title: ad libitum, 10-TNT, Rep 3

description: Western Fence Lizard

value: Liver

tag: gender

value: Adult

tag: treatment


title: ad libitum, 5-TNT, Rep 5

status: Public on Nov 15 2018

type: RNA

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

country: USA

institute: US Army ERDC

description: Western Fence Lizard

hyb_protocol: The Agilent 8 x 60K, 2µm feature size microarray platform (Custom Array: AMADID 028809) was used for transcript expression assays (Agilent Technologies). The Agilent One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations where 500 ng of total RNA was used as the starting material for each exposure replicate. At least 4 replicate liver samples (most treatments included 6 replicates) collected from individual lizards per experimental condition were hybridized to microarrays in a completely randomized design using a random number generator. Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: An Agilent SureScan Microarray Scanner (G2505 C, Agilent Technologies Inc.) was used to scan microarrays at 2 μm resolution.

data_processing: Data were extracted using Agilent Feature Extraction software, version 9.5.1 (Agilent Technologies). Internal control spots were analyzed to confirm that signal data was within the linear range of detection. GeneSpring version GX 11.0.2 (Agilent Technologies) was used to normalize data using quantile normalization followed by baseline transformation to the median of all samples. Statistical analysis was performed using GeneSpring where two-way ANOVA (p ≤ 0.05) with Benjamini-Hochberg multiple-testing correction and 1.5 fold-change cutoff was used to identify differentially expressed transcripts.

molecule: total RNA

organism: Sceloporus occidentalis

source_name: liver tissue

label_protocol: The Agilent One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations and 500 ng of total RNA extracted from liver tissues in each individual lizard replicate.

growth_protocol: The original laboratory colony of WFLs was established from lizards collected from the San Joaquin Valley in Fresno and Tulare Counties, California. Lizards for this study were males obtained from generations F4 and F5. Within 24 h after hatching, lizards were housed 10–15 per cage on corncob substrate in 74.2 l glass aquaria that were covered with a 3-mm steel mesh lid. Heat and light were provided by a 40-W incandescent light bulb positioned over one end of each cage to permit thermoregulation across an approximate temperature gradient of 26–40 C. Ambient room temperature was maintained at approximately 22 C along with a 14:10 h light:dark light cycle. Lizards were provided with a water source and fed daily with house crickets (Acheta domesticus) that were fed a mixture consisting of ground poultry laying pellets, Herptivite, and Rep-Cal (Rep-Cal Research Labs, Los Gatos, CA, USA). At 6 months of age, male lizards were randomly separated into groups for the different phases of the study.

extract_protocol: At the completion of the exposures, animals were euthanized by CO2 asphyxia, and dissected. Liver tissues were fixed in RNA Later™ (Ambion, Austin, TX) following manufacturer's recommendations and stored at -80°C until RNA extraction. RNA extraction was conducted using RNeasy Mini RNA extraction kits (Qiagen Inc., Valencia, CA). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) with RNA 6000 Nano LabChips® RNA. Only samples with a 28s/18s ratio ≥2.0 and RNA integrity number (RIN) ≥7.0 were used for downstream applications.

treatment_protocol: Exposure 1 - TNT x food limitation: The study incorporated a factorial treatment arrangement within a completely randomized experimental design. The food limitation treatments included an ad libitum control (fed 10 crickets daily) and a reduced food ration (2 crickets daily). The TNT exposures consisted of daily oral doses of corn oil control or a corn oil-TNT suspension at 5, 10, 20, mg/kg/day. All treatments included 10 biological replicates (10 individually caged lizards) per condition.

tag: tissue

value: Male

tag: age

tag: diet

value: ad libitum

value: 5 mg/kg/d TNT


title: adcp1-1_H3_ChIPSeq_rep2

type: SRA

city: Beijing

first: QIANWEN

last: SUN

address: Zhongguancun Street

department: School of life sciences

country: China

institute: Tsinghua University

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with trim_galore.
ChIP-seq reads were aligned to the TAIR10 genome using Bowtie 2 version 2.3.2. BS-seq reads were aligned to TAIR10 using bismark_v0.18.1. RNA-seq reads were aligned to TAIR10 genome using HISAT2 version 2.0.5.
Peaks were called using MACS2.
Reads coverage nomalized to reads per kilobase per million mapped reads (RPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files were generated using Computematrix,gtf files include FPKM values for each Sample.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: leaves

extract_protocol:
For H3K9me2 ChIP-seq, nuclei were extracted with Honda buffer and digested with MNase, the resulting histone-DNA complexes were isolated with antibody. For GFP ChIP-seq, the nuclei were cross-linked by 1% formaldehyde and sonicated,  histone-DNA complexes were isolated with antibody. For BS-seq, DNA was extracted from 14-day-old leaves with CTAB. After complete bisulfite conversion of 2μg DNA with EZ DNA Methylation-Gold Kit (Zymo Research ,D5005), the DNA was sonicated to 250bp (Covaris) for library construction. For RNA-seq, total RNA was extracted from 14-day-old leaves using Trizol (Ambion).
ChIP-seq Libraries were constructed using ACCEL-NGS®1S PLUS DNA LIBRARY KIT ( Swift Biosciences ,Cat. No. 18096) according to the manufacturer. BS-seq library was constructed following Illumina’s manufacturer Instructions(Swift Biosciences, ACCEL-NGS® METHYL-SEQ DNA LIBRARY KIT, 30024). For RNA-seq, Libraries for two biological replicates of each genotype were constructed and sequenced according to the manufacturer’s protocol (NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina®). The rRNA was depleted from total RNA using Ribo-ZeroTM rRNA removal Kit (Illumina). Illumina libraries were generated and sequenced using a 2x150 paired-end (PE) configuration on the HiSeq instrument (Illumina).

tag: developmental stage

tag: chip antibody

value: H3(Abcam, ab1791)

tag: genotype

value: mutant


title: ad libitum, 10-TNT, Rep 1

description: Western Fence Lizard

value: 10 mg/kg/d TNT


title: follicular phases ovary 5

city: Fuyang

first: Yong

last: Liu

address: Qinghe West Road

institute: Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province

library_source: transcriptomic

data_processing:
TruSeq PE Cluster Kit v3-cBot-HS (Illumina) was used to cluster the cBot clusters
(1) Transcripts with low expression levels, low credible single exon transcripts, and exon numbers <2 were filtered out; (2) transcripts <200 bp in length were filtered out; (3) through Cuffcompare software, the duplicated transcripts of the exon region of the database annotation were removed, and the lncRNA overlapped with the exon region of the splicing transcript; (4) the expression of each transcript was calculated by Cuffquant, and the transcript of FPKM<0.5 was filtered out; and (5) finally, we determined whether the encoding potential was the key condition to determine lncRNAs. We used three coding potential analysis programs (CNCI, CPC, and Pfam-sca) to screen the transcripts
The FPKM (the number of fragments per million fragments from a single gene) was used to estimate the expression levels of lncRNA and transcripts of uncertain coding potential (TUCP).
Filtering out the adaptor sequences, empty sequence, and low-quality sequences,
Genome_build: NC_030808.1
Supplementary_files_format_and_content: text files with FPKM

organism: Capra hircus

source_name: goat ovary

growth_protocol: The ovaries were washed with physiological saline containing double antibodies and then were placed into an RNase-free centrifuge tube, labeled, frozen in liquid nitrogen, and stored at -80°C within 20 days

extract_protocol:
Firsly,total RNA was extracted from the goat ovaries at the follicular and luteal phases.Finally, the RNA integrity was assessed by the RNA Nano 6000 assay kit (Agilent Technologies, CA, USA) with the Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: anhui white

value: ovary

tag: estrus phase

value: follicular phase


title: Col-0_H3_ChIPSeq_rep2

value: wild type


title: Col-0_H3K9me2_ChIPSeq_rep2

value: H3K9me2(Abcam, ab1220)


title: follicular phases ovary 4


title: adcp1-1_H3_ChIPSeq_rep1


title: luteal phases ovary 2

value: luteal phase


title: follicular phases ovary 3


title: ad libitum, 5-TNT, Rep 2

description: Western Fence Lizard


title: ad libitum, 5-TNT, Rep 3

description: Western Fence Lizard


title: ad libitum, 5-TNT, Rep 4

description: Western Fence Lizard


title: ad libitum, 0-TNT, Rep 6

description: Western Fence Lizard

value: 0 mg/kg/d TNT


title: adcp1-1_H3K9me2_ChIPSeq_rep1


title: ad libitum, 5-TNT, Rep 1

description: Western Fence Lizard


title: Col-0_H3_ChIPSeq_rep1


title: follicular phases ovary 2


title: ad libitum, 0-TNT, Rep 4

description: Western Fence Lizard


title: ad libitum, 0-TNT, Rep 5

description: Western Fence Lizard


title: Col-0_H3K9me2_ChIPSeq_rep1


title: follicular phases ovary 1


title: WT-CO [GC010323]

status: Public on Nov 14 2018

city: Leuven

first: Alvaro

last: Cortés Calabuig

address: Herestraat 49 PO box 602

country: Belgium

institute: Genomics Core Leuven

description: WT-CO       (WT_ M_ACE-I_M)

data_processing:
Raw read data was aligned to the mouse reference genome to with tophat 2.0.13
Gene count was performed with HT-Seq count 0.5.3p3, options -s no -a 10 -i gene_name
Differential expression analysis was performed with DESeq and edgeR
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: text file with raw counts

organism: Mus musculus

growth_protocol: DKO mice were backcrossed for at least 10 generations into the C57BL/6J background, resulting in mice having a 98.4% C57BL/6J background. Homozygous DKO (LDLR-/-;ob/ob) mice were generated using classical intercrossing strategies, for which heterozygous ob/+ and C57BL/6 (WT) mice were purchased from Harlan Laboratory. The mice were genotyped by PCR for LDLR and ob genotype as described before7.

extract_protocol:
Hearts were collected at the age of 24 weeks. Three hearts per group were snap-frozen in liquid nitrogen. Total RNA was extracted using the TRIzol reagent protocol (Invitrogen), purified on an RNeasy spin column (Qiagen), and DNase treated. RNA sample quality was assessed by Nanodrop.
Illumina True Seq Stranded

treatment_protocol: The effect of 12-week ACE-I treatment on gene expression in the heart was investigated. In the ACE-I treated groups (DKO-AI and WT-AI) mice were injected with ACE-inhibitor captopril (10 mg/kg/day IP) between 12 and 24 weeks of age. In the control groups (DKO-CO and WT-CO), animals received an equal volume of physiological saline NaCl 0.9%.

