title: H1299__2Gy_irradiated_Lys05_48H_rep2

source_name: H1299, 2Gy_irradiated_Lys05, 48H


title: OE1_0h_H3K27me3_15u

status: Public on Feb 04 2020

type: SRA

city: Boston

first: Andrew

last: Lane

state: MA

address: 450 Brookline Ave

country: USA

institute: Dana-Farber Cancer Institute

description:
H3K27me3_ChIP-seq
processed data file: H3K27me3_OE_0h.tdf

library_source: genomic

data_processing:
Demultiplex Illumina NextSeq sequencing libraries using .bcl2fastq2-2.15.0.4.
Demultiplex reads based on barcode at the start of Read1, trim adapter barcode (the provided fastqs are trimmed).
Alignment of fastqs to mm9 using BWA.
Filter improperly paired and collapse duplicated reads from bam file.
Convert to bed files using BEDTools and call peaks using Homer.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: tdf files for IGV visualization.

molecule: genomic DNA

organism: Mus musculus

source_name: myeloid cells

growth_protocol: HMGN1 over expressing mouse myeloid cells in vitro.

extract_protocol:
Lysis and chromatin digestion with MNase (15 units or 60 units) as described in the Mint-ChIP3 protocol on https://www.protocols.io/view/mint-chip3-a-low-input-chip-seq-protocol-using-mul-wbefaje
T7 adapter ligation, linear amplification, reverse transcription and PCR as described in the Mint-ChIP3 protocol.

treatment_protocol: Over expression of control (WT) or HMGN1 (OE), and induction of differentiation by E2 depletion (0-36-96h).

tag: cell type

value: Myeloid cells

tag: genotype/variation

value: HMGN1 over expression

tag: differentiation time

tag: mnase units

tag: chip antibody

tag: replicate

value: Replicate 1


title: WT1_36h_H3K27me3_60u

description:
H3K27me3_ChIP-seq
processed data file: H3K27me3_WT_36h.tdf

value: Control


title: OE1_96h_H3K27ac_60u

description:
H3K27ac_ChIP-seq
processed data file: H3K27ac_OE_96h.tdf


title: IkBa ChIP-seq from P6 WT intestinal cells [W4CI]

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

description: No use of DSP crosslink

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC software was used to summarize the quality of the sequenced reads
Reads were aligned to the mm10 genome assembly using Bowtie2 (see materials and methods main paper)
htseq software was used to estimate the raw gene counts
peaks were called using MACS2 with the following setting: ChIP threshold FDR (0.1)
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph and bigWig files are generated from MACS2 peak calling output using bamtools

source_name: Intestine

extract_protocol:
Cells were crosslinked with 0.5% formaldehyde and lysated. Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. DNA purification with GFX Kit [GE Healthcare Life Sciences Ref.28-9034-71]
Samples were digested with 0.1% collagenase and single-cell suspension was stained as described. Different subpopulations were directly sorted in a total volume of 10  ml of reaction buffer and processed for obtaining cDNA following manufacture’s protocol. cDNA amplification was performed by Long Distance PCR (LD-PCR) and the PCR-amplified cDNA purified by immobilization on AMPure XP beads (Agencourt AMPure XP kit). Samples were analyzed with Agilent High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). Covaris shearing was used for Illumina Low input sample preparation and Double last bead purification was performed to remove fragments below 200 bp. Next, samples were used to generate an Illumina sequencing library by NEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer and total cDNA was sequenced using an Illumina HiSeq 2000 sequencer.

treatment_protocol: Starting material was directly extracted P6 intestines, which were frozen and smashed with liquid nitrogen in ceramic mortar and pestle.

tag: tissue

value: Intestine

tag: strain

tag: age

value: IkappaBalpha, Abcam ab32518


title: WT2_96h_H3K27me3_15u

description:
H3K27me3_ChIP-seq
processed data file: H3K27me3_WT_96h.tdf

value: Replicate 2


title: H1299__Lys05_48H_rep1

type: RNA

city: Hradec Kralove

first: Lucie

last: Cechakova

address: Trebesska 1575

department: Department of Radiobiology

country: Czech Republic

institute: University of Defense in Brno

hyb_protocol: Hybridization of the labelled samples to microarrays was performed using Gene Expression Hybridization Kit (Agilent). Two samples (each 900 ng), one labelled Cy3-CTP and the other Cy5-CTP, were hybridized to one microarray. Hybridization was carried out for 17 hours at 65 ° C in a rotating hybridization oven (Agilent). The microarray slide washes were performed with the Gene Expression Wash Pack (Agilent) kit on the following day.

scan_protocol: The slides were then scanned using a GenePix 4000B scanner (Molecular Devices) at a resolution of 5 μm.

data_processing: Data were processed in R. Each channel was treated as a separate sample. Data were normalized with quantile normalization and color batch effects were removed. Probes with flags in 15 of 32 slides were removed from the analysis. The experimental groups were compared with limma package with linear regression with Empirical Bayes correction. P values were adjusted for multiple testing with Benjamini-Hochberg method.

molecule: total RNA

organism: Homo sapiens

label_protocol: Synthesis of aRNA was performed from a total template RNA (500 ng) using Low Input Quick Amp Labeling Kit (Agilent) with Cy3-CTP and Cy5-CTP (GE Healthcare) fluorescence nucleotides. The labelled aRNA was purified by RNeasy Mini Kit (Qiagen) and measured spectroscopically (NanoDrop OneC, ThermoFisher).

growth_protocol: Non-small cell lung carcinoma cells (H1299) were obtained from the American Type Culture Collections (Manassas, VA, USA). The cells were cultured at 37°C in a humidified incubator under a controlled 5% CO2 atmosphere and maintained in RPMI medium 1640 (Gibco, Paisley, UK) supplemented with 10% fetal bovine serum, 150 UI/ml penicillin and 50 mg/ml streptomycin (all from Sigma-Aldrich, St. Louis, MO, USA). The culture was divided twice per week by dilution to a concentration of 2x105 cells/10ml. The cell line in the maximal range of up to 15 passages was used for this study.

extract_protocol: Total mRNA was extracted from the samples with RNeasy Mini Kit (Qiagen) according to manufacturer's instructions. Quantity of the RNA was measured spectrophotometrically with NanoDrop OneC. Quality of the RNA was evaluated with Agilent Bioanalyzer 2100 (Agilent). The samples had RIN 9.2 or above.

treatment_protocol: The cells were treated by autophagy inhibitors Lys05 (a kind gift from Dr. Amaravadi, Pennsylvania University, Philadelphia, USA) and Spautin-1 (Calbiochem, Ukraine) in various concentrations of 2, 5 and 10 μM and Baf in 15 nM concentration.  Inhibitors were added to the cells 1 hour prior to irradiation. The cells in either flask, tube, or 6-well plate, were irradiated using a 60Co gamma-ray source with a dose-rate of 0.44 Gy.min-1. After irradiation, the cells were transferred back into an incubator and cultivated further for the prescribed time according to the particular experiment.

tag: cell line

tag: treatment

tag: time


title: H1299__control_48H_rep2

source_name: H1299, control, 48H

value: control


title: SUZ12 ChIP-seq from P6 IkBa KO intestinal cells [K8SZ]

description: No use of DSP crosslink

value: SUZ12, Abcam ab12073


title: SUZ12 ChIP-seq from P6 WT intestinal cells [W1SZ]

description: No use of DSP crosslink


title: H3K27me3 ChIP-seq from P6 WT intestinal cells [W1H3]

description: No use of DSP crosslink

value: H3K27me, Millipore #07-449


title: MHCII low scMacs 5 days after nerve crush SnMac_MHCII_lo_D5_1

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description:
MHCII low scMacs 5 days after nerve crush
MHCII low scMacs 5 days after nerve crush

hyb_protocol: All Methods listed in Ydens et al.  Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system . Nature Neuroscience. 2019.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using limma Bioconductor. Normalisation was done by RMA.

label: biotin

source_name: Sciatic Nerve


title: p65 ChIP-seq from P6 IkBa KO intestinal cells [K9P6]

description: No use of DSP crosslink

value: NF-kappaB p65, abcam ab16502


title: IkBa ChIP-seq from P6 WT intestinal cells [W4DI]

description: Cells treated with DSP crosslink


title: H1299__spautin_48H_rep2

source_name: H1299, spautin, 48H

value: spautin


title: p65 ChIP-seq from P6 IkBa KO intestinal cells [K8P6]

description: No use of DSP crosslink


title: WT2_0h_H3K27me3_15u

description:
H3K27me3_ChIP-seq
processed data file: H3K27me3_WT_0h.tdf


title: H1299__2Gy_irradiated_spautin_24H_rep3

source_name: H1299, 2Gy_irradiated_spautin, 24H


title: SUZ12 ChIP-seq from P6 IkBa KO intestinal cells [K9SZ]

description: No use of DSP crosslink


title: p65 ChIP-seq from P6 WT intestinal cells [W2P6]

description: No use of DSP crosslink


title: WT1_96h_H3K27me3_15u


title: input WT

city: Milan

first: Chiara

last: Lanzuolo

address: Via Francesco Sforza 35

country: Italy

institute: CNR and Istituto Nazionale Genetica Molecolare

data_processing:
Basecalls performed using Phred33 quality score
Sequenced reads were trimmed for quality and adaptor sequence using Trimmomatic v0.32 with ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35 parameters in single-end mode
Trimmed reads were mapped to mm10 and dm6 genomes using Bowtie v1.0.1 with -m 1 parameter and PCR duplicates removed with samtools rmdup
Reads ambiguously mapping to both genomes were removed and the steps repeated for both mm10 and dm6 genomes
Genome_build: mm10, dm6
Supplementary_files_format_and_content: wiggle files with smoothed signal generated using spp R package

source_name: Muscle stem (satellite) cells_Lmna Δ8-11 +/+

extract_protocol:
cell extraction protocol: Satellite cells were isolated from hind-limb muscle and fixed before sorting using FACS
Cells were sonicated and for spike-in experiments a 5% of sheared drosophila chromatin was added to each sample. Satellite cells from pools of 6-9 mice per genotype were used
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: Lmna {delta}8-11 +/+

value: Post natal day 19

value: Muscle stem (satellite) cells


title: SUZ12 ChIP-seq from P6 WT intestinal cells [W2SZ]

description: No use of DSP crosslink


title: WT1_36h_H3K27me3_15u


title: H3K4me3 WT

value: H3K4me3 (Millipore 07-473)


title: input HOM spike-in

source_name: Muscle stem (satellite) cells_Lmna Δ8-11 -/-

value: Lmna {delta}8-11 -/-


title: input WT spike-in


title: WT1_0h_H3K27me3_15u

value: Myeloid cells


title: H3K27me3 HOM spike-in

value: H3K27me3 (Millipore 07-449)


title: H1299__2Gy_irradiated_Lys05_24H_rep3

source_name: H1299, 2Gy_irradiated_Lys05, 24H


title: OE2_96h_H3K27ac_15u

value: HMGN1 over expression


title: H1299__2Gy_irradiated_spautin_24H_rep1


title: Hx 2 RNAseq

city: Madison

first: Jyoti

last: Watters

state: WI

address: 2015 Linden Drive

department: CBS

institute: University of Wisconsin-Madison

library_source: transcriptomic

data_processing:
ChIP-seq: Base calls were made using Illumina 1.9 software
ChIP-seq: Alignment was performed by ProteinCT using bowtie2
ChIP-seq: Homer v4.8 was used to create normalized genome coverage files with duplicate removal
ChIP-seq: Homer v4.8 vwas used to generate tag directories and perform peak calling
ChiP-seq: Homer v4.8 was used to perform differential peak analysis between Nx and Hx samples
RNAseq: Base calls made using Illumina 1.9 software
RNAseq: Alignment made using Tophat v2.1
RNAseq: Differential expression analyses performed using Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: ChIP bedGraph files for each individual sample and consensus files for all samples in treatment;

source_name: N9 microglia

growth_protocol: N9 microglia cultured in DMEM and supplemented with 10% fetal bovine serum and 1% penicillin streptomycin

extract_protocol:
For ChIP-seq, lysates were sonicated manually and cleared prior to antibody incubation.For RNA seq, cells were lysed in Trizol.
ChIP-seq libraries prepared according to Illumina's instructions; RNA stranded libraries prepared according to Illumina protocols

treatment_protocol: Cells were treated for 16 hours with either 1% O2 or 21% O2, in an incubator maintained at 5% CO2 and 37 °C.

