title: WT [June29_KW.66.featurecounts]

description:
June29_KW.66.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.64.featurecounts]

status: Public on Jun 03 2018

type: SRA

city: Stanford

first: Aparna

middle: Rajiv

last: Rajpurkar

state: CA

address: 279 Campus Drive

department: Genetics

country: USA

institute: Stanford University

description:
June29_KW.64.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda

library_source: transcriptomic

data_processing:
Reads were aligned to the GRCm38 build of the Mus musculus genome using STAR (release 020201) with standard parameters. Initial cell filtering was performed by setting a minimum threshold of 40% total reads mapping to the genome.
Read counting to genes was performed with featureCounts (version 1.5.3) from the Subread package. Non-default parameters used were --primary. Gene filtering was performed by setting a minimum threshold of 10 reads in a total of  5 cells. Cell filtering was performed by requiring a minimum of 750 genes expressed with 10 reads. Futhermore, we required cells to have a minimum of 100,000 total reads mapping to known genes and less than 10% of reads mapping to mitochondrial genes. This retained 197 WT cells and 95 AireKO cells for downstream analysis.
Normalization was performed using the indeXplorer pipeline (https://git.embl.de/velten/indeXplorer) (version ad03ee7f), depending on SCDE version 2.6.0. Normalized files are provided. Mitochondrial read count effect was regressed out of the data. All downstream analysis was performed using R version 3.4.0.
All analysis code and pipelines are provided at the publically available repository https://github.com/mTEC-pipelines/tufts-pipelines.
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression matriix of post-normalized read counts for all retained cells.
Supplementary_files_format_and_content: aireko_counts.txt: tab-separated file of raw counts, aireKO samples
Supplementary_files_format_and_content: all_wt_counts.txt: tab-separated file of raw counts, wild-type samples
Supplementary_files_format_and_content: POR_all_data.txt: tab-separated file of normalized expression counts
Supplementary_files_format_and_content: samples_all.txt: tab-separated metadata file with sample batch information
Supplementary_files_format_and_content: POR_all_data.rda: Rdata file of normalized expression counts

molecule: polyA RNA

organism: Mus musculus

source_name: Thymus epithelium

extract_protocol:
For thymic epithelium, thymi were isolated, cleaned of fat and transferred to DMEM + 2% FBS on ice. Thymi were minced with a razor blade and tissue pieces were moved with a glass Pasteur pipette to 15 ml tubes and vortexed briefly in 10 ml of media. Fragments were allowed to settle before removing the media and replacing it with 4 ml of digestion media containing 2% FBS, 100 μg mL-1 DNase I (Roche), and 100 μg mL-1 Liberase TM (Sigma-Aldrich) in DMEM. Tubes were moved to a 37° C water bath and fragments were triturated through a glass Pasteur pipette at 0 min and 6 min to mechanically aid digestion. At 12 min, tubes were spun briefly to pellet undigested fragments and the supernatant was moved to 20 ml of 0.5% BSA (Sigma-Aldrich), 2 mM EDTA (TekNova), in PBS (MACS buffer) on ice to stop the enzymatic digestion. This was repeated twice for a total of three 12 min digestion cycles, or until there were no remaining tissue fragments. The single cell suspension was then pelleted and washed once in MACS Buffer. Density-gradient centrifugation using a three-layer Percoll gradient (GE Healthcare) with specific gravities of 1.115, 1.065, and 1.0 was used to enrich for stromal cells. Cells isolated from the Percoll- light fraction, between the 1.065 and 1.0 layers, were then washed and resuspended for staining. Cells were stained with fluorescently labeled antibodies and sorted via flow cytometry into single wells of 96 well plates containg 5 ul of lysis buffer. cDNA libraries were prepared using the standard smartSeq-2 protocol including ERCC control RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype

tag: age

value: 6 weeks

tag: Sex

value: Mixed

tag: mouse status

value: Naive

tag: sorting gate


title: WT [June29_KW.62.featurecounts]

description:
June29_KW.62.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.65.featurecounts]

description:
June29_KW.65.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.63.featurecounts]

description:
June29_KW.63.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.60.featurecounts]

description:
June29_KW.60.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.61.featurecounts]

description:
June29_KW.61.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.59.featurecounts]

description:
June29_KW.59.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.55.featurecounts]

description:
June29_KW.55.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.58.featurecounts]

description:
June29_KW.58.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.56.featurecounts]

description:
June29_KW.56.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.54.featurecounts]

description:
June29_KW.54.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.53.featurecounts]

description:
June29_KW.53.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.52.featurecounts]

description:
June29_KW.52.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.51.featurecounts]

description:
June29_KW.51.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.49.featurecounts]

description:
June29_KW.49.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.4.featurecounts]

description:
June29_KW.4.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.50.featurecounts]

description:
June29_KW.50.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.48.featurecounts]

description:
June29_KW.48.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.47.featurecounts]

description:
June29_KW.47.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.46.featurecounts]

description:
June29_KW.46.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.45.featurecounts]

description:
June29_KW.45.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.5.featurecounts]

description:
June29_KW.5.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.42.featurecounts]

description:
June29_KW.42.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.43.featurecounts]

description:
June29_KW.43.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.57.featurecounts]

description:
June29_KW.57.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.41.featurecounts]

description:
June29_KW.41.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.3.featurecounts]

description:
June29_KW.3.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.38.featurecounts]

description:
June29_KW.38.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.37.featurecounts]

description:
June29_KW.37.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.39.featurecounts]

description:
June29_KW.39.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.40.featurecounts]

description:
June29_KW.40.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.35.featurecounts]

description:
June29_KW.35.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.36.featurecounts]

description:
June29_KW.36.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.34.featurecounts]

description:
June29_KW.34.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.31.featurecounts]

description:
June29_KW.31.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.29.featurecounts]

description:
June29_KW.29.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.2.featurecounts]

description:
June29_KW.2.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.30.featurecounts]

description:
June29_KW.30.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.44.featurecounts]

description:
June29_KW.44.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.27.featurecounts]

description:
June29_KW.27.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.26.featurecounts]

description:
June29_KW.26.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.28.featurecounts]

description:
June29_KW.28.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.22.featurecounts]

description:
June29_KW.22.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.24.featurecounts]

description:
June29_KW.24.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.21.featurecounts]

description:
June29_KW.21.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.23.featurecounts]

description:
June29_KW.23.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.20.featurecounts]

description:
June29_KW.20.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.25.featurecounts]

description:
June29_KW.25.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.19.featurecounts]

description:
June29_KW.19.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.18.featurecounts]

description:
June29_KW.18.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.14.featurecounts]

description:
June29_KW.14.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.16.featurecounts]

description:
June29_KW.16.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.15.featurecounts]

description:
June29_KW.15.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.33.featurecounts]

description:
June29_KW.33.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.32.featurecounts]

description:
June29_KW.32.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.13.featurecounts]

description:
June29_KW.13.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.11.featurecounts]

description:
June29_KW.11.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.10.featurecounts]

description:
June29_KW.10.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.12.featurecounts]

description:
June29_KW.12.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.1.featurecounts]

description:
June29_KW.1.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.17.featurecounts]

description:
June29_KW.17.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: Jejunum, LB81 yogurt intake mice, 28 months of age

status: Public on Jun 02 2018

type: RNA

city: Tokyo

first: Yuki

last: Usui

state: Tokyo

address: 4-6-1 Shirokanedai, Mintato-ku, Tokyo, Japan

department: Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

description: Gene expression data from jejunum of LB81 yogurt intake mice at 28 months of age.

hyb_protocol: cRNA were hybridized to Affymetrix Mouse Genome 430 2.0 chip (GPL1261; 45,101 probes) (n=1 per group).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 7G System.

data_processing: The CEL files were normalized by frozen robust multi-array analysis using frma and mouse4302frmavecs packages from Bioconductor in the R statistical language. The detection calls were calculated by MAS5.0 using the affy package from Bioconductor.

label: biotin

molecule: total RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix manual uisng GeneChip 3’IVT Express kit.

growth_protocol: The eight-month-old ICR male mice obtained from Japan SLC (Hamamatsu, Japan) were fed on a normal diet (AIN-93) (Oriental Yeast, Tokyo) or the same diet containing 1–2% LB81 yogurt until they were 28 months of age. Mice were maintained under specific-pathogen free conditions. Each mouse was reared in a single cage.

extract_protocol: Jejunum, ileum, distal colon, liver and spleen tissues were isolated from the control mice (n=9) and the LB81 yogurt intake mice (n=10) at the 28 months of age. Total RNA was extracted from individual tissues of each mice and equal amount of RNA from same group samples were pooled and mixed.

treatment_protocol: The eight-month-old ICR male mice were on a normal diet (AIN-93) or the same diet containing 1–2% LB81 yogurt until they were 28 months of age.

tag: tissues

value: Jejunum

value: 28 months of age

tag: gender

value: male

value: ICR


title: Jejunum, control mice, 28 months of age

description: Gene expression data from jejunum of control mice at 28 months of age.

source_name: Jejunum, control mice, 28 months of age


title: Ileum, control mice, 28 months of age

description: Gene expression data from ileum of control mice at 28 months of age.

source_name: Ileum, control mice, 28 months of age

value: Ileum


title: Liver, control mice, 28 months of age

description: Gene expression data from liver of control mice at 28 months of age.

source_name: Liver, control mice, 28 months of age

value: Liver


title: Ileum, 28-month-old

description: Gene expression data from ileum tissues of 28-month-old mice.

source_name: Ileum, 28-month-old


title: 686-2010--12DIV01

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

description: Gene expression at 12DIV in cultured mouse hippocampal neurons

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneChip scanner GSC3000 (Affymetrix, Santa Clara, CA)

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA algorithm (Irizarry et al., 2003)

source_name: Hippocampal neurons, 12DIV, replicate 2

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Pregnant RjOrl:SWISS female mice were purchased from Janvier Labs. Hippocampal and cortical cell cultures were prepared from e17.5-18.5 mouse embryos. Briefly, hippocampi were dissected,treated with 0.25% trypsin (Life Technologies) during 15 min at 37ºC and dissociated into single cells by gentle trituration. Neurons were seeded on glass coverslips or plastic plates coated with 0.1 mg/ml Poly-D-lysine (Sigma) at ~105 cells/cm2 or 2x104 cells/cm2 for low-density cultures. Neurons were plated in DMEM containing 10% fetal bovine serum (FBS), penicillin/streptomycin (pen/strep), and 1-2 hours later medium was replaced by Neurobasal medium supplemented with 2% B27, pen/strep, 0.6% Glucose and Glutamax (all reagents from Life Technologies). Cytosine arabinoside (1 µM; Sigma) was added to cultures at 3 days in vitro (DIV) and 1/3 of the medium was refreshed every 4-5 days

extract_protocol: RNA was prepared using the QIAGEN Rneasy Mini Kit - Total RNA Purification kit following the manufacturers instructions

treatment_protocol: No treatments were performed

tag: time

value: 12 days

tag: replicate

value: A


title: 687-2010--15DIV01

description: Gene expression at 15DIV in cultured mouse hippocampal neurons

source_name: Hippocampal neurons, 15DIV, replicate 2

value: 15 days


title: Jejunum, 4-month-old mice

description: Gene expression data from jejunum tissues of 4-month-old mice.

