title: control_day14_rep4


title: P7-R

status: Public on Aug 14 2021

type: SRA

city: Beijing

first: Wei

last: Liu

address: 20 Dong-Da Street, Fengtai District

country: China

institute: Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity

library_source: transcriptomic

data_processing:
FASTQ files of each sample were processed by using Cell Ranger (v.3.0.2) count pipeline coupled with human reference version GRCh38 to generate feature-barcode matrices.
Genome_build: GRCh38
Supplementary_files_format_and_content: tar file of gene expression matrix generated by Cell Ranger (v.3.0.2)

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were isolated from human peripheral blood samples. Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (16 rxns PN-1000075) was used with PBMCs  for the construction of 10x ScRNA sequencing libraries according to protocol provided by 10x Genomics.
10x ScRNA libraries were prepared for sequencing using standard Illumina and 10x Genomics protocols

tag: disease state

value: Severe fever with thrombocytopenia syndrome (SFTS)

tag: illness phase

value: Convalescent

tag: cell type

value: Peripheral blood mononuclear cells

tag: age

tag: Sex

value: male


title: control_day7_rep2

type: RNA

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

country: USA

institute: Columbia University Medical Center

description: Gene expression in blood, un-irradiated control

hyb_protocol: Agilent recommended protocols were used for hybridizations

scan_protocol: Slides were  scanned with the Agilent DNA Microarray Scanner (G2505B), and the images were analyzed (Agilent Feature Extraction Software ver. 10.7) with default parameters for background correction and flagging non-uniform features.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

label_protocol: We processed 152 samples from each of the following groups: 0 (control), 158, 191, 215 and 259 uCi at days 2, 3, 5, 7  and day 14 RNA for microarray hybridization.

growth_protocol: We obtained whole blood samples from injected mice (days 2, 3, 5, 7 and 14) from 6 replicates mice exposed to an internal emitter (cesium) in amounts of 0, 158, 191, 215 and 259 microCurie.

extract_protocol: We isolated RNA from the blood using the PAXgene Blood RNA method (PreAnalytix GmBH, catalog#762165), and then depleted Globin transcripts using the Ambion GLOBINclear-Mouse kit (Life Technologies, Grand Island, NY, catalog#AM1980). We evaluated the samples for RNA integrity using the Agilent 2100 bioanalyzer and samples with RINs >8.0 were used for further analysis.

treatment_protocol: Mice were injected with of 0, 158, 191, 215 and 259 microCurie of 137 CsCl solution.

tag: tissue

value: whole blood

tag: injected uci

tag: day


title: P7-A

value: Acute


title: control_day7_rep1


title: P6-A


title: WT BMDM 3h CL075 Rep1

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description:
rRNA-depleted RNA
WT CL075 1
WT_CLO75_1

data_processing:
Base calling was carried out through an integrated primary analysis software called RTA (Real TimeAnalysis).
Reads were mapped against mm10 using kallisto 0.46.1.
Raw read counts and transcripts per million were extracted from abundance files and combined into a count matrix.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: gene_counts.txt: Matrix table with raw gene counts.
Supplementary_files_format_and_content: tpm_values.txt: TPM values for every gene and every sample.

source_name: Primary bone marrow-derived macrophages

growth_protocol: Bone marrow was flushed from the femurs and tibiae of 8-week-old female mice. pBMDM were generated from the bone marrow using L929-conditioned media as a source of M-CSF.

extract_protocol:
Supernatants were removed and total RNA was isolated using Roche High Pure RNA Isolation kit.
Library was prepared by Macrogen Inc. using Illumina TruSeq Stranded Total RNA with ribo-zero.

treatment_protocol: BMDM from each mouse were either left untreated of stimulated with CL075 for 3h.

tag: strain

tag: genotype

value: WT

value: Female

value: pBMDM

tag: treatment

value: Treated for 3h with 5 ug/ml CL075


title: WT BMDM 3h CL075 Rep2

description:
rRNA-depleted RNA
WT CL075 2
WT_CLO75_2


title: control_day5_rep6


title: control_day5_rep2


title: Sarm1-/-BMDM Unstimulated Rep3

description:
rRNA-depleted RNA
SKO U 3
SKO_U_3

value: B6.129X1-Sarm1tm1Aidi /J

value: Untreated


title: control_day5_rep3


title: P5-A


title: P5-R


title: Sarm1-/-BMDM Unstimulated Rep5

description:
rRNA-depleted RNA
SKO U 5
SKO_U_5


title: WT BMDM 3h CL075 Rep5

description:
rRNA-depleted RNA
WT CL075 5
WT_CLO75_5


title: P6-R


title: control_day5_rep4


title: control_day3_rep2


title: P4-A


title: WT BMDM 3h CL075 Rep3

description:
rRNA-depleted RNA
WT CL075 3
WT_CLO75_3


title: Sarm1-/-BMDM Unstimulated Rep1

description:
rRNA-depleted RNA
SKO U 1
SKO_U_1


title: control_day3_rep3


title: control_day5_rep5


title: control_day3_rep6


title: P4-R


title: HFD-4

city: Ann Arbor

first: Dave

last: Bridges

state: MI

address: 1415 Washington Heights

department: Nutritional Sciences

institute: University of Michigan

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on Mouse Gene 2.1 ST, and were washed and stained using the Affymetrix Gene Atlas system (software version 2.0.0.460).

scan_protocol: Peg Arrays were scanned using the Affymetrix Gene Atlas system (software version 2.0.0.460).

data_processing: RMA was used to fit log2 expression values to the data using the oligo bioconductor package in R version 3.4.3

label: biotin

source_name: Liver

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: Mouse offspring were raised from dams either fed a 60% high fat diet during lactation (D12492) or a standard chow diet (5L0D). At 24 weeks of age livers were removed at necropsy and RNA prepared for sequencing.

extract_protocol: RNA was extracted using an RNeasy Mini Kit (QIAGEN, Gaithersburg, MD, USA) according to the manufacturer’s instructions

treatment_protocol: No treatments were give aside to the in vivo lactational exposures. Upon liver removal at necropsy livers were flash frozen on liquid nitrogen and stored at -80 until RNA isolation.

tag: diet

value: HFD


title: Sarm1-/-BMDM Unstimulated Rep2

description:
rRNA-depleted RNA
SKO U 2
SKO_U_2


title: control_day3_rep4


title: P2-A

value: female


title: P2-R


title: control_day3_rep5


title: Control-4

value: Control


title: control_day5_rep1


title: P1-R


title: P3-A


title: WT BMDM Unstimulated Rep3

description:
rRNA-depleted RNA
WT U 3
WT_U_3


title: control_day3_rep1


title: WT BMDM Unstimulated Rep5

description:
rRNA-depleted RNA
WT U 5
WT_U_5


title: P1-A


title: P3-R


title: WT BMDM Unstimulated Rep2

description:
rRNA-depleted RNA
WT U 2
WT_U_2


title: C3


title: Dox induced ZGLP1 rep1

city: BOSTON

first: George

last: Church

state: MA

address: CLS, 528/7A, 3 Blackfan Cir.

department: Genetics

institute: Harvard Medical School

description: overexpressed gene is uniquely barcoded

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were mapped to hg19 genome with STAR Aligner
DEGs and p-values were determined using DESeq2
Gene Barcodes were identified with BBMap
barcode counts were then manually added to transcriptome counts matrix and used in DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: The DESeq2 output is given as a list of mapped genes with a log2fc between ZGLP1 and GFP control and its associated p-value

source_name: rRNA depleted RNA ATCC BXS0116 hiPSC

growth_protocol: Cells were grown on Corning Matrigel in MTeSR Plus media at 37 C, 5% CO2, normal oxygen

extract_protocol:
Total RNA was extracted with Qiagen RNAeasy plus mini kit
Library was constructed with KAPA RNA HyperPrep with Riboerase

treatment_protocol: Dox was added at 1ug/ml for 3 days to induce gene induction

value: hiPSCs

tag: ovrexpressed gene

tag: induction time

value: 48 hrs


title: Dox induced ZGLP1 rep2

description: overexpressed gene is uniquely barcoded


title: C4


title: OCP, DMEM

city: Chongqing

first: Ziming

last: Wang

address: #10, Changjiang Branch road

institute: Army Medical Center, Army Medical University

description: Gene expression data in primary osteoclast precursors treated by normal culture medium

hyb_protocol: After 16 hours of hybridization remove the array from the hybridization oven. Vent the array by inserting a clean pipette tip into one of the septa, and extract the hybridization cocktail with a pipettor through the remaining septum. The used hybridization cocktail can be rehybed on another array if necessary. Store the cocktail at -20°C.

scan_protocol: scan on the GeneChip Scanner 3000.

data_processing: Affymetrix Expression Console Software.

label_protocol: RNAs were isolated and labeled using biotin and detected with Ambion WT Expression Kit according to the standard Affymetrix protocol.

growth_protocol: early OCPs were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100U/ml penicillin and 100 U/ml streptomycin (Gibco, Thermo Fisher Scientific，Waltham, MA, USA) and M-CSF (50 ng/ml) (Biolegend, San Diego, CA, USA). For osteoclastogenic induction, early OCPs were stimulated by M-CSF (50 ng/ml) and RANKL (50 ng/ml) for at least 4-6 days. In some experiments, early OCPs under osteoclastogenic induction were cultured with conditioned medium (CM) from CT-26 for 4 days.

extract_protocol: Total RNA was extracted from early OCPs.

treatment_protocol: OCPs were treated by normal culture medium or CT-26 conditioned medium (CM:DMEM=1:1)

value: BALB/c mice

value: primary osteoclast precursors


title: OCP, CM

description: Gene expression data in primary osteoclast precursors treated by CT-26 CM


title: Sox2-Ctrl rep1

city: Sacramento

first: Fuzheng

last: Guo

state: CA

address: 2425 Stockton Blvd

institute: University of California Davis

data_processing:
Raw image data file from high-throughput sequencing(Illumina ) was transformed to Sequenced Reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base  Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality.
Paired-end clean reads were aligned to the reference genome (mouse genome mm10) using STAR version2.5 (Spliced Transcripts Alignment to a Reference).
HTseq v0.6.1 was used to count the read numbers mapped of each gene. Readcount and normalized FPKM was calculated to indicate the expression level of all genes.
Differentially expressed genes (DEGs) were analyzed using DESeq version 2.1.6.3 and adjusted p value padj < 0.05 was assigned as DEGs.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of FPKM values for all samples and all genes
Supplementary_files_format_and_content: tab-delimited text file of readcount values for all samples and all genes

source_name: spinal cord

extract_protocol:
Total RNA was prepared from the adult spinal cord  (P80) using QIAGEN RNeasy for lipid tissues with on-column DNase I digestion. The quality of RNA samples was determined by the Bioanalyzer 2100 system (Agilent Technologies). The RNA integrity number (RIN) of all our RNA samples used for RNA-seq was greater than 6.8.
mRNA from the spinal cord was purified from total RNA using poly-T oligo-attached magnetic beads. The resulting mRNA was fragmented randomly by addition of fragmentation buffer. The cDNA library was prepared using the NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs). The first strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). The second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.

value: spinal cord

value: post natal day 90 (P90)

value: spinal cord cells


title: Sox2-Ctrl rep3


title: WT BMDM Unstimulated Rep1

description:
rRNA-depleted RNA
WT U 1
WT_U_1


title: Sox2-Ctrl rep2


title: HFD-3


title: control_day2_rep3

value: whole blood


title: G56_miRNA

city: Nanjing

first: Wenshuang

last: Jia

address: NO.129 Jiangjun Road

institute: Nanjing University

data_processing:
The cDNA library was sequenced using Illumina Solexa following version 8 multiplexed single-read sequencing recipe.
Fastx (fastx_toolkit-0.0.13.2) was used to preprocess the original reads of the sequence.
The CLC genomics_workbench5.5 was applied to match the preprocessed sequence to the Sanger miRBase database (version 19.0).
Genome_build: Sanger miRBase database (version 19.0)
Supplementary_files_format_and_content: .csv file includes small RNA sequences and counts
Supplementary_files_format_and_content: .xls file includes effective reads and fold changes

organism: Danio rerio

source_name: G56, embryos

growth_protocol: Zebrafish were housed in the zebrafish room of Model Animal Research Center, Nanjing University, in accordance with IACUC-approved protocol. All methods were performed in accordance with the relevant guidelines and regulations.

extract_protocol:
Total RNA was isolated from 80 of the 14 hpf embryos, and its quantity was examined by electrophoresis using Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, US). The miRNA was isolated using mirVana miRNA Isolation Kit (Life technologies, USA) from the total RNA.
The 3’- and 5’-adaptors were added to the miRNA sequentially. cDNA was then reverse transcribed from the miRNA and amplified using a PCR reaction (98℃ 30 s, 11 × (98℃ 10 s, 60℃ 30 s, 72 ℃ 15 s) for 72 ℃ 10 min, 4℃). The cDNA was separated by 6% Novex TBE PAGE Gel for collecting the fragments with 147-157 nt long. The cDNA library was constructed and the quantity was examined using a commercial kit (Qubit™ dsDNA HS, Aglient 2100). The concentration of the library was no lower than 0.5 ng/µl and the size of cDNA was 140-160 bp.

treatment_protocol: Morpholinos (MOs) were purchased from Gene Tools (http://www.gene-tools.com). MOs were dissolved in nanopure water and microinjected into the embryos at 1-cell stages. The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO, or 7.5 ng control MO per embryo. The embryos microinjected with control MO or gata5/6 MOs at 1-cell stage were collected at 14 hpf for analyzing the miRNA expression changes affected by knocking down gata4/5/6.