value: Hypoxia

tag: passages


title: Hx 3 RNAseq


title: H1299__2Gy_irradiated_control_24H_rep2

source_name: H1299, 2Gy_irradiated_control, 24H


title: p65 ChIP-seq from P6 WT intestinal cells [W1P6]

description: No use of DSP crosslink

value: Intestine


title: Hx 1 RNAseq


title: Nx 3 RNAseq

value: Normoxia


title: H1299__2Gy_irradiated_Lys05_24H_rep1


title: Nx 2 RNAseq


title: OE2_0h_H3K27ac_15u

description:
H3K27ac_ChIP-seq
processed data file: H3K27ac_OE_0h.tdf

value: Replicate 2


title: H1299__Lys05_24H_rep2


title: Nx 1 RNAseq


title: Hx 3 10% Input


title: H1299__control_24H_rep3

source_name: H1299, control, 24H

value: control


title: H1299__spautin_24H_rep1

source_name: H1299, spautin, 24H


title: Nx 3 10% Input


title: Hx 2 10% Input


title: OE1_36h_H3K27ac_15u

description:
H3K27ac_ChIP-seq
processed data file: H3K27ac_OE_36h.tdf

value: Replicate 1


title: H1299__2Gy_irradiated_control_1H_rep3

source_name: H1299, 2Gy_irradiated_control, 1H


title: OE2_36h_H3K27ac_15u


title: Hx 1 10% Input


title: H1299__control_24H_rep1


title: Nx 1 10% Input


title: Hx 3 H3K4me3_ChIPSeq

tag: antibody

value: Abcam ab8580


title: H1299__2Gy_irradiated_spautin_1H_rep2

source_name: H1299, 2Gy_irradiated_spautin, 1H


title: Hx 1 H3K4me3_ChIPSeq


title: Nx 3 H3K4me3_ChIPSeq


title: Nx 2 H3K4me3_ChIPSeq


title: WT2_96h_H3K27ac_15u

description:
H3K27ac_ChIP-seq
processed data file: H3K27ac_WT_96h.tdf

value: Control


title: Nx 2 10% Input


title: WT2_0h_H3K27ac_15u

description:
H3K27ac_ChIP-seq
processed data file: H3K27ac_WT_0h.tdf


title: OE1_0h_H3K27ac_15u


title: OE1_96h_H3K27ac_15u


title: WT2_36h_H3K27ac_15u

description:
H3K27ac_ChIP-seq
processed data file: H3K27ac_WT_36h.tdf


title: H3K27me3 WT spike-in


title: WT1_96h_H3K27ac_15u


title: Nx 1 H3K4me3_ChIPSeq


title: WT1_36h_H3K27ac_15u


title: H1299__2Gy_irradiated_control_1H_rep1


title: Hx 2 H3K4me3_ChIPSeq


title: H1299__2Gy_irradiated_Lys05_1H_rep2

source_name: H1299, 2Gy_irradiated_Lys05, 1H


title: H1299__spautin_1H_rep2

source_name: H1299, spautin, 1H

value: spautin


title: Brain microglia, replicate 5

description: Brain microglia, replicate 5

data_processing:
Image analysis and base calling resulted in .bcl files, which were converted into .fastq files with the CASAVA1.8.2 software.
No Quality Trimming was done.
Star was used for mapping with Star version 2.5.2b and the following command line: STAR --runThreadN 10 --genomeDir XXX --genomeLoad LoadAndKeep --limitBAMsortRAM 20000000000 --readFilesIn SampleFastQs --readFilesCommand zcat --outFileNamePrefix YYY --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --seedSearchStartLmax 30 --outSAMtype BAM SortedByCoordinate
featureCounts v1.5.1 was used for count file generation with the following command line: featureCounts –a GTFFile –G FASTAFile –o OutFile -p -F GTF -g gene_name -t exon -T 10 –largestOverlap
Genome_build: Gencode M11 was used for mapping and counting (mm10)
Supplementary_files_format_and_content: tab-delimited text files including raw counts for each sample

source_name: Brain

growth_protocol: All Methods listed in Ydens et al.  Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system . Nature Neuroscience. 2019.


title: OE2_96h_H3_15u

description:
H3_ChIP-seq
processed data file: H3_OE_96h.tdf

source_name: myeloid cells


title: Brain microglia, replicate 4

description: Brain microglia, replicate 4

extract_protocol: All Methods listed in Ydens et al.  Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system . Nature Neuroscience. 2019.


title: H1299__spautin_1H_rep3


title: OE2_36h_H3_15u

description:
H3_ChIP-seq
processed data file: H3_OE_36h.tdf


title: H1299__control_1H_rep2

source_name: H1299, control, 1H


title: Brain microglia, replicate 2

description: Brain microglia, replicate 2


title: Brain microglia, replicate 3

description: Brain microglia, replicate 3


title: OE2_0h_H3_15u

description:
H3_ChIP-seq
processed data file: H3_OE_0h.tdf


title: AG83

city: Kolkata

first: Syamal

last: Roy

state: West Bengal

address: Chunilal Bhawan 168, Maniktala Main Road, Kol

department: Infectious Disease and Immunology

country: India

institute: Former: CSIR-IICB, Present: NIPER, Kolkata

hyb_protocol: Microarray analysis was done on a Custom Agilent One color (AMADID: 035638(L. donovani)) platform using total RNA isolated from SbRLD or SbSLD

scan_protocol: iLife Discoveries (Gurgaon, India) performed the analysis, and the data were analyzed after background noise correction and normalization. Differential mRNA expression, fold change analysis and cluster analysis was done using GeneSpring GX12.6 and Genesis software. All the data have been filtered based on detection; differential p value ≤ 0.05.

data_processing: The background correction and normalization was done using limma library in R3.5.0

organism: Leishmania donovani

source_name: Client ID 8

label_protocol: Cy3 labelling was used with Custom Agilent One color (AMADID: 035638(L. donovani)

growth_protocol: Three clinical isolates representing SbRLD (BHU575, BHU814 and BHU138_Clone1) and three clinical isolates representing SbSLD (BHU77, BHU581 and BPK206) along with sensitive reference strain Ag83 and reference resistant BHU138_Clone2 were grown in 75cm2 tissue culture flask.

extract_protocol: The total RNA was extracted using standard Trizol method

treatment_protocol: There was no treatment done to the cells. This experiment was designed to check the differences between the resistant and sensitive strains.

tag: group


title: BHU 138_Clone2

description: BHU 138_Clone2

source_name: Client ID 7


title: OE1_96h_H3_15u


title: WT1_0h_H3K27ac_15u


title: BHU 581

description: BHU 581

source_name: Client ID 5

value: Sensitive


title: BPK 206

description: BPK 206

source_name: Client ID 6


title: BHU 777

description: BHU 777

source_name: Client ID 4


title: H1299__Lys05_1H_rep1


title: BHU 138_Clone1

description: BHU 138_Clone1

source_name: Client ID 3

value: Resistant


title: BHU 814

description: BHU 814

source_name: Client ID 2


title: OE1_36h_H3_15u


title: Sciatic nerve macrophage, replicate 4

description: Sciatic nerve macrophage, replicate 4

source_name: Sciatic nerve


title: OE1_0h_H3_15u


title: BHU 575

description: BHU 575

source_name: Client ID 1


title: WT2_96h_H3_15u

description:
H3_ChIP-seq
processed data file: H3_WT_96h.tdf


title: Sciatic nerve macrophage, replicate 2

description: Sciatic nerve macrophage, replicate 2


title: WT2_36h_H3K27me3_15u


title: Sciatic nerve macrophage, replicate 1

description: Sciatic nerve macrophage, replicate 1


title: Brain microglia, replicate 1

description: Brain microglia, replicate 1


title: Optic nerve macrophage, replicate 4

description: Optic nerve macrophage, replicate 4

source_name: Optic nerve


title: Optic nerve macrophage, replicate 3

description: Optic nerve macrophage, replicate 3


title: WT2_36h_H3_15u

description:
H3_ChIP-seq
processed data file: H3_WT_36h.tdf


title: WT1_96h_H3_15u


title: WT1_36h_H3_15u


title: WT2_0h_H3_15u

description:
H3_ChIP-seq
processed data file: H3_WT_0h.tdf


title: OE2_96h

data_processing:
alignment: HiSat using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. FPKM values were ERCC normalized. See methods for further details
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file matix containing raw FPKM values for each transcript

molecule: polyA RNA

extract_protocol:
Trizol RNA
TruSeq RNA Library Preparation Kit v2, Set A

tag: Stage


title: Optic nerve macrophage, replicate 1

description: Optic nerve macrophage, replicate 1


title: Control_9_Semen_WGBS

city: New York

first: Deli

last: Liu

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

description: WGBS

data_processing:
WGBS data were aligned to the bisulfite-converted hg19 reference genome using Bismark v0.19.020. We extracted methylation status with the bismark methylation extractor script in Bismark.
Only CpGs with at least three reads covering them were used for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Bismark methylcall output files are in .txt format

source_name: Semen samples

extract_protocol:
The study protocol was approved by the Ethics Committee of Fujian Province Hospital and all volunteers provided written informed consent. 17 volunteers were asked to donate semen. They were requested to abstain from ejaculation for at least 3 days, but no more than 10 days prior to their visit. Semen samples were collected from age-matched male volunteers in their reproductive age (20-45 years). 9 were controls with no diabetes (Fasting plasma glucose 3.9-6.1mmol/L) and 8 were T2DM patients (Fasting plasma glucose > 6.1mmol/L). Study cohorts are further detailed in Supplemental Information: Table S1.
The DNA of seventeen Semen samples was isolated using a tissue/cell genome DNA isolation kit (Aidlab Biotechnlogies co., Ltd.), according to the manufacturer's protocol. The quality of the genomic DNA was checked with a NANODROP UV-2100 DNA analyzer (Amersham, USA), and then bisulfite conversion was performed using the EZ DNA Methylation-Gold Kit (ZYMO) according to the manufacturer's instructions. Genomic DNA was fragmented by ultrasonication.
The fragments were then end-repaired, 3-end-adenylated and ligated with adapters. 2% agarose gel electrophoresis was used to select fragments of 200-250 bp in length. The selected fragments were treated with bisulfite and subjected to PCR amplification to form the sequencing library. Then, the qualified library was sequenced using an IlluminaHiSeq™2500 system (BGI, Beijing, China). The peak signal produced by the Illumina HiSeq was transformed into base sequence by base calling as Raw Data or Raw Reads. The Raw Reads were then filtered for subsequent information analysis to ensure the quality of information analysis, including the removal of reads that have adapters and filtration of reads with more than 10% N content or more than 50% low quality bases. The final filtered data are called clean reads.

treatment_protocol: No treatments were applied prior to genomic DNA extraction

value: semen

tag: disease state

value: non-diabetic control


title: Sciatic nerve macrophage, replicate 3

description: Sciatic nerve macrophage, replicate 3


title: Optic nerve macrophage, replicate 2

description: Optic nerve macrophage, replicate 2


title: OE1_96h


title: WT2_96h


title: WT1_96h


title: Control_8_Semen_WGBS

description: WGBS


title: Control_7_Semen_WGBS

description: WGBS


title: OE2_36h


title: WT1_0h_H3_15u

tag: cell type

tag: genotype/variation


title: Control_5_Semen_WGBS

description: WGBS


title: OE1_36h


title: Control_6_Semen_WGBS

description: WGBS


title: WT2_36h


title: S60_9

city: Princeton

first: Ian

middle: Michael

last: Traniello

state: NJ

address: Princeton University

department: Lewis-Sigler Insitute for Genomic Biology

institute: Princeton University

data_processing:
FASTQ files were aligned to the honey bee genome using STAR 2.5.3a.
Raw counts were generated using the "featureCounts" function in Sumbread 1.5.2
Genome_build: Amel_HAv3.1

organism: Apis mellifera

source_name: mushroom bodies

growth_protocol: Honey bee (Apis mellifera) drones were obtained from colonies maintained in apiaries according to standard commercial methods by the University of Illinois Bee Research Facility, Urbana, IL. For the RNA-Seq experiment, only one colony was used. One-day-old adult drones were obtained by removing frames of honeycomb containing pupae from colonies, placing them in an incubator (34°C, 50% relative humidity), and then monitoring their emergence every 24 h.

