title: NS15_23_SD_Rep2

city: Melbourne

first: Avilash

last: Singh Yadav

state: Victoria

address: Innovation Walk 18, Monash University Clayton Campus

department: School of Biological Sciences

institute: Monash University

description: Clean fasta file generated by BGI-Shenzen containing unique small RNA read sequences. The raw read counts for each read is provded in the sequence header alognwith the unique read ID

data_processing:
Low quality reads were removed (by  BGI-Shenzen)
3' adapter sequences were trimmed (by  BGI-Shenzen)
5' adapter contaminants were removed (by  BGI-Shenzen)
Short reads (<18 bp) were removed (by  BGI-Shenzen)
Clean.fa files (for each sample ) was generated by  BGI-Shenzen. These fasta files contains unique small RNA read sequences. The read counts for each read is provded in the sequence header along with the unique read ID.
clean.fa files  (generated by  BGI-Shenzen) were used for mapping.
small RNA reads were mapped to either TAIR 10 genome (Col-0 samples) or bur-0 genome (for Bur-0 and NS15 samples) using SOAPAligner or Bowtie1 or SCRAM2.
Genome_build: TAIR 10 (for Col-0 samples) and bur-0 genome (Gan et al., 2011, doi:10.1038/nature10414) for Bur-0 and NS15 samples.

organism: Arabidopsis thaliana

source_name: Total shoot tissue

growth_protocol: Plants were grown for 45 days under short day photoperiodic conditions at 23°C or 27°C.

extract_protocol:
Total RNA was extracted from total shoot tissue which was harvested 5 hours after light exposure in the growth rooms (beginning of the day). Total RNA was extracted by TRIzol™ Reagent (Ambion® | Thermo Fisher Scientific). Two biological replicates were used.
small RNA sequencing was performed by  BGI-Shenzen (Beijing Genomics Institute on Illumina HiSeqTM 2000 platform.

tag: accession

tag: growth temperature

tag: photoperiodic conditions

value: short day (8h light/16h dark)

value: 45 day old


title: NS15_23_SD_Rep1

status: Public on Jul 25 2018

type: SRA

country: Australia

library_source: transcriptomic

molecule: total RNA

tag: age


title: NS15_27_SD_Rep1


title: NS15_27_SD_Rep2


title: Bur-0_27_SD_Rep2


title: Caput4C_28

city: Philadelphia

first: Colin

last: Conine

state: Pennsylvania

address: 421 Curie Blvd BRB 1213

department: Genetics and Neonatology

country: USA

institute: UPenn Perelman SOM and CHOP

data_processing:
Reads were aligned to mm10 RefSeq using Bowtie software in a sequencial manner first to rRNA, snRNA and miRNAs to eliminate any reads coming from them and then aligned to the genome.
Genome_build: mm10
Supplementary_files_format_and_content: excel file with normalized gene counts (in multiple spreadsheets)

organism: Mus musculus

growth_protocol: After fertilization by ICSI Zygotes developed in KSOM medium at 37 °C in 5% CO2 5% O2 for 28 hours

extract_protocol:
Embryos were collected at 28 hours post-ICSI in 5ul of buffer TCL with 1% beta mercaptoethanol and frozen at -80C.
single-cell RNA-seq/Nextera kit
single embryo RNA-seq (Smart-seq 2 protocol)

treatment_protocol: Zygotes were generated by ICSI from sperm isolated from the testis, caput epididymis, or cauda epididiymis. Following fertilization by ICSI zygotes were developed to different stages of preimplantation development and were harvested for single-embryo RNA-Seq (Smart-Seq 2 protocol). For RNA injection experiments 3 hours after fertilization by ICSI RNA was injected using an Eppendorf Femtojet injection setup.

tag: strain

value: FVB

tag: deveopmental stage

value: 4C embryo

tag: sperm source

value: caput

tag: rna injected


title: Bur-0_23_SD_Rep2


title: Caput4C_25


title: Bur-0_27_SD_Rep1


title: Caput4C_27


title: CA_8C_15

source_name: CA

value: 8C embryo

value: cauda


title: Bur-0_23_SD_Rep1


title: Caput4C_26


title: Col-0_27_SD_Rep2


title: caput4C_22


title: caput4C_7


title: caput4C_24


title: Col-0_23_SD_Rep2


title: caput4C_23


title: Col-0_27_SD_Rep1


title: caput4C_21


title: caput4C_2


title: Col-0_23_SD_Rep1


title: ES49_Input

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

library_source: genomic

data_processing:
Base calls were performed using Bowtie 1.1.1.
ChIP-Seq reads were aligned to the mm9 genome assembly using samtools 1.2.
Peak calls was performed using MACS1.4.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *_peaks.bed: For every 300 bp window, the mapped tag count for ChIP, Cc and that for Input, Ci were used for calculation. Ec and Ei indicates the estimate count for 300 bp window for ChIP and Input. Signal ratio of ‘target TF’ was calculated as, Cc/Ec + 1 ÷ Max(1, Ci/Ei + 1).
Supplementary_files_format_and_content: *.sorted.bam.tdf: Binary files that can be loaded into the Inegrated Genomics Viewer (IGV).

molecule: genomic DNA

source_name: Ewing sarcoma

growth_protocol: Ewing sarcoma cells are maintained in IMDM supplemented with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and immunoprecipitated with each antibodies.
Libraries were prepared according to Illumina's instructions accompanying the ThruPLEX DNA-seq 6S (12) Kit (R400523). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No special treatment was performed.

tag: strain/background

value: Balb/c

tag: cell line

tag: cell type

value: EWS-FLI1-induced murine Ewing sarcoma cells

tag: chip antibody


title: ES48_H3K27Ac


title: Caput4C_30


title: caput4C_20


title: Caput4C_29


title: caput4C_19


title: ES48_EWS-FLI1

value: FLAG (Sigma, F7425, lot 085M4774V)


title: caput4C_18


title: caput4C_17


title: ES49_H3K27Me3


title: caput4C_15


title: ES49_H3K27Ac


title: caput4C_14


title: caput4C_16


title: caput4C_13


title: caput4C_12


title: ES49_EWS-FLI1


title: caput4C_11


title: caput4C_10


title: caput4C_1


title: cauda4C_9


title: cauda4C_8


title: cauda4C_6


title: cauda4C_7


title: cauda4C_5


title: Cauda4C_31


title: Cauda4C_32


title: cauda4C_4


title: cauda4C_3


title: L29PB_D8_5224

type: RNA

city: Bethesda

first: Delong

last: Liu

state: MD

address: 10 Center Drive

institute: NHLBI/NIH

hyb_protocol: Biotin-labeled RNA (20 µg) was fragmented to ~200 bp and hybridized to U133 Plus 2.0 chips for 16 hours, washed, and stained on a fluidics station.

scan_protocol: GeneChip operating software Version 1.4 was used to calculate signal intensity and present calls on the hybridized chip

data_processing: Affymetrix Expression Console software was used to calculated signal intensities and present calls on the hybridized chips. The signal intensity values of the probe sets were normalized by RMA across the chips. Only probe sets with signal on > 5 arrays were used for analysis.

label: biotin

organism: Homo sapiens

source_name: PB

label_protocol: standard Affymetrix protocol

growth_protocol: Total RNA (1 μg) was isolated from CD19+ selected PBMCs and LN core biopsies.

extract_protocol: Microarray analysis was performed on Affymetrix U133 plus 2.0 chips (Santa Clara, CA) as described (22).

tag: subject id

tag: subject status

value: chronic lymphocytic leukemia

tag: tissue

value: Peripheral blood

value: CD19+ selected PBMCs

tag: drug

value: Lenalidomide

tag: date


title: L27PB_D0_5184


title: Cauda4C_29


title: Cauda4C_28


title: L28PB_D8_5214


title: Cauda4C_30


title: L14PB_D0_4637


title: Cauda4C_27


title: L12PB_D8_4600


title: L16PB_D8_4682


title: L27PB_D8_5188


title: L13PB_D0_4622


title: L14PB_D8_4654


title: L16PB_D0_4674


title: Cauda4C_26


title: L13PB_D8_4632


title: L29PB_D0_5215


title: L07PB_D8_4368


title: L09PB_D8_4438


title: L12PB_D0_4590


title: L04PB_D8_4306


title: L28PB_D0_5205


title: L07PB_D0_4361


title: L09PB_D0_4436


title: Cauda4C_25


title: cauda4C_24


title: L02PB_D8_4291


title: cauda4C_23


title: cauda4C_22


title: L16LNM_D8_5309

source_name: LNM

value: LN core biopsies


title: cauda4C_21


title: cauda4C_20


title: cauda4C_2


title: cauda4C_19


title: cauda4C_18


title: L04PB_D0_4293


title: L02PB_D0_4272


title: L16LNM_D0_5308


title: cauda4C_14


title: cauda4C_15


title: cauda4C_16


title: L14LNM_D8_5297


title: cauda4C_13


title: L14LNM_D0_5307


title: L13LNM_D0_5306


title: cauda4C_12


title: cauda4C_10


title: cauda4C_11


title: cauda4C_1


title: cauda4C_17


title: L11LNM_D0_5070


title: L11LNM_D8_5069


title: L12LNM_D8_5293


title: L07LNM_D0_5064


title: L07LNM_D8_5056


title: L09LNM_D8_5291


title: cauda28_9

value: 2C embryo


title: L09LNM_D0_5290


title: L13LNM_D8_5295


title: L05LNM_D8_5342


title: cauda28_7


title: cauda28_5


title: L04LNM_D0_5062


title: cauda28_4


title: L05LNM_D0_5341


title: cauda28_3


title: L04LNM_D8_5052


title: mo5_HA

city: Rochester

first: Xuewei

last: Wang

address: 200 1st street

institute: Mayo Clinic

data_processing:
Base calling by CASAVA
Alignment by Tophat2
Gene count by featureCount
Normalization by RPKM
Genome_build: mm10
Supplementary_files_format_and_content: excel file for rpkm values of genes

source_name: 24mo male RiboTag (old)

