title: NCoR1 ChIPseq 6hr CpG

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.2.6 with --qc-filter -P -t  -q. Uniquely aligned reads were taken for downstream analysis and
peaks were called using findPeaks form HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph files were generated using HOMER tool and further converted to BigWig using bedGraphToBigWig


title: 24uv4_L_1: 24hour_MONDNJ_LPS_rep1

status: Public on Oct 18 2019

type: RNA

city: Oxford

first: Andrew

middle: Cameron

last: Sayce

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol using iScan system

data_processing: Bead-level data were processed in Illumina GenomeStudio analytical software to generate mappings and probe-level intensities. Probe-level data was imported into R Bioconductor v2.14 using the lumi package. Data were normalised using neqc protocol. Inclusion criteria for further analysis required a detection p-value <0.01 for at least 1 of the 48 samples for a given probe. This analysis identified 21,705 expressed probes for further evaluation.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Monocyte-derived macrophage, MON-DNJ treated, LPS treated, 24 hours

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit for Illumina arrays.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats by centriguation through Ficoll-Paque PLUS density gradient. Monocytes were isolated by adherence to tissue culture plates coated in 2% bovine gelatin, transferred to 6 well plates seeded at 3x10^6 cells, and cultured in X-VIVO 10 supplemented with 1% (v/v) donor-autologous heat-inactivated human plasma and 25 ng/mL recombinant human interleukin-4 for 3 days at 37°C, 5% CO2 to differentiate into macrophages.

extract_protocol: Samples were washed in 37°C PBS containing calcium and magnesium once followed by lysis in TRIzol reagent for 5 minutes. Samples were applied to a Direct-zol RNA Mini-prep column (Zymo Research) and treated according to manufacturer's instructions to collect total RNA.

treatment_protocol: At 3 days, media was removed, and infectious stimuli diluted in X-VIVO 10 (or X-VIVO 10 only) were added to samples. Infection (or mock-infection) occurred at room temperature (20°C) with rocking for 90 minutes. Mock-media and DENV-media were removed at 90 minutes and replaced with MON-DNJ or control media containing 1% autologous plasma. LPS treatments were diluted to a final concentration of equivalent drug and autologous plasma. Treatmentwith drug or control was continued such that total time of treatment including the 90 minute infection was 6 hours or 24 hours.

tag: tissue

value: Monocyte-derived macrophage

tag: time point

value: 24 hours p.i.

tag: drug treatment

value: MON-DNJ, 25 μM

tag: infection

value: LPS, S. enterica, 200 ng/mL pulse, 100 ng/mL sustained

tag: replicate


title: 24uv4_D_4: 24hour_MONDNJ_DENV_rep4

source_name: Monocyte-derived macrophage, MON-DNJ treated, dengue infected, 24 hours


title: Empty CpG Rep1

type: SRA

city: Bhubaneswar

first: Sunil

middle: Kumar

last: Raghav

state: Odisha

address: Nalco Square

department: Infectious Disease Biology

country: India

institute: Institute of Life Sciences

description:
CpG activation (Control)
Emp_CpG_NCoR1_CpG.txt

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were checked for quality using FastQC v0.11.5, then mapped to mm10 whole genome using TopHat v2.1.0 with defult parameters
Fragment Per Kilobase of exon per Megabase of library size (FPKM) and differential expression were calculated using cufflinks v2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff output

organism: Mus musculus

source_name: CpG activation (Control)

growth_protocol: The CD8α+ DC lines were grown in IMDM medium supplemented with 10% FBS and antibiotic solution (Gibco), 5x10-5M 2-mercaptoethanol,sodiumbicarbonate, hepes. The cells were maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
The cells were thawed by placing the plates/tubes on ice. Total RNA was isolated using RNeasy plus kit (Qiagen) according to vendor recommended protocol. RNA concentration was estimated by nanodrop (Thermo)
2 ug of total RNA was used to isolate mRNA through magnetic beads using mRNA isolation kit (PolyA mRNA isolation Module, NEB) followed by RNA-seq library preparation using mRNA library preparation kit (NEB) strictly following the vendor recommended protoco.l

treatment_protocol: DCs were plated in 6 well plates at a density of 5 x 10^6 cells/ml overnight. Cells were challenged with different activation media containing TLR9 agonist CpG-B, TLR3 agonist pIC for different time points. cells were washed in the plate once with PBS followed by addition of RNA-later (RLT) buffer (Qiagen) for lysis of cells. The plates were then stored at -80oC until further RNA isolation and processing of samples.

tag: genotype/variation

value: wildtype

tag: cell line

tag: cell line genetic background strain

tag: cell type

value: Dendritic cell


title: 24uv4_D_2: 24hour_MONDNJ_DENV_rep2


title: 24uv4_D_3: 24hour_MONDNJ_DENV_rep3


title: 24uv4_L_3: 24hour_MONDNJ_LPS_rep3


title: 101178130143_R05C02

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Illumina protocol.

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

data_processing:
Minfi preprocessIllumina was used to process samples (for background subtraction and colour correction).
Average Beta (after minfi::preprocessIllumina in R).

label: Cy5 and Cy3

molecule: genomic DNA

source_name: buccal swab genomic DNA

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted using the Masterpure system (Epicentre, USA) and quantified using a NanoPhotometer P300 (Implen, Germany). Bisulfite converted using the EZ DNA Methylation Kit™ (Zymo Research).

value: Buccal epithelial cells

tag: age

tag: gender

value: Female


title: 24uv4_D_1: 24hour_MONDNJ_DENV_rep1


title: 101178130143_R03C02


title: Empty Uns Rep2

description:
Unstimulated (Control)
Emp_Uns_NCoR1_Uns.txt

source_name: Unstimulated (Control)


title: 101178130143_R02C02


title: Empty Uns Rep1


title: 24uv4_U_4: 24hour_MONDNJ_uninfected_rep4

source_name: Monocyte-derived macrophage, MON-DNJ treated, uninfected, 24 hours

value: Uninfected


title: 101178130143_R01C02


title: 101178130143_R06C01


title: brain_wild-type_E14.5_replicate3

city: Kyoto

first: Keiichi

last: Ishihara

state: Kyoto

address: 5 Misasagi Nakauchi-cho, Yamashina-ku

department: Department of Pathological Biochemistry

country: Japan

institute: Kyoto Pharmaceutical University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity > 8 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes. On completion of the fragmentation reaction, hybridized to SurePrint G3 Mouse GE 8x60 K microarray (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting. (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with GeneSpring GX (ver 12.0.0) (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: wild-type, brain

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the The Low Input Quick Amp Labeling kit, one color (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini kit (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using RNAiso (Takara) according to the manufacturer's instructions, followed by treatment with DNase I.

tag: strain

tag: genotype

value: wild-type

value: whole brain


title: brain_wild-type_E14.5_replicate2


title: brain_Ts1Cje_E14.5_replicate2

source_name: Ts1Cje, brain


title: brain_Ts1Cje_E14.5_replicate1


title: brain_Ts1Cje_E14.5_replicate3


title: 24uv4_U_3: 24hour_MONDNJ_uninfected_rep3


title: 24uv4_U_2: 24hour_MONDNJ_uninfected_rep2


title: ChIP_FGO_Setd2_Con_H3K27ac_rep1

city: Beijing

first: Wei

last: Xie

address: Haidian District

department: School of Life Science

country: China

institute: Tsinghua University

description:
processed data file:
ChIP_FGO_Setd2_Con_H3K27ac.bed.gz

library_source: genomic

data_processing:
STAR ChIP-seq datasets were mapped to the mouse mm9 reference genome using Bowtie2 (version 2.2.2) with the parameter:–t –q –N 1 –L 25. Multiple mapped reads and PCR duplicates were removed. After validating the reproducibility, replicates were pooled for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files for STAR ChIP-seq contains the RPKM value in 100bp bin across the mm9 genome.

source_name: oocyte

extract_protocol:
The DNA extraction follows STAR ChIP-seq protocol
The STAR ChIP-seq libraries were generated following the protocol as described previously(Zhang et al., 2016).

treatment_protocol: 8-week-old females were intraperitoneally injected with PMSG and hCG. Oocytes and embryos were harvested in M2 medium at following time point after hCG: MII oocytes, 13h; Zygotes 30 h; late-two cell embryos, 47 h; blastocyst, 98 h. Germinal versicle stageᕈᕧᕴᖧᖽᗬᗺᘈᘬᘺᙬᙹᚘᚥᚳᛐᛝᜐ᜼ᝉ᝗ᝥជផ៏៥៸᠅᠓ᠳᡀᡳᢌᢜᢩᢷᣜᣩᤜ᤽᥶ᦰ᧩ᨢᩜ᪕ᫎᬈᭁ᭻᮴ᯏᯗᯧᰠ᱄ᱨᲉᲣ᲻᳔ᳫᴎᴳᵚᵱᶪᷝḖḣḾṟṹẳẼỆồựἪ὜ᾃ᾽᾽῭‽⁜₎€⃊⃨ℐ℮⅖ⅾ↠⇗∐∮≨⊡⋓⌍⌿⍸⎱⏣␕⑇⑹⒫ⓝ─┳║╯▍▷◱☏☭♋⚄⚣⛁⛳✬❎❰➓➵⟗⠅⠳⡍⡦⢑⢯⣮⤍⤯⥒⥰⦝⧄⧿⨸⩱⪪⫤⬝⭖⮐⯊ⰃⰼⱵⲯ⳨ⴢ⴯ⴽ

value: oocyte

tag: developmental stage

value: FGO

tag: chip-antibody

value: H3K27ac (Active Motif, Cat.39133)


title: 101178130143_R04C01


title: PC3_shE2F1_2

city: Nanning

first: Qingniao

last: Zhou

state: Guangxi

address: 22 Shuangyong road

institute: Guangxi Medical Universtiy

data_processing:
RNA-seq alignment (1.1.1) in Illumina BaseSpace platform was used for processing data.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR aligner in RNA-seq alignment application.
Reads Per Kilobase of exon per Megabase of library size (RPKM) estimation of reference genes and transcripts using Cufflinks 2, assembly of novel transcripts with Cufflinks 2.
Variant calling (SNVs and small indels) with the Isaac Variant caller, Manta is used for Optional fusion calling.
Genome_build: hg38
Supplementary_files_format_and_content: text files include RPKM values for each Sample

growth_protocol: PC3 and DU145 were cultured at 37 ℃ in RPMI-1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
RNA was harvested using  AxyPrep TM Multisource Total RNA Miniprep Kit (Corning Incorporated; NY, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Prostate cancer

value: Prostate cancer cells

value: E2F1 knockdown


title: D32.DHA.FGF1.2

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

country: USA

institute: NIH

description: iPSC derived retinal organoids at D32 supplemented with DHA+FGF1 replicate 2

data_processing:
Fastq files were generated from reads passing chastity filter and used for further analysis. Illumina adapter, polyA, and polyT sequence trimming was performed with Trimmomatic v0.36.
Transcript level quantitation was performed using Kallisto v0.45.0 employing a merged transcript cDNA and ncRNA FASTA file downloaded from the Ensembl ftp site. Gene level quantification was generated by summarization of the transcript level quantitation using tximport v1.8.0 with the option “countFromAbundance=lengthScaledTPM”. The gene level count values were TMM normalized and converted to count per million (CPM) via edgeR.
Genome_build: GRCm38.p6 using Ensembl v94 annotation

molecule: polyA RNA

source_name: iPSC derived Retina organoids_D32_DHA+FGF1

growth_protocol: The mouse Nrl-GFP wild-type (WT) induced pluripotent stem cells (iPSC) clone was generated, characterized and maintained as previously described (PMID: 27667917). Briefly, the iPSC clone was reprogrammed from fibroblasts of embryonic day 14.5 WT Nrl-GFP mice, by infection of individual Doxycyclin-inducible lentiviral vectors carrying Oct3/4, Sox2, Klf4, and c-Myc genes. Embryonic stem cell-like colonies were picked and evaluated by morphology, proliferation rate and Nanog expression. The selected Nrl-GFP iPSCs were maintained on feeder cells (Millipore) at 37℃, 5% CO2. Maintenance medium was comprised of Knockout DMEM (Life Technologies), 1x MEM non-essential amino acids (NEAA)(Sigma), 1x GlutaMAX (Life Technologies), 1x Penicillin-Streptomycin (PS) (Life Technologies), 2000 U/ml LIF (Millipore), and 15% ES cell-qualified fetal bovine serum (FBS) (Life Technologies). Media were full changed performed every day, with 1x 2-Mercaptoethanol (2-ME) (Life Technologies) freshly added. Cells were passaged using TrypLE Express (Life Technologies) every two days.

