of total RNA was separated on a 10% polyacrylamide gel, the region containing 65-85 nts was removed and RNA was purified as previously described in Burgess et al. 2015.
Libraries were prepared as per manufacturer's instruction with NEB Ultradirectional RNA library kit

tag: background ecotype

value: Columbia

tag: genotype

value: whole seedlings

value: 10 days

tag: rna fraction

value: tRNA size selection


title: Caco2_D21.1_Control

description:
lab ID:
JR, 20160603, 0513 seeded

source_name: in vitro  cell culture, adherent


title: CRL1790_miR890.2

description:
lab ID:
SA_51a, 20150423

value: CCD841CoN (CRL1790)


title: trm5-1 mutant Rep 2 (tRNA)

tag: tissue


title: 2-B

value: LS

value: 10 weeks


title: Wild type Col-0 Ecotype Rep 3 (tRNA)

value: wild type


title: trm5-1 mutant Rep 3 (tRNA)


title: Caco2_D18.1_Control

description:
lab ID:
JR, 20160518, 0501 seeded


title: Wild type Col-0 Ecotype Rep 2 (tRNA)


title: Sample_SC-876951_G1

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

description:
scRNAseq_counts.txt
cell_metadata.txt

data_processing:
Bulk RNA-seq reads in fastq files were aligned to hg19 using Tophat (version 2.0.13).
Gene-level read counts were quantified using htseq-count 62 using Ensembl GRCh37 gene annotations.
ChIP-seq reads in fastq files were aligned to hg19 using Bowtie2(version 2.2.9)
CellRanger from 10X Genomics was used to align and quantify single cell RNA-seq data
Seurat was used to filter out low quality cells and normalize gene expression values
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file of gene-level read counts for each bulk RNAseq sample.
Supplementary_files_format_and_content: tab-delimited file of gene-level read counts for each cell that passed quality check
Supplementary_files_format_and_content: tab-delimited file of metadata for each cell

source_name: MiMac + fatty acid HADHA mutant

growth_protocol: The hESC line RUES2 (NIHhESC-09-0013) and hiPSC line WTC #11, previously derived in the Conklin laboratory 101, were cultured on Matrigel growth factor-reduced basement membrane matrix (Corning) in mTeSR media (StemCell Technologies).  A monolayer-based directed differentiation protocol was followed to generate hESC-CMs and hiPSC-CMs, as done previously 25.  hiPSC-CM cardiolipin assay was done with a small molecule monolayer-based directed differentiation protocol, as done previously 102.  15 days after differentiation hPSC-CMs were enriched for the cardiomyocyte population using a lactate selection process 103.  We generated cardiomyocyte populations ranging from 40-60% that were then enriched to 75-80% cardiomyocytes after 4 days of lactate enrichment.

extract_protocol:
RNA libraries were prepared for sequencing using standard 10X Genomics protocols
RNA was extracted from cells using Trizol and analyzed with SYBR green qPCR using the 7300 real-time PCR system (Applied Biosystems).  Primers used are listed in Supplemental Table S14.  Linear expression values for all qPCR experiments were calculated using the delta-delta Ct method.

treatment_protocol: HADHA line creation: Using LentiCrisprV2 plasmid104 (lentiCRISPRV2 was a gift from Feng Zhang (Addgene plasmid # 52961) two different gRNAs targeted to Exon 1 of HADHA were designed using CRISPRScan105.  Sequences for the gRNAs can be found in Supplemental Table S12.  The gRNA and Cas9 expressing plasmids were transiently transfected into the WTC line using GeneJuice (EMD Millipore).  24 hours after transfection, WTCs were puromycin selected for two days and then clonally expanded.  DNA of the clones was isolated, the region around the targeting guides was PCR amplified (see guides in Supplemental Table S12) and sequenced to determine the insertion and deletion errors generated by CRISPR-Cas9 system in exon 1 of HADHA.  Western analysis was performed to determine the levels of HADHA protein in HADHA mutants.  31 clones were sent for sequencing from gRNA1 experiment, 6 clones (19%) had no mutations while 25 clones (81%) were found to have mutations.  24 clones were sent for sequencing from gRNA2, 1 clone had no mutations (4%) while 23 clones (96%) were found to have mutations. Two of the mutant lines were analyzed further in this study. microRNA Overexpression and Knockout:  We used LentiCrisprV2 plasmid (Addgene 52961) to KO microRNAs-141, -200a, -205 and -122.  gRNAs for each miR that had either the protospacer adjacent motif (PAM) NGG cut site adjacent or in the seed region of the mature microRNA were chosen to test.  gRNAs can be found in Supplement Table S12.  The global reduction of each miR was assessed via TaqMan RT-qPCR with probes specific against the mature form of each respective miR.

tag: culture media

value: Fatty acid media

tag: sequencing technology

value: Single cell RNAseq


title: Sample_SC-876951_C1

description:
scRNAseq_counts.txt
cell_metadata.txt

source_name: Let7 + miR-452

value: Glucose media


title: Sample_SC-876951_B1

description:
scRNAseq_counts.txt
cell_metadata.txt

source_name: MiMac


title: Sample_SC-876951_F1

description:
scRNAseq_counts.txt
cell_metadata.txt

source_name: MiMAC + fatty acid + SS-31 wild type


title: Sample_SC-876951_E1

description:
scRNAseq_counts.txt
cell_metadata.txt

source_name: MiMAC + fatty acid wild type


title: Sample_SC-876951_A1

description:
scRNAseq_counts.txt
cell_metadata.txt

source_name: EV


title: EV rep 6

description:
bulk_RNAseq_counts.txt
US-1622989

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA was extracted from cells using Trizol and analyzed with SYBR green qPCR using the 7300 real-time PCR system (Applied Biosystems).  Primers used are listed in Supplemental Table S14.  Linear expression values for all qPCR experiments were calculated using the delta-delta Ct method.

