title: LK-17-ACTGAT

city: Stanford

first: Lisa

middle: M

last: Kronstad

state: CA

address: S131 Grant Building

department: Medicine

institute: Stanford  University

data_processing:
The raw influenza sequencing reads were aligned using STAR (47) to the influenza genome of each strain downloaded from the Influenza Research Database (A/California/07/09 (Cal/09), CY121687; A/Vic/361/2011 (Vic/11), KJ942683).
The raw human sequencing reads were aligned to the Genome Reference Consortium Human Build 38 genome, downloaded from the Illumina web server. Alignment was performed using Bowtie2vand TopHat to produce a parsimonious transcriptome assembly.
The differential transcriptome assembly was analyzed using the DEseq2 R package from Bioconductor.
Differentially expressed genes were mapped to known protein-protein networks derived from the STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) database using the BioNet R package from Bioconductor.
Count normalization performed with RNA-seq

source_name: primary monocytes

growth_protocol: Monocytes were suspended in RPMI media

extract_protocol:
Tel TEST RNA-bee total RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Infection with A/California/07/2009 (MOI 10) or A/Victoria/361/2001 (MOI 0.2)

value: primary monocytes

tag: donor

tag: infection

tag: hpi

value: 24 HPI


title: LK-16-GAGTGG

status: Public on Jul 28 2018

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

value: Uninfected


title: LK-18-ATTCCT


title: A498 DGAT1/2 shRNA xenograft, 200mg/kg doxycycline chow, 5 days, biol repl 1

type: RNA

city: Philadelphia

first: Daniel

last: Ackerman

state: PA

address: 421 Curie Blvd, BRB II/III, Rm 646

institute: University of Pennsylvania

description: Gene expression data from A498 cells following DGAT knockdown

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Transcriptome 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: RMA-sst was applied using Affymetroix Transcriptome Analysis Console (TAC) with default settings

label: biotin

source_name: A498 DGAT1/2 shRNA tumor from mouse treated with 200mg/kg doxycycline chow

label_protocol: 250ng of total RNA was converted to biotinylated cDNA using standard protocols used by the Molecular Profiling Core at the University of Pennsylvania

growth_protocol: After subcutaneous injection of 5e6 A498 cells in NIH-III mice, tumors were allowed to grow to 300mm3 and were then randomly assigned to the two treatment groups

extract_protocol: total RNA extraction was performed with RNEasy columns according to the manufacturer's instructions

treatment_protocol: Mice were fed either control or doxycycline chow for 5 days ad lititum

tag: tissue

value: A498 xenograft tumor

value: Clear cell renal cell carcinoma (ccRCC)

tag: treatment

value: doxycycline

tag: genotype/variation

value: DGAT1/2 knockdown


title: A498 DGAT1/2 shRNA xenograft, control chow, 5 days, biol repl 4

description: Gene expression data from A498 cells without DGAT knockdown

source_name: A498 DGAT1/2 shRNA tumor from mouse treated with control chow

value: vehicle

value: wildtype


title: 60-SMA

city: Ann Arbor

first: Simpa

middle: S

last: Salami

state: MI

address: 1500 E Medical Center Dr

department: Urology

institute: University of Michigan

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data processing, quality control and differential gene expression analysis were performed in R (version 3.4.4). BeadArray-specific variance stabilization, normalization, and gene annotation were performed using the lumi package. Data from all three batches were combined prior to quantile normalization using the normalizeBetweenArrays function from the limma package

source_name: severe malaral anemia

label_protocol: Total RNA was purified from PAXgene-stabilized whole blood and depleted of globin mRNA transcripts using GLOBINclear Kits. RNA quality was assessed with either an Agilent 2100 Bioanalyzer or a Perkin Elmer LabChip GX and quantity was assessed with a NanoDrop 1000A Spectrophotometer. After RNA purification and quality assessment, 20 samples from each group were randomly selected for transcriptome analyses based on sufficient RNA yield and RNA integrity numbers (>6.1). Approximately 300 ng of total RNA was used in Illumina TotalPrep RNA Amplification Kits to produce cRNA. Whole genome expression analyses were performed using HumanHT-12 v4 Expression BeadChips and an Illumina BeadArray Reader.