tag: strain

value: whole heart

value: post natal 24 weeks


title: WT-CO [GC010324]

description: WT-CO       (WT_ M_ACE-I_M)


title: WT-AI [GC010327]

description: WT-AI       (WT_HPC-M_ACE-I_P)

source_name: Heart _WT_ACE-I


title: WT-AI [GC010326]

description: WT-AI       (WT_HPC-M_ACE-I_P)


title: WT-AI [GC010325]

description: WT-AI       (WT_HPC-M_ACE-I_P)


title: WT-CO [GC010322]

description: WT-CO       (WT_ M_ACE-I_M)


title: P2143_N712-S517

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

data_processing:
Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Reads were demultiplexed according to the cell barcodes.
Libraries were inspected with the FastQC suite to assess the quality of the reads.
Sequenced reads were filtered for low-complexity or low-quality sequence.
Reads were mapped on the mouse reference genome with the RNA pipeline of the GEMTools 1.7.0 suite as paired-end reads using default parameters.
Low-quality cells were filtered out based on the distribution of the number of non-zero count genes per cell (minimum number of genes detected), to remove cells with less than two median absolute deviations (MAD) with respect to the median. Genes expressed in less than five cells, poorly annotated genes (GM identifiers), and histone gene clusters were also discarded from the dataset. The final dataset included 385 cells and 11,327 genes for experiment 1, and 287 cells and 11,303 genes for experiment 2.
Genome_build: Gencode release M15, assembly GRCm38
Supplementary_files_format_and_content: Tab-separated values (.tsv) files containing gene expression values (rows) as raw read counts for each cell (columns) in pool.

molecule: polyA RNA

source_name: skin

growth_protocol: Mice were bred and aged at the animal facilities of the Barcelona Science Park and fed standard rodent chow.

extract_protocol:
For FACS sorting, mice were sacrificed between 8 am and 10 am. Skin was shaved and then dissected, anagen patches were removed, and the subdermis was scraped off with a scalpel. The tissue was then chopped with a tissue chopper (McILWAIN tissue chopperref.) until skin pieces were smaller than 0.5 mm in diameter. Skin pieces were then digested in 20 ml DMEM-Ca (Cat. 21068028Ref) containing 10% FBS and 2.5 mg/ml collagenase 1 (Sigma-Aldrich) at 37ºC for 1 hour on the shaker, after which 5 µg/ml DNase 1 was added, and the solution was incubated for 15 min at 37ºC without shaking. Liberated cells were then sequentially filtered through a 100 µm filter and 40 µm filter. Centrifugation steps were carried out at 300g for 10 minutes at 4ºC. Cells were then stained with antibodies (as stated) in staining buffer (EMEM, 15% FBS). To isolate fibroblasts, cells were stained with the following antibodies: CD45-biotin, CD117-biotin, EpCam-biotin, CD24-biotin, SA-APC, CD31-PerCP/Cy5.5, CD34-FITC, Pdgfrαa-PE, without using CD24 antibody for lineage selection, to avoid negative selection of fibroblasts with pre-adipogenic characteristics. To isolate the different fibroblast subpopulations from newborn skin, cells were stained with CD45-biotin, CD117-biotin, EpCam-biotin, CD31-biotin, SA-APC-Cy7, CD34-FITC, Pdgfrα-APC, Dlk1-PE, CD26-PerCp-Cy5.5, and Sca1-BV605. To assess viability, cells were stained with DAPI (1 μg/ml) in PBS with 2% FBS immediately prior to sorting. Fibroblasts were sorted using a FACS ARIA Fusion instrument.
Full-length single-cell RNA-seq libraries were prepared using the Smart-seq2 protocol with minor modifications. Briefly, freshly harvested single cells were sorted into 96-well plates containing the lysis buffer (0.2% Triton-100). Reverse transcription was performed using SuperScript II (Invitrogen) in the presence of oligo-dT30VN, template-switching oligonucleotides, and betaine. cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kappa Biosystems) and ISPCR primer, with 23 cycles of amplification. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitivity DNA Kit (Agilent Technologies). A total of 200 ng of the amplified cDNA was fragmented using Nextera® XT (Illumina) and amplified with indexed Nextera® PCR primers. Products were purified twice with Agencourt Ampure XP beads and quantified again using a Bioanalyzer High Sensitivity DNA Kit.
Pooled sequencing of Nextera® libraries was carried out using a HiSeq2000 (Illumina) to an average sequencing depth of 1.2 million reads per cell in experiment 1, and 1.4 million reads per cell in experiment 2. Sequencing was carried out as paired-end (PE75) reads with library indexes corresponding to cell barcodes.

treatment_protocol: To perform the transcriptomic analysis of aging dermal fibroblasts, two-month-old mice (young) and 18-month-old mice (old) were used. For the transcriptome analysis of fibroblast subpopulations from newborn mice, female littermates at the age of P2 were used.

tag: cell type

value: dermal fibroblast

value: old

tag: experiment


title: P2143_N712-S508


title: AromhumH Replicate 1

city: Chicago

first: Hong

last: Zhao

state: IL

address: 303 E. Superior St., Suite 4-121

department: OB/GYN

institute: Northwestern university

description: replicate 4

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

label: biotin

source_name: Lower abdominal muscle tissue

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

growth_protocol: We used low abdominal muscle tissues from 1-month-old male mice

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.

treatment_protocol: WT mice is the control mice. Both AromhumL and AromhumH mice are humanized aromatase trasgenic mice. Human aromatase expression levels are higher in AromhumH mice and Lower in AromhumL.

