title: Input WT

city: Denver

first: Christopher

last: Phiel

state: CO

address: 1150 12th Street SI 4111

department: Integrative Biology

institute: University of Colorado Denver

data_processing:
Library strategy: m6A-seq
m6A-seq reads were aligned to the reference genome using Bowtie 2.
The DESeq package in StrandNGS software was used to quantify mRNA and identify mRNAs with differential amounts of m6A between WT and Gsk-3 DKO ESCs.
Genome_build: mm9
Supplementary_files_format_and_content: Peaks_with_gene_annotations_filtered_ERD_sorted

source_name: Embryonic stem cells

growth_protocol: Feeder-free ESCs were grown on 10 cm plates coated with 0.1 % gelatin. Media was high glucose DMEM supplemented with 15% FBS, 1% non-essential amino acids, 1% sodium pyruvate, 1% L-glutamine, 1% penicillin/streptomycin, and 55 μM β-mercaptoethanol.

extract_protocol:
Purified total RNA was then incubated with oligo (dT) beads to isolate mRNA. m6A mRNA was subsequently isolated using Dynabeads coupled with m6A antibody.
m6A mRNA and total mRNA was chemically fragmented by incubating with 100 mM Tris HCl, pH 7.0 and 100 mM ZnCl2 at 94°C for 5 minutes. 100 ng of RNA were used to prepare libraries according to Ion XpressRNA-seq barcoding kit protocols.

treatment_protocol: Cells were grown in the absence of LIF for 14 days before isolating total RNA using Trizol.

tag: strain

tag: antibody

tag: genotype/variation

value: wildtype


title: NmeCas9 - T gRNA

status: Public on Dec 21 2017

type: SRA

city: Raleigh

first: Chase

last: Beisel

state: NC

address: 840 Main Campus Drive

department: Chemical and Biomolecular Engineering

country: USA

institute: North Carolina State University

library_source: genomic

data_processing:
see the following website: https://bitbucket.org/csmaxwell/crispr-txtl-pam-counting-script/overview
Real Time Analysis for basecalling.
Supplementary_files_format_and_content: 2017-12-07-nme-pam-log2-4nts.csv: A list of the depletion of PAMs from NmeCas9 in a PAM determination assay. We used a plasmid containing a  randomized 10nt library PAM flanked by a targeting site for our system (see https://benchling.com/s/seq-3orlk0nTK6xPHJMMKZRC for the reference    sequence). If this particular Cas9 was able to cleave this plasmid, then it is considered a functional PAM and is NOT able to be sequenced, while the plasmid containing non-functional PAMs were left in the reaction. The remaining plasmids were then PCR amplified and prepared  for NGS. Since the total number of unique sequences containing 10 nucleotides is extremely large, we trimmed down the length of the randomized PAM from 10 to 4 since it seemed like the four nucleotides were the most important, in terms of allowing/not allowing the Cas9 cleavage.
2017-12-07-nme-pam-log2-5nts.csv: same contents as above except it looked at  5 nucleotides within the 10N library.
nme-counts-q10.csv: The total read sequences that matched our reference (see https://benchling.com/s/seq-3orlk0nTK6xPHJMMKZRC for the reference sequence). We were only interested in the 10Ns that were present in the reference (position 1070-1082 in the sequence).

molecule: genomic DNA

organism: synthetic construct

source_name: plasmid DNA

extract_protocol:
myTXTL extract purchased from Arbor Biosciences.
The samples were PCR amplified twice. The 1st PCR involved attachment of unique adapters that provided a landing site for the 2nd PCR. The 2nd PCR involved attachment of i5 and i7 Nextera low plex pooling indices.

treatment_protocol: Prior to library construction, the TXTL reaction should be diluted 1:10 for successful amplification using a high-fidelity polymerase.

tag: in vitro environment

value: myTXTL from Arbor Biosciences

tag: grna

value: Targets the randomized PAM library

tag: illumina nextera indices


title: m6A-seq WT

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: m6A antibody, NEB, E1611A, lot 0011602


title: NmeCas9 - NT gRNA

value: Non-targeting gRNA


title: m6A-seq Gsk-3 DKO

value: Gsk-3 DKO


title: Input Gsk-3 DKO


title: Neonate_3M003_6h_subj3 [mDC]

type: RNA

city: Vancouver

first: Edgardo

last: Fortuno III

state: BC

department: Paediatrics

country: Canada

institute: Child & Family Research Institute - University of British Columbia

description: Neonate subject 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with no background subtraction using Illumina's BeadStudio software version 3.1.3.0

label: biotin

organism: Homo sapiens

source_name: Cord blood

label_protocol: Biotinylated cRNA were prepared with the Ambion's Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit with in-column DNAseI treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: age group

value: Neonate

tag: subject

tag: gender

value: Female

tag: tissue

value: Cord blood

tag: cell type

value: mDC

tag: agent

tag: time


title: Neonate_Unstim_0h_subj3 [mDC]

description: Neonate subject 3

value: Unstim


title: Neonate_3M003_1h_subj2 [mDC]

description: Neonate subject 2


title: Neonate_3M003_6h_subj2 [mDC]

description: Neonate subject 2


title: Neonate_3M003_1h_subj3 [mDC]

description: Neonate subject 3


title: Adult_Unstim_0h_subj1 [mDC]

description: Adult subject 1

source_name: Peripheral blood

value: Adult

value: Peripheral blood


title: radiated_IgG_sample_4.2

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

description: Gene expression data from A549 (ATCC CCL185) cells radiated followed by immunoprecipiation of IgG

hyb_protocol: The samples were hybridized to the Affymetrix GeneTitan:HumanGene 2.1 ST Array Plate for 18 h.

scan_protocol: HT Array Plates were scanned using the HT Scanner (Affymetrix GeneChip®HT)

data_processing: The data was analyzed using robust multi-array average (RMA) analysis using the rma() function from the R package oligo (version 1.30.0) with default setting (target=core).

source_name: A549 (ATCC CCL185) cells ;treatment: radiated ;immunoprecipiation with: IgG

label_protocol: 100 ng of quality controlled (using Bioanalyzer) total RNA were used for the processing of the biotinylated cRNA.

growth_protocol: A549 cells (ATCC CL-185) were grown to confluence in DMEM 10% f.c.s.

extract_protocol: RNA was transcribed to cDNA (Quiagen, according to the manufacturer's instructions)

treatment_protocol: Cells were irradiated with 4 Gy and after 24h EGFR was immuno-precipitated

tag: cell line

tag: treatment

value: radiated

tag: construct

value: IgG


title: radiated_IgG_sample_4.3


title: Neonate_Unstim_0h_subj1 [mDC]

description: Neonate subject 1


title: Neonate_Unstim_0h_subj2 [mDC]

description: Neonate subject 2


title: non-radiated_IgG_sample_3.3

description: Gene expression data from A549 (ATCC CCL185) cells non-radiated followed by immunoprecipiation of IgG

source_name: A549 (ATCC CCL185) cells ;treatment: non-radiated ;immunoprecipiation with: IgG

value: non-radiated


title: non-radiated_IgG_sample_3.2


title: radiated_IgG_sample_4.1


title: ribo_20_WT_w/o_CHX_1

city: Bethesda

first: Jon

middle: R.

last: Lorsch

state: MD

address: BG 49 RM 2C08, 49 Convent Dr.

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development,

institute: National Institutes of Health

data_processing:
The ribosome profiling and mRNA sequencing data were processed as described in Ingolia, N.T. (2010). Genome-wide translational profiling by ribosome footprinting.  Methods Enzymol. 470, 119–142. Breifly, the sequnce linker and the first nucleotide of each read were removed using fastx_toolkit/0.0.13 (fastx_clipper and fastx_trimmer, respectively). Ribosome RNAs were removed using bowtie/2-2.2.5  alignment agains year ribosome RNA sequences.The non-rRNA reads were mapped to yeast geneome sacCer3 (http://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/chromFa.tar.gz)using TopHat/2.0.13.
Wiggle files were produced from the alignment files using RiboSeq (https://github.com/ingolia-lab/RiboSeq), Two replicates of mRNA or foot-print alignment files were merged for generating two wiggle files, each for genes on the Watson or Crick strand. The total reads on both strands were summed and a normalization factor q was calculated as 1000,000,000/(total reads on W+C strands). Wiggle files were then regenerated by multiplying all reads by the factor q, yielding the number of reads per 1000 million total reads (rpkm).
For uORF identification, we employed the "yassour-uorf" program in RiboSeq (https://github.com/ingolia-lab/RiboSeq), to identify all potential uORFs within annotated 5’UTRs initiating with either AUG or a near-cognate codons. We use the perameter -c15-r4-z0.5 in the relevant line of code. This analysis was conducted on multiple published datasets listed in (Dataset-list.docx) and all unpublished ribosome profiling datasets in this study.  After excluding uORFs shorter than 3 codons, we identified 564 AUG initiated uORFs and 5497 near-cognate uORFs with evidence of translation in one or more experiments. The characteristics of all uORFs, including uORF_name,  gene_name, position from 5' end (cap), position to main AUG, uORF_length, context, start codon and start_codon_type are listed in supplimentary file "all_uorf_info.xlsx".
Genome_build: sacCer3
Supplementary_files_format_and_content: a bed file for all yeast uORFs
Supplementary_files_format_and_content: wig
Supplementary_files_format_and_content: "Dataset-list.pdf" is for the published datasets we used in uORF identification, and “all_uorf_info.xlsx” listed all information for the uORFs we identified

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7  in synthetic complete medium at 20°C,without treatment with cycloheximide before harvesting.

extract_protocol: Cells were rapidly vacuum filtered and flash frozen. Whole cell extracts were prepared by breaking cells in freezer mill in cell lysis buffer containing 500 µg/ml cycloheximide. Whole cell extracts were RNase treated, and run over sucrose gradients to extract the monosome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification. Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos.

treatment_protocol: No additional treatment


title: ribo_30_WT_w/o_CHX_2

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7  in synthetic complete medium at 30°C,without treatment with cycloheximide before harvesting.


title: ribo_37_WT_with_CHX_2

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7 in synthetic complete medium at 37℃.

extract_protocol: Cells were rapidly vacuum filtered and flash frozen. Whole cell extracts were prepared by breaking cells in freezer mill in cell lysis buffer containing 100 µg/ml cycloheximide. Ribosome profiling (Rnase I footprinting, size selection,RNA extraction,  linker ligation, reverse transcription, cDNA circularization, subtractive hybridization, PCR amplification) was done as described Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324(5924):218-223

treatment_protocol: Cultures were treated with cycloheximide (100 µg/ml) for 2 min prior to harvesting


title: ribo_30_WT_w/o_CHX_1


title: ribo_25_WT_w/o_CHX_2

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7  in synthetic complete medium at 25°C,without treatment with cycloheximide before harvesting.


title: ribo_25_WT_w/o_CHX_1


title: Neonate_3M003_1h_subj1 [mDC]

description: Neonate subject 1


title: radiated_EGFR_sample_2.2

description: Gene expression data from A549 (ATCC CCL185) cells radiated followed by immunoprecipiation of EGFR

source_name: A549 (ATCC CCL185) cells ;treatment: radiated ;immunoprecipiation with: EGFR

value: EGFR


title: ribo_37_WT_w/o_CHX_1

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7  in synthetic complete medium at 37°C,without treatment with cycloheximide before harvesting.


title: radiated_EGFR_sample_2.1


title: Neonate_3M003_6h_subj1 [mDC]

description: Neonate subject 1


title: non-radiated_IgG_sample_3.1


title: ribo_20_WT_w/o_CHX_2


title: non-radiated_EGFR_sample_1.2

description: Gene expression data from A549 (ATCC CCL185) cells non-radiated followed by immunoprecipiation of EGFR

source_name: A549 (ATCC CCL185) cells ;treatment: non-radiated ;immunoprecipiation with: EGFR


title: ribo_37_WT_with_CHX_1


title: ribo_37_WT_w/o_CHX_2


title: non-radiated_EGFR_sample_1.3


title: radiated_EGFR_sample_2.3


title: non-radiated_EGFR_sample_1.1


title: ribo_20_WT_with_CHX_2

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7 in synthetic complete medium at 20℃.