extract_protocol:
For RNA extraction, 1-2 million induced pluripotent stem cells from neural retina were dissected from intact retinal organoids (12 from D12 to D32) using a moria nickel-plated pin holder (Fine Science Tools) with 0.25 mm-diameter tungsten needles (Fine Science Tools), before being lysed in 0.5 ml TriPure isolation reagent. RNA was extracted following manufacturer’s instructions and the quality was assessed using Agilent 4200 TapeStation system (Agilent).
Directional RNA-seq library construction was performed from 100 ng of high quality RNA (RIN > 8.0) using the Illumina Stranded mRNA Library Prep Kit (Illumina). Library construction from two or three biological replicates for all time points was performed.

treatment_protocol: Nrl-GFP iPSCs were differentiated into retinal organoids using the modified HIPRO protocol (PMID: 27667917). At differentiation day (D) 0, iPSCs were plated in PrimeSurface low adhesion U-shaped 96-well plate (Wako) at a density of 3000 cells per well in 100 ml retinal differentiation medium constituted by GMEM (Life Technologies), 1x NEAA (Sigma), 1x sodium pyruvate (Sigma) and 1.5%(v/v) knockout serum replacement (Life Technologies). 20 ml diluted Matrigel (120 ml >9.5 mg/ml Matrigel diluted in 900 ml retinal differentiation medium) (Corning) was added to each well at D1. At D7, Retinal organoids were transferred a 100 mm Poly(2-hydroxyethyl methacrylate) (Sigma)-coated petri dish with 10 ml DMEM/F12 with GlutaMAX (Life Technologies) supplemented with 1x N2 supplement (Life Technologies) and 1x PS (Life Technologies). From D10 to D26, retinal organoids were maintained in DMEM/F12 with GlutaMAX (Life Technologies), 1x PS (Life Technologies), 1x N2 supplement (Life Technologies), 1 mM taurine (Sigma), 500 nM 9-cis retinal (Sigma) and 100 ng/ml insulin-like growth factor 1 (Life Technologies). From D26 and onward, 1x NEAA acid (Sigma), 1x B27 supplement without Vitamin A (Life Technologies) and 2%(v/v) FBS (Atlanta Biologicals) were added to the culture. Half-media exchanges were performed every two days. 1x 2-ME was freshly added to media. The cultures were incubated in 5% O2 from D0 to D10 and in 20% O2 from D10 onwards. In the fatty acid supplementation experiments, cis-4,7,10,13,16,19-Docosahexaenoic acid (DHA) (Sigma) and linoleic acid (LA) (Sigma) were conjugated with bovine serum albumin (BSA) (Sigma) and supplied to retinal organoids from D10 and onward at a final concentration of 26 M. Fibroblast growth factor 1 (FGF1) was added to the organoid culture from D26 and onward to reach a final concentration of 200 ng/ml.

value: iPSC derived Retina organoids

tag: supplement


title: D32.DHA.FGF1.1

description: iPSC derived retinal organoids at D32 supplemented with DHA+FGF1 replicate 1


title: 101178130143_R03C01

tag: tissue


title: D32.LA.FGF1.3

description: iPSC derived retinal organoids at D32 supplemented with LA+FGF1 replicate 3

source_name: iPSC derived Retina organoids_D32_LA+FGF1

tag: time point


title: D32.LA.FGF1.2

description: iPSC derived retinal organoids at D32 supplemented with LA+FGF1 replicate 2


title: 101178130143_R05C01


title: 24U_L_4: 24hour_untreated_LPS_rep4

source_name: Monocyte-derived macrophage, untreated, LPS treated, 24 hours

value: Monocyte-derived macrophage

value: 24 hours p.i.

tag: drug treatment

value: Untreated


title: 24uv4_U_1: 24hour_MONDNJ_uninfected_rep1

value: MON-DNJ, 25 μM

tag: infection


title: MDA-P, biological replicate 1

city: San Juan de Alicante

first: Angela

last: Nieto

state: Alicante

address: Av. Ramón y Cajal s/n

department: Developmental Neurobiology

country: Spain

institute: Instituto de Neurociencias (CSIC-UMH)

description: Gene expression data from MDA231 cells with PRRX1 overexpression

hyb_protocol: Three independent samples per condition from MDA231-C and MDA231-P cells, were hybridized to Human Gene 2.0 ST expression arrays (Affymetrix)

scan_protocol: Done according to manufacturer's protocol

data_processing:
Microarray data was analyzed using R and Bioconductor. Expression data was preprocessed and normalized using the RMA algorithm
Differential expression analysis was performed using limma t- test to extract statistically significant changes between PRRX1 and control samples

label: biotin

source_name: Parental MDA-MB-231

growth_protocol: Cells were cultured in DMEM:F12 HAM media (1:1), and SUM149PT cells in  F12 HAM media, supplemented with 10% heat inactivated fetal bovine serum (FBS) (Sigma), 10 μg/ml insulin (Roche), 1% Gentamicin (Sigma) and 1% amphotericin (Sigma).

extract_protocol: RNA extractions were performed from cells in 70% confluency in 10cm plates, using miRvana kit following manufacturer's instructions.

treatment_protocol: Cells were transduced using a lentiviral system to stably express control GFP (MDA231-Control, MDA231-C) and PRRX1 (MDA231-PRRX1, MDA231-P)

value: Triple-negative, mesenchymal


title: MDA-P, biological replicate 3

label_protocol: Done according to manufacturer's protocol


title: 24U_L_3: 24hour_untreated_LPS_rep3

value: LPS, S. enterica, 200 ng/mL pulse, 100 ng/mL sustained

tag: replicate


title: 101178130143_R01C01

value: Buccal epithelial cells

value: Female


title: MDA-C, biological replicate 3

description: Gene expression data from MDA231 control cells


title: MDA-C, biological replicate 1


title: 24U_L_2: 24hour_untreated_LPS_rep2


title: 101178130032_R06C02


title: brain_wild-type_E14.5_replicate1

value: wild-type


title: 24U_L_1: 24hour_untreated_LPS_rep1


title: 24U_D_4: 24hour_untreated_DENV_rep4

source_name: Monocyte-derived macrophage, untreated, dengue infected, 24 hours


title: D32.BSA.FGF1.3

description: iPSC derived retinal organoids at D32 supplemented with BSA+FGF1 replicate 3

source_name: iPSC derived Retina organoids_D32_BSA+FGF1


title: D32.BSA.FGF1.2

description: iPSC derived retinal organoids at D32 supplemented with BSA+FGF1 replicate 2


title: D32.LA.FGF1.1

description: iPSC derived retinal organoids at D32 supplemented with LA+FGF1 replicate 1


title: 101178130143_R02C01


title: MDA-P, biological replicate 2


title: D32.DHA.2

description: iPSC derived retinal organoids at D32 supplemented with DHA replicate 2

source_name: iPSC derived Retina organoids_D32_DHA

value: DHA


title: D32.BSA.FGF1.1

description: iPSC derived retinal organoids at D32 supplemented with BSA+FGF1 replicate 1


title: D32.DHA.3

description: iPSC derived retinal organoids at D32 supplemented with DHA replicate 3


title: MDA-C, biological replicate 2


title: D32.DHA.1

description: iPSC derived retinal organoids at D32 supplemented with DHA replicate 1


title: D32.LA.3

description: iPSC derived retinal organoids at D32 supplemented with LA replicate 3

source_name: iPSC derived Retina organoids_D32_LA

value: LA


title: 101178130032_R05C02


title: D32.LA.2

description: iPSC derived retinal organoids at D32 supplemented with LA replicate 2


title: 101178130032_R03C02


title: 101178130032_R01C02


title: D32.BSA.3

description: iPSC derived retinal organoids at D32 supplemented with BSA replicate 3

source_name: iPSC derived Retina organoids_D32_BSA

value: BSA


title: 101178130032_R06C01


title: D32.BSA.2

description: iPSC derived retinal organoids at D32 supplemented with BSA replicate 2


title: 24U_D_2: 24hour_untreated_DENV_rep2


title: 24U_D_3: 24hour_untreated_DENV_rep3


title: 24U_D_1: 24hour_untreated_DENV_rep1


title: D32.BSA.1

description: iPSC derived retinal organoids at D32 supplemented with BSA replicate 1


title: 101178130032_R04C01


title: D26.LA.1

description: iPSC derived retinal organoids at D26 supplemented with LA replicate 1

source_name: iPSC derived Retina organoids_D26_LA


title: 101178130032_R03C01


title: 101178130032_R05C01


title: D26.DHA.1

description: iPSC derived retinal organoids at D26 supplemented with DHA replicate 1

source_name: iPSC derived Retina organoids_D26_DHA


title: D26.LA.2

description: iPSC derived retinal organoids at D26 supplemented with LA replicate 2


title: D26.BSA.1

description: iPSC derived retinal organoids at D26 supplemented with BSA replicate 1

source_name: iPSC derived Retina organoids_D26_BSA


title: D32.LA.1

description: iPSC derived retinal organoids at D32 supplemented with LA replicate 1


title: 24U_U_2: 24hour_untreated_uninfected_rep2

source_name: Monocyte-derived macrophage, untreated, uninfected controls, 24 hours

value: Uninfected


title: D26.DHA.2

description: iPSC derived retinal organoids at D26 supplemented with DHA replicate 2


title: pol II ChIPseq 0hr control

data_processing:
Basecalls performed using integrated primary analysis software called RTA (Real TimeAnalysis. v1.18) for pol II datasets.
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.2.6 with --qc-filter -P -t  -q
Uniquely aligned reads were taken for downstream analysis
peaks were called using findPeaks form HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph files were generated using HOMER tool and further converted to BigWig using bedGraphToBigWig

source_name: DC1940 cell line

extract_protocol:
Cell pellets were treated with different chromatin extraction buffer supplemented with protease and phosphatase inhibitors (Roche)  then clarified from sonicated nuclei and histone-DNA complexes were isolated with respective antibodies. 50 µl blocked protien A sepharose beads were added to each sample and incubated for 2.5h at 4°C to pull down the respective antibody-chromatin complexes. The beads were then washed with different washing buffers. Protein-bound chromatin complexes were eluted from beads for 30 min using elution buffer followed by reverse-crosslinked by incubating the eluted supernatant at 65°C overnight. Next day DNA was purified from the reverse cross-linked chromatin by proteinase-K and RNase digestion followed by purification using PCR purification kit (Qiagen).
For ChIP-seq library preparation, 30 µl ChIP-DNA was processed for library preparation according to ChIP-seq library preparation recommended protocol (NEB)

treatment_protocol: DCs were plated in 15 cm plates at a density of 30 x 106 cells/ml overnight. cells were then challenged with different activation media containing TLR9 agonist CpG-B, TLR3 agonist pIC for different time points. the cells were cross-linked using 1% formaldehyde (sigma) for 10 min at room temperature followed by quenching the reaction using 2.5 M glycine (sigma) for 10 min. The plates were placed on ice and the cells were scraped and collected in 50 ml conical tubes. The cells were then washed three times using cold 1 x PBS and cell pellets were stored at -80°C.

value: Dendritic cell

tag: chip antibody

value: polII


title: 101178130032_R02C01

source_name: buccal swab genomic DNA


title: pol II ChIPseq 6hr CpG control


title: pol II ChIPseq 6hr CpG NCoR1 KD


title: PU.1 ChIPseq 0hr control

data_processing:
Basecalls performed using integrated primary analysis software called RTA (Real TimeAnalysis. v1.18) for PU.1 datasets.
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.2.6 with --qc-filter -P -t  -q
Uniquely aligned reads were taken for downstream analysis
peaks were called using findPeaks form HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated using HOMER tool

tag: genotype/variation

value: Empty vector

tag: cell line


title: 24U_U_3: 24hour_untreated_uninfected_rep3


title: 24U_U_1: 24hour_untreated_uninfected_rep1


title: 24U_U_4: 24hour_untreated_uninfected_rep4


title: 6uv4_L_3: 6hour_MONDNJ_LPS_rep3

source_name: Monocyte-derived macrophage, MON-DNJ treated, LPS treated, 6 hours

value: 6 hours p.i.