extract_protocol:
To investigate alterations in the microglial translatome during normal aging, systemic inflammation, amyloidoisis and tauopathy, RNA was isolated from microglia using the RiboTag translational Cre/Lox-based profiling system for microglial transcript isolation based on expression of a hemagluttanin (HA) epitope-tagged core ribosomal protein (RPL22) in a cell type of interest. A tamoxifen inducible Cx3cr1 promoter for Cre and eYFP expression (Cx3cr1-CreERT2-IRES-eYFP was crossed to RiboTag mice to generate double heterozygous Cx3cr1CreERT2-IRES-eYFP/+; Rpl22HA/+ mice (referred to as RiboTag). For comparisons of RiboTag vs cellular isolation strategies at baseline and following LPS injection, microglia were also isolated from the forebrain of PBS perfused tamoxifen injected RiboTag mice using cellular isolation strategies where cells underwent a 20 minute collagenase enzymatic digestion followed by a Percoll gradient for myelin removal and sorting based on staining for CD45 and CD11b (7AAD- CD11b+ CD45lo/int  microglial population were sorted to  >98% purity). Cells were sorted into Buffer RLT supplemented with 2-β-mercaptoethanol and RNA was isolated using a Qiagen RNeasy microkit with in column DNaseI digestion. For all RiboTag studies, RiboTag mice (Cx3Cr1cre/+; Rpl22HA/+) were injected for 3 consecutive days with 100μg/g tamoxifen and allowed to rest for a week prior to harvesting or systemic challenge followed by harvest. PBS perfused forebrains were immediately sonicated in homogenization buffer (50mM Tris pH 7.4, 100mM KCl, 12mM MgCl2, 1% NP-40) supplemented with 1mM DTT, 1x protease/phosphatase inhibitors, 200U/mL RNAsin, 100 μg/mL cycloheximide, and 1mg/mL heparin. Lysates were centrifuged at 4°C at 10,000g for 10 minutes. Supernatants were incubated with anti-HA antibodies and rotated at 4°C for 4 hours prior to incubation with protein G magnetic beads overnight at 4°C while rotating. Beads were magnetized and non-HA containing supernatants were removed prior to washing with a high salt buffer (50mM Tris, 300mM KCl, 12mM MgCl2, 10% NP-40, 1mM DTT, 100μg/mL cycloheximide). Three washes were conducted prior to magnetizing the beads, removing all supernatants and then releasing HA bound transcripts from the beads using Buffer RLT supplemented with 2-β-mercaptoethanol. RNA was purified using a Qiagen RNeasy microkit followed by in-column DNase I treatment according to manufacturer’s instructions. For LPS and poly I:C studies, animals were injected with 2μg/g LPS or 12μg/g poly I:C intraperitoneally (i.p.), respectively and microglial were isolated 24 hours post systemic challenge. For amyloidosis studies, 9-10 month old male APPswe/PS1ΔE9 (APP/PS1) and littermate controls were used for RNAseq studies. For tauopathy studies, 9-10 month old male Cx3Cr1creER/+; Rpl22HA/+ that were injected previously injected intracerebroventricularly (ICV) with 2.7E+10 viral particles/ventricle and 2uL/ventricle of rAAV1-TauP301L and rAAV1-GFP on postnatal day 0 were used for to isolate RNA. Finally, in the normal aging study, male or female RiboTag mice (Cx3Cr1cre/+; Rpl22HA/+) were harvested at either 3 months (young), 12 months (middle), or 24 months (old) of age for RiboTag mediated RNA isolation.
Samples were amplified for RNAseq by cDNA library preparation using a NuGen Ovation RNA v2 kit (NuGen, San Carlos, CA) according to manufacturer’s instructions.

value: forebrain microglia

tag: protocol

value: RiboTag


title: L12LNM_D0_5305


title: L02LNM_D8_5061


title: cauda28_24


title: cauda28_8


title: L01LNM_D8_5289


title: mo1_HA


title: cauda28_23


title: mm4_HA

source_name: 12mo male RiboTag (middle-aged)


title: cauda28_21


title: mm3_HA


title: cauda28_6


title: cauda28_22


title: cauda28_19


title: mm2_HA


title: my4_HA

source_name: 3mo male RiboTag (young)


title: mm1_HA


title: my5_HA


title: cauda28_17


title: L01LNM_D0_5288


title: my2_HA


title: mo4_HA


title: L02LNM_D0_5060


title: cauda28_16


title: mo2_HA


title: cauda28_15


title: my1_HA


title: cauda28_14


title: fo5_HA

source_name: 24mo female RiboTag (old)


title: cauda28_2


title: fo3_HA


title: fo1_HA


title: cauda28_11


title: cauda28_10


title: cauda28_12


title: fo2_HA


title: fm4_HA

source_name: 12mo female RiboTag (middle aged)


title: cauda28_1


title: cauda24_9


title: cauda28_20


title: cauda28_13


title: fm3_HA


title: my3_HA


title: fm5_HA


title: cauda24_8


title: fm2_HA


title: cauda28_18


title: cauda24_6


title: cauda24_5


title: fm1_HA


title: fy5_HA

source_name: 3mo female RiboTag (young)


title: fy4_HA


title: cauda24_4


title: fy3_HA


title: cauda24_3


title: cauda24_1


title: cauda18_9


title: fy1_HA


title: s_HA_P5

source_name: 9-10mo rAAV1-TauP301L injected RiboTag


title: cauda18_7


title: cauda18_6


title: s_HA_P3


title: s_HA_P2


title: cauda18_5


title: cauda24_7


title: cauda18_3


title: s_HA_G8

source_name: 9-10mo rAAV1-GFP injected RiboTag control for tauopathy


title: s_HA_P1


title: cauda18_4


title: s_HA_G5


title: cauda18_25


title: cauda18_27


title: s_HA_G3


title: s_HA_G2


title: cauda18_26


title: cauda18_24


title: fy2_HA


title: s_HA_G1


title: cauda18_22


title: cauda18_23


title: s_HA_A3

source_name: 9-10mo APP/PS1 RiboTag


title: s_HA_A4


title: s_HA_A5


title: cauda18_8


title: s_HA_A2


title: cauda18_20


title: cauda18_19


title: cauda18_21


title: cauda18_18


title: s_HA_W7

source_name: 9-10mo RiboTag control for APP/PS1


title: s_HA_P4


title: s_HA_A1


title: cauda18_2


title: s_HA_W4


title: s_HA_W3


title: cauda18_15


title: cauda18_14


title: s_HA_W1


title: s_HA_W2


title: cauda18_11


title: cauda18_16


title: s_HAS_3

source_name: Saline control for Poly(I:C) study


title: cauda18_13


title: s_HAP_1

source_name: 24 hours post Poly(I:C) i.p. challenge


title: caput28_8


title: s_HAP_2


title: caput28_7


title: cauda18_12


title: cauda18_10


title: s_HAS_2


title: s_HAS_1


title: s_S4_T

source_name: total input (bulk)

value: forebrain


title: caput28_6

value: FVB


title: s_S3_T


title: s_L4_HA

source_name: 24 hours post LPS i.p. challenge


title: caput28_4


title: caput28_3


title: s_S1_T


title: s_L1_HA


title: s_L3_C

value: cellular isolation/ cell sorting


title: s_S2_T


title: caput28_5

value: caput


title: s_L2_C


title: s_HAP_3


title: s_L1_C


title: s_S4_HA

source_name: Saline control for LPS study


title: s_S3_HA


title: caput28_2


title: caput28_24


title: caput28_23


title: caput28_26


title: caput28_25


title: caput28_22


title: s_S1_HA


title: caput28_20


title: caput28_27


title: caput28_21


title: caput28_18


title: s_S3_C


title: s_L3_HA


title: s_S2_C


title: caput28_16


title: s_S1_C


title: caput28_13


title: caput28_15


title: caput28_14


title: caput28_12


title: caput28_1


title: caput28_11


title: s_S2_HA


title: caput24_8


title: caput24_7


title: caput24_5


title: caput24_4


title: caput28_17


title: caput24_3


title: caput28_10


title: caput24_9


title: caput18_7


title: caput18_21


title: caput24_1


title: caput18_20


title: caput24_11


title: caput18_8


title: caput18_6


title: caput24_12


title: caput18_5


title: caput18_4


title: caput18_3


title: caput24_2


title: caput18_13


title: caput18_19


title: caput18_15


title: caput18_2


title: caput18_17


title: caput18_14


title: caput18_12


title: caput18_18


title: caput24_10


title: caput18_16


title: KLM1_methanol_PBS

first: Jinguo

last: Chen

department: NIAID

institute: NIH

data_processing:
cellranger version 2.0.1_mkfastq: bcl2fastq v1.9
cellranger version 2.0.1_count: The 98-bp-long read 2 containing the cDNA sequence was aligned using STAR against the GRCh38 human reference transcriptome. Unique molecular identifier (UMI) quantification, GemCode, and cell barcodes filtering based on error detection by Hamming distance were performed as described by Zheng et al
cellranger version 2.0.1_aggr: It normalizes multiple runs to the same sequencing depth (default=mapped) and then re-computes and produces a new single gene-barcode matrix containing all the data for correlation analysis.
Loupe™ Cell Browser (v2.0) was used to view the entire dataset and interactively find significant genes, cell types, and substructure within cell clusters.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files with filtered_gene_bc_matrices

molecule: polyA RNA

source_name: Pancreatic cancer cell line

extract_protocol:
Human PBMCs were obtained from anonymous, healthy donors of the NIH Blood Bank. Cells were separated with LeucoSep tube filled with Ficoll-Paque-plus (GE Healthcare, Pittsburgh, PA) according to the manufacturer’s instruction. single-cell suspension was prepared following 10X Genomics Single cell protocols: Cell preparation guide (CG00053, Rev C).
Droplet-based single-cell partitioning and single-cell RNA-Seq libraries were generated using the Chromium Single-Cell 3′ Reagent v2 Kit (10X Genomics, Pleasanton, CA) as per the manufacturer’s protocol based on the 10X GemCode proprietary technology

tag: isolation

tag: fixation

value: Methanol

tag: resuspension

value: PBS


title: caput18_11

tag: strain


title: KLM1_live

value: Live


title: KLM1_methanol_SSC

value: SSC


title: CD8+_methanol_SSC

source_name: whole blood

value: MACS


title: SortSeq_Mixture 383 samples

first: Shian

last: Su

address: 1G Royal Parade

department: Molecular Medicine

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
gene counting matrix generated using scPipe 1.3.0
reads were aligned using Rsubread 1.29.6
Genome_build: ENSEMBL Homo_sapiens.GRCh38.88
Supplementary_files_format_and_content: gene counting matrix, rows repsent genes and each column is a well

source_name: lung adenocarcinoma

growth_protocol: The human lung adenocarcinoma cell lines H2228, H1975 and HCC827 were retrieved from ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum (FCS) and 1% Penicillin-Streptomycin.  The cells were grown independently at 37C  with 5% carbon dioxide until near 100% confluency.