extract_protocol: Peripheral blood was collected by venipuncture on hospital admission (CM and SMA) or as an outpatient (CC) for thin and thick smears, hematological testing, plasma, and filter paper blood spots. Whole blood was collected for RNA using the PAXgene Blood RNA System (PreAnalytiX GmbH; Hombrechtikon, Switzerland). Plasma and PAXgene whole-blood samples were stored at -80°C until further processing and analysis.

tag: diagnosis

value: severe malaral anemia

tag: processing batch

tag: age

tag: Sex

value: Male

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype

value: SS

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: A498 DGAT1/2 shRNA xenograft, control chow, 5 days, biol repl 2

tag: tissue

tag: cell type

tag: treatment


title: C396_C6K5PANXX_ACTTGA_L004: Donor C396 white blood cells

city: Parkville

first: CSL

last: Research

state: VIC

address: 30 Flemington Rd

country: Australia

institute: CSL Limited / bio21 Institute

description: Donor C396 white blood cells

data_processing:
Reads were mapped to Homo sapiens GRCh37.p10 genome, using TopHat (TopHat v2.1.0, bowtie v2.2.5; Trapnell et al.,2009).
Mapped reads were summaried on a gene level using Ensembl ID gene annotation (Ensembl Release 70 based on GRCh37.p10 genome build) and featureCounts (Rsubread package v1.23.2; Yang et al., 2014) software.
Summarised read counts in this submission were NOT normalised nor filtered. We recommend using Bioconductor edgeR package functions: i) calcNormFactors (TMM method) to normalise between samples based on library sizes,  and ii) rpkm function to normalise between genes within a sample based on gene lengths.
Genome_build: GRCh37.p10
Supplementary_files_format_and_content: All processed data files are in a tab delimited file format. They contain raw read counts summarised on a gene level according to Ensembl Release 70 annotation.

molecule: polyA RNA

source_name: RNA from white blood cells

extract_protocol:
RNA was extracted using RNeasy Mini Kit (QIAGEN, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Peripheral blood was collected in EDTA vacutainers and red blood cells (RBC) lysed in ammonium chloride lysing solution. The remaining white blood cells (WBC) were stored in RNAprotect (QIAGEN, Germany) for later use

value: Blood

value: White blood cells

tag: donor

tag: gender

value: F

tag: ancestry

tag: phenotype

value: Healthy

tag: das score

tag: disease activity

tag: arthropathymeds

tag: nsaids

tag: steroids

tag: biologics

tag: plaquenil

tag: leflumide

tag: sulfasalazine

tag: rituximab

tag: othermeds


title: C148_C6K5PANXX_AGTCAA_L007: Donor C148 white blood cells

description: Donor C148 white blood cells

tag: tissue

tag: cell type

tag: age


title: A498 DGAT1/2 shRNA xenograft, 200mg/kg doxycycline chow, 5 days, biol repl 2