value: gata4/5/6 knockdown

tag: developmental stage

value: embryos


title: Sox2-cKO rep2


title: control_day2_rep1


title: Dox induced GFP rep 1

description: overexpressed gene is uniquely barcoded

value: sfGFP


title: control_day2_rep6


title: control_day2_rep4


title: Control-3


title: C1

value: Peripheral blood mononuclear cells

value: male


title: control_day2_rep2


title: HFD-2


title: HFD-1


title: Sox2-cKO rep1


title: Control-1


title: C2


title: Control-2


title: control_day2_rep5


title: Sox2-cKO rep3


title: WT_miRNA

source_name: WT, embryos

value: wild type


title: met1-7, Roots, Ground control, replicate 3 [MRG3]

status: Public on Aug 13 2021

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

description: diff_expr_genes_root_direct_11_07_2017.xlsx

data_processing:
The quality of the RNA-Seq sequence data was first evaluated using FastQC prior to further downstream analysis. Low quality sequences were removed and poor quality part of the reads were trimmed using Trimmomatic. Star Aligner was used to map high quality paired-end reads to TAIR10 genome. Gene expression was obtained using RSEM. The expected read counts and Fragments Per Kilobase of transcript per Million mapped reads (FPKM), were extracted for further analysis. A generalized linear regression model was built to perform the differential gene analysis using edgeR. Prior to the differential analysis, hierarchical clustering and Principal Component Analysis (PCA) were conducted to identify the potential outlier of the samples. The thresholds for calling significantly differential expressed genes were set at FDR 0.05, the fold change of greater than 2, and the average FPKM for at least one of each comparison group is higher than 0.
Genome_build: TAIR10
Supplementary_files_format_and_content: .xls spreadsheets containing lists of genes,  FPKM values, and CPM values.

organism: Arabidopsis thaliana

source_name: solid 0.5x MS media plates; grown on the ground, 11 days old plant harvested into KFT containing RNAlater fixative

growth_protocol: The laboratory preparations and launch conditions: Dry, sterilized Arabidopsis seeds were planted aseptically on the surface of 10-cm2 solid media plates comprised of 0.5% Phytagel/0.5× MS media, and then immediately wrapped in light-tight black cloth (Duvetyne, SeattleFabrics.com) and transported to KSC (Kennedy Space Center), FL, USA. The wrapped plates were stored at temperatures between 4 and 10 °C until launch within a cold stowage bag nominally at 4 °C. The seeds remained dormant until removed from cold stowage and exposed to light at the initiation of the experiment on the ISS (International Space Station). Plant growth on the ISS and ISSES: The plates were installed into the Vegetable Production System (Veggie) hardware on the ISS and a comparable set installed into the Veggie hardware on the ISS Environmental Simulator (ISSES) chamber at Kennedy Space Center (KSC). These plates made up the NASA Advanced Plant Experiment 04 – Epigenetic Expression (APEX04-EPX) experiment that was launched on the SpaceX mission CRS-10. Plants in the Veggie hardware were exposed to constant light conditions of 100-135 µmoles/m2/s PAR and grown for eleven days (11d) before being harvested into Kennedy Space Center Fixation Tubes (KFTs) and fixed in RNAlater™ (Ambion, Grand Island, NY, USA). Samples from each plate were harvested into individual KFTs. The KFTs were then stowed at -80°C in the MELFI freezer aboard the ISS. The ground control plates were grown inside the Veggie ground unit within the ISSES (International Space Station Environment Simulator) chamber at KSC with the 48-h delay. The ISSES chamber replicated the temperature, CO2 levels and lighting that had been experienced by the spaceflight plants in the previous 48 h. Ground control plants were harevested after 11 days of growth into KFTs with RNAlater™ and stored in a at -80°C freezer.

extract_protocol:
Seedlings stored in RNA later were recovered from -80°C freezer. Each tube containing the seedlings was allowed to thaw in the fridge overnight. After completely thawing the samples to room temperature, the seedlings were observed under the microscope. The preserved seedlings from the spaceflight and ground control harvests were dissected into distinct plant parts: leaf, hypocotyl, and root. Total RNA extraction: Total RNA was extracted using Qiashredder and RNAeasy™ kits from QIAGEN (QIAGEN Sciences, MD, USA) according to the manufacturer’s instructions. Residual DNA was removed by performing an on-column digestion using an RNase Free DNase (QIAGEN GmbH, Hilden, Germany). Integrity of the RNA was evaluated using the Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA).
Library preparation:  RNAseq library were constructed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Basically, 2ul of of 1:200 diluted RNA spike-in ERCC (half amount of suggested in the ERCC user guide: Cat# 4456740) spike to 1000 ng of total RNA followed by mRNA isolating using NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs, catalog # E7490). Then followed by RNA library construction with NEBNext Ultra Directional Lib Prep (New England Biolabs, catalog #E7420) according to the manufacturer's user guide. Briefly, RNA is fragmented in NEBNext First Strand Synthesis Buffer by heating at 94 °C for desired time. This step is followed by first strand cDNA synthesis using reverse transcriptase and oligodT primers.  Synthesis of ds cDNA is performed using the 2nd strand master mix provided in the kit, followed by end-repair and adaptor ligation.  At this point, Illumina adaptors are ligated to the sample.  Finally, library is enriched (each library has a unique barcode) by 10 cycles of amplification, and purified by Agencourt AMPure beads (Beckman Coulter, catalog # A63881). 48 barcoded libraries were sized on the bioanalyzer, quantitated by QUBIT. Finally, 48 individual libraries were pooled with equimolar.
Illumina sequencing:  Sequencing experiments were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) gene expression and sequencing core, University of Florida. Uniquely barcoded libraries were normalized to 2.5 nM and pooled (equimolarly) for sequencing on the HiSeq3000 Illumina sequencer. Bisulfite-converted sequencing libraries were sequenced together with RNAseq libraries (uniquely barcoded) to maximize data output. The RNAseq libraries in the pool served to compensate for the low base diversity of bisulfite-converted genomic libraries. The final library was created by mixing RNA-seq vs bisulfite-converted libraries at a 60%:40% ratio, with a mere 1% PhiX spike-in. Library pools were processed according the Illumina protocol (HiSeq3000) for clustering on the cBOT machine. After denaturation, neutralization and mixing with the ExAmp reagent, the final pool concentration for clustering was 0.25 nM. Sequencing was done using a 2x101 cycles format (paired-end configuration). The 48-sample project was sequenced on 12 lanes for a robust reads/lane output.

treatment_protocol: On Orbit Operations and harvest:  At 11 days, seedlings were harvested by an astronaut into KFT (Kennedy Fixation Tube) containing RNAlater solutions. Once the plants were placed in the KFTs, the KFT was actuated with RNAlater to preserve the sample. At 24 hours post-harvest, KFTs were then transferred to MELFI freezer. Following Dragon Capsule splashdown in the Pacific Ocean, the KFTs transferred to the Cold Stowage charter plane at the Long Beach Airport, placed into an insulated shipper with dry ice, and flown to Johnson Space Center (JSC). The KFTs were then transferred via FedEx ground to the Kennedy Space Center. The KFTs were removed from dry ice and transferred to a -80°C freezer. The PIs retrieved the plant samples from the KFTs and transferred the samples back to the University of Florida.  The harvested material was used to compare the transcriptomes of each genotype. The patterns of gene expression and the genome-wide methylation profiles were compared between treatments (spaceflight versus ground control) and within each genotype.

tag: cultivar

value: Roots

tag: organism part

value: Whole roots from 11 day old seedling

value: 11 days old plants, 24hr light grown

tag: biosource type

value: RNAlater fixed_sample


title: met1-7, Roots, Ground control, replicate 2 [MRG2]


title: met1-7, Roots, Flight, replicate 4 [MRF4]

source_name: solid 0.5x MS media plates; grown on the ISS, 11 days old plant harvested into KFT containing RNAlater fixative


title: met1-7, Roots, Ground control, replicate 1 [MRG1]


title: met1-7, Roots, Ground control, replicate 4 [MRG4]


title: Dox induced GFP rep 2

description: overexpressed gene is uniquely barcoded

value: hiPSCs

value: 48 hrs


title: met1-7, Leaves, Flight, replicate 4 [MLF4]

description: diff_expr_genes_leaf_direct_11_07_2017.xlsx

value: Leaves

value: All leaves from 11 day old seedling


title: met1-7, Leaves, Ground control, replicate 3 [MLG3]


title: met1-7, Leaves, Flight, replicate 3 [MLF3]


title: met1-7, Roots, Flight, replicate 2 [MRF2]


title: No Akt_Rep2

type: other

city: Boston

first: Philip

middle: A

last: Cole

state: Massachusetts

address: 77 Avenue Louis Pasteur, 168 New Research Building

department: Department of Medicine

institute: Brigham and Womens Hospital

description: There were no cells, organisms, or extracts used in this study. Control with no Akt

hyb_protocol: Microarrays were blocked in TBS-T containing 5% BSA for 1 hour at room temperature in a slow shaker, removed from TBS-T and incubated for 90 min at 30 °C with 0.5 μM Akt, 5 mM ATP, 0.08 mg/mL BSA and 1 mM DTT in 120 μL reaction buffer (50 mM HEPES pH 7.5, 12 mM MgCl2, 1 mM EGTA and 0.01% NP-40). The reaction was quenched by the addition of buffer containing: 50 mM HEPES pH 7.5, 1 mM EGTA and 0.01% NP-40, 100 mM EDTA and 500 mM NaCl, and washed 3 times for 10 min in a slow shaker. Subsequent washes were performed for 10 min and 3 times for each of the following conditions: 1% SDS in reaction buffer, 1% SDS in TBS-T and TBS-T. Microarrays were incubated in TBS-T containing 5% BSA with Akt phosphorylated substrate antibody recognizing K/RXK/RXXS*/T* (Lifespan #S-C63885) in a 1:500 dilution overnight at 4C. Microarrays were washed 4 times for 10 minutes with TBS-T and incubated with secondary antibody Alexa-Fluor 555 (Thermo Fisher Scientific # A21428) at 1:2000 in TBS-T with 5% BSA for 90 min. Then, microarrays were washed 4 times for 10 min with TBS-T, water. Microarrays were centrifuged at 1000 rpm for 2 min and allowed to dry for 5 min away from the light.

scan_protocol: Microarrays were scanned in a GenePix 4400 Microarray Scanner (Molecular Devices)

data_processing: The signal intensity of each spot on the microarray was defined as the value of the median foreground intensity minus the median background intensity. Values were normalized according to CDI recommendations by using the signal intensity (median foreground intensity minus median background intesity) and calulating the average and standard deviation value for all spots. Then using the following formula to obtain the values recorded in the follwing tables:  z = [α – α(avg)] / α(std) α(avg)]; where α  is the signal intensity.

molecule: other

organism: synthetic construct

source_name: no enzyme, reaction mixture only

treatment_protocol: Microarrays were incubated with kinase assay reaction buffer (500 nM Akt) for 90 min at 30C

tag: protein tag

value: no tag


title: met1-7, Roots, Flight, replicate 3 [MRF3]


title: met1-7, Leaves, Ground control, replicate 1 [MLG1]


title: Akt_O-GlcNAcSer473_Rep1

type: protein

description: There were no cells, organisms, or extracts used in this study. Semisynthetic Akt (500 nM) was used to catalyze phosphorylation of the proteins spotted on the microarray.

molecule: protein

source_name: semisynthetic O-GlcNAcSer473 Akt protein

label_protocol: Microarrays were incubated in TBS-T containing 5% BSA with Akt phosphorylated substrate antibody recognizing K/RXK/RXXS*/T* (Lifespan #S-C63885) in a 1:500 dilution overnight at 4C. Microarrays were washed 4 times for 10 minutes with TBS-T and incubated with secondary antibody Alexa-Fluor 555 (Thermo Fisher Scientific # A21428) at 1:2000 in TBS-T with 5% BSA for 90 min

value: Flag, HA, 6HIS


title: met1-7, Roots, Flight, replicate 1 [MRF1]


title: elp2-5, Roots, Ground control, replicate 3 [ERG3]


title: elp2-5, Leaves, Ground control, replicate 4 [ELG4]


title: met1-7, Leaves, Flight, replicate 2 [MLF2]


title: met1-7, Leaves, Ground control, replicate 2 [MLG2]


title: met1-7, Leaves, Flight, replicate 1 [MLF1]


title: elp2-5, Roots, Ground control, replicate 2 [ERG2]


title: elp2-5, Roots, Ground control, replicate 1 [ERG1]


title: met1-7, Leaves, Ground control, replicate 4 [MLG4]


title: elp2-5, Roots, Ground control, replicate 4 [ERG4]


title: No Akt_Rep1

label: Alexa-Fluor 555 (Thermo Fisher Scientific # A21428)


title: Akt_O-GlcNAcSer473_Rep2


title: elp2-5, Leaves, Ground control, replicate 3 [ELG3]


title: Akt_pSer473_Rep1

source_name: semisynthetic phosphoSer473 Akt protein


title: elp2-5, Roots, Flight, replicate 4 [ERF4]


title: elp2-5, Roots, Flight, replicate 2 [ERF2]


title: Akt_pSer473_Rep2


title: elp2-5, Leaves, Ground control, replicate 1  [ELG1]


title: elp2-5, Roots, Flight, replicate 1 [ERF1]


title: Col-0, Roots, Ground control, replicate 4 [CRG4]

value: Wild Type

value: Whole roots form 11 day old seedling


title: elp2-5, Leaves, Flight, replicate 1 [ELF1]


title: elp2-5, Leaves, Flight, replicate 3 [ELF3]


title: elp2-5, Leaves, Ground control, replicate 2 [ELG2]


title: Col-0, Roots, Ground control, replicate 2 [CRG2]


title: elp2-5, Roots, Flight, replicate 3 [ERF3]


title: elp2-5, Leaves, Flight, replicate 4 [ELF4]


title: Col-0, Roots, Ground control, replicate 3 [CRG3]


title: Col-0, Roots, Ground control, replicate 1 [CRG1]


title: Col-0, Roots, Flight, replicate 1 [CRF1]


title: Col-0, Leaves, Ground control, replicate 4 [CLG4]


title: Col-0, Roots, Flight, replicate 3 [CRF3]


title: Col-0, Roots, Flight, replicate 2 [CRF2]


title: Col-0, Leaves, Ground control, replicate 3 [CLG3]


title: Col-0, Leaves, Flight, replicate 4 [CLF4]


title: Col-0, Roots, Flight, replicate 4 [CRF4]