value: Male

value: FVB/N

value: 1 month


title: ad libitum, 0-TNT, Rep 3

description: Western Fence Lizard

value: Liver

value: Adult

value: ad libitum


title: Wild type ( WT) Replicate 3

description: replicate 4


title: Wild type ( WT) Replicate 4

description: replicate 4


title: AromhumL Replicate 2

description: replicate 4


title: P2143_N712-S503


title: P2143_N712-S506


title: P2143_N712-S507


title: P2143_N712-S505


title: P2143_N711-S517


title: AromhumH Replicate 3

description: replicate 4


title: AromhumH Replicate 2

description: replicate 4


title: ad libitum, 0-TNT, Rep 2

description: Western Fence Lizard


title: Wild type ( WT) Replicate 2

description: replicate 4


title: AromhumH Replicate 4

description: replicate 4


title: AromhumL Replicate 3

description: replicate 4


title: AromhumL Replicate 1

description: replicate 4


title: ad libitum, 0-TNT, Rep 1

description: Western Fence Lizard


title: Wild type ( WT) Replicate 1

description: replicate 4


title: AromhumL Replicate 4

description: replicate 4


title: P2143_N711-S508


title: P2143_N712-S504


title: P2143_N712-S502


title: P2143_N711-S502


title: P2143_N711-S507


title: P2143_N711-S505


title: P2143_N711-S506


title: P2143_N711-S504


title: P2143_N711-S503


title: P2143_N710-S517


title: P2143_N710-S507


title: P2143_N710-S508


title: P2143_N710-S506


title: P2143_N710-S504


title: P2143_N710-S505


title: P2143_N709-S503


title: P2143_N709-S508


title: P2143_N709-S517


title: P2143_N709-S502


title: P2143_N709-S504


title: P2143_N710-S503


title: P2143_N709-S506


title: P2143_N708-S506


title: P2143_N709-S505


title: P2143_N708-S508


title: P2143_N708-S517


title: P2143_N708-S507


title: P2143_N708-S505


title: P2143_N708-S504


title: P2143_N708-S503


title: P2143_N710-S502


title: P2143_N707-S508

value: young


title: P2143_N707-S506


title: P2143_N707-S517


title: P2143_N707-S507


title: P2143_N708-S502


title: P2143_N707-S504


title: P2143_N707-S505


title: P2143_N707-S503


title: P2143_N706-S517


title: P2143_N707-S502


title: P2143_N706-S508


title: P2143_N706-S502


title: P2143_N706-S503


title: P2143_N706-S504


title: P2143_N706-S506


title: P2143_N706-S505


title: P2143_N706-S507


title: P2143_N705-S506


title: P2143_N705-S504


title: P2143_N704-S508


title: P2143_N704-S517


title: P2143_N705-S502


title: P2143_N705-S503


title: P2143_N705-S505


title: P2143_N704-S507


title: P2143_N705-S508


title: P2143_N703-S517

value: newborn


title: P2143_N704-S504


title: P2143_N703-S508


title: P2143_N704-S502


title: P2143_N704-S503


title: P2143_N703-S507


title: P2143_N703-S506


title: P2143_N703-S505


title: P2143_N703-S504


title: P2143_N705-S507


title: P2143_N705-S517


title: P2143_N709-S507


title: P2143_N702-S504


title: P2143_N704-S505


title: P2143_N702-S508


title: P2143_N702-S506


title: P2143_N702-S517


title: P2143_N702-S505


title: P2143_N704-S506


title: P2143_N702-S503


title: P2143_N701-S507


title: P2143_N703-S502


title: P2143_N701-S506


title: P2143_N702-S507


title: P2143_N701-S517


title: P2143_N701-S505


title: P2143_N701-S508


title: P2143_N701-S504


title: P2143_N701-S503


title: P2143_N701-S502


title: P2139_N712-S517


title: P2139_N712-S508


title: P2139_N712-S506


title: P2139_N712-S505


title: P2143_N703-S503


title: P2139_N712-S502


title: P2139_N712-S503


title: P2139_N711-S517


title: P2139_N711-S505


title: P2139_N711-S508


title: P2139_N711-S507


title: P2139_N711-S506


title: P2139_N711-S502


title: P2139_N711-S503


title: P2139_N711-S504


title: P2139_N710-S506


title: P2139_N710-S508


title: P2139_N712-S507


title: P2139_N710-S504


title: P2139_N710-S517


title: P2139_N710-S507


title: P2143_N702-S502


title: P2139_N709-S508


title: P2139_N709-S517


title: P2139_N710-S503


title: P2139_N712-S504


title: P2139_N709-S506


title: P2139_N709-S507


title: P2139_N709-S505


title: P2139_N710-S502


title: P2139_N709-S504


title: P2139_N709-S503


title: P2139_N709-S502


title: P2139_N708-S508


title: P2139_N708-S507


title: P2139_N708-S517


title: P2139_N710-S505


title: P2139_N708-S504


title: P2139_N708-S506


title: P2139_N708-S502


title: P2139_N708-S505


title: P2139_N707-S517


title: P2139_N707-S503


title: P2139_N707-S507


title: P2139_N707-S508


title: P2139_N707-S502


title: P2139_N707-S504


title: P2139_N707-S506


title: P2139_N707-S505


title: P2139_N705-S507


title: P2139_N705-S508


title: P2139_N706-S506


title: P2139_N706-S505


title: P2139_N706-S503


title: P2139_N706-S504


title: P2139_N705-S517


title: P2139_N706-S507


title: P2139_N706-S508


title: P2139_N706-S502


title: P2139_N705-S505


title: P2139_N705-S506


title: P2139_N705-S504


title: P2139_N705-S502


title: P2139_N705-S503


title: P2139_N708-S503


title: P2139_N704-S517


title: P2139_N706-S517


title: P2139_N704-S507


title: P2139_N704-S506


title: P2139_N703-S508


title: P2139_N704-S504


title: P2139_N703-S503


title: P2139_N703-S505


title: P2139_N703-S502


title: P2139_N703-S506


title: P2139_N702-S508


title: P2139_N703-S507


title: P2139_N702-S507


title: P2139_N701-S508


title: P2139_N701-S507


title: P2139_N702-S504


title: P2139_N703-S504


title: P2139_N702-S503


title: P2139_N704-S508


title: P2139_N701-S504


title: P2139_N702-S517


title: P2139_N704-S505


title: P2139_N701-S506


title: P2139_N702-S502


title: P2139_N701-S503


title: P2139_N704-S503


title: P2139_N703-S517


title: P2135_N712-S517


title: P2139_N701-S502


title: P2139_N701-S505


title: P2139_N704-S502


title: P2139_N702-S505


title: P2135_N712-S508


title: P2139_N701-S517


title: P2135_N712-S507


title: P2139_N702-S506


title: P2135_N712-S506


title: P2135_N712-S505


title: P2135_N712-S504


title: P2135_N712-S503


title: P2135_N711-S508


title: P2135_N711-S517


title: P2135_N711-S505


title: P2135_N711-S504


title: P2135_N711-S506


title: P2135_N711-S507


title: P2135_N710-S517


title: P2135_N711-S503


title: P2135_N711-S502


title: P2135_N710-S507


title: P2135_N710-S508


title: P2135_N709-S517


title: P2135_N710-S503


title: P2135_N710-S504


title: P2135_N709-S508


title: P2135_N710-S502


title: P2135_N710-S505


title: P2135_N710-S506


title: P2135_N709-S506


title: P2135_N709-S505


title: P2135_N709-S504


title: P2135_N709-S503


title: P2135_N708-S517


title: P2135_N709-S507


title: P2135_N708-S507


title: P2135_N708-S506


title: P2135_N708-S508


title: P2135_N712-S502


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title: P1961_N708-S504


title: P1962_N703-S504


title: P1961_N707-S507


title: P1961_N708-S502


title: P1961_N707-S517


title: P1961_N707-S508


title: P1961_N707-S505


title: P1961_N707-S504


title: P1961_N707-S502


title: P1961_N707-S506


title: P1961_N706-S508


title: P1961_N706-S507


title: P1961_N706-S505


title: P1961_N707-S503


title: P1961_N706-S506


title: P1961_N709-S505


title: P1961_N706-S517


title: P1961_N706-S502


title: P1961_N706-S504


title: P1961_N705-S508


title: P1961_N705-S503


title: P1961_N705-S502


title: P1961_N705-S507


title: P1961_N705-S506


title: P1961_N705-S505


title: P1961_N705-S504


title: P1961_N708-S503


title: P1961_N704-S508


title: P1961_N704-S517


title: P1961_N704-S507


title: P1961_N704-S506


title: P1961_N704-S504


title: P1961_N704-S502


title: P1961_N703-S508


title: P1961_N706-S503


title: P1961_N703-S506


title: P1961_N703-S517


title: P1961_N704-S503


title: P1961_N703-S503


title: P1961_N703-S507


title: P1961_N703-S504


title: P1961_N704-S505


title: P1961_N705-S517


title: P1961_N702-S508


title: P1961_N702-S517


title: P1961_N702-S505


title: P1961_N702-S503


title: P1961_N702-S507


title: P1961_N703-S505


title: P1961_N701-S508


title: P1961_N702-S504


title: P1961_N702-S502


title: P1961_N701-S506


title: P1961_N702-S506


title: P1961_N701-S517


title: P1961_N701-S504


title: P1961_N701-S507


title: P1961_N701-S505


title: P1961_N701-S502


title: P1960_N712-S517


title: P1961_N701-S503


title: P1960_N712-S507


title: P1960_N712-S505


title: P1960_N712-S504


title: P1960_N712-S508


title: P1961_N703-S502


title: P1960_N712-S503


title: P1960_N712-S506


title: P1960_N711-S507


title: P1960_N711-S508


title: P1960_N712-S502


title: P1960_N711-S506


title: P1960_N711-S517


title: P1960_N711-S505


title: P1960_N711-S504


title: P1960_N711-S502


title: P1960_N710-S507


title: P1960_N710-S506


title: P1960_N710-S517


title: P1960_N710-S508


title: P1960_N711-S503


title: P1960_N710-S503


title: P1960_N710-S505


title: P1960_N709-S508


title: P1960_N710-S504


title: P1960_N709-S507


title: P1960_N709-S517


title: P1960_N709-S506


title: P1960_N709-S504


title: P1960_N709-S503


title: P1960_N709-S502


title: P1960_N708-S507


title: P1960_N708-S508


title: P1960_N708-S506


title: P1960_N708-S517


title: P1960_N708-S505


title: P1960_N707-S508


title: P1960_N708-S503


title: P1960_N708-S502


title: P1960_N707-S517


title: P1960_N707-S507


title: P1960_N707-S506


title: P1960_N707-S505


title: P1960_N707-S504


title: P1960_N707-S502


title: P1960_N710-S502


title: P1960_N706-S517


title: P1960_N707-S503


title: P1960_N706-S508


title: P1960_N709-S505


title: P1960_N706-S507


title: P1960_N706-S505


title: P1960_N706-S504


title: P1960_N706-S503


title: P1960_N705-S517


title: P1960_N706-S506


title: P1960_N705-S508


title: P1960_N708-S504


title: P1960_N705-S507


title: P1960_N705-S505


title: P1960_N705-S506


title: P1960_N705-S503


title: P1960_N705-S504


title: P1960_N704-S517


title: P1960_N705-S502


title: P1960_N704-S507


title: P1960_N704-S506


title: P1960_N704-S508


title: P1960_N704-S505


title: P1960_N704-S502


title: P1960_N703-S517


title: P1960_N704-S503


title: P1960_N704-S504


title: P1960_N703-S508


title: P1960_N703-S507


title: P1960_N706-S502


title: P1960_N702-S517


title: P1960_N703-S506


title: P1960_N703-S504


title: P1960_N703-S503


title: P1960_N702-S508


title: P1960_N702-S506


title: P1960_N702-S507


title: P1960_N702-S505


title: P1960_N702-S503


title: P1960_N701-S517


title: P1960_N701-S507


title: P1960_N701-S508


title: P1960_N701-S504


title: P1960_N701-S505


title: P1960_N701-S506


title: P1960_N701-S502


title: P1960_N703-S505


title: P1960_N703-S502


title: P1960_N702-S504


title: P1960_N702-S502


title: P1960_N701-S503


title: 5786049042_J: Sputum_Placebo_Post-treatment_M027

city: Newcastle

first: Thomas

middle: K

last: Wright

state: NSW

address: Callaghan

department: Faculty of Health and Medicine

country: Australia

institute: The University of Newcastle

data_processing: Microarray data were exported using GenomeStudio (Illumina) and analysed using GeneSpring GX12.5 (Agilent Technologies). Data were log transformed and quantile normalisation performed.

organism: Homo sapiens

source_name: Sputum, Placebo, Post-treatment

label_protocol: Biotinylated cRNA was prepared from 500ng of extracted RNA using the Illumina Total Prep RNA Amplification Kit as standard for Illumina arrays

extract_protocol: RNA was extracted from sputum plugs stored in Buffer RLT using the Rneasy Mini Kit (Qiagen), whereas blood was extracted from PAXgene Blood RNA tubes using the PAXgene Blood RNA Kit (Qiagen) as per manufacturers instructions.