extract_protocol:
For the three cell lines, cells were dissociated into single cell suspensions in FACS buffer and sorted for 9-cell-mixture and single cell experiment (see below for sorting strategy).   The remaining cells were centrifuged and frozen at -80C for later RNA extraction. The RNA was then extracted using a Qiagen RNA miniprep kit. The amount of RNA was quantified using both Invitrogen Qubit fluorometric quantitation and an Agilent 4200 bioanalyzer to get an accurate estimation. The extracted RNA was then diluted to 60 ng\ul and then mixed in different proportions, according to the study design. The different mixtures were further diluted to create an RNA series that ranged from 3.75pg to 30pg that was dispensed into CEL-seq2 and SORT-seq primer plates using a Nanodrop II dispenser. Prepared RNA mixture plates were sealed and immediately frozen upside down at -80C.
For CEL-seq2, Single cells were flow sorted into chilled 384-well PCR plates containing 1.2ul of primer/ERCC mix using a BD FACSAria III flow cytometer. Sorted plates were sealed and immediately frozen upside down at -80C. Then these plates, together with the mRNA mixture plates, were taken from -80C and processed using an adapted Cel-Seq2 protocol with the following variations. The second strand synthesis was performed using NEBNext Second Strand Synthesis module in a final reaction volume of 8 ul and NucleoMag NGS Clean-up and Size select magnetic beads were used for all DNA purification and size selection steps. For the 9-cell-mixture plates, clean up of the PCR product was performed with 2X0.7-0.9 bead/DNA ratio. For the single cell and mRNA mixture plates, two different clean up ratios for the PCR product were used (0.8 followed by 0.9). The choice of clean-up ratio was optimized from the QC results of the 9-cell-mixture data and the SORT-seq protocols.

value: lung adenocarcinoma cells


title: DTM-Y_PBMC_methanol-3W+SSC

value: Ficoll

value: PBMC


title: DTM-X_PBMC_methanol-3H+SSC


title: DTM-X_PBMC_live


title: caput18_1

tag: deveopmental stage


title: PC9 Gefitinib DTC rep2

city: Richmond

first: Timothy

middle: L

last: Lochmann

state: VA

address: 521 N 11th St

department: OCMB

institute: Virginia Commonwealth University

data_processing:
RNA-seq quality was confirmed by FastQC
RNA-seq data was mapped to ENSEMBL hg38 release 85 assembly using the STAR aligner under default settings
Aligned read files were counted using SummerizedExperiment in R.
Genes with no reads across all samples within each cell line were removed from analysis prior to differential analysis.
Summarized data sets were compared for differential expression by DESeq2 under default settings.
Genome_build: hg38
Supplementary_files_format_and_content: csv file of differential expression between DTC compared to parental

source_name: NSCLC

growth_protocol: Cells were grown in RPMI1680 supplemented with 10% FBS.

extract_protocol:
RNA was isolated with TriZol.
Libraries were created with the KAPA Stranded mRNA-seq Kit.

treatment_protocol: PC9 cells were treated with 50nM gefitinib for 6-days, followed by 3-days of growth media.

value: NSCLC cell line


title: PC9 Gefitinib DTC rep1


title: PC9 Parental rep2


title: PC9 Parental rep1


title: PC9 Parental rep3


title: DTM-X_PBMC_methanol-3W+SSC


title: TDP43OE_bruseq_iPSC_overexpression_rep2

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

description: bru-labeled RNA

data_processing:
Library strategy: bru-seq
Illumina Casava v1.8.2 software used for basecalling.
Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using Bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1
Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: Please refer to Table S1 (Supplemntary Info) for information on patient subtypes and replicate information. The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score (placeholder); (6) strand; (7) gene span; (8) feature_type;  (9)  length (sum of feature lengths, e.g. introns and exons); (10) length (sum of feature lengths, e.g. introns and exons); (11) read count (sense strand); (12) density (RPK) – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6)

source_name: iPSC

growth_protocol: Fibroblasts were grown in DMEM (4.5 g/L D-glucose, +glutamine, no pyruvate (Gibco/Thermo Fisher) supplemented with 10% heat inactivated fetal bovine serum (FBS) (Gibco/Thermo Fisher), 1X Glutamax-1 (Gibco/Thermo Fisher), and 1X MEM NEAA (Gibco/Thermo Fisher)]). Fibroblasts were reprogrammed into iPSCs using two protocols as outlined in the methods. iPSC were cultured in E8 media (Gibco/ThermoFisher) on plates coated with vitronectin (diluted 1:100 in PBS, Gibco/ThermoFisher), and passaged every 5-6 d by adding 0.5 mM EDTA (Gibco/ThermoFisher) dissolved in PBS (no Ca/Mg; Gibco/ThermoFisher) followed by gentle trituration in E8 media using a P1000 pipette.

extract_protocol:
For bruseq and bruchaseseq, total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then  synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

value: iPSC

tag: subtype

value: TDP43 overexpression

tag: bru labeling time

value: 0.5 hours

tag: assay

value: bruseq

tag: time between bru labeling and rna extraction

value: 0 hours

tag: labeling agent

value: Bromouridine (Bru)


title: TDP43OE_bruseq_iPSC_control_rep2

description: bru-labeled RNA

tag: cell type

value: GFP control for TDP43 overexpression


title: LAIV_nasal cells_S00172127

city: Liverpool

first: Simon

last: Jochems

address: Pembroke Place

country: United Kingdom

institute: Liverpool School of Tropical Medicine

data_processing:
Quality control of raw sequencing data was done using fastQC.
Mapping to a human reference genome assembly (GRCh38) was done using STAR 2.5.0a.
Read counts from the resulting BAM alignment files were obtained with featureCounts using a GTF gene annotation from the Ensembl database.
The R/Bioconductor package DESeq2 was used to identify differentially expressed genes among the samples, after removing absent features (zero counts in more than 75% of samples). Genes with an FDR value < 0.1 and an absolute fold change (FC) > 1.5 were identified as differentially expressed.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

source_name: LAIV_nasal cells_D9

extract_protocol:
Nasal cells were collected in RNALater (ThermoFisher) at -80C until extraction. Extraction was performed using the RNEasy micro kit (Qiagen) with on column DNA digestion. Extracted RNA was quantified using a Qubit™  (ThermoFisher).
Sample integrity assessment (Bioanalyzer, Agilent), library preparation and RNA-sequencing (Illumina Hiseq 4000, 20M reads, 100 paired-end reads) were performed at the Beijing Genome Institute (China).

tag: subject id

value: healthy volunteers experimentally challenged with pneumococcus

tag: vaccine

value: live attenuated influenza vaccine (LAIV)

tag: timepoint

tag: carriage status

value: NEG

value: nasal cells


title: TIV_nasal cells_S00170778

source_name: TIV_nasal cells_D2

tag: subject status

value: tetravalent inactivated influenza vaccine (TIV)

value: POS


title: TIV_nasal cells_S00172130

source_name: TIV_nasal cells_D9


title: LAIV_nasal cells_S00170772

source_name: LAIV_nasal cells_D2


title: TDP43OE_bruseq_iPSC_overexpression_rep1

description: bru-labeled RNA


title: TIV_nasal cells_S00170770


title: Control KO

city: Buffalo

first: Amanda

last: Perez

state: NY

address: Elm and Carlton Streets

institute: Roswell Park Cancer Institute

description: replicate 1

hyb_protocol: 1500ng of the labeled probes are then mixed with hybridization reagents and hybridized overnight at 58°C to the WG-6 BeadChips (Illumina, Inc).

scan_protocol: Following washing and staining with Cy3-streptavidin conjugate, the BeadChips are imaged using the Illumina iScan Reader to measure fluorescence intensity at each probe. The intensity of the signal corresponds to the quantity of the respective mRNA in the original sample.

data_processing: BeadChip data files are analyzed with Illumina’s GenomeStudio (v2011.1) gene expression module (v1.9.0) to report both un-normalized and quantile normalized, background corrected gene expression signal levels.

source_name: BAMC from mouse BM

label_protocol: Expression profiling is accomplished using the Mouse WG-6  whole-genome gene expression array and direct hybridization assay (Illumina, Inc).  Initially, 500ng total RNA is converted to cDNA, followed by in vitro transcription to generate biotin labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.) as per manufacturer’s instructions.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNAseI 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: BAMC were isolated from WT and p53-null irradiated (13 GY, 24h) and non-irradiated mice as described in (Hsiao FS et al, 2010).

value: p53-null on C57Bl/6 b.

tag: gender

value: male

tag: age

value: 3 months

tag: tissue

value: bone marrow (BM)


title: TIV_nasal cells_S00172125


title: TIV_nasal cells_S00170765


title: 24 Hr after 13Gy KO

description: replicate 1


title: TIV_nasal cells_S00170058

source_name: TIV_nasal cells_D-4


title: TDP43OE_bruchaseseq_iPSC_overexpression_rep2

description: bru-labeled RNA

data_processing:
Library strategy: bruchase-seq
Illumina Casava v1.8.2 software used for basecalling.
Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using Bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1
Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: Please refer to Table S1 (Supplemntary Info) for information on patient subtypes and replicate information. The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score (placeholder); (6) strand; (7) gene span; (8) feature_type;  (9)  length (sum of feature lengths, e.g. introns and exons); (10) length (sum of feature lengths, e.g. introns and exons); (11) read count (sense strand); (12) density (RPK) – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6)

value: iPSC

value: bruchaseseq

value: 6 hours


title: TDP43OE_bruseq_iPSC_control_rep1

description: bru-labeled RNA

value: 0.5 hours

value: bruseq


title: 48 Hr after 1 3 Gy KO

description: replicate 1


title: Podocyte primary culture 4days tamoxifen-treated No.2

city: Isehara

first: Masaru

last: Motojima

state: Kanagawa

address: 143 Shimokasuya

department: Clinical Pharmacology

institute: Tokai University School of Medicine

description: Gene expression data

hyb_protocol: 600 ng of Cy3-labelled cRNA were hybridized using Gene Expression Hybridization Kit according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner ( G2600D SG13164306) using one color scan setting for 4x44k array slides using scan protocol AgilentHD_HiSen_GX_1Color.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 026655_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the LowInput QuickAmp Labeling Kit (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.