tag: treatment

tag: genotype/variation


title: C141_C6K5PANXX_CGTACG_L007: Donor C141 white blood cells

description: Donor C141 white blood cells

tag: donor

tag: gender

value: M

tag: ancestry

tag: phenotype


title: A498 DGAT1/2 shRNA xenograft, control chow, 5 days, biol repl 1


title: A498 DGAT1/2 shRNA xenograft, control chow, 5 days, biol repl 3


title: LK-14-GTTTCG

value: primary monocytes

tag: infection

tag: hpi

value: 7 HPI


title: 47-CC

source_name: community children without Plasmodium falciparum infection

tag: diagnosis

value: no Plasmodium falciparum infection

tag: processing batch

tag: Sex

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype

value: AA

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: LK-15-CGTACG

tag: cell type

tag: donor


title: C137_C6K5PANXX_ACTGAT_L004: Donor C137 white blood cells

description: Donor C137 white blood cells

tag: tissue

tag: gender

tag: age

tag: ancestry

tag: phenotype

tag: das score

tag: disease activity

tag: arthropathymeds

tag: nsaids

tag: steroids

tag: biologics

tag: plaquenil

tag: leflumide

tag: sulfasalazine

tag: rituximab

tag: othermeds


title: LK-13-GTGGCC

tag: cell type

tag: donor

tag: infection

value: Uninfected

tag: hpi


title: Healthy human PBMCs

first: Saskia

last: Freytag

state: Victoria

address: 1G Royal Parade

department: Population Health and Immunity

institute: WALTER AND ELIZA HALL INST MEDICAL RES

data_processing:
Data was processed according to the Cell Ranger protocol. Note that the data were aligned to a full reference genome.
Genome_build: GRCh38 version 90
Supplementary_files_format_and_content: Compressed sparse column format for storing expression counts.

extract_protocol:
PBMCs were isolated from whole blood using density centrifugation. Cells were then processed by the 10X Genomics Chromium single cell platform using the manufacturer’s 3' protocol to obtain a pooled library.
The 10x Genomics Chromium machine partitions cells into Gel Bead-In-EMulsions (GEMs), where all generated cDNA share a common 10x Genomics barcode but uses a pool of about 750,000 barcodes to separately index each cell’s transcriptome. The P7 and R2 primers were added during the GEM incubation and the P5, and R1 during library construction via end repair, A-tailing, adaptor ligation and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The library was prepared for sequencing using an Illumina 150 cycle (v2 chemistry) high output kit and sequenced on an Illumina HiSeq 2500 to obtain paired-end reads.

tag: subject status

value: healthy donor

value: Peripheral blood mononuclear cells (PBMCs)

tag: barcode coordinate

value: tag CB

tag: umi coordinate

value: tag UB


title: LK-12-GTGAAA

value: 24 HPI


title: Control C360

first: Steven

middle: K

last: Lundy

address: 4043 Biomedical Sciences Research Bldg 109 Zina Pitcher Place

department: Internal Medicine

institute: University of Michigan Medical School

description: 100ng whole blood total RNA was hybridized to NanoString Human Immunology panel and analyzed using nCounter

hyb_protocol: 100 ng of RNA was hybridized to NanoString Human Immunology Panel using manufacturer's protocol

scan_protocol: Scan was performed on nCounter Analyzer

data_processing: The raw data were filtered to include mRNA expression above 32 copies/100 ng total RNA then linearized and Voom normalized using R statistics package. Batch effects were corrected using the Combat method.

source_name: blood RNA

label_protocol: Total RNA (400ng) was sent to Michigan State University core NanoString facility

extract_protocol: Whole blood RNA was isolated from PAXgene tubes using Qiagen RNA isolation kit

tag: tissue

value: whole blood

tag: diagnosis

tag: anti-retinal ab bands on wb

tag: age (years)