extract_protocol:
Heads were removed while frozen and incubated for 16 h in RNAlater ICE (Ambion). Brains were dissected to obtain samples containing the MB and surrounding nuclei, following an established protocol (Sen Sarma et al., 2009; Lutz and Robinson, 2013; McNeill et al., 2016). RNA was extracted using Picopure RNA isolation kits (Applied Biosystems)
Poly-adenylated RNA was enriched using Oligo(dT)25 Dynabeads (Thermo Fisher Scientific). RNA was fragmented and converted to cDNA (as per instructions in the NEXTflex Directional RNA-Seq Kit, Bioo Scientific Corporation). Average fragment sizes were estimated with a BioAnalyzer High Sensitivity DNA assay (Agilent Technologies). cDNA libraries were labeled with NEXTflex RNA-Seq Barcodes for multiplexing during sequencing. Final cDNA library concentrations were estimated using a Qubit (Thermo Fisher Scientific), and then eight barcoded libraries were pooled for sequencing, preserving information to allow data to be resolved at the individual bee level. The total concentration of all adapter-ligated fragments within each assembled library pools was confirmed using KAPA Library Quantification kits (Kapa Biosystems). The pooled libraries were sequenced on a HiSeq 2000 (Illumina) at the W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign.

treatment_protocol: Drones were either administered a sucrose reward or a water control and collected 60 min later.

value: sucrose

value: mushroom bodies

tag: caste

value: drone

tag: time collected

value: 60 min

tag: colony

value: RX

tag: percent dwv


title: Control_4_Semen_WGBS

description: WGBS

tag: tissue


title: S60_8


title: WT1_36h


title: S60_30


title: OE1_0h


title: Control_3_Semen_WGBS

description: WGBS


title: Control_2_Semen_WGBS

description: WGBS


title: T2DM_8_Semen_WGBS

description: WGBS

value: type 2 diabetes mellitus (T2DM)


title: Control_1_Semen_WGBS

description: WGBS


title: T2DM_7_Semen_WGBS

description: WGBS


title: S60_25


title: S60_27


title: S60_26


title: S60_15


title: S60_14


title: S60_6


title: S60_13


title: OE2_0h


title: WT1_0h


title: T2DM_6_Semen_WGBS

description: WGBS


title: C60_9


title: C60_8


title: fibro_st_S5P_ChIP-MNase

city: Nice

first: Dominic

last: van Essen

address: 28 Avenue Valombrose

country: France

institute: Institute for Research on Cancer & Aging, Nice (IRCAN)

data_processing:
alignment to mm9 reference genome (bowtie v 2 -a -m 5 --tryhard)
removal of duplicates (reads that mapped to the exact same genomic location were eliminated if there were significantly more than expected based on the local read density in a range of ±2bp at a p-value of 0.05)
selection of reads mapping to refGene promoters ±10kb (intersectBed)
normalization (read counts in overlapping 60bp windows at 10bp intervals were normalized by the local read density in the surrounding 600bp window)
mapping around promoters (mean normalized signal in 3 adjacent bins was calculated at 10bp intervals surrounding and centred-on refGene promoters ±1kb)
Genome_build: mm9
Supplementary_files_format_and_content: matrix files = gzip-compressed files of comma-separated values, representing normalized nucleosome occupancy at 10bp intervals surrounding refGene promoters, beginning at position -1000bp and ending at position +1000bp relative to the direction of transcription; promoter_data.bed file = list of refGene promoters used in BED+4 format, score indicates ChIP-MNase coverage level, additional fields indicate FPKM expression in DCs & fibroblasts, and log2-fold stimulus-driven activatio of inducible genes n in DCs & fibroblasts; example.r = example R script using matrix files & promoter_data.bed file to analyse nucleosome occupancies at distinct classes of genes.

source_name: 3T3 fibroblasts, 1hr after TNF-alpha treatment

extract_protocol:
Cells were fixed for 10minutes with 4% formaldehyde and used to prepare chromatin.  Chrromatin was fragmented to approximately 5-10kb fragments and used for ChIP.  ChIP-enriched chromatin was then digested using micrococcal nuclease (MNase) to generate approximately 80% mononucleosomal fragments.
NebNext Ultra II DNA library kit

value: 3T3 fibroblast

tag: bafkd

value: no

value: TNFa 5ng/ml

tag: chip target

value: RNA pol II S5P


title: T2DM_5_Semen_WGBS

description: WGBS


title: T2DM_4_Semen_WGBS

description: WGBS


title: WT_Adam10inhibitor

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Ave, Room 1080

country: Canada

institute: Lunenfeld- Tanenbaum Research Institute

description: Cut&Run

data_processing:
Library strategy: Cut&Run
Reads aligned to mm10 usingHisat2 (2.1.0) with parameters --no-spliced-alignment and --no-unal
Duplicate reads removed with Picard; Non-uniquely aligned reads removed (hisat flag ZS:i), Remove reads aligned to ambiguous chromosomes; remove reads in mm10 blacklist regions (https://www.nature.com/articles/s41598-019-45839-z).
CPM normalization using bedtools genomecov with -scale x (x = 1/million aligned reads).
IgG signal was removed from corresponding sample file using macs2 bdgcmp -m subtract and mac2 bdgpeakcall was used to call peaks.
Custom script was used to calculate area under the peaks (AUC) from bedgraph signal files.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_peaks.bed: Peak file in bed format. Column 4: Peak AUC, column 5: Peak summit pileup.

source_name: Cultured Mouse Keratinocytes

extract_protocol:
Zymoresearch DNA purification kit.
DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: EDTA for 30mins, 15 mins recovery in growth media.

value: Primary keratinocytes culture

value: abcam RBPJ ChIP grade Ab (cat # 25949)


title: C60_27

tag: treatment

value: control


title: C60_14


title: C60_26


title: T2DM_3_Semen_WGBS

description: WGBS


title: AjubaKO

description: Cut&Run


title: C60_6


title: T2DM_2_Semen_WGBS

description: WGBS


title: WT_EDTA

description: Cut&Run


title: C60_30


title: C60_25


title: C60_13


title: A77 1726 +Nucleotides 25uM_r3

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description:
hg19_A375_PROseq_A77Nuc_N3_spikenorm_dedup_F.bedGraph.gz
hg19_A375_PROseq_A77Nuc_N3_spikenorm_dedup_R.bedGraph.gz

data_processing:
Base calling and generation of FASTQ files performed using standard bcl2fastq2 for NextSeq  PRO-seq read pairs containing one or more members with mean quality score <20 filtered and trimmed to 50nt, for adapter using cutadapt 1.14, pairs containing reads trimmed shorter than 20 nt filtered  PRO-seq mapped to index composed of spike-in genome (dm3), successfully aligned pairs filtered, remaining mapped to reference (hg19) using bowtie 1.2.2 retaining uniquely mappable pairs only, allowing 2 mismatches  PROseq strand-specific bedGraphs generated using custom scripts based on 3' mapping location, with all replicates combined;
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

source_name: A375 cell lines

growth_protocol: Human A375 malignant melanoma cells (ATCC) are grown on standard tissue culture plates in filter sterilized DMEM (Life Technologies) with 10% heat-inactivated FBS (Atlanta Biologicals), 1X GlutaMAX (Life Technologies) and 1% Penicillin-Streptomycin (Life Technologies).

extract_protocol:
Cells were washed in PBS. Cells were detached using accutase and collected in 50ml tube. Cells were spin 300gx4mins washed with washing buffer :10mM Tris-Cl, pH 8.0, 10mM KCl, 250mM sucrose, 5mM MgCl2, 0.5mM DTT, 10% Glycerol. Cells were spin again and then resuspended in permeablization buffer (Washing+0.1% Igepal). Cells were incubated 2mins at RT and then spin again and resupended in Freezing buffer (50mM Tris-CL pH 8.3, 40% glycerol, 5mM MgCl2, 0.5mM DTT. Nuclei were counted and aliquoted in 1million/tube and flash frozen.
using 1 million cells per sample. Samples were spiked with 40,000 Drosophila S2 cells as a normalization spike-in control. Samples were sequenced on the NextSeq using a High Output 75-cycle kit, generating paired end 42 nt reads. Libraries were sequenced to an average read depth of 10 million mappable reads per sample.
Pro-Seq

treatment_protocol: 10 million A375 cells per condition were treated with DMSO or 25 μM A771726.  After a 24 hr treatment, nuclei were isolated counted carefully and 5x1Million aliquotes were prepared for test and library prep.

tag: cell line


title: T2DM_1_Semen_WGBS

description: WGBS


title: WT2_0h

source_name: myeloid cells


title: A77 1726 +Nucleotides 25uM_r2


title: A77 1726 25uM_r3

description:
hg19_A375_PROseq_A77_N3_spikenorm_dedup_F.bedGraph.gz
hg19_A375_PROseq_A77_N3_spikenorm_dedup_R.bedGraph.gz


title: A77 1726 +Nucleotides 25uM_r1


title: Adam10_Hom_Tumor_Rep2

description: processed data file: Tumors_Adam10_KO_deseq2.xlsx

data_processing:
Reads were aligned to mm10 using Hisat2 (2.1.0).
Raw reads obtained from bam files using featureCounts and mm10 annotation file from Ensembl (Mus_musculus.GRCm38.94.gtf).
DESeq2 package in R was used to determine differentially expressed genes between samples.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_deseq2.xlsx: Differential gene expression analysis

source_name: CD104+ SCC Tumors

extract_protocol:
Zymoresearch RNA Extraction Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Primary tumor cells

tag: marker


title: A77 1726 25uM_r2


title: A77 1726 25uM

data_processing:
Following paper was followed B. J. Zarnegar et al., irCLIP platform for efficient characterization of protein-RNA interactions. Nat Methods 13, 489-492 (2016)
Genome_build: GRCh38
Supplementary_files_format_and_content: BigWig files containing RT stops normalized to 10,000,000 reads total across all files

extract_protocol:
Following paper was followed B. J. Zarnegar et al., irCLIP platform for efficient characterization of protein-RNA interactions. Nat Methods 13, 489-492 (2016)
Following paper was followed B. J. Zarnegar et al., irCLIP platform for efficient characterization of protein-RNA interactions. Nat Methods 13, 489-492 (2016)
irCLIP

treatment_protocol: 60 million A375 cells per condition were treated with DMSO or 25 μM A771726.  After a 24 hr treatment, cells were UV crosslinked to a total of 0.35 J/cm2


title: Adam10_Hom_Tumor_Rep1


title: dmso_r2

description:
hg19_A375_PROseq_DMSO_N3_spikenorm_dedup_F.bedGraph.gz
hg19_A375_PROseq_DMSO_N3_spikenorm_dedup_R.bedGraph.gz


title: dmso


title: A77 1726 +Nucleotides 25uM


title: Adam10_Het_Tumor_Rep3


title: dmso_r1


title: A77 1726 25uM_r1


title: A77+Nucleotides_48hrs_r3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to hg19 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: hg19
Supplementary_files_format_and_content: excel files include RPKM values for each Sample ...

extract_protocol:
Treated A375  cells were washed and libearse was used.  Total RNA was extracted with TrizolPlus RNeasy mini kit from Qiagen.
Total RNA was depleted of ribosomal RNA with the RiboZero gold kit (Epicentre). Enriched mRNA was then applied to library preparation according to manufacturer’s protocol (NEBNext Ultra). After repeated quality control for average DNA input size of 300 bp, the samples were sequenced on a HiSeq Illumina sequencer with 2x100bp paired-end reads.