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

source_name: Jejunum, 4-month-old mice

growth_protocol: The eight-month-old ICR male mice obtained from Japan SLC (Hamamatsu, Shizuoka, Japan) were fed on a normal diet (AIN-93) (Oriental Yeast, Tokyo) until they were 28 months of age. The 2-month-old ICR male mice obtained from Japan SLC (Hamamatsu, Shizuoka, Japan) and were fed on a normal diet (AIN-93) (Oriental Yeast, Tokyo) until 4 months of age. Mice were maintained under specific-pathogen free conditions. Each mouse was reared in a single cage.

extract_protocol: Jejunum, ileum, distal colon, liver and spleen tissues were isolated from the 4-month-old mice (n=6) and the 28-month-old mice (n=9). Total RNA was extracted from individual tissues of each mice and equal amount of RNA from same group samples were pooled and mixed.

value: 4 months of age


title: Spleen, control mice, 28 months of age

description: Gene expression data from spleen of control mice at 28 months of age.

source_name: Spleen, control mice, 28 months of age

value: Spleen


title: Distal colon, 4-month-old mice

description: Gene expression data from distal colon tissues of 4-month-old mice.

source_name: Distal colon, 4-month-old mice

value: Distal colon


title: Distal colon, 28-month-old

description: Gene expression data from distal colon tissues of 28-month-old mice.

source_name: Distal colon, 28-month-old


title: Spleen, LB81 yogurt intake mice, 28 months of age

description: Gene expression data from spleen of LB81 yogurt intake mice at 28 months of age.


title: Distal colon, control mice, 28 months of age

description: Gene expression data from distal colon of control mice at 28 months of age.


title: Jejunum, 28-month-old

description: Gene expression data from jejunum tissues of 28-month-old mice.

source_name: Jejunum, 28-month-old


title: 760-2010--3DIV

description: Gene expression at 3DIV in cultured mouse hippocampal neurons

source_name: Hippocampal neurons, 3DIV, replicate 1

value: 3 days

value: B


title: 762-2010--12DIV

source_name: Hippocampal neurons, 12DIV, replicate 1


title: 685-2010--6DIV01

description: Gene expression at 6DIV in cultured mouse hippocampal neurons

source_name: Hippocampal neurons, 6DIV, replicate 2

value: 6 days


title: 681-2010--0DIV01

description: Gene expression at 0DIV in cultured mouse hippocampal neurons

source_name: Hippocampal neurons, 0DIV, replicate 2

value: 0 days


title: 684B-2010--3DIV01

source_name: Hippocampal neurons, 3DIV, replicate 2


title: 763-2010--15DIV

source_name: Hippocampal neurons, 15DIV, replicate 1


title: 682-2010--20h01

description: Gene expression at 1DIV in cultured mouse hippocampal neurons

source_name: Hippocampal neurons, 1DIV, replicate 2

value: 20 hours


title: 757-2010--0DIV

source_name: Hippocampal neurons, 0DIV, replicate 1


title: Liver, LB81 yogurt intake mice, 28 months of age

description: Gene expression data from liver of LB81 yogurt intake mice at 28 months of age.


title: Liver, 4-month-old mice

description: Gene expression data from liver tissues of 4-month-old mice.

source_name: Liver, 4-month-old mice


title: NICDID3

city: State College

first: Aswathy

last: Sebastian

address: University Park

institute: PennState

data_processing:
Illumina Truseq Stranded mRNA Librarykit was used and data was sequnced using Illumina HiSeq2500. Base calling was done using bcl2fastq v1.8.4 software and quality reports were generated using fastqc.
Trimmomatic (v0.32) was used for adapter trimming and low quality base removal
Data was processed using Tuxedo pipeline.Data mapping to the mm10 reference genome was done using Tophat2.
Transcriptome assembly was obtained using cufflinks and cuffmerge utilities.
Differential expression results were obtained using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Tab delimited text files include gene-level raw read counts for each sample

source_name: whole brain (including cerebellum)

extract_protocol:
Whole brains were removed and placed into RNAlater.  RNA was extracted using the Qiagen Rneasy Midi Kit. The libraries were made with the Illumina TruSeq RNA Sample Prep Kit (FC-122-1001). We used 100 ng of total RNA as input. The pool of libraries was sequenced on the Illumina HiSeq 2500 in Rapid Mode using 150 nt single read sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Nicotine Treatment: Mice were randomly assigned into four groups: Water-Water (WW), Water-Ethanol (WE), Nicotine-Water (NW), or Nicotine-Ethanol (NE). During the first six days of the experiment, mice were exposed to 3 glass drinking bottles filled with water or nicotine for 22 h a day, and a single water bottle for 2 h each day (Fig 1). For the WW and WE groups, all 3 bottles were filled with tap water. For the NW and NE groups, all 3 bottles were filled with 200 µg/ml (−)-nicotine freebase (Sigma–Aldrich, St. Louis, MO) dissolved in tap water. Bottles were placed on the cages at 1500 h and were removed and replaced with the single water bottle at 1300 h the next day. The three bottles were read and nicotine consumption (mg/kg) was calculated for each mouse. The 2 h single bottle was weighed and water consumption (ml) was calculated. Leakage/evaporation was accounted for by tubes on control cages handled using the same protocol, but with no animal present. We subtracted the volume lost in control tubes from individual drinking values. These procedures continued throughout the experiment. However, during the last 4 days (PND 42-45) mice were exposed to ethanol via the drinking-in-the-dark (DID) protocol.
Drinking-in-the-dark: During experimental days (7-10) nicotine exposure continued as detailed above (22 h/day), however, at 1300 h, all 3 bottles (nicotine or water) were removed and replaced with a single 10 ml serological pipette fitted with a ball bearing drinking spout containing either ethanol or water. Ethanol was prepared from ethyl alcohol (200 proof; Koptec 200) diluted in tap water to produce a 20% v/v solution. Mice had 2 h access to a single bottle of water or ethanol for three days (PND 42-44). On the final day (PND 45), mice had 4 h access to the ethanol bottle. Leakage/evaporation was accounted for by tubes on control cages as described above. At the end of the 4 h drinking session on the final day, blood samples were collected from the tail vein (10µl) and mice were sacrificed via cervical dislocation, whole brains including the cerebellum were dissected and placed into RNAlater® for subsequent RNA extraction.

tag: group

value: NE

value: female

tag: tissue

value: whole brain (including cerebellum)

value: PND 45 (when sacrificed)


title: Spleen, 4-month-old mice

description: Gene expression data from spleen tissues of 4-month-old mice.

source_name: Spleen, 4-month-old mice

value: male

value: ICR


title: Ileum, LB81 yogurt intake mice, 28 months of age

description: Gene expression data from ileum of LB81 yogurt intake mice at 28 months of age.

value: Ileum

value: 28 months of age


title: Ileum_6w_SPF_no_3

city: Berlin

first: Franziska

last: Schmidt

address: Hindenburgdamm 30

department: Medizinische Klinik für Gastroenterologie, Infektiologie and Rheumatology

country: Germany

institute: Charité-Universitätsmedizin Berlin

data_processing:
Base calling and barcode filtering were performed using Torrent Suite (5.8.0)
From single end reads (FASTQ files) adopters were removed and reads were cropped at 200 bp using Trimmomatic (0.36)
Sequencing quality was checked using FASTQC (0.11.5)
Reads were mapped using STAR aligner (2.5.3a) on mouse genome version mm10 (UCSC) with RefGene annotation and index with 200 bp splice junction overhang.
HTSeq were used to quantify gene raw counts.
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: text-files include raw counts

source_name: terminal ileum

extract_protocol:
total RNA was extracted by Qiazol lysis reagent
generation of 3’ polyA tag mRNA libraries was performed using the QuantSeq 3′ mRNA-Seq Library Prep Kit for Ion Torrent (Lexogen, Vienna Biocenter)

value: 6 weeks

value: terminal ileum

tag: microbial colonization status

value: specific-pathogen free

tag: treatment

value: no


title: BRAF_219

first: Markus

last: Morkel

address: Charitéplatz 1

department: Dept. of Pathology

institute: Charité - Universitätsmedizin Berlin

data_processing:
The following Illumina HiSeq software suite versions were employed: HCS 2.2.58; RTA: 1.18.64; BCL Converter: 2.17.1.14
RNAseq reads were aligned to the mouse genome GRCm38 using STAR aligner and Gencode exon annotations
Read counts were calculated for each gene_id using HTSeq
After removal of ribosomal reads, raw counts were normalized using the DESeq function estimateSizeFactors, and dispersion in replicates were calculated using the DESeq function estimateDispersions with default parameters
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file containing processed read counts (fpkm values) per gene_id and sample

source_name: small intestinal organoids

growth_protocol: Organoid cultures of transgenic mouse small intestine were propagated as described in Sato et al., Gastroenterology (2011), using 48-well plates with 15µl droplets of medium and Matrigel (BD) per well overlaid with 300µl CCM-REN.

extract_protocol:
Total RNA from sorted cells was extracted using the RNeasy micro Kit (Qiagen)
100ng total RNA were used for library preparation with the ScriptSeq Kit (Illumina) according to the manufacturer’s instructions

treatment_protocol: Transgenes (luc-tdTomato, KRASG12V-tdTomato, BRAFV600E-tdtomato) were induced by adding 2µg/ml doxycycline to the cultures for 24h. Fluorescence activated cell sorting was done after dissociation in TrypLE (Gibco) and 100U/µl DNAseI (Sigma) for 15min. at 37°C, followed by filtering through a 30µM strainer (Costar), using an ARIA II SORP (BD). Cells positive for the tdTomato transgene and negative for a green live/dead stain were collected.

value: intestine, duodenum

tag: dev. stage

value: adult

tag: transgene


title: BRAF_231


title: KRAS_1


title: KRAS_369


title: Spleen, 28-month-old mice

description: Gene expression data from spleen tissues of 28-month-old mice.