tag: gender

value: Male


title: Control C324

value: Female


title: Control C364


title: Control C363


title: Control C323


title: Control C361


title: LK-9-ATGTCA


title: Control C010


title: Control C273


title: Control C230


title: LK-10-CCGTCC


title: RP patient R300

value: Retinitis pigmentosa


title: Control C249

value: nd


title: LK-11-GTCCGC


title: LK-7-CTTGTA


title: LK-8-AGTTCC


title: RP patient R261


title: RP patient R281


title: Control C275


title: RP patient R253


title: RP patient R271


title: Control C319


title: LK-6-GGCTAC


title: LK-5-TAGCTT


title: LK-4-GATCAG


title: RP patient R245


title: LK-3-ACAGTG


title: RP patient R294


title: RP patient R201


title: Control C272


title: RP patient R188


title: LK-1-CGATGT


title: RP patient R172


title: LK-2-TGACCA


title: Infected_3

city: Madison

first: CHIA-WEI

last: WU

state: WI

address: 1656 Linden Dr

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

data_processing:
CASAVA v 1.7 for basecallng
Raw RNA-Seq data was proccessed with CLC Genomics Workbench 8.5 .
Adaptor sequences were trimmed. The ambiguous trim limit was set at 1 and quality trim limit was at 0.05.  Reads shorter than 25 nucleotides were excluded.
Trimmed sequences were mapped to to the reference genome sequence of Capra hircus assembly ARS1, with the parameters: mismatch cost, 2; insertion and deletion cost, 3; length and similarity fraction, 0.8.
Unique gene reads from each sample were exported from CLC Genomics Workbench and used for normalization and differential gene expression analysis with an R package, DESeq2 version 1.16.1
Genome_build: ARS1
Supplementary_files_format_and_content: Tab-delimited text files containing serial ID, gene name, chromosome, gene region and Normalized unique gene reads.

organism: Capra hircus

source_name: Goat PBMC

extract_protocol:
RNA was extracted from stimulated PBMC’s using TRIzol® and RNeasy® Mini Kit (Qiagen®) according to manufacturer’s directions for the remainder of the extraction.  TURBO DNA-free™ DNase Treatment (Ambion®) was used to eliminate residual genomic DNA.
A total of 1 µg of RNA was used as input for TruSeq RNA Sample Prep Rev.F (March 2014, Illumina)

treatment_protocol: PBMC’s were plated at a density of 1.0E+06 cells per well in 96 well plates with 10 µg/ml M. paratuberculosis whole cell lysate (WCL) and 100 U/ml IL-2 for 24 hours.  The WCL was prepared by resuspending the centrifuged cell pellet of actively grown M. paratuberculosis (O.D. ~ 1.0) in protein lysis buffer (100mM Tris–Cl, 100mM NaCl, 5mM MgCl2, 1mM PMSF, complete ultra-protease inhibitor cocktail (Roche, Indianapolis, IN; pH 7.5) and bead-beating to homogenize (maximum pulse for 45 sec for a total of 4 pulses; with cooling on on ice for 30 sec between pulses).

value: PBMC

tag: vaccination

value: PBS buffer

value: M. paratuberculosis strain JTC1285

tag: time point

value: One month post-infection


title: RP patient R152


title: MEF_RING1Bfl_TAM_ATAC_rep3

city: London

first: Hamish

middle: W

last: King

address: 4 Newark St

department: Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

library_source: genomic

data_processing:
Paired-end reads were aligned to the mouse mm10 genome using bowtie2 (Langmead and Salzberg, 2012) with the “—no-mixed” and “—no-discordant” options. Non-uniquely mapping reads and reads mapping to custom “blacklist” of artificially high regions of the genome were discarded. PCR duplicates were removed using SAMtools (Li et al., 2009). Biological replicates were randomly downsampled to contain the same number of reads for each individual replicate and merged.
Merged BAM files were used to make a genome track using DANPOS2, with a Tn5 digestion control provided as background.
Peakcalling was performed using the DANPOS2 dpeak function using untreated and treated samples with biological replicates and a Tn5 gDNA control digestion as background.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files representing genome coverage (with background subtracted) for merged biological triplicate were generated using DANPOS2.