value: Bulk RNAseq


title: Sample_SC-876951_D1

description:
scRNAseq_counts.txt
cell_metadata.txt


title: MiMac rep 1

description:
bulk_RNAseq_counts.txt
US-1622976


title: miR-122 KO

description:
bulk_RNAseq_counts.txt
US-1601933

source_name: miR-122 KO


title: miR-205 KO

description:
bulk_RNAseq_counts.txt
US-1601905

source_name: miR-205 KO


title: EV rep 3

description:
bulk_RNAseq_counts.txt
US-1601896


title: EV rep 5

description:
bulk_RNAseq_counts.txt
US-1601928


title: EV rep 4

description:
bulk_RNAseq_counts.txt
US-1601897


title: miR-452 OE

description:
bulk_RNAseq_counts.txt
US-1601925

source_name: miR-452 OE


title: miR-378e OE

description:
bulk_RNAseq_counts.txt
US-1601893

source_name: miR-378e OE


title: miR-208b OE

description:
bulk_RNAseq_counts.txt
US-1555515

source_name: miR-208b OE


title: EV rep 2

description:
bulk_RNAseq_counts.txt
US-1601875


title: shLuc-Etn

city: guangzhou

first: Yi

last: Wu

state: guangdong

address: Kaiyuan road 190

institute: guangzhou institutes of biomedicine and health

description:
cells were transfected with shLuc in iCD1 medium deprivation of Etn
A5

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: mouse embryonic fibroblasts

growth_protocol: Cells were cultured in iCD1 medium or iCD1 medium deprivation of Etn

extract_protocol:
1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x100 paired end flow cell.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with indicated shRNAs

tag: reprogramming days

value: 2 days

tag: strain

value: CBA/CaJ X C57BL/6J

tag: shRNA

value: shLuc-Etn


title: EV rep 1

description:
bulk_RNAseq_counts.txt
US-1555436


title: Wild type Col-0 Ecotype Rep 4 (tRNA)


title: KO

city: Tokyo

first: Yoshiaki

last: Kubota

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Anatomy

country: Japan

institute: Keio University School of Medicine

data_processing:
We used a HiSeq3000 platform (Illumina, San Diego, CA) to generate 28 and 98 base paired-end reads. RNA-seq tags from the Chromium experiments were aligned using the Cell Ranger 3.0 software (10×Genomics). Using Cell Ranger, sequences with low quality and PCR duplicates were removed.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered raw counts output by Cell Ranger count

source_name: mesenteric CD31+cells

growth_protocol: Mice care was performed according to the standard method.

extract_protocol:
CD31+ cells were isolated using Dynabeads (Veritas) from the mesentery at P8. We constructed the libraries using a commercial micro-droplet based platform, Chromium Single Cell 3’ v3 (10×Genomics, Pleasanton, CA) according to the manufacturer’s instructions.
We used a HiSeq3000 platform (Illumina, San Diego, CA) to generate 28 and 98 base paired-end reads. RNA-seq tags from the Chromium experiments were aligned using the Cell Ranger 3.0 software (10×Genomics). Using Cell Ranger, sequences with low quality and PCR duplicates were removed.

treatment_protocol: For the tamoxifen-inducible expression of Cre, 4-hydroxytamoxifen (40 ug) was subcutaneously injected at P2, P3.5, P5, and P6.5.

value: mesentery

tag: Stage

value: postnatal day 8


title: shPebp1

description:
cells were transfected with shPebp1 in iCD1 medium
A6


title: Sample_SC-876951_H1

description:
scRNAseq_counts.txt
cell_metadata.txt

source_name: MiMac + fatty acid + SS-31 HADHA mutant


title: s100-2_lncRNA

city: Beijing

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

institute: Peking Union Medical College

description: lncRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome
Gene expression levels were expected of fragments per kilobase of transcript sequence per millions base pairs mapped (FPKM) using Cufflinks v2.1.0
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: MGC-803 cells

growth_protocol: gastric cancer cells MGC-803 were grown in DMEM with 10% FCS

extract_protocol:
MGC-803 cells were transfected with IBA57-AS1, KLRC2 or S100A1 and TMEM54 siRNAs, 48 hours later, MGC-803 cells were collected,total RNA was extracted from the cells with TRIzol reagent
The cDNA libraries were generated in as described previously. Zhao H, et al. Nat Commun. 2017 Nov 10;8(1):1428.

treatment_protocol: MGC-803 cells were transfected with IBA57-AS1, KLRC2 for overexpression or S100A1 and TMEM54 siRNAs

value: S100A1 knockdown


title: s100-1_lncRNA

description: lncRNA


title: cont


title: shLuc-rep2

description:
cells were transfected with shLuc in iCD1 medium Replicate 2
A4

value: shLuc


title: siTM2_lncRNA

description: lncRNA

value: TMEM54 knockdown


title: shPcyt2

description:
cells were transfected with shPcyt2 in iCD1 medium
A3


title: sic2_lncRNA

description: lncRNA

value: miR-574 knockdown


title: siTM1_lncRNA

description: lncRNA


title: KLRC2_lncRNA

description: lncRNA

value: KLRC2 overexpression


title: shEtnk1/2

description:
cells were transfected with shEtnl1/2 in iCD1 medium
A2


title: shLuc-rep1

description:
cells were transfected with shLuc in iCD1 medium, Replicate 1
A1


title: sic1_lncRNA

description: lncRNA


title: KLRC1_lncRNA

description: lncRNA


title: IBA1_lncRNA

description: lncRNA

value: IBA57-AS1 overexpression


title: IBA2_lncRNA

description: lncRNA


title: Control_lncRNA

description: lncRNA

value: control


title: HME1-E6_AdCycE_9

city: La Jolla

first: SERVANDO

last: GIRALDEZ MACIAS

state: CA

address: 10010 N Torrey Pines Rd

department: REGULATORY BIOLOGY

institute: THE SALK INSTITUTE FOR BIOLOGICAL STUDIES

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Raw CNA data was pre-processed using the affy2s package[34] in R using the CytoScanHD Array NA33 reference model and annotation database. . B allele frequency values were input into PennCNV using the hhall hidden Markov model. PennCNV calls were used in downstream analyses.   Copy number variable regions (CNVR) in each sample were defined after merging CNV calls within 1 Mb of a neighboring CNV.  Association of each CNVR (using average copy number) with treatment and control groups was tested using Mann-Whitney U tests. Enrichment of associations across the genome was tested by comparing the resulting p-values to a uniform distribution using a one-sided KS test. All analyses were performed in R (version 3.3.2).
the Processed data-NEW1.xlsx" was generated from the analysis of .CEL files coming from Affymetrix CytoScan HD Array. This file includes the average copy number over copy number variable regions for all samples (columns 4-22). Regions are defined according to chromosome and base pair start and stop coordinates (columns 1-3). Genes found within each region are included in column 23.