title: ribo_30_WT_with_CHX_2

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7 in synthetic complete medium at 30℃.


title: ribo_25_WT_with_CHX_2

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7 in synthetic completemedium at 25℃.


title: ribo_SUI1-L96P_w/o_CHX_1


title: ribo_SUI1-L96P_w/o_CHX_2


title: ribo_25_WT_with_CHX_1

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7 in synthetic complete medium at 25℃.


title: ribo_WT(for SUI1-L96P)_with_CHX_1

source_name: ribo_WT(for SUI1-L96P)_with_CHX_1

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7 in synthetic complete medium at 33℃.

extract_protocol: Cells were rapidly vacuum filtered and flash frozen. Whole cell extracts were prepared by breaking cells in freezer mill in cell lysis buffer containing 100 ug/ml cycloheximide. Ribosome profiling (Rnase I footprinting, size selection,RNA extraction,  linker ligation, reverse transcription, cDNA circularization, subtractive hybridization, PCR amplification) was done as described Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324(5924):218-223

treatment_protocol: Cultures were treated with cycloheximide (100 ug / ml) for 2 min prior to harvesting


title: ribo_WT(for SUI1-L96P)_w/o_CHX_1

source_name: ribo_WT(for SUI1-L96P)_w/o_CHX_1


title: ribo_WT(for SUI1-L96P)_with_CHX_2

source_name: ribo_WT(for SUI1-L96P)_with_CHX_2


title: ribo_tif3△_2

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7 in YPD medium at 23℃.


title: ribo_SUI1-L96P_with_CHX_1


title: ribo_WT(for tif3)_2

source_name: ribo_WT(for tif3)_2


title: ribo_SUI1-L96P_with_CHX_2


title: ribo_SUI3-2(for SUI1_T15A)_1

source_name: ribo_SUI3-2(for SUI1_T15A)_1


title: ribo_SUI-T15A_2


title: ribo_SUI1-T15A_1


title: ribo_WT(for SUI1-T15A)_1

source_name: ribo_WT(for SUI1-T15A)_1


title: ribo_WT(for SUI1-T15A)_2

source_name: ribo_WT(for SUI1-T15A)_2


title: ribo_SUI3-2(for TIF11-R13P)_2

source_name: ribo_SUI3-2(for TIF11-R13P)_2


title: ribo_SUI3-2(for TIF11-R13P)_1

source_name: ribo_SUI3-2(for TIF11-R13P)_1


title: ribo_tif3△_1


title: ribo_SUI3-2/TIF11_R13P_2


title: ribo_WT(for TIF11_R13P)_2

description: ribo_ tif11-R13P_fwd.wig, ribo_tif11-R13P_rev.wig

source_name: ribo_WT(for TIF11_R13P)_2


title: ribo_SUI3-2(for SUI1_T15A)_2

source_name: ribo_SUI3-2(for SUI1_T15A)_2


title: ribo_SUI3-2/TIF11_R13P_1


title: ribo_20_WT_with_CHX_1


title: ribo_TIF11_R13P_1

description: ribo_TIF11_fwd.wig, ribo_TIF11_rev.wig


title: ribo_30_WT_with_CHX_1


title: ribo_WT(for TIF11_R13P)_1

source_name: ribo_WT(for TIF11_R13P)_1


title: ribo_WT(for SUI1-L96P)_w/o_CHX_2

source_name: ribo_WT(for SUI1-L96P)_w/o_CHX_2


title: mRNA_WT(for TIF11_R13P)_2

description: mrna-TIF11_fwd.wig, mrna-TIF11_rev.wig

source_name: mRNA_WT(for TIF11_R13P)_2

extract_protocol: Cells were rapidly vacuum filtered and flash frozen. Whole cell extracts were prepared by breaking cells in freezer mill in cell lysis buffer containing 500 µg/ml cycloheximide. Total mRNA isolated from whole cell extract using miRNeasy minikt (Qiagen). Total RNA fragmentation, Size selection,  linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324(5924):218-223. Ribo-Zero Gold rRNA Removal Kit (Illumina) was used to to remove ribosome contamination after linker ligation step.


title: ribo_SUI3-2/SUI-T15A_2


title: mRNA_TIF11_R13P_1

description: mrna-tif11-R13P_fwd.wig, mrna-tif11-R13P_rev.wig


title: mRNA_TIF11_R13P_2


title: mRNA_WT(for TIF11_R13P)_1

description: mrna-TIF11_fwd.wig, mrna-TIF11_rev.wig

source_name: mRNA_WT(for TIF11_R13P)_1


title: ribo_TIF11_R13P_2

description: ribo_TIF11_fwd.wig, ribo_TIF11_rev.wig


title: ribo_WT(for tif3)_1

source_name: ribo_WT(for tif3)_1


title: ribo_SUI3-2/SUI-T15A_1


title: Myeloid dendritic cells, sample 4

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
Circulating BDCA-1+ myeloid dendritic cells (MDC) were positively enriched from PBMC, obtained from buffy coats of healthy donors using BDCA-1 MicroBeads (cell purity > 95%). Four samples of MDC (immediately after MACS sorting) were used for microarray preparation as they passed the purity criteria; all samples were processed separately. Sufficient amounts of high quality RNA were isolated and transcriptomes were assessed using the HG-U133A Affymetrix microarray. No significant difference in the present call rate as well as the overall variance was seen.
Keywords = myeloid antigen presenting cells
Keywords = dendritic cell subsets


title: Mature monocyte-derived dendritic cells, sample 2

description:
Circulating CD14+ monocytes were positively enriched from PBMC, obtained from buffy coats of healthy donors using CD14 MicroBeads (cell purity > 95%). Monocyte-derived dendritic cells (mo-DC) were generated from the CD14+ monocytes in a serum-free medium (CellGro) supplemented with 2mM glutamine, 500 U/ml IL-4 and 800 U/ml GM-CSF for seven days to generate immature mo-DC (cytokines were replenished on day 3 and 5) and consequently for three days with anti-CD40 antibody and TNFalpha to generate mature mo-DC.
Four samples of mature mo-DC (harvested on day 10 of culture) were used for microarray preparation as they passed the purity criteria; all samples were processed separately. Sufficient amounts of high quality RNA were isolated and transcriptomes were assessed using the HG-U133A Affymetrix microarray. No significant difference in the present call rate as well as the overall variance was seen.
Keywords = myeloid antigen presenting cells
Keywords = dendritic cell subsets

source_name: In vitro generated mature monocyte-derived dendritic cells


title: Mature monocyte-derived dendritic cells, sample 4


title: Immature monocyte-derived dendritic cells, sample 4

description:
Circulating CD14+ monocytes were positively enriched from PBMC, obtained from buffy coats of healthy donors using CD14 MicroBeads (cell purity > 95%). Monocyte-derived dendritic cells (mo-DC) were generated from the CD14+ monocytes in a serum-free medium (CellGro) supplemented with 2mM glutamine, 500 U/ml IL-4 and 800 U/ml GM-CSF for seven days to generate immature mo-DC (cytokines were replenished on day 3 and 5) and consequently for three days with anti-CD40 antibody and TNFalpha to generate mature mo-DC.
Four samples of immature mo-DC (harvested on day 7 prior to start of maturation) were used for microarray preparation as they passed the purity criteria; all samples were processed separately. Sufficient amounts of high quality RNA were isolated and transcriptomes were assessed using the HG-U133A Affymetrix microarray. No significant difference in the present call rate as well as the overall variance was seen.
Keywords = myeloid antigen presenting cells
Keywords = dendritic cell subsets

source_name: In vitro generated immature monocyte-derived dendritic cells


title: Monocytes, sample 3

description:
Circulating CD14+ monocytes were positively enriched from PBMC, obtained from buffy coats of healthy donors using CD14 MicroBeads (cell purity > 95%).
Four samples of monocytes (immediately after MACS sorting) were used for microarray preparation as they passed the purity criteria; all samples were processed separately. Sufficient amounts of high quality RNA were isolated and transcriptomes were assessed using the HG-U133A Affymetrix microarray. No significant difference in the present call rate as well as the overall variance was seen.
Keywords = myeloid antigen presenting cells
Keywords = dendritic cell subsets

source_name: Circulating CD14+ monocytes


title: Mature monocyte-derived dendritic cells, sample 3


title: Immature monocyte-derived dendritic cells, sample 1


title: Myeloid dendritic cells, sample 3

source_name: Circulating BDCA-1+ myeloid dendritic cells


title: Immature monocyte-derived dendritic cells, sample 2


title: Monocytes, sample 1


title: Eosinophils KO +

city: Uchinada Kahoku

first: Toshiki

last: Yabe-Wada

state: Ishikawa

address: 1-1 Daigaku

department: School of Medicine

country: Japan

institute: Kanazawa Medical University

hyb_protocol: Affymetrix GeneChip Hybridization, Wash, and Stain Kit was used for hybridization according to the manufacture’s instructions.

scan_protocol: The signals were quantified using Affymetrix CeneChip Scanner 3000.

data_processing: The data were normalized using the Robust Multichip Average (RMA) algorithm in the “affy” package of the Bioconductor project (http://www.bioconductor.org/), after which transcript signals were calculated by log2-transformation of the normalized data.

label: Biotin

source_name: Eosinophils stimulated with LPS derived from SLPI deficient bone marrow cells

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit was used for labeling according to the manufacturer's instructions.

growth_protocol: Bone marrow cells were cultured in RPMI 1640 medium containing with fetal calf serum and recombinant mouse cytokines (basophils and mast cells : interleukin 3, eosinophils : Flt 3 ligand, stem cell factor, interleukin 5) with at 37˚C in humidified atmosphere in the presence of 5% CO2.

extract_protocol: Total RNAs were prepared by miRNeasy (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Basophils were cultured with or without trinitrophenol (TNP)-ovalbumin for 12 hours following 1 hour incubation of cells with or without anti-TNP-IgE before RNA isolation. Eosinophils were cultured with or without lipopolysaccharide for 3 hours followed by RNA isolation.

value: bone marrow

value: Eosinophils

tag: genotype

value: Slpi-/-

tag: stimulation

value: LPS stimulated


title: Mature monocyte-derived dendritic cells, sample 1


title: Eosinophils WT +

source_name: Eosinophils stimulated with LPS derived from wild type bone marrow cells

tag: strain

value: wildtype


title: Control vs. shDEK SK-Mel-103 Replicate 2

city: Madrid

first: Metehan

last: Cifdaloz

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology Program

country: Spain

institute: CNIO

description: Biological replicate 2 of 3. shDEK vs. scrambled control infected melanoma cells.

hyb_protocol: Microarray: Human WHG 4X44K (Agilent microarray design ID 014850, P/N G4112F). Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 825 ng. Volume: 100 uL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2565C DNA microarray scanner (Agilent). Hybridized microarray images were analyzed by Agilent Feature Extraction Software (ver. 10.1), which performed feature quantitation, background subtraction [by spatial detrending] and dye bias normalization [after bias detection by linear and Lowess curve fitting methods].

data_processing: Raw data were normalized using loess within array normalization and quantiles for between-arrays normalization. Normexp method was applied for background correction.

source_name: scrambled control infected SK-Mel-103 melanoma cell line

label_protocol: 1µg of RNA was labeled by commercial Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit following manufacturer instructions.  Amplification: by RNA polymerases. Agilent manual G4140-90050 Ver. 5.7 March 2008. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores.  Labeled samples were purified with silica-based RNeasy spin columns (Qiagen).

growth_protocol: SK-Mel-103 cell line was grown in DMEM medium supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin (Gibco), and maintained at 37°C in humidified 5% CO2 atmosphere.

extract_protocol: RNA was isolated by Qiagen RNeasy Kit following manufacturer instructions.

treatment_protocol: Cells were plated at 70% confluence and infected with lentivirus either KH1-GFP scramble control or KH1-GFP-shDEK(2) virus. At day2 cells were selected with puromycin selection. At day 4.5 cells were harvested.

tag: lentivirus

value: KH1-GFP scramble control

tag: day after infection

source_name: shDEK infected SK-Mel-103 melanoma cell line

tag: shRNA seq


title: Immature monocyte-derived dendritic cells, sample 3


title: Myeloid dendritic cells, sample 1


title: Myeloid dendritic cells, sample 2


title: Monocytes, sample 4


title: Monocytes, sample 2


title: Control vs. shDEK SK-Mel-103 Replicate 3

description: Biological replicate 3 of 3. shDEK vs. scrambled control infected melanoma cells.