treatment_protocol: 1 million A375 cells per condition were treated with DMSO or 25 μM A771726.  After a 24 hr  or 48hrs treatment, cells were fixed in 11% formaldehyde and subjected to chromatin immunoprecipitation with DDX21 (Novus Biologicals) or Cdk9 (C-20),

tag: sample type

value: rRNA depleted RNA


title: MO9: kera_diff_donor4

type: genomic

city: Nijmegen

first: Jos

last: Smits

state: Gelderland

address: Rene Descartesdreef 1

department: Dermatology

country: Netherlands

institute: Radboudumc

hyb_protocol: bisulphite converted DNA was fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: rnbeads, methylumi norm; Limma M value differential expression

source_name: primary keratinocytes, fully differentiated status

label_protocol: Standard Illumina Protocol

growth_protocol: primary keratinocytes were cultured in KGM +growth factors untill ~50% confluency (proliferation status) or allowed to reach 100% confluency, switch to KGM lacking growth factors, and allowed to differentiate for an additional 6 days

extract_protocol: DNA was extracted using the QIAamp DNA blood mini kit according to the manufacturers protocol

treatment_protocol: primary keratinocytes were cultured to 50% confluency (proliferation status) or allowed to full differentiate (fully differentiated status)

value: skin

value: primary keratinocytes


title: SWH

city: Urrbrae

first: Haipei

state: South Australia

address: PMB1 Waite Building, School AFW

country: Australia

institute: The University of Adelaide

data_processing:
Sequencing analysis was performed using the in-house ACGT101-miR program (LC Sciences, Houston, Texas, USA). Raw sequencing reads were first processed by removing low-quality reads and adapter sequences to obtain clean sequences.
Reads with a nucleotide (nt) length <18nt or > 25nt were removed.
Common non-coding RNA families (rRNA, tRNA, snRNA and snoRNA), repeats and mRNA sequences were then discarded using RFam, Repbase and durum wheat NCBI mRNA entries as references. Unique sRNA sequences were then obtained for each library.
Conserved mature miRNAs and 3p- or 5p- derived miRNA variants were identified by BLAST search against miRNA precursors in the miRBase (Release 22.1).
The remaining unmatched sRNA sequences were used to identify novel durum miRNAs. Sequences were BLASTed to the durum wheat genome. To identify miRNA precursors, secondary hairpin structures containing matched sequences were predicted using RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi) from 120 nt of flanking genome sequences. The following criteria were used for the prediction of secondary structure: 1) the length of hairpin (two stems and the terminal loop) is ≥50nt; 2) the length of the hairpin loop region is ≤200 nt; 3) the cut-off of free energy is ≤-15kCal/mol; 4) the stem region of the predicted hairpin is ≥16 bp in length; 5) for each bulge in the stem, the nucleotide length is ≤12 nt; 6) for each bulge in the mature region of the predicted hairpin, the nucleotide length is ≤4 nt; 7) the number of biased match in each bulge in the mature region is ≤2; (8) the number of biased bulges in the mature region is ≤2; 9) the number of mismatches in the mature region is ≤4; 10) the mature region is ≥12 bp in length; and 11) the mature region in the stem is ≥80%.
Genome_build: Triticum turgidum subsp. durum assembly Svevo.v1, 3439611 [UID], 11200738 [GenBank]
Supplementary_files_format_and_content: Expression value (raw and normalised count) of all miRNAs in four libraries

organism: Triticum turgidum subsp. durum

source_name: Durum wheat young seedlings

growth_protocol: For each group, 16 randomly selected germinated seeds were transferred into pots (one seedling per pot). Each pot contained 1.2 kg of N40 sand with 0.5% CaCO3 and nutrient solution was provided. Seedlings were grown under controlled glasshouse conditions with day/night temperature of 24˚C/18˚C and a photoperiod of 16 h/8 h.

extract_protocol:
Total RNA was extracted from young seedlings using Tri reagent (Sigma-Aldrich) and treated with TURBO DNase (ThermoFisher Scientific) following the manufacturer’s instructions. The concentration and quality of RNA samples were measured on a NanoDrop Lite spectrophotometer (ThermoFisher Scientific). RNA integrity was assessed by agarose gel electrophoresis and a Bioanalyzer (RIN > 9).
Total RNA from eight biological replicates in each group were pooled for small RNA sequencing. Four small RNA libraries (TCG, TWH, SCG, SWH) were constructed using the TruSeq Small RNA Sample Prep Kit from the four groups. Single-end sequencing (50bp) was performed on an Illumina HiSeq2500 by LC-Bio (Hangzhou, China).

treatment_protocol: Seedling height, shoot fresh weight and root fresh weight were measured on 12-day old seedlings. Shoot dry weight and root dry weight were measured after overnight oven drying at 65˚C. Fresh shoots were collected and snap-frozen in liquid nitrogen for RNA extraction. Eight biological replicates were used for seedling measurements and eight biological replicates were used for RNA extraction.

tag: genotype

tag: parent treatment

value: Water-deficit and heat stress

value: shoot


title: Adam10_Het_Tumor_Rep2


title: MO3: kera_prolif_donor3

source_name: primary keratinocytes, proliferation status


title: SCG

value: Control


title: MO10: kera_diff_donor5


title: TWH

value: DBA Aurora


title: Adam10_Het_Tumor_Rep1


title: MO8: kera_diff_donor3


title: TCG


title: WT_Tumor_Control2


title: A77+Nucleotides_48hrs_r1


title: A77+Nucleotides_48hrs_r2


title: A771726_48hrs_r3


title: R45_9_3_9_W

data_processing:
FASTQ files were aligned to the honey bee genome using STAR 2.5.3a.
Raw counts were generated using the "featureCounts" function in Subread 1.5.2
Genome_build: Amel_HAv3.1

source_name: whole brain

growth_protocol: Honey bee (Apis mellifera) workers were obtained from colonies maintained in apiaries according to standard commercial methods by the University of Illinois Bee Research Facility, Urbana, IL. For the RNA-Seq experiment, two colonies were used, each headed by a queen artificially inseminated with semen from a single drone. One-day-old adult drones were obtained by removing frames of honeycomb containing pupae from colonies, placing them in an incubator (34°C, 50% relative humidity), and then monitoring their emergence every 24 h.

extract_protocol:
Bee heads were separated from bodies on dry ice and placed in a dissection dish with pure ethanol and dry ice to prevent RNA degradation during dissection. The cuticle of the head capsule was removed and each head was placed in RNAlaterICE (Life Technologies) at -20ºC for 14 to 18 h. The heads were then opened, the hypopharyngeal glands removed, and the whole brain removed. Using a fine scalpel, the optic lobes were removed and a horizontal incision was made across the midbrain through the posterior protocerebral lobe. The lower part of the midbrain containing the antennal lobes and the subesophageal ganglion were removed. The upper part of the midbrain containing mostly the mushroom bodies (MB) and the central brain was used for gene expression analysis. The MBs were placed in a new 1.5ml tube and kept frozen (-80°C) until RNA extraction. RNA extraction was performed with a PicoPure RNA Isolation Kit (Applied Biosystems; Lot #: 1210063) and the standard protocol, including DNase treatment (QIAGEN) to remove genomic DNA contamination.
RNA-Seq libraries were constructed with the TruSeq® Stranded mRNA HT (high throughput kit, Illumina cat #: RS-122-2103) using an ePMotion 5075 robot (Eppendorf) The libraries were pooled in equimolar concentration as per instructions and each pool was quantitated by qPCR. Paired-end sequencing (read length = 100nt) was performed on an Illumina HiSeq2000 using a TruSeq SBS sequencing kit version 3.

treatment_protocol: Workers

value: worker

value: brain


title: MO5: kera_prolif_donor5


title: R45_9_3_9_GOL


title: R45_9_3_8_BY


title: WT_Tumor_Control1


title: A771726_48hrs_r2


title: A771726_48hrs_r1


title: MO6: kera_diff_donor1


title: Nucleotide_48hrs_r2


title: R45_9_3_6_B


title: R45_9_3_8_BC


title: dmso_r3


title: MO4: kera_prolif_donor4


title: R45_9_3_8_B


title: MO7: kera_diff_donor2


title: MO2: kera_prolif_donor2


title: R45_9_3_5_GY


title: MO1: kera_prolif_donor1


title: R45_9_3_6_BO


title: MCF10DCIS.com tet-pLKO.1-puro-shNRF2v1 Day 10 spheroids replicate 1

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

data_processing:
Adapters were trimmed using fastq-mcf in the EAutils package (version ea-utils.1.1.2-537) with the following options: -q 10 -t 0.01 -k 0 (quality threshold 10, 0.01% occurrence frequency, no nucleotide skew causing cycle removal).
Datasets were aligned to the human (GRCh38.86) genome using HISAT2 with the option: --rna-strandness RF (for paired end reads generated by the TruSeq strand-specific library).
Alignments were assembled into transcripts using Stringtie (version 1.3.4) with the reference guided option
Supplementary_files_format_and_content: tab separated files- read counts resulting from HISAT2 alignment and TPM normalization resulting from Stringtie

source_name: MCF10DCIS.com 3D spheroids

growth_protocol: MCF10A-5E and MCF10DCIS.com spheroids were grown atop Matrigel, cultured in MCF10A assay media with media refeed every 4 days.

extract_protocol:
RNA was extracted at Day 10 of 3D culture by lysing individual wells in 500 μl RNA STAT-60
Total RNA was diluted to 50 ng/μl and prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina).

treatment_protocol: Cells were pretreated with 1 µg/ml doxycycline for three days before 3D culture and doxycycline was maintained in the 3D culture medium throughout the experiment to induce short hairpin RNA expression


title: Nucleotide_48hrs_r3


title: MCF10DCIS.com tet-pLKO.1-puro-shNRF2v1 Day 10 spheroids replicate 2


title: WT

description: Cut&Run

tag: antibody


title: R45_9_3_5_GW


title: R45_9_3_6_BC


title: MCF10DCIS.com tet-pLKO.1-puro-shNRF2v1 Day 10 spheroids replicate 4


title: MCF10DCIS.com tet-pLKO.1-puro-shNRF2v1 Day 10 spheroids replicate 3


title: MCF10DCIS.com tet-pLKO.1-puro-shLacZv3 Day 10 spheroids replicate 4


title: R45_9_3_3_G


title: R45_9_3_2_BY


title: Nucleotide_48hrs_r1


title: MCF10DCIS.com tet-pLKO.1-puro-shLacZv3 Day 10 spheroids replicate 3


title: R45_9_3_2_B


title: MCF10DCIS.com tet-pLKO.1-puro-shLacZv3 Day 10 spheroids replicate 2


title: dmso_48hrs_r2


title: R45_9_3_1_GW


title: R45_9_3_1_GY


title: dmso_48hrs_r1


title: MCF10DCIS.com tet-pLKO.1-puro-shLacZv3 Day 10 spheroids replicate 1


title: A77+Nucleotides_24hrs_r3


title: R45_9_11_9_GW


title: R45_9_11_8_Y


title: R45_9_3_3_GO


title: R45_9_11_8_GY


title: MCF10A-5E tet-pLKO.1-puro-shNRF2v4 Day 10 spheroids replicate 2

source_name: MCF10A-5E 3D spheroids


title: MCF10A-5E tet-pLKO.1-puro-shNRF2v4 Day 10 spheroids replicate 4


title: A77+Nucleotides_24hrs_r2


title: R45_9_11_8_W


title: R45_9_11_4_BY


title: R45_9_11_8_GO


title: A77+Nucleotides_24hrs_r1


title: A771726_24hrs_r2


title: A771726_24hrs_r3


title: R45_9_11_4_B


title: MCF10A-5E tet-pLKO.1-puro-shNRF2v4 Day 10 spheroids replicate 3


title: MCF10A-5E tet-pLKO.1-puro-shNRF2v4 Day 10 spheroids replicate 1


title: R45_9_11_3_GY


title: MCF10A-5E tet-pLKO.1-puro-shNRF2v1 Day 10 spheroids replicate 4


title: R45_9_11_3_GW


title: R45_9_11_2_BO


title: A771726_24hrs_r1


title: Nucleotide_24hrs_r3


title: R45_9_11_11_G


title: AjubaKO_EDTA

description: Cut&Run


title: R45_9_3_10_BO


title: MCF10A-5E tet-pLKO.1-puro-shNRF2v1 Day 10 spheroids replicate 2


title: R45_9_11_12_BY


title: R45_9_11_12_C


title: dmso_48hrs_r3


title: MCF10A-5E tet-pLKO.1-puro-shNRF2v1 Day 10 spheroids replicate 1


title: R45_9_11_10_BY


title: R45_9_11_10_B


title: R45_9_11_11_GO


title: Nucleotide_24hrs_r1


title: R45_9_11_10_BO


title: Nucleotide_24hrs_r2


title: MCF10A-5E tet-pLKO.1-puro-shGFP Day 10 spheroids replicate 4

value: shGFP


title: MCF10A-5E tet-pLKO.1-puro-shNRF2v1 Day 10 spheroids replicate 3


title: R45_9_11_2_O


title: R45_9_10_9_G


title: MCF10A-5E tet-pLKO.1-puro-shGFP Day 10 spheroids replicate 3


title: R45_9_10_9_BC


title: R45_9_10_7_G


title: dmso_24hrs_r3


title: dmso_24hrs_r2


title: R45_9_10_1_W


title: R45_9_10_1_GW


title: dmso_24hrs_r1


title: MCF10A-5E tet-pLKO.1-puro-shGFP Day 10 spheroids replicate 2


title: R45_9_10_12_C


title: MCF10A-5E tet-pLKO.1-puro-shGFP Day 10 spheroids replicate 1


title: Input A77 1726plus nucleotides  treated cells

data_processing:
ChIP-Seq aligned to hg19 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Genome_build: hg19
Supplementary_files_format_and_content: bed file

extract_protocol:
After chromatin immunoprecipitation, cross-link reversal is carried out and precipitated DNA is purified by phenol:chloform:isoamyl alcohol extraction.
The End-It DNA End-Repair Kit (Epicentre) was used to turn DNA overhangs into phosphorylated blunt ends and the Agencourt AMPure XP PCR Purification Kit (Beckman Coulter) was used to purify the resulting samples using a 1.8X ratio of beads to sample. Next, a single A in the 3’ end was added to samples using the Klenow Fragment enzyme (NEB) to allow for directional ligation and the AMPure Kit was again used to purify samples. Illumina adaptor oligos (1:10 dilution) were added to samples using the Quick Ligation Kit (NEB) and NEBNext Multiplex Oligos for Illumina Kit (NEB), and samples were purified with the AMPure Kit. Samples were then size-selected with the AMPure beads with a 0.9X bead to sample ratio. Multiplexing primers from the NEBNext Multiplex Oligos Kit were added during the 18-cycle PCR enrichment step, which utilized the Phusion High-Fidelity PCR Master Mix (NEB), to generate indexed libraries. Indexed libraries were beads purified. The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script.