extract_protocol: Total RNA was prepared from cultured podocytes or isolated glomeruli by RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s instruction.

treatment_protocol: Tamoxifen was i.p. injected for 3 consecutive days at 8 weeks of age and glomeruki were isolated on 7th day. Podocytes expanded from isolated glomeruli of adult mice was treated with tamoxifen for 4days or 7 days before RNA isolation.

value: Primary culture podocytes

tag: time point

tag: agent

value: Tamoxifen

tag: genotype


title: Podocyte primary culture 7days mock-treated No.2

description: Gene expression data

value: mock


title: TDP43OE_bruchaseseq_iPSC_control_rep2

description: bru-labeled RNA

tag: subtype

value: GFP control for TDP43 overexpression

value: Bromouridine (Bru)


title: Podocyte primary culture 4days tamoxifen-treated No.1

description: Gene expression data


title: Control WT

description: replicate 1

tag: strain


title: LAIV_nasal cells_S00170052

source_name: LAIV_nasal cells_D-4

value: healthy volunteers experimentally challenged with pneumococcus

value: live attenuated influenza vaccine (LAIV)

value: NEG

value: nasal cells


title: 24 Hr after 13Gy WT

description: replicate 1

value: male


title: Glomeruli of tamoxufen-treated mouse No.1

description: Gene expression data

value: Isolated glomeruli


title: Glomeruli of tamoxufen-treated mouse No.2

description: Gene expression data


title: TIV_nasal cells_S00170050

value: tetravalent inactivated influenza vaccine (TIV)

value: POS


title: Podocyte primary culture 7days tamoxifen-treated No.1

description: Gene expression data


title: TDP43OE_bruchaseseq_iPSC_overexpression_rep1

description: bru-labeled RNA

value: iPSC

value: TDP43 overexpression

tag: bru labeling time

tag: assay

value: bruchaseseq


title: TIV_nasal cells_S00170045


title: sALS4_bruseq_iPSC_rep2

description: bru-labeled RNA

value: sALS

value: 0.5 hours

value: bruseq

tag: time between bru labeling and rna extraction

value: 0 hours

tag: labeling agent


title: TDP43OE_bruchaseseq_iPSC_control_rep1

description: bru-labeled RNA

tag: cell type

value: GFP control for TDP43 overexpression

value: 6 hours


title: Glomeruli of control mouce No.2

description: Gene expression data

source_name: Glomeruli of control mouce No.2


title: TIV_nasal cells_S00170043

tag: subject id

value: healthy volunteers experimentally challenged with pneumococcus

tag: vaccine


title: Podocyte primary culture 7days tamoxifen-treated No.2

description: Gene expression data

value: Primary culture podocytes

value: Tamoxifen


title: Podocyte primary culture 7days mock-treated No.1

description: Gene expression data

value: mock


title: Glomeruli of control mouse No.1

description: Gene expression data

source_name: Glomeruli of control mouse No.1


title: Podocyte primary culture 4days mock-treated No.2

description: Gene expression data


title: TIV_nasal cells_S00169436

tag: timepoint

tag: carriage status

value: nasal cells


title: Podocyte primary culture 4days mock-treated No.1

description: Gene expression data


title: sALS4_bruseq_iPSC_rep1

description: bru-labeled RNA

value: Bromouridine (Bru)


title: sALS4_bruchaseseq_iPSC_rep2

description: bru-labeled RNA


title: TIV_nasal cells_S00169418

tag: subject status

value: tetravalent inactivated influenza vaccine (TIV)


title: TIV_nasal cells_S00168897

value: POS


title: LAIV_nasal cells_S00169416

value: live attenuated influenza vaccine (LAIV)


title: sALS4_bruchaseseq_iPSC_rep1

description: bru-labeled RNA

value: iPSC


title: TIV_nasal cells_S00168894


title: sALS2_bruseq_iPSC_rep1

description: bru-labeled RNA


title: sALS2_bruchaseseq_iPSC_rep2

description: bru-labeled RNA

value: bruchaseseq


title: sALS2_bruchaseseq_iPSC_rep1

description: bru-labeled RNA

value: sALS


title: LAIV_nasal cells_S00168888


title: TIV_nasal cells_S00168170


title: TIV_nasal cells_S00168118


title: C9A4_bruseq_iPSC_rep1

description: bru-labeled RNA

value: 0.5 hours


title: dupKi-hom 11

city: ANN ARBOR

first: Yao

last: Xiao

state: MICHIGAN

address: 100 Washtenaw Ave

institute: UNIVERSITY OF MICHIGAN

data_processing:
Basecalls performed using CASAVA version 1.8.2
Library generation (Illumina TruSeq) sequenced on Illumina HiSeq 2000
Quality control performed using FastQC
Removing contamination of pri- mers/adapters performed using Trimmomatic
Alignment performed using TopHat2
The number of differential expressed transcripts were identified through DESeq
Normalized FPKM values were generated through CuffDiff
Heat map was generated through MultiExperiment Viewer
Gene enrichment analysis was done in ToppFun under the ToppGene suite
Genome_build: mm7 and mm8
Supplementary_files_format_and_content: Processed data are excel files with FPKM values for each sample for each gene.

source_name: pons

extract_protocol:
RNA prepared via Trizol-Chloroform extraction, further purified with Qiagen Rneasy kit.
Library construction performed by University of Michigan DNA sequencing core.

value: SCA3 knock-in mouse, homozygoous for duplicated Q82 repeat


title: ATXN3-KO 2

value: Mouse knockout for ATXN3


title: ATXN3-KO 3


title: dupKi-hom 12


title: Unknown (repeat run) 1

value: Unknown (repeat run) 1


title: ATXN3-KO 1


title: C9A4_bruchaseseq_iPSC_rep2

description: bru-labeled RNA

value: 6 hours


title: wild-type 19

value: wild-type


title: C9A4_bruseq_iPSC_rep2

description: bru-labeled RNA

value: bruseq

value: 0 hours


title: TIV_nasal cells_S00167298

value: healthy volunteers experimentally challenged with pneumococcus


title: dupKi-hom 13


title: wild-type 17


title: wild-type 18


title: YAC15Q-hemi 4

value: Transgenic mouse with human ATXN3 containing Q15 repeat


title: TIV_nasal cells_S00166686

value: NEG

value: nasal cells


title: Unknown (repeat run) 2

value: Unknown (repeat run) 2


title: YAC15Q-hemi 3


title: C9A4_bruchaseseq_iPSC_rep1

description: bru-labeled RNA

value: Bromouridine (Bru)


title: C9A2_bruseq_iPSC_rep2

description: bru-labeled RNA

value: iPSC


title: LAIV_nasal cells_S00166393

value: live attenuated influenza vaccine (LAIV)

value: POS


title: wild-type 15


title: C9A2_bruseq_iPSC_rep1

description: bru-labeled RNA

value: 0.5 hours


title: ki-het 4

value: SCA3 knock-in mouse, heterozygous for single Q82 repeat in Atxn3 gene


title: wild-type 16


title: YAC84Q-hemi 4

value: Transgenic mouse with human ATXN3 containing Q84 repeat


title: YAC84Q-hemi 3


title: ki-hom 4

value: SCA3 knock-in mouse, homozygous for single Q82 repeat in Atxn3 gene


title: C9A2_bruchaseseq_iPSC_rep2

description: bru-labeled RNA

value: bruchaseseq

value: 6 hours


title: Ki-het 3


title: TIV_nasal cells_S00165555

value: tetravalent inactivated influenza vaccine (TIV)


title: dupKi-het 5

value: SCA3 knock-in mouse, heterozygous for duplicated Q82 repeat in Atxn3 gene


title: C9A2_bruchaseseq_iPSC_rep1

description: bru-labeled RNA


title: wild-type 14

value: wild-type


title: TIV_nasal cells_S00167654

value: healthy volunteers experimentally challenged with pneumococcus


title: dupKi-het 6


title: TIV_nasal cells_S00165547

value: NEG


title: sALS2_bruseq_iPSC_rep2

description: bru-labeled RNA

value: sALS

value: bruseq

value: 0 hours


title: C4_bruseq_iPSC_rep2

description: bru-labeled RNA

value: iPSC

value: Control

value: Bromouridine (Bru)


title: C4_bruseq_iPSC_rep1

description: bru-labeled RNA

value: 0.5 hours


title: YAC15Q-hemi 2

value: Transgenic mouse with human ATXN3 containing Q15 repeat


title: TIV_nasal cells_S00165556

value: POS

value: nasal cells


title: TIV_nasal cells_S00165164


title: YAC15Q-hemi 1


title: C4_bruchaseseq_iPSC_rep2

description: bru-labeled RNA

value: bruchaseseq


title: wild-type 13


title: YAC84Q-hemi 2

value: Transgenic mouse with human ATXN3 containing Q84 repeat


title: YAC84Q-hemi 1


title: LAIV_nasal cells_S00165160

value: live attenuated influenza vaccine (LAIV)


title: Ki-hom 2

value: SCA3 knock-in mouse, homozygous for single Q82 repeat in Atxn3 gene


title: LAIV_nasal cells_S00165524


title: wild-type 12

value: wild-type


title: KI-hom 1


title: LAIV_nasal cells_S00165153

value: healthy volunteers experimentally challenged with pneumococcus


title: C1_bruseq_iPSC_rep1

description: bru-labeled RNA


title: C1_bruseq_iPSC_rep2

description: bru-labeled RNA


title: TIV_nasal cells_S00163923

value: tetravalent inactivated influenza vaccine (TIV)

value: NEG


title: wild-type 11


title: dupki-het 3

value: SCA3 knock-in mouse, heterozygous for duplicated Q82 repeat in Atxn3 gene


title: Ki-het 1

value: SCA3 knock-in mouse, heterozygous for single Q82 repeat in Atxn3 gene


title: dupki-het 2


title: TIV_nasal cells_S00163883


title: C1_bruchaseseq_iPSC_rep1

description: bru-labeled RNA

value: iPSC

value: 6 hours


title: C1_bruchaseseq_iPSC_rep2

description: bru-labeled RNA

value: Control

value: Bromouridine (Bru)