label: Biotin

source_name: Human mammary epithelial cell line after Cyclin E adenoviral overexpression

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from HME1 derivative cell line (HME1-E6) constitutively expressing the human papilloma virus (HPV) E6 protein and after transient adenoviral overexpression of GFP (control) or Cyclin E using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

treatment_protocol: HME1-E6 cells were transduced with Ad-GFP or Ad-Cyc E three times per week during two weeks at 48-hour intervals. Single live cells were sorted into 96-wells plates 48 hours after the sixth transduction using a FACSAria (BD Biosciences). Sorted cells were cultured and amplified into populations of approximately 10 million derivatives, and then analyzed.

value: hTERT-HME1 Expressing HPV-E6 protein


title: HME1-E6_AdCycE_10

value: Human mammary epithelial cell line after Cyclin E adenoviral overexpression


title: HME1-E6_AdCycE_11


title: HME1-E6_AdCycE_5


title: HME1-E6_AdCycE_7


title: HME1-E6_AdCycE_4


title: HME1-E6_AdCycE_6


title: HME1-E6_AdCycE_8


title: Control2_lncRNA

description: lncRNA


title: S_T-2

description:
Small RNA
S_T2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome
Gene expression levels were expected of fragments per kilobase of transcript sequence per millions base pairs mapped (FPKM) using Cufflinks v2.1.0
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for  important smallRNA genes in each sample

extract_protocol:
MGC-803 cells were transfected with IBA57-AS1, KLRC2, S100A1 and TMEM54 overexpression construct or controls, 48 hours later, MGC-803 cells were collected,total RNA was extracted from the cells with TRIzol reagent
The cDNA libraries were generated in as described previously. Zhao H, et al. Nat Commun. 2017 Nov 10;8(1):1428.

tag: genotype/variation


title: HME1-E6_AdCycE_3


title: S_T

description:
Small RNA
S_T

treatment_protocol: MGC-803 cells were transfected with IBA57-AS1, KLRC2, S100A1 and TMEM54 overexpression construct


title: TMEM54

description:
Small RNA
TMEM

value: TMEM54 overexpression


title: TMEM54-2

description:
Small RNA
TMEM2


title: HME1-E6_AdGFP_7

source_name: Human mammary epithelial cell line after GFP adenoviral overexpression


title: HME1-E6_AdCycE_1


title: HME1-E6_AdCycE_2


title: HME1-E6_AdGFP_6

value: Human mammary epithelial cell line after GFP adenoviral overexpression


title: HME1-E6_AdGFP_5


title: I_K-2

description:
Small RNA
I_K2


title: HME1-E6_AdGFP_4


title: HME1-E6_AdGFP_3


title: I_K

description:
Small RNA
I_K


title: KLRC

description:
Small RNA
KLRC

value: KLRC overexpression


title: HOPX_OE rep 2

description:
bulk_RNAseq_counts.txt
WHHUMnirRAAHRAAPEI-22_1

value: Glucose media

value: Bulk RNAseq


title: KLRC-2

description:
Small RNA
KLRC2


title: HME1-E6_AdGFP_2


title: trm5-1 mutant Rep 4

description:
Sample_trm5_3
normalized_abundance_measurement.txt
raw_counts.txt

data_processing:
Base calling was done using CASAVA v1.8 in Illumina Hiseq X Ten.
Adapters were trimmed using Trim Galore v0.4.2. RNA-seq reads were aligned to Arabidopsis thaliana TAIR10 genome using STAR v2.5.3 with default parameters;the tRNA reads were aligned to GtRNAdb Arabidopsis thaliana tRNA reference (generated from tRNA-Scan SE based on Arabidopisis thaliana reference genome TAIR10) using segemehl v0.2.0 with default parameters.
SNPs were called using HaplotypeCaller of GATK v.3.7 for tRNA deep sequencing data; differential expression analysis was performed on the RNA-seq data using Deseq2, raw counts were normalised with Sample-wise size factor.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab delimited text files include SNP counts for each sample, raw counts from fetaureCounts and Sample-wide size factor normalised counts with Deseq2.

source_name: 20-day-old leaf sample

extract_protocol:
Total RNA was isolated from wild type and trm5 10-day-old Arabidopsis seedlings using the Spectrum Plant total RNA kit (SIGMA-ALDRICH) and contaminating DNA removed using DNase I (SIGMA-ALDRICH). To enrich for tRNAs, 10μg of total RNA was separated on a 10% polyacrylamide gel, the region containing 65-85 nts was removed and RNA was purified as previously described in Burgess et al. 2015.
Libraries were prepared as per manufacturer's instruction with Illumina’s TruSeq RNA sample kit v2

value: Columbia

value: leaf

tag: age

value: 20 days

value: total RNA


title: Negative_control(for HOPX) rep 2

description:
bulk_RNAseq_counts.txt
WHHUMnirRAAFRAAPEI-20_1

source_name: Negative_control(for HOPX)