treatment_protocol: 40 million A375 cells per condition were treated with DMSO or 25 μM A771726.  After a 24 hr treatment, cells were fixed in 11% formaldehyde and subjected to chromatin immunoprecipitation with DDX21 (Novus Biologicals) or Cdk9 (C-20),

tag: chip antibody


title: R45_8_25_7_Y


title: R45_9_10_12_B


title: Input A77 1726  treated cells


title: R45_8_25_7_GO


title: R45_9_10_12_BC


title: Input DMSO treated cells


title: R45_8_25_5_GO


title: R45_8_25_5_W


title: CDK9 Chip on  A77 1726plus nucleotides

value: CDK9 Santa Cruz sc484


title: 446_SP day 7 ZT4

city: Edinburgh

first: Matthew

middle: M

last: Hindle

state: Midlothian

address: Easter Bush

department: Functional Genetics and Development

country: United Kingdom

institute: The Roslin Institute

description: mRNASeq of Ovis aries pars tuberalis for sample PT446 SP day 7 ZT4

data_processing:
The FASTQ files were trimmed with TrimGalore v0.4.0
TopHat 2.1.0 and Bowtie v2.3.5 were used for mapping
StringTie and TAMA were used to combine RNASeq transcript predictions with PacBio IsoSeq data
featureCount (Subread v1.6.3) was used to count features (mapped pairs) for genes
Voom was used to normalise data and estimate precision weights
Genome_build: GCA_002742125.1 Oar_rambouillet_v1.0
Supplementary_files_format_and_content: TSV (tab separated) file containing raw featureCount output; GTF file containing StringTie merge output; XLSX files contain raw counts, voom normalised log2CPM (counts per million) and the precision weighted mean from voom.

organism: Ovis aries

source_name: SP day 7 ZT4

growth_protocol: Scottish blackface castrate male lambs were obtained from local farms

extract_protocol:
Samples were frozen on dry ice.  RNA was extracted from the pars tuberalis using Qiagen's TissueLyser II and RNeasy tissue kit. The quality of the extracted RNA was assessed using the Agilent 2100 Bioanalyser; all RNA integrity numbers (RINs) were above 8, indicating that good quality RNA had been extracted. Poly-A selection was used.
RNA prepared with TruSeq Stranded mRNA Sample Preparation Guide, (15031047 Rev. E, Oct 2013) and sequenced on HiSeq 2500 High Output V4 2x125 PE

treatment_protocol: All animal experiments were undertaken in accordance with the Home Office Animals (Scientific Procedures) Act (1986), UK, under a Project License held by A.S.I.L. Scottish blackface castrate males were housed in artificial light dark cycles, either 8:16 h light ⁄ dark cycle for short photoperiod (SP) or 16:8 h light ⁄ dark cycle for long photoperiod (LP). All animals were killed by an overdose of barbiturate (Euthatal; Rhone Merieux, Essex, UK) administered intravenously

tag: strain

value: scottish blackface

value: pars tuberalis

tag: Sex

value: male

tag: age

value: 1 year

tag: photoperiod

value: SP

tag: zt


title: R42_9_7_9_W

tag: caste

tag: colony

tag: percent dwv


title: 456_SP day 7 ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT456 SP day 7 ZT4

tag: tissue


title: DDX21 Chip on A77 1726plus nucleotides

value: DDX21 Novus Biologicals NB100-17-18


title: R42_9_7_9_GO


title: 444_SP day 7 ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT444 SP day 7 ZT4


title: R42_9_7_8_BC


title: R42_9_7_7_W


title: C60_15

tag: treatment

value: control

value: mushroom bodies

value: drone

tag: time collected

value: 60 min

value: RX


title: 465_SP day 1 ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT465 SP day 1 ZT4

source_name: SP day 1 ZT4


title: R42_9_7_6_O


title: CDK9 Chip on A77 1726  treated cells


title: DDX21 Chip on A77 1726  treated cells


title: R42_9_7_3_W


title: 461_SP day 1 ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT461 SP day 1 ZT4


title: R45_8_25_7_GW


title: CDK9 Chip on DMSO treated cells


title: R42_9_7_1_GO


title: R42_9_7_3_GO


title: DDX21 Chip on DMSO treated cells


title: 507_SP day 1 ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT507 SP day 1 ZT4


title: GBM_TMZ+4Gy_2

city: Leipzig

first: Susann

last: Haehnel

address: Liebigstrasse 13

department: Institute of Anatomy

country: Germany

institute: University of Leipzig

data_processing:
Illumina bcl2fastq v1.84 software was used for basecalling.
For adaptor trimming AdaptorRemoval v.2.2.0 was used with additional parameters as follows: --trimns –trimqualities –minquality 20, and –minlength 20 in order to trim terminating ambiguous bases or bases with a quality score less than 20 and to discard reads shorter than 20 bases.
Trimmed reads were mapped to the human reference genome version GRCh38/hg38 by segemehl v0.2.0 in split read mode (option --splits) and with additional parameters as follows: --hitstrategy 1 and --differences 1.
Expression quantification for the human reference gene annotation Gencode v25 was obtained by using HTSeq v0.6.1 with the following parameters: –stranded=reverse, --type=exon, --idattr=gene_id and --mode=intersection-strict.
Transcripts per million were calculated using the function "calculateTPM" from the R library scater v1.6.1 (https://bioconductor.org/packages/release/bioc/html/scater.html).
Genome_build: hg38
Supplementary_files_format_and_content: text file containing tpm counts for each sample with the corresponding ensembl_id

source_name: glioblastoma tissue (zone I)

growth_protocol: Glioblastoma and peritumoral brain tissue was surgically resected (Department of Neurosurgery, University Hospital Leipzig, Germany), processed in 350 µm tissue slices and cultivated on membrane inserts on a liquid-air-interface. Cultivation medium consisted of MEM (Gibco) with 25 % Hank's Balanced Salt Solution (HBSS, ThermoFisher Scientific), 10 % heat-inactivated horse serum (Gibco), 1 % L-glutamine (Gibco), 1 % Glucose (Mediatech Inc.), and 1 % penicillin/streptomycin (Gibco), was exchanged every 2 to 3 days. Tissue slices were cultivated in a humidified incubator at 37°C and 5 % CO2.

extract_protocol:
After radiochemotherapy, all 3 slices of each insert were pooled together, transferred to the QIAzol Lysis Reagent (Qiagen) and homogenized by a hollow needle attached to a syringe. The extraction of total RNA was performed using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. Isolated RNA was diluted in 30 µl of RNAse-free water and stored at -80°C.
RNA concentration was determined using the Qubit 2.0 (Life Technologies). The quality of the isolated RNA was determined by the Bioanalyzer 2100 using the RNA 6000 Nano-Kit (Agilent Technologies). RNA was DNase-digested twice using the TURBO DNA free Kit (Ambion®, ThermoFisher Scientific). For library preparation with the Truseq-Stranded Total RNA Sample Prep Kit (Illumina) up to 200 ng RNA per sample were used. An rRNA depletion step was conducted according to the manufacturer’s protocol and – depending on the quality of each sample – a fragmentation was done. Every library was equipped with two barcodes to allow multiplexing of the samples. Concentrations were determined using the Qubit DNA Kit and the DNA quality was detected by the Bioanalyzer 2100 (DNA1000 Kit). According to the average size, which is determined by the Bioanalyzer, and the exact concentration of the samples, the molarity of each library was calculated. The samples were sequenced at the HiSeq2500 with 2 x 126 bp paired-end reads. 12 pM of DNA were put on the flowcell using one lane per sample. The number of reads obtained was between 243 and 368 x 106 reads per sample. Sequencing was performed with 2 x 126 bp paired-end reads at a HiSeq2500 (Illumina) with one sample per lane.

treatment_protocol: Tissue slices were randomly distributed to the membrane inserts with 3 individual slices per insert. 24 hours prior to x-irradiation, slices were pre-treated with 200 µM temozolomide or DMSO as vehicle control. Total x-irradiation dose was 4 Gy. 24 hours after x-irradiation, the slices received fresh temozolomide- or DMSO-supplemented medium. After a total incubation time of 72 hours, total RNA was isolated or slices were fixed with 4 % paraformaldehyde for histology.

value: glioblastoma

value: temozolomide + x-irradiation

tag: concentration


title: R42_9_7_12_BO

value: worker


title: R42_9_7_12_C

value: brain


title: R42_9_6_9_Y


title: R42_9_7_10_C


title: 514_LP 16 weeks ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT514 LP 16 weeks ZT4

source_name: LP 16 weeks ZT4

value: LP


title: R42_9_7_12_O


title: R42_9_6_9_GW


title: GBM_untreated_2

value: 0 mM


title: GBM_TMZ+4Gy_1


title: R42_9_6_9_GY


title: R42_9_7_7_GY


title: 439_LP 16 weeks ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT439 LP 16 weeks ZT4

value: scottish blackface


title: HxLPS 5 RNAseq

data_processing:
RNAseq: Base calls made using Illumina 1.9 software
RNAseq: Alignment made using Tophat v2.1
RNAseq: Differential expression analyses performed using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff output

source_name: N9 microglia

extract_protocol: For RNAseq, cells were lysed in Trizol

treatment_protocol: Cells were treated for 16 hours with either 1% O2 or 21% O2, in an incubator maintained at 5% CO2 and 37 °C. Following 16 hrs, cells were exposed to 3 hrs of 100 ng/mL LPS.

value: Hypoxia LPS

tag: passages


title: 309_LP day 7 ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT309 LP day 7 ZT4

source_name: LP day 7 ZT4

value: pars tuberalis

value: male


title: 315_LP day 7 ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT315 LP day 7 ZT4

value: 1 year


title: R42_9_7_10_BC


title: HxLPS 4 RNAseq


title: GBM_untreated_1


title: peritumoral_untreated_2

source_name: peritumoral brain tissue (zone III)

value: peritumoral brain


title: peritumoral_untreated_1


title: HxLPS 3 RNAseq


title: R42_9_6_8_O


title: R42_9_6_8_B


title: 516_LP 16 weeks ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT516 LP 16 weeks ZT4


title: 393_LP day 1 ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT393 LP day 1 ZT4

source_name: LP day 1 ZT4


title: HxLPS 2 RNAseq


title: R42_9_6_8_BO


title: 383_LP day 1 ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT383 LP day 1 ZT4


title: HxLPS 1 RNAseq


title: 382_LP day 1 ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT382 LP day 1 ZT4


title: R42_9_6_9_G


title: NxLPS 5 RNAseq

value: Normoxia LPS


title: R42_9_6_7_W


title: NxLPS 4 RNAseq


title: R42_9_6_5_W


title: 388_SP 12 weeks ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT388 SP 12 weeks ZT4

source_name: SP 12 weeks ZT4

value: SP


title: 308_LP day 7 ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT308 LP day 7 ZT4


title: R42_9_6_4_O


title: R42_9_6_5_GW


title: 494_SP 4 weeks ZT24

description: mRNASeq of Ovis aries pars tuberalis for sample PT494 SP 4 weeks ZT24

source_name: SP 4 weeks ZT24


title: R42_9_6_4_B


title: NxLPS 2 RNAseq


title: NxLPS 1 RNAseq


title: COPT1 over expressor line versus Col-0 grown in MS with cupper replicate 2

city: Valencia

first: Francisco

last: Vera-Sirera

address: Ingeniero Fausto Elio, s/n

institute: IBMCP (UPV-CSIC)