source_name: Spleen, 28-month-old mice

value: Spleen


description: Gene expression data from distal colon of LB81 yogurt intake mice at 28 months of age.

source_name: Distal colon, LB81 yogurt intake mice, 28 months of ages

value: Distal colon


title: Ileum, 4-month-old mice

description: Gene expression data from ileum tissues of 4-month-old mice.

source_name: Ileum, 4-month-old mice

value: 4 months of age


title: Liver, 28-month-old mice

description: Gene expression data from liver tissues of 28-month-old mice.

source_name: Liver, 28-month-old mice

value: Liver


title: 758-2010--1DIV

source_name: Hippocampal neurons, 1DIV, replicate 1

value: 20 hours

value: B


title: NICDID5

value: NE

value: female

value: whole brain (including cerebellum)

value: PND 45 (when sacrificed)


title: NICDID7

value: NW


title: 761-2010--6DIV

source_name: Hippocampal neurons, 6DIV, replicate 1

value: 6 days


title: Ileum_6w_COL_no_2

value: 6 weeks

value: terminal ileum

value: germ free mice, colonized in week 5 of age with SPF microbiota


title: NICDID4


title: NICDID2


title: NICDID16

value: WE


title: LUC_989

value: intestine, duodenum

value: adult

value: luc-tdTomato


title: NICDID11


title: Ileum_6w_COL_no_1

value: no


title: Ileum_6w_SPF_no_2

value: specific-pathogen free


title: Ileum_6w_SPF_no_1


title: NICDID10


title: NICDID8


title: Ileum_6w_COL_no_3


title: Ileum_6w_GF_no_2

value: germ free


title: Ileum_6w_GF_no_3


title: LUC_987


title: Ileum_10w_GF_no_1

value: 10 weeks


title: Ileum_10w_GF_no_2


title: Ileum_6w_GF_no_1


title: Ileum_10w_GF_no_3


title: NICDID20

value: WW


title: NICDID19

value: female


title: Ileum_10w_SPF_no_2


title: NICDID18

value: whole brain (including cerebellum)


title: Ileum_10w_COL_no_2


title: Colon_10w_SPF_no_1

source_name: distal colon

value: colon


title: NICDID13

value: PND 45 (when sacrificed)


title: NICDID15


title: Colon_10w_SPF_no_2


title: NICDID21


title: Colon_10w_COL_no_2


title: Colon_10w_COL_no_1


title: Colon_10w_SPF_DSS_3

value: 1,5 % DSS 4 days plus 2 days water


title: Colon_10w_SPF_DSS_2


title: NICDID14


title: Ileum_10w_SPF_no_3


title: Ileum_10w_SPF_no_1


title: Ileum_10w_COL_no_3


title: H358 GFP-TNFa

city: Hangzhou

first: Qiong

last: Zhang

address: 866 YuHangTang Rd, Medical Research Building A212, ZiJinGang Campus, Zhejiang University

country: China

institute: Zhejiang University

description:
WTTNF
gene expression after 1 hr treatment of TNFa

hyb_protocol: Fluorescent targets were hybridized to the Human Whole Genome OneArray with Phalanx hybridization buffer using the Phalanx Hybridization System. After 16 hr of hybridization at 50 °C, non-specific binding targets were washed away by three different washing steps (wash I 42 °C 5 min; wash II 42 °C, 5 min, 25 °C 5 min; wash III rinse 20 times) then dried immediately by brief centrifugation.

scan_protocol: Slides were scanne on the Agilent G2505C scanner (Agilent Technologies, Santa Clara, CA, USA)

data_processing: The Cy5 fluorescence intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices). The signal intensity of each spot was loaded into the Rosetta Resolver System (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System could remove both systematic and random errors from the data. We filtered out spots for which the flag was less than 0. Spots that passed the criteria were normalized by the 50% media scaling normalization method. The technically repeated data were tested by the Pearson correlation coefficient calculation to check the reproducibility (R value > 0.975). Normalized spot intensities were transformed to gene expression log2 ratios between the control and treatment groups. The spots with log2 ratio ≥ 1 or log2 ratio ≤ −1 and P-value < 0.05 were tested for further analysis.

organism: Homo sapiens

source_name: H358 GFP, TNFa, 60 min

label_protocol: Target preparation was performed using an Eberwine-based amplification method with Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, AM1753) to generate amino-allyl antisense RNA(aa-aRNA). Labeled aRNA coupled with NHS-CyDye was prepared and purified prior to hybridization

growth_protocol: H358 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (Gibco), penicillin (100 U/ml), and streptomycin (100 mg/ml) at 37 °C in 5% CO2 (v/v).

extract_protocol: RNA was extracted by Trizol (Invitrogen) following the manufacturer's instructions.

treatment_protocol: Each cell line was treated with 10 g/ml TNF-a, 10 g/ml IL-1b or vehicle for 1 hour before harvest.

tag: cell line

value: bronchioalveolar carcinoma cell line H358

value: control

value: TNFa


title: Colon_10w_COL_no_3

tag: strain

value: germ free mice, colonized in week 5 of age with SPF microbiota


title: Colon_10w_SPF_no_3


title: Ileum_10w_COL_no_1

value: terminal ileum


title: Colon_10w_COL_DSS_2


title: Colon_10w_COL_DSS_3


title: Colon_10w_COL_DSS_1


title: Colon_10w_SPF_DSS_1


title: H358 YAP(5SA)-TNFa

description:
SATNF
gene expression after 1 hr treatment of TNFa

source_name: H358 YAP(5SA), TNFa, 60 min

tag: genotype

value: expressing YAP(5SA)


title: H358 GFP-IL-1b

description:
WTIL1
gene expression after 1 hr treatment of IL-1b

source_name: H358 GFP, IL-1b, 60 min


title: H358 YAP(5SA)-vehicle

description:
SAC
gene expression after 1 hr treatment of vehicle

source_name: H358 YAP(5SA), vehicle, 60 min

value: vehicle


title: OXA treated vs non-treated 3

city: Olsztyn

first: Kamil

last: Dobrzyn

state: Warminsko-Mazurskie

address: Oczapowskiego, 1A

department: Department of Animal Anatomy and Physiology

country: Poland

institute: University of Warmia and Mazury

description: US45103052_252644011040_S01_GE2_107_Sep09_1_3.txt:cy5ByCy3Signal(normalized)

hyb_protocol: Two differentially labelled samples (from OXA treated and non-treated, control samples) were placed on each array (one slide, n = 4) in a balanced block design with dye swaps. Hybridization was carried out in an Agilent hybridization oven for 17 h at 60°C. After the hybridization process, the microarrays were washed.

scan_protocol: Microarrays were scanned at 5 μm resolution with an Agilent’s High-Resolution C Microarray Scanner according to the manufacturers's protocol.

data_processing: The TIFF image, generated after the scanning process, was used for: data extraction and detailed analysis, background subtraction from features, and dye normalizations (linear and LOWESS); in the Feature Extraction Software. Gene expression data were analysed in GeneSpring GX 12 software (Agilent Technologies, USA) to identify the genes that were differentially expressed in pigs that were and were not treated with OXA.

organism: Sus scrofa domesticus

source_name: endometrium non-treated

label_protocol: The RNA isolated from the control and OXA treated tissues were labelled with Cyanine-3 (Cy-3) and Cyanine-5 (Cy-5), respectively. Quantity and purity of obtained cRNA were measured with NanoQuant plates on the Infinite M200 Pro plate reader . 825 ng of Cy-3 and 825 ng of Cy-5-labeled cRNA were mixed together (for each microarray). According to microarray manufacturer’s protocol, cRNA was fragmented and mixed with hybridization buffer.

growth_protocol: Four mature gilts (Large White x Polish Landrace) were used in the study (n = 4). All individuals were descended from private breeding farm. The gilts were at the age of 7-8 months and the weight of 120 to 130 kg. All animals used in the study were on days 15 to 16 of gestation. The day after coitus was marked as the first day of gestation. Insemination was performed on days 1 to 2 of the oestrous cycle. Pregnancy was confirmed by the presence of conceptuses. 15 to 16 days after coition, gilts were sacrificed. Pigs were slaughtered by qualified abattoir worker.

extract_protocol: Total RNA was extracted from tissues using peqGOLD TriFast isolation system according to the manufacturer’s instructions. RNA purity and quantity were measured spectrophotometrically . RNA quality was checked using RNA 6000 Nano Assay Kit on an Agilent 2100 Bioanalyzer. RNA integrity number (RIN) score between 8 and 10 were used for microarray analysis and quantitative real-time PCR (qPCR) experiments. RNAs were stored at −80 °C until the microarray analysis.

treatment_protocol: The endometrial explants obtained from the middle of uterine horns were cut into small, irregular slices (3 mm of thickness, 100 mg ± 10%). Tissue explants were washed three times in medium M199. The tissue explants were placed in the separate sterile culture vials with 2 mL medium 199 containing. Cultures were preincubated for 2 h (37°C, 95% O2, 5% CO2). To determine the influence of OXA on the global gene expression in the endometrium, slices were treated with OXA  at the concentration of 10 nM and incubated for another 24 h at the same conditions. Control tissues were incubated without any treatment. All cultures were prepared in duplicates in four separate experiments for each group (n = 4). The endometrial tissue explants were frozen and stored at -80°C for further analyses.

tag: race

value: Large White x Polish Landrace

tag: gilts age and weight

value: mature/7-8 months/120 to 130 kg

tag: period of pregnancy

value: days 15 to 16

value: endometrium

source_name: endometrium OXA-treated

value: 10 nM OXA


title: SK04_Huvec UT-1

status: Public on Jun 01 2018

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

label: Biotin

source_name: Huvec primary cells

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix human 1.0 ST  (Affymetrix, Inc).   Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to labeling.  300ng of total RNA was used for labeling with the Affymetrix WT plus kit. After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

growth_protocol: HUVEC were purchased from Lonza. cells were cultured using EGM2 medium containing penicillin, streptomycin, and glutamine. MDA-MB-231, breast carcinoma cells was cultured using RPM1640 complete media.