title: IBA57-AS1

description:
Small RNA
IBA


title: HOPX_OE rep 1

description:
bulk_RNAseq_counts.txt
WHHUMnirRAAGRAAPEI-21_1


title: IBA57-AS1-2

description:
Small RNA
IBA2


title: CC_M1

city: Nanjing

first: Xiaqing

last: Yu

address: Weigang No.1

institute: Nanjing Agricultural University

description: mature leaf

data_processing:
After sequencing, raw reads were further analysed using the ACGT101-miR program (LC Sciences, Houston, Texas, USA). After removing junk reads and sequences < 18 nt and > 25 nt, remaining sequences were aligned using Rfam (http://rfam.janelia.org), Cucumber Genome Network database (http://www.icugi.org/cgi-bin/ICuGI/index.cgi) and repeat database (http://www.girinst.org/repbase). The sequences that matched Rfam, mRNA, rRNA, tRNA, snoRNA, snRNA, other non-coding RNAs and repeat sequences were filtered out. The valid sequences were blasted against the reported pre-miRNAs and mature miRNAs in plants from miRBase 21.0 (ftp://mirbase.org/pub/mirbase/21/). A maximum of one mismatch between target and known miRNAs from miRBase database was allowed. Moreover, only the pre-miRNAs with stable hairpin structures were considered and secondary structures of the pre-miRNAs were predicted using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi).. miRNAs that are conserved among plants as compared with miRBase 21.0 and with stable hairpin structures were divided to conserved miRNAs. Minimal folding free energy index (MFEI) is another important factor for miRNA identification52. Novel miRNAs were only considered when minimal folding free energy index (MFEI) of their pre-miRNAs were ≥ 0.80 in this study. Moreover, the normalized copy number of the novel miRNAs was required to be ≥ 10 in at least one sample.
Target genes of miRNAs identified in Cucumis were predicted with Targetfinder. To clarify the functions of the target genes, GO functional annotation and KEGG pathway analysis of the miRNA targets were performed using GO database (http://www.geneontology.org/) and KEGG database (http://www.genome.jp/kegg/),
The alignment software, bowtie 0.12.8, was used to map the reads back to the transcriptome. Then, the number of mapped clean reads for each unigene was counted and normalized into a RPKM value (Reads Per kb per Million reads), which is widely used to calculate the unigene expression (Mortazavi et al., 2008). To detect differentially expressed genes, statistical analyses among libraries were performed following the formula as described (Shen et al., 2012), where FDR (false discovery rate) were used to determine the threshold the P value in multiple tests and analyses using the q-value package (Benjamini et al., 2001). In our work, the differentially expressed unigenes between two samples were screened with the threshold of FDR ≤ 0.001 and the absolute value of log2Ratio ≥ 1. Furthermore, the GO classifications and the KEGG pathway enrichments were compared between up-regulated and down-regulated  unigenes.
Genome_build: http://www.icugi.org/cgi-bin/ICuGI/index.cgi, genome v2
Supplementary_files_format_and_content: expression data of miRNA  (raw reads and norm reads)

organism: Cucumis sativus

source_name: Cucumis sativus L.‘BejingJietou’, ‘BejingJietou’, mature leaf

growth_protocol: The young leaf (first leaf counting from the top) and the mature leaf (the first fully developed leaf) of self-cross plants (S10) of synthesized new species, Cucumis ×hytivus J. F. Chen & J. H. Kirkbr. and the mature leaves of the diploid parents, C. hystrix Chakr. and C. sativus ‘BeijingJietou’ were the plant material for sequencing. Single seeds were sown in a plug tray after soaking and pre-germination and then cultured in climate chambers (RDN-1000E-4, Dongnan Instrument Co, Ltd, Ningbo, China) at an air temperature of 25/20°C (14 h/10 h, day/night), a light intensity of 280±20 µmol m-2 s-1 and 60±10% relative humidity. On the 20th day after sowing, healthy and uniform seedlings were transferred to plastic plots (11 cm diameter, 9 cm height) and cultured in the climate chambers with the same climate setting. The seedlings were irrigated by flooding the bench for 10 min two times per day with 1/2 nutrient solution, according to the Japanese Garden test formula.

extract_protocol:
Total RNA was extracted using the TRIzol Reagent. The mRNA was isolated using oligo (dT)-attached magnetic beads. The four libraries were sequenced using IlluminaHiSeqTM 2500.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: BeijingJietou

tag: ploidy

value: diploid

tag: leaf developmental stage

value: mature

tag: harvest stage

value: the first fully developed leaf


title: CC_M2

description: mature leaf


title: S100A1

description:
Small RNA
S100A

tag: cell line

value: S100A1 overexpression


title: MiMac rep 3

description:
bulk_RNAseq_counts.txt
WHHUMnirRAADRAAPEI-18_1

source_name: MiMac


title: Wild type Col-0 Ecotype Rep 4

description:
Sample_col_3 (wt3)
normalized_abundance_measurement.txt
raw_counts.txt

tag: background ecotype

value: wild type


title: trm5-1 mutant Rep 3

description:
Sample_trm5_2
normalized_abundance_measurement.txt
raw_counts.txt

tag: genotype


title: con

description:
Small RNA
con1

value: control


title: Wild type Col-0 Ecotype Rep 3

description:
Sample_col_2 (wt2)
normalized_abundance_measurement.txt
raw_counts.txt

tag: rna fraction


title: HHCC_M2

description: mature leaf

organism: Cucumis x hytivus

source_name: Cucumis ×hytivus J.F. Chen & J.H. Kirkbride, C. ×hytivus, mature leaf

value: allotetraploid

tag: tissue


title: Wild type Col-0 Ecotype Rep 2

description:
Sample_col_1 (wt1)
normalized_abundance_measurement.txt
raw_counts.txt


title: HME1-E6_AdGFP_1

value: hTERT-HME1 Expressing HPV-E6 protein

tag: cell type


title: 4TO7 cells

city: Kowloon

first: Minh

middle: TN

last: Le

state: Hong Kong

address: Tat Chee Avenue, Kowloon Tong

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
NEB index primer 12
jINGMINsNALLrna4_CTTGTA_L006

data_processing:
Sequencing reads were processed by Cutadapt (Martin, 2011) to trim the cloning adaptor sequences using default parameters.
The sequences were aligned to mouse miRNA sequences and genome sequence (mm9 genome assembly) using Bowtie (Langmead et al, 2009)
Analysis of the aligned data was performed using BEDTools Multicov (Quinlan & Hall, 2010).
Genome_build: mm9
Supplementary_files_format_and_content: multiple spreadsheets containing bowtie align reads length, miRNA read counts, Genome Clusters data

source_name: 4TO7 cells

growth_protocol: DMEM with 10% EV-free FBS

extract_protocol:
RNAs were extracted using Trizol. Ribosomal RNAs were removed using a Ribozero kit.
RNAs were separated by denaturing polyacrylamide gel electrophoresis and stained with SYBR-Gold (Invitrogen). miRNA-sized small RNAs were excised from the polyacrylamide gel. Small RNAs were eluted in 0.3 M NaCl from crushed gel pieces. After recovery, precipitation and washing, small RNAs were suspended in nuclease-free water. The RNAs were converted to cDNAs using a NEBNext® small RNA library prep kit (New England Biolabs, USA) according to the manufacturer’s instructions.