tag: diagnosis

value: neutrophilic COPD

value: Female

value: Sputum


title: 6007254006_D: Sputum_Placebo_Post-treatment_M040


title: 5786049042_D: Sputum_Placebo_Post-treatment_M014


title: 6007254005_H: Sputum_Placebo_Post-treatment_M076


title: 5786049053_J: Sputum_Placebo_Post-treatment_M007


title: 6007254006_B: Sputum_Placebo_Post-treatment_M033


title: 6007254006_J: Sputum_Placebo_Post-treatment_M057


title: 6007254006_H: Sputum_Placebo_Post-treatment_M047


title: 6007254006_L: Sputum_Placebo_Post-treatment_M060


title: 6007254005_L: Sputum_Placebo_Post-treatment_M079


title: 5786049053_K: Sputum_Placebo_Post-treatment_M006


title: 6007254005_K: Sputum_Placebo_Pretreatment_M079

source_name: Sputum, Placebo, Pretreatment


title: 6007254005_G: Sputum_Placebo_Pretreatment_M076


title: 5786049053_H: Sputum_Placebo_Post-treatment_M005


title: 6007254006_K: Sputum_Placebo_Pretreatment_M060


title: 5786049053_I: Sputum_Placebo_Pretreatment_M006


title: 6007254006_C: Sputum_Placebo_Pretreatment_M040


title: 5786049053_L: Sputum_Placebo_Pretreatment_M007


title: 6007254006_I: Sputum_Placebo_Pretreatment_M057


title: 6007254005_D: Sputum_Azithromycin_Post-treatment_M065

source_name: Sputum, Azithromycin, Post-treatment


title: 5786049042_C: Sputum_Placebo_Pretreatment_M014


title: 5786049042_E: Sputum_Placebo_Pretreatment_M020


title: 6007254005_F: Sputum_Azithromycin_Post-treatment_M069


title: 5786049042_I: Sputum_Placebo_Pretreatment_M027


title: 5786049042_F: Sputum_Placebo_Post-treatment_M020


title: 6007254006_G: Sputum_Placebo_Pretreatment_M047


title: 6007254005_B: Sputum_Azithromycin_Post-treatment_M061


title: 5786049053_G: Sputum_Placebo_Pretreatment_M005


title: 6007254006_A: Sputum_Placebo_Pretreatment_M033


title: 6007254005_J: Sputum_Azithromycin_Post-treatment_M078


title: 5786049042_H: Sputum_Azithromycin_Post-treatment_M023


title: 5786049042_B: Sputum_Azithromycin_Post-treatment_M008


title: 6007254005_E: Sputum_Azithromycin_Pretreatment_M069

source_name: Sputum, Azithromycin, Pretreatment


title: 5786049053_F: Sputum_Azithromycin_Post-treatment_M004


title: 6007254006_F: Sputum_Azithromycin_Post-treatment_M045


title: 6007254005_I: Sputum_Azithromycin_Pretreatment_M078


title: 5786049042_K: Sputum_Azithromycin_Pretreatment_M029


title: 5786049042_G: Sputum_Azithromycin_Pretreatment_M023


title: 5786049053_D: Sputum_Azithromycin_Post-treatment_M003


title: 5786049053_C: Sputum_Azithromycin_Pretreatment_M003


title: 5786049042_A: Sputum_Azithromycin_Pretreatment_M008


title: 5786049016_B: Blood_Placebo_Post-treatment_M040

source_name: Blood, Placebo, Post-treatment

value: Blood


title: 5786049053_B: Sputum_Azithromycin_Post-treatment_M002


title: 6007254005_C: Sputum_Azithromycin_Pretreatment_M065


title: 5786049053_A: Sputum_Azithromycin_Pretreatment_M002


title: 6007254006_E: Sputum_Azithromycin_Pretreatment_M045


title: 5786049024_F: Blood_Placebo_Post-treatment_M027


title: 5786049053_E: Sputum_Azithromycin_Pretreatment_M004


title: 5786049042_L: Sputum_Azithromycin_Post-treatment_M029


title: 5786049016_H: Blood_Placebo_Post-treatment_M047


title: 6007254005_A: Sputum_Azithromycin_Pretreatment_M061


title: 5786049024_J: Blood_Placebo_Post-treatment_M033


title: 5786049063_F: Blood_Placebo_Post-treatment_M005


title: 5786049024_B: Blood_Placebo_Post-treatment_M014


title: 5786049018_J: Blood_Placebo_Post-treatment_M076


title: 5786049018_I: Blood_Placebo_Pretreatment_M076

source_name: Blood, Placebo, Pretreatment


title: 5786049016_J: Blood_Placebo_Post-treatment_M057


title: 5786049016_L: Blood_Placebo_Post-treatment_M060


title: 5786049063_H: Blood_Placebo_Post-treatment_M006


title: 5786049024_D: Blood_Placebo_Post-treatment_M020


title: 5786049016_I: Blood_Placebo_Pretreatment_M057


title: 5786049024_C: Blood_Placebo_Pretreatment_M020


title: 5786049018_H: Blood_Azithromycin_Post-treatment_M073

source_name: Blood, Azithromycin , Post-treatment


title: 5786049024_I: Blood_Placebo_Pretreatment_M033


title: 5786049063_E: Blood_Placebo_Pretreatment_M005


title: 5786049016_A: Blood_Placebo_Pretreatment_M040


title: 5786049016_G: Blood_Placebo_Pretreatment_M047


title: 5786049024_L: Blood_Azithromycin_Post-treatment_M037


title: 5786049018_F: Blood_Azithromycin_Post-treatment_M069


title: 5786049016_K: Blood_Placebo_Pretreatment_M060


title: 5786049016_F: Blood_Azithromycin_Post-treatment_M045


title: 5786049024_H: Blood_Azithromycin_Post-treatment_M029


title: 5786049063_B: Blood_Azithromycin_Post-treatment_M003


title: 5786049016_D: Blood_Azithromycin_Post-treatment_M041


title: 5786049018_D: Blood_Azithromycin_Post-treatment_M065


title: 5786049024_A: Blood_Placebo_Pretreatment_M014


title: 5786049018_E: Blood_Azithromycin_Pretreatment_M069

source_name: Blood, Azithromycin , Pretreatment


title: 5786049063_G: Blood_Placebo_Pretreatment_M006


title: 5786049024_E: Blood_Placebo_Pretreatment_M027


title: 5786049018_B: Blood_Azithromycin_Post-treatment_M061


title: 5786049016_E: Blood_Azithromycin_Pretreatment_M045


title: 5786049018_A: Blood_Azithromycin_Pretreatment_M061


title: 5786049018_G: Blood_Azithromycin_Pretreatment_M073


title: 5786049063_L: Blood_Azithromycin_Post-treatment_M008


title: 5786049063_D: Blood_Azithromycin_Post-treatment_M004


title: 5786049024_K: Blood_Azithromycin_Pretreatment_M037


title: 5786049024_G: Blood_Azithromycin_Pretreatment_M029


title: 5786049016_C: Blood_Azithromycin_Pretreatment_M041


title: 5786049063_K: Blood_Azithromycin_Pretreatment_M008


title: 5786049018_C: Blood_Azithromycin_Pretreatment_M065


title: 5786049063_C: Blood_Azithromycin_Pretreatment_M004


title: SNF237_D28_batch5

city: Singapore

first: Vipin

last: Narang

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

hyb_protocol: Labelled cRNAs were hybridized to Illumina human HT-12 V4.0 chips for 16 hours at 58°C in batches of 96 samples. The arrays were then washed and stained base on Illumina Wash Protocol.

scan_protocol: The human chips were scanned using BeadArray Scanner 500GX and the images were analyzed using Illumina GenomeStudio Gene Expression v 2011.1.

data_processing: Illumina Genome Studio was used to export the data in raw format. Raw expression data was loaded into R/Bioconductor and normalized using log2 quantile normalization method of the lumi R package.

label: Biotin

source_name: PBMC Day 28 post-vaccination

label_protocol: Biotinylated cRNA was prepared according to the Illumina® Ambion TotalPrep™ 96 RNA Amplification kit (Thermo Fisher Scientific, San Jose, CA, USA) using 300ng of RNA.

growth_protocol: No growth protocol was used. PBMCs isolated from whole blood were directly processed for RNA isolation.

extract_protocol: PBMCs were isolated from whole blood. 1 million PBMCs were washed with 1 mL of PBS and centrifuged. The supernatant was removed. The cell pellet was loosened and lysed in mirVana Lysis/Binding buffer and stored in -80degC before extraction. Total RNA was isolated from PBMCs using mirVana™ miRNA isolation kit (Thermo Fisher Scientific, San Jose, CA, USA). Total RNA integrity was assessed by Agilent Bioanalyzer.

treatment_protocol: No treatment of PBMCs was performed.

value: PBMC

value: Vaxigrip influenza vaccine

tag: time point

value: Day 28

tag: subject id

tag: age (years)