extract_protocol: Total RNA from HUVEC treated with EVs from MDA231 differentiated breast cancer cells were extracted and qualitative analysis were performed using the Agilent Bioanalyzer.Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Before EV isolation, the cells were cultured using low human AB serum in the respective media for one passage.  The cells were cultured in 75 cm2 flasks and conditioned media (100 ml) was collected and concentrated to 1 ml using Centricon filters (EMD Millipore) with a cutoff of 10 kDa. A 250 µl volume of concentrated conditioned medium from the respective cells was used to isolate EVs. The EVs were isolated using ExoQuick kit according to the manufacturer’s instructions (SBI Biosciences).  The isolated EVs were washed with PBS (Ca and Mg free) and analyzed using flow cytometry as described earlier (Kaur et al., 2014b). HUVEC cells were treated with MDA-MB-231 exosomes for 3-days

value: endothelial

value: HuVEC

value: untreated


title: SK01_Huvec exo-1

hyb_protocol: After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

value: treated MDA231 exosomes


title: H358 YAP(5SA)-IL-1b

description:
SAIL1
gene expression after 1 hr treatment of IL-1b

source_name: H358 YAP(5SA), IL-1b, 60 min


title: OXA treated vs non-treated 1

description: US45103052_252644011040_S02_GE2_107_Sep09_1_1.txt:cy5ByCy3Signal(normalized)


title: OXA treated vs non-treated 4

description: US45103052_252644011040_S01_GE2_107_Sep09_1_4.txt:cy3ByCy5Signal(normalized)


title: SK05_Huvec UT-2


title: SK06_Huvec UT-3


title: H358 GFP-vehicle

description:
WTC
gene expression after 1 hr treatment of vehicle

source_name: H358 GFP, vehicle, 60 min


title: OXA treated vs non-treated 2

description: US45103052_252644011040_S01_GE2_107_Sep09_1_2.txt:cy3ByCy5Signal(normalized)


title: DMSO treated control cells, biological replicate 2

city: Gothenburg

first: Mattias

last: Andersson

address: Medicinaregatan 1F

department: Sahlgrenska Cancer Center

country: Sweden

institute: University of Gothenburg

description: epithelial

hyb_protocol: Hybridization to Affymetrix Human Gene 1.0 ST arrays was performed using standard Affymetrix protocols.

scan_protocol: Arrays were scanned using a GeneChip scanner 3000 and image analysis was performed using the GeneChip Operating Software.

data_processing: Probe summarization and data normalization were performed using Robust Multi-array Analysis (RMA) with the Expression Console Software v1.1.2.

source_name: lacrimal gland

label_protocol: Biotin labled cRNA was syntesized from 200 ng total RNA according to standard Affymetrix protocols.

growth_protocol: Cells were grown in DMEM/F12 based medium at 37 degrees Celsius and in 5% CO2.

extract_protocol: Total RNA was isolated using the Trizol reagent (Life Technologies) followed by the RNeasy Mini kit (Qiagen).

treatment_protocol: Cells were treated with either 50 nM siRNA for 48 hours or 1 micromolar of linsitinib or BMS-754807 for 24 hours in biological triplicates.

tag: agent

value: DMSO

tag: sirna

tag: cell type

value: adenoid cystic carcinoma cells


title: SK03_Huvec exo-3


title: DMSO treated control cells, biological replicate 3

description: epithelial


title: BMS-754807 treated cells, biological replicate 1

description: epithelial


title: MYB siRNA 2 treated cells, biological replicate 3

description: epithelial

value: MYB siRNA 2


title: BMS-754807 treated cells, biological replicate 3

description: epithelial


title: ACC xenograft ACCX6

data_processing:
Probe summarization and data normalization were performed using Robust Multi-array Analysis (RMA) with the Expression Console Software v1.4.1.
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: ACC xenograft

value: lung metastasis, primary tumor oral cavity

tag: cells

value: adenoid cystic carcinoma cells (xenograft)

value: epithelial


title: MYB siRNA 2 treated cells, biological replicate 1

description: epithelial


title: BMS-754807 treated cells, biological replicate 2

description: epithelial


title: ACC xenograft ACCX5M1

value: lung metastasis, primary tumor parotid gland


title: linsitinib treated cells, biological replicate 3

description: epithelial

value: linsitinib


title: SK02_Huvec exo-2


title: MYB siRNA 2 treated cells, biological replicate 2

description: epithelial


title: FatMinus_RMM104

city: Singapore

first: Daniel

last: Carbajo

state: Singapore

address: 8A Biomedical Grove, Immunos Building levels 3 & 4

department: Bioinformatics

country: Singapore

institute: SIgN (A*STAR)

description: Fat3 Lyve1- macrophages

data_processing:
Paired-end reads were mapped to reference genome using STAR version 2.5.2b
Mapped paired-end reads were summarized to gene level using featureCounts v1.5.0 and with GENCODE GRCm38 vM7 gene annotation
Counts per million were calculated in R_3.3.0 using edgeR_3.14.0 over TMM-normalized read counts summarized at gene level; CPM values were log2-transformed
Genome_build: GRCm38
Supplementary_files_format_and_content: log2-transformed CPM values calculated on TMM-normalized read counts summarized at gene level; raw counts per sample

source_name: Fat Lyve1- macrophages

extract_protocol:
Total RNA was extracted using Arcturus PicoPure RNA Isolation kit (Thermofisher, KIT0204) according to manufacturer’s protocol.
cDNA libraries were prepared using 2ng of total RNA and 1ul of a 1:50,000 dilution of Ambion ERCC RNA Spike-in Controls (Thermofisher, 4456740) using the SMARTSeq v2 protocol described in Nature Protocols volume 9, pages 171-181 (Picelli et al., 2014) with the following modifications: 1. Use of 20mM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Nextera XT kit (Illumina, FC-131). 12 samples were subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2000 (20 samples/lane) and 1 sample was subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2500 Rapid mode (14 samples/lane).

tag: genotype/variation

value: wid type

value: Adipose tissue

value: sorted Lyve1- macrophages


title: AortaMinus_RHH1775

description: Aorta2 Lyve1- macrophages

source_name: Aorta Lyve1- macrophages

value: Aorta


title: FatPlus_RMM101

description: Fat3 Lyve1+ macrophages

source_name: Fat Lyve1+ macrophages

value: sorted Lyve1+ macrophages


title: FatMinus_RMM102

description: Fat1 Lyve1- macrophages


title: FatMinus_RMM103

description: Fat2 Lyve1- macrophages


title: AortaMinus_RHH1776

description: Aorta3 Lyve1- macrophages


title: linsitinib treated cells, biological replicate 2

description: epithelial


title: linsitinib treated cells, biological replicate 1

description: epithelial


title: Treg_CT5

city: Boston

first: Irene

last: Ghobrial

state: MA

address: 4 Blackfan Circle, 2nd Floor, Suite 240

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
We used Picard and STAR to process and align the RNA-seq reads with mouse reference genome (mm10) and to compute a series of quality control metrics.
RNA-seq transcript abundances were estimated using RSEM.
Genes with low expression (RSEM expected counts) were filtered out and differential gene expression between different samples was determined using DESeq2.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: RSEM output

source_name: BM of control mice

extract_protocol:
Total RNA was isolated from flow-sorted CD4+FOXP3-GFP+ cells acquired from the BM of Vk*MYC-injected and control mice using Rneasy Micro kit (QIAGEN).
NEBNext Ultra RNA Library prep kit

tag: condition

value: Control


title: AortaPlus_RHH1773

description: Aorta3 Lyve1+ macrophages

source_name: Aorta Lyve1+ macrophages

tag: tissue


title: Treg_CT1


title: DMSO treated control cells, biological replicate 1

description: epithelial


title: control siRNA treated cells, biological replicate 3

description: epithelial

value: control siRNA


title: MYB siRNA 1 treated cells, biological replicate 3

description: epithelial

value: MYB siRNA 1


title: deletion SIRT1, rep3

city: Geneva

first: Giorgio

last: Ramadori

address: Michel Servet 1

country: Switzerland

institute: University of Geneva

description: POOLF

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R.

source_name: ventromedial hypothalamus, SIRT1 deletion

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain/background

value: mixed genetic background

value: Sf1-Cre; Sirt1loxP/loxP

tag: age

value: 16 weeks

value: ventromedial hypothalamus


title: MYB siRNA 1 treated cells, biological replicate 1

description: epithelial

value: adenoid cystic carcinoma cells


title: control siRNA treated cells, biological replicate 2

description: epithelial


title: deletion SIRT1, rep1

description: POOLD


title: control, rep1

description: POOLA

source_name: ventromedial hypothalamus, control


title: control, rep3

description: POOLC


title: control, rep2

description: POOLB


title: deletion SIRT1, rep2

description: POOLE


title: CMP_replicate2

city: shang hai

first: Qian

address: xiangyin road 800

institute: Second military medical university

data_processing:
Illumina Casava1.6 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads) as described in article: Mortazavi, A., B. A. Williams, et al. (2008).
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 5(7): 621-8.
A strict algorithm was developed to identify differentially expressed genes refering to Audic, S. and J. M. Claverie (1997). The significance of digital gene expression profiles. Genome Res 7(10): 986-95.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with mean value of gene expression.

source_name: bone marrow

growth_protocol: The above cell subsets were isolated from spleen of tumor-bearing mice,embryonic liver (E14.5) and bone marrow of wild type mice by cell sorter respectively. Cells with purity >98% were used for subsequent experiments.

extract_protocol:
RNA was harvested using Trizol reagent, and isolated using an RNA isolation kit (QIAGEN). TruSeqRNASample Preparation Kit (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: common myeloid progenitor cells isolated from bone marrow

value: bone marrow

tag: cell markers

value: wild type


title: HSC_repicate2

value: hematopoietic stem cells  isolated from bone marrow

value: c-Kit+Sca-1+Lin−, purity >98%


title: MEP_replicate1

value: megakaryocyte-erythroid progenitor cells isolated from bone marrow


title: HSC_replicate1


title: CLP_replicate1

value: common lymphoid progenitor cells isolated from bone marrow

value: c-Kit+Sca-1+IL-7R+Lin−,purity >98%


title: AortaMinus_RHH1774

description: Aorta1 Lyve1- macrophages

value: wid type

value: Aorta

value: sorted Lyve1- macrophages


title: EL Ter cells_replicate1

source_name: embryonic liver

value: Ter-119+CD45-Lin- cells sorted from embryonic liver (E14.5)