title: Eosinophils WT -

source_name: Unstimulated eosinophils derived from wild type bone marrow cells

value: not stimulated


title: Mast cells WT

source_name: Unstimulated mast cells derived from wild type bone marrow cells

value: Mast cells


title: RXRα-KD

city: Beijing

first: Zhiyi

last: Jing

address: 7 Science Park Road ZGC Life Science Park

country: China

institute: NIBS

data_processing:
Basecalls performed using CASAVA.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human transcriptome using TopHat2.
Cufflinks 2.1.1 was used for transcripts assembly, abundance estimation and differential expression analysis using a known set of reference transcripts from Ensembl v.73.
Genome_build: human reference genome release GRCh37
Supplementary_files_format_and_content: FPKM

source_name: HepG2 cells

growth_protocol: HepG2-NTCP  cell  clones  were  generated  by  expressing  human  NTCP  with  a  C-terminal  tag  (C9, TETSQVAPA),  and  were  selected  with  G418  treatment  (500  μg/ml).  These  cells  were  cultured  in Dulbecco’s modification of Eagle’s medium (DMEM, Invitrogen) supplemented with 10% fetal bovine serum  (FBS,  Gibco). A custom TALEN plasmid targeting the human RXRα gene (NR2B1) was constructed. Donor DNA was generated by inserting two arms that are homologous with RXRα gene sequence into the PLKO.1 plasmid, which contains a puromycin resistance gene expression cassette. Wild-type HepG2 cells expressing NTCP (HepG2-NTCP/WT), or HepG2 cells with a disrupted RXRα gene (HepG2-NTCP/RXRα-KD) were seeded on 10-cm plates, 3h after cell attachment, the original DMEM (10% FBS) medium was replaced with PMM. Total RNAs was isolated from the cells after incubation in PMM for 24h.

extract_protocol:
Total RNA was isolated with Trizol reagent (Invitrogen) and transcribed into cDNA with random primers (PrimeScript RT kit; Takara).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HepG2-NTCP cells

value: liver

value: RXRalpha-KD


title: Basophils WT -

source_name: Unstimualted basophils derived from wild type bone marrow cells

value: Basophils


title: Eosinophils KO -

source_name: Unstimulated eosinophils derived from SLPI deficient bone marrow cells


title: Mast cells KO

source_name: Unstimulated mast cells derived from SLPI deficient bone marrow cells


title: WT

value: wild type


title: Basophils KO +

source_name: Basophils stimulated with IgE derived from SLPI deficient bone marrow cells

value: IgE stimulated


title: Basophils KO -

source_name: Unstimulated basophils derived from SLPI deficient bone marrow cells


title: Control vs. shDEK SK-Mel-103 Replicate 1

description: Biological replicate 1 of 3. shDEK vs. scrambled control infected melanoma cells.


title: Basophils WT +

source_name: Basophils stimulated with IgE derived from wild type bone marrow cells


city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

description: Wild type Mouse (4-week 20% Alcohol) Forestomach replicate 3

hyb_protocol: Cy3 or Cy5 labeled, linearly amplified cRNA samples were hybridized with Gene Expression Hybridization Kit (Agilent p/n 5188-5242) according to the user guide.

scan_protocol: Scanned on an Agilent Microarray Scanner p/n G2565BA

data_processing: Agilent Feature Extraction Software 9.1 was used for background subtraction and LOWESS normalization.

source_name: Whole Forestomach of C57BL/6J mouse at OE27C

label_protocol: 1 µg of total RNA were labled with Agilent Low RNA Input Linear Amplification Kit, PLUS, Two-Color( Agilent p/n 5188-5340) according to the provided protocol.

growth_protocol: OE27A mice were given supersaccharin without alcohol. OE27C mice were treated with 20% alcohol in supersaccharin for 4 weeks.  OE26F mice were treated with 15% alcohol for 40 weeks.

extract_protocol: Forestomach  were dissected and snap-frozen for extraction of total RNA. Total RNA was extracted from mouse forestomach tissue using RNeasy Fibrous Tissue Mini Kit (Qiagen; Valencia, CA).

tag: age

value: Adult

value: Forestomach

source_name: Agilent's Universal Mouse Reference RNA

tag: manufacturer

value: Agilent


description: Wild type Mouse (40-week 15% Alcohol) Forestomach replicate 3

source_name: Whole Forestomach of C57BL/6J mouse at OE26F


description: Wild type Mouse (4-week 20% Alcohol) Forestomach replicate 1


description: Wild type Mouse (40-week 15% Alcohol) Forestomach replicate 1


description: Wild type Mouse (4-week 20% Alcohol) Forestomach replicate 4


description: Wild type Mouse (40-week 15% Alcohol) Forestomach replicate 4


description: Wild type Mouse (Negative control) Forestomach replicate 4

source_name: Whole Forestomach of C57BL/6J mouse at OE27A


description: Wild type Mouse (4-week 20% Alcohol) Forestomach replicate 2


description: Wild type Mouse (Negative control) Forestomach replicate 3


title: SRFHKO +PE heart at D25, biological rep1

city: Châtenay-Malabry

first: Mathias

last: Mericskay

address: 5, Rue Jean-Baptiste Clément

department: Signalling and Cardiovascular Pathophysiology

country: France

institute: INSERM - University Paris-Sud

description: Gene expression data from cardiac ventricles from 10 week-old mice

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip450 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The raw data were analyzed with GeneChip Operationg Software version 1.4 (GCOS) and statistical analyses were carried out with the BioConductor suite.

source_name: cardiac ventricular tissue from 10 week-old mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

extract_protocol: Trizol extraction

treatment_protocol: Control and SRFHKO mutant mice were injected i.p. with 0.7mg of tamoxifen for 3 days. All control (SRF-flex2neo littermates) and SRFHKO mice were systematically injected with tamoxifen to normalize for any effects due to tamoxifen. For the mice treated with phenylephrine (PE), the drug was administrated at 80 mg/kg/day from day 10 to day 25 after the first day of tamoxifen injection, using Alzet osmotic minipumps

tag: Sex

value: male


title: SRFHKO +PE heart at D25, biological rep3


title: SRFHKO +PE heart at D25, biological rep2


description: Wild type Mouse (Negative control) Forestomach replicate 2


description: Wild type Mouse (40-week 15% Alcohol) Forestomach replicate 2


title: MTB infected 48h replicate 12

city: London

first: Maurice

last: Berk

address: St Mary's Campus

country: United Kingdom

institute: Imperial College London

description:
replicate 12
M-F48+

data_processing: The discovery and validation cohorts were normalised separately. In both cases, the data were quantile normalised and log2 transformed using the normaliseIllumina function in the beadarray R package. For the discovery data set, negative values were transformed prior to log2 transformation by adding the absolute largest negative value plus one to the entire data set

source_name: MTB infected 48h_whole blood_discovery

label_protocol: The Illumina TotalPrep RNA amplification kit (Applied Biosystems) was used to convert samples to biotin labelled cRNA

growth_protocol: M. tuberculosis was grown in a shaking incubator at 37 oC until mid-log phase in Middlebrook 7H9 broth (Difco, MI) medium containing 0.2% glycerol (Sigma-Aldrich), 0.05% tween 80 (Sigma-Aldrich), 10% ADC enrichment (Difco, MI). Aliquots were frozen in 15% glycerol and stored at -80 oC. The number of colony forming units (CFU)/ml was determined by serial dilution on 7H11 agar (Difco, Detroit, MI) containing 0.5% glycerol, 10% oleic acid-albumin-dextrose-catalase (Difco, MI) enrichment. Prior to infection assays, a vial of mycobacteria was defrosted and grown to mid log  9  phase. Cultures were centrifuged at 3200 rpm for 10 minutes, supernatant decanted and the cell pellet was resuspended in phosphate buffered saline (PBS) (Sigma-Aldrich) and further diluted in PBS to the required mycobacterial inoculum.

extract_protocol: RNA was extracted using the RNeasy and miRNeasy whole blood RNA extraction kit (Qiagen, Valencia CA) for mRNA and miRNA respectively according to the manufacturer’s protocol

treatment_protocol: mycobacteria were inoculated into the 2 ml aliquots of diluted whole blood samples to give a final inoculum of 1 CFU : 1 monocyte (multiplicity of infection [MOI] 1:1) assuming an average of 2 x 105 monocytes/ml of diluted whole blood. Uninfected whole blood samples served as matched controls at each time point

tag: cohort

value: discovery

tag: infected/uninfected

value: infected

tag: bacterium

value: MTB

tag: hours

value: Whole blood


title: SRFHKO heart at D25, biological rep3


title: MTB infected 96h replicate 12

description:
replicate 12
M-F96+

source_name: MTB infected 96h_whole blood_discovery

tag: tissue


title: SRFHKO heart at D25, biological rep2


title: MTB uninfected 96h replicate 12

description:
replicate 12
M-F96-

source_name: MTB uninfected 96h_whole blood_discovery

value: uninfected


title: MTB uninfected 48h replicate 12

description:
replicate 12
M-F48-

source_name: MTB uninfected 48h_whole blood_discovery


title: control heart +PE at D25, biological rep3


title: MTB uninfected 72h replicate 12

description:
replicate 12
M-F72-

source_name: MTB uninfected 72h_whole blood_discovery


description: Wild type Mouse (Negative control) Forestomach replicate 1


title: MTB infected 72h replicate 12

description:
replicate 12
M-F72+

source_name: MTB infected 72h_whole blood_discovery


title: MTB uninfected 24h replicate 12

description:
replicate 12
M-F24-

source_name: MTB uninfected 24h_whole blood_discovery


title: SRFHKO heart at D25, biological rep1


title: control heart +PE at D25, biological rep2


title: MTB uninfected 6h replicate 12

description:
replicate 12
M-F06-

source_name: MTB uninfected 6h_whole blood_discovery


title: MTB infected 6h replicate 12

description:
replicate 12
M-F06+

source_name: MTB infected 6h_whole blood_discovery


title: MTB infected 24h replicate 12

description:
replicate 12
M-F24+

source_name: MTB infected 24h_whole blood_discovery


title: MTB infected 72h replicate 10

description:
replicate 10
M-C72+


title: MTB uninfected 0h replicate 12

description:
replicate 12
M-F0

source_name: MTB uninfected 0h_whole blood_discovery


title: MTB uninfected 96h replicate 10

description:
replicate 10
M-C96-


title: control heart at D25, biological rep3


title: control heart at D25, biological rep2


title: MTB uninfected 72h replicate 10

description:
replicate 10
M-C72-


title: control heart at D25, biological rep1


title: SRFHKO heart at D8, biological rep3


title: control heart +PE at D25, biological rep1


title: MTB infected 96h replicate 10

description:
replicate 10
M-C96+


title: SRFHKO heart at D8, biological rep4


title: MTB infected 48h replicate 10

description:
replicate 10
M-C48+


title: SRFHKO heart at D8, biological rep2


title: SRFHKO heart at D8, biological rep1


title: MTB infected 24h replicate 10

description:
replicate 10
M-C24+


title: MTB uninfected 24h replicate 10

description:
replicate 10
M-C24-


title: MTB infected 6h replicate 10

description:
replicate 10
M-C06+


title: control heart at D8, biological rep2


title: control sample 16

type: genomic

city: Helsinki

first: Juha

last: Kere

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

hyb_protocol: Bisufite-treated genomic DNA was amplified, fragmented, and hybridized to the Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol.

scan_protocol: Beadchips were imaged using Illumina iScan scanner.

data_processing: The .idat files were imported in R and analyzed using the minfi package. After quality check, the data were normalized using the subset-quantile within array normalization (SWAN) method. The probes overlapping with known SNPs as well as probes prone to cross-hybridization problems were removed. The M-values were extracted and the batch effects removed using the ComBat method.

label: Cy3, Cy5

source_name: whole blood

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA from whole blood samples was extracted using standard protocols.