title: sALS5_bruseq_fib

description: bru-labeled RNA

source_name: Fibroblasts

value: Fibroblasts

value: sALS

value: 0.5 hours

value: bruseq

value: 0 hours


title: wild-type 10


title: TIV_nasal cells_S00163882

value: nasal cells


title: dupki-het 1


title: wild-type 9


title: ki-hom 3

value: SCA3 knock-in mouse, homozygous for single Q82 repeat in Atxn3 gene


title: LAIV_nasal cells_S00165162

value: live attenuated influenza vaccine (LAIV)

value: POS


title: sALS5_bruchaseseq_fib

description: bru-labeled RNA

value: bruchaseseq


title: dupKi-het 4


title: LAIV_nasal cells_S00163879

value: healthy volunteers experimentally challenged with pneumococcus


title: C4_bruchaseseq_iPSC_rep1

description: bru-labeled RNA


title: wild-type 7

value: wild-type


title: wild-type 8


title: wild-type 6


title: KI-het 2

value: SCA3 knock-in mouse, heterozygous for single Q82 repeat in Atxn3 gene


title: TIV_nasal cells_S00164485

value: tetravalent inactivated influenza vaccine (TIV)

value: NEG


title: sALS4_bruseq_fib

description: bru-labeled RNA


title: LAIV_nasal cells_S00163867


title: wild-type 5


title: sALS4_bruchaseseq_fib

description: bru-labeled RNA

value: 6 hours


title: LAIV_nasal cells_S00163865


title: dupKi-hom 10

value: SCA3 knock-in mouse, homozygoous for duplicated Q82 repeat in Atxn3 gene


title: wild-type 4


title: dupKi-hom 9


title: TIV_nasal cells_S00163708


title: TIV_nasal cells_S00163710


title: dupKi-hom 6


title: LAIV_nasal cells_S00163706


title: sALS2_bruseq_fib

description: bru-labeled RNA

value: Fibroblasts

value: Bromouridine (Bru)


title: sALS3_bruseq_fib

description: bru-labeled RNA

value: sALS

value: 0.5 hours


title: dupKi-hom 5


title: dupKi-hom 7


title: sALS3_bruchaseseq_fib

description: bru-labeled RNA


title: dupKi-hom 4


title: dupKi-hom 8


title: wild-type 3

source_name: deep cerebellar nucleus


title: dupKi-hom 3


title: dupKi-hom 2


title: wild-type 2


title: LAIV_nasal cells_S00163689


title: wild-type 1


title: sALS1_bruchaseseq_fib

description: bru-labeled RNA


title: TIV_nasal cells_S00163688


title: TIV_nasal cells_S00162947


title: TIV_nasal cells_S00162946


title: Liver_txj_control_4

city: Davis

first: Charles

middle: E

last: Mordaunt

state: CA

address: 3318 Tupper Hall, One Shields Ave

department: Medical Microbiology and Immunology

institute: University of California, Davis

data_processing:
Filter using Illumina flag
Separate and trim reads based on adapter contamination
Align to mm10 using BSSeeker2
Combine aligned reads, both trimmed and no adapter contamination
Convert sam files to percent methylation bed files
Genome_build: mm10
Supplementary_files_format_and_content: Percent Methylation Bed file containing single base methylation information with ranged color coding

source_name: fetal liver

extract_protocol:
DNA was isolated using the QIAamp DNA Mini Kit (Qiagen).
Diluted DNA was bisulfite converted using the EZ DNA Methylation Lightning kit (Zymo) according to the manufacturer’s instructions. WGBS libraries were prepared using the TruSeq DNA Methylation kit (Illumina) with indexed PCR primers and a 14-cycle PCR program.

value: tx-j

tag: diet

value: Control


title: Liver_txj_choline_2

value: Choline


title: Liver_txj_choline_4


title: Liver_txj_choline_3


title: Liver_txj_choline_1


title: C9A3_bruseq_fib

description: bru-labeled RNA

value: bruseq

value: 0 hours


title: C9A4_bruchaseseq_fib

description: bru-labeled RNA

value: bruchaseseq


title: C9A3_bruchaseseq_fib

description: bru-labeled RNA


title: LAIV_nasal cells_S00162943

value: healthy volunteers experimentally challenged with pneumococcus

value: live attenuated influenza vaccine (LAIV)

value: POS

value: nasal cells


title: C9A2_bruseq_fib

description: bru-labeled RNA


title: LAIV_nasal cells_S00163703


title: Liver_txj_control_2


title: Liver_txj_control_3


title: sALS2_bruchaseseq_fib

description: bru-labeled RNA


title: Liver_WT_choline_4


title: sALS1_bruseq_fib

description: bru-labeled RNA


title: Liver_WT_choline_3


title: TIV_nasal cells_S00162916

value: tetravalent inactivated influenza vaccine (TIV)


title: C9A4_bruseq_fib

description: bru-labeled RNA


title: dupKi-hom 1


title: TIV_nasal cells_S00162914


title: Liver_WT_choline_2


title: C9A2_bruchaseseq_fib

description: bru-labeled RNA

value: 6 hours


title: Liver_WT_choline_1


title: C9A1_bruseq_fib

description: bru-labeled RNA


title: Liver_WT_control_4


title: LAIV_nasal cells_S00162912


title: Liver_txj_control_1


title: Liver_WT_control_3


title: Liver_WT_control_2


title: TIV_nasal cells_S00162922

value: NEG


title: Ezh2_WT-Osx_P29

first: Asha

last: Nair

address: 200 1ST ST SW

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: calvaria

extract_protocol:
RNA was isolated utilizing Ultra Turrax T25 (IKA) and Direct-zol™ RNA kit (Zymo Research).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: calvaria

value: wild type (WT, Ezh2_WT_Osx)

tag: age

value: 2 to 3 day-old


title: C5_bruseq_fib

description: bru-labeled RNA

value: Fibroblasts

value: 0.5 hours

value: Bromouridine (Bru)


title: Liver_WT_control_1

value: Control


title: LAIV_nasal cells_S00162909


title: Ezh2_WT-Osx_P27


title: Ezh2_cKO-Osx_P8

value: Ezh2 conditional knockout (Ezh2 cKO, Ezh2_cKO-Osx)


title: TIV_nasal cells_S00162143


title: Ezh2_cKO-Osx_P37


title: Ezh2_cKO-Osx_P10


title: C5_bruchaseseq_fib

description: bru-labeled RNA


title: TIV_nasal cells_S00162798


title: LAIV_nasal cells_S00162044


title: TIV_nasal cells_S00162043


title: LAIV_nasal cells_S00160323


title: C3_bruchaseseq_fib

description: bru-labeled RNA


title: C9A1_bruchaseseq_fib

description: bru-labeled RNA


title: LAIV_nasal cells_S00162799


title: C4_bruseq_fib

description: bru-labeled RNA

value: bruseq

value: 0 hours


title: TIV_nasal cells_S00160302

value: healthy volunteers experimentally challenged with pneumococcus


title: C2_bruchaseseq_fib

description: bru-labeled RNA

value: bruchaseseq


title: C1_bruseq_fib

description: bru-labeled RNA


title: LAIV_nasal cells_S00160131

value: live attenuated influenza vaccine (LAIV)


title: Ezh2_WT-Osx_P14


title: LAIV_nasal cells_S00160130

value: POS

value: nasal cells


title: C4_bruchaseseq_fib

description: bru-labeled RNA

value: 6 hours


title: C1_bruchaseseq_fib

description: bru-labeled RNA


title: LAIV_nasal cells_S00158485


title: TIV_nasal cells_S00158476

value: tetravalent inactivated influenza vaccine (TIV)

value: NEG


title: C3_bruseq_fib

description: bru-labeled RNA


title: M: High metastastic cell line SACC-LM

city: Guangzhou

first: jinsong

last: Li

address: Yanjiang west road

country: China

institute: sun yat-sen university

description: High metastastic cell line SACC-LM

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: High metastastic cell line SACC-LM

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: All cells were cultivated in RPMI-1640 medium (Gibco, Rockville, MD) supplemented with 10% FBS (Invitrogen, Carlsbad, CA).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: SACC-LM are highly metastatic cells derived from lung metastases of SACC-83 xenografts.

tag: cell line

value: SACC-LM


title: H596IFN3

city: Barcelona

first: Anna

last: Esteve-Codina

address: Carrer Baldiri Reixac 4-8

country: Spain

institute: CNAG-CRG

description:
AE1158
COUNTS_genes_LUNGCANCER_10

data_processing:
RNA-seq reads were mapped with STAR 2.5.3a
Genes were quantified with RSEM 1.3.0
with genome annotation GENCODE v27
Estimated RSEM counts were used for downstream analysis
Genome_build: GRCh38_primary_assembly

source_name: Lung cancer cell line

extract_protocol:
Maxell® RSC SimplyRNA Tissue
TruSeq Stranded mRNA (polyA)

tag: disease state

value: Lung adenocarcinoma

tag: treatment

value: Interferon γ


title: H596IFN2

description:
AE1154
COUNTS_genes_LUNGCANCER_10


title: A3: Parental SACC-83 cells

description: parental SACC-83 cells

source_name: parental SACC-83 cells


title: LAIV_nasal cells_S00157829


title: H596IFN1

description:
AE1150
COUNTS_genes_LUNGCANCER_10


title: C2_bruseq_fib

description: bru-labeled RNA

value: Fibroblasts

tag: subtype

value: 0.5 hours


title: LAIV_nasal cells_S00157828


title: H596HGF3

description:
AE1157
COUNTS_genes_LUNGCANCER_10

value: Hepatocyte growth factor (HGF)


title: H596HGF1

description:
AE1149
COUNTS_genes_LUNGCANCER_10


title: H596HGF2

description:
AE1153
COUNTS_genes_LUNGCANCER_10


title: TIV_nasal cells_S00157821


title: H596CrizoH3

description:
AE1159
COUNTS_genes_LUNGCANCER_10

value: Crizotinib +HGF


title: S42

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: combined.results.csv.gz

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the rat (Rattus norvegicus) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 100 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

organism: Rattus norvegicus

source_name: Sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley®™SD®™ (Harlan) at about 70 to 100 days of age were fed ad lib with a standard rat diet and ad lib tap water for drinking. To obtain time-pregnant females, the female rats in proestrus were pair-mated with male rats. The sperm-positive (day 0) rats were monitored for diestrus and changes in body weight. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1 generation. Non-littermate females and males aged 70-90 days from F1 generation control or atrazine lineages were bred to obtain F2 generation offspring. The F2 generation rats were bred to obtain F3 generation offspring.