tag: ethnicity

value: Chinese

tag: microarray batch


title: SNF238_D0_batch6

source_name: PBMC Day 0 pre-vaccination

tag: treatment

value: Day 0

tag: gender


title: 5786049063_A: Blood_Azithromycin_Pretreatment_M003

tag: age

tag: tissue


title: SNF238_D28_batch6


title: SNF240_D28_batch7

value: Male


title: SNF234_D2_batch2

source_name: PBMC Day 2 post-vaccination

value: Day 2


title: SNF240_D7_batch7

source_name: PBMC Day 7 post-vaccination

value: Day 7


title: SNF240_D0_batch7


title: SNF236_D0_batch4


title: SNF233_D7_batch2


title: SNF236_D28_batch4


title: SNF239_D7_batch8


title: SNF239_D0_batch8


title: SNF234_D7_batch2


title: SNF233_D2_batch2


title: SNF238_D7_batch6


title: SNF239_D28_batch8


title: SNF237_D7_batch5


title: SNF237_D0_batch5


title: SNF233_D28_batch2


title: SNF232_D7_batch1


title: SNF233_D0_batch2


title: SNF234_D28_batch2


title: SNF240_D2_batch7


title: SNF237_D2_batch5


title: SNF236_D2_batch4


title: SNF238_D2_batch6


title: SNF236_D7_batch4


title: SNF234_D0_batch2


title: SNF232_D28_batch1


title: SNF231_D2_batch2


title: SNF230_D7_batch2


title: SNF231_D28_batch2


title: SNF230_D28_batch2


title: SNF230_D0_batch2


title: SNF232_D0_batch1


title: SNF232_D2_batch1


title: SNF231_D7_batch2


title: SNF226_D7_batch2


title: SNF231_D0_batch2


title: SNF228_D0_batch3


title: SNF225_D7_batch2


title: SNF228_D2_batch3


title: SNF226_D2_batch2


title: SNF230_D2_batch2


title: SNF225_D28_batch2


title: SNF228_D28_batch3


title: SNF228_D7_batch3


title: SNF226_D0_batch2


title: SNF226_D28_batch2


title: SNF225_D2_batch2


title: SNF223_D2_batch3


title: SNF224_D7_batch7


title: SNF224_D2_batch7


title: SNF225_D0_batch2


title: SNF223_D0_batch3


title: SNF223_D7_batch3


title: SNF223_D28_batch3


title: SNF224_D28_batch7


title: SNF224_D0_batch7


title: SNF222_D7_batch7


title: SNF222_D2_batch7


title: SNF222_D28_batch7


title: SNF220_D28_batch7


title: SNF220_D2_batch7


title: SNF220_D0_batch7


title: SNF219_D7_batch3


title: SNF219_D2_batch3


title: SNF218_D0_batch7


title: SNF219_D28_batch3


title: SNF218_D7_batch7


title: SNF219_D0_batch3


title: SNF220_D7_batch7


title: SNF217_D28_batch3


title: SNF216_D2_batch4


title: SNF216_D28_batch4


title: SNF222_D0_batch7


title: SNF216_D7_batch4


title: SNF217_D2_batch3


title: SNF216_D0_batch4


title: SNF215_D2_batch1


title: SNF218_D28_batch7


title: SNF217_D0_batch3


title: SNF218_D2_batch7


title: SNF215_D7_batch1


title: SNF217_D7_batch3


title: SNF214_D7_batch1


title: SNF215_D28_batch1


title: SNF215_D0_batch1


title: SNF214_D28_batch1


title: SNF213_D0_batch6


title: SNF214_D2_batch1


title: SNF213_D2_batch6


title: SNF213_D28_batch6


title: SNF210_D0_batch1


title: SNF209_D7_batch2


title: SNF209_D2_batch2


title: SNF214_D0_batch1


title: SNF209_D28_batch2


title: SNF210_D7_batch1


title: SNF213_D7_batch6


title: SNF210_D28_batch1


title: SNF206_D28_batch6F


title: SNF208_D28_batch4


title: SNF206_D0_batch8


title: SNF204_D28_batch8


title: SNF209_D0_batch2


title: SNF205_D2_batch7


title: SNF208_D7_batch4


title: SNF208_D0_batch4


title: SNF205_D0_batch7


title: SNF204_D2_batch8


title: SNF204_D0_batch8


title: SNF205_D28_batch7


title: SNF206_D7_batch6R


title: SNF206_D2_batch6F


title: SNF205_D7_batch7


title: SNF204_D7_batch8


title: SNF203_D7_batch2


title: SNF202_D0_batch4


title: SNF201_D0_batch3


title: SNF203_D28_batch2


title: SNF203_D0_batch2


title: SNF201_D28_batch3


title: SNF200_D28_batch8


title: SNF200_D7_batch8


title: SNF202_D28_batch4


title: SNF201_D2_batch3


title: SNF202_D2_batch4


title: SNF203_D2_batch2


title: SNF199_D7_batch4


title: SNF197_D0_batch1


title: SNF200_D0_batch8


title: SNF199_D28_batch4


title: SNF202_D7_batch4


title: SNF199_D0_batch4


title: SNF197_D2_batch1


title: SNF199_D2_batch4


title: SNF201_D7_batch3


title: SNF196_D28_batch3


title: SNF197_D28_batch1


title: SNF197_D7_batch1


title: SNF196_D2_batch3


title: SNF195_D7_batch1


title: SNF195_D2_batch1


title: SNF195_D28_batch1


title: SNF195_D0_batch1


title: SNF196_D0_batch3


title: SNF194_D7_batch3


title: SNF190_D28_batch4


title: SNF194_D2_batch3


title: SNF191_D7_batch8


title: SNF194_D0_batch3


title: SNF189_D7_batch3


title: SNF189_D0_batch3


title: SNF190_D0_batch4


title: SNF187_D28_batch6R


title: SNF190_D2_batch4


title: SNF191_D2_batch8


title: SNF191_D28_batch8


title: SNF186_D28_batch1


title: SNF191_D0_batch8


title: SNF194_D28_batch3


title: SNF189_D28_batch3


title: SNF190_D7_batch4


title: SNF186_D7_batch1


title: SNF189_D2_batch3


title: SNF186_D2_batch1


title: SNF183_D7_batch4


title: SNF187_D0_batch8


title: SNF187_D2_batch6F


title: SNF184_D2_batch5


title: SNF184_D7_batch5


title: SNF184_D0_batch5


title: SNF184_D28_batch5


title: SNF187_D7_batch6F


title: SNF186_D0_batch1


title: SNF196_D7_batch3


title: SNF181_D7_batch7


title: SNF179_D28_batch4


title: SNF183_D2_batch4


title: SNF179_D7_batch4


title: SNF182_D28_batch8


title: SNF182_D0_batch8


title: SNF182_D7_batch8


title: SNF179_D0_batch4


title: SNF181_D28_batch7


title: SNF179_D2_batch4


title: SNF183_D0_batch4


title: SNF181_D0_batch7


title: SNF183_D28_batch4


title: SNF174_D7_batch3


title: SNF174_D2_batch3


title: SNF175_D2_batch4


title: SNF175_D7_batch4


title: SNF181_D2_batch7


title: SNF173_D7_batch3


title: SNF182_D2_batch8


title: SNF175_D28_batch4


title: SNF173_D2_batch3


title: SNF173_D28_batch3


title: SNF174_D28_batch3


title: SNF175_D0_batch4


title: SNF174_D0_batch3


title: SNF172_D7_batch1


title: SNF172_D28_batch1


title: SNF173_D0_batch3


title: SNF171_D2_batch2


title: SNF171_D0_batch2


title: SNF170_D7_batch6R


title: SNF171_D7_batch2


title: SNF170_D0_batch6R


title: SNF168_D7_batch8


title: SNF172_D2_batch1


title: SNF169_D28_batch2


title: SNF172_D0_batch1


title: SNF169_D7_batch2


title: SNF167_D28_batch1


title: SNF171_D28_batch2


title: SNF170_D28_batch6F


title: SNF167_D7_batch1


title: SNF169_D0_batch2


title: SNF168_D2_batch8


title: SNF169_D2_batch2


title: SNF168_D28_batch8


title: SNF165_D28_batch1


title: SNF165_D2_batch1


title: SNF161_D0_batch4


title: SNF165_D7_batch1


title: SNF165_D0_batch1


title: SNF161_D7_batch4


title: SNF170_D2_batch6R


title: SNF160_D28_batch5


title: SNF167_D0_batch1


title: SNF161_D28_batch4


title: SNF160_D0_batch5


title: SNF156_D7_batch4


title: SNF167_D2_batch1


title: SNF161_D2_batch4


title: SNF156_D28_batch4


title: SNF168_D0_batch8


title: SNF155_D2_batch8


title: SNF156_D2_batch4


title: SNF154_D7_batch6


title: SNF160_D2_batch5


title: SNF154_D2_batch6


title: SNF160_D7_batch5


title: SNF155_D0_batch8


title: SNF156_D0_batch4


title: SNF153_D2_batch8


title: SNF153_D28_batch8


title: SNF154_D0_batch6


title: SNF150_D7_batch5


title: SNF152_D7_batch1


title: SNF153_D7_batch8


title: SNF152_D0_batch1


title: SNF154_D28_batch6


title: SNF152_D2_batch1


title: SNF152_D28_batch1


title: SNF153_D0_batch8


title: SNF155_D28_batch8


title: SNF150_D28_batch5


title: SNF147_D2_batch6


title: SNF150_D2_batch5


title: SNF145_D7_batch1


title: SNF146_D28_batch5


title: SNF146_D0_batch5


title: SNF150_D0_batch5


title: SNF147_D0_batch6


title: SNF149_D2_batch4


title: SNF147_D28_batch6


title: SNF149_D0_batch4


title: SNF149_D7_batch4


title: SNF145_D28_batch1


title: SNF149_D28_batch4


title: SNF145_D2_batch1


title: SNF144_D7_batch6


title: SNF142_D2_batch4


title: SNF144_D0_batch6


title: SNF143_D28_batch4


title: SNF146_D2_batch5


title: SNF143_D7_batch4


title: SNF146_D7_batch5


title: SNF145_D0_batch1


title: SNF144_D2_batch6


title: SNF144_D28_batch6


title: SNF143_D2_batch4


title: SNF142_D7_batch4


title: SNF139_D2_batch5


title: SNF139_D7_batch5


title: SNF138_D7_batch6


title: SNF139_D0_batch5


title: SNF143_D0_batch4


title: SNF137_D7_batch6


title: SNF142_D28_batch4


title: SNF137_D2_batch6


title: SNF138_D2_batch6


title: SNF136_D7_batch5


title: SNF132_D28_batch4


title: SNF132_D0_batch4


title: SNF138_D28_batch6


title: SNF137_D0_batch6


title: SNF136_D2_batch5


title: SNF135_D0_batch4


title: SNF142_D0_batch4


title: SNF135_D28_batch4


title: SNF137_D28_batch6


title: SNF135_D7_batch4


title: SNF136_D28_batch5


title: SNF139_D28_batch5


title: SNF136_D0_batch5


title: SNF132_D7_batch4


title: SNF135_D2_batch4


title: SNF138_D0_batch6


title: SNF147_D7_batch6


title: SNF132_D2_batch4


title: SNF129_D7_batch1


title: SNF129_D28_batch1


title: human naïve CD4 rep2

city: ShangHai

first: Chao

last: Wang

address: 1954HuaShan road

institute: Shanghai Jiao Tong University

description:
processed data file:
CD4lowHLA-G_vs_human_N_CD4.xls
CD4lowHLA-G_vs_human_N_CD4_diff.xls

data_processing:
Raw fastq was analyzed using FastQC and Trimmomatic to remove adapters and low quality reads.
Clean reads were mapped to hg19 or mm9 using STAR.
Raw read counts were calculated by HTseq-count.
DEseq2 was applied to calculated the normalized gene counts and differential expressed genes.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: normalized gene counts and differential expressed genes.

source_name: human naïve CD4 cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA LT V2 Sample Prep Kit(Illumina, Sandiego) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: healthy donors (HD)

value: peripheral blood

value: human naive CD4 cells


title: CD4lowHLA-G+ T cells rep1

source_name: CD4lowHLA-G+ T cells

value: prostate cancer (PCa) patient with androgen deprivation therapy (ADT)

value: CD4lowHLA-G+ T cells


title: SNF129_D0_batch1


title: CD4lowHLA-G+ T cells rep2


title: SNF126_D2_batch1


title: SNF128_D2_batch5


title: SNF126_D7_batch1


title: SNF128_D28_batch5


title: SNF129_D2_batch1


title: SNF128_D7_batch5


title: SNF128_D0_batch5


title: SNF126_D28_batch1


title: human naïve CD4 rep1


title: SNF125_D7_batch4


title: FB_ATAC_rep1

city: Baltimore

first: Andy

last: McCallion

state: MD

address: 733 N Broadway, MRB 446

department: Institute of Genetic Medicine

institute: Johns Hopkins School of Medicine

data_processing:
Individual ATAC-seq libraries were sequenced on the Illumina MiSeq to a minimum depth of 20 million, 2x75bp reads per library. A single MB ATAC-seq library was sequenced on the Illumina HiSeq in Rapid Run mode with 2x100bp reads, to a depth of ≥350 million paired-end reads. Quality of sequencing was evaluated using FastQC (v0.11.2; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to mm9 using Bowtie2 (v2.2.5), under --local mode. Reads aligning to the mitochondrial genome, unknown and random chromosomes, and PCR duplicates were removed prior to peak calling (SAMtools). Peaks were called on individual libraries and on a concatenated file combining all MB and all FB libraries (“Joint”) using MACS2 (v2.1.1.20160309) “callpeak” with options: --nomodel --nolambda -B -f BAMPE --gsize mm --keep-dup all.
Supplementary_files_format_and_content: tab-delimited text file containing the peak calls from MACS2
Genome_build: mm9

source_name: E15.5 forebrain dopaminergic neurons

growth_protocol: Tg(Th-EGFP)DJ76Gsat mice (Th-EGFP) were generated by the GENSAT Project and purchased through the Mutant Mouse Resource and Research Centers Repository. Colony maintenance matings were between hemizygous male Th-EGFP mice and female Swiss Webster (SW) mice, obtained from Charles River Laboratories. This same mating scheme was used to establish timed matings, generating litters for assay; day on which vaginal plug is observed, E0.5.