title: Col-0, Leaves, Flight, replicate 2 [CLF2]


title: Col-0, Leaves, Flight, replicate 3 [CLF3]


title: Col-0, Leaves, Ground control, replicate 2 [CLG2]


title: Col-0, Leaves, Ground control, replicate 1  [CLG1]


title: Ground control, met1-7, Roots, replicate 4

description:
FMR.vs.GMR.full.CG.txt
FMR.vs.GMR.full.CHG.txt
FMR.vs.GMR.full.CHH.txt
FMR.vs.GMR.genes01.full.CG.txt
FMR.vs.GMR.genes01.full.CHG.txt
FMR.vs.GMR.genes01.full.CHH.txt
FMR.vs.GMR.genes02.full.CG.txt
FMR.vs.GMR.genes02.full.CHG.txt
FMR.vs.GMR.genes02.full.CHH.txt
FMR.vs.GMR.genes03.full.CG.txt
FMR.vs.GMR.genes03.full.CHG.txt
FMR.vs.GMR.genes03.full.CHH.txt
FMR.vs.GMR.genes04.full.CG.txt
FMR.vs.GMR.genes04.full.CHG.txt
FMR.vs.GMR.genes04.full.CHH.txt
FMR.vs.GMR.genes05.full.CG.txt
FMR.vs.GMR.genes05.full.CHG.txt
FMR.vs.GMR.genes05.full.CHH.txt
GER.vs.GMR.full.CG.txt
GER.vs.GMR.full.CHG.txt
GER.vs.GMR.full.CHH.txt
GER.vs.GMR.genes01.full.CG.txt
GER.vs.GMR.genes01.full.CHG.txt
GER.vs.GMR.genes01.full.CHH.txt
GER.vs.GMR.genes02.full.CG.txt
GER.vs.GMR.genes02.full.CHG.txt
GER.vs.GMR.genes02.full.CHH.txt
GER.vs.GMR.genes03.full.CG.txt
GER.vs.GMR.genes03.full.CHG.txt
GER.vs.GMR.genes03.full.CHH.txt
GER.vs.GMR.genes04.full.CG.txt
GER.vs.GMR.genes04.full.CHG.txt
GER.vs.GMR.genes04.full.CHH.txt
GER.vs.GMR.genes05.full.CG.txt
GER.vs.GMR.genes05.full.CHG.txt
GER.vs.GMR.genes05.full.CHH.txt
GMR.vs.GCR.full.CG.txt
GMR.vs.GCR.full.CHG.txt
GMR.vs.GCR.full.CHH.txt
GMR.vs.GCR.genes01.full.CG.txt
GMR.vs.GCR.genes01.full.CHG.txt
GMR.vs.GCR.genes01.full.CHH.txt
GMR.vs.GCR.genes02.full.CG.txt
GMR.vs.GCR.genes02.full.CHG.txt
GMR.vs.GCR.genes02.full.CHH.txt
GMR.vs.GCR.genes03.full.CG.txt
GMR.vs.GCR.genes03.full.CHG.txt
GMR.vs.GCR.genes03.full.CHH.txt
GMR.vs.GCR.genes04.full.CG.txt
GMR.vs.GCR.genes04.full.CHG.txt
GMR.vs.GCR.genes04.full.CHH.txt
GMR.vs.GCR.genes05.full.CG.txt
GMR.vs.GCR.genes05.full.CHG.txt
GMR.vs.GCR.genes05.full.CHH.txt
GMR-winavg.CG.txt
GMR-winavg.CHG.txt
GMR-winavg.CHH.txt

library_source: genomic

data_processing:
The short reads from the uniquely barcoded bisulfite-converted genomic libraries were trimmed using trimmomatic v 0.36 and quality control on the original and trimmed reads was performed using FastQC v 0.11.4 and MultiQC v 1.1. The bisulfite-converted reads were aligned to the TAIR10 genome using BSMAP. Methylation calling was performed with CSCALL and the differential methylation analysis was performed using the MCOMP program, which is part of the MOABS package.
A cytosine site that had at least a 10x read coverage in at least 2 out of the 4 replicates were included in the downstream analyses. Methylated cytosine sites for which the p-value of the difference between test and control methylation rates was below 0.01 were considered differentially methylated cytosines (DmCs). Differentially methylated regions were defined by comparing the average methylation levels within a 100 bp window between spaceflight and ground controls and those with statistical significance (p<0.01) were used in the analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: .csv files containing methylation levels in a 100 bp sliding window across the genome and differential methylation between the spaceflight vs. ground control comparisons.

molecule: genomic DNA

extract_protocol:
Seedlings stored in RNA later were recovered from -80°C freezer. Each tube containing the seedlings was allowed to thaw in the fridge overnight. After completely thawing the samples to room temperature, the seedlings were observed under the microscope. The preserved seedlings from the spaceflight and ground control harvests were dissected into distinct plant parts: leaf, hypocotyl, and root. DNA extraction was done using a modified phenol/chloroform protocol (LeFrois et al., 2016) and genomic-wide bisulfite sequencing was performed using a similar procedure as described by (Wang et al., 2013). 700-1700 ng of genomic DNA (>5 Kb in length) observed on the TapeStation Genomic Screen Tape (Agilent) was processed for sequencing library construction.
Library preparation:  DNA was transferred into 6x16 mm glass microtubes with AFA fiber and pre-slit snap caps (Cat# 520045, Covaris, Inc.) and sheared into average fragments size of ~400 bp, using the Covaris S220 ultrasonic disruptor. Short DNA fragments (<100 bp) were removed using AMPure magnetic beads (Cat# A63881, Beckman Coulter) at a 1:1 bead to sample ratio.  100-250 ng of clean, fragmented DNA was used for the Illumina sequencing library construction.  The NEBNext® UltraTM II DNA Illumina construction kit (Cat# E7645S, NEB) in conjunction with the Illumina-specific methylated and dual-index barcoded adaptors (Cat# E7600S NEB) were used as described in the manufacturer’s guidelines. Illumina libraries (containing methylated adaptors) were subjected to sodium bisulfite treatment using the EZ DNA Methylation Direct kit (ZYMO Research, Cat #D5020) according to the manufacturer's instructions. The resulting libraries were enriched by a 13-15 cycle amplification using an uracil-insensitive polymerase (EpiMark hot start Taq polymerase, NEB, Cat#M0490S). The amplified library products were separated on a 2% agarose gel from which library fragments in the 250-500 bp range were excised (QIAquick gel extraction kit, Cat# 28704, QIAGEN) and AMPure purified (Cat# A63881, Beckman Coulter). Gel staining was done with SYBR safe (Life Technologies) and visualized on a blue light transilluminator (Life Technologies) to avoid UV damage to the DNA. The final libraries were quantitated by the QUBIT fluorometer, sized on the Agilent TapeStation (DNA5000 Screen Tape) and by qPCR with the Kapa SYBR Fast qPCR reagents (Cat# KK4824, Kapa Biosystems) with monitoring on an ABI7900HT real-time PCR system (LifeTechnologies). The average library size was 350 bp. Care was taken to generate WGBS libraries that were approximately the same size as the RNA-Seq libraries.
Illumina sequencing:  Sequencing experiments were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) gene expression and sequencing core, University of Florida. Uniquely barcoded libraries were normalized to 2.5 nM and pooled (equimolarly) for sequencing on the HiSeq3000 Illumina sequencer. Bisulfite-converted sequencing libraries were sequenced together with RNAseq libraries (uniquely barcoded) to maximize data output. The RNAseq libraries in the pool served to compensate for the low base diversity of bisulfite-converted genomic libraries. The final library was created by mixing RNA-seq vs bisulfite-converted libraries at a 60%:40% ratio, with a mere 1% PhiX spike-in. Library pools were processed according the Illumina protocol (HiSeq3000) for clustering on the cBOT machine. After denaturation, neutralization and mixing with the ExAmp reagent, the final pool concentration for clustering was 0.25 nM. Sequencing was done using a 2x101 cycles format (paired-end configuration). The 48-sample project was sequenced on 12 lanes for a robust reads/lane output.


title: elp2-5, Leaves, Flight, replicate 2 [ELF2]


title: Ground control, met1-7, Roots, replicate 2


title: Ground control, met1-7, Roots, replicate 1


title: Ground control, met1-7, Leaves, replicate 4

description:
FML.vs.GML.full.CG.txt
FML.vs.GML.full.CHG.txt
FML.vs.GML.full.CHH.txt
FML.vs.GML.genes01.full.CG.txt
FML.vs.GML.genes01.full.CHG.txt
FML.vs.GML.genes01.full.CHH.txt
FML.vs.GML.genes02.full.CG.txt
FML.vs.GML.genes02.full.CHG.txt
FML.vs.GML.genes02.full.CHH.txt
FML.vs.GML.genes03.full.CG.txt
FML.vs.GML.genes03.full.CHG.txt
FML.vs.GML.genes03.full.CHH.txt
FML.vs.GML.genes04.full.CG.txt
FML.vs.GML.genes04.full.CHG.txt
FML.vs.GML.genes04.full.CHH.txt
FML.vs.GML.genes05.full.CG.txt
FML.vs.GML.genes05.full.CHG.txt
FML.vs.GML.genes05.full.CHH.txt
GEL.vs.GML.full.CG.txt
GEL.vs.GML.full.CHG.txt
GEL.vs.GML.full.CHH.txt
GEL.vs.GML.genes01.full.CG.txt
GEL.vs.GML.genes01.full.CHG.txt
GEL.vs.GML.genes01.full.CHH.txt
GEL.vs.GML.genes02.full.CG.txt
GEL.vs.GML.genes02.full.CHG.txt
GEL.vs.GML.genes02.full.CHH.txt
GEL.vs.GML.genes03.full.CG.txt
GEL.vs.GML.genes03.full.CHG.txt
GEL.vs.GML.genes03.full.CHH.txt
GEL.vs.GML.genes04.full.CG.txt
GEL.vs.GML.genes04.full.CHG.txt
GEL.vs.GML.genes04.full.CHH.txt
GEL.vs.GML.genes05.full.CG.txt
GEL.vs.GML.genes05.full.CHG.txt
GEL.vs.GML.genes05.full.CHH.txt
GML.vs.GCL.full.CG.txt
GML.vs.GCL.full.CHG.txt
GML.vs.GCL.full.CHH.txt
GML.vs.GCL.genes01.full.CG.txt
GML.vs.GCL.genes01.full.CHG.txt
GML.vs.GCL.genes01.full.CHH.txt
GML.vs.GCL.genes02.full.CG.txt
GML.vs.GCL.genes02.full.CHG.txt
GML.vs.GCL.genes02.full.CHH.txt
GML.vs.GCL.genes03.full.CG.txt
GML.vs.GCL.genes03.full.CHG.txt
GML.vs.GCL.genes03.full.CHH.txt
GML.vs.GCL.genes04.full.CG.txt
GML.vs.GCL.genes04.full.CHG.txt
GML.vs.GCL.genes04.full.CHH.txt
GML.vs.GCL.genes05.full.CG.txt
GML.vs.GCL.genes05.full.CHG.txt
GML.vs.GCL.genes05.full.CHH.txt
GML-winavg.CG.txt
GML-winavg.CHG.txt
GML-winavg.CHH.txt


title: Ground control, met1-7, Roots, replicate 3


title: Ground control, met1-7, Leaves, replicate 2


title: Flight, met1-7, Roots, replicate 1

description:
FER.vs.FMR.full.CG.txt
FER.vs.FMR.full.CHG.txt
FER.vs.FMR.full.CHH.txt
FER.vs.FMR.genes01.full.CG.txt
FER.vs.FMR.genes01.full.CHG.txt
FER.vs.FMR.genes01.full.CHH.txt
FER.vs.FMR.genes02.full.CG.txt
FER.vs.FMR.genes02.full.CHG.txt
FER.vs.FMR.genes02.full.CHH.txt
FER.vs.FMR.genes03.full.CG.txt
FER.vs.FMR.genes03.full.CHG.txt
FER.vs.FMR.genes03.full.CHH.txt
FER.vs.FMR.genes04.full.CG.txt
FER.vs.FMR.genes04.full.CHG.txt
FER.vs.FMR.genes04.full.CHH.txt
FER.vs.FMR.genes05.full.CG.txt
FER.vs.FMR.genes05.full.CHG.txt
FER.vs.FMR.genes05.full.CHH.txt
FMR.vs.FCR.full.CG.txt
FMR.vs.FCR.full.CHG.txt
FMR.vs.FCR.full.CHH.txt
FMR.vs.FCR.genes01.full.CG.txt
FMR.vs.FCR.genes01.full.CHG.txt
FMR.vs.FCR.genes01.full.CHH.txt
FMR.vs.FCR.genes02.full.CG.txt
FMR.vs.FCR.genes02.full.CHG.txt
FMR.vs.FCR.genes02.full.CHH.txt
FMR.vs.FCR.genes03.full.CG.txt
FMR.vs.FCR.genes03.full.CHG.txt
FMR.vs.FCR.genes03.full.CHH.txt
FMR.vs.FCR.genes04.full.CG.txt
FMR.vs.FCR.genes04.full.CHG.txt
FMR.vs.FCR.genes04.full.CHH.txt
FMR.vs.FCR.genes05.full.CG.txt
FMR.vs.FCR.genes05.full.CHG.txt
FMR.vs.FCR.genes05.full.CHH.txt
FMR.vs.GMR.full.CG.txt
FMR.vs.GMR.full.CHG.txt
FMR.vs.GMR.full.CHH.txt
FMR.vs.GMR.genes01.full.CG.txt
FMR.vs.GMR.genes01.full.CHG.txt
FMR.vs.GMR.genes01.full.CHH.txt
FMR.vs.GMR.genes02.full.CG.txt
FMR.vs.GMR.genes02.full.CHG.txt
FMR.vs.GMR.genes02.full.CHH.txt
FMR.vs.GMR.genes03.full.CG.txt
FMR.vs.GMR.genes03.full.CHG.txt
FMR.vs.GMR.genes03.full.CHH.txt
FMR.vs.GMR.genes04.full.CG.txt
FMR.vs.GMR.genes04.full.CHG.txt
FMR.vs.GMR.genes04.full.CHH.txt
FMR.vs.GMR.genes05.full.CG.txt
FMR.vs.GMR.genes05.full.CHG.txt
FMR.vs.GMR.genes05.full.CHH.txt
FMR-winavg.CG.txt
FMR-winavg.CHG.txt
FMR-winavg.CHH.txt