treatment_protocol: EVs were purified from the cells using differential centrifugation including 2 rounds of ultracentrifugation

value: breast cancer cell line

tag: molecule subtype

value: cellular small RNAs


title: 4TO7 EVs

description:
NEB index primer 6
jINGMINsNALLrna2_GCCAAT_L006

source_name: Extracellular vesicles from 4TO7 cells

value: Extracellular vesicles small RNAs


title: MiMac rep 2

description:
bulk_RNAseq_counts.txt
WHHUMnirRAACRAAPEI-17_1

tag: culture media

value: Glucose media

tag: sequencing technology

value: Bulk RNAseq


title: EV rep 7

description:
bulk_RNAseq_counts.txt
WHHUMnirRAAARAAPEI-15_1

source_name: EV


title: 4T1 cells

description:
NEB index primer 9
jINGMINsNALLrna3_GATCAG_L006

source_name: 4T1 cells


title: HHCC_M1

description: mature leaf

value: leaf


title: EV rep 8

description:
bulk_RNAseq_counts.txt
WHHUMnirRAABRAAPEI-16_1


title: Negative_control(for HOPX) rep 1

description:
bulk_RNAseq_counts.txt
WHHUMnirRAAERAAPEI-19_1


title: HH_M1

description: mature leaf

organism: Cucumis hystrix

source_name: Cucumis hystrix Chakr., C. hystrix, mature leaf


title: HHCC_Y2

description: young leaf

source_name: Cucumis ×hytivus J.F. Chen & J.H. Kirkbride, C. ×hytivus , young leaf

value: young

value: first leaf counting from the top


title: HHCC_Y1

description: young leaf


title: con-2

description:
Small RNA
con2


title: 4T1 EVs

description:
NEB index primer 4
jINGMINsNALLrna1_TGACCA_L006

source_name: Extracellular vesicles from 4T1 cells


title: sample34_sm

status: Public on Aug 24 2019

city: Berlin

first: Gesa

middle: Marijke

last: Richter

address: Assmannshauser Str. 4-6

institute: Charité - University Medicine Berlin

data_processing:
RNA-seq samples were mapped to the transcriptome (Ensembl 96, GRCh38) using the transcript abundance quantification method Salmon (v0.13.1)
Transcript level estimates were summarised for the gene level and imported into R using the package tximport (v1.12.3)
Differential expression analysis between current and never smokers was performed with DESeq2 (v1.24.0)
Genome_build: Ensembl 96, GRCh38
Supplementary_files_format_and_content: Textfile including ENSGIDs and corresponding lenght-scaled TPM-values per sample

source_name: Oral mucosa

extract_protocol:
total RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Hilden, Germany)
TruSeq Stranded mRNA (Illumina, San Diego, USA)

value: Masticatory mucosa

tag: extraction site

value: palatal, regio 24/25

tag: smoking status

value: current smoker


title: sample33_sm


title: sample36_sm


title: sample32_sm


title: S100A1-2

description:
Small RNA
S100A2

tag: genotype/variation


title: trm5-1 mutant Rep 2

description:
Sample_trm5_1
normalized_abundance_measurement.txt
raw_counts.txt

value: Columbia

tag: age

value: 20 days

value: total RNA


title: sample38_sm


title: sample35_sm


title: sample29_sm


title: sample30_sm


title: sample27_sm


title: sample28_sm


title: sample31_sm


title: sample26_sm


title: sample25_sm


title: HH_M2

description: mature leaf

value: diploid

value: mature

value: the first fully developed leaf


title: sample23_sm


title: sample21_nonsm

value: never smoker


title: sample20_nonsm


title: sample24_sm


title: sample19_nonsm


title: sample18_nonsm


title: sample17_nonsm


title: sample15_nonsm


title: sample37_sm


title: sample16_nonsm


title: sample12_nonsm


title: sample13_nonsm


title: sample14_nonsm


title: sample10_nonsm


title: sample9_nonsm


title: sample11_nonsm


title: sample8_nonsm


title: sample7_nonsm


title: sample22_sm


title: sample4_nonsm


title: sample3_nonsm


title: WT: N-cre replicate 1

city: Bethesda

first: Skyler

middle: Alexander

last: Kuhn

address: 41 CENTER DR, BG 41 RM B620

department: National Cancer Institute

institute: National Institutes of Health

description:
RawCountsMatrix_RSEM_isoforms.txt
processed data header: control_S22

data_processing:
Base calling was performed using RTA version 2.7.7
Demultiplexing and fastq file generation was conducted using bcl2fastq
The sequencing quality was evaluated using FastQC (version 0.11.5), Preseq (version 2.0.3), Picard tools (version 1.119) and RSeQC (version 2.6.4).
Reads were trimmed using Cutadapt (1.18) to remove adapter sequences, prior to mapping to the mm10 mouse reference genome using STAR (version 2.5.2b) in two-pass mode.
Gene and transcript expression levels were quantified using RSEM (version 1.3.0) with gencode’s M16 mouse annotation
EBSeq (version 1.22.1) was used to test for differential isoform expression between experimental conditions. Group-based TPM filtering was applied to remove lowly expressed transcripts. Significant differentially expressed isoforms were identified with a false-discovery rate < 0.05.
Genome_build: mm10 with M16 GENCODE annotation
Supplementary_files_format_and_content: Tab-delimeted text file contain raw isoform counts for each sample

source_name: Hippocampus

extract_protocol:
Hippocampi were collected, flash frozen in dry ice, and RNA was extracted by using RNeasy Plus Universal Kit (Qiagen, Cat.No. 73404).
Libraries were constructed from hippocampal total RNA using Illumina’s TruSeq Stranded Total RNA Kit (RS-122-2201). RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: 3 months

tag: animal tag number


title: TG: N-cre; Fox1 replicate 2

description:
RawCountsMatrix_RSEM_isoforms.txt
processed data header: Rbfox1_S26

value: TG:N-cre; Fox1


title: TG: N-cre; Fox1 replicate 3

description:
RawCountsMatrix_RSEM_isoforms.txt
processed data header: Rbfox1_S27


title: WT: N-cre replicate 2

description:
RawCountsMatrix_RSEM_isoforms.txt
processed data header: control_S23


title: sample2_nonsm


title: WT: N-cre replicate 3

description:
RawCountsMatrix_RSEM_isoforms.txt
processed data header: control_S24


title: sample6_nonsm


title: sample1_nonsm


title: Adult BM_LSKCD105+CD48neg_rep1

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® MouseGene1.0st and MouseGene2.0st (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. Brain array CDF file V19 was used for annotation.