extract_protocol:
Pooled brain regions were dissociated using the Papain Dissociation System (Worthington Biochemical Corporation). The tissue was dissociated in the papain solution for 30 minutes at 37°C, with gentle trituration every 10 minutes using a sterile Pasteur pipette. Following dissociation, cells were passed through a 40µm cell strainer into a 50mL conical, centrifuged for 5 minutes at 300g, resuspended in albumin-inhibitor solution containing DNase, applied to a discontinuous density gradient, and centrifuged for 6 minutes at 70g. The resulting cell pellet was resuspended in HBSS with Mg2+ and Ca2+ and submitted to FACS. Aliquots of 50,000 EGFP+ cells were sorted directly into 300µL HBSS with Mg2+ and Ca2+ with 10% FBS for ATAC-seq. Aliquots containing ≥50,000 EGFP+ cells were sorted into kit-provided lysis buffer for RNA-seq.
ATAC-seq library preparation generally follows the steps as set out in the original ATAC-seq paper with minor modifications. Aliquots of 50,000 EGFP+ cells were centrifuged for 5 minutes at 4°C and 500g, washed with 50µL of chilled PBS and centrifuged again for 5 minutes at 4°C and 500g. The cell pellet was resuspended in lysis buffer, as set out in the protocol, and cells were left to lyse for 5 minutes at 4°C before being centrifuged for 10 minutes at 4°C at 500g. The resulting nuclei pellet was transposed, as written, using the transposase from the Nextera DNA Library Preparation Kit. Following transposition, DNA was purified with the MinElute Reaction Clean-up Kit (Qiagen) and eluted in 10µL elution buffer. Libraries were amplified according to the original ATAC-seq protocol. The qPCR surveillance steps were modified such that the additional number of cycles of amplification were calculated as ¼ maximum intensity, so as to limit PCR duplication rates in the final libraries. Amplified libraries were purified with Ampure XP beads (Beckman Coulter) following the Nextera DNA Library Prep Protocol Guide. Libraries were quantified using the Qubit dsDNA High Sensitivity Assay (Invitrogen) in combination with the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Assay (Agilent).

treatment_protocol: Pregnant SW mice were euthanized at E15.5 and the embryos were removed and immediately placed in chilled Eagle’s Minimum Essential Media (EMEM) on ice. Embryos were decapitated and brains were removed into Hank’s Balanced Salt Solution without Mg2+ and Ca2+ (HBSS w/o) on ice. Under a fluorescent microscope, EGFP+ brains were identified and microdissected to yield the desired forebrain (FB) and midbrain (MB) regions desired. Microdissected regions were placed in fresh HBSS w/o on ice, and pooled per litter for dissociation.

value: Tg(Th-EGFP)DJ76Gsat x Swiss Webster

value: Forebrain

value: Th-EGFP+ sorted dopaminergic neurons


title: FB_ATAC_rep2


title: FB_ATAC_rep3


title: SNF125_D2_batch4

value: Female


title: MB_ATAC_rep3

source_name: E15.5 midbrain dopaminergic neurons

value: Midbrain


title: SNF125_D28_batch4

value: PBMC

value: Vaxigrip influenza vaccine


title: MB_ATAC_rep2


title: SNF124_D28_batch6F

value: Day 28

value: Chinese


title: SNF125_D0_batch4

value: Day 0


title: SNF123_D28_batch1

value: Male


title: SNF124_D7_batch6R

value: Day 7


title: SNF123_D7_batch1


title: SNF124_D0_batch6F


title: SNF126_D0_batch1


title: SNF124_D2_batch8

value: Day 2


title: MB_ATAC_rep1


title: SNF123_D2_batch1


title: SNF122_D0_batch3


title: IPEC 03-2016_14 low glucose

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

description: Transcriptome profile from intestinal porcine enterocytes (jejunum)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

organism: Sus scrofa

source_name: Jejunum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: Different Deoxynivalenol concentrations applied to apical or basolateral under high/low glucose in vitro

tag: agent

value: Deoxynivalenol

tag: concentration

tag: application site

value: ap

tag: glucose status

value: low


title: SNF122_D2_batch3

tag: cell type


title: SNF123_D0_batch1


title: SNF109_D7_batch8


title: IPEC 03-2016_06 low glucose

value: Control


title: SNF122_D7_batch3


title: SNF118_D2_batch1


title: IPEC 03-2016_02 low glucose

value: 200 ng/mL


title: SNF118_D7_batch1


title: SNF119_D7_batch5


title: SNF118_D0_batch1


title: SNF122_D28_batch3


title: IPEC 03-2016_15 low glucose

value: bl


title: IPEC 03-2016_11 low glucose


title: IPEC 03-2016_05 low glucose


title: IPEC 03-2016_03 low glucose


title: IPEC 03-2016_12 low glucose


title: SNF119_D2_batch5


title: IPEC 03-2016_13 low glucose


title: SNF119_D0_batch5


title: SNF116_D7_batch8


title: IPEC 03-2016_10 low glucose


title: SNF109_D28_batch8


title: IPEC 03-2016_04 low glucose


title: IPEC 03-2016_08 low glucose


title: SNF116_D0_batch8


title: IPEC 03-2016_09 low glucose


title: IPEC 03-2016_07 low glucose


title: IPEC 03-2016_01 low glucose


title: SNF109_D2_batch8


title: SNF108_D28_batch6


title: SNF108_D7_batch6


title: IPEC_J2_DON2000bl_3

value: basolateral

value: high


title: IPEC_J2_DON2000ap_2

value: apical


title: IPEC_J2_DON2000ap_1


title: IPEC_J2_DON2000bl_2


title: IPEC_J2_DON200bl_1


title: IPEC_J2_DON2000bl_1


title: SNF107_D28_batch5

value: PBMC


title: SNF107_D2_batch5

value: Vaxigrip influenza vaccine


title: SNF105_D7_batch2

value: Female


title: IPEC_J2_DON200bl_3


title: IPEC 03-2016_15


title: SNF108_D2_batch6

value: Chinese


title: SNF107_D0_batch5

value: Day 0


title: IPEC_J2_DON200ap_2


title: SNF105_D2_batch2


title: SNF105_D28_batch2

value: Day 28


title: IPEC_J2_DON200bl_2


title: IPEC_J2_DON2000ap_3


title: SNF107_D7_batch5

value: Day 7

value: Male


title: IPEC 03-2016_14

value: Deoxynivalenol


title: IPEC 03-2016_13


title: SNF104_D7_batch7


title: SNF105_D0_batch2


title: SNF104_D2_batch7

value: Day 2


title: IPEC 03-2016_12

value: low


title: IPEC 03-2016_10


title: SNF102_D7_batch4


title: IPEC_J2_DON200ap_1


title: SNF102_D28_batch4


title: IPEC 03-2016_05


title: SNF100_D7_batch5


title: IPEC 03-2016_07


title: IPEC 03-2016_08


title: SNF100_D2_batch5


title: IPEC 03-2016_09


title: SNF100_D28_batch5


title: IPEC 03-2016_04


title: IPEC 03-2016_02


title: IPEC 03-2016_03


title: 8Gy4h_#2

city: Chiba

first: Atsuko

last: Ishikawa

state: Chiba

address: Anagawa 4-9-1

department: Research Center for Charged Particle Therapy

country: Japan

institute: National Institute of Radiologocal Sciences

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Ver 2.0, 4x44K (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (Protocol: GE1-v1_95_Feb07 and Grid: 026655_D_F_20150604) to obtain background subtracted and spatially determined Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Small intestine_4hr_8Gy

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (one-color) (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Trizol reagent (Life Technologies, Carlsbad, CA) and RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: BALB/cA Jcl mice were irradiated with C-ion after intraperitnial administration of saline or FGF1 or FGF1/CPP-C. Four hours later, small intestine was sampled and immediately frozen using liquid nitrogen, and then stored at -80 °C.

tag: strain

value: BALB/cA Jcl

value: female

tag: pre-treated with

value: saline

tag: treated with

value: 8Gy Carbon-ion irradiation

value: small intestine


title: SNF102_D0_batch4

tag: time point

tag: subject id


title: SNF100_D0_batch5

tag: age (years)

tag: ethnicity


title: SNF096_D7_batch9

tag: treatment

tag: microarray batch


title: FGF1CPPC+8Gy4h_#2

source_name: Small intestine_4hr_FGF1CPPC+8Gy

tag: gender

tag: age


title: FGF1+8Gy4h_#2

source_name: Small intestine_4hr_FGF1+8Gy

tag: tissue


title: SNF099_D0_batch3


title: SNF104_D28_batch7


title: SNF095_D7_batch9


title: FGF1CPPC+8Gy4h_#1


title: 0Gy4h_#2

source_name: Small intestine_4hr_0Gy


title: FGF1+8Gy4h_#1


title: SNF099_D2_batch3


title: SNF104_D0_batch7


title: SNF094_D7_batch1


title: SNF096_D0_batch9


title: HC13

city: Sydney

first: Fatemeh

last: Vafaee

state: UNSW

address: Gate 11 Botany Street, UNSW Sydney, School of BABS

department: School of Biotechnology and Biomolecular Sciences

institute: University of New South Wales

data_processing:
Illumina Casava1.7 software used for basecalling.
Data pre-processing was performed using a pipeline comprising of adapter trimming (cutadapt), followed by genome alignment to human genome hg 19 using Bowtie (18 bp seed, 1 error in seed, quality score sum of mismatches<70). Where multiple best strata alignments existed, tags were randomly assigned to one of those coordinates. Tags were annotated against mirBase 20 and filtered for at most one base error within the tag.
Counts for each miRNA were tabulated and adjusted to counts per million miRNAs passing the mismatch filter.
Supplementary_files_format_and_content: All samples achieved miRNA read counts >45,000 read counts and miRNAs with low abundance (<50 read counts across more than 20% of samples) were removed.

source_name: healthy control_Serum_Exosome

extract_protocol:
Exosomes were isolated from 1 mL RNase A (37 °C for 10 min; 100 ng/ml; Qiagen, Australia) treated serum, by size exclusion chromatography (qEV iZONE Science). Then, Serum exosomes were processed for RNA extraction using the Plasma/Serum Circulating & Exosomal RNA Purification Mini Kit (Norgen Biotek, Cat. 51000) according to the manufacturer’s protocol.
Exosome RNA sequencing libraries were then constructed using the NEBNext Multiplex Small RNA Library Prep Kit for Illumina (BioLabs, New England) according to the manufacturer’s instructions.