title: pol II ChIPseq 0hr NCoR1 KD

tag: cell type


title: 6uv4_L_2: 6hour_MONDNJ_LPS_rep2

value: Monocyte-derived macrophage


title: 6uv4_L_4: 6hour_MONDNJ_LPS_rep4


title: D26.BSA.2

description: iPSC derived retinal organoids at D26 supplemented with BSA replicate 2

value: iPSC derived Retina organoids


title: 101178130032_R01C01

tag: age


title: 101070190069_R05C02

tag: gender


title: RNA_F_EB45.5

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

description:
polyA RNA
processed data file: annot_daphplx17evigenes_mod.gff.gz
processed data file: expression_EBseq_gene_FvsM.txt.gz
processed data file: expression_EBseq_tr_FvsM.txt.gz
processed data file: splicing_KisSplice_reads.fa.gz
processed data file: splicing_kissDE_FvsM.txt.gz

data_processing:
RNA-Seq: Illumina adapters (using core sequence: AGATCGGAAGAGC) and nucleotides with low quality (Phred score < 20) were removed with cutadapt (v.1.11).
RNA-Seq: The filtered reads were mapped to the reference genome of Daphnia pulex PA42 (GCA_900092285.1; Ye et al. 2017) using RSEM (v.1.3.0; Li & Dewey 2011) using STAR aligner (2.5.3a; Dobin et al. 2013) for the RNA-seq samples, with default settings.
RNA-Seq: The Daphnia pulex gene models used in the analysis are from November 2017 obtained from the arthropod database in eugenes (Genomic Information for Eukaryotic Organisms; http://arthropods.eugenes.org) produced by Don Gilbert using EvidentialGene (Gilbert 2016).
RNA-Seq: Expression changes were analysed at gene and transcript levels using EBSeq (v.1.20.0) (Leng et al. 2013), with default settings. Genes and transcripts with significant expression difference between males and females (with posterior probability of differential expression < 0.05) were analysed further.
Genome_build: GCA_900092285.1
Supplementary_files_format_and_content: RNA-Seq: txt (differential expression analysis results at gene level: expression_EBseq_gene_FvsM.txt.gz and transcriptome level: expression_Ebseq_tr_FvsM.txt.gz)
Supplementary_files_format_and_content: RNA-Seq: txt (de-novo differential splicing analysis results: splicing_kissDE_FvsM.txt.gz), fasta (de-novo splicing events detected by kisSplice: splicing_KisSplice_reads.fa.gz)

organism: Daphnia pulex

source_name: whole organism

growth_protocol: Cultures of Daphnia pulex Eloise Butler strain (genotypes EB31 and EB45, originally sampled from Eloise Butler pond in Minnesota (Yampolsky et al. 2014)) were maintained in a 16:8 h light:dark photoperiod and temperature of 20 ± 1 °C, in standard COMBO medium (COMBO). Media were prepared using a protocol adapted from Kilham et al. (1998), and renewed every other day. Animals were fed every other day with Chlorella vulgaris at a concentration of ~27,550 cells of algae per individual Daphnia. Oxygen concentrations were continuously monitored using an oxygen sensor (Unisense microrespiration system, Denmark). Daphnia samples were flash frozen in liquid nitrogen and stored in -80C until further use.

extract_protocol:
Total RNA was extracted from the samples using RNeasy micro kit ((Qiagen Ltd, UK) according to the manufacturer's protocol.
The RNA-seq libraries were prepared using the Illumina TruSeq standard mRNA kit and sequenced (1x85bp) using Illumina NextSeq 500 platform at the Centre for Genomics and Bioinformatics, Indiana University.

treatment_protocol:
To induce male Daphnia, sexually matured individual female Daphnia were treated with the crustacean reproductive hormone, methyl (2E, 6E)-farnesoate (MF) at a final concentration of 400nM. This concentration is sufficient to induce male Daphnia at 100% efficiency (Olmstead & Leblanc 2002). Due to the instability of MF, media was changed daily to ensure consistent exposure. The first brood was discarded and male neonates were collected from 2nd–3rd broods. Female and male cultures were maintained separately.
Maintained under standard condition with normal levels of oxygen (6 mg/L) for 3, 8 and 15 days.

tag: strain

value: Eloise Butler (45)

tag: clone

value: Clone 45

value: female

value: Mix of ages of 3, 8 and 15 days

value: whole body

tag: exposure

value: control

tag: culturing media

value: Standard COMBO


title: 6uv4_D_3: 6hour_MONDNJ_DENV_rep3

source_name: Monocyte-derived macrophage, MON-DNJ treated, dengue infected, 6 hours

value: MON-DNJ, 25 μM


title: PU.1 ChIPseq 6hr CpG control

value: Empty Vector

tag: cell line genetic background strain


title: RNA_M_EB45.5

value: male


title: WGBS_M_EB45.2

description:
Bisulphite-treated genomic DNA
processed data file: annot_daphplx17evigenes_mod.gff.gz
processed data file: methylation_MethylKit_FvsM.txt.gz

data_processing:
Bisulfite-Seq: Illumina adapters (using core sequence: AGATCGGAAGAGC) and nucleotides with low quality (Phred score < 20) were removed with cutadapt (v.1.11) while processing both read pairs at the same time.
Bisulfite-Seq: The filtered reads were mapped to the reference genome of Daphnia pulex PA42 (GCA_900092285.1; Ye et al. 2017) using BWA Meth (v.0.10; Pedersen et al. 2014) for the bisulfite treated DNA samples, with default settings.
Bisulfite-Seq: The Daphnia pulex gene models used in the analysis are from November 2017 obtained from the arthropod database in eugenes (Genomic Information for Eukaryotic Organisms; http://arthropods.eugenes.org) produced by Don Gilbert using EvidentialGene (Gilbert 2016).
Bisulfite-Seq: Methylated CpG sites were called from mapped reads using MethylDackel (v.0.2.1; github.com/dpryan79/MethylDackel). Both uniquely mapped singletons and discordant reads were retained, while reads with low mapping quality (MAPQ < 10) and nucleotides with low base calling quality (Phred < 30) were excluded. Seven base pairs from both ends of the reads were also excluded, as they showed an excessive amount of methylation potentially due to adapter contamination.
Bisulfite-Seq: Differential methylation analysis was done using methylKit (v.1.3.0; Akalin et al. 2012). Akalin et al. 2012). CpG sites with abnormally high (>98 percentile) coverage were removed, as well as sites that were not covered in all samples or had zero methylated reads in more than half of the samples (n=6/12). Logistic regression was used to analyse differential CpG methylation between males and females, using genotype (EB31 and EB45) as a co-variable. The Q-values were adjusted using the SLIM method (Wang et al. 2011).
Genome_build: GCA_900092285.1
Supplementary_files_format_and_content: Bisulfite-Seq: bed (CpG-methylation calls from MethylDackel in methylKit format:*CpG.methylKit.gz)
Supplementary_files_format_and_content: Bisulfite-Seq: txt (differential CpG-methylation analysis results from methylKit: methylation_MethylKit_FvsM.txt.gz)
Supplementary_files_format_and_content: Bisulfite-Seq: gff (Daphnia pulex gene models used in the analysis are from November 2017 obtained from the arthropod database in eugenes (Genomic Information for Eukaryotic Organisms; http://arthropods.eugenes.org) produced by Don Gilbert using EvidentialGene (Gilbert 2016))

extract_protocol:
Genomic DNA was extracted from the samples using MasterPure DNA purification kit (Epicentre, USA) following Athanasio et al. (2016).
Libraries for sodium bisulfite treated samples were prepared following the EpiGnome Methyl-Seq kit (Epicentre, USA) protocol. Briefly, DNA samples (50 ng for sodium bisulfite converted and 20 ng for non-converted samples) were diluted in 9 μL of nuclease-free water, mixed with 2 μL of DNA synthesis primer and incubated at 95°C for 5 minutes. Samples were placed on ice and 5 μL of the mastermix (containing 4 μL of EpiGnome DNA synthesis premix, 0.5 μL of 100 mM DTT and 0.5 μL of EpiGnome polymerase) was added to each sample. The reactions were incubated as 25°C for 5 minutes, 42°C for 30 minutes and 37°C for 2 minutes. Then, 1 μL of exonuclease I was added to each sample and incubated for 10 minutes at 37°C, 3 minutes at 95°C followed by 2 minutes at 25°C. DNA samples were tagged by addition of TT master mix (7.5 μL of EpiGnome terminal tagging premix and 0.5 μL of DNA polymerase). Samples were incubated at 25°C for 30 minutes followed by 3 minutes at 95°C. Reactions were cooled to 4°C and purified using AMPure XP system (1.6x beads) (Beckman Coulter Inc., USA) as recommended. The final step of library construction comprised the amplification of the libraries and addition of barcodes. Each reaction contained 22.5 μL of the purified tagged DNA, 25 μL of FailSafe PCR premix E, 1 μL EpiGnome forward primer, 1 μL of EpiGnome index PCR primer and 0.5 μL of FailSafe PCR enzyme (1.25 U). PCR was performed according to the manufactures guidelines. Amplified samples were purified using AMPure XP beads (1x beads). Samples were re-suspended in 20 μL of nuclease-free water and quantity and quality of the sequencing libraries were assessed. Daphnia pulex libraries were sequenced using Illumina NextSeq-500 platform at the Centre for Genomics and Bioinformatics, Indiana University, USA.


title: 6uv4_L_1: 6hour_MONDNJ_LPS_rep1

value: LPS, S. enterica, 200 ng/mL pulse, 100 ng/mL sustained


title: 6uv4_D_2: 6hour_MONDNJ_DENV_rep2


title: WGBS_M_EB45.1


title: 101070190069_R04C02

value: Buccal epithelial cells

value: Female


title: RNA_M_EB45.4


title: 6uv4_D_4: 6hour_MONDNJ_DENV_rep4


title: 101070190069_R03C02


title: RNA_M_EB45.2


title: 101070190069_R06C01


title: RNA_F_EB45.4


title: AVN_LCM_HET7

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

data_processing:
RNA-seq: reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al., 2013).
RNA-seq: Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: AVN_LCM_counts.xlsx (Excel file with normalized (DESeq2) count data per gene & differential expression analysis).

source_name: Tbx3 +/- GFP-positive AV node

growth_protocol: Animal care was in accordance with guidelines from the European Union and Amsterdam University Medical Centers. Tbx3CreERT2 and BAC-Tbx3-Egfp were maintained on a FVB/NJ background commercially obtained from Jackson laboratory (stock number 100800).

extract_protocol:
Hearts from ND8-10 pups were removed, the AV node region microdissected (based on fluorescence) and immediately embedded in O.C.T. (Tissue-Tek, 621232) in the -20°C for 10 minutes. Cryosectioning was performed with a cryostat (Leica biosystems, CM1950) and AV node tissue was sectioned at a thickness of 8 µm. Five consecutive sections were collected and mounted onto PEN-membrane coated slides (MembraneSlide 1.0 PEN, Carl Zeiss Microscopy, 415190-9041-001). Microdissection was performed immediately afterwards with a Laser Microdissection Microscope (Leica microsystems, LMD6) and the AV node identified visually based on fluorescence. AV node tissue was collected in a tube containing the lysis buffer of the PicoPure RNA isolation kit (ThermoFisher Scientific, KIT0204) and the first step of manufacturer’s protocol conducted before storing the samples in the -80°C. After all samples were collected the PicoPure RNA isolation kit (ThermoFisher Scientific, KIT0204) was followed according to manufacturer’s protocol with an on column DNAse treatment (RNAse-free DNAse, Qiagen, 79254). RNA integrity and concentration was determined using the Bioanalyzer RNA 6000 Pico materials (Agilent Technologies, 5067-1513 and 5067-1535).
The Ovation RNA-seq system V2 (Nugen, 7102-32) was used for cDNA synthesis with a RNA input between approximately 300 and 2000 pg. Quality of the cDNA library was determined by Bioanalyzer DNA 7500 (Agilent Technologies, 5067-1506), purity by the Nanodrop (Isogen Life Science, ND-1000) and quantity by the Qubit dsDNA HS (ThermoFisher Scientific, Q32854). RNA-sequencing libraries were made using Ovation Ultralow Library System V2 (Nugen, 0344-32) and sequenced on the HiSeq4000.