source_name: Adult mouse BM

label_protocol: around 5ng of total RNA is reverse transcribed  following the Ovation Pico System V2  (Nugen) Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 3,6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen). After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® MouseGene1.0st and MouseGene2.0st  (Affymetrix) at 45°C for 17 hours.

extract_protocol: RNeasy Plus Micro Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: Bone marrow

value: Adult

tag: sorted cell


title: KO6: 700

city: Montreal

first: Anna

middle: K

last: Naumova

state: QC

address: 1001 Decarie Blvd

department: Obstetrics and Gynecology

institute: McGill University

data_processing:
Trimming and filtering, TRIMMOMATIC v0.36
Alignment to GRCm38, STAR v2.5.3a
Mark duplicates, Picard v2.9.0
Produce raw counts, HTSeq-Count v0.6.0
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV, Raw Counts

source_name: lung

extract_protocol:
Trizol extraction followed by purification with RNAeasy (Qiagen, NL)
Truseq RNA, mRNA Seq stranded

value: lung

tag: time

value: Zpbp2 KO


title: Adult BM_LSKCD105+CD48neg_rep3


title: WT6: 183

value: WT


title: sample5_nonsm

value: Masticatory mucosa


title: KO4: 694


title: Adult BM_Lin+_rep2

value: Lin+


title: Adult BM_LSKCD105+CD48neg_rep2


title: Adult BM_LSKCD105+CD48neg_rep4


title: Adult BM_Lin+_rep3


title: TG: N-cre; Fox1 replicate 1

description:
RawCountsMatrix_RSEM_isoforms.txt
processed data header: Rbfox1_S25


title: Adult BM_Lin+_rep4


title: Adult BM_Lin+_rep1


title: Y3 primed OT-I with corticosteroid, biological rep1

city: Shimotogari, Nagaizumi-cho

first: Akihiro

last: Tokunaga

state: Shizuoka

institute: Kyowa kirin Co., Ltd

hyb_protocol: Following fragmentation, ssDNA were hybridized for 17 hr on GeneChip Clariom D Array, mouse. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Clariom D Arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Raw data were processed with the Guanine Cytosine Count Normalization (GCCN) and Signal Space Transformation (SST) algorithms prior to Robust Multiarray Average (RMA) using Expresson Console Software (ThermoFisher Scientific) according to the default analysis settings (Exon Level-SST-Alt Splice Analysis).

source_name: Y3 primed, corticosteroid treated, 4 days

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 5.5 ug ssDNA.

growth_protocol: OT-I cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum and 4 mmol/L of L-glutamine.

extract_protocol: Total RNA was isolated with the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: OT-I cells were stimulated with N4 or Y3 peptide and treated with corticosteroids in vitro for 4 days.

value: splenocyte

tag: cell line

value: OT-I


title: Y3 primed OT-I, biological rep3

source_name: Y3 primed, 4 days


title: Y3 primed OT-I with corticosteroid, biological rep3


title: Y3 primed OT-I with corticosteroid, biological rep2


title: Y3 primed OT-I, biological rep1


title: Y3 primed OT-I, biological rep2


title: WT5: 182


title: KO5: 697


title: WT4: 181


title: patient_day7

city: Saint Petersburg

last: Kostareva

address: Ulitsa Akkuratova, 2

country: Russia

institute: Almazov National Medical Research Centre

data_processing:
Individual fastqs were aligned to hg38 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6  --outSAMstrandField All.
Gene expression was obtained via RSEM with Gencode v26 annotation
Genome_build: hg38
Supplementary_files_format_and_content: Counts

source_name: Skeletal muscle stromal cells

growth_protocol: DMEM10% FCS serum

extract_protocol:
Total RNAs were isolated using standard isolated with Trizol reagent (Sigma, USA) according to standard method of Phenol-chloroform extraction (Sambrook J et al. 1989).
Libraries for RNA sequencing were prepared using TruSeq Stranded mRNA kit (Illumina, USA), according to manufacturer recommendation

treatment_protocol: Low serum 2% horse serum

value: Skeletal muscle

value: stromal cells

tag: treatment

value: Myogen differentiated


title: donor_day7

tag: genotype


title: patient_day0

value: Ctrl


title: Th0 plus stim KO3

city: Boston

first: Takayuki

last: Katsuyama

address: 3 Blackfan Circle, CLS-948

department: Rheumatology and Clinical Immunology

institute: Beth Israel Deaconess Medical Center

data_processing:
Samples were sequenced on an Illumina NextSeq500 run with single-end 75-bp reads.
Cufflinks
STAR Align
STAR Gene counts
Genome_build: mm9

source_name: Th0 Effector CD4 T cells

growth_protocol: Naïve CD4 T cells were isolated from spleens using CD4+CD62L+ T cell isolation kit II (Miltenyi)

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were stimulated with anti-CD3 (0.5μg/mL) and anti-CD28 (1μg/mL) for 72 hours, and re-stimulated with PMA (100ng/mL) and Ionomycin (1μM) for 4 hours.