value: embryonic liver

value: Ter-119+CD45- Lin-, purity >98%


title: MYB siRNA 1 treated cells, biological replicate 2

description: epithelial

value: MYB siRNA 1


title: AortaPlus_RMM106

description: Aorta2 Lyve1+ macrophages

value: sorted Lyve1+ macrophages


title: FatPlus_RMM099

description: Fat1 Lyve1+ macrophages

value: Adipose tissue


title: Ter cells_replicate1

source_name: tumor stage -spleen

value: Ter-119+CD45-Lin-cells sorted from spleen of tumor-bearing mice

value: tumor stage -spleen

value: Ter-119+CD45-Lin-, purity >98%


title: Treg_MM5

source_name: BM of Vk-MYC-injected mice

value: Multiple Myeloma


title: Treg_CT3

value: Control


title: Treg_MM4


title: FatPlus_RMM100

description: Fat2 Lyve1+ macrophages


title: CMP_replicate1

value: common myeloid progenitor cells isolated from bone marrow

value: bone marrow

value: wild type


title: CLP_replicate2

value: common lymphoid progenitor cells isolated from bone marrow

value: c-Kit+Sca-1+IL-7R+Lin−,purity >98%


title: Treg_MM3


title: MEP_replicate2

value: megakaryocyte-erythroid progenitor cells isolated from bone marrow


title: Control_replicate1

value: CD45+Ter-119- cells sorted from spleen of tumor-bearing mice


title: EL Ter cells_replicate2

value: Ter-119+CD45-Lin- cells sorted from embryonic liver (E14.5)

value: embryonic liver


title: Ter cells_replicate2

value: Ter-119+CD45-Lin- cells sorted from spleen of tumor-bearing mice


title: Control_replicate2


title: wt_emb_MNase-seq_rep2_16U_ml

city: Cambridge

first: Julie

last: Ahringer

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

library_source: genomic

data_processing:
Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.
Improperly paired, low-quality (q<10), mitochondrial, and modENCODE-blacklisted reads were discarded.
Normalised coverage was calculated from <300bp reads using MACS2: --format BAMPE --bdg --SPMR --gsize ce --nolambda, and smoothed by binning the signal at 10bp resolution.
Genome_build: WBcel215/ce10 (WS220)
Supplementary_files_format_and_content: Genome-wide accessibility profiles by stage/concentration/replicate.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: mixed embryos

growth_protocol: Wild-type N2 were grown at 20°C in liquid culture to the adult stage using standard S-basal medium with HB101 bacteria, animals bleached to obtain embryos, and the embryos hatched without food in M9 buffer for 24 hrs at 20°C to obtain synchronized starved L1 larvae. L1 larvae were grown in a further liquid culture at 20°C to the desired stage, then collected, washed in M9, floated on sucrose, washed again in M9, then frozen into "popcorn" by dripping embryo or worm slurry into liquid nitrogen. Popcorn were stored at -80°C until use. Times of growth were L1 (4 hrs), L2 (20 hrs), L3 (30 hrs), L4 (45 hrs), young adults (60 hrs). Mixed populations of embryos were collected by bleaching cultures of synchronized one day old adults. glp-1(e2144) were raised at 15°C on standard NGM plates seeded with OP50 bacteria. Embryos were obtained by bleaching gravid adults and then approximately 6000 placed at 25°C on 150mm 2% NGM plates seeded with a 30X concentrated overnight culture of OP50. For harvest, worms were washed 3X in M9 and then worm slurry was frozen into popcorn by dripping into liquid nitrogen and stored at -80°C. Harvest times after embryo plating were D1/YA (53 hrs), D2 (71 hrs), D6 (167 hrs), D9 (239 hrs), D13 (335 hrs).

extract_protocol:
Frozen embryos or worms were broken by grinding in a mortar and pestle or smashing using a Biopulverizer, then the frozen powder was thawed in 10 ml Egg buffer (25 mM HEPES pH 7.3, 118 mM NaCl, 48 mM KCl, 2 mM CaCl2, 2 mM MgCl2). Ground worms were pelleted by spinning at 1500 g for 2 minutes, then resuspended in 10ml working Buffer A (0.3M sucrose, 10 mM Tris pH 7.5, 10 mM MgCl2, 1mM DTT, 0.5 mM spermidine 0.15 mM spermine, protease inhibitors (Roche complete, EDTA free) containing 0.025% IGEPAL CA-630. The sample was dounced 10X in a 14ml stainless steel tissue grinder (VWR), then the sample spun 100g for 6 min to pellet large fragments. The supernatant was kept and the pellet resuspended in a further 10 ml Buffer A, then dounced for 25 strokes. This was spun 100g for 6 min to pellet debris and the supernatants, which contain the nuclei, were pooled, spun again at 100g for 6 min to pellet debris, and transferred to a new tube. Nuclei were counted using a hemocytometer. Twenty million nuclei were transferred to a 1.5 ml tube and spun 2000g for 10min to pellet.
Replicate concentration courses of DNase I were performed for each stage as follows. Twenty million nuclei were digested for 10 minutes at 25C using 2.5, 5, 10, 25, 50, 100, 200, and 800 units/ml DNase I (Roche), then EDTA was added to stop the reactions. Embryo micrococcal nuclease (MNase) digestion concentration courses for embryos were made by digesting nuclei with 0.025, 0.05, 0.1, 0.25, 0.5, 1, 4, 8, or 16 units/ml MNase in 10mM Tris pH 7.5, 10mM MgCl2, 4mM CaCl2 for 10 minutes at 37C. Reactions were stopped by the additon of EDTA. Following digestions, total DNA was isolated from the nuclei following proteinase K and RNase A digestion, then large fragments removed by binding to Agencourt AMPure XP beads (0.5 volumes). Small double cut fragments < 300 bp were isolated either using a Pippen prep gel (protocol 1) or using Agencourt AMPure XP beads (protocol 2). DNA was converted into sequencing libraries using the Illumina Truseq kit.

value: wild-type N2

value: mixed embryos

tag: protocol


title: control siRNA treated cells, biological replicate 1

description: epithelial

value: control siRNA

value: adenoid cystic carcinoma cells


title: wt_emb_MNase-seq_rep2_8U_ml


title: wt_emb_MNase-seq_rep2_1U_ml


title: wt_emb_MNase-seq_rep2_0.5U_ml


title: wt_emb_MNase-seq_rep2_0.25U_ml


title: wt_emb_MNase-seq_rep2_0.1U_ml


title: wt_emb_MNase-seq_rep2_4U_ml


title: wt_emb_MNase-seq_rep1_16U_ml


title: wt_emb_MNase-seq_rep1_8U_ml


title: wt_emb_MNase-seq_rep2_0.025U_ml


title: wt_emb_MNase-seq_rep2_0.05U_ml


title: wt_emb_MNase-seq_rep1_1U_ml


title: wt_emb_MNase-seq_rep1_4U_ml


title: GBM primary cultures (p<2) NR12

city: Nantes

first: Raluca

last: TEUSAN

address: IRS-UN - 8 quai Moncousu - BP 70721

country: France

institute: Inserm

hyb_protocol: 20ug cRNA per hybridization; Incubation under rotation (60 rpm); GeneChip Fluidics Station 400; Agilent SurePrintG3 Human GE 8x60.

scan_protocol: The scanned images (Agilent Technologies Scanner G2505C) were analyzed with Feature Extraction Software (10.7.1.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

data_processing: The raw signals of each probe for all the arrays were normalized against a virtual median chip (median raw intensity per row) using a local weighted scattered plot smoother analysis.

source_name: GBM primary cultures (p<2), MES

label_protocol: 3 ug of total RNA of each sample as starting material. In vitro transcription with Enzo BioArray High Yield RNA Transcript Labeling kit; T7 RNA polymerase; one-cycle target labeling protocol; one-cycle EukGE-WS2v5 target labeling protocol.

growth_protocol: Samples were grown in defined media DMEM/F12 supplemented with penicillin, streptomycin, glutamine, N2, B27, EGF, FGF and heparin.

extract_protocol: All samples were stored at -80C. Total RNA extraction using RNeasy mini kit (Qiagen) according to the manufacturer's instructions. The quality of RNA was controlled by an Agilent 2100 Bioanalyser. RNAs were qualified if the 28S/18S ratio was more than 1.5.

treatment_protocol: No treatment.