hyb_protocol: DNA onto slides was rehydrated by placing the slide upside-down over a water bath at 60Â°C for 10 s, and snap dry onto a heat block at 65Â°C. Rehydratation was repeated 3 times. DNA was immobilized by UV light by exposing the slides DNA-side-up to 65 mJ in a UV cross-linker (Stratagene). Slides were then washed twice in 0.1% SDS and 4 times in water, 2 min each wash at RT, and finally dipped in 96% ethanol for 1 min and dried by centrifugation at 2000 rpm 1 min at RT. Slides were prehybridized for 30 min at 42Â°C with 100 ÂµL of prehybridization solution (6x SSC (Sigma), 1% BSA (Sigma) and 0.5% SDS (Sigma)), under a 60x22 mm coverslip LifterSlip (Erie Scientific) in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were rinsed 5 times in H2O in a slide rack at RT and dried by centrifugation at 2000 rpm 1 min at RT. Slides were hybridized immediately.  Both coupled aa-aRNA (Cy3 and Cy5) were mixed and fragmented in the presence of 20 Âµg of tRNA (Ambion) and 20 Âµg of poly(A) (Roche) using the RNA fragmentation Reagent (Ambion) as described by the manufacturer, in a final volume of 10 ÂµL. Fragmented aa-aRNA was used directly in the hybridization mix, which contains of 50 ÂµL deionized formamide (Sigma), 30 ÂµL 20x SSC, 5 ÂµL 100x DenhardtÂ´s solution (Sigma), and 5 ÂµL 10% SDS in a final volume of 100 ÂµL. Hybridization mixture was denatured at 95 Â°C for 5 min, spun briefly, and applied by capillary between a pre-treated slide (see above) and a 60x42 mm coverslip LifterSlip. Slides were incubated o/n at 37Â°C in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were washed sequentially once in 1x SSC 0.1% SDS 5 min at 30Â°C; once in 0.2x SSC 0.1% SDS 5 min at 30Â°C; twice in 0.1x SSC 2 min each at 30Â°C; and finally 0.01x SSC 10 sec at RT. Slides were dried by centrifugation at 2000 rpm 1 min at RT.

scan_protocol: Hybridized microarray slides were scanned at 532-nm for the Cy3 and 635-nm for the Cy5 dyes, with a GenePix 4000B scanner (Axon Molecular Devices, Sunnyvale CA), at 5-nm resolution and 100% laser power.

data_processing:
Spot intensities were quantified using GenePix Pro 6.0 microarray-analysis software (Axon Molecular Devices, Sunnyvale CA). Spots with a net intensity in both channels lower than the median signal background plus twice standard deviations were removed as low signal spots.  Data were normalized by median global intensity using the GenePix Pro 6.0 software.
Linear normalized log2 ratio (COPT1 OE/Col-0). Values for COPT1-OE vs Col Cu Def Rep1, COPT1-OE vs Col Cu Exc Rep2 and  COPT1-OE vs Col Cu Exc Rep3 have been dye-swap corrected

organism: Arabidopsis thaliana

source_name: COPT1 OE with cupper

label_protocol: RNA was amplified using the MessageAmp II aRNA Amplification kit (Ambion), basically as described by the manufacturer. 5-(3-aminoallyl)-UTP (aa-UTP) (Ambion) was incorporated into the amplified RNA (aRNA) at ratio 1:1 with UTP. After purification 7.5 Âµg of aminoallyl-aRNA (aa-aRNA) were used in a coupling reaction with either fluorescent Cy3 or Cy5 as reactive N-hydroxyl succinimidal dyes (NHS-dyes) (Amersham Pharmacia Biotech, Piscataway, NJ). For this, each aliquot of Cy3 or Cy5 were dissolved in 20 ÂµL of DMSO and used in four coupling reactions. aa-aRNA was dissolved in 15 ÂµL of freshly-made 0.1 M NaCO3 pH 9.0, and mixed with 5 Âµl of either Cy-3 or Cy-5 dye. Coupling was allowed for 1 h at RT in the dark. Reaction was stopped with 35 ÂµL of 100 mM sodium acetate pH 5.2 and incubated 5 min in the dark. Fluorescent aa-aRNA was purified using a MegaClear purification column (Ambion) as described by the manufacturer. Coupled aa-aRNA (250-300 pmol Cy dye in 5-7 Âµg aa-aRNA) was dried in a speedvac and dissolved in 2.5 ÂµL of filtered water.

growth_protocol: Seeds were surface sterilized by treatment with 70% ethanol for 20 min, followed by commercial bleach (2.5 % sodium hypochlorite) containing 0.05 % Triton X-100 for 10 min, and finally, four washes with sterile distilled water. Stratification of the seeds was conducted in the dark at 4ºC for 2 days. Seeds were sowed in  ½ MS medium (see specifications in treatment protocol) and grown for 6-7 days under  12 hours of light + 12 hours of darkness photoperiod conditions.

extract_protocol: Seedlings were frozen in liquid nitrogen, and grounded in mortars dipped in liquid nitrogen. Total RNA was extracted using the Quiagen Plant RNeasy Mini Kit followong the manufacturerÂ´s recommendations

treatment_protocol: Seeds of Arabidopsis thaliana, ecotype Columbia-0 (Col-0) and the transgenic lines COPT1OE were surface-sterilized and stratified for 2 d at 4°C and were germinated in ½ MS medium plates including 1% sucrose (Murashige, 1962)  supplemented or not with the indicated concentrations of cupper.  In order to know the effects of both Cu, the components of the ½ MS medium were prepared separately according to the conditions: macronutrients (10 mM NH4NO3, 9.4 mM KNO3, 0.37 mM MgSO4∙7H20, 0.62 mM KH2PO4 and 1.13 mM CaCl2), micronutrients (50 μM H3BO3, 36.6 μM MnSO4∙ H20, 15 μM ZnSO4∙7H20, 0.57 μM NaMoO4∙2H2O and 0.05 μM CoCl2∙6H20), 50 μM Fe-citrate 0.25 mM KI, 0.05% MES, 1% sucrose and 0.8% phytoagar; pH 5.7-5.8.  Seedlings were grown in Cu deficiency (0 μM CuSO4),or Cu excess (10 μM CuSO4).

tag: ecotype background

tag: genotype/variation

value: COPT1 over-expressor

value: 7 days seedling

tag: growth condition

value: MS withCupper

source_name: Col-0 with cupper

value: wild type


title: R42_9_6_3_Y


title: Beko_SCR_rep2

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

data_processing:
Quality control of FASTQ  files was done using fastqc.
Removal of low-quality reads was done using fastx-toolkit.
Read mapping was done using Bowtie2  called from Tophat based on  Illumina iGenome mm9 UCSC gene GTF gene definitions.
Mapped reads per gene were extracted using the summarizeOverlaps from the genomicAlignments package in R on  Illumina iGenome mm9 UCSC gene definitions.
The extracted read counts were analyzed with DESeq2 in order to obtain expression measures and differential gene expression measures.
Genome_build: mm9
Supplementary_files_format_and_content: Differential gene expression analysis summary from DESeq2 in tabular form.

growth_protocol: Mouse pre-T (Beko) cells were grown at 37°C with 5% CO2 in IMDM medium (Gibco 21980-065) supplemented with 2% FCS, peptone, insulin, nonessential aminoacids and penicillin/streptomycin.

extract_protocol:
Rneasy Mini Kit (Qiagen #74104) using the QIAshredder (Qiagen #79654) and  RNase-free DNase (Qiagen #79254).
Lybrary-prep kit: Illumina TruSeq® Stranded Total RNA LT - Ribo-Zero Gold (RS-122-2301/2).

treatment_protocol: Mouse pre-T (Beko) cells were treated for 24 hours with 0.01 µg/ml apicidin, 10 µg/ml  DAPT (GSI) or with DMSO as control. Alternatively, Beko cells were infected with plasmids driving the expression of shRNAs against Hdac3 or scrambled (SCR) as control.

tag: cell type

value: pre-T cells (Beko)

tag: infected with

value: plasmids driving the expression of scrambled (SCR) shRNAs as control.

tag: molecule subtype

value: RiboMinus - depleted total RNA


title: COPT1 over expressor line versus Col-0 grown in MS with cupper replicate 3


title: R42_9_6_3_W

value: worker

value: brain


title: COPT1 over expressor line versus Col-0 grown in MS with cupper replicate 4


title: 387_SP 12 weeks ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT387 SP 12 weeks ZT4

tag: strain

value: scottish blackface

tag: Sex

tag: age


title: COPT1 over expressor line versus Col-0 grown in MS with cupper replicate 1


title: 502_SP 4 weeks ZT24

description: mRNASeq of Ovis aries pars tuberalis for sample PT502 SP 4 weeks ZT24

tag: photoperiod

tag: zt


title: R42_9_6_3_GY

tag: caste

tag: colony

tag: percent dwv


title: 386_SP 12 weeks ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT386 SP 12 weeks ZT4

tag: tissue


title: COPT1 over expressor line versus Col-0 grown in MS without cupper replicate 2

source_name: COPT1 OE without cupper

value: MS without Cupper

source_name: Col-0 without cupper


title: COPT1 over expressor line versus Col-0 grown in MS without cupper replicate 3


title: R42_9_6_2_BO

source_name: whole brain


title: Beko_Hdac3_KD_rep2

value: plasmids driving the expression of shRNAs against Hdac3.


title: 486_SP 4 weeks ZT20

description: mRNASeq of Ovis aries pars tuberalis for sample PT486 SP 4 weeks ZT20

source_name: SP 4 weeks ZT20

value: pars tuberalis

value: male


title: 485_SP 4 weeks ZT20

description: mRNASeq of Ovis aries pars tuberalis for sample PT485 SP 4 weeks ZT20

value: 1 year


title: COPT1 over expressor line versus Col-0 grown in MS without cupper replicate 1


title: EC-E4

city: Luzhou

first: xu

last: liu

address: 25th Taiping Street

country: China

institute: The Affiliated Hospital of Southwest Medical University

hyb_protocol: sample was hybridized to the Affymetrix Clariom S Assay,human (Cat No 902926) for 16-18 h at 45°C. Following hybridization, the microarrays were washed and stained with Streptavidin Phycoerythrin on the Affymetrix Fluidics Station 450

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

data_processing:
The data were analyzed with the robust multichip analysis (RMA) algorithm using default analysis settings and global scaling as a normalization method Values are presented according to log2 RMA signal intensity
We defined the genes with a fold-change of more than 1.5 or less than 1.5 and a p-value of less than 0.05 as different expression genes, which were selected to undergo basic analysis

label_protocol: sample was labeled with biotin by terminal deoxynucleotidyl transferase (TdT)

extract_protocol: Total RNA was extracted by Trizol (Invitrogen, Carlsbad, CA, USA), and a total of 500 ng RNA was used for cDNA synthesis

tag: cell line

tag: genotype

value: overexpression of the EN2

value: esophageal squamous cell carcinoma


title: 492_SP 4 weeks ZT24

description: mRNASeq of Ovis aries pars tuberalis for sample PT492 SP 4 weeks ZT24

value: SP


title: Beko_DMSO_(GSI_ Ctrl)_rep2

source_name: Beko_DMSO_(GSI_ Ctrl)

tag: treated with

value: DMSO for 24hrs


title: R42_9_6_1_GY


title: R42_9_6_1_GO


title: EC-N4

value: control


title: EC-E3


title: 470_SP 4 weeks ZT16

description: mRNASeq of Ovis aries pars tuberalis for sample PT470 SP 4 weeks ZT16

source_name: SP 4 weeks ZT16


title: Beko_DMSO_(GSI_ Ctrl)_rep1


title: Beko_SCR_rep1


title: R42_9_6_12_O


title: Beko_GSI_rep2

value: 10 µg/ml  DAPT (GSI) for 24hrs


title: EC-N3


title: 482_SP 4 weeks ZT16

description: mRNASeq of Ovis aries pars tuberalis for sample PT482 SP 4 weeks ZT16


title: R42_9_6_12_BO


title: Beko_Hdac3_KD_rep1

value: pre-T cells (Beko)


title: 467_SP 4 weeks ZT16

description: mRNASeq of Ovis aries pars tuberalis for sample PT467 SP 4 weeks ZT16


title: ky-E2


title: Beko_GSI_rep1


title: R42_9_6_12_B


title: 471_SP 4 weeks ZT20

description: mRNASeq of Ovis aries pars tuberalis for sample PT471 SP 4 weeks ZT20


title: Beko_DMSO_(Apicidin_Ctrl)_rep2


title: R42_9_6_11_Y


title: osm-3 treatment 4

city: Cologne

first: Martin

last: Denzel

address: Joseph-Stelzmann-Str. 9b

institute: Max Planck Institute for Biology of Ageing

description: VST_log2_counts_deseq2.txt, noTreatment_vs_Treatment_in_osm3_deseq2.txt, WT_vs_osm3_Treatment_deseq2.txt

data_processing:
Reads were mapped and quantified to reference using kallisto 0.43.0-1 and the –fr-stranded option
Differential gene expression was estimated using DESeq2 R package (DESeq2 1.16.1)
Genome_build: WBCel235 (Ensemble release v94; accessed 2018-12-03).