tag: gender

tag: genotype/variation

value: control


title: MTB uninfected 48h replicate 10

description:
replicate 10
M-C48-


title: control sample 15


title: control sample 14


title: MTB uninfected 0h replicate 10

description:
replicate 10
M-C0


title: MTB infected 96h replicate 9

description:
replicate 9
M-B96+


title: MTB uninfected 6h replicate 10

description:
replicate 10
M-C06-


title: control sample 13


title: control sample 7


title: MTB infected 72h replicate 9

description:
replicate 9
M-B72+


title: control sample 12


title: control heart at D8, biological rep1


title: control sample 9


title: MTB infected 6h replicate 9

description:
replicate 9
M-B6+


title: control sample 8


title: MTB infected 48h replicate 9

description:
replicate 9
M-B48+


title: control sample 10


title: MTB uninfected 48h replicate 9

description:
replicate 9
M-B48-


title: control sample 6


title: MTB uninfected 72h replicate 9

description:
replicate 9
M-B72-


title: control sample 5

value: female


title: MTB uninfected 96h replicate 9

description:
replicate 9
M-B96-


title: control sample 3


title: control sample 4


title: control sample 2


title: MTB uninfected 6h replicate 9

description:
replicate 9
M-B06-


title: MTB uninfected 24h replicate 9

description:
replicate 9
M-B24-


title: control sample 11


title: SRS patient 42, 11p15 LOM

value: 11p15 LOM


title: MTB uninfected 0h replicate 9

description:
replicate 9
M-B0


title: control sample 1


title: SRS patient 44, UPD(7)mat


title: MTB infected 72h replicate 8

description:
replicate 8
M-A72+


title: MTB infected 24h replicate 9

description:
replicate 9
M-B24+


title: MTB uninfected 96h replicate 8

description:
replicate 8
M-A96-


title: SRS patient 40, UPD(7)mat


title: SRS patient 37, 11p15 LOM


title: SRS patient 41, UPD(7)mat


title: MTB infected 48h replicate 8

description:
replicate 8
M-A48+


title: SRS patient 38, 11p15 LOM


title: MTB uninfected 72h replicate 8

description:
replicate 8
M-A72-


title: SRS patient 34, clinical SRS

value: clinical SRS


title: MTB uninfected 48h replicate 8

description:
replicate 8
M-A48-


title: SRS patient 39, clinical SRS


title: MTB uninfected 6h replicate 8

description:
replicate 8
M-A06-


title: MTB infected 6h replicate 8

description:
replicate 8
M-A06+


title: SRS patient 43, 11p15 LOM


title: SRS patient 36, clinical SRS


title: MTB infected 24h replicate 8

description:
replicate 8
M-A24+


title: SRS patient 33, clinical SRS


title: MTB uninfected 24h replicate 8

description:
replicate 8
M-A24-


title: SRS patient 32, 11p15 LOM


title: UPD(7)pat


title: BCG infected 96h replicate 11

description:
replicate 11
B-E96+

source_name: BCG infected 96h_whole blood_discovery

value: BCG


title: MTB uninfected 0h replicate 8

description:
replicate 8
M-A0


title: BCG uninfected 96h replicate 11

description:
replicate 11
B-E96-

source_name: BCG uninfected 96h_whole blood_discovery


title: SRS patient 27, clinical SRS


title: BCG infected 48h replicate 11

description:
replicate 11
B-E48+

source_name: BCG infected 48h_whole blood_discovery


title: SRS patient 31, 11p15 LOM


title: SRS patient 26, UPD(7)mat


title: SRS patient 29, clinical SRS


title: BCG infected 24h replicate 11

description:
replicate 11
B-E24+

source_name: BCG infected 24h_whole blood_discovery


title: SRS patient 28, UPD(7)mat


title: SRS patient 30, clinical SRS


title: SRS patient 24, clinical SRS


title: BCG uninfected 24h replicate 11

description:
replicate 11
B-E24-

source_name: BCG uninfected 24h_whole blood_discovery


title: SRS patient 35, UPD(7)mat


title: SRS patient 23, 11p15 LOM


title: BCG uninfected 6h replicate 11

description:
replicate 11
B-E06-

source_name: BCG uninfected 6h_whole blood_discovery


title: BCG infected 6h replicate 11

description:
replicate 11
B-E06+

source_name: BCG infected 6h_whole blood_discovery


title: SRS patient 18, clinical SRS


title: non-Tg, biological rep3

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were imported into the Affymetrix Expression Console™ Software and CHP files were generated. RMA aoglrithm.

source_name: Cortex of non-Tg mouse

label_protocol: GeneChip® WT PLUS Reagent Kit (Affymetrix, Japan) were used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

growth_protocol: Each mouse was maintained in Specific-pathogen-free (SPF) condition and sacrificed at 12 months of age.

extract_protocol: Total RNA was isolated using Isogen (Nippon Gene) according to the manufacturers’ instructions.

treatment_protocol: Brains were removed from each mouse under pentobarbital anesthesia (i.p), after perfusion of 40 ml of saline via the left ventricle. Cortices were isolated and preserved at –80°C until RNA preparation.

value: Cortex

value: non-Tg

value: 12 months of age


title: SRS patient 25, 11p15 LOM


title: BCG infected 12h replicate 11

description:
replicate 11
B-E12+

source_name: BCG infected 12h_whole blood_discovery


title: BCG infected 72h replicate 11

description:
replicate 11
B-E72+

source_name: BCG infected 72h_whole blood_discovery


title: SRS patient 21, 11p15 LOM


title: MTB infected 96h replicate 8

description:
replicate 8
M-A96+

source_name: MTB infected 96h_whole blood_discovery


title: BCG uninfected 48h replicate 11

description:
replicate 11
B-E48-

source_name: BCG uninfected 48h_whole blood_discovery


title: non-Tg, biological rep2


title: BCG infected 96h replicate 10

description:
replicate 10
B-C96+


title: BCG uninfected 12h replicate 11

description:
replicate 11
B-E12-

source_name: BCG uninfected 12h_whole blood_discovery


title: BCG uninfected 0h replicate 11

description:
replicate 11
B-E0

source_name: BCG uninfected 0h_whole blood_discovery


title: SRS patient 19, 11p15 LOM


title: BCG uninfected 96h replicate 10

description:
replicate 10
B-C96-


title: SRS patient 17, 11p15 LOM


title: SRS patient 20, UPD(7)mat


title: 3xTg-AD-H, biological rep3

source_name: Cortex of 3xTg-AD-H mouse

value: 3xTg-AD-H Homo


title: BCG uninfected 72h replicate 11

description:
replicate 11
B-E72-

source_name: BCG uninfected 72h_whole blood_discovery


title: 3xTg-AD-H, biological rep2


title: SRS patient 12, 11p15 LOM

source_name: whole blood


title: BCG infected 72h replicate 10

description:
replicate 10
B-C72+


title: BCG uninfected 72h replicate 10

description:
replicate 10
B-C72-


title: 3xTg-AD-H, biological rep1


title: SRS patient 22, UPD(7)mat


title: BCG infected 48h replicate 10

description:
replicate 10
B-C48+


title: SRS patient 16, clinical SRS


title: non-Tg, biological rep1


title: BCG uninfected 48h replicate 10

description:
replicate 10
B-C48-


title: SRS patient 13, 11p15 LOM


title: SRS patient 15, 11p15 LOM


title: APPWT, biological rep1

source_name: Cortex of App+/+ mouse

value: App+/+


title: SRS patient 11, clinical SRS


title: BCG infected 24h replicate 10

description:
replicate 10
B-C24+


title: APPWT, biological rep3


title: APPNL-G-F, biological rep3

source_name: Cortex of AppNL-G-F/NL-G-F mouse

value: AppNL-G-F/NL-G-F Homo


title: APPNL-G-F, biological rep1

value: male


title: SRS patient 8, UPD(7)mat


title: APPNL-G-F, biological rep2


title: BCG uninfected 24h replicate 10

description:
replicate 10
B-C24-

value: discovery


title: APPWT, biological rep2


title: SRS patient 14, 11p15 LOM


title: BCG infected 6h replicate 10

description:
replicate 10
B-C06+

value: infected


title: BCG uninfected 12h replicate 10

description:
replicate 10
B-C12-


title: BCG infected 12h replicate 10

description:
replicate 10
B-C12+


title: SRS patient 5, 11p15 LOM


title: SRS patient 9, 11p15 LOM


title: SRS patient 7, clinical SRS


title: SRS patient 10, UPD(7)mat


title: SRS patient 6, clinical SRS


title: BCG uninfected 48h replicate 9

description:
replicate 9
B-B48-


title: BCG infected 96h replicate 9

description:
replicate 9
B-B96+

source_name: BCG infected 96h_whole blood_discovery


title: BCG uninfected 96h replicate 9

description:
replicate 9
B-B96-

source_name: BCG uninfected 96h_whole blood_discovery


title: BCG uninfected 6h replicate 10

description:
replicate 10
B-C06-


title: SRS patient 3, 11p15 LOM


title: BCG infected 72h replicate 9

description:
replicate 9
B-B72+


title: SRS patient 2, 11p15 LOM


title: BCG uninfected 0h replicate 10

description:
replicate 10
B-C0


title: BCG infected 48h replicate 9

description:
replicate 9
B-B48+

source_name: BCG infected 48h_whole blood_discovery


title: genomic DNA from Control 9

city: Taipei

first: Tzu-Pin

last: Lu

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Public Health, Institute of Epidemiology and Preventive Medicine

country: Taiwan

institute: National Taiwan University, Taiwan

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan Reader based on the recommended Illumina scanner setting (iScan Control Software v.3.3.28)

data_processing: GenomeStudio V2011.1

label: Cy3 and Cy5

source_name: Control 9

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: disease state

value: healthy control

value: peripheral blood

value: M

tag: creatnine

tag: smoking

tag: hyperlipidemia

tag: hypertension

tag: dm


title: SRS patient 1, 11p15 LOM


title: genomic DNA from Control 10

source_name: Control 10


title: SRS patient 4, clinical SRS


title: BCG infected 24h replicate 9

description:
replicate 9
B-B24+

source_name: BCG infected 24h_whole blood_discovery

value: Whole blood


title: BCG infected 12h replicate 9

description:
replicate 9
B-B12+

source_name: BCG infected 12h_whole blood_discovery


title: BCG uninfected 24h replicate 9

description:
replicate 9
B-B24-

source_name: BCG uninfected 24h_whole blood_discovery

value: uninfected


title: genomic DNA from Control 11

source_name: Control 11

value: F


title: BCG infected 6h replicate 9

description:
replicate 9
B-B06+

source_name: BCG infected 6h_whole blood_discovery


title: BCG uninfected 6h replicate 9

description:
replicate 9
B-B06-

source_name: BCG uninfected 6h_whole blood_discovery


title: BCG uninfected 12h replicate 9

description:
replicate 9
B-B12-

source_name: BCG uninfected 12h_whole blood_discovery


title: genomic DNA from Control 12

source_name: Control 12


title: genomic DNA from Control 8

source_name: Control 8


title: BCG uninfected 0h replicate 9

description:
replicate 9
B-B0

source_name: BCG uninfected 0h_whole blood_discovery


title: BCG infected 96h replicate 8

description:
replicate 8
B-A96+


title: genomic DNA from Control 3

source_name: Control 3


title: genomic DNA from Control 6

source_name: Control 6


title: genomic DNA from Control 4

source_name: Control 4


title: BCG infected 72h replicate 8

description:
replicate 8
B-A72+

source_name: BCG infected 72h_whole blood_discovery


title: genomic DNA from Control 5

source_name: Control 5


title: genomic DNA from Control 1

source_name: Control 1


title: genomic DNA from CAE patient 8

source_name: CAE patient 8

value: coronary artery ectasia (CAE)