value: glioblastoma multiforme (GBM) primary culture

tag: passage

tag: molecular subtype

value: MES


title: GBM primary cultures (p<2) NR09


title: wt_emb_MNase-seq_rep1_0.5U_ml

tag: strain


title: GBM primary cultures (p<2) NR05

source_name: GBM primary cultures (p<2), PROLIF/PN

value: PROLIF/PN


title: GBM primary cultures (p<2) NR07


title: GBM primary cultures (p<2) NR06


title: GBM primary cultures (p<2) NR11


title: GBM primary cultures (p<2) NR04


title: GBM primary cultures (p<2) NR03


title: GBM primary cultures (p<2) NR02


title: GBM primary cultures (p<2) NR08


title: GBM primary cultures (p<2) NR10


title: wt_emb_MNase-seq_rep1_0.1U_ml


title: wt_YA_DNase-seq_rep2_800U_ml

source_name: young adults

value: young adults


title: wt_YA_DNase-seq_rep2_400U_ml


title: wt_emb_MNase-seq_rep1_0.25U_ml


title: wt_YA_DNase-seq_rep2_50U_ml


title: wt_YA_DNase-seq_rep2_10U_ml


title: wt_YA_DNase-seq_rep2_5U_ml


title: wt_YA_DNase-seq_rep2_2.5U_ml


title: wt_YA_DNase-seq_rep2_100U_ml


title: wt_YA_DNase-seq_rep1_400U_ml


title: wt_YA_DNase-seq_rep1_800U_ml


title: wt_YA_DNase-seq_rep2_200U_ml


title: wt_YA_DNase-seq_rep2_25U_ml


title: wt_YA_DNase-seq_rep1_200U_ml


title: wt_YA_DNase-seq_rep1_25U_ml


title: wt_YA_DNase-seq_rep1_2.5U_ml


title: wt_YA_DNase-seq_rep1_10U_ml


title: wt_L4_DNase-seq_rep2_800U_ml

source_name: L4 larvae

value: L4 larvae


title: wt_L4_DNase-seq_rep2_400U_ml


title: wt_L4_DNase-seq_rep2_200U_ml


title: GBM primary cultures (p<2) NR01


title: wt_L4_DNase-seq_rep2_100U_ml


title: wt_YA_DNase-seq_rep1_100U_ml


title: wt_L4_DNase-seq_rep2_10U_ml


title: wt_L4_DNase-seq_rep2_25U_ml


title: wt_L4_DNase-seq_rep2_5U_ml


title: wt_L4_DNase-seq_rep2_50U_ml


title: wt_L4_DNase-seq_rep1_100U_ml


title: wt_L4_DNase-seq_rep1_200U_ml


title: wt_L4_DNase-seq_rep1_400U_ml


title: wt_YA_DNase-seq_rep1_50U_ml


title: wt_L4_DNase-seq_rep1_50U_ml


title: wt_L4_DNase-seq_rep1_25U_ml


title: wt_L3_DNase-seq_rep2_200U_ml

source_name: L3 larvae

value: L3 larvae


title: wt_L3_DNase-seq_rep2_100U_ml


title: wt_L4_DNase-seq_rep1_10U_ml


title: wt_L3_DNase-seq_rep2_5U_ml


title: wt_L3_DNase-seq_rep2_2.5U_ml


title: wt_L3_DNase-seq_rep2_10U_ml


title: wt_L3_DNase-seq_rep2_25U_ml


title: wt_L3_DNase-seq_rep2_400U_ml


title: wt_L3_DNase-seq_rep2_50U_ml


title: wt_L3_DNase-seq_rep1_800U_ml


title: wt_L3_DNase-seq_rep2_800U_ml


title: wt_L4_DNase-seq_rep2_2.5U_ml


title: wt_L4_DNase-seq_rep1_2.5U_ml


title: wt_L4_DNase-seq_rep1_800U_ml


title: wt_L3_DNase-seq_rep1_400U_ml


title: wt_L3_DNase-seq_rep1_50U_ml


title: wt_L3_DNase-seq_rep1_100U_ml


title: wt_L3_DNase-seq_rep1_200U_ml


title: wt_L3_DNase-seq_rep1_25U_ml


title: wt_L3_DNase-seq_rep1_10U_ml


title: wt_L2_DNase-seq_rep2_100U_ml

source_name: L2 larvae

value: L2 larvae


title: wt_L2_DNase-seq_rep2_25U_ml


title: wt_L4_DNase-seq_rep1_5U_ml


title: wt_L3_DNase-seq_rep1_2.5U_ml


title: wt_L2_DNase-seq_rep2_10U_ml


title: wt_L2_DNase-seq_rep2_200U_ml


title: wt_L2_DNase-seq_rep2_50U_ml


title: wt_L2_DNase-seq_rep1_800U_ml


title: wt_L2_DNase-seq_rep1_400U_ml


title: wt_L2_DNase-seq_rep1_200U_ml


title: wt_L2_DNase-seq_rep1_10U_ml


title: wt_L1_DNase-seq_rep2_400U_ml

source_name: L1 larvae

value: L1 larvae


title: wt_L2_DNase-seq_rep1_50U_ml


title: wt_L2_DNase-seq_rep1_25U_ml


title: wt_L1_DNase-seq_rep2_800U_ml


title: wt_L2_DNase-seq_rep1_2.5U_ml


title: wt_L1_DNase-seq_rep2_10U_ml


title: wt_L1_DNase-seq_rep2_5U_ml


title: wt_L1_DNase-seq_rep2_50U_ml


title: wt_L1_DNase-seq_rep2_100U_ml


title: wt_L2_DNase-seq_rep2_400U_ml


title: wt_L2_DNase-seq_rep2_800U_ml


title: wt_L1_DNase-seq_rep2_25U_ml


title: wt_L1_DNase-seq_rep2_2.5U_ml


title: wt_L1_DNase-seq_rep1_400U_ml


title: wt_L2_DNase-seq_rep2_5U_ml


title: wt_L1_DNase-seq_rep1_100U_ml


title: wt_L1_DNase-seq_rep1_200U_ml


title: wt_L2_DNase-seq_rep2_2.5U_ml


title: wt_L1_DNase-seq_rep1_10U_ml


title: wt_L1_DNase-seq_rep1_25U_ml


title: wt_L1_DNase-seq_rep1_5U_ml


title: wt_L2_DNase-seq_rep1_100U_ml


title: wt_L1_DNase-seq_rep1_50U_ml


title: wt_L2_DNase-seq_rep1_5U_ml


title: wt_L1_DNase-seq_rep1_2.5U_ml


title: wt_L1_DNase-seq_rep2_200U_ml


title: wt_emb_DNase-seq_rep2_800U_ml


title: wt_emb_DNase-seq_rep2_400U_ml


title: wt_emb_DNase-seq_rep2_10U_ml


title: wt_emb_DNase-seq_rep2_50U_ml


title: wt_emb_DNase-seq_rep2_100U_ml


title: wt_emb_DNase-seq_rep2_200U_ml


title: wt_emb_DNase-seq_rep2_25U_ml


title: wt_emb_DNase-seq_rep2_5U_ml


title: wt_emb_DNase-seq_rep1_800U_ml


title: wt_emb_DNase-seq_rep1_400U_ml


title: wt_emb_DNase-seq_rep1_200U_ml


title: wt_emb_DNase-seq_rep1_100U_ml


title: wt_emb_DNase-seq_rep2_2.5U_ml


title: wt_L1_DNase-seq_rep1_800U_ml


title: wt_emb_DNase-seq_rep1_25U_ml


title: wt_emb_DNase-seq_rep1_50U_ml


title: wt_emb_DNase-seq_rep1_10U_ml


title: wt_emb_DNase-seq_rep1_5U_ml


title: wt_emb_DNase-seq_rep1_2.5U_ml


title: Venous blood_d34_stress_4728

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

institute: INRAE

description: SAMPLE 17

hyb_protocol: 600 ng of Cy3-labelled cRNA were hybridized on the microarray slides following the manufacturer’s instructions.

scan_protocol: Immediately after washing, the slides were scanned on Agilent G2505C Microarray Scanner using Agilent Scan Control A.8.5.1 software.

data_processing:
The fluorescence signal extracted using Agilent Feature Extraction software v10.10.1.1 with default parameters.
Raw data (median signal intensity) were filtered, log2 transformed, and normalized using quantile method.

organism: Gallus gallus

source_name: female_stress_whole blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts). Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: Before extraction, 10µl of acetic acid 5N was added in each tube. Total RNA was extracted with TRIzol reagent (Invitrogen) according to the manufacturer’s protocol.

treatment_protocol: For 24h after leaving the hatchery, the chicks were kept without food and water in containers and subjected to a lower room temperature (22°C = cold vs 27°C = control) and shaking movements mimicking transport. Control animals were not be subjected to stressors after leaving the hatchery and were placed in standard rearing conditions. Venous blood was collected from the 24 chicks 34 days after laying, using vacuum tubes with EDTA. 100µl of whole blood were diluted in 1ml of trizol. After a strong shaking and 5 mn of incubation at RT, the tubes were frozen in liquid nitrogen and stored at -80°C until extraction.

tag: chicken id

value: chicken 4728

tag: gender

value: female

value: 34 days after birth

tag: sample group

value: stress

value: whole, venous blood


title: Venous blood_d34_ctrl_4699

description: SAMPLE 14

source_name: male_control_whole blood

value: chicken 4699

value: male

value: control


title: wt_YA_short_cap_RNAseq_rep2

data_processing:
Reads were trimmed using trim_galore, and aligned using bwa in single-end mode.
Low-quality (q<10), mitochondrial, tRNA, snoRNA, rRNA, or miRNA, and modENCODE-blacklisted reads were discarded.
Strand-specific coverage of 5’ ends of reads was generated.
Stage-specific tracks:  coverage of all 5' end reads in all replicates per stage.
Tracks pooled across all stages: coverage of 5' end reads was summed across all replicates in all stages, and filtered for reproducibility by only keeping signal at base pairs with non-zero coverage in at least two replicates.
Genome_build: WBcel215/ce10 (WS220)
Supplementary_files_format_and_content: Profiles of transcription initiation for each stage/strand; profiles of transcription initiation pooled across all stages & filtered for reproducible signal. For embyro (and pooled) data, we also included short cap replicates from (Chen et al., 2013; GSE42819).

growth_protocol: Wild-type N2 were grown at 20°C in liquid culture to the adult stage using standard S-basal medium with HB101 bacteria, animals bleached to obtain embryos, and the embryos hatched without food in M9 buffer for 24 hrs at 20°C to obtain synchronized starved L1 larvae. L1 larvae were grown in a further liquid culture at 20°C to the desired stage, then collected, washed in M9, floated on sucrose, washed again in M9, then frozen into "popcorn" by dripping embryo or worm slurry into liquid nitrogen. Popcorn were stored at -80°C until use. Times of growth were L1 (4 hrs), L2 (20 hrs), L3 (30 hrs), L4 (45 hrs), young adults (60 hrs). Mixed populations of embryos were collected by bleaching cultures of synchronized one day old adults.

extract_protocol:
Nuclei were isolated and then chromatin associated RNA was isolated as in (Pandya-Jones and Black 2009), resuspending washed nuclei in Trizol for RNA extraction. Following purification, RNA was of 17–200nt was isoated using Zymo clean and concentrate columns.
To profile transcription initiation ("short cap RNA-seq"), stranded libraries were prepared from 17–200nt RNA. Non-capped RNA was degraded by first converting uncapped RNAs into 5’-monophosphorylated RNAs using RNA polyphosphatase (Epibio), then treated with 5' Terminator nuclease (Epibio). The RNA was then treated with calf intestinal phosphatase to remove 5’ phosphates from undegraded RNA, and decapped using Tobacco Acid Pyrophosphatase (Epicentre, protocol 1), Cap-Clip Acid Pyrophosphatase (CellScript, protocol 2) or Decapping Pyrophosphohydrolase, (Dpph tebu-bio protocol 3) and then converted into sequencing libraries using the Illumina TruSeq Small RNA Preparation Kit kit. Libraries were size selected to be 145–225 bp long on a 6% acrylamide gel, giving inserts of 20–100 bp long. Libraries were made from two biological replicates for each developmental stage. During the course of this work, the TAP enzyme stopped being available; the Cap-Clip and Dpph enzymes perform less well than TAP. One L3 replicate and one YA replicate were made using a slightly different protocol (protocol 4) from Chen et al 2013 (doi: 10.1101/gr.153668.112).
RNA-seq of short (<100nt) capped chromatin associated RNA