title: Flight, met1-7, Roots, replicate 3


title: Ground control, met1-7, Leaves, replicate 3


title: Flight, met1-7, Leaves, replicate 1

description:
FEL.vs.FML.full.CG.txt
FEL.vs.FML.full.CHG.txt
FEL.vs.FML.full.CHH.txt
FEL.vs.FML.genes01.full.CG.txt
FEL.vs.FML.genes01.full.CHG.txt
FEL.vs.FML.genes01.full.CHH.txt
FEL.vs.FML.genes02.full.CG.txt
FEL.vs.FML.genes02.full.CHG.txt
FEL.vs.FML.genes02.full.CHH.txt
FEL.vs.FML.genes03.full.CG.txt
FEL.vs.FML.genes03.full.CHG.txt
FEL.vs.FML.genes03.full.CHH.txt
FEL.vs.FML.genes04.full.CG.txt
FEL.vs.FML.genes04.full.CHG.txt
FEL.vs.FML.genes04.full.CHH.txt
FEL.vs.FML.genes05.full.CG.txt
FEL.vs.FML.genes05.full.CHG.txt
FEL.vs.FML.genes05.full.CHH.txt
FML.vs.FCL.full.CG.txt
FML.vs.FCL.full.CHG.txt
FML.vs.FCL.full.CHH.txt
FML.vs.FCL.genes01.full.CG.txt
FML.vs.FCL.genes01.full.CHG.txt
FML.vs.FCL.genes01.full.CHH.txt
FML.vs.FCL.genes02.full.CG.txt
FML.vs.FCL.genes02.full.CHG.txt
FML.vs.FCL.genes02.full.CHH.txt
FML.vs.FCL.genes03.full.CG.txt
FML.vs.FCL.genes03.full.CHG.txt
FML.vs.FCL.genes03.full.CHH.txt
FML.vs.FCL.genes04.full.CG.txt
FML.vs.FCL.genes04.full.CHG.txt
FML.vs.FCL.genes04.full.CHH.txt
FML.vs.FCL.genes05.full.CG.txt
FML.vs.FCL.genes05.full.CHG.txt
FML.vs.FCL.genes05.full.CHH.txt
FML.vs.GML.full.CG.txt
FML.vs.GML.full.CHG.txt
FML.vs.GML.full.CHH.txt
FML.vs.GML.genes01.full.CG.txt
FML.vs.GML.genes01.full.CHG.txt
FML.vs.GML.genes01.full.CHH.txt
FML.vs.GML.genes02.full.CG.txt
FML.vs.GML.genes02.full.CHG.txt
FML.vs.GML.genes02.full.CHH.txt
FML.vs.GML.genes03.full.CG.txt
FML.vs.GML.genes03.full.CHG.txt
FML.vs.GML.genes03.full.CHH.txt
FML.vs.GML.genes04.full.CG.txt
FML.vs.GML.genes04.full.CHG.txt
FML.vs.GML.genes04.full.CHH.txt
FML.vs.GML.genes05.full.CG.txt
FML.vs.GML.genes05.full.CHG.txt
FML.vs.GML.genes05.full.CHH.txt
FML-winavg.CG.txt
FML-winavg.CHG.txt
FML-winavg.CHH.txt


title: Flight, met1-7, Roots, replicate 2


title: Ground control, met1-7, Leaves, replicate 1


title: Flight, met1-7, Leaves, replicate 2


title: Flight, met1-7, Leaves, replicate 4


title: Col-0, Leaves, Flight, replicate 1  [CLF1]


title: Flight, met1-7, Leaves, replicate 3


title: Ground control, elp2-5, Roots, replicate 4

description:
FER.vs.GER.full.CG.txt
FER.vs.GER.full.CHG.txt
FER.vs.GER.full.CHH.txt
FER.vs.GER.genes01.full.CG.txt
FER.vs.GER.genes01.full.CHG.txt
FER.vs.GER.genes01.full.CHH.txt
FER.vs.GER.genes02.full.CG.txt
FER.vs.GER.genes02.full.CHG.txt
FER.vs.GER.genes02.full.CHH.txt
FER.vs.GER.genes03.full.CG.txt
FER.vs.GER.genes03.full.CHG.txt
FER.vs.GER.genes03.full.CHH.txt
FER.vs.GER.genes04.full.CG.txt
FER.vs.GER.genes04.full.CHG.txt
FER.vs.GER.genes04.full.CHH.txt
FER.vs.GER.genes05.full.CG.txt
FER.vs.GER.genes05.full.CHG.txt
FER.vs.GER.genes05.full.CHH.txt
GER.vs.GCR.full.CG.txt
GER.vs.GCR.full.CHG.txt
GER.vs.GCR.full.CHH.txt
GER.vs.GCR.genes01.full.CG.txt
GER.vs.GCR.genes01.full.CHG.txt
GER.vs.GCR.genes01.full.CHH.txt
GER.vs.GCR.genes02.full.CG.txt
GER.vs.GCR.genes02.full.CHG.txt
GER.vs.GCR.genes02.full.CHH.txt
GER.vs.GCR.genes03.full.CG.txt
GER.vs.GCR.genes03.full.CHG.txt
GER.vs.GCR.genes03.full.CHH.txt
GER.vs.GCR.genes04.full.CG.txt
GER.vs.GCR.genes04.full.CHG.txt
GER.vs.GCR.genes04.full.CHH.txt
GER.vs.GCR.genes05.full.CG.txt
GER.vs.GCR.genes05.full.CHG.txt
GER.vs.GCR.genes05.full.CHH.txt
GER.vs.GMR.full.CG.txt
GER.vs.GMR.full.CHG.txt
GER.vs.GMR.full.CHH.txt
GER.vs.GMR.genes01.full.CG.txt
GER.vs.GMR.genes01.full.CHG.txt
GER.vs.GMR.genes01.full.CHH.txt
GER.vs.GMR.genes02.full.CG.txt
GER.vs.GMR.genes02.full.CHG.txt
GER.vs.GMR.genes02.full.CHH.txt
GER.vs.GMR.genes03.full.CG.txt
GER.vs.GMR.genes03.full.CHG.txt
GER.vs.GMR.genes03.full.CHH.txt
GER.vs.GMR.genes04.full.CG.txt
GER.vs.GMR.genes04.full.CHG.txt
GER.vs.GMR.genes04.full.CHH.txt
GER.vs.GMR.genes05.full.CG.txt
GER.vs.GMR.genes05.full.CHG.txt
GER.vs.GMR.genes05.full.CHH.txt
GER-winavg.CG.txt
GER-winavg.CHG.txt
GER-winavg.CHH.txt


title: Ground control, elp2-5, Roots, replicate 2


title: Ground control, elp2-5, Roots, replicate 3


title: Ground control, elp2-5, Leaves, replicate 1

description:
FEL.vs.GEL.full.CG.txt
FEL.vs.GEL.full.CHG.txt
FEL.vs.GEL.full.CHH.txt
FEL.vs.GEL.genes01.full.CG.txt
FEL.vs.GEL.genes01.full.CHG.txt
FEL.vs.GEL.genes01.full.CHH.txt
FEL.vs.GEL.genes02.full.CG.txt
FEL.vs.GEL.genes02.full.CHG.txt
FEL.vs.GEL.genes02.full.CHH.txt
FEL.vs.GEL.genes03.full.CG.txt
FEL.vs.GEL.genes03.full.CHG.txt
FEL.vs.GEL.genes03.full.CHH.txt
FEL.vs.GEL.genes04.full.CG.txt
FEL.vs.GEL.genes04.full.CHG.txt
FEL.vs.GEL.genes04.full.CHH.txt
FEL.vs.GEL.genes05.full.CG.txt
FEL.vs.GEL.genes05.full.CHG.txt
FEL.vs.GEL.genes05.full.CHH.txt
GEL.vs.GCL.full.CG.txt
GEL.vs.GCL.full.CHG.txt
GEL.vs.GCL.full.CHH.txt
GEL.vs.GCL.genes01.full.CG.txt
GEL.vs.GCL.genes01.full.CHG.txt
GEL.vs.GCL.genes01.full.CHH.txt
GEL.vs.GCL.genes02.full.CG.txt
GEL.vs.GCL.genes02.full.CHG.txt
GEL.vs.GCL.genes02.full.CHH.txt
GEL.vs.GCL.genes03.full.CG.txt
GEL.vs.GCL.genes03.full.CHG.txt
GEL.vs.GCL.genes03.full.CHH.txt
GEL.vs.GCL.genes04.full.CG.txt
GEL.vs.GCL.genes04.full.CHG.txt
GEL.vs.GCL.genes04.full.CHH.txt
GEL.vs.GCL.genes05.full.CG.txt
GEL.vs.GCL.genes05.full.CHG.txt
GEL.vs.GCL.genes05.full.CHH.txt
GEL.vs.GML.full.CG.txt
GEL.vs.GML.full.CHG.txt
GEL.vs.GML.full.CHH.txt
GEL.vs.GML.genes01.full.CG.txt
GEL.vs.GML.genes01.full.CHG.txt
GEL.vs.GML.genes01.full.CHH.txt
GEL.vs.GML.genes02.full.CG.txt
GEL.vs.GML.genes02.full.CHG.txt
GEL.vs.GML.genes02.full.CHH.txt
GEL.vs.GML.genes03.full.CG.txt
GEL.vs.GML.genes03.full.CHG.txt
GEL.vs.GML.genes03.full.CHH.txt
GEL.vs.GML.genes04.full.CG.txt
GEL.vs.GML.genes04.full.CHG.txt
GEL.vs.GML.genes04.full.CHH.txt
GEL.vs.GML.genes05.full.CG.txt
GEL.vs.GML.genes05.full.CHG.txt
GEL.vs.GML.genes05.full.CHH.txt
GEL-winavg.CG.txt
GEL-winavg.CHG.txt
GEL-winavg.CHH.txt


title: Ground control, elp2-5, Leaves, replicate 4


title: Ground control, elp2-5, Roots, replicate 1


title: Flight, elp2-5, Roots, replicate 4

description:
FER.vs.FCR.full.CG.txt
FER.vs.FCR.full.CHG.txt
FER.vs.FCR.full.CHH.txt
FER.vs.FCR.genes01.full.CG.txt
FER.vs.FCR.genes01.full.CHG.txt
FER.vs.FCR.genes01.full.CHH.txt
FER.vs.FCR.genes02.full.CG.txt
FER.vs.FCR.genes02.full.CHG.txt
FER.vs.FCR.genes02.full.CHH.txt
FER.vs.FCR.genes03.full.CG.txt
FER.vs.FCR.genes03.full.CHG.txt
FER.vs.FCR.genes03.full.CHH.txt
FER.vs.FCR.genes04.full.CG.txt
FER.vs.FCR.genes04.full.CHG.txt
FER.vs.FCR.genes04.full.CHH.txt
FER.vs.FCR.genes05.full.CG.txt
FER.vs.FCR.genes05.full.CHG.txt
FER.vs.FCR.genes05.full.CHH.txt
FER.vs.FMR.full.CG.txt
FER.vs.FMR.full.CHG.txt
FER.vs.FMR.full.CHH.txt
FER.vs.FMR.genes01.full.CG.txt
FER.vs.FMR.genes01.full.CHG.txt
FER.vs.FMR.genes01.full.CHH.txt
FER.vs.FMR.genes02.full.CG.txt
FER.vs.FMR.genes02.full.CHG.txt
FER.vs.FMR.genes02.full.CHH.txt
FER.vs.FMR.genes03.full.CG.txt
FER.vs.FMR.genes03.full.CHG.txt
FER.vs.FMR.genes03.full.CHH.txt
FER.vs.FMR.genes04.full.CG.txt
FER.vs.FMR.genes04.full.CHG.txt
FER.vs.FMR.genes04.full.CHH.txt
FER.vs.FMR.genes05.full.CG.txt
FER.vs.FMR.genes05.full.CHG.txt
FER.vs.FMR.genes05.full.CHH.txt
FER.vs.GER.full.CG.txt
FER.vs.GER.full.CHG.txt
FER.vs.GER.full.CHH.txt
FER.vs.GER.genes01.full.CG.txt
FER.vs.GER.genes01.full.CHG.txt
FER.vs.GER.genes01.full.CHH.txt
FER.vs.GER.genes02.full.CG.txt
FER.vs.GER.genes02.full.CHG.txt
FER.vs.GER.genes02.full.CHH.txt
FER.vs.GER.genes03.full.CG.txt
FER.vs.GER.genes03.full.CHG.txt
FER.vs.GER.genes03.full.CHH.txt
FER.vs.GER.genes04.full.CG.txt
FER.vs.GER.genes04.full.CHG.txt
FER.vs.GER.genes04.full.CHH.txt
FER.vs.GER.genes05.full.CG.txt
FER.vs.GER.genes05.full.CHG.txt
FER.vs.GER.genes05.full.CHH.txt
FER-winavg.CG.txt
FER-winavg.CHG.txt
FER-winavg.CHH.txt