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse embryonic fibroblasts, tamoxifen-treated, ATAC-seq

growth_protocol: Ring1a-/-;Ring1bfl/fl SV40-immortalised mouse embryonic fibroblasts (MEFs) were grown in DMEM supplemented with 7% FBS and penicillin/streptomycin and maintained in culture for less than 10 passages (Endoh et al. 2012; Jullien et al. 2017).

extract_protocol:
Chromatin accessibility was assayed using an adaptation of the assay for transposase accessible-chromatin (ATAC)-seq (Buenrostro et al., 2013). Briefly, 5 × 106 cells were harvested, washed with PBS and nuclei were isolated using 1 mL HS Lysis buffer (50 mM KCl, 10 mM MgSO4.7H20, 5 mM HEPES, 0.05 % NP40 (IGEPAL CA630)), 1 mM PMSF, 3 mM DTT)  for 1 min at room temperature. Nuclei were centrifuged at 1,000 × g for 5 min at 4°C, followed by a total of three washes with ice-cold RSB buffer (10mM NaCl, 10mM Tris (pH 7.4), 3mM MgCl2), to remove as much of contaminating cytoplasmic and mitochondrial material as possible. Nuclei were then counted, and 5×104 nuclei were resuspended in Tn5 reaction buffer (10mM TAPS, 5mM MgCl2, 10% dimethylformamide) and 2 µl of Tn5 transposase (25µM) made in house according to the previously described protocol (Picelli et al., 2014). Nuclei were then incubated for 30 min at 37°C, before isolation and purification of tagmented DNA using QiaQuick MinElute columns (Qiagen).
ATAC-seq libraries were prepared by PCR amplification using custom made Illumina barcodes previously described (Buenrostro et al., 2013) and the NEBNext® High-Fidelity 2X PCR Master Mix with 8-10 cycles. Libraries were purified with two rounds of AMPure XP bead cleanup (1.5X beads:sample), followed by quantification by qPCR using SensiMix SYBR (Bioline) and KAPA Library Quantification DNA standards (KAPA Biosystems). ATAC-seq libraries were sequenced on Illumina NextSeq500 using 80bp paired-end reads in biological triplicate.

treatment_protocol: Ring1a-/-;Ring1bfl/fl MEFs were treated with 800 nM 4-hydroxytamoxifen (TAM) for 96 h to ablate RING1B levels.

value: mouse embryonic fibroblasts

tag: genotype/variation

tag: replicate

tag: passage


title: Infected_2

tag: cell type


title: AIR patient A277

value: Autoimmune retinopathy


title: AIR patient A286


title: MEF_RING1Bfl_TAM_ATAC_rep2


title: RP patient R223


title: Infected_1


title: RP patient R215


title: AIR patient A166


title: Naive_3

value: One month post-vaccination


title: AIR patient A213


title: Naive_2


title: Infected_4


title: Naive_4


title: MEF_RING1Bfl_TAM_ATAC_rep1


title: AIR patient A178


title: MEF_RING1Bfl_UNT_ATAC_rep3

source_name: Mouse embryonic fibroblasts, untreated control, ATAC-seq


title: MEF_RING1Bfl_UNT_ATAC_rep2


title: Naive_1


title: AIR patient A135


title: LAV-vaccinated_4

value: delta-lipN mutant live-attenuated vaccine


title: MEF_RING1Bfl_UNT_ATAC_rep1


title: AIR patient A132


title: RING1Bfl_TAM_MNase_rep1

data_processing:
Paired-end reads were aligned to the mouse mm10 genome using bowtie2 (Langmead and Salzberg, 2012) with the “—no-mixed” and “—no-discordant” options. Non-uniquely mapping reads and reads mapping to custom “blacklist” of artificially high regions of the genome were discarded. PCR duplicates were removed using SAMtools (Li et al., 2009). Biological replicates were randomly downsampled to contain the same number of reads for each individual replicate and merged.
DANPOS2 was used to generated a genome coverage profile, identify nucleosome positions and calculate nucleosome occupancy (Chen et al. 2013).
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files representing genome coverage for merged biological triplicate were generated using DANPOS2.