treatment_protocol: No treatment conducted

value: FVB/NJ

value: Neonatal Day 10

value: Atrioventricular node


title: 101070190069_R02C02


title: WGBS_M_EB45.3


title: 101070190069_R01C02


title: AVN_LCM_HET4


title: 6uv4_D_1: 6hour_MONDNJ_DENV_rep1

value: Monocyte-derived macrophage

value: 6 hours p.i.


title: WGBS_F_EB45.2

value: Eloise Butler (45)

value: Clone 45


title: 101070190021_R05C02


title: WGBS_F_EB45.1

value: female

value: Mix of ages of 3, 8 and 15 days


title: 6uv4_U_4: 6hour_MONDNJ_uninfected_rep4

source_name: Monocyte-derived macrophage, MON-DNJ treated, uninfected, 6 hours

value: Uninfected


title: 6U_L_4: 6hour_untreated_LPS_rep4

source_name: Monocyte-derived macrophage, untreated, LPS treated, 6 hours

value: Untreated


title: WGBS_M_EB31.2

value: Eloise Butler (31)

value: Clone 31

value: whole body

value: control

value: Standard COMBO


title: 101070190069_R05C01

value: Buccal epithelial cells

value: Female


title: 101070190021_R06C02


title: WGBS_M_EB31.1

value: male


title: WGBS_F_EB45.3


title: 6uv4_U_3: 6hour_MONDNJ_uninfected_rep3

value: MON-DNJ, 25 μM


title: 6uv4_U_2: 6hour_MONDNJ_uninfected_rep2

value: Monocyte-derived macrophage


title: 101070190021_R03C02


title: WGBS_F_EB31.3


title: AVN_LCM_HET6

value: FVB/NJ

value: Neonatal Day 8

value: Atrioventricular node


title: AVN_LCM_WT6

source_name: WT GFP-positive AV node


title: 101070190021_R02C02


title: 101070190069_R03C01


title: WGBS_M_EB31.3


title: AVN_LCM_HET5

value: Neonatal Day 10


title: HeyA8-TR

city: Suita

first: Kenjiro

last: Sawada

state: Osaka

address: Yamadaoka 2-15

department: Obstetrics and Gynecology

institute: Osaka University Faculty of Medicine

description: test

data_processing:
Experimental data were analyzed by DataAssist™ Software (Thermo). Ct values were provided from all miRNAs represented on the cards and fold changes in expression were calculated using the delta delta Ct (ddCt) method. Expression levels of RNU44 on the array card were defined as an endogenous control for the purpose of ddCt calculation. Non-normalized data reports raw CT values in each sample. Normalized data reports Ct values of target gene signal normalized to that of RNU44. Target-control data reports relative gene expression of paclitaxel resistant/sensitive cells (i.e., SKOV3ip1-TR/SKOV3ip1) in each cell line.
Matrix normalized worksheet reports normalized signal (against RNU44). Fold Change worksheet reports test/control (i.e., SKOV3ip1-TR/SKOV3ip1) ratios.

label: FAM

source_name: ovarian cancer cell line

label_protocol: PCR assays were performed using TaqMan® MicroRNA Assays (Thermo) following the Manufacturer’s instructions. Reverse transcription reaction was performed using TaqMan® MicroRNA Reverse Trabnscription Kit (Thermo). Quantitative real-time PCR were performed with cycling condition of 95゜C for 10 min (followed by 95゜C for 15 sec and 60゜C for 60 sec) for a total of 40 cycles.

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS and 100 U/mL penicillin/streptomycin and incubated in 95% air/5% CO2 at 37°C. Cells were authenticated by short tandem repeat DNA profiling at Takara-Bio Inc. (Otsu, Japan) and were used for this study within 6 months of resuscitation.

extract_protocol: Total RNA was extracted from the four lines with TRIzol reagent (Thermo Fisher Scientific, Waltham, MA).

treatment_protocol: Two paclitaxel-resistant sublines from SKOV3ip1 and HeyA8 were developed by stepwise increases in paclitaxel concentration from 1 nM to 150–300 nM over a period of 3 months. The resulting paclitaxel-resistant sublines, designated as SKOV3ip1-TR and HeyA8-TR, respectively, were cultured with 150–300 nM paclitaxel in the culture medium to maintain paclitaxel resistance.

value: high grade serous ovarian cancer cell

tag: treatment

value: paclitaxel

tag: paclitaxel resistance

value: resistant


title: HeyA8

description: control

value: sensitive


title: AVN_LCM_HET3

tag: tissue


title: 6U_D_4: 6hour_untreated_DENV_rep4

source_name: Monocyte-derived macrophage, untreated, dengue infected, 6 hours

tag: time point

value: 6 hours p.i.

tag: drug treatment

value: Untreated


title: SKOV3ip1-TR

description: test


title: WGBS_F_EB31.2

value: Eloise Butler (31)

value: Clone 31

value: female

value: Mix of ages of 3, 8 and 15 days

value: whole body

value: control

tag: replicate


title: 6U_L_2: 6hour_untreated_LPS_rep2

value: Monocyte-derived macrophage

tag: infection

value: LPS, S. enterica, 200 ng/mL pulse, 100 ng/mL sustained


title: AVN_LCM_HET2

value: FVB/NJ

value: Neonatal Day 8


title: SKOV3ip1

description: control


title: 101070190021_R03C01

value: Buccal epithelial cells

value: Female


title: AVN_LCM_WT1

value: Atrioventricular node


title: 6U_D_2: 6hour_untreated_DENV_rep2


title: 6U_L_3: 6hour_untreated_LPS_rep3


title: 6U_L_1: 6hour_untreated_LPS_rep1


title: 6uv4_U_1: 6hour_MONDNJ_uninfected_rep1

value: MON-DNJ, 25 μM

value: Uninfected


title: 101070190021_R04C02


title: 101070190069_R01C01


title: 101070190021_R02C01


title: 101070190021_R04C01


title: breast cancer_41 [hov228]

city: Chennai

first: Rajkumar

last: T

state: Tamilnadu

address: Adyar

department: Molecular Oncology

institute: Cancer Institute (WIA)

hyb_protocol: The Cy3 and Cy5 labelled aRNA was used for hybridization onto the microarray chips from Stanford Functional Genomics Facility (SFGF, Stanford, CA) containing 44,544 spots, for 16 hrs in Lucidea SlidePro hybridization chamber. (GE Healthcare) at 42℃. The labeling for microarray experiments was standardized using the Amino Allyl MessageAmp II aRNA amplification kit (Ambion) as per the manufacturer’s instructions. Post hybridisation slides were washed in 0.1X SSC, 1X SSC followed by 0.1X SSC and dried

scan_protocol: The slides were scanned in ProScanArray (PerkinElmer, Shelton, CT, USA). Griding was done using Scan array Express software package (version -4). The integrated or mean intensity of signal within the spot was calculated. The files were saved as GPR files.

data_processing: The Foreground Median intensity for Cy3 and Cy5, Background Median intensity for Cy3 and Cy5, spot size data were imported into BRB-ArrayTools software using the Import wizard function. Background correction was not done. Global normalization was used to median centre the log-ratios on each array in order to adjust for differences in labelling intensities of the Cy3 and Cy5 dyes

source_name: tumour tissue from a patient with breast cancer

label_protocol: 1 µg of total RNA from the tumour sample and universal RNA (Stratagene; Cat no: 74000041) were reverse transcribed using Array script at 42°C for 2 hrs to obtain cDNA using the Amino Allyl MessageAmp II aRNA amplification kit (Ambion, Austin, Tx; Cat no: AM1797). The cDNA was amplified by in-vitro transcription in the presence of T7 RNA polymerase; aRNA thus obtained was purified and quantitated in NanoDrop (NanoDrop Technologies, Wilmington, DE, USA). 20 mg of tumour aRNA was labelled using NHS ester of Cy5 dye and control universal aRNA was labelled using NHS ester of Cy3 dye

extract_protocol: Total RNA extracted from tissue samples using RNeasy RNA extraction kit (Qiagen) according to manufacturer's instructions. Quantitated using Nanodrop and quality checked using Agilent BioAnalyzer

tag: histopathological examination (hpe); inflitrating lobular carcinoma (ilc); infiltrating ductal carcinoma (idc)

value: IDC

tag: cancer stage

tag: er status

value: Positive

tag: pr status

tag: her2 status

value: Negative

tag: tissue origin

value: breast

tag: sample type

value: surgery (frozen tissue)

source_name: Universal reference RNA

value: Stratagene Universal Human Reference RNA from 10 human cell lines


title: AVN_LCM_WT5

tag: strain

tag: age


title: paired normal of breast cancer_41 [hoae203]

source_name: morphologically normal tissue from a patient with breast cancer

tag: gender

value: Morphologically normal

value: Paired normal


title: 6U_U_2: 6hour_untreated_uninfected_rep2

source_name: Monocyte-derived macrophage, untreated, uninfected controls, 6 hours

value: Monocyte-derived macrophage

value: 6 hours p.i.

value: Untreated


title: BMP4_2

city: Rotterdam

first: Eskeatnaf

last: Mulugeta

address: Wytemaweg 80

department: Cell Biology

institute: Erasmus University Medical Center Rotterdam (Erasmus MC)

data_processing:
Quality of sequence reads evaluated using FastQC (version 0.11.2)
Low quality reads and and contaminants (e.g. sequence adapters) were removed using Trimmomatic (version 0.32)
Sequences were aligned to the mm10 genome using tophat2 (version 2.0.14), with bowtie2 (version 2.1.0) for the transfected cells or Cufflinks for the non-transfected cells.
Transcript abundance level (Transcript count) was generated using HTSeq (version 0.5.3p9)
The transcript counts were further processed using R software environment for statistical computing and graphics (version 3.4.0)
The transcript counts were further processed using R software environment for statistical computing and graphics (version 3.4.0)
Differential expression was performed using edgeR R package using the negative binomial GLM approach, or Cuffdiff (version 7)  for the non-transfected cells.
Genome_build: mm10

source_name: Adult hippocampal neural stem cells

growth_protocol: Cells were grown in basal medium (DMEM/F-12 + Glutamax (Invitrogen, 31331-093)) + 1x N2 supplement (R&D Systems, AR009) + 1x Penicillin-Streptomycin (ThermoFischer Scientific, 15140) + 2ug/ml Laminin (Sigma, L2020) + 5ug/mL Heparin + 20 ng/ml FGF2 (Peprotech, 450-33).