value: spleen

value: Th0 Effector CD4 T cells

value: 7 week

value: Srsf1-flox/flox dLck.Cre


title: Th0 plus stim KO2


title: HeLa_C

first: Tsuyoshi

last: Osawa

address: 4-6-1 Komaba, Meguro-ku

department: RCAST

institute: The University of Tokyo

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
RNA-seq reads were trimmed into 100bp and algined to human transcriptome (UCSC gene) and genome (GRCh37/hg19) references respectively using Burrows-Wheeler Aligner.  After transcript coordinate was converted to genomic positions, an optimal mapping result was selected either from transcript or genome mapping by comparing the minimal edit distance to the reference.
Local realignment was performed within in-house short reads aligner with smaller k-mer size (k=11).
Fragments per kilobase of exon per million fragment mapped (fpkm) values were calculated for each UCSC gene while considering strand-specific information.
Genome_build: NCBI Build #37 (UCSC hg19)
Supplementary_files_format_and_content: FPKM

source_name: HeLa control

growth_protocol: Human carvical cancer HeLa was maintained in Dulbecco's modified Eagle's medium (DMEM), supplemented with 10% fetal bovine serum (FBS) at 37 °C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted from cells using the Isogen reagent (Nippon Gene, Toyama, Japan). TruSeq RNA sample Preparation Kits v2 (Illumina, #RS-122) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared by TruSeq sample purification kit (Illumina) following manufacturer's protocol.

treatment_protocol: Cells were treated for 24 h under nutrient starvation (all nutrients 1/100) and nutrient starvation supplementated with 4mM glutamine conditions.

tag: culture condition

value: Control


title: HeLa_NSGLN

source_name: HeLa nutrient starvatin supplementated with glutamine

value: Nutrient Starvation + Glutamine


title: HeLa_NS

source_name: HeLa nutrient starvatin

value: Nutrient Starvation (all nutrients 1/1000)


title: donor_day0

tag: tissue


title: Eye disc rep 3

city: Baltimore

first: Robert

last: Johnston

address: 3400 N. Charles St.

department: Biology

institute: Johns Hopkins University

description:
Eye_disc_all_reps.cool.gz
Eye_disc_all_reps_DI.bedgraph
Eye_disc_all_reps_TADs.bed

data_processing:
Hi-C fastq reads were trimmed of the adapter sequence ‘GATCGAGCTCGAGAATTCTCGAGCTCGATC’. Read ends were then independently aligned using Bowtie2 v2.3.4.2 and default parameters. Pairing of mapped reads was done by custom script that removed PCR duplicates and filtered out reads aligning to more than two restriction enzyme fragments.
Hi-C read pairs were processed using HiFive, v1.4. Reads were filtered for a maximum insert size of 500bp, followed by filter of fragment-ends with fewer than 10 valid intra-chromosomal interactions larger than 100Kb. Linearly-interpolated log-log distance curves were calculated across 90 bins with a minimum interaction size of 200 and a maximum equal to the largest chromosome. Fragment-end corrections were calculated using the ‘express’ algorithm, an iterative correction procedure that removes distance effects prior to normalization. This was done using intra-chromosomal interactions only for 1000 iterations or until the largest parameter change was smaller than 1e-4.
TAD calls were performed using Hifive based on the directionality index (DI). DI was found using a 15Kb window considering interactions up to 100Kb tong. DI was calculated for each 5Kb step along the genome. TADs were called using a 3-state, 3-part Gaussian mixture model HMM initialized with an upstream, neutral, and downstream bias state. All mixture model components had variance of one and means in 0.5 increments centered on 1.0, 0.0, and -1.0 for the three states, respectively. Transitions to states (0, 1, 2) were set to (0.8, 0.05, 0.15), (0.25, 0.5, 0.25), and (0.15, 0.05, 0.8) for the downstream, neutral, and upstream states, respectively. Initial state frequencies were set at 0.3, 0.4, and 0.3. Parameters were learned from all chromosome DI scores after dividing each chromosome DI score set by its standard deviation. TADs were defined as starting at the first downstream bias state following an upstream bias state with any number of intervening neutral states.  TADs extended through the last upstream bias state followed by a downstream bias state with any number of intervening neutral states.
Genome_build: dm6
Supplementary_files_format_and_content: Hi-C files are in the cool format (https://github.com/mirnylab/cooler) and were created using a HiFive to Cool converter. Directionality Index (DI) files are in a BEDGRAPH format, and TADs are in BED format, both created using HiFive.