source_name: Embryonic stem cells, tamoxifen-treated, MNase-seq

growth_protocol: Mouse embryonic stem cell (ESCs) were grown on gelatin-coated plates in DMEM (Gibco) supplemented with 15% FBS, 10ng/mL leukemia-inhibitory factor, penicillin/streptomycin, beta-mercaptoethanol, L-glutamine and non-essential amino acids.

extract_protocol:
Nuclei were isolated from 5 × 10^7 Ring1a-/-;Ring1bfl/fl mouse embryonic stem cells with or without TAM-treatment with RSB buffer (10 mM Tris-HCl (pH 8), 10 mM NaCl, 3 mM MgCl2) supplemented with 0.1 % NP-40 and 5 mM N-ethylmaleimide. This was followed by MNase digestion for 5 min at 37°C with 16 U MNase (Fermentas, Waltham, MA) in 1 ml RSB supplemented with 0.25 M sucrose, 3 mM CaCl2 and 10 mM N-ethylmaleimide. After digestions were stopped with 4 mM EDTA, nuclei were pelleted by centrifugation at 1500 x g and the soluble S1 fraction collected. Pelleted nuclei were then resuspended in 300 µl nucleosome release buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 0.2 mM EDTA, 10 mM N-ethylmaleimide), incubated at 4°C for 1 hr with gentle rotation, and then gently passed through a 27G syringe needle five times. After the insoluble material was pelleted by centrifugation at 1500 x g, the soluble S2 fraction was collected and combined with the S1 fraction.
DNA was purified from chromatin corresponding to 5 × 10^6 cells using ChIP DNA Clean and Concentrator kit (Zymo, Irvine, CA). MNase-seq libraries were prepared from 500 ng of DNA using the NEBNext Ultra II DNA Library Prep Kit (NEB) according to the manufacturer’s protocol. DNA fragment size selection step was included to enrich for mono-nucleosome size fragments in the final libraries. Libraries were sequenced on Illumina NextSeq500 using 80 bp paired-end reads in biological triplicate.

treatment_protocol: Previously described Ring1a-/-;Ring1bfl/fl ESCs (Endoh et al., 2008) were adapted to grow under feeder-free culture conditions and were treated with 800 nM 4-hydroxytamoxifen (TAM) for 72 h to ablate RING1B levels.

value: mouse embryonic stem cells


title: RING1Bfl_TAM_MNase_rep2


title: LAV-vaccinated_2


title: LAV-vaccinated_1


title: AIR patient A125


title: AIR patient A061


title: AIR patient A145


title: AIR patient A052


title: Mycopar-vaccinated_1

value: Mycopar vaccine


title: RING1Bfl_UNT_MNase_rep2

source_name: Embryonic stem cells, untreated control, MNase-seq


title: AIR patient A048


title: AIR patient A134


title: LAV-vaccinated_3


title: Mycopar-vaccinated_3


title: Mycopar-vaccinated_2


title: RING1Bfl_UNT_MNase_rep1


title: RING1Bfl_UNT_MNase_rep3


title: RING1Bfl_TAM_MNase_rep3


title: AIR patient A001


title: untreated cells, replicate 5

status: Public on Jul 27 2018

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using bowtie2 against mm10 version of the human genome and RSEM v1.2.31 software was used to estimate raw read counts and FPKM values using transcriptome information from Ensemble v84 set
DESeq2 was used to estimate significance of differential expression between 5 replicates of untreated and BMS-595-treated samples
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contains the raw counts and FPKM values for each gene as estimated by RSEM

source_name: untreated_BM-drived HPC

growth_protocol: LLC-TB mice were treated for 2 weeks and hematopoietic progenitor cells (HPC) were isolated from the bone marrow

extract_protocol:
Total RNA was extracted from the HPC using the Qiagen’s Rneasy Mini Kit and RNA quality was assessed using the Agilent RNA ScreenTape Assay on Agilent’s 2200 TapeStation
RNA-seq library was prepared using TruSeq Stranded Total RNA kit (Illumina) and ran in a 75bp paired end run on Illumina NextSeq 500