extract_protocol:
Fifty to hundred ul of rat sperm suspension were used for DNA extraction, then 820 uL DNA extraction buffer and 80 ul 0.1M DTT added. The sample was incubated at 65C for 15 minutes. Following this incubation 80 ul proteinase K (20 mg/ml) was added and the sample was incubated at 55C for 2 hours under constant rotation. Then 300 ul of protein precipitation solution (Promega Genomic DNA Purification Kit, A795A) were added, the sample mixed thoroughly and incubated for 15 min on ice. The sample was centrifuged at 13,500 rpm for 20 minutes at 4C. One ml of the supernatant was transferred to a 2 ml tube and 2 ul of glycoblue and 1 ml of cold 100 % isopropanol were added. The sample was mixed well by inverting the tube several times then left in -20C freezer for at least one hour. After precipitation the sample was centrifuged at 13,500 rpm for 20 min at 4C. The supernatant was taken off and discarded without disturbing the (blue) pellet. The pellet was washed with 70% cold ethanol by adding 500ul of 70% ethanol to the pellet and returning the tube to the freezer for 20 minutes. After the incubation the tube was centrifuged for 10 min at 4C at 13,500 rpm and the supernatant discarded. The tube was spun again briefly to collect residual ethanol at bottom of tube and then as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes). Pellet was then resuspended in 100 ul of nuclease free water.
The MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed.

treatment_protocol: On days 8 through 14 of gestation, the F0 females were administered daily intraperitoneal injections of vinclozolin (25 mg/kg BW/day) or dimethyl sulfoxide (vehicle). The vinclozolin was obtained from Chem Service, Westchester PA and was injected in DMSO vehicle. The F1- F3 generation offspring were not themselves treated directly with vinclozolin.

value: vinclozolin

tag: generation


title: LAIV_nasal cells_S00156930


title: DMSO-treated HepG2

city: Beijing

first: Juan

last: Feng

address: No.30, Shuangqing Road, Haidian District

department: School of Medicine

institute: Tsinghua University

description: Analysis used DMSO-treated RNA as control samples for comparison to the experimental samples treated with hawk tea extracts

hyb_protocol: Hybridization was performed in an Agilent G4112F platform (Whole Human Genome Microarray 44k, AMADID 14850) using the One-Color gene expression system (Agilent Technologies) according to the manufacturer’s instructions. These microarrays contain around 41,000 human genes and transcripts with one 60-mer oligonucleotide probe representing each sequence.

scan_protocol: Arrays were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides

data_processing: Microarray data were extracted with Feature Extraction Software version 10.7 (Agilent Technologies)

source_name: HepG2 cells, DMSO treated, 24 h

label_protocol: cRNA was labelled with cyanine-3 (Cy3) for hybridization in an Agilent platform, according to the manufacturer’s instructions.

growth_protocol: HepG2 cells  were maintained in high-glucose Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 100 mg/mL streptomycin at 37°C in a humidified incubator under 5% carbon dioxide.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. RNA quality control was performed in a 2100 Bioanalyzer (Agilent Technologies). In all cases, RNA integrity number was above 8.

treatment_protocol: HepG2 cells  were treated hawk tea extracts for 24 h at a dose of 200 µg/mL. DMSO (1‰）was set as the control group.

value: DMSO treated, 24h


title: HTE-treated HepG2

source_name: HepG2 cells, HTE treated, 24h

value: Hawk tea extracts treated, 24h


title: H596CrizoH2

description:
AE1155
COUNTS_genes_LUNGCANCER_10


title: S41

description: combined.results.csv.gz


title: Eos_R5_dkPGD2

city: Allschwil

first: Axel

last: Klenk

address: Hegenheimermattweg 91

department: Research Informatics

country: Switzerland

institute: Idorsia Pharmaceuticals Ltd.

hyb_protocol: a pool of 300 ng of Cy3 labeled aRNA (examined sample) and 300 ng of Cy5 labeled aRNA human reference (Agilent, Austin TX, USA) were hybridized using the Agilent Hybridization kit (Agilent, Austin TX, USA) according to the manufacturer's instructions. Hybridization was performed for 17 hours and washed according to Agilent's instructions.

scan_protocol: Scanned on an Agilent G2565BA scanner using Agilent scan control (version 8.5.1). Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: BioConductor package vsn was used for variance-stabilizing normalization and glog transformation

source_name: eosinophils from donor R5, treated with dkPGD2

label_protocol: 50 ng of totRNA were labeled using the Low RNA Input QuickAmp Labeling kit (Agilent, Austin TX, USA) following the manufacturer's instructions.

extract_protocol: total RNA extracted  using MagMAX-96 for microarrays kit (Life technologies, Foster City CA, USA ) following the manufacturer's instructions

value: eosinophils

tag: donor

source_name: Stratagene Reference

value: Pool of 10 human cell lines


title: Eos_R1_IL5

source_name: eosinophils from donor R1, treated with IL5


title: H596CrizoH1

description:
AE1151
COUNTS_genes_LUNGCANCER_10

value: Crizotinib + Hepatocyte growth factor (HGF)


title: Eos_R2_Vehicle

source_name: eosinophils from donor R2, treated with Vehicle

value: Vehicle


title: TIV_nasal cells_S00156923

source_name: TIV_nasal cells_D-4

value: healthy volunteers experimentally challenged with pneumococcus

value: nasal cells


title: Eos_R1_Vehicle

source_name: eosinophils from donor R1, treated with Vehicle


title: Eos_R5_IL5

source_name: eosinophils from donor R5, treated with IL5


title: LAIV_nasal cells_S00157827

source_name: LAIV_nasal cells_D2

value: live attenuated influenza vaccine (LAIV)

value: POS


title: Eos_R3_Vehicle

source_name: eosinophils from donor R3, treated with Vehicle


title: Eos_R6_Vehicle

source_name: eosinophils from donor R6, treated with Vehicle


title: Eos_R2_IL5

source_name: eosinophils from donor R2, treated with IL5


title: Eos_R4_dkPGD2

source_name: eosinophils from donor R4, treated with dkPGD2


title: Eos_R4_IL5

source_name: eosinophils from donor R4, treated with IL5


title: S40

description: combined.results.csv.gz


title: LAIV_nasal cells_S00157823

source_name: LAIV_nasal cells_D9

value: NEG


title: H596B3

description:
AE1156
COUNTS_genes_LUNGCANCER_10

source_name: Lung cancer cell line

value: Lung adenocarcinoma

value: No treatment


title: S39

description: combined.results.csv.gz

source_name: Sperm


title: H596B2

description:
AE1152
COUNTS_genes_LUNGCANCER_10


title: S38

description: combined.results.csv.gz


title: TIV_nasal cells_S00156621

source_name: TIV_nasal cells_D9

value: tetravalent inactivated influenza vaccine (TIV)