title: Flight, elp2-5, Roots, replicate 2


title: Flight, elp2-5, Leaves, replicate 4

description:
FEL.vs.FCL.full.CG.txt
FEL.vs.FCL.full.CHG.txt
FEL.vs.FCL.full.CHH.txt
FEL.vs.FCL.genes01.full.CG.txt
FEL.vs.FCL.genes01.full.CHG.txt
FEL.vs.FCL.genes01.full.CHH.txt
FEL.vs.FCL.genes02.full.CG.txt
FEL.vs.FCL.genes02.full.CHG.txt
FEL.vs.FCL.genes02.full.CHH.txt
FEL.vs.FCL.genes03.full.CG.txt
FEL.vs.FCL.genes03.full.CHG.txt
FEL.vs.FCL.genes03.full.CHH.txt
FEL.vs.FCL.genes04.full.CG.txt
FEL.vs.FCL.genes04.full.CHG.txt
FEL.vs.FCL.genes04.full.CHH.txt
FEL.vs.FCL.genes05.full.CG.txt
FEL.vs.FCL.genes05.full.CHG.txt
FEL.vs.FCL.genes05.full.CHH.txt
FEL.vs.FML.full.CG.txt
FEL.vs.FML.full.CHG.txt
FEL.vs.FML.full.CHH.txt
FEL.vs.FML.genes01.full.CG.txt
FEL.vs.FML.genes01.full.CHG.txt
FEL.vs.FML.genes01.full.CHH.txt
FEL.vs.FML.genes02.full.CG.txt
FEL.vs.FML.genes02.full.CHG.txt
FEL.vs.FML.genes02.full.CHH.txt
FEL.vs.FML.genes03.full.CG.txt
FEL.vs.FML.genes03.full.CHG.txt
FEL.vs.FML.genes03.full.CHH.txt
FEL.vs.FML.genes04.full.CG.txt
FEL.vs.FML.genes04.full.CHG.txt
FEL.vs.FML.genes04.full.CHH.txt
FEL.vs.FML.genes05.full.CG.txt
FEL.vs.FML.genes05.full.CHG.txt
FEL.vs.FML.genes05.full.CHH.txt
FEL.vs.GEL.full.CG.txt
FEL.vs.GEL.full.CHG.txt
FEL.vs.GEL.full.CHH.txt
FEL.vs.GEL.genes01.full.CG.txt
FEL.vs.GEL.genes01.full.CHG.txt
FEL.vs.GEL.genes01.full.CHH.txt
FEL.vs.GEL.genes02.full.CG.txt
FEL.vs.GEL.genes02.full.CHG.txt
FEL.vs.GEL.genes02.full.CHH.txt
FEL.vs.GEL.genes03.full.CG.txt
FEL.vs.GEL.genes03.full.CHG.txt
FEL.vs.GEL.genes03.full.CHH.txt
FEL.vs.GEL.genes04.full.CG.txt
FEL.vs.GEL.genes04.full.CHG.txt
FEL.vs.GEL.genes04.full.CHH.txt
FEL.vs.GEL.genes05.full.CG.txt
FEL.vs.GEL.genes05.full.CHG.txt
FEL.vs.GEL.genes05.full.CHH.txt
FEL-winavg.CG.txt
FEL-winavg.CHG.txt
FEL-winavg.CHH.txt


title: Flight, elp2-5, Roots, replicate 3


title: Flight, met1-7, Roots, replicate 4


title: Flight, elp2-5, Leaves, replicate 2


title: Ground control, elp2-5, Leaves, replicate 3


title: Ground control, elp2-5, Leaves, replicate 2


title: Flight, elp2-5, Leaves, replicate 3


title: Flight, elp2-5, Roots, replicate 1


title: Ground control, Col-0, Roots, replicate 4

description:
FCR.vs.GCR.full.CG.txt
FCR.vs.GCR.full.CHG.txt
FCR.vs.GCR.full.CHH.txt
FCR.vs.GCR.genes01.full.CG.txt
FCR.vs.GCR.genes01.full.CHG.txt
FCR.vs.GCR.genes01.full.CHH.txt
FCR.vs.GCR.genes02.full.CG.txt
FCR.vs.GCR.genes02.full.CHG.txt
FCR.vs.GCR.genes02.full.CHH.txt
FCR.vs.GCR.genes03.full.CG.txt
FCR.vs.GCR.genes03.full.CHG.txt
FCR.vs.GCR.genes03.full.CHH.txt
FCR.vs.GCR.genes04.full.CG.txt
FCR.vs.GCR.genes04.full.CHG.txt
FCR.vs.GCR.genes04.full.CHH.txt
FCR.vs.GCR.genes05.full.CG.txt
FCR.vs.GCR.genes05.full.CHG.txt
FCR.vs.GCR.genes05.full.CHH.txt
GCR-winavg.CG.txt
GCR-winavg.CHG.txt
GCR-winavg.CHH.txt
GER.vs.GCR.full.CG.txt
GER.vs.GCR.full.CHG.txt
GER.vs.GCR.full.CHH.txt
GER.vs.GCR.genes01.full.CG.txt
GER.vs.GCR.genes01.full.CHG.txt
GER.vs.GCR.genes01.full.CHH.txt
GER.vs.GCR.genes02.full.CG.txt
GER.vs.GCR.genes02.full.CHG.txt
GER.vs.GCR.genes02.full.CHH.txt
GER.vs.GCR.genes03.full.CG.txt
GER.vs.GCR.genes03.full.CHG.txt
GER.vs.GCR.genes03.full.CHH.txt
GER.vs.GCR.genes04.full.CG.txt
GER.vs.GCR.genes04.full.CHG.txt
GER.vs.GCR.genes04.full.CHH.txt
GER.vs.GCR.genes05.full.CG.txt
GER.vs.GCR.genes05.full.CHG.txt
GER.vs.GCR.genes05.full.CHH.txt
GMR.vs.GCR.full.CG.txt
GMR.vs.GCR.full.CHG.txt
GMR.vs.GCR.full.CHH.txt
GMR.vs.GCR.genes01.full.CG.txt
GMR.vs.GCR.genes01.full.CHG.txt
GMR.vs.GCR.genes01.full.CHH.txt
GMR.vs.GCR.genes02.full.CG.txt
GMR.vs.GCR.genes02.full.CHG.txt
GMR.vs.GCR.genes02.full.CHH.txt
GMR.vs.GCR.genes03.full.CG.txt
GMR.vs.GCR.genes03.full.CHG.txt
GMR.vs.GCR.genes03.full.CHH.txt
GMR.vs.GCR.genes04.full.CG.txt
GMR.vs.GCR.genes04.full.CHG.txt
GMR.vs.GCR.genes04.full.CHH.txt
GMR.vs.GCR.genes05.full.CG.txt
GMR.vs.GCR.genes05.full.CHG.txt
GMR.vs.GCR.genes05.full.CHH.txt


title: Ground control, Col-0, Roots, replicate 3


title: Ground control, Col-0, Leaves, replicate 4

description:
FCL.vs.GCL.full.CG.txt
FCL.vs.GCL.full.CHG.txt
FCL.vs.GCL.full.CHH.txt
FCL.vs.GCL.genes01.full.CG.txt
FCL.vs.GCL.genes01.full.CHG.txt
FCL.vs.GCL.genes01.full.CHH.txt
FCL.vs.GCL.genes02.full.CG.txt
FCL.vs.GCL.genes02.full.CHG.txt
FCL.vs.GCL.genes02.full.CHH.txt
FCL.vs.GCL.genes03.full.CG.txt
FCL.vs.GCL.genes03.full.CHG.txt
FCL.vs.GCL.genes03.full.CHH.txt
FCL.vs.GCL.genes04.full.CG.txt
FCL.vs.GCL.genes04.full.CHG.txt
FCL.vs.GCL.genes04.full.CHH.txt
FCL.vs.GCL.genes05.full.CG.txt
FCL.vs.GCL.genes05.full.CHG.txt
FCL.vs.GCL.genes05.full.CHH.txt
GCL-winavg.CG.txt
GCL-winavg.CHG.txt
GCL-winavg.CHH.txt
GEL.vs.GCL.full.CG.txt
GEL.vs.GCL.full.CHG.txt
GEL.vs.GCL.full.CHH.txt
GEL.vs.GCL.genes01.full.CG.txt
GEL.vs.GCL.genes01.full.CHG.txt
GEL.vs.GCL.genes01.full.CHH.txt
GEL.vs.GCL.genes02.full.CG.txt
GEL.vs.GCL.genes02.full.CHG.txt
GEL.vs.GCL.genes02.full.CHH.txt
GEL.vs.GCL.genes03.full.CG.txt
GEL.vs.GCL.genes03.full.CHG.txt
GEL.vs.GCL.genes03.full.CHH.txt
GEL.vs.GCL.genes04.full.CG.txt
GEL.vs.GCL.genes04.full.CHG.txt
GEL.vs.GCL.genes04.full.CHH.txt
GEL.vs.GCL.genes05.full.CG.txt
GEL.vs.GCL.genes05.full.CHG.txt
GEL.vs.GCL.genes05.full.CHH.txt
GML.vs.GCL.full.CG.txt
GML.vs.GCL.full.CHG.txt
GML.vs.GCL.full.CHH.txt
GML.vs.GCL.genes01.full.CG.txt
GML.vs.GCL.genes01.full.CHG.txt
GML.vs.GCL.genes01.full.CHH.txt
GML.vs.GCL.genes02.full.CG.txt
GML.vs.GCL.genes02.full.CHG.txt
GML.vs.GCL.genes02.full.CHH.txt
GML.vs.GCL.genes03.full.CG.txt
GML.vs.GCL.genes03.full.CHG.txt
GML.vs.GCL.genes03.full.CHH.txt
GML.vs.GCL.genes04.full.CG.txt
GML.vs.GCL.genes04.full.CHG.txt
GML.vs.GCL.genes04.full.CHH.txt
GML.vs.GCL.genes05.full.CG.txt
GML.vs.GCL.genes05.full.CHG.txt
GML.vs.GCL.genes05.full.CHH.txt

value: All leaves form 11 day old seedling


title: Ground control, Col-0, Roots, replicate 2


title: Ground control, Col-0, Leaves, replicate 2


title: Flight, Col-0, Roots, replicate 3

description:
FCR.vs.GCR.full.CG.txt
FCR.vs.GCR.full.CHG.txt
FCR.vs.GCR.full.CHH.txt
FCR.vs.GCR.genes01.full.CG.txt
FCR.vs.GCR.genes01.full.CHG.txt
FCR.vs.GCR.genes01.full.CHH.txt
FCR.vs.GCR.genes02.full.CG.txt
FCR.vs.GCR.genes02.full.CHG.txt
FCR.vs.GCR.genes02.full.CHH.txt
FCR.vs.GCR.genes03.full.CG.txt
FCR.vs.GCR.genes03.full.CHG.txt
FCR.vs.GCR.genes03.full.CHH.txt
FCR.vs.GCR.genes04.full.CG.txt
FCR.vs.GCR.genes04.full.CHG.txt
FCR.vs.GCR.genes04.full.CHH.txt
FCR.vs.GCR.genes05.full.CG.txt
FCR.vs.GCR.genes05.full.CHG.txt
FCR.vs.GCR.genes05.full.CHH.txt
FCR-winavg.CG.txt
FCR-winavg.CHG.txt
FCR-winavg.CHH.txt
FER.vs.FCR.full.CG.txt
FER.vs.FCR.full.CHG.txt
FER.vs.FCR.full.CHH.txt
FER.vs.FCR.genes01.full.CG.txt
FER.vs.FCR.genes01.full.CHG.txt
FER.vs.FCR.genes01.full.CHH.txt
FER.vs.FCR.genes02.full.CG.txt
FER.vs.FCR.genes02.full.CHG.txt
FER.vs.FCR.genes02.full.CHH.txt
FER.vs.FCR.genes03.full.CG.txt
FER.vs.FCR.genes03.full.CHG.txt
FER.vs.FCR.genes03.full.CHH.txt
FER.vs.FCR.genes04.full.CG.txt
FER.vs.FCR.genes04.full.CHG.txt
FER.vs.FCR.genes04.full.CHH.txt
FER.vs.FCR.genes05.full.CG.txt
FER.vs.FCR.genes05.full.CHG.txt
FER.vs.FCR.genes05.full.CHH.txt
FMR.vs.FCR.full.CG.txt
FMR.vs.FCR.full.CHG.txt
FMR.vs.FCR.full.CHH.txt
FMR.vs.FCR.genes01.full.CG.txt
FMR.vs.FCR.genes01.full.CHG.txt
FMR.vs.FCR.genes01.full.CHH.txt
FMR.vs.FCR.genes02.full.CG.txt
FMR.vs.FCR.genes02.full.CHG.txt
FMR.vs.FCR.genes02.full.CHH.txt
FMR.vs.FCR.genes03.full.CG.txt
FMR.vs.FCR.genes03.full.CHG.txt
FMR.vs.FCR.genes03.full.CHH.txt
FMR.vs.FCR.genes04.full.CG.txt
FMR.vs.FCR.genes04.full.CHG.txt
FMR.vs.FCR.genes04.full.CHH.txt
FMR.vs.FCR.genes05.full.CG.txt
FMR.vs.FCR.genes05.full.CHG.txt
FMR.vs.FCR.genes05.full.CHH.txt