value: wild-type N2


title: wt_YA_short_cap_RNAseq_rep1


title: wt_L4_short_cap_RNAseq_rep2


title: Venous blood_d34_ctrl_4709

description: SAMPLE 15

value: chicken 4709


title: Venous blood_d34_ctrl_4693

description: SAMPLE 13

value: chicken 4693


title: Venous blood_d34_stress_4772

description: SAMPLE 22

value: chicken 4772


title: Venous blood_d34_stress_4773

description: SAMPLE 23

value: chicken 4773


title: Venous blood_d34_stress_4584

description: SAMPLE 11

value: chicken 4584


title: Venous blood_d34_ctrl_4641

description: SAMPLE 12

source_name: female_control_whole blood

value: chicken 4641


title: Venous blood_d34_ctrl_4763

description: SAMPLE 21

value: chicken 4763


title: Venous blood_d34_ctrl_4750

description: SAMPLE 20

value: chicken 4750


title: Venous blood_d34_stress_4545

description: SAMPLE 6

source_name: male_stress_whole blood

value: chicken 4545


title: Venous blood_d34_ctrl_4743

description: SAMPLE 19

value: chicken 4743

value: female


title: Venous blood_d34_ctrl_4560

description: SAMPLE 7

value: chicken 4560

value: 34 days after birth


title: Venous blood_d34_stress_4725

description: SAMPLE 16

value: chicken 4725

value: stress

value: whole, venous blood


title: Venous blood_d34_ctrl_4567

description: SAMPLE 8

value: chicken 4567

value: control


title: Venous blood_d34_stress_4737

description: SAMPLE 18

value: chicken 4737

value: male


title: Venous blood_d34_stress_4583

description: SAMPLE 10

value: chicken 4583


title: Venous blood_d34_ctrl_4515

description: SAMPLE 3

value: chicken 4515


title: Venous blood_d34_ctrl_4509

description: SAMPLE 2

value: chicken 4509


title: Venous blood_d34_stress_4544

description: SAMPLE 5

value: chicken 4544


title: Venous blood_d34_stress_4526

description: SAMPLE 4

value: chicken 4526


title: wt_L4_short_cap_RNAseq_rep1

value: wild-type N2

value: L4 larvae


title: Venous blood_d34_ctrl_4501

description: SAMPLE 1

value: chicken 4501


title: wt_L3_short_cap_RNAseq_rep2

value: L3 larvae


title: wt_L1_short_cap_RNAseq_rep1

value: L1 larvae


title: wt_L2_short_cap_RNAseq_rep1

value: L2 larvae


title: Venous blood_d34_stress_4778

description: SAMPLE 24

value: chicken 4778

value: female

value: 34 days after birth

value: stress


title: wt_L3_short_cap_RNAseq_rep1


title: wt_emb_short_cap_RNAseq_rep1

value: mixed embryos


title: wt_L2_short_cap_RNAseq_rep2


title: Capped nuclear RNA-seq of glp-1 day 13 adults, replicate 2

data_processing:
Reads were trimmed to 20bp, and aligned using bwa in paired-end mode.
Low-quality (q<10), mitochondrial, rRNA, and modENCODE-blacklisted reads were discarded.
Strand-specific paired-end coverage with regions between read pairs "filled in" were generated.
Read coverage was normalised by DESeq2 sizeFactors of gene-level read counts.
Stage-specific normalised coverage was calculated by averaging across two biological replicates, and smoothed by binning at 10bp resolution.
Normalised coverage was log2-scaled using the formula log2(n + 1).
Genome_build: WBcel215/ce10 (WS220)
Supplementary_files_format_and_content: Forward and reverse-strand normalised genome-wide read coverage in linear and log2 scales.

source_name: day 13 adults

extract_protocol:
Nuclei were isolated and then chromatin associated RNA (development series) or nuclear RNA (ageing series) was isolated. Chromatin associated RNA was isolated as in (Pandya-Jones and Black 2009), resuspending washed nuclei in Trizol for RNA extraction. To isolate nuclear RNA, nuclei were directly mixed with Trizol. Following purification, RNA >200nt was isolated using Zymo clean and concentrate columns.
RNA was treated with DNase I, then with 5' Terminator nuclease (Epibio) to remove rRNA, and then stranded libraries prepared using the NEB Next Ultra Directional RNA Library Prep Kit (#E7420S). Libraries were made from two biological replicates for each developmental stage and each ageing time point.
RNA-seq of >200nt capped nuclear RNA

tag: molecule

value: nuclear RNA


title: Capped nuclear RNA-seq of wild-type young adults, replicate 2

value: chromatin associated RNA


title: Capped nuclear RNA-seq of glp-1 day 13 adults, replicate 1


title: Capped nuclear RNA-seq of glp-1 day 9 adults, replicate 2

source_name: day 9 adults


title: Venous blood_d34_stress_4581

description: SAMPLE 9

value: chicken 4581

value: whole, venous blood


title: wt_L1_short_cap_RNAseq_rep2


title: Capped nuclear RNA-seq of wild-type L4 larvae, replicate 2


title: Capped nuclear RNA-seq of wild-type L3 larvae, replicate 2


title: Capped nuclear RNA-seq of glp-1 young adults, replicate 1

source_name: day 1 / young adults


title: Capped nuclear RNA-seq of glp-1 day 9 adults, replicate 1


title: Capped nuclear RNA-seq of wild-type L3 larvae, replicate 1


title: Capped nuclear RNA-seq of glp-1 day 6 adults, replicate 1

source_name: day 6 adults


title: Capped nuclear RNA-seq of glp-1 day 2 adults, replicate 2

source_name: day 2 adults


title: Capped nuclear RNA-seq of glp-1 day 2 adults, replicate 1


title: Capped nuclear RNA-seq of wild-type young adults, replicate 1


title: Capped nuclear RNA-seq of glp-1 young adults, replicate 2


title: Capped nuclear RNA-seq of glp-1 day 6 adults, replicate 2


title: wt_emb_short_cap_RNAseq_rep2

source_name: mixed embryos


title: Capped nuclear RNA-seq of wild-type L4 larvae, replicate 1


title: Capped nuclear RNA-seq of wild-type embryos, replicate 1


title: Capped nuclear RNA-seq of wild-type L2 larvae, replicate 2


title: Capped nuclear RNA-seq of wild-type L2 larvae, replicate 1


title: Capped nuclear RNA-seq of wild-type L1 larvae, replicate 1


title: Capped nuclear RNA-seq of wild-type embryos, replicate 2


title: H3K27me3_wt_l3_rep2

data_processing:
ChIP-seq reads were aligned to the WS220 assembly of the C. elegans genome using bwa.
Low-quality (q<10), and (McMurchy et al., 2017)-blacklisted reads were discarded.
ChIP-seq data were normalized using the BEADS algorithm (Cheung et al., 2011).
ChIP-seq signal was either log-transformed (H3K4me3, H3K4me1) or z-scored (H3K36me3, H3K27me3).
Stage-specific coverage was calculated by averaging across biological replicates, and smoothed by binning the signal at 10bp resolution.
Genome_build: WBcel215/ce10 (WS220)
Supplementary_files_format_and_content: Stage-specific normalized ChIP-seq profiles of histone marks.

extract_protocol:
Frozen worm pellets were ground, fixed for 10 minutes in 1% formaldehyde, fixative was quenched with 125 mM glycine and cross-linked tissue washed 2X with PBS + protease inhibitors, then resuspended in FA buffer and subjected to sonication in a Bioruptor or Bioruptor pico to an average DNA size of 200bp. Extracts were spun down and the soluble fraction used for ChIP.  For ChIPs of protein factors, 1mg of ChIP extract was incubated with 5ug antibody; for histone modifications, 500ug ChIP extract was incubated with 2ug of antibody.  After overnight incubation with rotation at 4C, 40ul of equilibrated magnetic beads (coupled to protein A or G, depending on antibody) were added and incubated for 2 hrs at room temperature with rotation. Washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer were performed and DNA was eluted in elution buffer (1% SDS in TE with 250 mM NaCl) two times with 57 ul volume each, at 65°C. Samples were treated with RNAse, proteinase K and then crosslinks were reversed overnight at 65°C. DNA was purified on Qiagen PCR purification columns and used for ChIP library preparation.
ChIP or input DNA is blunt ended, A-tailed, ligated to adaptors, amplified by PCR, then size selected using AMPure beads. Illumina TruSeq adaptors and barcodes were used. Samples were sequenced on a HiSeq1500

tag: antibody

tag: antibody id

tag: antibody manufacturer

value: WAKO


title: H3K27me3_wt_l2_rep2


title: H3K27me3_wt_l2_rep1


title: H3K27me3_wt_ya_rep1


title: H3K27me3_wt_l4_rep1


title: H3K27me3_wt_ya_rep2


title: Capped nuclear RNA-seq of wild-type L1 larvae, replicate 2


title: H3K27me3_wt_l1_rep1


title: H3K27me3_wt_l3_rep1


title: H3K27me3_wt_emb_rep2


title: Clone6 [methylation]

type: genomic

city: Baltimore

first: Jie

last: Wang

state: Maryland

address: 400 N Broadway

institute: Johns Hopkins University

description: SAMPLE 3

hyb_protocol: Performed by the Johns Hopkins Deep Sequencing and Microarray Core Facility

data_processing: We analyzed DNA methylation data to identify differential methylated sites and regions Using RnBeads. Normalization was performed according to internal controls

label: Cy5 and Cy3

source_name: Mutated SVG

growth_protocol: The human astroglial cell line SVG-10B1 was originally established by Dr. Major and obtained via a material transfer agreement

treatment_protocol: SVG cells were cultured in Dulbecco’s Minimum Essential Media (DMEM, Thermo Fisher Scientific, Grand Island, NY) supplemented with 10%  fetal calf serum (FCS, Gemini Bio-products, West Sacramento, CA). Cells were incubated in a humidified incubator containing 5% CO2/95% air at 37°C, and passaged every 2-4 days

tag: cell line background

tag: cell type

value: human astroglial cell line

tag: genotype/variation

value: IDH1 R132H/WT

tag: replicate


title: H3K36me3_wt_ya_rep2

value: Abcam


title: SVG [methylation]

description: SAMPLE 1

scan_protocol: Performed by the Johns Hopkins Deep Sequencing and Microarray Core Facility

source_name: Wild-type astroglial cell line SVG

value: wild-type


title: H3K27me3_wt_l1_rep2


title: H3K36me3_wt_ya_rep1

source_name: young adults


title: H3K36me3_wt_l4_rep2

source_name: L4 larvae


title: Clone2 [methylation]

description: SAMPLE 2

label_protocol: Performed by the Johns Hopkins Deep Sequencing and Microarray Core Facility


title: H3K36me3_wt_l4_rep1


title: H3K27me3_wt_l4_rep2


title: H3K36me3_wt_l3_rep2

source_name: L3 larvae


title: H3K36me3_wt_l2_rep2

source_name: L2 larvae


title: H3K36me3_wt_l3_rep1


title: H3K36me3_wt_l2_rep1


title: H3K36me3_wt_l1_rep2

source_name: L1 larvae


title: H3K36me3_wt_emb_rep2


title: H3K27me3_wt_emb_rep1


title: H3K36me3_wt_emb_rep1


title: H3K4me1_wt_ya_rep2


title: H3K4me1_wt_l4_rep1


title: H3K4me1_wt_ya_rep1


title: H3K4me1_wt_l3_rep2


title: H3K4me1_wt_l3_rep1


title: H3K4me1_wt_l2_rep2


title: H3K4me3_wt_ya_rep2


title: H3K4me1_wt_l1_rep1


title: H3K4me1_wt_l2_rep1


title: H3K36me3_wt_l1_rep1


title: H3K4me3_wt_ya_rep1


title: H3K4me1_wt_emb_rep1


title: H3K4me1_wt_l1_rep2


title: H3K4me1_wt_emb_rep2


title: H3K4me3_wt_l4_rep1


title: H3K4me3_wt_l4_rep2


title: H3K4me3_wt_emb_rep1


title: H3K4me3_wt_l2_rep2


title: H3K4me3_wt_l2_rep1


title: H3K4me3_wt_emb_rep2


title: H3K4me3_wt_l1_rep1


title: glp-1_day13adult_ATAC-seq_rep1

data_processing:
Reads were trimmed using trim_galore, and aligned using bwa in single-end mode.
Low-quality (q<10), mitochondrial, and modENCODE-blacklisted reads were discarded.
Normalised coverage was calculated using MACS2: --format BAM --bdg --SPMR --gsize ce --nolambda --nomodel --extsize 150 --shift -75 --keep-dup all
Stage-specific accessibility was calculated by averaging across biological replicates, and smoothed by binning the signal at 10bp resolution.
Genome_build: WBcel215/ce10 (WS220)
Supplementary_files_format_and_content: Stage-specific genome-wide accessibility profiles. Normalized data across replicates.