extract_protocol:
Total RNA from transfected and FACS sorted cells was extracted using Qiagen RNAeasy Micro kit (Qiagen, 74104) . Total RNA from non-transfected cells was extracted using Direct-zol™ RNA MiniPrep Kit (Zymo Research, R2052), according to manufacturer's instructions.
RNA concentration was quantified using the Qubit dsDNA BR/HS Assay Kit. A KAPA mRNA HyperPrep Kit (for Illumina) (KAPA Biosystems, Wilmington, MA, USA) has been used with 1000ng of RNA diluted to a final volume of 50µl. Each RNA sample was captured with 50µl of capture beads at 65°C for 2 min and 20°C for 5 min. For the second capture, 50µl of RNase free water was used at 70°C for 2 min and 20°C for 5 min. Captured RNA was subjected to the KAPA Hyper Prep assay: end-repair, A-tailing, and ligation by adding 11µl of Fragment, Prime and Elite Buffer (2X). To obtain a distribution of 200-300bp fragment on the library, the reaction was run for 6min at 94°C. cDNA synthesis was run in 2 steps following manufacturer’s instructions. The ligation step consisted of a final volume of 110 μL of the adaptor ligation reaction mixture with 60μL of input cDNA, 5 μL of diluted adaptor and 45μL of ligation mix (50µL of ligation buffer+ 10 μL of DNA ligase). The Kapa Dual-Indexed Adapters (KAPA Biosystems-KK8720) stock was diluted to 7µM (1.5mM or 7nM) to get the best adaptor concentration for library construction. The ligation cycle was run according to manufacturer’s instructions. To remove short fragments such as adapter dimers, 2 AMPure XP bead clean-ups were done (0.63 SPRI and 0.7SPRI). To amplify the library, 7 PCR cycles were applied to cDNA KAPA HP mix. Amplified libraries were purified using AMPure XP. The quality and fragment size distributions of the purified libraries was assessed by a 2200 TapeStation Instrument (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: To induce quiescence of "BMP4" samples, cells were plated into flasks in proliferation conditions and allowed to adhere overnight. Media was replaced the next day with basal media or basal media plus 20ng/mL recombinant mouse BMP4 (R&D Systems, 5020-BP), and cultured for 72h at 37C, 5% CO2.

value: wild type

tag: number of cells

tag: passage number


title: BMP4_1


title: 101070190021_R01C02

tag: tissue

value: Buccal epithelial cells


title: AVN_LCM_WT3

value: FVB/NJ

value: Neonatal Day 10


title: 101070190021_R05C01

value: Female


title: BMP4_3


title: WGBS_F_EB31.1

value: Eloise Butler (31)

tag: clone

value: Clone 31

value: female

value: Mix of ages of 3, 8 and 15 days

value: whole body

tag: exposure

value: control

tag: culturing media

value: Standard COMBO


title: 6U_D_3: 6hour_untreated_DENV_rep3

tag: time point

tag: drug treatment

tag: infection

tag: replicate


title: AVN_LCM_WT2

value: Neonatal Day 8

value: Atrioventricular node


title: FGF2_3


title: 101070190020_R05C02


title: FGF2_2


title: 101070190020_R04C02


title: 101070190020_R06C02


title: 101070190021_R01C01


title: 6U_U_1: 6hour_untreated_uninfected_rep1

value: Monocyte-derived macrophage

value: Uninfected


title: MoMacro Donor 6

city: Nantes

first: Aurelie

last: Moreau

address: 30 bd Jean Monnet

country: France

institute: INSERM U1064

description:
C7_D6
gene expression analysis of T7-amplified polyA RNA

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: Blood monocytes Donor 6

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: ATDCs were differentiated following a 6 day-culture of monocytes in AIMV medium supplemented with recombinant human GM-CSF at 100U/ml. MoDC were differentiated following a 6 day-culture of monocytes in IMDM medium supplemented with 10% FBS, 1000U/ml recombinant human GM-CSF and 1000U/ml recombinant human IL-4. MoMacro were obtained following a 7 day-culture of monocytes in RPMI 1640 medium supplemented with 20% FCS and 100ng/ml rhM-CSF.

extract_protocol: Total RNA was isolated using RNeasy Plus kits (Qiagen) as previously described (Riquelme, P et al. Mol Ther., 2013).

value: whole blood

tag: cell type

value: Monocyte-derived Macrophages (MoMacro)

value: male


title: 6U_U_3: 6hour_untreated_uninfected_rep3

data_processing: Bead-level data were processed in Illumina GenomeStudio analytical software to generate mappings and probe-level intensities. Probe-level data was imported into R Bioconductor v2.14 using the lumi package. Data were normalised using neqc protocol. Inclusion criteria for further analysis required a detection p-value <0.01 for at least 1 of the 48 samples for a given probe. This analysis identified 21,705 expressed probes for further evaluation.

value: 6 hours p.i.

value: Untreated


title: BMP E47_3

description: For overexpression of pCAGGS-E47-GFP, 5x106 cells per construct were nucleofected using the Amaxa mouse neural stem cell nucleofector kit (Lonza, VPG-1004) and Amaxa Nucleofector II (Lonza), using the program A-033, according to manufacturer’s instructions. Cells had been pre-treated with 20ng/mL BMP4 for 72h prior to transfection, to induce quiescence. Following transfection, cells were plated into flasks, in supplemented basal media, and incubated for 48h at 37C, 5% CO2. Cells transfected with E47 were cultured in the presence of 20ng/mL FGF2 and 20ng/mL BMP4.

value: wild type


title: FGF2_1


title: AVN_LCM_WT4

value: FVB/NJ

value: Neonatal Day 10


title: BMP E47_2


title: 6U_D_1: 6hour_untreated_DENV_rep1


title: 101070190020_R03C02

value: Buccal epithelial cells

value: Female


title: 101070190020_R01C02


title: 101070190020_R06C01


title: 101070190020_R02C02


title: 101070190020_R02C01


title: 101070190020_R04C01


title: BMP E47_1


title: FGF ID4_2

description: For overexpression of pBABE-Id4-FLAG, 5x106 cells per construct were nucleofected using the Amaxa mouse neural stem cell nucleofector kit (Lonza, VPG-1004) and Amaxa Nucleofector II (Lonza), using the program A-033, according to manufacturer’s instructions. In order to FACS sort transfecetd cells, cells were co-transfected with an empty pCAGGS-IRES-GFP construct at half the concentration of pBABE-Id4-FLAG, to increase the likelihood of GFP+ cells also being Id4+. ). Following transfection, cells were plated into flasks, in supplemented basal media, and incubated for 48h at 37C, 5% CO2. Cells transfected with Id4 were cultured in the presence of 20ng/mL FGF2.


title: FGF ID4_3


title: FGF ID4_1


title: 101070190020_R05C01


title: BMP GFP_3

description: Cells were cultured in basal media in the presence of 20ng/mL FGF2 and 20ng/mL BMP4 for 72h to induce quiescence. 5x106 cells per construct were nucleofected using the Amaxa mouse neural stem cell nucleofector kit (Lonza, VPG-1004) and Amaxa Nucleofector II (Lonza), using the program A-033, according to manufacturer’s instructions. These BMP4 control cells were nucleofected with pmaxGFP vector from the Amaxa kit (Lonza, VPG-1004). Following transfection, cells were plated into flasks, in supplemented basal media with 20ng/mL FGF2 and 20ng/mL BMP4, and incubated for 48h at 37C, 5% CO2.


title: 101070190020_R01C01


title: FGF GFP_3

description: Cells were cultured in basal media in the presence of 20ng/mL FGF2. 5x106 cells per construct were nucleofected using the Amaxa mouse neural stem cell nucleofector kit (Lonza, VPG-1004) and Amaxa Nucleofector II (Lonza), using the program A-033, according to manufacturer’s instructions. These FGF2 control cells were nucleofected with pmaxGFP vector from the Amaxa kit (Lonza, VPG-1004). Following transfection, cells were plated into flasks, in supplemented basal media with 20ng/mL FGF2, and incubated for 48h at 37C, 5% CO2.


title: BMP GFP_2


title: 101070190019_R06C02


title: paired normal of breast cancer_39 [hoae204]

tag: histopathological examination (hpe); inflitrating lobular carcinoma (ilc); infiltrating ductal carcinoma (idc)

value: Morphologically normal

tag: cancer stage

value: Paired normal

value: breast

value: surgery (frozen tissue)

value: Stratagene Universal Human Reference RNA from 10 human cell lines


title: breast cancer_39 [hov219]

value: IDC with DCIS

tag: er status

value: Positive

tag: pr status

tag: her2 status

value: Negative

tag: tissue origin

tag: sample type


title: breast cancer_37 [hov208]

tag: age

tag: gender

value: IDC


title: breast cancer_38 [hov212]


title: FGF GFP_2

tag: strain

tag: number of cells

tag: passage number


title: paired normal of breast cancer_40 [hov251]


title: paired normal of breast cancer_35 [hoae205]


title: paired normal of breast cancer_37 [hov253]


title: breast cancer_40 [hov224]

value: IDC with vascular emboli


title: BMP GFP_1


title: breast cancer_34 [hov162]


title: 101070190019_R03C02

tag: tissue


title: breast cancer_33 [hov158]


title: MoMacro Donor 1

description:
C7_D1
gene expression analysis of T7-amplified polyA RNA

source_name: Blood monocytes Donor 1

value: whole blood

value: Monocyte-derived Macrophages (MoMacro)

value: male


title: 101070190019_R05C02

source_name: buccal swab genomic DNA


title: 6U_U_4: 6hour_untreated_uninfected_rep4

value: Monocyte-derived macrophage

tag: time point

value: 6 hours p.i.

tag: drug treatment

value: Untreated

value: Uninfected


title: FGF GFP_1

value: wild type


title: MoMacro Donor 4

description:
C7_D4
gene expression analysis of T7-amplified polyA RNA

source_name: Blood monocytes Donor 4


title: MoMacro Donor 3

description:
C7_D3
gene expression analysis of T7-amplified polyA RNA

source_name: Blood monocytes Donor 3


title: paired normal of breast cancer_34 [hov179]

value: Female

value: Morphologically normal

value: Paired normal


title: breast cancer_35 [hov180]

value: breast

value: surgery (frozen tissue)

value: Stratagene Universal Human Reference RNA from 10 human cell lines


title: 101070190019_R01C02

value: Buccal epithelial cells


title: breast cancer_36 [hov192]

value: IDC

value: Positive

value: Negative


title: paired normal of breast cancer_33 [hoae172]


title: paired normal of breast cancer_38 [hov233]


title: Pho ChIP 14-16 hr

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz

country: Germany

institute: Max Planck Institute of Biochemistry

data_processing:
Reads from fastq files were aligned to the dm6 genome.
Bam files were used as inputs to run Bioconductor packages.
The STAN Bioconductor package (Zacher et al., 2014) was used to define the location of high-level H3K27me3 domains in 14-16 hr wt embryos.
Read numbers from the different H3K27me3 ChIP datasets were normalised based on the number of H3K27me3 molecules in each condition, as measured by mass spectrometry.
Pho peaks were identified using GenoGAM (Stricker et al., 2017).
Genome_build: dm6
Supplementary_files_format_and_content: Bedgraph files (for visualizing ChIP-seq datasets) contain the number of overlapping reads with 200 bp bins covering the 7 chromosomal arms of the Drosophila genome.
Supplementary_files_format_and_content: Bedgraph files (High Pho peaks and H3K27me3 domains) contain the position of the high Pho peaks and high-level H3K27me3 domains that were identified.

organism: Drosophila melanogaster

source_name: 14-16 hr old Oregon R embryos

growth_protocol: Drosophila embryos were grown on standard medium at 25˚C

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq kit.

tag: devepmental stage

value: 14-16 hr old embryo

tag: antibodies

value: Pho (Papp and Müller 2006)


title: 101070190019_R02C02

data_processing:
Minfi preprocessIllumina was used to process samples (for background subtraction and colour correction).
Average Beta (after minfi::preprocessIllumina in R).


title: 101070190019_R05C01


title: MoMacro Donor 5

description:
C7_D5
gene expression analysis of T7-amplified polyA RNA

source_name: Blood monocytes Donor 5

value: whole blood

tag: cell type

value: Monocyte-derived Macrophages (MoMacro)

value: male


title: 101070190019_R06C01


title: MoMacro Donor 2

description:
C7_D2
gene expression analysis of T7-amplified polyA RNA

source_name: Blood monocytes Donor 2


title: H3K27me3 ChIP 14-16 hr

value: H3K27me3 (Cell Signaling (C36B11))


title: 101070190019_R04C01


title: 16GSOTT_6_M_P14_CB

city: Urbana

first: Lisa

last: Stubbs

state: ILLINOIS

address: 2402 IGB, 1206 W. Gregory Drive, MC-195

department: Cell and Developmental Biology, Institute for Genomic Biology

institute: University of Illinois

data_processing:
Fastq files were generated with the software Casava 1.8.2 (Illumina)
read alignment: Tophat 2.0.8, default parameters
read quantification: Reads inside of exon features were counted in union mode using htseq version 0.6.1.
differential expression: Done in R using the Bioconductor package edgeR.  Pairwise comparisons between control and intruder conditions in each tissue and time after challenge were analyzed using the bin.loess version of trended dispersion in edgeR version 3.2.4 in R version 3.0.0.
Genome_build: mouse NCBI version 37.2
Supplementary_files_format_and_content: 16GSO_allcounts_for_GEO_2019-06-12.txt: Tab delimited text file of the matrix of raw read counts mapped to the mouse genome (Ensembl annotation of the NCBIM37 version of the mouse genome) as created by the edgeR function readDGE. TopHat2 version 2.0.8 (Kim et al. 2013) was used to align reads.  Reads inside of exon features were counted in union mode using htseq version 0.6.1 (Anders et al. 2015). Note that the counts include meta tags that are prefixed by "__" that were removed from counts before further processing.