title: LAIV_nasal cells_S00156618


title: Eos_R2_dkPGD2

source_name: eosinophils from donor R2, treated with dkPGD2


title: Eos_R6_dkPGD2

source_name: eosinophils from donor R6, treated with dkPGD2

source_name: Stratagene Reference


title: H596B1

description:
AE1148
COUNTS_genes_LUNGCANCER_10


title: S37

description: combined.results.csv.gz


title: LAIV_nasal cells_S00156613


title: Eos_R4_Vehicle

source_name: eosinophils from donor R4, treated with Vehicle


title: H1993IFN3

description:
AE1180
COUNTS_genes_LUNGCANCER_10

value: Interferon γ


title: H1993IFN2

description:
AE1178
COUNTS_genes_LUNGCANCER_10


title: TIV_nasal cells_S00156611

source_name: TIV_nasal cells_D2


title: LAIV_nasal cells_S00156620


title: S35

description: combined.results.csv.gz


title: S36

description: combined.results.csv.gz


title: LAIV_nasal cells_S00156442

source_name: LAIV_nasal cells_D-4


title: H1993B3

description:
AE1179
COUNTS_genes_LUNGCANCER_10


title: CD8+_live

source_name: whole blood

tag: isolation

value: MACS

tag: fixation

value: Live

tag: resuspension

value: PBS


title: Eos_R3_dkPGD2

source_name: eosinophils from donor R3, treated with dkPGD2


title: S34

description: combined.results.csv.gz

value: vinclozolin


title: Eos_R5_Vehicle

source_name: eosinophils from donor R5, treated with Vehicle

value: eosinophils


title: LAIV_nasal cells_S00156445

tag: subject id

tag: cell type


title: H1993IFN1

description:
AE1176
COUNTS_genes_LUNGCANCER_10


title: S33

description: combined.results.csv.gz


title: LAIV_nasal cells_S00156441

tag: vaccine

tag: timepoint


title: S32

description: combined.results.csv.gz


title: LAIV_nasal cells_S00155319

tag: subject status

tag: carriage status


title: H1993B1

description:
AE1175
COUNTS_genes_LUNGCANCER_10


title: S31

description: combined.results.csv.gz


title: H1993B2

description:
AE1177
COUNTS_genes_LUNGCANCER_10


title: TIV_nasal cells_S00155310


title: TIV_nasal cells_S00155317

source_name: TIV_nasal cells_D-4


title: H1573IFN3

description:
AE1174
COUNTS_genes_LUNGCANCER_10


title: H1573IFN2

description:
AE1172
COUNTS_genes_LUNGCANCER_10


title: S30

description: combined.results.csv.gz


title: LAIV_nasal cells_S00155308


title: S14

description: combined.results.csv.gz


title: H1573IFN1

description:
AE1170
COUNTS_genes_LUNGCANCER_10


title: TIV_nasal cells_S00155300


title: S13

description: combined.results.csv.gz


title: LAIV_nasal cells_S00155299

source_name: LAIV_nasal cells_D2


title: Eos_R1_dkPGD2

source_name: eosinophils from donor R1, treated with dkPGD2

tag: tissue

value: Pool of 10 human cell lines


title: S10

description: combined.results.csv.gz


title: S11

description: combined.results.csv.gz


title: S12

description: combined.results.csv.gz


title: Eos_R6_IL5

source_name: eosinophils from donor R6, treated with IL5


title: H1573B2

description:
AE1171
COUNTS_genes_LUNGCANCER_10


title: LAIV_nasal cells_S00154300


title: TIV_nasal cells_S00154296


title: Eos_R3_IL5

source_name: eosinophils from donor R3, treated with IL5


title: S8

description: combined.results.csv.gz


title: S9

description: combined.results.csv.gz


title: EBC1IFN1

description:
AE1161
COUNTS_genes_LUNGCANCER_10

source_name: Lung cancer cell line

value: Squamous cell carcinoma


title: LAIV_nasal cells_S00154295


title: H1573B3

description:
AE1173
COUNTS_genes_LUNGCANCER_10


title: EBC1IFN2

description:
AE1164
COUNTS_genes_LUNGCANCER_10


title: EBC1IFN3

description:
AE1167
COUNTS_genes_LUNGCANCER_10


title: S7

description: combined.results.csv.gz

source_name: Sperm


title: S6

description: combined.results.csv.gz


title: LAIV_nasal cells_S00154289


title: LAIV_nasal cells_S00154292


title: EBC1Crizo2

description:
AE1165
COUNTS_genes_LUNGCANCER_10

value: Crizotinib


title: LAIV_nasal cells_S00154288

value: healthy volunteers experimentally challenged with pneumococcus


title: EBC1Crizo1

description:
AE1162
COUNTS_genes_LUNGCANCER_10


title: LAIV_nasal cells_S00155297

value: nasal cells


title: S5

description: combined.results.csv.gz


title: TIV_nasal cells_S00153616


title: S4

description: combined.results.csv.gz


title: H1573B1

description:
AE1169
COUNTS_genes_LUNGCANCER_10


title: EBC1R3

description:
AE1166
COUNTS_genes_LUNGCANCER_10


title: EBC1Crizo3

description:
AE1168
COUNTS_genes_LUNGCANCER_10


title: EBC1R2

description:
AE1163
COUNTS_genes_LUNGCANCER_10


title: EBC1R1

description:
AE1160
COUNTS_genes_LUNGCANCER_10


title: S1

description: combined.results.csv.gz


title: S2

description: combined.results.csv.gz


title: LAIV_nasal cells_S00153614

value: live attenuated influenza vaccine (LAIV)


title: S3

description: combined.results.csv.gz


title: LAIV_nasal cells_S00153612

value: POS


title: LAIV_nasal cells_S00153615


title: G087_E07_241_HIG_PRE_STOUD

status: Public on Jul 24 2018

city: Wageningen

first: Roland

last: Hangelbroek

address: Stippeneng 4

department: Division of Human Nutrition

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of Affymetrix GeneChip Human Gene 1.1 ST arrays was carried out according to standard Affymetrix protocols (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner according to standard protocol.

data_processing: Expression estimates were calculated applying the robust microarray analysis (RMA) algorithm.

source_name: Muscle biopsy from vastus lateralis, isolated from subject HIG, before or without resistance-type exercise training

label_protocol: One hundred nanogram of total RNA was labelled using Ambion WT expression kit (Applied Biosystems, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Baseline transcriptome profiles were measured in muscle biopsies collected from 53 young, 73 healthy older subjects, and 61 frail older subjects. Follow‐up samples from these frail older subjects (31 samples) and healthy older subjects (41 samples) were collected after 6 months of progressive resistance‐type exercise training.

extract_protocol: Muscle samples were obtained with a 5 mm Bergstrom muscle biopsy needle from the Musculus vastus lateralis, after local anaesthesia of the skin and fascia. Samples were freed from any visible blood and non‐muscle tissue and immediately frozen in liquid nitrogen and then stored at −80°C. All samples were obtained in the morning, in an overnight fasted state, after at least 3 days of no heavy physical activity. Total RNA was isolated from the skeletal muscle tissue by using Trizol reagent (Invitrogen, Breda, Netherlands). Thereafter, RNA was purified using the Qiagen RNeasy Micro kit (Qiagen, Venlo, Netherlands), and RNA quality was checked using an Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, Netherlands).

treatment_protocol: Training for both frail and healthy older subjects and consisted of progressive full‐body resistance‐type exercise training. However, the frail older group had training sessions twice per week, whereas the healthy older group trained three times per week. In addition, subjects took a protein or control drink for the duration of the study. The healthy older group received a 15 g portion of milk protein or control supplement at breakfast. The frail older group received a similar drink containing 15 g supplement drink (milk protein or control) at breakfast and lunch.

value: vastus lateralis

tag: Sex

value: F

tag: subjectid

value: HIG

tag: age (yrs)

tag: height (m)

tag: weight (kg)

tag: bmi (kg/m2)

tag: supplement

value: protein

tag: received training

value: yes

tag: group

value: Healthy older (baseline)


title: G087_G07_237_PAM_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject PAM, before or without resistance-type exercise training

value: PAM


title: G087_H07_238_PAM_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject PAM, after resistance-type exercise training

value: Healthy older (after training)


title: G086_H01_19_DSMT26

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 26, before or without resistance-type exercise training

value: M

value: DSMT 26

value: placebo / no supplement

value: no

value: Young (baseline)


title: G087_F07_242_HIG_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject HIG, after resistance-type exercise training


title: G086_H09_222_LUR_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject LUR, after resistance-type exercise training

value: LUR


title: G087_H05_224_TIA_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject TIA, after resistance-type exercise training

value: TIA


title: G086_H08_188_MOH_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject MOH, after resistance-type exercise training

value: MOH


title: G087_B05_158_8083_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8083, after resistance-type exercise training

value: Frail (after training)


title: G086_H10_248_PEH_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject PEH, after resistance-type exercise training

value: vastus lateralis

value: PEH


title: G086_G12_263_KLE_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject KLE, before or without resistance-type exercise training

value: KLE


title: G087_A05_157_8083_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8083, before or without resistance-type exercise training

value: F

value: protein

value: Frail (baseline)


title: G086_H03_64_4024_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4024, before or without resistance-type exercise training


title: G086_H12_264_KLE_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject KLE, after resistance-type exercise training

value: yes


title: G086_H02_39_07LVR_MEAT_MILK

source_name: Muscle biopsy from vastus lateralis, isolated from subject 07LVR, before or without resistance-type exercise training


title: G086_H07_122_8031_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8031, after resistance-type exercise training


title: G086_G08_187_MOH_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject MOH, before or without resistance-type exercise training

value: Healthy older (baseline)


title: G086_H06_344_30RNN_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 30RNN, before or without resistance-type exercise training

value: M


title: G086_H11_256_VRH_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject VRH, after resistance-type exercise training

value: VRH

value: Healthy older (after training)


title: G086_G09_221_LUR_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject LUR, before or without resistance-type exercise training


title: G086_G03_63_4015_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4015, before or without resistance-type exercise training

value: placebo / no supplement

value: no


title: G087_C05_203_HOA_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject HOA, before or without resistance-type exercise training

value: HOA


title: G087_D05_204_HOA_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject HOA, after resistance-type exercise training


title: G086_G06_339_17RNS_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 17RNS, before or without resistance-type exercise training


title: G086_G11_255_VRH_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject VRH, before or without resistance-type exercise training


title: G086_G05_94_HEN_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject HEN, before or without resistance-type exercise training

value: HEN


title: G086_G10_247_PEH_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject PEH, before or without resistance-type exercise training


title: G086_G07_121_8031_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8031, before or without resistance-type exercise training


title: G086_G04_74_8005_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8005, before or without resistance-type exercise training


title: G087_G05_223_TIA_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject TIA, before or without resistance-type exercise training

value: TIA


title: G086_G02_37_01OIK_MEAT_MILK

source_name: Muscle biopsy from vastus lateralis, isolated from subject 01OIK, before or without resistance-type exercise training

value: Young (baseline)


title: G086_G01_14_DSMT20

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 20, before or without resistance-type exercise training

value: vastus lateralis

value: DSMT 20


title: G086_F12_262_VOM_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject VOM, after resistance-type exercise training

value: VOM


title: G086_F11_254_SPM_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject SPM, after resistance-type exercise training

value: F

value: SPM


title: G086_F08_186_LEJ_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject LEJ, after resistance-type exercise training

value: LEJ


title: G086_F10_228_PAA_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject PAA, after resistance-type exercise training

value: PAA

value: yes


title: G086_F05_93_ERG_STOUD_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject ERG, before or without resistance-type exercise training

value: ERG

value: Healthy older (baseline)


title: G086_F07_350_52CRR_PRO_CARB_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject 52CRR, before or without resistance-type exercise training

value: M

value: protein


title: G086_F03_57_55IRP_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 55IRP, before or without resistance-type exercise training

value: placebo / no supplement

value: no


title: G086_F04_73_4056_PROM_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4056, before or without resistance-type exercise training

value: Frail (baseline)


title: G086_F01_13_DSMT17

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 17, before or without resistance-type exercise training

value: DSMT 17


title: G086_F02_35_05IOE_MEAT_MILK

source_name: Muscle biopsy from vastus lateralis, isolated from subject 05IOE, before or without resistance-type exercise training

value: Young (baseline)


title: G086_F06_338_16CUE_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 16CUE, before or without resistance-type exercise training

value: vastus lateralis


title: G086_E12_261_VOM_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject VOM, before or without resistance-type exercise training


title: G086_E11_253_SPM_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject SPM, before or without resistance-type exercise training


title: G086_E06_337_19EES_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 19EES, before or without resistance-type exercise training


title: G086_E10_227_PAA_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject PAA, before or without resistance-type exercise training


title: G086_D11_252_ROL_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject ROL, after resistance-type exercise training

value: ROL

value: Healthy older (after training)


title: G086_D12_260_COM_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject COM, after resistance-type exercise training

value: COM


title: G086_E09_199_JAJ_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject JAJ, before or without resistance-type exercise training

value: JAJ


title: G086_E08_185_LEJ_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject LEJ, before or without resistance-type exercise training

value: LEJ


title: G086_E01_12_DSMT15

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 15, before or without resistance-type exercise training

value: DSMT 15


title: G086_E03_56_53ATR_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 53ATR, before or without resistance-type exercise training


title: G086_E02_33_03LIS_MEAT_MILK

source_name: Muscle biopsy from vastus lateralis, isolated from subject 03LIS, before or without resistance-type exercise training


title: G086_E05_88_BOI_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject BOI, before or without resistance-type exercise training

value: F

value: BOI


title: G086_F09_200_JAJ_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject JAJ, after resistance-type exercise training

value: yes


title: G086_E04_72_4054_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4054, before or without resistance-type exercise training

value: M


title: G086_E07_349_51UTN_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 51UTN, before or without resistance-type exercise training

value: protein

value: Healthy older (baseline)