tag: sample type

value: healthy control

tag: molecule subtype

value: small RNA


title: HC14


title: HC11


title: HC16


title: HC12


title: HC10


title: HC15


title: HC9


title: HC8


title: HC6


title: 8Gy4h_#1


title: HC7


title: SNF093_D2_batch5

value: PBMC

value: Vaxigrip influenza vaccine


title: SNF094_D2_batch1

value: Female

value: Chinese


title: SNF094_D0_batch1

value: Day 0


title: SNF094_D28_batch1

value: Day 28


title: IPEC_J2_DON200ap_3

tag: agent

tag: concentration

value: 200 ng/mL

tag: application site

value: apical

value: high


title: 0Gy4h_#1

tag: strain


title: SNF093_D7_batch5

tag: cell type

value: Day 7


title: SNF093_D28_batch5


title: SNF092_D7_batch8


title: SNF093_D0_batch5


title: SNF092_D28_batch8


title: SNF092_D0_batch8


title: SNF092_D2_batch8

value: Day 2


title: SNF091_D7_batch7


title: SNF091_D28_batch7


title: HC5


title: HC4


title: HC3


title: HC2


title: GII-III.10

source_name: IDH-mutant glioma grades II-III_Serum_Exosome

value: glioblastoma

value: mut (IDH2 R172K )

tag: atrx

tag: mgmt

value: Unmeth

value: 1p/19q codeletion

tag: pre-operation radiology

value: T2 hyperintensity; FLAIR high signal; contrast enhancement (recurrence)

tag: treatment effect

value: Hyalinised vessels; siderophages


title: GII-III.9

value: mut

value: Meth

value: T2 hyperintense; contrast enhancement anteriorly

value: No prior Rx

value: small RNA


title: HC1

value: healthy control


title: GII-III.7

value: Contrast enhancement; central diffusion restriction

value: Coagulative necrosis with microCa2+


title: GII-III.8

value: T2 hyperintense; contrast enhancement (recurrence)

value: No Rx effects


title: GII-III.6

value: not performed

value: T1 - hyperintense; contrast enhancing (recurrence)

value: Radionecrosis


title: SNF087_D7_batch2

value: PBMC

value: Vaxigrip influenza vaccine

tag: time point

value: Day 7

tag: subject id

tag: age (years)

value: Female

tag: ethnicity

value: Chinese


title: SNF087_D0_batch2

tag: treatment

value: Day 0

tag: gender

tag: microarray batch


title: GII-III.5

tag: sample type

value: glioblastoma

value: mut

value: Meth

value: T2 - hyperintense; T1 - isointense; no contrast enhancement (recurrence)

value: Rare hyalinised vessels

tag: molecule subtype


title: SNF108_D0_batch6


title: GII-III.2

value: 19q loss

value: T2 - hyperintense; T1 hypointense; rim peripheral restricted diffusion

value: No prior Rx

value: small RNA


title: GII-III.4

value: borderline

value: not performed

value: T2 - hyperintense; FLAIR - patchy suppression


title: GII-III.3

value: T2 - hyperintense; FLAIR - high signal; no contrast enhancement (recurrence)

value: No Rx effects


title: SNF090_D2_batch5

value: PBMC

value: Vaxigrip influenza vaccine

value: Day 2

value: Male


title: SNF090_D28_batch5

value: Day 28

value: Chinese


title: SNF091_D0_batch7

value: Day 0

value: Female


title: SNF090_D7_batch5

value: Day 7


title: SNF087_D2_batch2


title: SNF090_D0_batch5


title: SNF091_D2_batch7


title: GBM12

source_name: IDH-wildtype glioblastoma_Serum_Exosome

value: glioblastoma

value: wt

value: Unmeth

value: Heterogenously enhancing mass


title: SNF087_D28_batch2


title: GBM11

value: not performed

value: Rim enhancing lesion with central restricted diffusion

value: Treatment effects (tumour necrosis with mineralisation and hyalinised vessels)

value: small RNA


title: GII-III.1

value: mut

value: Meth

value: High FLAIR signal

value: No prior Rx


title: SNF085_D7_batch5

value: PBMC

value: Vaxigrip influenza vaccine


title: SNF086_D7_batch7

value: Male

value: Chinese


title: S40_RNASeq_3

city: Tallahassee

first: Brian

middle: P

last: Chadwick

state: FL

address: 319 Stadium Drive, King 3076

department: Biological Science

institute: Florida State University

description: rRNA-depleted total RNA

data_processing:
All ChIP-Seq processing and mapping to human genome build hg19 were performed through the full service of Zymo Research.
RNA-Seq analysis for generation of bigwig files was achieved by first using cutadapt to remove the TruSeq 3’ adapter sequence. Strand-specific alignment to the hg38 used hisat2 with rna-strandness command. Sam files were converted to bam files using samtools. Bam files were converted to bedgraph using bedtools before conversion to bigwig using bedgraphtobigwig.
Genome_build: hg19 for ChIP-Seq and hg38 for RNA-Seq
Supplementary_files_format_and_content: Processed data files are all bigwig format.

source_name: hTERT-Immortalized Retinal Pigment Epithelial Cells

extract_protocol:
For ChIP-Seq, 3 replicate pellet were prepared for each sample. Pellets consisted of at least 5 million cells, cross linked with 1% formaldehyde in phosphate buffered saline for 7 minutes before quenching with 125mM glycine for 5 minutes. Cells were pelleted before flash freezing and storing at -80C. Pellets were then shipped on dry ice to Zymo Research for ChIP preparation. For RNA-Seq, total RNA was extracted from three replicate cultures of each sample using the Machery Nagel Nucleospin RNA Plus kit according to the manufacturers recommendations. RNA samples were shipped on dry ice to Novogene Corporation for quality control analysis followed by rRNA depleted total RNA-Seq.
Libraries for ChIP-Seq and RNA-Seq were prepared using the services provided by Zymo Research and Novogene Corporation respectively.

tag: genotype

value: SETDB1 Knock-out

tag: chip antibody


title: S40_RNASeq_2

description: rRNA-depleted total RNA

value: hTERT-Immortalized Retinal Pigment Epithelial Cells


title: S6_RNASeq_3

description: rRNA-depleted total RNA


title: SNF086_D2_batch7

value: Day 2


title: SNF084_D2_batch3


title: SNF085_D2_batch5

value: Female


title: SNF085_D28_batch5

source_name: PBMC Day 28 post-vaccination

value: Day 28


title: SNF084_D7_batch3

value: Day 7


title: GBM10

value: glioblastoma

value: wt

value: not performed

value: Rim enhancing lesion with central restricted diffusion


title: S40_RNASeq_1

description: rRNA-depleted total RNA


title: SNF083_D28_batch6


title: SNF086_D0_batch7

source_name: PBMC Day 0 pre-vaccination

value: Day 0


title: SNF084_D28_batch3


title: SNF084_D0_batch3


title: SNF086_D28_batch7


title: SNF085_D0_batch5


title: GBM8

value: Unmeth

value: T2 hyperintense; FLAIR high signal; contrast enhancement

value: small RNA


title: SNF083_D7_batch6

value: PBMC

value: Vaxigrip influenza vaccine


title: S6_RNASeq_2

description: rRNA-depleted total RNA


title: GBM9

value: Meth

value: Rim enhancing lesion

value: No prior Rx


title: S6_RNASeq_1

description: rRNA-depleted total RNA

value: hTERT-Immortalized Retinal Pigment Epithelial Cells

value: SETDB1 Knock-out


title: SNF083_D2_batch6

source_name: PBMC Day 2 post-vaccination

value: Day 2

value: Female

value: Chinese


title: SNF083_D0_batch6


title: GBM7

value: glioblastoma

value: wt

value: T2 hyperintense; T1 hypointense; rim enhancing lesion


title: SNF082_D7_batch3

source_name: PBMC Day 7 post-vaccination

value: Day 7

value: Male


title: SNF082_D28_batch3

value: Day 28


title: GBM6

value: borderline

value: not performed

value: T2 hyperintense; central restricted diffusion; rim enhancing

value: small RNA


title: GBM5

value: Unmeth

value: T2 - hyperintense; T1 heterogenous intensity; contrast enhancing


title: RPE1_RNASeq_2

description: rRNA-depleted total RNA

value: hTERT-Immortalized Retinal Pigment Epithelial Cells

value: Wild type


title: RPE1_RNASeq_3

description: rRNA-depleted total RNA


title: GBM4

value: Meth

value: Contrast enhancement - post surgical change

value: No prior Rx


title: RPE1_RNASeq_1

description: rRNA-depleted total RNA


title: GBM3

value: glioblastoma

value: T2 hyperintense; contrast enhancement (recurrence)

value: Focal radionecrosis


title: GBM2

value: wt

value: Heterogeneous lesions with subtle diffusion restriction; extensive peri-tumor edema


title: SNF081_D28_batch3

value: PBMC

value: Vaxigrip influenza vaccine

value: Day 28

value: Male

value: Chinese


title: GBM1

value: Unmeth

value: not performed

value: T2 hyperintense; FLAIR high signal; contrast enhancement (recurrence)

value: small RNA


title: SNF082_D2_batch3

value: Day 2


title: SNF102_D2_batch4


title: SNF082_D0_batch3

value: Day 0


title: SNF081_D7_batch3

value: Day 7


title: Ribo-Seq (HepG2.215-SENP3KD)

city: Ithaca

first: Ji

last: Wan

state: NY

address: 303 Biotech 526 Campus Road

institute: Cornell University

data_processing:
Sequencing reads were mapped to genome and NCBI refseq genes by Tophat ((--bowtie1 --no-novel-juncs -G)
P-site of RPF (13th nt) was extracted
Genome_build: hg19
Supplementary_files_format_and_content: Normalized ribosome occupancy file

source_name: Human liver epithelial cells

extract_protocol:
Rnase I Digestion, RNA dephosphorylation, Size Selection
Poly-A Tailing, cDNA synthesis, Size selection, circularization, DNA precipitation, Linearization, PCR amplification

treatment_protocol: cycloheximide for 3 mins (100 ug/ml)

tag: cell line


title: Ribo-Seq (HepG2.215-control)


title: SNF080_D28_batch3

tag: cell type

value: Female


title: SNF081_D0_batch3


title: WT rep3

city: Shanghai

first: Xiaofen

last: Wu

address: 345 Lingling Rd

department: Shanghai Institute of Organic Chemistry

institute: Chinese Academy of Sciences

data_processing:
Sequencing reads were mapped to UCSC dm6(for sample 1-6) or flybase dm6_r6.05(for sample 7-18) with STAR by default parameter.
Read counts for each gene were calculated by HTSeq-count.
Count files were used as input to DESeq for normalization and differential expression analysis.
Genome_build: dm6
Supplementary_files_format_and_content: For sample1-6, differential expression between foxoc431/c431/WT was called using DESeq. For sample 7-18, sequencing depth was normalized to the same using DESeq.

organism: Drosophila melanogaster

source_name: fly head

growth_protocol: Flies were cultured in standard media at 25ºC with 60% humidity unless otherwise specified. The control (WT) line used was 5905 (FlyBase ID FBst0005905, w1118). The given genotype flies were collected at the day of eclosion and transferred to new vials every other day during aging process.