extract_protocol:
Freshly dissected tissue was flash-frozen in liquid nitrogen and frozen at -80° C until RNA could be extracted. Total RNA was disrupted in Trizol (Life Technologies, Carlsbad, CA, USA) with a mechanical pestle according manufacturer’s specifications. The aqueous phase was precipitated in isopropanol, resuspended in nuclease-free water, treated with DNase I (New England Biolabs, Ipswich, MA, USA), and cleaned up using a Zymo RNA Clean & Concentrator™-25 kit (Zymo Research, Irvine, CA, USA) according to manufacturer’s specifications. Prior to library preparation, total RNA was checked for purity using a NanoDrop ND-1000 spectrophotometer, integrity using RNA Nano chips on an Agilent 2100 Bioanalyzer, and concentration using a Qubit fluormeter.
RNA-Seq libraries were prepared from total RNA robotically using TruSeq Stranded mRNA HT (Illumina, San Diego, CA, USA) on an epMotion 5075 robot (Eppendorf, Hamburg, Germany).

tag: strain background

tag: genotype/variation

value: mutant

value: cerebellum


title: 16GSOTT_5_M_P14_CB


title: input 14-16 hr


title: 101070190019_R03C01

value: Female


title: H3K27me3 ChIP 2-4 hr

source_name: 2-4 hr old Oregon R embryos

value: 2-4 hr old embryo


title: 16GSOTT_4_M_P14_CB


title: Pho ChIP 2-4 hr


title: 101070190019_R02C01


title: paired normal of breast cancer_36 [hoae200]

tag: histopathological examination (hpe); inflitrating lobular carcinoma (ilc); infiltrating ductal carcinoma (idc)

value: Morphologically normal

tag: cancer stage

value: Paired normal

value: breast


title: WT3_M_P14_CB

source_name: wild type_P14_cerebellum

value: wild type


title: input 2-4 hr


title: 101070190019_R01C01

value: Buccal epithelial cells


title: WT2_M_P14_CB


title: HepG2_TGFBeta [3-T3]

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

growth_protocol: Cells were grown in monolayer culture system using MEM media with 10% FBS.

extract_protocol:
Cells were collected by scraping, RNA was extracted using TRIzol
TruSeq v2 for mRNA

treatment_protocol: Cells were plated at 70% confluency and left to adhere overnight. Cells were then treated with 5ng/mL of human recombinant TGFB1 ligand or respective vehicle for three hours.

tag: cell line

value: hepatocellular carcinoma cell line

tag: passage

tag: treatment

value: 5ng/mL of human recombinant TGFB1 ligand for 3 hrs


title: WT_1_M_P14_CB

tag: age


title: HA-28z_Batch3

city: PALO ALTO

first: Hima

last: Anbunathan

state: CA

address: 265 Campus Drive

institute: Stanford University

description:
Control HA_replicate3
HA_28Z_Bulk_Batch3
processed data file: Processed_TPMs_additional.csv

data_processing:
Expression levels of genes were quantified using Kallisto 0.44.0, with Gencode v27 reference transcriptome, and hg38 as the reference human genome.
TPMs were summed for transcript-level quantification.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Processed_TPMs_additional.csv: Comma-separated text file includes TPM values.

source_name: CAR T Cells

extract_protocol:
For T cell subset-specific RNA-seq, T cells were isolated from healthy donor buffy coats as described above. Before activation, naïve and central memory CD4+ or CD8+ subsets were isolated using a BD FACSAria cell sorter (Stem Cell FACS Core, Stanford University School of Medicine) using the following markers: Naïve (CD45RA+CD45RO-, CD62L+, CCR7+, CD95-, and CD122-), Central Memory (CD45RA-CD45RO+, CD62L+, CCR7+). Sorted starting populations were activated, transduced, and cultured as described above. On days 7, 10, and 14 of culture, CAR+ CD4+ and CD8+ cells were sorted, and RNA was isolated using Qiagen mRNeasy kit.
Samples library prep and sequencing were performed by BGI America (Cambridge, MA).

value: Bulk

value: Control HA

tag: timepoint


title: HepG2_TGFBeta [1-T3]


title: JUN-HA-28z_Batch3

description:
Jun overexpressed HA_replicate3
HA_28Z_Bulk_JUN_Batch3
processed data file: Processed_TPMs_additional.csv

value: Jun overexpressed HA


title: JUN-CD19-28z_Batch3

description:
Jun overexpressed CD19_replicate3
CD19_28Z_Bulk_JUN_Batch3
processed data file: Processed_TPMs_additional.csv

value: Jun overexpressed CD19


title: HepG2_vehicle [3-V3]

value: vehicle for 3 hrs


title: HepG2_TGFBeta [2-T3]


title: B6C3_M_P35_M28_CB

description: 816_B6C3_M_P35_M28_CB_ATTACTCG-TAATCTTA_L006

source_name: wild type_P35_cerebellum


title: CD19-28z_Batch3

description:
Control CD19_replicate3
CD19_28Z_Bulk_Batch3
processed data file: Processed_TPMs_additional.csv

value: Control CD19


title: HepG2_vehicle [2-V3]


title: B6C3_M_P35_M27_CB

description: 815_B6C3_M_P35_M27_CB_ATTACTCG-AGGCGAAG_L006


title: B6C3_M_P35_M29_CB

description: 817_B6C3_M_P35_M29_CB_ATTACTCG-CAGGACGT_L006


title: JUN_HA_28Z_Batch2

description:
Jun overexpressed HA_replicate2
HA_28Z_Bulk_JUN_Batch2
processed data file: Processed_TPMs_additional.csv


title: HepG2_vehicle [1-V3]


title: 16GSOTT_P35_C20_CB

description: 813_16gsoT_T_P35_C20_CB_ATTACTCG-CCTATCCT_L006

value: mutant


title: m6A enriched mRNA mock infected RNA2 A549

city: CHICAGO

first: Zijie

last: Zhang

state: IL

department: Chemistry

institute: University of Chicago

description: m6A enriched mRNA

data_processing:
Library strategy: MeRIP-seq
Seequencing reads were aligned to reference genome by Hisat2
gene level read counts were obtained using R package Rsubread
Genome_build: hg38
Supplementary_files_format_and_content: gene level read counts
4 of the datasets were processed by canonical analysis and thus has processed data file.  Other data sets doesn't have canonical processed data files and thus are not included here.^SAMPLE = GSM4041575

growth_protocol: A549(ATCC CCL-185) cell lines were purchased from the American Type Culture Collection (Manassas, VA) and were grown in Dulbecco's modified Eagle's medium (DMEM; Life Technologies) supplemented with 10% FBS.

extract_protocol:
TRIzol (Invitrogen) + polyT beads(thermo fisher)
Kapa hyper RNA library kit

treatment_protocol: RNAs were extracted from highly purified hMPV virions and purified with the RiboMinus Eukaryote System v2 kit (Thermo Fisher) to remove ribosome-derived RNA. For host cell,  total RNAs were extracted from mock or hMPV-infected A549 cells and polyadenylated RNAs were isolated using Dynabeads mRNA DIRECT Purification kit (Thermo Fisher).

tag: group

value: mock infected


title: 16GSOTT_P35_C21_CB

description: 814_16gsoT_T_P35_C21_CB_ATTACTCG-GGCTCTGA_L006

value: cerebellum


title: 16GSOTT_P35_C19_CB

description: 812_16gsoT_T_P35_C19_CB_ATTACTCG-ATAGAGGC_L006


title: m6A enriched mRNA mock infected RNA1 A549

description: m6A enriched mRNA


title: CD19_28Z_Batch2

description:
Control CD19_replicate2
CD19_28Z_Bulk_Batch2
processed data file: Processed_TPMs_additional.csv


title: JUN_CD19_28Z_Batch2

description:
Jun overexpressed CD19_replicate2
CD19_28Z_Bulk_JUN_Batch2
processed data file: Processed_TPMs_additional.csv


title: paired normal of breast cancer_32 [hov246]

tag: gender

value: Female

tag: tissue origin

tag: sample type

value: surgery (frozen tissue)

value: Stratagene Universal Human Reference RNA from 10 human cell lines


title: paired normal of breast cancer_29 [hoae189]

value: Morphologically normal

value: Paired normal

value: breast


title: breast cancer_27 [hoae168]

source_name: tumour tissue from a patient with breast cancer

value: IDC with extensive DCIS

tag: er status

value: Positive

tag: pr status

tag: her2 status

value: Negative


title: breast cancer_28 [hoae169]

value: IDC

source_name: Universal reference RNA


title: breast cancer_32 [hov157]

value: Both breast T2N0M0


title: JUN_HA_28Z_Batch1

description:
Jun overexpressed HA_replicate1
HA_28Z_Bulk_JUN_Batch1
processed data file: Processed_TPMs_additional.csv

tag: cell type

value: Bulk

value: Jun overexpressed HA


title: m6A enriched mRNA hMPV infected RNA2

description: m6A enriched mRNA

value: hMPV infected


title: paired normal of breast cancer_31 [hoae191]

source_name: morphologically normal tissue from a patient with breast cancer


title: breast cancer_31 [hoae174]


title: paired normal of breast cancer_30 [hoae192]


title: breast cancer_29 [hoae170]


title: paired normal of cancer_26 [hoae183]


title: paired normal of breast cancer_27 [hoae184]


title: breast cancer_30 [hoae173]


title: paired normal of breast cancer_25 [hoae195]


title: breast cancer_26 [hoae157]


title: paired normal of breast cancer_28 [hoae188]


title: W483_P35_B6C3_HC

description: 669_W483_P35_B6C3_HC_TAATGCGC-ACGTCCTG_L005

source_name: wild type_P35_hippocampus

tag: strain background

value: wild type

tag: tissue

value: hippocampus


title: W481_P35_B6C3_HC

description: 668_W481_P35_B6C3_HC_TAATGCGC-TAAGATTA_L005

tag: genotype/variation


title: breast cancer_25 [hoae151]

tag: histopathological examination (hpe); inflitrating lobular carcinoma (ilc); infiltrating ductal carcinoma (idc)

tag: cancer stage


title: m6A enriched mRNA Input hMPV infected RNA1

description: m6A enriched mRNA

tag: cell line


title: HA_28Z_Batch1

description:
Control HA_replicate1
HA_28Z_Bulk_Batch1
processed data file: Processed_TPMs_additional.csv

value: Control HA


title: HA_28Z_Batch2

description:
Control HA_replicate2
HA_28Z_Bulk_Batch2
processed data file: Processed_TPMs_additional.csv


title: N10_P35_M_B6C3_HC


title: JUN_CD19_28Z_Batch1

description:
Jun overexpressed CD19_replicate1
CD19_28Z_Bulk_JUN_Batch1
processed data file: Processed_TPMs_additional.csv

value: Jun overexpressed CD19


title: paired normal of breast cancer_24 [hoae190]

value: Female

value: surgery (frozen tissue)


title: m6A enriched RNA viral genome RNA2

description: m6A enriched RNA

value: viral genome


title: B11_P35_M_16GsoTT_HC

value: mutant


title: CD19_28Z_Batch1

description:
Control CD19_replicate1
CD19_28Z_Bulk_Batch1
processed data file: Processed_TPMs_additional.csv

value: Control CD19


title: breast cancer_24 [hoae150]