title: G086_D10_226_RAM_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject RAM, after resistance-type exercise training

value: RAM


title: G086_D08_184_KIJ_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject KIJ, after resistance-type exercise training

value: KIJ


title: G086_D07_348_33ELN_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 33ELN, before or without resistance-type exercise training

value: placebo / no supplement

value: no


title: G086_D03_55_46NEN_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 46NEN, before or without resistance-type exercise training

value: vastus lateralis

value: Young (baseline)


title: G086_D05_87_VEJ_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject VEJ, before or without resistance-type exercise training

value: VEJ


title: G086_D01_11_DSMT14

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 14, before or without resistance-type exercise training

value: DSMT 14


title: G086_C11_251_ROL_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject ROL, before or without resistance-type exercise training

value: ROL


title: G086_C10_225_RAM_PRE_STOUD_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject RAM, before or without resistance-type exercise training


title: G086_D06_329_AW11_CAS

source_name: Muscle biopsy from vastus lateralis, isolated from subject AW11, before or without resistance-type exercise training


title: G086_D02_31_SSMPRE_SCRECOVERY

source_name: Muscle biopsy from vastus lateralis, isolated from subject SSMpre, before or without resistance-type exercise training

value: SSMpre


title: G086_C12_259_COM_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject COM, before or without resistance-type exercise training

value: COM


title: G086_C07_347_40OTZ_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 40OTZ, before or without resistance-type exercise training


title: G086_C02_25_DSMT34

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 34, before or without resistance-type exercise training

value: DSMT 34


title: G086_C06_328_LW02_CAS

source_name: Muscle biopsy from vastus lateralis, isolated from subject LW02, before or without resistance-type exercise training


title: G086_B11_250_SOJ_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject SOJ, after resistance-type exercise training

value: SOJ

value: Healthy older (after training)


title: G086_B12_258_MEH_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject MEH, after resistance-type exercise training

value: M

value: MEH

value: yes


title: G086_C09_197_BOH_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject BOH, before or without resistance-type exercise training

value: BOH

value: protein

value: Healthy older (baseline)


title: G086_C04_68_4040_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4040, before or without resistance-type exercise training

value: placebo / no supplement

value: no

value: Frail (baseline)


title: G086_C05_82_8064_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8064, before or without resistance-type exercise training

value: vastus lateralis

value: F


title: G086_B08_124_8032_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8032, after resistance-type exercise training

value: Frail (after training)


title: G086_C01_09_DSMT12

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 12, before or without resistance-type exercise training

value: DSMT 12

value: Young (baseline)


title: G086_B09_190_RIC_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject RIC, after resistance-type exercise training

value: RIC


title: G086_C03_54_41OHT_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 41OHT, before or without resistance-type exercise training


title: G086_B07_346_36AIS_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 36AIS, before or without resistance-type exercise training


title: G086_C08_183_KIJ_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject KIJ, before or without resistance-type exercise training

value: KIJ


title: G086_B06_327_SO06_CAS

source_name: Muscle biopsy from vastus lateralis, isolated from subject SO06, before or without resistance-type exercise training


title: G086_B05_81_8059_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8059, before or without resistance-type exercise training


title: G086_B04_66_4032_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4032, before or without resistance-type exercise training


title: G086_B03_53_48OTF_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 48OTF, before or without resistance-type exercise training


title: G086_B02_24_DSMT33

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 33, before or without resistance-type exercise training

value: DSMT 33


title: G086_A09_189_RIC_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject RIC, before or without resistance-type exercise training


title: G086_A07_345_35ELN_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 35ELN, before or without resistance-type exercise training

value: M


title: G086_A12_257_MEH_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject MEH, before or without resistance-type exercise training

value: MEH


title: G086_B01_08_DSMT11

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 11, before or without resistance-type exercise training

value: DSMT 11


title: G086_A11_249_SOJ_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject SOJ, before or without resistance-type exercise training

value: SOJ

value: yes


title: G086_A08_123_8032_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8032, before or without resistance-type exercise training

value: protein


title: G086_D09_198_BOH_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject BOH, after resistance-type exercise training

value: BOH

value: Healthy older (after training)


title: G086_A04_65_4030_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4030, before or without resistance-type exercise training

value: placebo / no supplement

value: no

value: Frail (baseline)


title: G086_A03_52_01ASX_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 01ASX, before or without resistance-type exercise training

value: vastus lateralis


title: G086_A05_80_8052_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8052, before or without resistance-type exercise training


title: G085_H07_214_HEF_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject HEF, after resistance-type exercise training

value: HEF


title: G086_A02_21_DSMT29

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 29, before or without resistance-type exercise training

value: DSMT 29

value: Young (baseline)


title: G085_H05_152_8079_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8079, after resistance-type exercise training

value: F

value: Frail (after training)


title: G085_H10_246_WIC_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject WIC, after resistance-type exercise training

value: WIC


title: G085_H12_343_25EER_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 25EER, before or without resistance-type exercise training

value: M

value: Healthy older (baseline)


title: G085_H06_206_CLJ_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject CLJ, after resistance-type exercise training

value: CLJ


title: G085_H09_59_49ICS_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 49ICS, before or without resistance-type exercise training


title: G085_H01_23_DSMT32

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 32, before or without resistance-type exercise training

value: DSMT 32


title: G085_H02_51_20KNY_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 20KNY, before or without resistance-type exercise training

value: protein


title: G085_G09_58_56IPR_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 56IPR, before or without resistance-type exercise training


title: G085_G10_245_WIC_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject WIC, before or without resistance-type exercise training

value: yes


title: G085_G11_331_MG39_CAS

source_name: Muscle biopsy from vastus lateralis, isolated from subject MG39, before or without resistance-type exercise training


title: G086_A01_04_DSMT05

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 05, before or without resistance-type exercise training

value: DSMT 05


title: G085_G06_205_CLJ_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject CLJ, before or without resistance-type exercise training

value: placebo / no supplement


title: G085_G12_342_29EJS_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 29EJS, before or without resistance-type exercise training

value: no


title: G085_G02_50_43ETS_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 43ETS, before or without resistance-type exercise training


title: G085_G07_213_HEF_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject HEF, before or without resistance-type exercise training


title: G085_G01_22_DSMT30

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 30, before or without resistance-type exercise training

value: DSMT 30


title: G085_F11_330_PH37_CAS

source_name: Muscle biopsy from vastus lateralis, isolated from subject PH37, before or without resistance-type exercise training

value: vastus lateralis


title: G085_F08_220_ESM_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject ESM, after resistance-type exercise training

value: ESM

value: Healthy older (after training)


title: G085_H11_332_GB22_CAS

source_name: Muscle biopsy from vastus lateralis, isolated from subject GB22, before or without resistance-type exercise training


title: G085_F03_78_8023_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8023, before or without resistance-type exercise training

value: Frail (baseline)


title: G085_F10_244_WIJ_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject WIJ, after resistance-type exercise training

value: F

value: WIJ


title: G085_E12_340_28LUS_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 28LUS, before or without resistance-type exercise training


title: G085_E10_243_WIJ_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject WIJ, before or without resistance-type exercise training


title: G085_F02_49_38LES_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 38LES, before or without resistance-type exercise training

value: Young (baseline)


title: G085_F01_10_DSMT07

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 07 (DROPOUT), before or without resistance-type exercise training

value: M

value: DSMT 07 (DROPOUT)


title: G085_F07_212_PUJ_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject PUJ, after resistance-type exercise training

value: PUJ


title: G085_E01_7_DSMT08

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 08, before or without resistance-type exercise training

value: DSMT 08


title: G085_E03_77_8022_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8022, before or without resistance-type exercise training


title: G085_F05_150_8078_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8078, after resistance-type exercise training

value: Frail (after training)


title: G085_E08_219_ESM_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject ESM, before or without resistance-type exercise training

value: protein

value: yes

value: Healthy older (baseline)


title: G085_F09_236_TUY_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject TUY, after resistance-type exercise training

value: TUY


title: G085_E09_235_TUY_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject TUY, before or without resistance-type exercise training

value: placebo / no supplement


title: G085_F12_341_18ILS_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 18ILS, before or without resistance-type exercise training

value: vastus lateralis

value: no


title: G085_D12_336_09EZR_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 09EZR, before or without resistance-type exercise training


title: G085_D07_210_VAW_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject VAW, after resistance-type exercise training

value: VAW

value: Healthy older (after training)


title: G085_E05_149_8078_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8078, before or without resistance-type exercise training

value: Frail (baseline)


title: G085_E02_44_14ISR_MEAT_MILK

source_name: Muscle biopsy from vastus lateralis, isolated from subject 14ISR, before or without resistance-type exercise training


title: G085_D04_140_8067_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8067, after resistance-type exercise training

value: F


title: G085_D09_234_PAR_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject PAR, after resistance-type exercise training

value: PAR


title: G085_D06_202_RAJ_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject RAJ, after resistance-type exercise training

value: M

value: RAJ


title: G085_D03_76_8021_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8021, before or without resistance-type exercise training


title: G085_E07_211_PUJ_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject PUJ, before or without resistance-type exercise training

value: PUJ


title: G085_G05_151_8079_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8079, before or without resistance-type exercise training


title: G085_C09_233_PAR_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject PAR, before or without resistance-type exercise training


title: G085_C12_335_05EJN_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 05EJN, before or without resistance-type exercise training


title: G085_D05_148_8076_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8076, after resistance-type exercise training


title: G085_C07_209_VAW_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject VAW, before or without resistance-type exercise training


title: G085_C05_147_8076_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8076, before or without resistance-type exercise training


title: G085_C06_201_RAJ_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject RAJ, before or without resistance-type exercise training


title: G085_C04_139_8067_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8067, before or without resistance-type exercise training


title: G085_D01_6_DSMT07

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 07, before or without resistance-type exercise training

value: DSMT 07

value: Young (baseline)


title: G085_C03_75_8019_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8019, before or without resistance-type exercise training


title: G085_B10_240_EVE_POST_STOUD_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject EVE, after resistance-type exercise training

value: EVE


title: G085_B07_208_HAP_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject HAP, after resistance-type exercise training

value: HAP

value: protein

value: yes


title: G085_B12_334_03UTR_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 03UTR, before or without resistance-type exercise training

value: placebo / no supplement

value: Healthy older (baseline)