extract_protocol:
Frozen embryos or worms were broken by grinding in a mortar and pestle or smashing using a Biopulverizer, then the frozen powder was thawed in 10 ml Egg buffer (25 mM HEPES pH 7.3, 118 mM NaCl, 48 mM KCl, 2 mM CaCl2, 2 mM MgCl2). Ground worms were pelleted by spinning at 1500 g for 2 minutes, then resuspended in 10ml working Buffer A (0.3M sucrose, 10 mM Tris pH 7.5, 10 mM MgCl2, 1mM DTT, 0.5 mM spermidine 0.15 mM spermine, protease inhibitors (Roche complete, EDTA free) containing 0.025% IGEPAL CA-630. The sample was dounced 10X in a 14ml stainless steel tissue grinder (VWR), then the sample spun 100g for 6 min to pellet large fragments. The supernatant was kept and the pellet resuspended in a further 10 ml Buffer A, then dounced for 25 strokes. This was spun 100g for 6 min to pellet debris and the supernatants, which contain the nuclei, were pooled, spun again at 100g for 6 min to pellet debris, and transferred to a new tube. Nuclei were counted using a hemocytometer. Twenty million nuclei were transferred to a 1.5 ml tube and spun 2000g for 10min to pellet.
ATAC-seq was performed essentially as in (Buenrostro et al. 2013). Twenty million nuclei were resuspended in 47.5 ul of tagmentation buffer, incubated for 30 minutes at 37°C with 2.5 ul Tn5 enzyme (Illumina Nextera kit), and then tagmented DNA purified using a MinElute column (Qiagen) and converted into a library using the Nextera kit protocol. Typically, libraries were amplified using 12–16 PCR cycles.

tag: age

value: day 13 adults


title: H3K4me3_wt_l3_rep2


title: glp-1_day9adult_ATAC-seq_rep2

value: day 9 adults


title: glp-1_day9adult_ATAC-seq_rep1


title: H3K4me3_wt_l1_rep2


title: glp-1_day13adult_ATAC-seq_rep2


title: glp-1_day6adult_ATAC-seq_rep2

value: day 6 adults


title: glp-1_day6adult_ATAC-seq_rep1


title: glp-1_day2adult_ATAC-seq_rep2

value: day 2 adults


title: H3K4me1_wt_l4_rep2


title: glp-1_day2adult_ATAC-seq_rep1


title: H3K4me3_wt_l3_rep1


title: glp-1_YA_ATAC-seq_rep2

value: day 1 / young adults


title: wt_YA_ATAC-seq_rep2

value: young adults

value: wild-type N2


title: glp-1_YA_ATAC-seq_rep1


title: wt_L2_ATAC-seq_rep2

value: L2 larvae


title: wt_L1_ATAC-seq_rep2

value: L1 larvae


title: wt_L4_ATAC-seq_rep2

value: L4 larvae


title: wt_L3_ATAC-seq_rep2

value: L3 larvae


title: wt_YA_ATAC-seq_rep1


title: wt_L1_ATAC-seq_rep1


title: wt_L2_ATAC-seq_rep1


title: wt_L4_ATAC-seq_rep1


title: wt_L3_ATAC-seq_rep1


title: wt_emb_ATAC-seq_rep1

value: mixed embryos


title: wt_emb_ATAC-seq_rep2


title: VaMyb14-OE cold 8h rep2

city: Wuhan

first: Lingye

last: Su

address: Lumo Road, Moshan

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

description: Gene expression data from VaNAC26 transgenic Arabdopsis leaf under 5 day drought

hyb_protocol: 12.5 μg of labelled and fragmented cRNA probes were hybridized to the Arabidopsis arrays with the Hybridization, Wash and Stain Kit (Affymetrix, #900720) according to the manufacturer’s instructions

scan_protocol: The arrays were scanned using a GeneChip® Scanner 3000 (Affymetrix, #3000).

data_processing: The data were analyzed with Microarray Suite version 3.0 (MAS 3.0)

organism: Arabidopsis thaliana

source_name: VaMyb14 transgenic Arabdopsis leaf

label_protocol: The cRNA was labelled with a biotinylated ribonucleotide  analogue and was fragmented with fragmentation buffer using the MessageAmp™ Premier RNA Amplification Kit (Ambion, #1792).

growth_protocol: Plants were grown on soil in a greenhouse (16-h light/8-h dark) at 22 oC

extract_protocol: Total RNA was extracted from 100 mg samples by using the Column Plant RNAout 2.0 (Tiandz Inc., Beijing, China)

treatment_protocol: For cold treatment, seedlings of transgenic lines and wild-type Arabidopsis were grown in soil in 22 oC for 21 d. After irrigation, the phenotypes of plant were observed during the following 8 h 4℃ cold treatment.

tag: tissue

value: leaf

value: VaMyb14 transgenic

tag: treatment

value: under 8 h cold


title: mock_control_2

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

description:
K11
Gene expression data from 2 dpf sibling homozygous wildtype zebrafish embryos.

hyb_protocol: The labeled products were hybridized to Affymetrix Zebrafish Gene 1.0 ST Arrays at the Dartmouth Genomics and Microarray Laboratory.

scan_protocol: Arrays were scanned using the GeneChip 3000 7G scanner and exported as standard .CEL files.

data_processing: Expression was extracted using Bioconductor in R using the GCRMA package.

organism: Danio rerio

source_name: Sibling homozygous wildtype embryos

label_protocol: Input RNA was 100ng and labeled using the Affymetrix GeneChip WT PLUS Reagent Kit.

growth_protocol: Growth at 28.5°C for 48 hpf.

extract_protocol: Column purification - RNeasy Mini Kit (Qiagen).

treatment_protocol: None, morpholino injection or TALEN induced gene-editing.

value: whole embryo

value: 2 dpf


title: wild type cold 8h rep2

description: Gene expression data from wild type Arabdopsis leaf under 5 day drought

source_name: wild type Arabdopsis leaf

value: wild type


title: mock_control_1

description:
K10
Gene expression data from 2 dpf sibling homozygous wildtype zebrafish embryos.


title: VaMyb14-OE cold 8h rep1


title: VaMyb14-OE control rep2

description: Gene expression data from VaNAC26 transgenic Arabdopsis leaf under normal conditon

source_name: VaMyb14 transgenic Arabdopsis leaf under

value: normal condition


title: Mutant_2

description:
K14
Gene expression data from 2 dpf sibling homozygous islet2a mutant zebrafish embryos.

source_name: Sibling homozygous mutant islet2a embryos


title: Morphant_2

description:
K8
Gene expression data from 2 dpf wildtype zebrafish embryos injected with translation blocking morpholino targeting islet2a.

source_name: Translation blocking islet2a morpholino-injected embryos


title: control_cultivar4_timepoint1_rep3

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

institute: IRHS

hyb_protocol: The hybridization performed on a AryANE 12x135k array (NimbleGen Hybridization System, Roche) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. Pair-data files were extracted from the scanned images using DEVA 1.2 software (Roche).

data_processing: Statistical analyses were performed using R version 2.14.1 (R Development Core Team, 2011) and the package LIMMA 3.10.1 (Smyth G.K., 2005) from the Bioconductor project. Data were normalized by the lowess method from LIMMA.

organism: Malus domestica

source_name: Apple 'Linda' fruit flesh

label_protocol: 200ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. Five µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of cyanine-3 (Cy3) or cyanine-5 (Cy5) (Interchim, France), then purified with QIAquick PCR Purification Kit (QIAGEN) according to manufacturer’s instructions. Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized.

growth_protocol: Apples fruits were harvested from a commercial orchard at a preclimatric stage.

extract_protocol: Total RNA was extracted from frozen samples as described by Gasic et al. (2004) and Chang et al. (1993)

treatment_protocol:
protocol 1: Harvested fruits were washed with tap water, surface-sterilized by 2% sodium hypochlorite for 2 min, and then washed with sterilized water, air-dried and finally inoculated with 20 µl (1×105 conidia mL-1) of P. expansum on opposite sides of each fruit, and stored in open-faced plastic boxes at 2°C.
protocol 2: Samples were then taken from each control and inoculated fruits at 3 time points. i.e. one hour, one week and six weeks post inoculation.

tag: organ

value: Mature fruit

tag: tissus

value: parenchyma

tag: genetic background

value: Linda

tag: phenotype

value: Susceptible

tag: treatment 1

tag: treatment 2

value: 1h cold storage 2°C


title: wild type cold 8h rep1


title: Morphant_3

description:
K9
Gene expression data from 2 dpf wildtype zebrafish embryos injected with translation blocking morpholino targeting islet2a.


title: wild type control rep2

description: Gene expression data from wild type Arabdopsis leaf under normal conditon


title: WT_control_2

description:
K3
Gene expression data from 2 dpf uninjected wildtype zebrafish embryos.

source_name: Uninjected embryos


title: Morphant_1

description:
K7
Gene expression data from 2 dpf wildtype zebrafish embryos injected with translation blocking morpholino targeting islet2a.


title: Mutant_1

description:
K13
Gene expression data from 2 dpf sibling homozygous islet2a mutant zebrafish embryos.


title: WT_control_1

description:
K2
Gene expression data from 2 dpf uninjected wildtype zebrafish embryos.


title: Mutant_3

description:
K15
Gene expression data from 2 dpf sibling homozygous islet2a mutant zebrafish embryos.