title: Ground control, Col-0, Leaves, replicate 1


title: Ground control, Col-0, Leaves, replicate 3


title: Flight, Col-0, Roots, replicate 4


title: Flight, Col-0, Roots, replicate 2


title: Flight, Col-0, Leaves, replicate 3

description:
FCL.vs.GCL.full.CG.txt
FCL.vs.GCL.full.CHG.txt
FCL.vs.GCL.full.CHH.txt
FCL.vs.GCL.genes01.full.CG.txt
FCL.vs.GCL.genes01.full.CHG.txt
FCL.vs.GCL.genes01.full.CHH.txt
FCL.vs.GCL.genes02.full.CG.txt
FCL.vs.GCL.genes02.full.CHG.txt
FCL.vs.GCL.genes02.full.CHH.txt
FCL.vs.GCL.genes03.full.CG.txt
FCL.vs.GCL.genes03.full.CHG.txt
FCL.vs.GCL.genes03.full.CHH.txt
FCL.vs.GCL.genes04.full.CG.txt
FCL.vs.GCL.genes04.full.CHG.txt
FCL.vs.GCL.genes04.full.CHH.txt
FCL.vs.GCL.genes05.full.CG.txt
FCL.vs.GCL.genes05.full.CHG.txt
FCL.vs.GCL.genes05.full.CHH.txt
FCL-winavg.CG.txt
FCL-winavg.CHG.txt
FCL-winavg.CHH.txt
FEL.vs.FCL.full.CG.txt
FEL.vs.FCL.full.CHG.txt
FEL.vs.FCL.full.CHH.txt
FEL.vs.FCL.genes01.full.CG.txt
FEL.vs.FCL.genes01.full.CHG.txt
FEL.vs.FCL.genes01.full.CHH.txt
FEL.vs.FCL.genes02.full.CG.txt
FEL.vs.FCL.genes02.full.CHG.txt
FEL.vs.FCL.genes02.full.CHH.txt
FEL.vs.FCL.genes03.full.CG.txt
FEL.vs.FCL.genes03.full.CHG.txt
FEL.vs.FCL.genes03.full.CHH.txt
FEL.vs.FCL.genes04.full.CG.txt
FEL.vs.FCL.genes04.full.CHG.txt
FEL.vs.FCL.genes04.full.CHH.txt
FEL.vs.FCL.genes05.full.CG.txt
FEL.vs.FCL.genes05.full.CHG.txt
FEL.vs.FCL.genes05.full.CHH.txt
FML.vs.FCL.full.CG.txt
FML.vs.FCL.full.CHG.txt
FML.vs.FCL.full.CHH.txt
FML.vs.FCL.genes01.full.CG.txt
FML.vs.FCL.genes01.full.CHG.txt
FML.vs.FCL.genes01.full.CHH.txt
FML.vs.FCL.genes02.full.CG.txt
FML.vs.FCL.genes02.full.CHG.txt
FML.vs.FCL.genes02.full.CHH.txt
FML.vs.FCL.genes03.full.CG.txt
FML.vs.FCL.genes03.full.CHG.txt
FML.vs.FCL.genes03.full.CHH.txt
FML.vs.FCL.genes04.full.CG.txt
FML.vs.FCL.genes04.full.CHG.txt
FML.vs.FCL.genes04.full.CHH.txt
FML.vs.FCL.genes05.full.CG.txt
FML.vs.FCL.genes05.full.CHG.txt
FML.vs.FCL.genes05.full.CHH.txt


title: Flight, Col-0, Roots, replicate 1


title: Flight, Col-0, Leaves, replicate 4


title: Flight, Col-0, Leaves, replicate 2


title: SC226

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

institute: University of Pittsburgh

description: SSC

data_processing:
10X Genomics' Cell Ranger 3.0.2 software's mkfastq command was used for basecalling.  It is a wrapper for Illumina's bcl2fastq
Sequenced reads were then mapped to GRCh38-3.0.0 whole genome using 10X Genomics' Cell Ranger 3.0.2 software's cellranger count function
Cell Ranger output files included: raw_feature_bc_matrix.h5.  The raw_feature_bc_matrix.h5 files were utilized for further downstream analysis in R with the package Seurat V2.3.4 only cells expressing at least 200 genes were kept for downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: .h5 files contain the UMI (transcript) counts assigned to each cell barcode for each gene; each .h5 file corresponds to one sample/biopsy

molecule: polyA RNA

source_name: dorsal, mid-forearm skin biopsy

extract_protocol:
Biopsies were finely diced using a scalpel and placed in a Miltenyi C tube.  The enzymes from the Miltenyi whole skin dissociation kit, human, were used to digest cells over a period of 2 hours at 37 degrees.  Biopsies were then further mechanically separated using the h_skin_01 program on the Miltenyi OctoDissociator.  The resulting single cell suspension was filtered through a 70 micron filter, a 30 micron filter, and finally resuspended in PBS containing 0.04% BSA.  Cells were loaded into the the 10X Genomics Chromium instrument according to the manufacturer's directions.
Libraries were constructed according to 10X Genomics' Single Cell 3’ Reagent Kits v2 User Guides

tag: chemistry

value: 10X Genomics 3 Prime V2 chemistry

value: skin

value: scleroderma


title: Flight, Col-0, Leaves, replicate 1

tag: age


title: SC240

description: SSC


title: Flight, elp2-5, Leaves, replicate 1


title: SC224

description: SSC


title: SC202

description: SSC


title: SC212

description: SSC


title: SC184

description: SSC


title: SC169

description: SSC


title: SC164

description: SSC


title: SC160

description: SSC


title: Ground control, Col-0, Roots, replicate 1


title: SC237

description: SSC


title: SC159

description: SSC


title: SC163

description: SSC


title: WT Rep 3

city: Glasgow

first: Dustin

last: Flanagan

state: Glasgow

address: Garscube Estate, Switchback Road, , Bearsden

country: United Kingdom

institute: Cancer Research UK Beatson Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Genome_build: GRCm38.98
Supplementary_files_format_and_content: Raw counts matrix

source_name: Small Intestinal Tissue

extract_protocol:
RNA extraction perfomed with Qiagen RNeasy kit using Qiagen protocols
Libraries for cluster generation and DNA sequencing were prepared following a previously described method (Fisher et al. 2011) using TruSeq RNA sample prep kit v2 (Illumina)
The libraries were run on Illumina Next Seq using the High Output 75 cycles kit (2x36 cycles, paired end reads, single index)

treatment_protocol: Where stated, mice were treated with…

value: VilCreER


title: B (0.3×10^9/mL PA-MSHA treatment)

city: Hefei

first: Wulin

last: Shan

state: Anhui

address: Huanhudong Road 107

institute: The First Affiliated Hospital of University of Science and Technology of China

data_processing:
The original image data was transformed into Sequenced Reads for Base Calling analysis using software BCL2FASTQ2 (V2.19.0).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GCF_000001405.38_GRCh38.p12 genome.
FPKM were calculated. The analysis method of miRNA expression abundance is to count according to the mapping position of read on the genome. It is necessary to verify whether the position of read is consistent with the mature sequence of known miRNA, and if the position is inconsistent, no statistics will be taken.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Abundance of miRNA expression of each sample.

source_name: colorectal cancer

extract_protocol:
RNA was harvested from cells using Trizol reagent. Illumina TruSeq RNA Sample was used with 1 ug of total RNA for the construction of sequencing libraries.
miRNAs libraries start from the RNA that has passed the quality inspection, the 3' -end adaptor is linked, the reverse primer is hybridized, the 5' -end adaptor is linked, the reverse transcription is made into DNA, and then PCR amplification is performed.

treatment_protocol: Cells were treated with Pseudomonas aeruginosa-mannose sensitive hemagglutinin (PA-MSHA).

tag: cell line

tag: cell type

value: cetuximab-resistant colorectal cancer cells

value: 0.3x10^9/mL PA-MSHA


title: A (0×10^9/mL PA-MSHA treatment)

value: 0x10^9/mL PA-MSHA


title: C (0.4×10^9/mL PA-MSHA treatment)

value: 0.4x10^9/mL PA-MSHA


title: SC247

description: SSC

tag: tissue


title: Alk5 Rep 7

value: VilCreER LSL-Alk5 hom


title: Alk5 Rep 5


title: Alk5 Rep 6


title: Alk5 Rep 4

value: VilCreER LSL-Alk5/+

value: 100ul oral gavage twice daily 0.5% w/v HPMC (hydroxyl propyl methyl cellulose) 0.1% Tween80 in deionised water.


title: Alk5 Rep 1

value: VilCreER LSL-Alk5/LSL-ALk5


title: WT Rep 1


title: Alk5 Rep 3


title: Apc Kras Alk5 Smad4 Rep 2

value: VilCreER Apc f/f [new] KRasG12D/+ Smad4 f/f LSL-Alk5ca hom


title: WT Rep 2


title: Apc Kras Alk5KO Rep 2

value: VilCreER Apc fl/fl KRasG12D/+ Alk5 fl/fl


title: Apc Kras Alk5 EGFRi Rep 1

value: VilCreER Apc f/f KrasG12D/+ LSL-Alk5/+

value: AZD8931 25mg/kg oral gavage twice daily


title: Apc Kras Alk5 EGFRi Rep 3

value: VilCreER Apc f/f KrasG12D/+ LSL-Alk5/LSL-Alk5


title: Apc Kras Alk5 6244 Rep 1

value: AZD6244 50mg/kg oral gavage twice daily.


title: Alk5 Rep 2


title: Apc Kras Alk5 Rep 7

value: VilCreER Apc fl/fl KRasG12D/+ LSL-Alk5 hom


title: Apc Kras Alk5KO Rep 3


title: Apc Kras Alk5 Smad4 Rep 1


title: Apc Kras Alk5 Smad4 Rep 3

value: VilCreER Apc f/f [new] KRasG12D/+ Smad4 f/f LSL-Alk5ca het


title: Apc Kras Alk5KO Rep 1


title: Apc Kras Alk5 Rep 5


title: Apc Kras Alk5 6244 Rep 2


title: Apc Kras Alk5 EGFRi Rep 2


title: Apc Kras Alk5 Rep 4

value: VilCReER Apc fl/fl KrasG12D/+ LSL-Alk5/LSL-Alk5


title: Apc Kras Alk5 Rep 2


title: Apc Kras Alk5 6244 Rep 3


title: Apc Alk5 Rep 4

value: VilCreER Apc fl/fl LSL-Alk5/+


title: Apc Alk5KO Rep 2

value: VilCreER Apc fl/fl Alk5 fl/fl


title: Apc Kras Rep 3

value: VilCreER Apc fl/fl KrasG12D/+


title: Apc Kras Alk5 Rep 1

value: VilCReER Apc fl/fl KrasG12D/+ LSL-Alk5/+


title: Apc Alk5KO Rep 1


title: Apc Kras Alk5 Rep 6


title: Apc Alk5KO Rep 3


title: Apc Kras Rep 2


title: Apc Rep 2

value: VilCreER Apc fl/fl


title: Apc Alk5 Rep 2


title: Apc Kras Rep 1


title: Apc Alk5 Rep 1

value: VilCreER Apc fl/fl LSL-Alk5/LSL-Alk5


title: Apc Rep 4


title: Apc Rep 5


title: Apc Alk5 Rep 3


title: Apc Kras Alk5 Rep 3


title: ctrl_5

city: Nashville

first: Christopher

middle: Scott

last: Wilson

state: Tennessee

address: 2213 Garland Ave, MRBIV (Langford) 7415

institute: Vanderbilt University Medical Center

data_processing:
Base calling was done by CASAVA 1.8
Data filtering steps included
1. Removal of reads containing adaptors; 2. Removal of reads containing >10% bases that could be determined; 3. Only using reads with Qscore of over 50% bases that is <or=5; 4. Reads were aligned to mm10 by utilzing STAR software
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Purified CD4+ T cells

extract_protocol:
Qiagen Rneasy kit following manufaturer's protocols.
Briefly, mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beads (For prokaryotes, mRNA was purified through the removal of rRNA by using kit). The mRNA is first fragmented randomly by addition of fragmentation buffer. According to demand of customer, we have NEB library and strand specific library to choose
First strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization(1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads

value: Purified CD4+ T cells


title: SLE_1


title: ctrl_3


title: Apc Rep 1


title: Apc Rep 3


title: SLE_2


title: a_CD45_1

value: 100ug of anti-CD45RB (MB23G2)


title: ctrl_4


title: a_CD45_3


title: SLE_C_1


title: Apc Alk5 Rep 5


title: SLE_C_3


title: SLE_3


title: a_CD45_5


title: P90_SCI_rep1_7days

city: Norwich

first: Darrell

last: Green

address: Earlham Road

department: Norwich Medical School

institute: University of East Anglia

data_processing:
The original fastq files were converted to fasta format and reads without Ns were kept for further analysis.
The 3' adapter and HD signatures [Sorefan et al. 2012] were trimmed and the files were converted from redundant to non-redundant format.
The reads were mapped to the reference genome, allowing 00 mis-matches and 0 gaps using PatMaN [Pruffer et al. 2008].
The reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRBase, release 21.
The abundances of the reads were normalized using the RPM method [Mortazavi et al. 2008].
The differential expression was called on offset fold change on confidence intervals built on replicates, offset = 20.
Genome_build: GRCm38
Supplementary_files_format_and_content: *csv: Comma-separated text files include raw abundances.

source_name: sensorimotor cortex, P90, SCI, 7 days

growth_protocol: All procedures involving live animals were performed according to European Community Council Directive of 24 November 1986 (86/609/EEC) and University of Turin's institutional guidelines on animal welfare (DL 116/92). C57BL/6J mice were bred in Neuroscience Institute Cavalieri Ottolenghi animals facility. All animals had free access to food and water and were used for SCI surgery.

extract_protocol:
Seven days after injury, WT and SCI mice were sacrificed by cervical dislocation, the brains removed and the sensorimotor cortex rapidly isolated: under a dissecting microscope we isolated the sensorimotor cortex. The samples were collected individually and stored at -80°C until the total RNA extraction.
RNA was extracted using the mirVana kit.
HD sRNA libraries created with HiSeq2500 adapters (Xu et al. 2015).
The sequencing was done at the Earlham Institute (UK), single end, 50nt reads.

treatment_protocol: Adult (P90) C57BL/6J male mice were used to produce the SCI model or control group (WT). Animals were deeply anaesthetized with 3% isoflurane vaporized in O2/N2O 50:50 in order to perform the spinal cord transection. The cervical spine was exposed, the spinal muscles displaced laterally and the lesion performed as follows: using a 27-gauge½ needle, the entire spinal cord was dorsally exposed and transacted at C5/6 level. In the control group, the spinal cord was simply exposed without any damage.

tag: strain/background

tag: gender

value: male

value: sensorimotor cortex

value: spinal cord injury (SCI)

tag: time point

value: 7 days post injury


title: P90_wt_rep2_7days

source_name: sensorimotor cortex, P90, control, 7 days

tag: treatment

value: control surgery


title: P90_wt_rep3_7days


title: P90_SCI_rep3_7days


title: P90_wt_rep1_7days


title: Apc Rep 6

tag: genotype


title: S12A.WB2.Tp_Blood_EDTA+Tempus

city: Rome

first: Giscard

middle: Humberto Oliveira

last: Lima

address: Piazza Lauro de Bosis, 15

country: Italy

institute: University of Rome Foro Italico

description: Transcriptome Analyses Console (TAC) software 4.0; Array Type: HTA-2_0  (Life Technologies, Carlsbad, CA, USA); Analysis Type: Expression (Gene); Summarization Method: Gene Level - SST-RMA

hyb_protocol: 200µL hybridization cocktail (containing approximately 5.2µg fragmented and labelled single-stranded complimentary DNA targets) was loaded to the GeneChip® Human Transcriptome Array 2.0 (Thermo Fisher Scientific, Waltham, MA, US).