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: L1 WT and osm-3(dh441)IV larvae were syncronized by harvesting worms that hatched within a one hour time period and allowed to grow to day one of adulthood at 20 degrees.

extract_protocol:
Worms were removed and flash frozen in liquid nitrogen in using Trizol reagent. Ribosomal RNA was depleted from 2.5 ug of total RNA using Illumina Ribo-zero Gold kit (Illumina). Strand specific RNA-seq libraries were constructed using SMARTer Stranded RNA-Seq HT Kit (Clontech #634829) according to manufacturer's protocol
Strand specific RNA-seq libraries were constructed using SMARTer Stranded RNA-Seq HT Kit (Clontech #634829) according to manufacturer's protocol
Based on rRNA depleted input amount, 15 cycles of amplificatoin were performed to generate RNA seq libraries.

treatment_protocol: Day one worms were transferred to either vehicle or 10 ug/ml tunicamycin plates for six hours before they were harvested and snap frozen in trizol

tag: dev stage

value: Day 1

tag: treatment

value: 10 ug/mL Tunicamycin


title: osm-3 treatment 3


title: Beko_DMSO_(Apicidin_Ctrl)_rep1

tag: cell type

value: RiboMinus - depleted total RNA


title: osm-3 treatment 2


title: ky-E1


title: Beko_Apicidin_rep2

value: 0.01 µg/ml  apicidin for 24hrs


title: R42_9_6_11_GY

value: worker

value: brain


title: osm-3 treatment 1


title: Beko_Apicidin_rep1


title: 479_SP 4 weeks ZT12

description: mRNASeq of Ovis aries pars tuberalis for sample PT479 SP 4 weeks ZT12

source_name: SP 4 weeks ZT12

value: scottish blackface


title: R42_8_24_6_GY


title: ky-N1


title: 481_SP 4 weeks ZT12

description: mRNASeq of Ovis aries pars tuberalis for sample PT481 SP 4 weeks ZT12

value: pars tuberalis


title: 460_SP 4 weeks ZT8

description: mRNASeq of Ovis aries pars tuberalis for sample PT460 SP 4 weeks ZT8

source_name: SP 4 weeks ZT8

value: male


title: ky-N2


title: 513_SP 4 weeks ZT8

description: mRNASeq of Ovis aries pars tuberalis for sample PT513 SP 4 weeks ZT8

value: 1 year


title: LYS14_ALL_Kang2020

city: St. Louis

first: Yiming

last: Kang

state: MO

address: 1 Brookings Dr

department: Computer Science and Engineering

institute: Washington University in St. Louis

description: Calling Card Assay for in vivo Transcription Factor Binding: a retrotransposon is directed into the genome at loci bound by a given transcription factor

data_processing:
Library strategy: "Calling Card" Assay
Paired-End sequence reads were filtered for presence of Read1 initial 5bp barcode followed by unique 17-mer sequence (AATTCACTACGTCAACA) and Read2 initial 8bp barcode.
The remaining sequence after the 17-mer sequence of Read1 was mapped to the 2008 S. cerevisiae reference genome (R-61-1-1) sequence using NovoAlign with default parameter settings.
Insertion position and number of reads mapping to each insertion are reported in gnashy file.
Genome_build: S288C-R61
Supplementary_files_format_and_content: gnashy: a table indicating genomic position of the retrotransposon insertion and number of reads aligning to that position

organism: Saccharomyces cerevisiae

growth_protocol: The indicated yeast strain was co-transformed with a plasmid carrying the indicated transcription factor fused at the C-terminus to Sir4p and a plasmid carrying a barcoded HIS3-carrying Ty5 retrotransposon under the control of the GAL1/10 promoter.  A single clone was then incubated for 3 days on selective media with galactose as the carbon source.  Plates were then sequentially replica-plated to YPD (2 days), followed by SC-HIS with 5'FOA agar plates (3 days).

extract_protocol:
Genomic DNA was extracted from all cells using standard glass bead-beating, phenol chloroform isoamyl alcohol purification, and NH4Ac ethanol protocol.
Genomc DNA was digested in three separate restriction enzyme digests (HinPI1, HpaII, and Taq-alphaI), self-ligated with T4 DNA ligase, and an inverse PCR reaction was performed to amplify genomic DNA downstream of each inserted Ty5 retrotransposon.
"Calling Card" Assay to identify in vivo genomic targets of DNA-binding factors

treatment_protocol: "Calling Card" Assay performed as previously described: 1. "Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins." Wang H, Mayhew D, Chen X, Johnston M, Mitra RD.  Genome Research, 2011, May 21(5):748-55. PMID 21471402. 2. "Calling Card Analysis in Budding Yeast." Mayhew D, Mitra RD.  Cold Spring Harbor Protocols, 2016, Feb 1, 2016(2). PMID 26832687.

tag: transcription factor


title: NxLPS 3 RNAseq

first: Jyoti

address: 2015 Linden Drive

institute: University of Wisconsin-Madison

source_name: N9 microglia

value: Normoxia LPS

tag: passages


title: R42_8_24_6_G


title: 512_SP 4 weeks ZT8

description: mRNASeq of Ovis aries pars tuberalis for sample PT512 SP 4 weeks ZT8

tag: strain


title: wt treatment 3

description: VST_log2_counts_deseq2.txt, noTreatment_vs_Treatment_in_WT_deseq2.txt, WT_vs_osm3_Treatment_deseq2.txt


title: 466_SP 4 weeks ZT12

description: mRNASeq of Ovis aries pars tuberalis for sample PT466 SP 4 weeks ZT12

tag: Sex


title: 511_SP 4 weeks ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT511 SP 4 weeks ZT4

source_name: SP 4 weeks ZT4

tag: age


title: R42_8_24_5_C


title: sox10 + cells Leflunomide+Progesterone

city: Boston

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to hg19 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: Zv9
Supplementary_files_format_and_content: excel files include RPKM values for each Sample ...

organism: Danio rerio

source_name: sox10 + cells

growth_protocol: Zebrafish embryos are grown at 28C in E3 1X.

extract_protocol:
Total RNA was extracted with TrizolPlus RNeasy mini kit from Qiagen.
Total RNA was depleted of ribosomal RNA with the RiboGone Kit (Clonetech). Enriched mRNA was then applied to library preparation according to manufacturer’s protocol (Smart Low input Protocol, Clonetech). After repeated quality control for average DNA input size of 300 bp, the samples were sequenced on a HiSeq Illumina sequencer with 2x100bp paired-end reads.

treatment_protocol: Embryos were treated with DMSO, leflunomide 7UM,  16uM Progesterone  or the combination of the two chemiclas from 50% epibolfy till 15somites. Embryos were dissociated and sox10 cells were sorted.

tag: sample type

value: rRNA depleted RNA


title: R42_9_6_11_W


title: R42_8_24_5_BY


title: wt treatment 2


title: sox10 + cells Progesterone 16uM


title: wt treatment 1


title: 416_SP 4 weeks ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT416 SP 4 weeks ZT4

tag: photoperiod

value: SP

tag: zt


title: R42_8_24_3_GY

tag: caste

tag: colony


title: 425_SP 4 weeks ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT425 SP 4 weeks ZT4

tag: tissue


title: 498_SP 4 weeks ZT0

description: mRNASeq of Ovis aries pars tuberalis for sample PT498 SP 4 weeks ZT0

source_name: SP 4 weeks ZT0


title: sox10 + cells leflunomide 7uM


title: sox10 + cells dmso


title: wt treatment 4


title: osm-3 no treatment 4

description: VST_log2_counts_deseq2.txt, noTreatment_vs_Treatment_in_osm3_deseq2.txt, WT_vs_osm3_noTreatment_deseq2.txt

value: Vehicle


title: GCN4_ALL_Kang2020


title: osm-3 no treatment 3


title: 490_SP 4 weeks ZT0

description: mRNASeq of Ovis aries pars tuberalis for sample PT490 SP 4 weeks ZT0


title: 497_SP 4 weeks ZT0

description: mRNASeq of Ovis aries pars tuberalis for sample PT497 SP 4 weeks ZT0


title: R42_8_24_3_GO

tag: percent dwv


title: R42_8_24_2_GO


title: osm-3 no treatment 2

tag: genotype


title: R42_8_24_2_O


title: sox10 + cells ctr9 Mo-pro-exp2

treatment_protocol: Embryos were injected with a morpholino for ctr9 and then treated with DMSO or 32uM Progesterone from 50% epibolfy till 15somites. Embryos were dissociated and sox10 cells were sorted.


title: osm-3 no treatment 1


title: sox10 + cells ctr9 Mo-dmso-exp2


title: sox10 + cells ctr9 Mo-pro-exp1


title: R42_8_24_2_C


title: wt no treatment 4

description: VST_log2_counts_deseq2.txt, noTreatment_vs_Treatment_in_WT_deseq2.txt, WT_vs_osm3_noTreatment_deseq2.txt


title: R42_8_24_1_GO


title: wt no treatment 3


title: sox10 + cells ctr9 Mo-dmso-exp1


title: sox10 + cells unij-Pro exp1


title: 303_LP 4 weeks ZT24

description: mRNASeq of Ovis aries pars tuberalis for sample PT303 LP 4 weeks ZT24

source_name: LP 4 weeks ZT24

value: LP


title: 331_LP 4 weeks ZT24

description: mRNASeq of Ovis aries pars tuberalis for sample PT331 LP 4 weeks ZT24


title: wt no treatment 2


title: EDS1_ALL_Kang2020


title: 341_LP 4 weeks ZT20

description: mRNASeq of Ovis aries pars tuberalis for sample PT341 LP 4 weeks ZT20

source_name: LP 4 weeks ZT20


title: wt no treatment 1


title: 336_LP 4 weeks ZT20

description: mRNASeq of Ovis aries pars tuberalis for sample PT336 LP 4 weeks ZT20


title: 332_LP 4 weeks ZT24

description: mRNASeq of Ovis aries pars tuberalis for sample PT332 LP 4 weeks ZT24


title: 335_LP 4 weeks ZT20

description: mRNASeq of Ovis aries pars tuberalis for sample PT335 LP 4 weeks ZT20


title: ML3

city: Anyang

first: Jianyong

last: Wu

address: Huanghe Dadao 38#

institute: Institute of Cotton Research, CAAS

description: 1st true leaves fully expanded

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Supplementary_files_format_and_content: xls include FPKM values for each Sample

organism: Gossypium hirsutum

source_name: Leaf

growth_protocol: Standard Hydroponic solution in the Lab

extract_protocol:
T.RNA with Sigma Spectrum Plant Total RNA kit (Sigma-  448 Aldrich, USA)
Accordance with the protocol for the mRNA-Seq sample preparation kit   (Illumina, San Diego, USA)

tag: cultivar

value: Leaf

tag: developmental stage

value: Seedling stage


title: 330_LP 4 weeks ZT16

description: mRNASeq of Ovis aries pars tuberalis for sample PT330 LP 4 weeks ZT16

source_name: LP 4 weeks ZT16


title: MR3

description: 1st true leaves fully expanded

source_name: Root

value: Root


title: 329_LP 4 weeks ZT16

description: mRNASeq of Ovis aries pars tuberalis for sample PT329 LP 4 weeks ZT16


title: ML1

description: 1st true leaves fully expanded


title: Sample_I32_24h_C6

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

institute: IRSN

description: Control

data_processing:
Quality (selection of Q>30) and adapter trimming with Trimgalor v0.4.2
Mapping with 2PASS STAR v020201 against  GRCz11 zebrafish reference genome and Ensembl v95 exon-exon junctions
Quantification and normalization with Desq2 v1.22.2
Genome_build: GRCz11
Supplementary_files_format_and_content: Raw reads in fastq
Supplementary_files_format_and_content: Read count files from RNAstar

source_name: entire embryos

growth_protocol: Zebrafish eggs were collected just after fertlization and grown in 9mm Petri dishes with embryo medium (60mg/L Instant Ocean, 0.01 % (w/v) of methylene blue). Eggs were grown in Panasonic incubator (MIRE) at 28°C.