title: genomic DNA from Control 2

source_name: Control 2


title: BCG uninfected 96h replicate 8

description:
replicate 8
B-A96-

source_name: BCG uninfected 96h_whole blood_discovery

value: BCG


title: BCG uninfected 12h replicate 8

description:
replicate 8
B-A12-


title: BCG infected 24h replicate 8

description:
replicate 8
B-A24+

source_name: BCG infected 24h_whole blood_discovery


title: BCG infected 48h replicate 8

description:
replicate 8
B-A48+

source_name: BCG infected 48h_whole blood_discovery


title: BCG uninfected 72h replicate 8

description:
replicate 8
B-A72-

source_name: BCG uninfected 72h_whole blood_discovery


title: genomic DNA from CAE patient 7

source_name: CAE patient 7


title: genomic DNA from CAE patient 10

source_name: CAE patient 10


title: BCG uninfected 72h replicate 9

description:
replicate 9
B-B72-


title: BCG uninfected 48h replicate 8

description:
replicate 8
B-A48-

source_name: BCG uninfected 48h_whole blood_discovery


title: genomic DNA from CAE patient 11

source_name: CAE patient 11


title: BCG uninfected 0h replicate 8

description:
replicate 8
B-A0

source_name: BCG uninfected 0h_whole blood_discovery


title: BCG infected 6h replicate 8

description:
replicate 8
B-A06+

source_name: BCG infected 6h_whole blood_discovery


title: BCG infected 12h replicate 8

description:
replicate 8
B-A12+

source_name: BCG infected 12h_whole blood_discovery


title: BCG uninfected 6h replicate 8

description:
replicate 8
B-A06-

source_name: BCG uninfected 6h_whole blood_discovery


title: genomic DNA from CAE patient 9

source_name: CAE patient 9


title: genomic DNA from CAE patient 6

source_name: CAE patient 6


title: BCG uninfected 24h replicate 8

description:
replicate 8
B-A24-

source_name: BCG uninfected 24h_whole blood_discovery


title: genomic DNA from CAE patient 5

source_name: CAE patient 5


title: genomic DNA from CAE patient 2

source_name: CAE patient 2


title: genomic DNA from CAE patient 4

source_name: CAE patient 4


title: genomic DNA from CAE patient 1

source_name: CAE patient 1


title: genomic DNA from Control 7

source_name: Control 7


title: MTB infected 96h replicate 5

description:
replicate 5
MR+_96

source_name: MTB infected 96h_whole blood_validation

value: validation

value: MTB


title: MTB infected 96h replicate 6

description:
replicate 6
PL+_96


title: MTB infected 96h replicate 1

description:
replicate 1
DB+_96


title: MTB infected 96h replicate 4

description:
replicate 4
ME+_96


title: genomic DNA from CAE patient 3

source_name: CAE patient 3


title: MTB infected 72h replicate 7

description:
replicate 7
SP+_72

source_name: MTB infected 72h_whole blood_validation


title: MTB infected 96h replicate 2

description:
replicate 2
DMS+_96


title: MTB infected 72h replicate 6

description:
replicate 6
PL+_72


title: MTB infected 96h replicate 7

description:
replicate 7
SP+_96


title: MTB infected 72h replicate 1

description:
replicate 1
DB+_72


title: MTB infected 24h replicate 5

description:
replicate 5
MR+_24

source_name: MTB infected 24h_whole blood_validation


title: MTB infected 24h replicate 1

description:
replicate 1
DB+_24


title: MTB infected 72h replicate 5

description:
replicate 5
MR+_72


title: MTB infected 24h replicate 6

description:
replicate 6
PL+_24


title: MTB infected 24h replicate 2

description:
replicate 2
DMS+_24


title: MTB infected 48h replicate 5

description:
replicate 5
MR+_48

source_name: MTB infected 48h_whole blood_validation


title: MTB infected 48h replicate 4

description:
replicate 4
ME+_48


title: MTB infected 48h replicate 6

description:
replicate 6
PL+_48


title: MTB infected 72h replicate 2

description:
replicate 2
DMS+_72


title: MTB infected 72h replicate 4

description:
replicate 4
ME+_72


title: MTB infected 48h replicate 1

description:
replicate 1
DB+_48


title: MTB uninfected 96h replicate 1

description:
replicate 1
DB-_96

source_name: MTB uninfected 96h_whole blood_validation


title: MTB infected 24h replicate 7

description:
replicate 7
SP+_24


title: MTB infected 24h replicate 4

description:
replicate 4
ME+_24


title: MTB infected 48h replicate 2

description:
replicate 2
DMS+_48


title: MTB uninfected 96h replicate 5

description:
replicate 5
MR-_96


title: MTB uninfected 96h replicate 4

description:
replicate 4
ME-_96


title: MTB uninfected 72h replicate 2

description:
replicate 2
DMS-_72

source_name: MTB uninfected 72h_whole blood_validation


title: MTB uninfected 48h replicate 5

description:
replicate 5
MR-_48

source_name: MTB uninfected 48h_whole blood_validation


title: MTB uninfected 72h replicate 1

description:
replicate 1
DB-_72


title: MTB uninfected 72h replicate 4

description:
replicate 4
ME-_72


title: MTB uninfected 72h replicate 7

description:
replicate 7
SP-_72


title: MTB uninfected 96h replicate 6

description:
replicate 6
PL-_96


title: MTB uninfected 48h replicate 4

description:
replicate 4
ME-_48


title: MTB uninfected 48h replicate 2

description:
replicate 2
DMS-_48


title: MTB uninfected 96h replicate 2

description:
replicate 2
DMS-_96


title: MTB uninfected 48h replicate 6

description:
replicate 6
PL-_48


title: MTB uninfected 72h replicate 5

description:
replicate 5
MR-_72


title: MTB uninfected 72h replicate 6

description:
replicate 6
PL-_72


title: MTB uninfected 48h replicate 1

description:
replicate 1
DB-_48


title: SKMEL103 shCUGBP1 rep2

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description: SK-Mel-103 shCUGBP1 infection replicate 2

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were normalized using Expression Console from Affymetrix (RMA analyses). Probeset-level RMA values are available in the sample tables. Gene-level RMA values are available on the series record.
probe group file: HJAY_r2.pgf
meta-probeset file: HJAY_r2.full.mps

source_name: shRNA mediated CUGBP1 depleted SK-Mel-103

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: SK-mel-103 and UACC-62 human melanoma cell lines were grown in DMEM medium supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin (Gibco), and maintained at 37°C in humidified 5% CO2 atmosphere.

treatment_protocol: Cells were plated at 70% confluence and infected with lentivirus either scramble control or shCUGBP1-1. Cell were selected at day 2 after infection with puromycin (1ug/ml). Two days after, day 4 of infection, pellets were collected.

tag: cell line

tag: cell type

value: melanoma

tag: time point

value: Day 4 after infection

tag: knockdown target


title: SKMEL103 shCUGBP1 rep3

description: SK-Mel-103 shCUGBP1 infection replicate 3


title: SKMEL103 shcont rep3

description: SK-Mel-103 control infection replicate 3

source_name: control infected SK-Mel-103 cell line

value: control


title: MTB infected 48h replicate 7

description:
replicate 7
SP+_48

tag: cohort


title: MTB uninfected 24h replicate 2

description:
replicate 2
DMS-_24

source_name: MTB uninfected 24h_whole blood_validation

tag: infected/uninfected


title: MTB uninfected 24h replicate 5

description:
replicate 5
MR-_24

tag: bacterium


title: MTB uninfected 48h replicate 7

description:
replicate 7
SP-_48

tag: hours


title: MTB uninfected 24h replicate 4

description:
replicate 4
ME-_24

tag: tissue


title: UACC 62 shCUGBP1 rep3

description: UACC-62 shCUGBP1 infection replicate 3

source_name: shRNA mediated CUGBP1 depleted UACC-62


title: MTB uninfected 24h replicate 1

description:
replicate 1
DB-_24


title: UACC 62 shcont rep2

description: UACC-62 control infection replicate 2

source_name: control infected UACC-62 cell line


title: SKMEL103 shcont rep2

description: SK-Mel-103 control infection replicate 2


title: MTB uninfected 0h replicate 1

description:
replicate 1
DB_0

source_name: MTB uninfected 0h_whole blood_validation


title: MTB uninfected 0h replicate 4

description:
replicate 4
ME_0


title: MTB uninfected 24h replicate 7

description:
replicate 7
SP-_24


title: MTB uninfected 0h replicate 6

description:
replicate 6
PL_0


title: SKMEL103 shCUGBP1 rep1

description: SK-Mel-103 shCUGBP1 infection replicate 1


title: UACC 62 shCUGBP1 rep2

description: UACC-62 shCUGBP1 infection replicate 2


title: UACC 62 shCUGBP1 rep1

description: UACC-62 shCUGBP1 infection replicate 1


title: MTB uninfected 24h replicate 6

description:
replicate 6
PL-_24


title: UACC 62 shcont rep1

description: UACC-62 control infection replicate 1


title: SKMEL103 shcont rep1

description: SK-Mel-103 control infection replicate 1


title: UACC 62 shcont rep3

description: UACC-62 control infection replicate 3


title: MTB uninfected 0h replicate 2

description:
replicate 2
DMS_0


title: MTB uninfected 0h replicate 7

description:
replicate 7
SP_0


title: BCG infected 96h replicate 4

description:
replicate 4
BCG_ME+_96

source_name: BCG infected 96h_whole blood_validation


title: BCG infected 72h replicate 1

description:
replicate 1
BCG_DB+_72

source_name: BCG infected 72h_whole blood_validation


title: BCG infected 96h replicate 6

description:
replicate 6
BCG_PL+_96


title: BCG infected 72h replicate 3

description:
replicate 3
BCG_K+_72


title: BCG infected 48h replicate 7

description:
replicate 7
BCG_SP+_48

source_name: BCG infected 48h_whole blood_validation


title: Sara_5

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

data_processing:
Bcl files were converted into fastq by bcl2fastq v2.17.1.14. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).
Adapters and low quality bases were removed from the raw reads using cutadapt version 1.8.3 (parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{100}" -a "T{100}" --times 2 --cut 3 -q 20  -m 30 )
The remaining reads (raw data submitted)  were mapped to the Mus musculus genome (mm10) using tophat2.
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from igenomes UCSC), which was modified to contain a window surrounding the 3' UTR. Duplicate reads were marked and filtered based on having the same UMI and mapping to the same gene, using a python script.
Genes were filtered out if thier sum counts after UMI filter <=10 or  maximum value <= 5. In addition three genes: Ddx3y, Eif2s3y, Xist were removed from further analysis.  Normalization and differential expression analysis was performed using the DESeq2 R-package (Bioconductor, https://bioconductor.org/packages/release/bioc/html/DESeq2.html). Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Genome_build: mm10
Supplementary_files_format_and_content: Report_UMI_filtered.xlsx contains UMI counts  for 10,412 genes10,415 genes remained after filtering based on expression levels (sum normalized count in all samples greater than 10, and maximum expression level higher than 5), normalized counts and log2 normalized counts (rld) done by DESeq2. In addition contains results of DESeq2 contrasts run with a model containing two factors: activation status (i.e. CD40 mAb activated or resting) and bone marrow genotype (WT or ICAM-1/2-DKO).  In addition, three genes which were sex linked were removed (Ddx3y, Eif2s3y, Xist), to eliminate the male/female bias of the bone marrow used for the WT vs DKO bone marrow transplantation.

source_name: activated DCs from WT/WT chimeric mice

growth_protocol: 104 cells were sorted in 40 ul of Lysis/Binding Buffer (Life technologies), lysed for 5 min and frozen at -80C.

extract_protocol:
Cell lysates were thawed and messanger RNA was captured with 15ul of Dynabeads oligo(dT) (Life technologies), and washed according to manufacture guidelines.
Purified messanger RNA was eluted at 70C with 6ul of 10mM Tris-Cl pH 7.5 and stored at -80C.For library preparation RNA was used for the bulk MARS-seq  protocol (Jaitin et al. 2014 Science.343:776-9). MARS-seq libraries were sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).