value: breast

value: Stratagene Universal Human Reference RNA from 10 human cell lines


title: GD2_CD8_N_Day14

description:
GD2_CD8_Naive_Day14_BigBulk
processed data file: Processed_TPMs_additional.csv

tag: compartment

value: Naive


title: Input mock infected RNA2 A549

description:
Input RNA
A549_readCount.txt

value: mock infected


title: B10_P35_M_16GsoTT_HC

tag: age


title: m6A enriched RNA viral genome RNA1

description: m6A enriched RNA


title: GD2_CD8_N_Day7

description:
GD2_CD8_Naive_Day7_BigBulk
processed data file: Processed_TPMs_additional.csv

tag: timepoint


title: Input hMPV infected RNA2

description:
Input RNA
A549_readCount.txt

tag: group


title: Input hMPV infected RNA1

description:
Input RNA
A549_readCount.txt


title: GD2_CD8_N_Day10_rep2

description:
GD2_CD8_Naive_Day10_Bulk2
processed data file: Processed_TPMs_additional.csv


title: N5_P14_M_B6C3_HC

source_name: wild type_P14_hippocampus


title: N4_P14_M_B6C3_HC


title: Input mock infected RNA1 A549

description:
Input RNA
A549_readCount.txt


title: B12_P35_M_16GsoTT_HC


title: A18_P14_M_16GSOTT_HC


title: GD2_CD4_N_Day7

description:
GD2_CD4_Naive_Day7_BigBulk
processed data file: Processed_TPMs_additional.csv


title: GD2_CD4_N_Day14

description:
GD2_CD4_Naive_Day14_BigBulk
processed data file: Processed_TPMs_additional.csv


title: Input viral genome RNA1

description: Input RNA

data_processing:
Library strategy: MeRIP-seq
Seequencing reads were aligned to reference genome by Hisat2
gene level read counts were obtained using R package Rsubread
Genome_build: hg38
Supplementary_files_format_and_content: gene level read counts


title: breast cancer_21 [hov191]

tag: gender

value: IDC

value: Negative

value: Positive

value: trucut (frozen tissue)


title: breast cancer_22 [hov201]

tag: tissue origin


title: breast cancer_20 [hov184]

value: positive

tag: sample type


title: breast cancer_23 [hov213]

tag: er status


title: A14_P14_M_16GSOTT_HC

value: hippocampus


title: gun5-1+NF3

city: Rostock

first: Andreas

middle: Sven

last: Richter

address: Albert-Einstein-Strasse 3

department: Institute for Biosciences

institute: University of Rostock

description:
treatment with 5µM Noflurazon
Cuffdiff_Col-0+NF_gun5-1+NF

data_processing:
Analysis was performed using GALAXY-Webserver
Trimmomatic
TopHat alignment of reads to Arabidopsis thaliana Col-0 genome build (NCBI GenBank BioProject PRJNA10719), Araport11 Official Release
Cufflinks on TopHats "accepted hits"
Cuffmerge of all assembled transcripts togehter with Col-0 Araport11 (s.a.) annotation
Cuffdiff
Down stream analysis using GALAXY-tools (Filter, Cut, Paste), Microsoft Excel (offline handling of datasets), Perseus-Software (generation of heatmaps on FC, MPI biochemistry)
Genome_build: Arabidopsis thaliana Col-0 genome build (NCBI GenBank BioProject PRJNA10719)
Supplementary_files_format_and_content: Processed data files contain log2(FC) and p-value of control (Col-0+NF or gun5-1+NF for gun5-1+NF+PIP) vs mutant (gun1-1+NF, gun4-1+NF, gun5-1+NF, gun5-1+NF+PIP)

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: 5d, 100µl photons m-2 s-1

extract_protocol:
RNA-extraction protocol using citric acid described by Onate-Sanchez and Vicente-Carbajosa (2008). Total RNA of 5d old seedlings was extracted.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: 5µM Norflurazon (+NF) in growth media (MS). Additionally the gun5-1 mutant was germinated in the presence of 100µM piperonylic acid (+PIP) and +5µM NF

tag: genotype

value: whole seedling

tag: ecotype background

value: 5d after germination

tag: treatment

value: 5µM Norflurazon


title: GD2_CD8_N_Day10_rep1

description:
GD2_CD8_Naive_Day10_BigBulk
processed data file: Processed_TPMs_additional.csv

tag: cell type


title: N6_P14_M_B6C3_HC

tag: strain background

value: wild type

tag: tissue


title: A13_P14_M_16GSOTT_HC

tag: genotype/variation


title: breast cancer_19 [hov168]

value: Female

tag: histopathological examination (hpe); inflitrating lobular carcinoma (ilc); infiltrating ductal carcinoma (idc)

value: ILC

tag: cancer stage

tag: pr status

tag: her2 status

value: surgery (frozen tissue)


title: breast cancer_17 [hoae196]

tag: age

value: breast

value: trucut biopsy (frozen tissue)


title: gun5-1+NF2


title: GD2_CD4_N_Day10_rep2

description:
GD2_CD4_Naive_Day10_Bulk2
processed data file: Processed_TPMs_additional.csv

tag: compartment

value: Naive

tag: timepoint


title: GD2_CD4_N_Day10_rep1

description:
GD2_CD4_Naive_Day10_BigBulk
processed data file: Processed_TPMs_additional.csv


title: Input viral genome RNA2

description: Input RNA

data_processing:
Library strategy: MeRIP-seq
Seequencing reads were aligned to reference genome by Hisat2
gene level read counts were obtained using R package Rsubread
Genome_build: hg38
Supplementary_files_format_and_content: gene level read counts
4 of the datasets were processed by canonical analysis and thus has processed data file.  Other data sets doesn't have canonical processed data files and thus are not included here.^SAMPLE = GSM4041575
Library strategy: MeRIP-seq
Seequencing reads were aligned to reference genome by Hisat2
gene level read counts were obtained using R package Rsubread
Genome_build: hg38
Supplementary_files_format_and_content: gene level read counts
4 of the datasets were processed by canonical analysis and thus has processed data file.  Other data sets doesn't have canonical processed data files and thus are not included here.^SAMPLE = GSM4041575

tag: group

value: viral genome

tag: cell line


title: Input_M_EB45.0

description: processed data file: annot_daphplx17evigenes_mod.gff.gz

data_processing:
ChIP-Seq: Illumina adapters (using core sequence: AGATCGGAAGAGC) and nucleotides with low quality (Phred score < 20) were removed with cutadapt (v.1.11).
ChIP-Seq: The filtered reads were mapped to the reference genome of Daphnia pulex PA42 (GCA_900092285.1; Ye et al. 2017) using BWA-MEM (v.0.7.15-r1140; Li & Durbin 2009) for the non-bisulfite treated DNA samples (ChIP-seq and reference DNA), with default settings.
ChIP-Seq: The Daphnia pulex gene models used in the analysis are from November 2017 obtained from the arthropod database in eugenes (Genomic Information for Eukaryotic Organisms; http://arthropods.eugenes.org) produced by Don Gilbert using EvidentialGene (Gilbert 2016).
ChIP-Seq: The ChIP-seq reads were filtered by mapping quality (MAPQ > 30) to reduce background noise from unspecific mapping. The peaks corresponding to histone modifications (H3K4me3 and H3K27me3) were called with MACS2 (v 2.1.0.20151222; Zhang et al. 2008), separately for each sample without sifting model building using 132Mbp as an estimate of the mappable genome size and predicted fragments sizes 134bp (for H3K4me3) and 144bp (for H3K27me3) as estimated from the data.
ChIP-Seq: Differential analysis of histone peaks (narrowPeak) were achieved using DiffBind (v. 2.8.0; Stark & Brown 2011), by comparing the male and female samples against each other (n=3 for both sexes and histone modifications) and against the input controls (n=2). The peaks for H3K27me3 were mapped to the nearest transcript, and the peaks for H3K4me3 were mapped against the nearest exon 1. Differential peaks (FDR<0.05) within 200bp of known transcripts (H3K27me3) or exon 1 (H3K4me3) were retained for further analysis.
Genome_build: GCA_900092285.1
Supplementary_files_format_and_content: ChIP-Seq: bed (ChIP-seq histone modification peaks called using MACS2 in narrowPeak format: *peaks.narrowPeak.gz)
Supplementary_files_format_and_content: ChIP-Seq: txt (differential ChIP-seq peak analysis using DiffBind for H3K27me3: chipseq_DiffBind_H3K27me3_FvsM.txt.gz, and H3K4me3: chipseq_DiffBind_H3K4me3_FvsM.txt.gz)

source_name: whole organism

extract_protocol:
Daphnia samples (30 mg wet tissue per sample) were homogenised in 1 ml of PBS/1%formaldehyde using Dounce homogenizer.
The chromatin immunoprecipitation sequencing libraries (ChIP-seq) were prepared using the iDeal-seq kit, H3K4me3 (C15410003-50, 1 ug/reaction), H3K27me3 (C15410195, 1 µg/reaction) antibodies and sequenced using Illumina HiSeq 2500 (1x50 bp) as part of a service provided by Diagenode (Belgium). Briefly, Daphnia samples (30 mg wet tissue per sample) were homogenised in 1 ml of PBS/1%formaldehyde using Dounce homogenizer. The collected cells were lysed and the nuclei were collected and sonicated to a final size of 80-400 bp. The mentioned antibodies were used to prepare test samples according to the manual for the iDeal ChIP-seq kit. The IP samples and input samples were quantified using the Qubit dsDNA HS kit. Library preparation was performed on the IP and input samples using the MicroPLEX library preparation protocol on 500 pg of DNA. The amplified libraries (13 PCR cycles) were purified using AMPure beads, quantified using the Qubit ds DNA HS kit and analysed on Bioanalyzer. The prepared libraries were then sequenced on HiSeq 2500.

tag: strain

value: Eloise Butler (45)

tag: clone

value: Clone 45

tag: gender

value: male

value: Mix of ages of 3, 8 and 15 days

value: whole body

tag: exposure

value: control

tag: culturing media

value: Standard COMBO

tag: chip antibody

tag: replicate


title: Mock_CD8_N_Day10

description:
Mock_CD8_Naive_Day_10_Bulk2
processed data file: Processed_TPMs_additional.csv

tag: cell type


title: gun5-1+NF1

tag: genotype

tag: tissue

value: whole seedling

tag: ecotype background

value: 5d after germination

tag: treatment


title: breast cancer_18 [hoae187]

tag: age

tag: histopathological examination (hpe); inflitrating lobular carcinoma (ilc); infiltrating ductal carcinoma (idc)

value: IDC

tag: cancer stage

tag: er status

value: Negative

tag: pr status

tag: her2 status

value: positive

tag: tissue origin

tag: sample type

value: Stratagene Universal Human Reference RNA from 10 human cell lines


title: breast cancer_16 [hoae231]

tag: gender

value: Female

value: Block not available

value: breast

value: surgery (frozen tissue)


title: gun4-1+NF3

description:
treatment with 5µM Noflurazon
Cuffdiff_Col-0+NF_gun4-1+NF

value: 5µM Norflurazon


title: breast cancer_15 [hoae230]

value: Positive


title: Mock_CD4_N_Day10

description:
Mock_CD4_Naive_Day_10_Bulk2
processed data file: Processed_TPMs_additional.csv

tag: compartment

value: Naive

tag: timepoint


title: gun4-1+NF2


title: H3K4me3_M_EB45.3

description:
processed data file: annot_daphplx17evigenes_mod.gff.gz
processed data file: chipseq_DiffBind_H3K4me3_FvsM.txt.gz

tag: strain

value: Eloise Butler (45)

tag: clone

value: Clone 45

value: male

value: Mix of ages of 3, 8 and 15 days

tag: exposure

tag: culturing media

tag: chip antibody

tag: replicate


title: Input_F_EB45.0

value: female

tag: age

tag: tissue

value: whole body

value: control

value: Standard COMBO


title: gun4-1+NF1

tag: genotype

value: whole seedling

tag: ecotype background

value: 5d after germination

tag: treatment


title: gun1-1+NF3

description:
treatment with 5µM Noflurazon
Cuffdiff_Col-0+NF_gun1-1+NF


title: H3K4me3_M_EB45.2


title: gun1-1+NF2


title: H3K4me3_F_EB45.3


title: gun1-1+NF1


title: H3K4me3_F_EB45.2


title: Col-0 + NF3

description: treatment with 5µM Noflurazon

value: wild-type


title: breast cancer_14 [hoae229]