extract_protocol:
Total RNA extraction with trizol no DNaseI treatment, followed by two rounds of mRNA extraction with illumina magnetic Beads
Stranded mRNAseq v2 Illumina with dual UDT indexes

treatment_protocol: External continuous irradiation to gamma radiation (137Cs) at 0.5mGy/h, 5mGy/h 50mGy/h or non-exposed controls

value: entire embryos

tag: genetic background

value: AB

tag: irradiation batch

tag: dose rate in mgy/h

value: Control


title: Sample_I32_24h_C5

description: Control


title: 20ng_cMO_st41_repl3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Fluorescence images were transformed to BCL files with the Illumina BaseCaller software and samples were demultiplexed to FASTQ files using bcl2fastq 2.17.1.14
Assessment of quality control of sequences using FastQC 0.11.5
Alignment of sequences to Xenopus Laevis reference genome using STAR 2.5.2a
Counting unique reads within genes using featureCounts 1.5.0-p1
Data normalization and testing for differentially expressed genes using DESeq2 1.8.2
Genome_build: Xenla9.1 (http://www.xenbase.org)
Supplementary_files_format_and_content: gene counts

organism: Xenopus laevis

growth_protocol: Injected and uninjected Xenopus laevis embryos were cultivated in 0.1x MBS culture buffer.

extract_protocol:
Total RNA was extracted using Trizol reagent (peqGOLD TriFast reagent, peQlab) according to instructions.
TruSeq RNA Library Preparation Kit v2, Set A (48 samples, 12 indexes)

value: stage 41

tag: injected morpholino

value: 20 ng cMO

value: whole embryo


title: MR2

description: 1st true leaves fully expanded


title: 328_LP 4 weeks ZT16

description: mRNASeq of Ovis aries pars tuberalis for sample PT328 LP 4 weeks ZT16

tag: strain

value: scottish blackface

value: pars tuberalis


title: 10ng_ERFE_MO1_st41_repl3

value: 10 ng ERFE-MO1


title: Sample_I32_24h_C3

description: Control


title: sox10 + cells unij-dmo-exp2


title: Sample_I32_24h_C1

description: Control


title: 10ng_cMO_st41_repl3

value: 10 ng cMO


title: LL3

description: 1st true leaves fully expanded


title: sox10 + cells uni-dmso-exp1

value: rRNA depleted RNA


title: Sample_I32_24h_C2

description: Control


title: 354_LP 4 weeks ZT12

description: mRNASeq of Ovis aries pars tuberalis for sample PT354 LP 4 weeks ZT12

source_name: LP 4 weeks ZT12

tag: Sex

value: male

value: 1 year


title: Sample 2_ovary

city: New York

first: Maija

last: Slaidina

state: NY

address: 540 1st ave

department: Skirball Institute

institute: New York University School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: dm6
Supplementary_files_format_and_content: Indexed BAM files containing position-sorted reads aligned to the genome and gene-barcode matrices.

organism: Drosophila melanogaster

source_name: LL3 ovary single cells

growth_protocol: conrmeal-molasses meadia, 25 C

extract_protocol:
15 – 50 LL3 ovaries were dissected per sample in ice-cold DPBS; majority of associated fat body was removed with forceps and dissection needles. For dissociation, ovaries were transferred to 9-well glass plates and incubated in dissociation solution (0.5% Type I Collagenase, 1% Trypsin 1:250 in DPBS) for 15 minutes with gentle rotation. The suspension was vigorously pipetted multiple times during the dissociation to enhance the dissociation efficiency. Enzymatic dissociation was stopped by adding Schneider cell culture media with fetal bovine serum (S-FBS). Starting from this step, all plastic materials – pipet tips, tubes, filters – were coated with S-FBS. Cell suspension was filtered through a custom-made 40micron cell strainer. The strainer was built by securing nylon mesh in a cap of a 0.2 ml PCR tube and cutting the bottom of the tube and the cap. Upon filtering, dissociated cells were purified by fluorescence activated cell sorting (FACS) using a 100- micron nozzle on Sony SY3200 Cell Sorter.
Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics)

value: ovary

tag: age


title: 342_LP 4 weeks ZT12

description: mRNASeq of Ovis aries pars tuberalis for sample PT342 LP 4 weeks ZT12

value: LP


title: Sample_I32_24h_0.5mG_E6

description: Exposed


title: LL2

description: 1st true leaves fully expanded

value: Leaf

value: Seedling stage


title: 20ng_ERFE_MO2_st37_38_repl3

value: stage 37/38

value: 20 ng ERFE-MO2


title: Sample 1_ovary


title: 337_LP 4 weeks ZT12

description: mRNASeq of Ovis aries pars tuberalis for sample PT337 LP 4 weeks ZT12


title: 352_LP 4 weeks ZT8

description: mRNASeq of Ovis aries pars tuberalis for sample PT352 LP 4 weeks ZT8

source_name: LP 4 weeks ZT8


title: Sample_I32_24h_0.5mG_E5

description: Exposed

value: entire embryos

value: AB


title: 20ng_cMO_st37_38_repl3

value: 20 ng cMO


title: 350_LP 4 weeks ZT8

description: mRNASeq of Ovis aries pars tuberalis for sample PT350 LP 4 weeks ZT8


title: LR3

description: 1st true leaves fully expanded

value: Root


title: MR1

description: 1st true leaves fully expanded


title: Sample_I32_24h_0.5mG_E4

description: Exposed


title: Sample_I32_24h_0.5mG_E3

description: Exposed


title: 10ng_ERFE_MO1_st37_38_repl3

value: whole embryo


title: 348_LP 4 weeks ZT8

description: mRNASeq of Ovis aries pars tuberalis for sample PT348 LP 4 weeks ZT8

value: scottish blackface

value: pars tuberalis


title: LR2

description: 1st true leaves fully expanded


title: Sample_I32_24h_0.5mG_E2

description: Exposed


title: LR1

description: 1st true leaves fully expanded


title: 363_LP 4 weeks ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT363 LP 4 weeks ZT4

source_name: LP 4 weeks ZT4


title: uninjected_st41_repl3

value: stage 41


title: 10ng_cMO_st37_38_repl3

value: 10 ng cMO


title: Sample_I32_24h_0.5mG_E1

description: Exposed


title: HL3

description: 1st true leaves fully expanded


title: 359_LP 4 weeks ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT359 LP 4 weeks ZT4

value: male


title: uninjected_st37_38_repl3


title: 20ng_ERFE_MO2_st35_36_repl3

value: stage 35/36


title: LL1

description: 1st true leaves fully expanded


title: 314_LP 4 weeks ZT4

description: mRNASeq of Ovis aries pars tuberalis for sample PT314 LP 4 weeks ZT4

value: 1 year


title: HL2

description: 1st true leaves fully expanded


title: HL1

description: 1st true leaves fully expanded


title: Sample_I17_96h_C9

description: Control

value: Control


title: Sample_I17_96h_C11

description: Control


title: ML2

description: 1st true leaves fully expanded

value: Leaf


title: 372_LP 4 weeks ZT0

description: mRNASeq of Ovis aries pars tuberalis for sample PT372 LP 4 weeks ZT0

source_name: LP 4 weeks ZT0

value: LP


title: 20ng_cMO_st35_36_repl3


title: Sample_I17_96h_5mG_E9

description: Exposed


title: HR2

description: 1st true leaves fully expanded

value: Seedling stage


title: 10ng_cMO_st35_36_repl3


title: 10ng_ERFE_MO1_st35_36_repl3

value: 10 ng ERFE-MO1


title: 367_LP 4 weeks ZT0

description: mRNASeq of Ovis aries pars tuberalis for sample PT367 LP 4 weeks ZT0


title: HR3

description: 1st true leaves fully expanded


title: uninjected_st35_36_repl3


title: HR1

description: 1st true leaves fully expanded


title: 20ng_ERFE_MO2_st41_repl2

value: 20 ng ERFE-MO2


title: DL3

description: 1st true leaves fully expanded


title: Sample_I17_96h_5mG_E10

description: Exposed

value: entire embryos

value: AB


title: DL2

description: 1st true leaves fully expanded


title: Sample_I17_96h_50mG_E9

description: Exposed


title: 370_LP 4 weeks ZT0

description: mRNASeq of Ovis aries pars tuberalis for sample PT370 LP 4 weeks ZT0


title: Sample_I17_96h_50mG_E11

description: Exposed


title: DL1

description: 1st true leaves fully expanded


title: Sample_I17_96h_C10

description: Control


title: 10ng_ERFE_MO1_st41_repl2


title: DR3

description: 1st true leaves fully expanded

value: Root


title: Sample_I17_96h_50mG_E10

description: Exposed


title: 10ng_cMO_st41_repl2

value: whole embryo


title: DR2

description: 1st true leaves fully expanded


title: DKO_Ctrl_P15_3

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

hyb_protocol: Following fragmentation and labelling, 2.5 ug of cDNA were hybridized for 16 hr at 45°C onto Affymetrix Mouse ClariomS arrays. Then microarrays were  washed and stained using Affymetrix Fluidics FS450 machines.

scan_protocol: Microarrays were scanned using an Affymetrix GCS3000 7G system

data_processing: Data were normalized using Expression Console from Affymetrix (RMA-GENE analysis)

source_name: P15_DKO_mammary cells

label_protocol: Biotinylated cDNA were prepared according to the Ovation® Pico WTA System V2 protocol and the Nugen Encore Biotin Module from 500pg total RNA

growth_protocol: Not applied (fresh tissue)

extract_protocol: Qiagen micro-columns

tag: cell type

value: Mammary cells

tag: cell subtype

value: a3a6KO luminall cells


title: Sample_I17_48h_C8

description: Control


title: DKO_Ctrl_P15_2


title: 20ng_ERFE_MO2_st37_38_repl2

value: stage 37/38


title: Sample_I17_48h_C7

description: Control


title: Sample_I17_96h_5mG_E11

description: Exposed


title: uninjected_st41_repl2

value: stage 41


title: 20ng_cMO_st41_repl2

value: 20 ng cMO


title: DR1

description: 1st true leaves fully expanded


title: 20ng_cMO_st37_38_repl2


title: CL3

description: 1st true leaves fully expanded


title: Sample_I17_48h_C5

description: Control


title: DKO_Ctrl_P15_1


title: 10ng_ERFE_MO1_st37_38_repl2


title: Sample_I17_48h_5mG_E8

description: Exposed


title: Lu_Ctrl_P15_3

source_name: P15_Ctrl_mammary cells

value: Ctrl luminal cells


title: CL2

description: 1st true leaves fully expanded


title: CL1

description: 1st true leaves fully expanded


title: Lu_Ctrl_P15_4


title: Sample_I17_48h_5mG_E7

description: Exposed


title: Lu_Ctrl_P15_2


title: 10ng_cMO_st37_38_repl2

value: 10 ng cMO


title: uninjected_st37_38_repl2


title: CR3

description: 1st true leaves fully expanded


title: Sample_I17_48h_5mG_E5

description: Exposed


title: 20ng_ERFE_MO2_st35_36_repl2

value: stage 35/36


title: CR1

description: 1st true leaves fully expanded


title: Sample_I17_48h_50mG_E6

description: Exposed


title: Sample_I17_48h_50mG_E8

description: Exposed


title: 10ng_ERFE_MO1_st35_36_repl2


title: Sample_I17_48h_50mG_E5

description: Exposed


title: 20ng_cMO_st35_36_repl2


title: Lu_Ctrl_P15_1


title: BL3

description: 1st true leaves fully expanded

value: Leaf


title: 10ng_cMO_st35_36_repl2


title: Sample_I17_24h_C4

description: Control

value: Control


title: Sample_I17_24h_C3

description: Control


title: BL1

description: 1st true leaves fully expanded

value: Seedling stage


title: 20ng_ERFE_MO2_st41_repl1


title: BL2

description: 1st true leaves fully expanded


title: Sample_I17_24h_C1

description: Control


title: BR3

description: 1st true leaves fully expanded


title: BR2

description: 1st true leaves fully expanded


title: Sample_I17_24h_5mG_E4

description: Exposed


title: BR1

description: 1st true leaves fully expanded


title: 10ng_ERFE_MO1_st41_repl1

value: 10 ng ERFE-MO1


title: Sample_I17_24h_5mG_E2

description: Exposed


title: CR2

description: 1st true leaves fully expanded