treatment_protocol: None (resting) or intra-footpad injection of aCD40 mAb (10 µg, activated)

tag: strain

value: Popliteal lymph nodes

tag: age

value: 16-weeks (8 wks post BMT)

tag: treatment

value: activ (CD40 mAb)

tag: genotype

value: wild-type

value: activated dendritic cells (DCs)


title: Sara_7

source_name: activated  DCs from  ICAM-1/2 DKO/WT chimeric mice

value: ICAM-1/2 DKO


title: Sara_4

source_name: resting classical DCs from ICAM-1/2 DKO/WT chimeric mice

value: rest

value: resting classical dendritic cells (DCs)


title: Sara_8


title: BCG infected 72h replicate 7

description:
replicate 7
BCG_SP+_72

value: infected

value: Whole blood


title: Sara_2

source_name: resting classical DCs from  WT/WT chimeric mice


title: Sara_6


title: BCG infected 24h replicate 3

description:
replicate 3
BCG_K+_24

source_name: BCG infected 24h_whole blood_validation


title: BCG infected 72h replicate 4

description:
replicate 4
BCG_ME+_72


title: Sara_3


title: BCG infected 48h replicate 1

description:
replicate 1
BCG_DB+_48


title: BCG infected 48h replicate 3

description:
replicate 3
BCG_K+_48


title: BCG uninfected 96h replicate 1

description:
replicate 1
BCG_DB-_96

source_name: BCG uninfected 96h_whole blood_validation

value: uninfected


title: BCG infected 48h replicate 6

description:
replicate 6
BCG_PL+_48

value: BCG


title: BCG infected 24h replicate 7

description:
replicate 7
BCG_SP+_24

value: validation


title: BCG infected 24h replicate 1

description:
replicate 1
BCG_DB+_24


title: BCG infected 24h replicate 6

description:
replicate 6
BCG_PL+_24


title: BCG uninfected 96h replicate 3

description:
replicate 3
BCG_K-_96


title: BCG infected 24h replicate 4

description:
replicate 4
BCG_ME+_24


title: Sara_1


title: BCG uninfected 96h replicate 7

description:
replicate 7
BCG_SP-_96


title: BCG uninfected 96h replicate 6

description:
replicate 6
BCG_PL-_96


title: Pool 09

city: University Park

first: John

middle: Everett

last: Parkinson

state: PA

address: 208 Mueller Lab

department: Biology

institute: Penn State University

description:
P09: hW1 (hot; Winter1; Miami Nursery)
final_all_counts.txt
final_host_counts.txt
final_sym_counts.txt

data_processing:
Adapters and low quality nucleotides (<20 Phred score in ASCII 33 format) were removed from raw reads with Trimmomatic v0.3 (Bolger et al. 2014). Note that adapter sequences are included in the name of each library file.
Reads were mapped to the Acropora cervicornis holobiont transcriptome of Libro et al. (2013) with Bowtie2 v2.1.0 (Langmead and Salzberg 2012)
Reads were quantified with eXpress v1.5.1 (Roberts and Pachter 2013) to arrive at effective counts per transcript—the basis for differential expression analysis.
The A. cervicornis holobiont transcriptome includes genes from the coral host, algal symbiont, and potentially other contaminants. To determine the partner origin of each transcript, all reads were mapped against the A. digitifera genome (Shinzato et al. 2011) and the Symbiodinium minutum (ITS2 type B11) genome (Shoguchi et al. 2013) to generate exomes of known origin. Because these species are distantly related to A. cervicornis and S. ‘fitti’ (ITS2 type A3Caribbean), reads were also mapped against the more closely related A. palmata draft genome (Baums et al. unpublished data) and S. microadriaticum (ITS2 type A1) transcriptome (Bayer et al. 2012). The A. cervicornis transcripts were then BLASTed against these exomes, and an e-value cutoff value of e-10 was used to assign a host or symbiont origin to transcripts with high similarity. The host gene set (n = 22,772; matching to A. digitifera and/or A. palmata) was analyzed separately from the symbiont gene set (n = 21,094; matching to S. minutum and/or S. microadriaticum). Transcripts with unassigned or ambiguous origin (n = 21,669; matching no references genomes or at least one host and one symbiont genome simultaneously) were excluded from further analysis.
Genome_build: We used the Acropora cervicornis holobiont transcriptome of Libro et al. (2013), found in Bioproject PRJNA222758.
Supplementary_files_format_and_content: final_all_counts.txt, final_host_counts.txt, and final_sym_counts.txt are all matrix tables containing processed data for all samples (all=every transcript; host=host-only transcripts; sym=symbiont-only transcripts)

organism: Acropora cervicornis

source_name: Coral holobiont tissue (host, symbiont, etc.)

growth_protocol: Three in-water coral propagation nurseries in Florida were targeted for this experiment: the University of Miami nursery in Miami (referred to as the Miami nursery; 25°28'24.24"N, 80°07'42.24"W), the Coral Restoration Foundation nursery in Tavernier (Upper Keys nursery; 24°58'55.84"N, 80°26'10.69"W), and the MOTE Marine Lab / Nature Conservancy nursery in Summerland Key (Lower Keys nursery; 24°33'45.68"N, 81°24'00.54"W) (Fig. 1a). These three locations fall within the biogeographic range of one intermixing A. cervicornis population near the northernmost boundary of the species (Baums et al. 2010; Drury et al. 2016). All colonies had been growing in their respective common garden nurseries for at least one year prior to experimentation, minimizing environmental variation. At the Miami nursery, the annual linear tissue extension rates, annual mortality rates among replicate colonies, and relative bleaching sensitivities for each genotype were monitored throughout the experimental period. As part of the initial collection when the nurseries were established, donor colonies were genotyped at four host-specific microsatellite loci (Baums et al. 2005) to establish each colony’s genet identity. Subsequently, the dominant Symbiodinium ‘fitti’ strain in each colony was genotyped at 13 symbiont-specific loci (Pinzon et al. 2011; Baums et al. 2014). Host genets with anecdotally variable growth rates, mortality rates, and bleaching susceptibilities were chosen from each nursery (Miami: n = 10; Upper Keys: n = 11; Lower Keys: n = 10). Each collection included seven unique S. ‘fitti’ strains. No host genets or symbiont strains were shared across nurseries. To examine intraindividual variation, three physically distinct colonies of one genet at each nursery were sampled (three ramets of the same genet), so a total of 37 colonies were included in the study. To examine the effect of genotypic variation in the dominant symbiont, collections at each nursery included at least three genetically distinct colonies each associating with the same S. ‘fitti’ strain (‘monotypic’ group), as well as three colonies each associating with unique S. ‘fitti’ strains (‘diverse’ group’).

extract_protocol:
Total RNA was extracted with TriReagent (Thermo Fisher Scientific, Waltham, MA) then isolated and cleaned with the RNeasy Kit (Qiagen, Venlo, The Netherlands) according to the manufacturer's protocols. RNA quality for each sample was assessed using a Bioanalyzer 2000 (Agilent, Santa Clara, CA). Samples were pooled in equimolar concentrations based on total RNA amount prior to library preparation.
Following the manufacturer’s protocol, 150 bp single reads were generated from oligo(dT)-selected total RNA using the Illumina TruSeq Stranded mRNA HT Kit. mRNA sequencing libraries were individually barcoded, multiplexed in equal quantities, and run on three lanes of the Illumina HiSeq 2000 platform.  The data were demultiplexed into 12 individual library files. Note that each library file name includes its tag sequence.

treatment_protocol: A single branch (~9 cm) from each colony at each nursery was clipped underwater via SCUBA. Corals were sampled within two hours of solar noon and the growing tips were removed to minimize effects of diel cycle and branch position on gene expression (Hemond and Vollmer 2015). The remaining branch was divided into three equal fragments. Fragments were exposed to one of three treatments: extreme hot (35 ºC), extreme cold (10 ºC), and ambient (season-dependent: 24-28 ºC). Treatments were conducted shipboard immediately after collection. Temperatures were maintained in insulated water buckets using temperature regulators connected to aquarium heaters and/or ice as needed. This set-up was designed to be relatively inexpensive and simple for restoration workers to repeat, and based on an instant-read thermometer maintained target temperatures for the one hour treatment duration. After the temperature exposure, fragments were preserved in RNALater. The experiment was repeated four times over a 12-month period: June 2011 (Summer 1), September 2011 (Summer 2), February 2012 (Winter 1), and May 2012 (Winter 2; Fig. 1b). The Summer collections were scheduled to capture gene expression before and after the Summer thermal maximum. Due to logistical issues, it was impossible to sample around the Winter thermal minimum in the same way. Instead, the Winter collections began immediately after the Winter thermal minimum and spanned the same time interval as the Summer collections. From 2010-2011, a total of 444 Acropora cervicornis experimental fragments were collected from the Florida coral nurseries (37 colonies x 3 temperature treatments x 4 seasons). First, an RNAseq experiment was carried out on a subset of samples to identify important stress response genes that could later be assayed in all samples using HTqPCR. The subset included seven genets each from two of the three nurseries (Miami and Lower Keys), two of the four seasonal collections (Summer 1 and Winter 1), and all three temperature treatments (ambient, hot, and cold), resulting in 12 libraries. For each library, RNA from seven of the 10+ genotypes at each nursery were pooled (84 samples total; the design is provided in the Penn State ScholarSphere database). Due to the random distribution of missing data, seven genets was the maximum set that could be included while ensuring completely equal representation in each library.

tag: temperature

value: hot

tag: season

value: winter

tag: nursery

value: Miami


title: BCG uninfected 72h replicate 6

description:
replicate 6
BCG_PL-_72

source_name: BCG uninfected 72h_whole blood_validation


title: Pool 12

description:
P12: hW2 (hot; Winter1; Lower Keys Nursery)
final_all_counts.txt
final_host_counts.txt
final_sym_counts.txt

value: Lower Keys


title: Pool 10

description:
P10: aW1 (ambient; Winter1; Lower Keys Nursery)
final_all_counts.txt
final_host_counts.txt
final_sym_counts.txt

value: ambient


title: BCG uninfected 96h replicate 4

description:
replicate 4
BCG_ME-_96


title: BCG uninfected 72h replicate 4

description:
replicate 4
BCG_ME-_72


title: BCG uninfected 72h replicate 1

description:
replicate 1
BCG_DB-_72


title: BCG uninfected 72h replicate 7

description:
replicate 7
BCG_SP-_72


title: BCG uninfected 72h replicate 3

description:
replicate 3
BCG_K-_72


title: BCG uninfected 0h replicate 1

description:
replicate 1
BCG_DB_0

source_name: BCG uninfected 0h_whole blood_validation


title: BCG uninfected 48h replicate 7

description:
replicate 7
BCG_SP-_48

source_name: BCG uninfected 48h_whole blood_validation


title: BCG uninfected 24h replicate 6

description:
replicate 6
BCG_PL-_24

source_name: BCG uninfected 24h_whole blood_validation


title: BCG uninfected 24h replicate 4

description:
replicate 4
BCG_ME-_24


title: BCG uninfected 0h replicate 4

description:
replicate 4
BCG_ME_0


title: BCG uninfected 24h replicate 7

description:
replicate 7
BCG_SP-_24


title: BCG uninfected 48h replicate 3

description:
replicate 3
BCG_K-_48


title: BCG uninfected 0h replicate 7

description:
replicate 7
BCG_SP_0


title: BCG uninfected 24h replicate 1

description:
replicate 1
BCG_DB-_24


title: Pool 11

description:
P11: cW2 (cold; Winter1; Miami Nursery)
final_all_counts.txt
final_host_counts.txt
final_sym_counts.txt

value: cold


title: BCG uninfected 48h replicate 1

description:
replicate 1
BCG_DB-_48


title: Pool 07

description:
P07: aW1 (ambient; Winter1; Miami Nursery)
final_all_counts.txt
final_host_counts.txt
final_sym_counts.txt


title: Pool 08

description:
P08: cW1 (cold; Winter1; Lower Keys Nursery)
final_all_counts.txt
final_host_counts.txt
final_sym_counts.txt


title: mated females_DR 7 days_rep 3

city: Kiel

first: Christine

last: Fink

address: Am Botanischen Garten 1-9

department: Zoological Institute

institute: Kiel University

hyb_protocol: 200 pmol of the labelled samples (corresponding to approx. 2-3 µg cRNA) in hybridisation buffer containing salmon testes DNA and yeast tRNA were hybridized to the array at 42°C overnight. After hybridization, slides were washed twice with1 × SSC at RT for 1 h; 1 × SSC, 0.1% Triton-X- 100 at 60°C for 30 minutes and with 0.1 × SSC, 0.1% Tri- ton-X-100 at 37°C for 30 min. Subsequently, they were washed with 0.1 × SSC for 30 seconds at RT and rinsed with water before dried.