extract_protocol:
Heads were removed at the given age, RNA was harvested using Trizol reagent, and polyA tail RNAs were selected.
NEBNext Ultra RNA library Prep Kit for Illumina (NEB, E7530L) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: post eclosion day 3

tag: Sex

value: female


title: foxo-/- rep1


title: foxo-/- rep2


title: SNF079_D28_batch2


title: SNF081_D2_batch3


title: SNF080_D0_batch3


title: SNF079_D7_batch2


title: SNF080_D7_batch3


title: SNF079_D2_batch2


title: foxo-/- rep3


title: SNF078_D2_batch2


title: SNF095_D0_batch9


title: SNF080_D2_batch3


title: WT rep1


title: SNF079_D0_batch2


title: Sendai virus-infected rep2

city: Evanston

first: Roli

last: Mandhana

state: Illinois

address: 2205 Tech Drive

institute: Northwestern University

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat (v. 2.0.10)
The mapped reads for each sample were independently assembled into transcripts using Cufflinks (v. 2.1.1). Read counts were generated using HTSeq (v. 0.6.0) and differential expression analysis was done using DESeq2 (v. 1.2.10) .
Genome_build: hg19
Supplementary_files_format_and_content: CSV file includes normalized abundance measurements from DESeq2 formatted as a matrix table for all samples

source_name: Sendai virus-infected B cells

growth_protocol: Namalwa B cells were cultured in RPMI 1640 medium supplemented with 10% calf serum and 1% penicillin-streptomycin

extract_protocol:
RNA was harvested using Trizol reagent and treated with Dnase I.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were mock-infected or infected with 5 pfu/cell of Sendai virus for 6 hours

value: Namalwa B cells

tag: infection

value: Sendai virus


title: SNF078_D7_batch2

value: PBMC


title: SNF077_D7_batch5

value: Vaxigrip influenza vaccine


title: WT rep2


title: Sendai virus-infected rep1


title: ML 31 dCap-D3 mutant Wing Discs

city: Cleveland

first: Michelle

middle: Suzanne

last: Longworth

state: OH

address: 9500 Euclid Ave NE20

department: Molecular Genetics

institute: Cleveland Clinic Foundation

data_processing:
Adapters and low quality bases were trimmed with Trim Galore (v.0.3.3) and controlled for quality with FastQC (v0.11.3).
Trimmed reads were first aligned to the Drosophila genome assembly BDGP6 (Flybase FB2015_01 released February 24th, 2015 with Ensembl 6.04 annotations) using BWA aln/sampe (v.07.12) with default settings.
Unmapped reads were then aligned using TopHat (v.2.0.8b), -r 150 --mate-std-dev 100 --b2-sensitive –I 5000) to retrieve splice junctions.
Picard tools (v.1.119) were used to convert formats and to merge alignment files.
HTSeq (v.0.6.1) was used to count transcripts.
Genome_build: BDGP6
Supplementary_files_format_and_content: raw_counts.xls contains HTSeq read counts for each transcript and sample, excluding cases where all samples had zero reads.
Supplementary_files_format_and_content: wing_capd3-wt.xls contains lists of up- and down-regulated genes in wing discs in one tab and details of differential expression (DE) analysis in the second tab.
Supplementary_files_format_and_content: salivary_capd3-wt.xls contains lists of up- and down-regulated genes in salivary glands in one tab and details of differential expression (DE) analysis in the second tab.

source_name: 3rd instar larval wing discs

growth_protocol: All stocks were maintained at 25 C on standard dextrose media

extract_protocol:
RNA was isolated from Drosophila larval tissue using standard TriZol methods. Each salivary gland and wing disc sample consisted of 50 and 150 tissues respectively. Samples were cleaned and concentrated using the Qiagen Mini RNeasy Kit
Directional (wing disc) or non-directional (salivary gland) cDNA libraries made from cellular mRNAs were generated from the other 8 samples and sequenced (paired-end sequencing of 50 bp reads) in the Genomics Core at the University of Chicago on an Illumina HiSeq2500, according to standard protocols

tag: developmental stage

value: 3rd instar larval

tag: strain

tag: tissue

value: wing discs


title: Mock infected rep2

source_name: Mock infected B cells

value: control


title: ML 30 dCap-D3 mutant Wing Discs


title: Mock infected rep1


title: ML 59 Wild Type Wing Discs


title: SNF077_D28_batch5

tag: time point

value: Day 28

tag: subject id

tag: age (years)

value: Chinese


title: SNF076_D28_batch6

tag: treatment

tag: gender

tag: ethnicity


title: ML 29 Wild Type Wing Discs


title: SNF078_D28_batch2

value: Male

tag: microarray batch


title: SNF078_D0_batch2


title: SNF077_D2_batch5


title: SNF077_D0_batch5


title: SNF076_D0_batch6


title: SNF075_D7_batch5


title: SNF075_D28_batch5


title: ML 27 dCap-D3 mutant Salivary Glands

source_name: 3rd instar larval salivary glands

value: salivary glands


title: SNF075_D2_batch5

value: Day 2


title: Sample_17_TMD8_MALT1_sh2_repl2

city: New York

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to hg19 using STAR with default parameters
CPM were obtained using Rsubread
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited CPM

source_name: TMD8 cell line

extract_protocol: RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

value: lentiviral infection with shRNA hairpin2 targeting MALT1

value: TMD8 cell line


title: ML 28 Wild Type Wing Discs


title: ML 26 dCap-D3 mutant Salivary Glands


title: Sample_14_TMD8_MALT1_sh1_repl2

value: lentiviral infection with shRNA hairpin1 targeting MALT1


title: Sample_16_TMD8_MALT1_sh2_repl1


title: SNF074_D7_batch5

value: Day 7


title: SNF076_D2_batch6

value: Female


title: Sample_15_TMD8_MALT1_sh1_repl3


title: ML 25 dCap-D3 mutant Salivary Glands


title: Sample_13_TMD8_MALT1_sh1_repl1


title: SNF074_D28_batch5


title: SNF074_D0_batch5

value: Day 0


title: SNF075_D0_batch5


title: SNF074_D2_batch5


title: SNF073_D28_batch7


title: SNF073_D2_batch7


title: SNF073_D0_batch7


title: Sample_18_TMD8_MALT1_sh2_repl3


title: ML 23 Wild Type Salivary Glands


title: ML 24 Wild Type Salivary Glands


title: Sample_10_TMD8_shCntrl_repl1

value: lentiviral infection with nontargeting shRNA


title: SNF073_D7_batch7

value: PBMC


title: SNF071_D2_batch8

value: Vaxigrip influenza vaccine


title: SNF071_D28_batch8


title: Sample_8_OCILy3_MALT1_sh2_repl2

source_name: OCI-Ly3 cell line

value: OCI-Ly3 cell line


title: SNF071_D7_batch8


title: Sample_12_TMD8_shCntrl_repl3


title: Sample_11_TMD8_shCntrl_repl2


title: ML 22 Wild Type Salivary Glands

value: 3rd instar larval


title: Sample_9_OCILy3_MALT1_sh2_repl3


title: Sample_7_OCILy3_MALT1_sh2_repl1


title: Sample_5_OCILy3_MALT1_sh1_repl2


title: Sample_6_OCILy3_MALT1_sh1_repl3


title: Sample_4_OCILy3_MALT1_sh1_repl1


title: SNF070_D7_batch5


title: SNF070_D28_batch5


title: SNF071_D0_batch8


title: SNF070_D0_batch5


title: SNF070_D2_batch5


title: SNF069_D7_batch7


title: SNF068_D7_batch5


title: Sample_3_OCILy3_shCntrl_repl3


title: Sample_2_OCILy3_shCntrl_repl2


title: SNF069_D2_batch7


title: SNF068_D2_batch5


title: SNF068_D0_batch5


title: SNF067_D28_batch4


title: SNF069_D0_batch7


title: SNF067_D2_batch4


title: SNF069_D28_batch7


title: Sample_1_OCILy3_shCntrl_repl1


title: Sample_24_TMD8_compound3_24h_repl3

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to hg19 using STAR with default parameters
CPM were obtained using Rsubread
Genome_build: hg19
Supplementary_files_format_and_content: CPM

treatment_protocol: Included as additional column of SAMPLES section

value: treated with 100nM compound 3 for 24h


title: Sample_22_TMD8_compound3_24h_repl1


title: Sample_23_TMD8_compound3_24h_repl2


title: SNF064_D2_batch7


title: SNF064_D7_batch7


title: Sample_21_TMD8_DMSO_24h_repl3

value: treated with DMSO for 24h


title: SNF063_D2_batch1

value: Chinese


title: Sample_20_TMD8_DMSO_24h_repl2


title: Sample_19_TMD8_DMSO_24h_repl1


title: SNF067_D0_batch4


title: Sample_18_TMD8_compound3_8h_repl3

value: treated with 100nM compound 3 for 8h


title: SNF064_D0_batch7

value: Male


title: SNF062_D28_batch4

value: Day 28


title: SNF062_D7_batch4


title: SNF068_D28_batch5


title: SNF062_D0_batch4


title: SNF067_D7_batch4


title: SNF060_D7_batch6


title: SNF064_D28_batch7


title: SNF060_D28_batch6


title: SNF063_D7_batch1


title: SNF063_D28_batch1


title: SNF063_D0_batch1


title: SNF062_D2_batch4

value: Day 2


title: Sample_17_TMD8_compound3_8h_repl2

value: TMD8 cell line


title: SNF060_D0_batch6


title: SNF060_D2_batch6


title: SNF059_D7_batch5


title: Sample_15_TMD8_DMSO_8h_repl3

value: treated with DMSO for 8h


title: SNF059_D2_batch5


title: SNF058_D7_batch3

value: Day 7


title: Sample_16_TMD8_compound3_8h_repl1


title: Sample_14_TMD8_DMSO_8h_repl2


title: Sample_12_OCILy3_compound3_24h_repl3


title: Sample_13_TMD8_DMSO_8h_repl1


title: Sample_11_OCILy3_compound3_24h_repl2


title: SNF058_D2_batch3

value: Female


title: SNF057_D7_batch3


title: Sample_9_OCILy3_DMSO_24h_repl3


title: SNF059_D28_batch5


title: Sample_8_OCILy3_DMSO_24h_repl2


title: SNF056_D2_batch3


title: SNF057_D28_batch3


title: SNF059_D0_batch5

value: Day 0


title: SNF056_D28_batch3


title: SNF057_D2_batch3


title: SNF054_D7_batch6


title: SNF058_D0_batch3


title: SNF057_D0_batch3


title: Sample_7_OCILy3_DMSO_24h_repl1


title: SNF056_D7_batch3


title: SNF055_D7_batch6R


title: SNF056_D0_batch3


title: SNF058_D28_batch3


title: SNF055_D28_batch8


title: Sample_6_OCILy3_compound3_8h_repl3


title: Sample_10_OCILy3_compound3_24h_repl1


title: SNF055_D0_batch6F


title: SNF055_D2_batch6F


title: Sample_5_OCILy3_compound3_8h_repl2


title: SNF054_D28_batch6


title: Sample_4_OCILy3_compound3_8h_repl1