scan_protocol: The GeneChip arrays were incubated in the GeneChip Hybridization Oven 645 for 16hrs, washed and stained on the GeneChip Fluidics Station 450. Subsequently, arrays were scanned using the GeneChip® Scanner 3000 7G. Expression Console (Thermo Fisher Scientific, Waltham, MA, US) was used to perform initial data QC and visualisation of the data generated following array scanning.

data_processing: Data analysis and statistical evaluations were performed with Transcriptome Analyses Console (TAC) software 4.0. A False Discovery Ratio of ≤ 0.05 and a fold-change > 1.1 or < –1.1 was applied.

source_name: Healthy male

label_protocol: One hundred nanogram of total RNA was used to process the Affymetrix GeneChip® Human Transcriptome 2.0 Array using the GeneChip® WT Plus Reagent Kit according to the manufacturer instructions (Thermo Fisher Scientific, Waltham, MA, US). Single-stranded cDNA (ss-cDNA) was synthesized by the reverse transcription of complimentary RNA (cRNA).

growth_protocol: RNA was extracted from whole blood just after collection or stored at -80°C into K2EDTA or Tempus™ tubes prior to extraction.

extract_protocol: Tempus™ Spin RNA Isolation Kit: RNA was isolated from 3 mL of whole blood according to the manufacturer’s instructions. Inclusion: Some samples were collected and stored into K2EDTA tubes, then transfered to Tempus tube prior to RNA extraction. GeneJET RNA Purification Kit: RNA was isolated from 250 µL of whole blood according to the manufacturer instructions.

value: Whole blood

tag: Sex


title: S13A.Tp.WB2_Blood_EDTA+Tempus


title: S12.WB2.Th_Blood_EDTA+GeneJET


title: S13.Tp.Fz_Blood_Tempus_Frozen


title: S12.WB1.Th_Blood_GeneJET_Aliquoted


title: SLE_C_2

tag: strain


title: S11.WB2.Th_Blood_EDTA+GeneJET


title: P90_SCI_rep2_7days


title: S13.WB1.Th_Blood_GeneJET_Aliquoted


title: S9.Tp.Fz_Blood_Tempus_Frozen


title: S11.WB1.Th_Blood_GeneJET_Aliquoted


title: S12.Tp.Fz_Blood_Tempus_Frozen


title: S10.Tp.Fz_Blood_Tempus_Frozen


title: S7.WB2.Th_Blood_EDTA+GeneJET


title: S10.WB1.Th_Blood_GeneJET_Aliquoted


title: S11A.WB2.Tp_Blood_EDTA+Tempus


title: S13.WB2.Th_Blood_EDTA+GeneJET


title: S10A.WB2.Tp_Blood_EDTA+Tempus


title: S6.WB2.Th_Blood_EDTA+GeneJET


title: S9.WB1.Th_Blood_GeneJET_Aliquoted


title: S7.Tp.Fz_Blood_Tempus_Frozen


title: Apc Alk5 Rep 6


title: Cclt2

first: Xianda

last: Hu

address: 218 Anwaixiaoguanbeili St

institute: Beijing Tibetan Hospital, CTRC

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Trimmed reads were used for de novo assembly using Trinity v2.5.1 with parameters --min_contig_length 150  --CPU 8 --min_kmer_cov 3 --min_glue 3 --bfly_opts '-V 5 --edge-thr=0.1 --stderr'
All contig sequences assembled were annotated using Blast2GO pipeline. The RNA-seq reads were mapped to the built reference transcriptome using Bowtie2 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed -- no-discordant -p 1 -k 200,  and fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using RSEM software..

organism: Papilio clytia

source_name: fatbody

extract_protocol:
The fatbody tissue of Papilio clytia and Atrophaneura mencius with or without LPS were collected and total RNAs were extracted with Trizol reagent, from which mRNAs were purified by poly-T oligo-attached magnetic beads.
Libraries were constructed for sequencing using a Superscript Double-Stranded cDNA Synthesis kit according to manufacturer's specifications.

value: fatbody

value: lipopolysaccharide challenge

tag: developmental stage

value: final instar


title: Cclt1

value: control


title: S9.Th.WB2_Blood_EDTA+GeneJET


title: mammary gland epithelial cells, WT_p6_3696

city: Smithville

first: Evangelia

last: Koutelou

state: TX

address: 1808 Park Road 1C

department: Epigenet & Mol Carcinogenesis

institute: MD Anderson Cancer Center

data_processing:
Basecalling was done by HiSeq Control Software (HD 3.4.0.38).
The reads were mapped to the mouse genome (mm10) using TopHat (version 2.0.10).
The number of fragments in each known gene from GENCODE Release M21 was enumerated using htseq-count from the HTSeq package (version 0.6.0)
Genes with at least 10 fragments in at least 7 samples were retained, and then the normalized count value for each gene was calculated by R/Bioconductor package DESeq (version 1.18.0).
Genome_build: mm10
Supplementary_files_format_and_content: Column "GeneID" is Ensembl ID. Column "GeneSymbol" is gene symbol. Column "Biotype" is gene biotype from GENCODE. The other columns are normalized count values (estimated by DESeq) for all the samples.

source_name: mammary gland

growth_protocol: The glands were minced into a paste and incubated in DME/F-12 (HyClone) with 2 mg/ml collagenase A (Roche), 100 units/ml hyaluronidase (Sigma-Aldrich, H3506) for 1 h at 37°C with 180 rpm rotation along with manual shaking every 15 minutes. The cells were washed with DME/F-12 and centrifuged twice at 450 g for 10 minutes to remove the fatty layer. The cells were incubated in DME/F-12 with 2 units/ml DNase I (Sigma-Aldrich, D2463) at room temperature for 3 minutes and centrifuged at 450 g for 10 minutes. Then the pellets were resuspended in Red blood Cell Lysis buffer (Stemcell technology) on ice for 2 minutes and washed with DME/F-12 at 450 g for 10 minutes. Differential centrifugation (pulse centrifugation to 450 g for 10 seconds) was used to separate stroma from organoids. The supernatant from two spins containing the fibroblasts, macrophage and endothelial cells was pelleted and used as stroma fraction. To obtain fibroblasts, the pellets were resuspended in DME/F-12 containing 10% FBS on a 10 cm tissue culture plate. After plating the resuspended cells for 45 minutes, the plates were washed 3 times with PBS and attached cells were collected as fibroblasts. The pellets from 2 round pulse centrifugations were organoids, mainly consisting of mammary gland epithelial cells. The organoids were digested with 0.05% Trypsin/EDTA (HyClone) with 2 unit/ml of DNase I for 3 minutes and an equal volume of DME/F-12 containing 10% FBS was added and the cells were pipetted 20 times and filtered through 40 μm strainer. After 3 minutes at 600g centrifugation, single epithelial cells were obtained for experimental use.

extract_protocol:
Left and right number 2, 3 and 4 mammary glands from three-and-a-half-month-old Usp22-overexpressing and wildtype mice were dissected with lymph nodes removed from number 4 glands
1 µg of total RNA was used to prepare RNA-seq libraries with the Illumina TruSeq mRNA Kit according to the manufacturer's protocol.

value: mammary gland epithelial cells

value: mammary gland

value: wild-type

value: 3.5 months old

tag: developlemental stage

value: nulliparous

value: female


title: S9A.WB2.Tp_Blood_EDTA+Tempus


title: mammary gland epithelial cells, WT_p7_4239


title: S6.WB1.Th_Blood_GeneJET_Aliquoted


title: S5A.WB2.Tp_Blood_EDTA+GeneJET


title: S11.Tp.Fz_Blood_Tempus_Frozen


title: S6.WB2.Tp_Blood_EDTA+Tempus


title: mammary gland epithelial cells, WT_p5_3616


title: S7A.WB2.Tp_Blood_EDTA+Tempus


title: mammary gland epithelial cells, WT_p8_4267


title: S6.Tp.Fz_Blood_Tempus_Frozen


title: S10.WB2.Th_Blood_EDTA+GeneJET


title: S5.WB1.Th_Blood_GeneJET_Aliquoted


title: mammary gland epithelial cells, WT_p1_1686


title: mammary gland epithelial cells, WT_p4_3554


title: mammary gland epithelial cells, OE_p8_4268

value: USP22 OE


title: mammary gland epithelial cells, OE_p6_3698


title: mammary gland epithelial cells, OE_p4_3555


title: SC230

description: SSC

value: 10X Genomics 3 Prime V2 chemistry

value: skin

value: scleroderma


title: mammary gland epithelial cells, OE_p1_1683


title: mammary gland epithelial cells, WT_p3_3398


title: mammary gland epithelial cells, OE_p7_4240


title: LUNG31

city: Rochester

first: Irfan

last: Rahman

address: 601 elmwood ave

department: Environmental Medicine

institute: University of Rochester Medical Center

data_processing:
The raw sequence reads analyzed by the team of bioinformaticians at Norgen using their advanced analysis pipeline for the processing of raw counts and alignment to endogenous genome and annotated transcriptome
The miRNA data from various batches normalized using trimmed mean of M-values (TMM) normalization method
EdgeR statistical software package used for DE analysis. The DE was considered significant if log fold change of ≥ 1 or ≤ -1 at p- value and FDR of ≤ 0.05 was reported for the miRNA target.
GO analyses and KEGG analyses performed on the data
Genome_build: hg18
Supplementary_files_format_and_content: .txt files for DE analysed files and significantly varied files
Supplementary_files_format_and_content: .txt files for TMM

source_name: Lung Tissue

extract_protocol:
BALF exosome isolation using Plasma/Serum Exosome Purification and RNA Isolation Midi Kit from Norgen Biotek. Lung tissue exosome isolated using optimized protocol described by Dooner et al (2018). RNA isolation using Exosomal RNA isolation kit (for BALF) from Norgen and miRNeasy Mini Kit (for lung tissues)from Qiagen.
The library preparation was performed using the standard library preparation workflow of Norgen using Norgen Biotek Small RNA Library Prep Kit

tag: group

value: Smoker


title: LUNG30


title: LUNG29


title: LUNG28


title: LUNG26


title: LUNG32


title: S5.WB2.Th_Blood_EDTA+Tempus

value: male


title: mammary gland epithelial cells, OE_p3_3402


title: LUNG24

value: IPF


title: LUNG25


title: S7.WB1.Th_Blood_GeneJET_Aliquoted

value: Whole blood


title: mammary gland epithelial cells, OE_p5_3612


title: LUNG27


title: LUNG23


title: LUNG21


title: ALVACComp_P863_Euth

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

country: Canada

institute: RPM Bioinfo Solutions

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: Biotin

organism: Macaca mulatta

source_name: post-4th immunization_4 weeks

label_protocol: Isolated mRNA was amplified and biotinylated using the TargetAmpTM 2-Round Biotin-aRNA Amplification Kit 3.0 for microarray studies

growth_protocol: Not applicable. Cells were isolated directly from PBMCs

extract_protocol: RNA was extracted from PBMC using TRIzol and phenol-chloroform extraction

treatment_protocol: Not applicable. Cells were taken directly from blood

tag: subject

tag: vaccination number

value: post-4th immunization

tag: vaccination time

value: Week 25

tag: time after immunization

value: 4 weeks

tag: immunogen

value: PBMC

value: blood


title: ALVACComp_P863_post4th_16h

source_name: post-4th immunization_16 hours

value: 16 hours

tag: cell type


title: ALVACComp_P862_post4th_24h

source_name: post-4th immunization_24 hours

value: 24 hours

tag: tissue


title: ALVACComp_P851_post4th_72h

source_name: post-4th immunization_72 hours

value: 72 hours


title: ALVACComp_P851_Euth


title: ALVACComp_P841_post4th_24h


title: ALVACComp_P851_post4th_16h


title: ALVACComp_P464_post4th_72h


title: ALVACComp_P862_post4th_48h

source_name: post-4th immunization_48 hours

value: 48 hours


title: LUNG22


title: LUNG17


title: ALVACComp_P836_Euth


title: SC229

description: SSC

tag: chemistry


title: ALVACComp_P841_Euth


title: ALVACComp_P862_post4th_72h


title: LUNG16

value: COPD


title: LUNG20


title: LUNG19


title: LUNG18


title: LUNG11


title: ALVACComp_P836_post4th_16h


title: LUNG13


title: LUNG12


title: ALVACComp_P863_post4th_24h


title: ALVACComp_P851_post4th_48h


title: ALVACComp_P836_post4th_48h


title: LUNG14


title: LUNG8

value: Non-smoker


title: LUNG6


title: LUNG15


title: LUNG10


title: LUNG9


title: ALVACComp_P464_post4th_48h


title: ALVACComp_P836_post4th_24h


title: ALVACComp_P851_post4th_24h


title: LUNG4


title: ALVACComp_P863_post4th_72h


title: ALVACComp_P862_Euth


title: ALVACComp_P464_Euth


title: LUNG7


title: ALVACComp_P862_post4th_16h


title: ALVACComp_P841_post4th_48h


title: LUNG5


title: BAL40

source_name: BALF


title: ALVACComp_P841_post4th_16h


title: S5.Tp.Fz_Blood_Tempus


title: ALVACComp_P863_post4th_48h


title: LUNG3


title: ALVACComp_P464_post4th_16h


title: LUNG2


title: ALVACComp_P836_post1st_24h

source_name: post-1st immunization_24 hours

value: post-1st immunization

value: Week 0


title: BAL37


title: ALVACComp_P464_post1st_24h


title: BAL39


title: ALVACComp_P464_post4th_24h


title: ALVACComp_P841_post4th_72h


title: BAL36


title: ALVACComp_P862_post3rd_72h

source_name: post-3rd immunization_72 hours

value: post-3rd immunization

value: Week 4


title: ALVACComp_P836_post4th_72h


title: BAL38


title: BAL30

value: IPF


title: BAL34


title: BAL33


title: BAL28


title: BAL27


title: BAL32


title: BAL31


title: LUNG1


title: BAL26


title: BAL35


title: BAL29


title: ALVACComp_P851_post1st_48h

source_name: post-1st immunization_48 hours


title: ALVACComp_P841_post2nd_16h

source_name: post-2nd immunization_16 hours

value: post-2nd immunization

value: Week 12


title: ALVACComp_P862_post1st_72h

source_name: post-1st immunization_72 hours


title: ALVACComp_P863_post3rd_72h


title: ALVACComp_P851_post3rd_48h

source_name: post-3rd immunization_48 hours


title: ALVACComp_P863_post3rd_24h

source_name: post-3rd immunization_24 hours


title: BAL24


title: ALVACComp_P863_post3rd_48h


title: ALVACComp_P841_post1st_24h


title: ALVACComp_P836_post3rd_16h

source_name: post-3rd immunization_16 hours


title: ALVACComp_P862_post1st_48h


title: ALVACComp_P841_post3rd_16h


title: ALVACComp_P841_post3rd_72h


title: ALVACComp_P862_post1st_16h

source_name: post-1st immunization_16 hours


title: ALVACComp_P863_post2nd_72h

source_name: post-2nd immunization_72 hours


title: ALVACComp_P863_post1st_16h


title: ALVACComp_P862_post1st_24h


title: ALVACComp_P841_post2nd_24h

source_name: post-2nd immunization_24 hours


title: BAL22


title: BAL23


title: ALVACComp_P464_post3rd_16h


title: BAL25


title: A375_KO_eIF4B_vem_18h

city: Koto-ku

first: Hitomi

last: Shirahama

state: Tokyo

address: Ariake 3-8-31

country: Japan

institute: Japanese Foundation for Cancer Research

description: A375 eIF4B-rescued cells treated with vemurafenib  for 18 h

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hours at 45℃ on GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix, CA, USA). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Thermo Fisher Scientific, MA, USA).

data_processing: Normalization of microarray data was carried out by the Robust Multichip Average method using R software with affy package.