scan_protocol: The slides were scanned with the GenePixTM 4000B scanner (Axon Instruments, Molecular Devices, Munich, Germany). For spot finding and generating preliminary result files, the raw scanned image files were analyzed using GenePixPro version 6.0 (Axon Instruments), whereas data normalization and further data filtering were performed with Acuity 4.1 (Axon Instruments).

data_processing: Ratio-based normalization using default settings in Acuity. Criteria for inclusion of data in further analysis: Signal-to noise-ratio for at least one of the wavelengths > 3; -10 > log2 ratio ch2/ch1> 10; features is not flagged bad or absent in previous GenePix analysis.

label: Alexa Fluor 555

organism: Drosophila melanogaster

source_name: fat body, animals on control medium

label_protocol: In brief, cDNA synthesis from RNA isolated from fat bodies was performed with Prime Script RT (Takara) using the following primers: OdT T7 I (5’-GAG AGA GGA TCC AAG TAC TAA TAC GAC TCA CTA TAG GGA GAT TTT TTT TTT TTT TTT TTT TTT T G/A/C-3’) and CapFinder Sp6rG (5’-CAG CGG CCG CAG ATT TAG GTG ACA CTA TAG A rGrGrG-3’). cDNA was amplified with OdT T7 II (5’-GAG AGA GGA TCC AAG TAC TAA TAC GAC TCA CTA TAG G-3’) and Adaptor Sp6rG (5’-GAC GCC TGC AGG CGA TGA ATT TAG G-3’) and LA Taq polymerase. cDNA was transcribed with MEGAscript® T7 (Ambion) including aminoallyl-UTP (Ambion) and subsequently labeled with Alexa Fluor 555 or 647 (Invitrogen) for control or experimental sample, respectively.

growth_protocol: Fly stocks were raised on standard cornmeal-agar medium at 25 °C under a 12 h/12 h light/dark cycle.

extract_protocol: Isolation of total RNA with Trizol (RNAmagic, Biobudget).

treatment_protocol: Flies were kept on the dietary medium for 1, 3 or 7 days.

tag: gender

value: female

value: fat body

tag: age at start of treatment

label: Alexa Fluor 647

source_name: fat body, animal on dietary restriction medium

tag: time period of dr treatment


title: mated females_DR 7 days_rep 2


title: Pool 03

description:
P03: hS1 (hot; Summer1; Miami Nursery)
final_all_counts.txt
final_host_counts.txt
final_sym_counts.txt

value: summer


title: Pool 04

description:
P04: aS2 (ambient; Summer1; Lower Keys Nursery)
final_all_counts.txt
final_host_counts.txt
final_sym_counts.txt


title: mated females_DR 3 days_rep 3


title: Pool 02

description:
P02: cS1 (cold; Summer1; Lower Keys Nursery)
final_all_counts.txt
final_host_counts.txt
final_sym_counts.txt


title: mated females_DR 7 days_rep 1


title: Pool 06

description:
P06: hS2 (hot; Summer1; Lower Keys Nursery)
final_all_counts.txt
final_host_counts.txt
final_sym_counts.txt


title: mated females_DR 3 days_rep 2


title: mated females_DR 1 day_rep 2


title: mated females_DR 1 day_rep 3


title: Pool 01

description:
P01: aS1 (ambient; Summer1; Miami Nursery)
final_all_counts.txt
final_host_counts.txt
final_sym_counts.txt


title: Pool 05

description:
P05: cS2 (cold; Summer1; Miami Nursery)
final_all_counts.txt
final_host_counts.txt
final_sym_counts.txt


title: mated females_DR 1 day_rep 1


title: mated females_DR 3 days_rep 1


title: 1-ChIP-seq of K562: modification H3K4me3

status: Public on Dec 20 2017

city: Nashville

first: Andrea

last: Perreault

state: TN

address: 746 Robinson Research Building

institute: Vanderbilt University

description:
1-ChIPseq_H3K4me3
processed data file: ChIP_seqMerge_H3K4me3_v2.bw

data_processing:
To estimate variance across biological replicates, the Pearson correlation coefficient for pairwise gene RPKM was computed using the HOMER suite (Hypergeometric Optimization of Motif EnRichment)
Biological replicates were then merged and converted to bigWig files
Genome_build: hg19
Supplementary_files_format_and_content: each bigWig file build from merged biological replicates for ChIP-exo or ChIP-seq of Pol 2, H2A.z, or H3K4me3

growth_protocol: 37oC in 5% CO2 between 0.1-1 million cells/ml in DMEM (Dulbecco’s Modified Eagle Media) containing 10% bovine calf serum and 1% Penicillin/Streptomycin

extract_protocol:
Cells were lysed, then nuclei lysed. Purified chromatin was sonicated to obtain fragments of 100-500 basepairs
ChIPexo and ChIPseq libraries were prepared using the standard protocols

tag: cell line

tag: chip antibody

tag: chip antibody info.

value: Abcam ab8580


title: 2-ChIP-exo of K562: RNA polymerase II

description:
2-ChIPexo_Pol2
processed data file: ChIP_exoMerge.bw

value: Santa Cruz sc899


title: 2-ChIP-exo of K562: modification H3K4me3

description:
2-ChIPexo_H3K4me3
processed data file: ChIP_exoMerge_H3K4me3.bw


title: BCG infected 96h replicate 7

description:
replicate 7
BCG_SP+_96

tag: cohort

tag: infected/uninfected


title: Acute EBV ED483

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

hyb_protocol: The biotin-labeled cRNAs (5000 ng) were hybridized onto the HTA2.0 arrays following Affymetrix standard protocols.

scan_protocol: After washing and staining, the arrays were scanned by the GeneChip 3000 7G Scanner.

data_processing: The signal intensity data of the HTA2.0 arrays were processed through Affymetrix Expression Console (v1.4.1.46) with standard configuration for expression arrays, including robust multi-array average (RMA) background correction, median polish probe-level signal summarization, and quantile normalization. The detectable genes were defined for those whose signals were with a detection p-value <0.05 for > 50% of probe sets in at least 1 of all samples.

source_name: peripheral blood cells

label_protocol: The RNAs were subjected to the Ambion Whole-Transcript (WT) RNA Amplification system and GeneChip WT Terminal Labeling kit, which is biotin-based labeling. The assays started with 100 ng of total RNA for cDNA synthesis and amplification and then proceeded to fragmentation and labeling reactions.

extract_protocol: The blood samples were first subjected to the Ficoll process to isolate the mononuclear cells from the whole blood specimens. The RNA extraction was then carried out using the RNeasy Mini Kit from Qiagen AB (Cat. # 74104, Sollentuna, German) following manufacturer’s standard protocol. All RNA samples had both 18S and 28S bands with OD260:280 at 1.8 to 2.0 and were free of DNA and protein contaminations.

treatment_protocol: Peripheral blood mononulear cells were isolated from the whole blood specimens using the Ficoll method. No additional treatment was used for any samples.

value: M

value: peripheral blood mononuclear cells

tag: diagnosis

value: acute infectious mononucleosis (AIM)


title: Healthy Control C23

value: 3 y

tag: tissue

value: healthy


title: 2-ChIP-seq of K562: RNA polymerase II

description:
2-ChIPseq_Pol2
processed data file: ChIP_seqMerge.bw


title: 2-ChIP-exo of K562: histone H2AZ

description:
2-ChIPexo_H2AZ
processed data file: ChIP_exoMerge_H2AZ.bw

value: EMD Millipore 07-594


title: 2-ChIP-seq of K562: histone H2AZ

description:
2-ChIPseq_H2AZ
processed data file: ChIP_seqMerge_H2AZ.bw


title: 2-ChIP-seq of K562: modification H3K4me3

description:
2-ChIPseq_H3K4me3
processed data file: ChIP_seqMerge_H3K4me3_v2.bw


title: Acute EBV ED490


title: Healthy Control C21

value: F

value: 1 y


title: Chronic EBV 15VC2295

value: chronic active EBV infection (CAEBV)


title: Healthy Control C13


title: Healthy Control C15


title: Acute EBV 15VC2293

value: 4 y


title: 1-ChIP-seq of K562: histone H2AZ

description:
1-ChIPseq_H2AZ
processed data file: ChIP_seqMerge_H2AZ.bw


title: Chronic EBV 15VC2414


title: Healthy Control C22


title: Chronic EBV 15VC3454


title: Acute EBV 15VC1803


title: Chronic EBV 15VC2656

value: 2 y


title: Chronic EBV 15VC2407

value: 9 y


title: Acute EBV 15VC1799


title: Acute EBV 15VC2386


title: 1-ChIP-exo of K562: modification H3K4me3

description:
1-ChIPexo_H3K4me3
processed data file: ChIP_exoMerge_H3K4me3.bw


title: 1-ChIP-exo of K562: RNA polymerase II

description:
1-ChIPexo_Pol2
processed data file: ChIP_exoMerge.bw


title: Healthy Control C24


title: 1-ChIP-seq of K562: RNA polymerase II

description:
1-ChIPseq_Pol2
processed data file: ChIP_seqMerge.bw


title: 1-ChIP-exo of K562: histone H2AZ

description:
1-ChIPexo_H2AZ
processed data file: ChIP_exoMerge_H2AZ.bw


title: BCG uninfected 24h replicate 3

description:
replicate 3
BCG_K-_24

value: validation

value: uninfected

tag: bacterium

value: BCG

tag: hours

value: Whole blood


title: pLD401_3xFLAG_elution_2

city: New York

last: LaCava

address: 1230 York ave

institute: The Rockefeller University

description:
Processed_RNA-Seq_combined.xlxs
6_401-3xFlag-2

data_processing:
FASTAQ files were trimmed via trimmomatic (Bolger et al, 2014) using the following parameters: -phred33 -threads 8, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:16 MINLEN:25
mapping was performed via STAR (Dobin et al, 2013) version 2.5.3a (https://github.com/alexdobin/STAR) using the following parameters: -runThreadN 8, --quantMode GeneCounts, --outSAMtype BAM SortedByCoordinate, --outFilterMatchNmin 30
the results were output to one binary alignment map file for each sample matched to the reference
genes with the coverage of 10 or more reads in at least 3 experiments were selected
data was normalized using the ‘DESeq2’ (Love et al, 2014) R package version 1.14.1.
Genome_build: Human genome hg19 GRCh37.87 (FASTA) and annotation (GTF file) were downloaded from ENSEMBL (ftp://ftp.ensembl.org/pub/grch37/release-90) and reference FASTA and GTF files were created by combining the human genome and ORFeus-Hs from pLD401 (DOI: 10.1016/j.cell.2013.10.021)
Supplementary_files_format_and_content: Single Excel spreadsheet

growth_protocol: Suspension growth as described in DOI: 10.1007/978-1-4939-3372-3_20

extract_protocol:
Cryomilling and affinity capture as descibed DOI: 10.1007/978-1-4939-3372-3_20 ; and 10.3791/54518. RNAs were further extracted and purified in a multi-stage procedure as described in the main research article, see summary, above.
5 µl of purified RNA was used directly in RNA fragmentation.  Libraries were prepared according to Illumina's instructions with unique barcodes and were pooled at equimolar ratios.