organism: Drosophila melanogaster

source_name: Eye disc

extract_protocol:
Larval eye discs and antennal discs were prepared for Hi-C using the following steps: 3 replicates of 125 third instar larval eye or antennal discs (i.e. N=3, n=125) were dissected in 1X PBS and stored in 1X PBS on ice until fixation. Eye and antennal discs were separated manually by dissection. After all discs were collected, discs were centrifuged at 17,600g for 1 minute and PBS was removed. Residual PBS was removed with a pipette, and discs were left to air dry for 3 minutes. Fixative (750 uL heptane, 237.4 uL cross-linking solution, 12uL fresh 37% formaldehyde) was added to the discs, and discs were fixed for 15 minutes with vigorous shaking. Discs were then centrifuged at 17,600g for 1 minute and fixative was removed. 1 mL of glycine solution (125 mM glycine, 0.1% Triton in PBS) was added to the discs, and the discs were incubated for 1 minute with vigorous shaking to quench the crosslinking reaction. Discs were then centrifuged at 17,600g for 1 minute and glycine solution was removed. Discs were then washed 2X with 1 mL of ice-cold PBX and centrifuged at 17,600g for 1 minute. PBX was removed, and discs were then centrifuged again at 17,600g for 1 minute. Any residual PBX was removed with a pipette, and discs were air dried for 3 minutes. Discs were then snap-frozen in liquid nitrogen and stored at -80 degrees C. Cross-linking solution: 50 mM Hepes (11.92 g), 1 mM EDTA (0.292 g), 0.5 mM EGTA (0.19 g), 100 mM NaCl (5.844 g) in 1L ultra-pure water. Solution was brought to pH 8, sterile filtered, and stored at room temperature. Glycine solution: 0.14 g glycine, 15 mL 1X PBS, 15 mL Triton-X. Solution was made fresh for each experiment and was stored at 4 degrees C until use.
Prior to the Hi-C experiment, biotinylated bridge oligos were prepared as follows: 10 μl 10X NEBuffer 2 was mixed with 90 μl of a 100 μM mixture of the two oligos (Bridge oligo forward: GATCGAGCTCGAGAA/iBiodT/T, Bridge oligo reverse: CTCGAGCTC). The mixture was heated to 98°C for 6 min, then ramped down to RT at -0.1°C / sec and stored at -20°C until use. Antennal and eye discs were thawed on ice and 1 ml of lysis buffer (10 mM Tris-Cl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, 1x cOmplete protease inhibitor (Roche, Cat. No. 11 873 580 001)) was added. Samples were incubated on ice for 30 min and then spun at 1000g at 4°C for 5 min. The supernatant was removed and pellets were resuspended in 200 μl of 0.5% SDS and incubated at 65°C for 10 min. The SDS was then quenched by adding 100 μl of 10% Triton X-100 and incubating at 37°C for 15 min. 50 μl of 10x NEBuffer 3.1, 130 μl nuclease-free H2O and 8 μl of DpnII (NEB) were added and samples were incubated at 37°C overnight. Tubes were centrifuged for 5 min at 1000g at RT and pellets were resuspended in 30 μl nuclease-free H2O. 5 μl biotinylated bridge oligos (90 uM) were ligated to the DNA fragments overnight at 16°C using 1 μl of T4 DNA ligase HC (Thermo Fisher), 5 μl ligation buffer, 4 μl 10x BSA, and 5 μl PEG 4000. After adding 2.5 μl of 0.5 M EDTA, the samples were centrifuged at 1000g at RT for 5 min and resuspended in 300 μl 1x BSA and 0.2% SDS in water. The pellets were centrifuged again at 1000xg at RT for 5 min and the pellets were resuspended in 300 μl 1x BSA and 0.1% SDS in water. This step was repeated for a second time. After another centrifugation, the samples were resuspended in 245 μl of 1.22x BSA and 0.2% Triton X-100 in water. The bridge oligos were phosphorylated by adding 30 μl 10x T4 ligase buffer (Thermo Fisher) and 20 μl PNK (10 U/ μl, NEB). Tubes were incubated at 37°C for 1h. Bridge oligos were ligated to each other using 5 μl T4 DNA ligase HC (Thermo Fisher), 70 μl 10x T4 ligase buffer, 7 μl 100x BSA and 618 μl nuclease-free H2O. Samples were incubated for 4 h at RT. The samples were then spun down at 1000g at 4°C for 5 min and the pellet was resuspended in 500 μL of extraction buffer (50 mM Tris-Cl pH 8.0, 50 mM NaCl, 1 mM EDTA, 1% SDS). To digest proteins, 20 μL of 20 mg/ml Proteinase K (Invitrogen) was added and the mixture was incubated at 55°C at 1000 rpm on a thermal shaker for 30 min. For decrosslinking, 130 μL of 5 M sodium chloride were added and the mixture was incubated at 68°C at 1000 on a thermal shaker overnight. To precipitate DNA, 63 μL of 3 M sodium acetate pH 5.2, 2 μL of 15 mg/ml GlycoBlue (Thermo Fisher) and 1000 μL of absolute ethanol were mixed with the sample, followed by incubation at -80°C for 1 hour. The samples were then spun at 20,000xg at 4°C for one hour. The supernatant was removed and the DNA pellet was washed two times using 800 μL of 70% ethanol. All traces of remaining supernatant were removed; the was pellet air-dried for 2 min and then solubilized in 99 μl of 10 mM Tris-Cl pH 8.0. RNA was digested by incubation with 1 μL of 10 mg/ml RNase A at 37°C for 15 min. The DNA was sheared in a total volume of 100μl to ∼200-400 bp with Diagenode Bioruptor Pico (4°C, ON/OFF 30’’/90’’, 8 cycles). DNA fragments were size-selected with SPRIselect Beads (Beckman Coulter) following the manufacturer’s instructions. For right side size selection, 0.6x volume of beads were used, and for left side size selection 1x was used. DNA was eluted in 100μL of 10mM Tris-Cl pH 8.0. For biotin enrichment, 30 μl of Dynabeads Streptavidin M-280 (Life Technologies) per sample were prepared following the manufacturer’s instructions and added to the purified DNA. The biotinylated bridge oligos were allowed to bind to the beads for 20 min at RT. The beads were washed 4 times with 200 μL each of 1x B&W buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl) + 0.1% Tween-20. This was followed by 2 washes with 10 mM Tris-Cl pH 8.0. The beads were then resuspended in 40 μL of the same solution. Library preparation was performed using the Swift Biosciences Accel-NGS 2S Plus DNA Library Kit, with the following modification: throughout the library preparation there was no SPRIselect clean-up performed. Instead, the samples were washed using the already bound Streptavidin beads. Each of the SPRI steps were replaced by the washes described hereafter: Samples were placed against the magnet and incubated until the solution was clear. The supernatant was discarded and samples removed from the magnet. Beads were resuspended in 150 μL of 1x B&W buffer + 0.1% Tween-20, and incubated at 55°C in a thermal cycler for 2 min. This wash step was repeated a second time. An additional wash step with 100μL of 10 mM Tris-Cl pH 8.0 was performed. Here, the samples were immediately put against the magnet after resuspension, without any incubation. The supernatant was discarded and samples removed from the magnet. Beads were resuspended in the mixes as described in the Swift Biosciences Library Kit for Repair II, Ligation I and Ligation II. After Ligation II and the above described washes, beads were resuspended in 20μL of 10 mM Tris-Cl pH 8.0.

tag: developmental stage

value: third instar larvae

value: eye imaginal disc


title: Antennal disc rep 2

description:
Antennal_disc_all_reps.cool.gz
Antennal_disc_all_reps_DI.bedgraph
Antennal_disc_all_reps_TADs.bed

source_name: Antennal disc

value: antennal imaginal disc


title: Antennal disc rep 1


title: Eye disc rep 2


title: Th0 plus stim KO1

tag: cell type


title: Antennal disc rep 3


title: Th0 plus stim WT3

value: WT


title: Th0 plus stim WT2


title: N4 primed OT-I with corticosteroid, biological rep3

source_name: N4 primed, corticosteroid treated, 4 days

value: splenocyte


title: N4 primed OT-I with corticosteroid, biological rep1

value: OT-I