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 µg total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were cultured in RPMI1640 supplemented with 10% fetal bovine serum and 100 µg/ml kanamycin.

extract_protocol: Total RNA was extracted from cultured cells using QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).

treatment_protocol: A375 eIF4B-knockout (KO/LacZ) and eIF4B-rescued (KO/eIF4B) cells were treated with vehicle (DMSO) or vemurafenib (10 µM) for 6 or 18 hours.

tag: cell line

value: KO/eIF4B (eIF4B-rescued, WT)

value: 10 µM vemurafenib 18h


title: BAL21


title: BAL20


title: ALVACComp_P862_post2nd_24h

value: PBMC


title: ALVACComp_P862_post3rd_48h

value: blood


title: A375_KO_eIF4B_vem_6h

description: A375 eIF4B-rescued cells treated with vemurafenib for 6 h

value: 10 µM vemurafenib 6h


title: BAL19


title: M11538_2

first: Hongjian

last: Zhou

address: No.1 Wenyuan Road, Xianlin University Town, Nanjing

institute: Nanjing Normal University

data_processing:
RNA integrity was assessed with the RNA nano 6000 assay kit for the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Briefly, mRNA was purified from total RNA with poly T oligo-attached magnetic beads. Fragmentation was conducted at high temperature with divalent cations in 5× first-strand synthesis reaction buffer. To select cDNA fragments 370–420 bp long, library fragments were purified in an AMPure XP system (Beckman Coulter, Beverly, MA, USA).
PCR was performed with Phusion high-fidelity DNA polymerase, universal PCR primers, and index (X) primer. The PCR products were purified in the AMPure XP system (Beckman Coulter, Beverly, MA, USA) and library quality was assessed in the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Index-coded samples were clustered on a cBot cluster generation system using a TruSeq PE cluster kit v3-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
The reference genome index was built and paired-end clean reads were aligned to the reference genome with Hisat2 v2.0.5. FeatureCounts v. 1.5.0-p3 enumerated the reads mapped to each gene. Differential expression analysis was performed in the DESeq2 package of R v. 1.20.0 (R Core Team, Vienna, Austria).
Genome_build: dm6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: drosophila melanogaster

extract_protocol:
RNA integrity was assessed with the RNA nano 6000 assay kit for the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Briefly, mRNA was purified from total RNA with poly T oligo-attached magnetic beads. Fragmentation was conducted at high temperature with divalent cations in 5× first-strand synthesis reaction buffer. To select cDNA fragments 370–420 bp long, library fragments were purified in an AMPure XP system (Beckman Coulter, Beverly, MA, USA). PCR was performed with Phusion high-fidelity DNA polymerase, universal PCR primers, and index (X) primer. The PCR products were purified in the AMPure XP system (Beckman Coulter, Beverly, MA, USA) and library quality was assessed in the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Index-coded samples were clustered on a cBot cluster generation system using a TruSeq PE cluster kit v3-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The reference genome index was built and paired-end clean reads were aligned to the reference genome with Hisat2 v2.0.5. FeatureCounts v. 1.5.0-p3 enumerated the reads mapped to each gene. Differential expression analysis was performed in the DESeq2 package of R v. 1.20.0 (R Core Team, Vienna, Austria).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gal80ts; Tub> CR11538

value: 12 hours after injection of M. luteus

value: adult


title: ALVACComp_P836_post1st_72h

value: 72 hours


title: ALVACComp_P863_post2nd_48h

source_name: post-2nd immunization_48 hours

value: 48 hours


title: A375_KO_LacZ_vem_6h

description: A375 eIF4B-knockout cells treated with vemurafenib for 6 h

value: KO/LacZ (eIF4B-knockout, KO)


title: BAL18

value: COPD


title: ALVACComp_P464_prevax

value: pre-vaccination

value: Day 0

value: pre


title: A375_KO_LacZ_vehicle

description: A375 eIF4B-knockout cells without drug treatment (control)

value: Vehicle (DMSO)


title: M11538_3


title: BAL17


title: M11538_1


title: BAL16

value: Smoker


title: ALVACComp_P836_post2nd_16h

value: post-2nd immunization

value: Week 12

value: 16 hours


title: A375_KO_LacZ_vem_18h

description: A375 eIF4B-knockout cells treated with vemurafenib for 18 h

value: 10 µM vemurafenib 18h


title: M25C_3

value: Gal80ts; Tub-Gal4/P{CaryP}attP40


title: ALVACComp_P862_post2nd_48h

value: PBMC

value: blood


title: ALVACComp_P851_post3rd_72h

value: post-3rd immunization

value: Week 4


title: ALVACComp_P841_post3rd_48h

value: 48 hours


title: ALVACComp_P851_post3rd_24h

value: 24 hours


title: ALVACComp_P851_post3rd_16h


title: BAL15


title: ALVACComp_P836_prevax


title: ALVACComp_P851_post1st_72h

value: post-1st immunization

value: Week 0

value: 72 hours


title: A375_KO_eIF4B_vehicle

description: A375 eIF4B-rescued cells without drug treatment (control)

value: KO/eIF4B (eIF4B-rescued, WT)


title: ALVACComp_P836_post2nd_48h


title: ALVACComp_P841_post1st_72h


title: M25C_1

value: 12 hours after injection of M. luteus

value: adult


title: BAL13

value: Smoker


title: BAL11


title: M25C_2


title: ALVACComp_P464_post2nd_16h

value: post-2nd immunization

value: Week 12


title: BAL14


title: BAL12


title: S111_grade3

description: Small RNA seq

data_processing:
The original fastq files were converted to fasta format and reads without Ns were kept for further analysis
The 3' adapter and HD signatures [Sorefan et al. 2012] were trimmed and the files were converted from redundant to non-redundant format
The reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al. 2008]
The reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
The abundances of the reads were normalized using the RPM method [Mortazavi et al. 2008]
The differential expression was called on offset fold change on confidence intervals built on replicates, offset = 20
Genome_build: GRCh38
Supplementary_files_format_and_content: *csv: Comma-separated text files include sequences and raw abundances.

source_name: blood spot

extract_protocol:
Fingerstick samples were used for RNA extraction before construction of small RNA libraries
Illumina compatible method with HD adapters

tag: disease state

value: grade 3 chondrosarcoma


title: S118_grade2

description: Small RNA seq

value: grade 2 chondrosarcoma


title: S117_grade3

description: Small RNA seq


title: BAL9


title: S121_grade3

description: Small RNA seq


title: BAL10


title: S99_grade2

description: Small RNA seq


title: ALVACComp_P841_post3rd_24h

value: PBMC


title: ALVACComp_P851_post2nd_16h

value: 16 hours

value: blood


title: ALVACComp_P851_post2nd_72h


title: ALVACComp_P841_post1st_16h


title: ALVACComp_P862_post2nd_72h


title: S103_grade2

description: Small RNA seq


title: ALVACComp_P464_post1st_72h


title: ALVACComp_P863_post1st_48h


title: ALVACComp_P862_prevax

value: pre-vaccination

value: Day 0

value: pre


title: ALVACComp_P841_post1st_48h

value: post-1st immunization

value: 48 hours


title: ALVACComp_P851_post2nd_24h

value: 24 hours


title: BAL8

value: Non-smoker


title: BAL7


title: ALVACComp_P862_post3rd_24h

value: post-3rd immunization

value: Week 4


title: ALVACComp_P464_post3rd_72h

value: 72 hours


title: BAL6


title: ALVACComp_P464_post2nd_48h

value: post-2nd immunization


title: ALVACComp_P464_post2nd_24h

value: Week 12


title: S125_grade1

description: Small RNA seq

value: grade 1 chondrosarcoma


title: S135_grade1

description: Small RNA seq


title: ALVACComp_P851_prevax


title: BAL5


title: ALVACComp_P851_post1st_24h

value: Week 0


title: ALVACComp_P862_post2nd_16h

value: PBMC


title: ALVACComp_P464_post2nd_72h


title: ALVACComp_P836_post3rd_48h


title: ALVACComp_P836_post3rd_72h


title: S123_grade1

description: Small RNA seq


title: S124_grade1

description: Small RNA seq


title: S120_grade1

description: Small RNA seq


title: BAL3


title: BAL4


title: S119_grade1

description: Small RNA seq


title: BAL2


title: S106_grade1

description: Small RNA seq


title: S96_grade1

description: Small RNA seq


title: ALVACComp_P863_post3rd_16h

value: 16 hours


title: MCC_H441_rep3

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

description: Micrococcal nuclease digested 3C library, enriched for fragments of interest by oligonucleotide pulldown

data_processing:
Library strategy: Micro Capture-C (MCC)
The raw fastq file is processed to reconstruct a single read from the paired end sequencing. This is then mapped to the 800bp sequence surrounding the capture oligonucleotide using the non-stringent aligner BLAT. This allows the reads to be cut into ‘slices’ depending on whether they align to the sequence around the capture site. This strategy allows ligation junctions in the read to be determined with base pair accuracy. The resulting fastq file is aligned to the genome using bowtie and replicates for each cell type merged.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: NCI-H441 Lung Epithelia

growth_protocol:
NCI-H441 cells (ATCC HTB-174) were grown in RPMI 1640 medium (Gibco) supplemented with 10% non-heat inactivated FBS (Sigma) and 1% Penicillin-Streptomycin (Gibco), cells were given fresh media every two days and passaged by light trypsination twice weekly
Cells were resuspended in aliquots of 1 x 107 in 10 ml media with 10% FCS in a 15-ml conical centrifuge tube using an automated cell counter (CountessII, Thermo Fisher). Formaldehyde (37% (vol/vol)) was added to each aliquot to make a final concentration of 2% (vol/vol) and the cells were incubated on a roller mixer for 10 minutes at room temperature. The crosslinking reaction was quenched with cold 1 M glycine to a final concentration 130 mM and the sample was centrifuged (5 min at 220 g). The supernatant was discarded and the cell pellet was washed with 10 ml cold Phosphate Buffered Saline (PBS) and reconstituted in 1 ml PBS. An automated cell count on was performed on 10 ml of the cell suspension to reconfirm the cell number. Digitonin (Sigma D-141) was prepared fresh for each experiment (0.5% in dimethylsulfoxide (DMSO) (wt/vol)). Each batch of digitonin was tested for its ability to permeabilise cells at a concentration of 0.005% (wt/vol). 10 ml digitonin was added to make a final concentration of 0.005% (wt/vol). For standard nuclear preparation, the pellet was resuspended in 5ml cold lysis buffer (TRIS-HCl pH 8 10 mM, NaCl 10 mM, Igepal NP-40 (Sigma I8896) 0.2%, cOmplete proteinase inhibitor cocktail (PIC) (Roche 4693116001) (x1 tablet / 50 ml)) and incubated on ice for 20 min. The nuclei were centrifuged (300 g, 5 min) and resuspended in 1ml lysis buffer.

extract_protocol:
Qiagen DNeasy blood and tissue kit
7-10 µg of each 3C library was sonicated to a mean fragment size of 200 bp using a Covaris S220 Focussed Ultrasonicator (1-3 cycles of 60s: duty cycle 10%; intensity 5; cycles per burst 200). The library size was assessed using an Agilent TapeStation (DNA 1000) and an Ampure XP (Beckman Coulter) bead clean-up was performed once the sample had been adequately sonicated. To maximise library complexity three aliquots, each containing 2 µg sonicated 3C library, were processed in parallel for each sample to add sequencing adaptors. NEB Ultra II reagents were used following the standard protocol with the following modifications: first, additional adapter was added into the ligation reactions (7.5 µl rather than 2.5 µl); no size selection was performed (Ampure XP bead clean ups were always performed with a sample:bead ratio of 1:1.8) and the final PCR to add indices was amplified in triplicate from each aliquot using the Herculase II PCR kit (Agilent) to maximise DNA yield. All parallel library preparations and PCR reactions were pooled for each reaction.

value: Epithelial cell


title: ALVACComp_P841_prevax

value: pre-vaccination

value: blood


title: ALVACComp_P863_post1st_24h