value: Female

tag: histopathological examination (hpe); inflitrating lobular carcinoma (ilc); infiltrating ductal carcinoma (idc)

value: IDC

tag: cancer stage

tag: er status

tag: pr status

tag: her2 status

value: Negative

value: trucut biopsy (frozen tissue)

value: Stratagene Universal Human Reference RNA from 10 human cell lines


title: H3K4me3_F_EB45.1

tag: gender


title: H3K4me3_M_EB45.1

tag: strain


title: H3K27me3_M_EB45.3

description:
processed data file: annot_daphplx17evigenes_mod.gff.gz
processed data file: chipseq_DiffBind_H3K27me3_FvsM.txt.gz

tag: clone


title: H3K27me3_M_EB45.2

tag: exposure


title: Col-0 + NF2

description: treatment with 5µM Noflurazon

value: 5µM Norflurazon


title: breast cancer_12 [hoae227]

value: Positive

value: positive

tag: tissue origin

value: breast

tag: sample type


title: Col-0 + NF1

description: treatment with 5µM Noflurazon


title: breast cancer_13 [hoae228]


title: donor 3_PD-L1-

city: Houston

first: Stephen

last: Wong

state: TX

address: 6670 Bertener

department: Systems Medicine and Bioengineering Department

institute: Houston Methodist Neal Cancer Center

description: gene expression data in PD-L1- NK cells

hyb_protocol: 5.2ug of labeled and fragmented and biotin-labeled ss-cDNA was hybridized at 45C for 16 hours at 60rpm in affymetrix Hybridization oven 645. GeneChips were then washed and stained on the Affymetrix Fluidics Station 450 according to the manufacturer’s protocol.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 7G.  Data files were generated and processed with Affymetrix software and Expression Console.

data_processing:
The data were analyzed with transcriptome analysis console (TAC) 3.0 software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Clariom_D_Human
program-name = Expression Console
program-version = 1.4.1.46

label_protocol: 100ng RNA was used to generate biotinylated ss-cDNA according to the manufacturer’s protocol in the GeneChip® WT PLUS Reagent Kit

growth_protocol: Human primary NK cells were enriched from healthy donors based on CD3-CD56+ gating.

extract_protocol: Total RNA was extracted from the CD3-CD56+PD-L1+ or CD3-CD56+PD-L1- cells according to the manufacturer's instructions using RNeasy Mini Kit (Cat No./ID: 74104).

treatment_protocol: The enriched human primary NK cells were co-incubated with K562 myeloid leukemia cells for 24h in the presence of 10ng/ml IL-2 and then sorted based on CD3-CD56+PD-L1+ or CD3-CD56+PD-L1-.

tag: subject status

value: healthy donor

tag: cell type

value: human primary NK cells

tag: co-incubation

value: K562 myeloid leukemia target cells for 24 h

tag: sorted fraction

value: PD-L1- NK cells


title: breast cancer_10 [hoae225]

tag: age


title: breast cancer_8 [hoae223]


title: breast cancer_7 [hoae222]


title: donor 3_PD-L1+

description: gene expression data in PD-L1+ NK cells

value: PD-L1+ NK cells


title: breast cancer_11 [hoae226]


title: breast cancer_6 [hoae212]


title: breast cancer_5 [hoae211]

value: ILC


title: H3K27me3_M_EB45.1

value: Eloise Butler (45)

value: Clone 45

value: male

value: Mix of ages of 3, 8 and 15 days

tag: tissue

value: whole body

value: control

tag: culturing media

value: Standard COMBO

tag: chip antibody

tag: replicate


title: donor 2_PD-L1-

description: gene expression data in PD-L1- NK cells


title: breast cancer_9 [hoae224]

value: Female

tag: histopathological examination (hpe); inflitrating lobular carcinoma (ilc); infiltrating ductal carcinoma (idc)

value: IDC

tag: cancer stage

tag: er status

value: Negative

tag: pr status

value: trucut biopsy (frozen tissue)

value: Stratagene Universal Human Reference RNA from 10 human cell lines


title: circRNA day_0_3D - donor#3 - replicate#2

city: Davos Platz

first: Martin

last: Stoddart

address: Clavadelerstrasse 8

country: Switzerland

institute: AO Research Institute Davos

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

source_name: Human mesenchymal stromal cells from bone marrow (vertebra)

label_protocol: the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000

growth_protocol: MSCs were seeded at an initial cell density of 3x103 cells/cm2 and grown until passage 2 in α-MEM with 10% MSC-qualified FBS, 100 U/mL penicillin, 100 μg/mL streptomycin and 5 ng/ml basic Fibroblast Growth Factor. Cultures were maintained at 37°C/5% CO2, and the medium was refreshed every second day.

extract_protocol: Total RNA was isolated from day 0 2D and 3D samples collected in TRIreagent following manufacturer's instructions. Briefly, 100 µl of 1-Bromo-3-chloropropane (Sigma-Aldrich, St. Louis, MO, USA) were added to TRIreagent, mixed thoroughly and the samples were centrifuged at 12000 g for 15 min at 4°C. The recovered aqueous phase was mixed with 500 µl of 2-propanol (Sigma-Aldrich) and precipitation of RNA was carried out overnight at -20°C for enhanced recovery of small RNA species. RNA pellet was then washed with 75% EtOH (Sigma-Aldrich) and resuspended in 20 µl of DEPC-treated H2O. Total RNA concentration was measured with NanoDrop 1000 (Thermo Fisher) and purity was assessed by evaluation of the A260/280 and A260/230 ratios.

treatment_protocol: Cells were further expanded in the same expansion medium. When the cells were 70% confluent, cells were collected for RNA extraction. Monolayer of cells in triplicate, grown in 25 cm2 flasks (day 0 2D), were lysed directly with 1 ml of TRIreagent. The other cells were detached with 0.05% Trypsin-EDTA and counted. For each donor, three different aliquots of 1x106 cells each (day 0 3D) were lysed in 1 ml of TRIreagent within 30 minutes from trypsinization.

tag: age of donor

value: 55 years

tag: sex of donor

tag: cell status

value: trypsinized cells


title: donor 2_PD-L1+

description: gene expression data in PD-L1+ NK cells

value: healthy donor

value: human primary NK cells

value: K562 myeloid leukemia target cells for 24 h


title: circRNA day_0_3D - donor#3 - replicate#1

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.


title: donor 1_PD-L1+

description: gene expression data in PD-L1+ NK cells

value: PD-L1+ NK cells


title: H3K27me3_F_EB45.3

tag: strain

value: Eloise Butler (45)

tag: clone

value: Clone 45

tag: gender

value: female

tag: exposure


title: donor 1_PD-L1-

description: gene expression data in PD-L1- NK cells

tag: subject status

tag: cell type

tag: co-incubation

tag: sorted fraction

value: PD-L1- NK cells


title: H3K27me3_F_EB45.1

tag: age

value: Mix of ages of 3, 8 and 15 days

tag: tissue

value: whole body

value: control

tag: culturing media

tag: chip antibody


title: d_whiA_Exponential_3

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

description: ribosomal RNA depleted

data_processing:
Torrent Suite version 5.2.2 was used for basecalling.
The sequenced reads were trimmed for adaptor sequences.
The sequenced reads were mapped using Tmap (mapall -f $db -r $readPath/$i.bam -g 3 -a 1 -n 30 -v stage1 map1 map2 map3), and counted using Htseq (-a 10 -t gene -i Name $i"_*.sam" *.gff > *_$i.txt).
The data was normalized and analysed for differential expression using R statistical software and the DESeq2 package(Love et al., 2014).
Genome_build: NC_000964.3
Supplementary_files_format_and_content: tab-delimited text files containing read counts per gene for each sample.

organism: Bacillus subtilis

source_name: batch culture

growth_protocol: Luria-Bertani (LB) medium was used for routine selection and maintenance of B. subtilis. The defined buffered minimal (Amber) medium consisted of 70 mM K2HPO4 and 30 mM KH2PO4 (adjusted to pH 7.4), 15 mM sodium chloride, 10 mM (NH4)2SO4, 0.002 mM of trace elements [ZnCl2, MnSO4, CuCl2, CoCl2 and Na2MoO4], 22 mM glucose, 0.25 mM tryptophan, 10 mM glutamate, 1 mM MgSO4, 0.1 mM calcium chloride and 0.01 mM ammonium ferric citrate. When indicated the medium was supplemented with 22 mM final concentration: malate, fumarate or citrate. All strains were grown at 37 oC at 250 rpm. B. subtilis strains used in this study are listed in Table S4.

extract_protocol:
Cells (2 ml cultures) were spun down (30 s Eppendorf centrifuge, 14,000 rpm, 4°C), resuspended in 0.4 ml ice-cold growth medium and added to a screw cap Eppendorf tube containing 1.5 g glass beads (0.1 mm), 500 ul phenol:chloroform:isoamyl alcohol (25:24:1), 50 ul 10% SDS and 50 ul RNAse free water (Hamoen et al., 2002). All solutions were prepared with diethylpyrocarbonate (DEPC)-treated water. After vortexing, tubes were frozen in liquid nitrogen and stored at -80°C. Cells were broken using a bead-beater for 4 min at room temperature. After centrifugation, the water phase was transferred to a clean tube containing 400 ul chloroform, after vortexing and centrifugation, the water phase was used for RNA isolation with High Pure RNA Isolation Kit (Roche Diagnostics GmbH, Mannheim, Germany), yielding >3 ug total RNA per sample. TapeStation System (Agilent) was used for checking the integrity of the RNA, and RIN values of 8.3 – 9.2 were obtained.
For next-generation sequencing, a ribosomal RNA depletion was performed on the total RNA using the Ribo-Zero rRNA Removal Kit (Gram-Positive Bacteria) (Illumina). Bar-coded RNA libraries were generated according to the manufacturers’ protocols using the Ion Total RNA-Seq Kit v2 and the Ion Xpress RNA-Seq barcoding kit (Thermo Fisher Scientific). The size distribution and yield of the barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1000 ScreenTapes (Agilent Technologies). Sequencing templates were prepared on the Ion Chef System using the Ion PI Hi-Q Chef Kit (Thermo Fisher Scientific). Sequencing was performed on an Ion Proton System using a Ion PI v3 chip (Thermo Fisher Scientific) according to the instructions of the manufacturer.

tag: growth

value: Exponential

tag: experiment

value: whiA markerless mutant (KS696) (Surdova et.al. 2013)

tag: replicate


title: 168_Exponential_3

description: ribosomal RNA depleted

value: wild type


title: 168_Exponential_2

description: ribosomal RNA depleted


title: H3K27me3_F_EB45.2

value: Standard COMBO


title: circRNA day_0_3D - donor#2 - replicate#1

tag: age of donor

value: 80 years

tag: sex of donor

value: Male


title: circRNA day_0_3D - donor#2 - replicate#2

tag: cell status

value: trypsinized cells


title: circRNA day_0_3D - donor#1 - replicate#2

value: 59 years


title: circRNA day_0_3D - donor#1 - replicate#1


title: breast cancer_2 [hoae197]

data_processing: The Foreground Median intensity for Cy3 and Cy5, Background Median intensity for Cy3 and Cy5, spot size data were imported into BRB-ArrayTools software using the Import wizard function. Background correction was not done. Global normalization was used to median centre the log-ratios on each array in order to adjust for differences in labelling intensities of the Cy3 and Cy5 dyes

value: Female

tag: histopathological examination (hpe); inflitrating lobular carcinoma (ilc); infiltrating ductal carcinoma (idc)

value: Infiltrating mammary carcinoma, probably ILC

tag: cancer stage

tag: er status

value: Positive

tag: pr status

tag: her2 status

value: Negative

tag: tissue origin

value: breast

tag: sample type

value: trucut biopsy (frozen tissue)

value: Stratagene Universal Human Reference RNA from 10 human cell lines


title: breast cancer_3 [hoae198]

tag: age

tag: gender

value: IDC