tag: rip antibody

value: anti-FLAG; Sigma #F1804

tag: growth

value: suspension


title: pLD624_3xFLAG_elution

description:
Processed_RNA-Seq_combined.xlxs
4_624-3xFlag-1


title: pLD401_α-ORF1p_elution_1

description:
Processed_RNA-Seq_combined.xlxs
4_401-TandemElu-1

value: anti-ORF1; Abmart custom made clone 4H1 (Taylor et al. 2013)


title: pLD567_3xFLAG_elution_1

description:
Processed_RNA-Seq_combined.xlxs
6_567-3xFlag-1


title: pLD401_α-ORF1p_supernatant_2

description:
Processed_RNA-Seq_combined.xlxs
7_401-TandemSup-2


title: pLD401_3xFLAG_elution_1

description:
Processed_RNA-Seq_combined.xlxs
2_401-3xFlag-1


title: pLD401_α-ORF1p_elution_2_rRNA

description:
rRNA depleted total RNA
Processed_RNA-Seq_combined.xlxs
N/A


title: pLD401_α-ORF1p_elution_2

description:
Processed_RNA-Seq_combined.xlxs
8_401-TandemElu-2


title: pLD567_3xFLAG_elution_2

description:
Processed_RNA-Seq_combined.xlxs
2_567-3xFlag-2


title: pLD401_α-ORF1p_elution_1_rRNA


title: pLD401_α-ORF1p_supernatant_1

description:
Processed_RNA-Seq_combined.xlxs
3_401-TandemSup-1


title: Tf2(247)

city: Moscow

first: Sergei

last: Funikov

state: Moscow

address: Vavilov str. 32

country: Russia

institute: Engelhardt Insitute of Molecular Biology

description: small RNAs (21-29 nts)

data_processing:
As a result of deep-sequencing we obtained 5-14 million reads of small RNAs for each library. Pre-processing procedure included: 3’-adapter cropping, filtration of reads by length filtration (>18 nt) and quality (80% of nt have ≥ 20 Phred quality). Pre-processed reads were further subjected to subtraction of reads matching to all rRNA, tRNA, snRNA and miRNA sequences. The selected reads were mapped to the latest release of D. virilis genome by Bowtie (Langmead et al., 2009) with requiring of perfect match. In order to identify siRNAs and piRNAs, the sequenced reads were mapped to the canonical sequences of TEs obtained from combined libraries of annotated and computationally predicted D. virilis transposons and repeats sequences (Erwin et al., 2015). Length distribution and counting of siRNAs and piRNAs reads, nucleotide biases, ping-pong signatures, coverage of transposon sequence by piRNAs were analyzed with accordance to the well-described technique (Brennecke et al., 2007; Song et al., 2014) using custom scripts written in Python.
genome build: droVir2 (Aug, 2005)
Supplementary_files_format_and_content: Excel file with CPM

organism: Drosophila virilis

extract_protocol:
Total RNA was extracted from ovaries of 7-10 days old females using Extract RNA reagent (Evrogen, Russia). To prepare small RNA fraction for cloning, total RNA from ovaries (~ 25 µg) was separated, using 15% polyacrylamide gel electrophoresis containing 8 M Urea. After incubation in an ethidium bromide solution (0.5 µg/ml) gel fragments corresponding to the small RNA fraction were excised, using chemically synthesized RNA corresponding to 21 and 29 nts as size markers.
Cloning of small RNA libraries was performed by Illumina TruSeq Small RNA prep kit (Illumina, USA) according to the manufacturer’s protocol.

value: Ovaries

tag: strain

tag: rna fraction

value: Gel extraction of small RNAs (21-29 nts)


title: Tf1(165)

description: small RNAs (21-29 nts)


title: 9(w3)

description: small RNAs (21-29 nts)


title: CA3V_hippocampus_P30_Seizures_6

city: São Paulo

first: Hatylas

last: Azevedo

state: Sao Paulo

address: Doutor Arnaldo Avenue, 455

department: Pediatrics

country: Brazil

institute: University of São Paulo

description: Gene expression profiling of CA3 ventral hippocampus at P30

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028282_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: CA3 ventral hippocampus, P30, Hyperthermic Seizures

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Microarray-Based Gene Expression Analysis - Low Input RNA (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol:
[experimental protocol] Brain tissue samples were collected from the ventral CA3 hippocampus at 1 (P12), 19 (P30), 49 (P60) and 109 (P120) days after hyperthermic-induced seizures. Brain microdissection was performed as described in (Gorter et al., 2006). Briefly, after decapitation, the temporal lobe and hippocampus were removed by incision at the ventrocaudal part underneath the rhinal fissure, until 5 mm posterior to bregma. Then, the hippocampus was cut into smaller pieces (200-300 uM) and the CA3 region was selected and removed in phosphate buffered saline (PBS) at 4°C under a dissecting microscope. The material obtained from the ventral CA3 region was placed in Eppendorf tubes containing RNA later (Qiagen) for subsequent extraction of total RNA
Total RNA was isolated from CA3 ventral hippocampus samples using Trizol reagent (Life Technologies) and purified using RNeasy Spin Columns (Qiagen, USA). RNA quantity was determined using a Nanovue spectrophotometer (GE Healthcare, USA). The RNA quality was performed using a 2100 Bioanalyzer with an RNA 6000 Nano kit and Ladder (Agilent Technologies, USA), according to the manufacturer’s instructions.

value: CA3 ventral hippocampus

tag: time period

tag: group

value: Hyperthermic seizures


title: 160_x_101(N)(rec)

description: small RNAs (21-29 nts)

source_name: hybrid (101(N) and 160)

value: hybrid (101(N) and 160)


title: CA3V_hippocampus_P12_Control_7

description: Gene expression profiling of CA3 ventral hippocampus at P12

source_name: CA3 ventral hippocampus, P12, Normothermic Controls

value: Normothermic Controls


title: CA3V_hippocampus_P12_Control_5


title: CA3V_hippocampus_P12_Seizures_6

source_name: CA3 ventral hippocampus, P12, Hyperthermic Seizures


title: CA3V_hippocampus_P12_Control_2


title: CA3V_hippocampus_P12_Control_4


title: CA3V_hippocampus_P12_Seizures_5


title: CA3V_hippocampus_P12_Control_6


title: CA3V_hippocampus_P12_Seizures_7


title: CA3V_hippocampus_P12_Seizures_4


title: Mag_x_160(dys)

description: small RNAs (21-29 nts)

source_name: hybrid (Magarach and 160)

value: hybrid (Magarach and 160)


title: 101(N)_x_160(dys)

description: small RNAs (21-29 nts)


title: BCG uninfected 48h replicate 4

description:
replicate 4
BCG_ME-_48


title: 160_x_Mag(rec)

description: small RNAs (21-29 nts)


title: CA3V_hippocampus_P12_Control_1


title: CA3V_hippocampus_P30_Seizures_5


title: 160_x_Arg(rec)

description: small RNAs (21-29 nts)

source_name: hybrid (Argentina and 160)

value: hybrid (Argentina and 160)


title: CA3V_hippocampus_P30_Seizures_4


title: CA3V_hippocampus_P12_Seizures_3


title: Arg_x_160(dys)

description: small RNAs (21-29 nts)


title: CA3V_hippocampus_P30_Seizures_2


title: CA3V_hippocampus_P30_Seizures_3


title: CA3V_hippocampus_P12_Seizures_1


title: CA3V_hippocampus_P12_Control_3


title: CA3V_hippocampus_P12_Seizures_2


title: 160_x_140(rec)

description: small RNAs (21-29 nts)

source_name: hybrid (140 and 160)

value: hybrid (140 and 160)


title: 140_x_160(dys)

description: small RNAs (21-29 nts)


title: CA3V_hippocampus_P30_Seizures_1


title: 101(M)_x_160(dys)

description: small RNAs (21-29 nts)

source_name: hybrid (101(M) and 160)

value: hybrid (101(M) and 160)


title: 160_x_101(M)(rec)

description: small RNAs (21-29 nts)


title: 101(M)

description: small RNAs (21-29 nts)

source_name: 101 (M-strain)

value: 101 (M-strain)


title: CA3V_hippocampus_P30_Control_6

source_name: CA3 ventral hippocampus, P30, Normothermic Controls


title: 13

description: small RNAs (21-29 nts)

source_name: 13 (M-strain)

value: 13 (M-strain)


title: 160_x_13(rec)

description: small RNAs (21-29 nts)

source_name: hybrid (13 and 160)

value: hybrid (13 and 160)


title: 101(N)

description: small RNAs (21-29 nts)

source_name: 101 (N-strain)

value: 101 (N-strain)


title: 13_x_160(dys)

description: small RNAs (21-29 nts)


title: CA3V_hippocampus_P30_Control_4


title: CA3V_hippocampus_P30_Control_3


title: CA3V_hippocampus_P30_Control_5


title: CA3V_hippocampus_P60_Seizures_1

description: Gene expression profiling of CA3 ventral hippocampus at P60

source_name: CA3 ventral hippocampus, P60, Hyperthermic Seizures


title: CA3V_hippocampus_P60_Seizures_8


title: CA3V_hippocampus_P60_Seizures_3


title: CA3V_hippocampus_P30_Control_1


title: CA3V_hippocampus_P60_Seizures_6


title: CA3V_hippocampus_P60_Seizures_7


title: CA3V_hippocampus_P60_Seizures_4


title: CA3V_hippocampus_P60_Seizures_5


title: CA3V_hippocampus_P60_Control_6

source_name: CA3 ventral hippocampus, P60, Normothermic Controls


title: CA3V_hippocampus_P60_Control_5


title: CA3V_hippocampus_P60_Control_3


title: CA3V_hippocampus_P60_Seizures_2


title: Pat79 Whole Blood

first: Hakim

last: hocini

address: 101 Rue de Tolbiac

institute: INSERM

description: SAMPLE 79

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Assay

scan_protocol: iScan Illumina scanning protocol using iScan control software

data_processing: neqc of limma package

source_name: Pat79 Whole Blood

label_protocol: In vitro transcription was generated from 150 ng of RNA using Ambion Illumina TotalPrep RNA Amplification Kits (Applied Biosystems/Ambion).

extract_protocol: RNA were purified using RNeasy Plus Micro Kit (Qiagen, France) and quantified using a ND-8000 spectrophotometer (NanoDrop Technologies) before being checked for integrity on the 2100 BioAnalyzer (Agilent Technologies).

tag: patient name

tag: groups

value: chronically HIV-1 infected individuals with controlled virus replication under combined antiretroviral therapy

value: Whole Blood


title: Pat80 Whole Blood

description: SAMPLE 80

source_name: Pat80 Whole Blood


title: CA3V_hippocampus_P60_Control_4


title: Pat78 Whole Blood

description: SAMPLE 78

source_name: Pat78 Whole Blood


title: CA3V_hippocampus_P30_Control_2


title: Pat75 Whole Blood

description: SAMPLE 75

source_name: Pat75 Whole Blood


title: Pat77 Whole Blood

description: SAMPLE 77

source_name: Pat77 Whole Blood


title: CA3V_hippocampus_P60_Control_1


title: CA3V_hippocampus_P60_Control_2


title: CA3V_hippocampus_P120_Seizures_7

description: Gene expression profiling of CA3 ventral hippocampus at P120

source_name: CA3 ventral hippocampus, P120, Hyperthermic Seizures


title: Pat70 Whole Blood

description: SAMPLE 70

source_name: Pat70 Whole Blood


title: CA3V_hippocampus_P120_Seizures_6


title: CA3V_hippocampus_P120_Seizures_8


title: CA3V_hippocampus_P120_Seizures_5


title: Pat76 Whole Blood

description: SAMPLE 76

source_name: Pat76 Whole Blood


title: Pat73 Whole Blood

description: SAMPLE 73

source_name: Pat73 Whole Blood


title: Pat72 Whole Blood

description: SAMPLE 72

source_name: Pat72 Whole Blood


title: Pat71 Whole Blood

description: SAMPLE 71

source_name: Pat71 Whole Blood


title: Pat68 Whole Blood

description: SAMPLE 68

source_name: Pat68 Whole Blood


title: Pat69 Whole Blood

description: SAMPLE 69

source_name: Pat69 Whole Blood


title: CA3V_hippocampus_P120_Seizures_4


title: CA3V_hippocampus_P120_Seizures_3


title: CA3V_hippocampus_P120_Seizures_2


title: Pat67 Whole Blood

description: SAMPLE 67

source_name: Pat67 Whole Blood


title: Pat74 Whole Blood

description: SAMPLE 74

source_name: Pat74 Whole Blood


title: Pat63 Whole Blood

description: SAMPLE 63

source_name: Pat63 Whole Blood


title: Pat66 Whole Blood

description: SAMPLE 66

source_name: Pat66 Whole Blood


title: CA3V_hippocampus_P120_Seizures_1


title: Pat61 Whole Blood

description: SAMPLE 61

source_name: Pat61 Whole Blood


title: Pat58 Whole Blood

description: SAMPLE 58

source_name: Pat58 Whole Blood


title: Pat65 Whole Blood

description: SAMPLE 65

source_name: Pat65 Whole Blood


title: Pat59 Whole Blood

description: SAMPLE 59

source_name: Pat59 Whole Blood


title: CA3V_hippocampus_P120_Control_7

source_name: CA3 ventral hippocampus, P120, Normothermic Controls