treatment_protocol: LLC-TB mice were treated with vehicle (untreated) or 60 mg/kg of CK2 inhibitor BMS-595 (CK2i) for 2 weeks

tag: strain

value: Lewis Lung Carcinoma (LLC)-tumor bearing (TB) mouse

tag: treated with

value: vehicle (untreated)

value: bone marrow derived hematopoietic progenitor cells (HPC)


title: CK2i treated cells, replicate 1

source_name: CK2i treated_BM-drived HPC

value: 60 mg/kg of CK2 inhibitor BMS-595 (CK2i) for 2 weeks


title: CK2i treated cells, replicate 5


title: CK2i treated cells, replicate 4


title: untreated cells, replicate 3


title: untreated cells, replicate 4


title: CK2i treated cells, replicate 2


title: CK2i treated cells, replicate 3


title: untreated cells, replicate 2


title: untreated cells, replicate 1


title: CFLD3

city: Brisbane

first: Diego

middle: A

last: Calvopina

state: QLD

address: 300 Herston Rd

department: Hepatic Fibrosis

institute: QIMR-Berghofer

description: total free circulating and exosomal RNA

data_processing:
Torrent Suite v5.0.4 (Thermo Fisher) software used for basecalling.
mirPRo software pipeline from Shi et al., Sci Rep, 2015. was used to perform quality control (QC), alignment and small RNA counting.
Adapters were trimmed, clean, collapsed and count raw reads after which were mapped to the miRBase miRNA hairpin database (miRBase v21).
Initial threshold filtering was performed on raw count data as follows: miRNA with two or fewer non-zero counts were selected as noise, with 10 counts selected as noise threshold. The miRNA read counts identified by the mirPRo pipeline were normalized for compositional bias in sequenced libraries and library size using the DESeq2 v1.15.28 package.
Differential expression analysis was performed in R v3.3.2. Differential expression of miRNA read counts was performed using DESeq2. Pair-wise comparisons were generated between the different conditions of interest.
Genome_build: miRBase miRNA hairpin database (miRBase v21)
Supplementary_files_format_and_content: tab-delimited text file includes matrix of normalized abundance measurement for each library

source_name: Serum

extract_protocol:
Total circulatory RNA was extracted from from 200µL serum using the Plasma/Serum RNA Purification Mini Kit (Norgen Biotek Corporation, Thorold, Canada).
Libraries were prepared using the Ion Total RNA-Seq Kit v2 protocol (Thermo Fisher, Revision E) using an equal RNA input of 5µL from every sample pooled into its respective library

tag: condition

value: Cystic fibrosis liver disease

value: Serum

tag: metavir score


title: 64-SMA

value: severe malaral anemia

tag: processing batch

tag: age

tag: Sex

value: Male

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype

value: SS

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: Control 3

description: total free circulating and exosomal RNA

value: Healthy control

tag: tissue


title: Control 1

description: total free circulating and exosomal RNA

tag: condition


title: CFnoLD2

description: total free circulating and exosomal RNA

value: Cystic fibrosis no liver disease

tag: metavir score


title: CFnoLD1

description: total free circulating and exosomal RNA


title: Control 2

description: total free circulating and exosomal RNA


title: X021618_96

city: La Jolla

first: Fred

middle: H

last: Gage

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

data_processing:
Reads trimmed with Solexa-QA++ dynamic trim
Trimmed reads aligned to mm10 with Ensembl annotation using RSEM (bowtie)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files contain either raw counts or tpm normalized counts

extract_protocol:
The nuclei dissociation protocol is similar to the previously described protocol with some modifications. Hippocampus was carefully excised and immediately placed into a nuclei isolation medium (sucrose 0.25 M, KCl 25 mM, MgCl2 5 mM, TrisCl 10 mM, dithiothreitol, 0.1 % Triton, protease inhibitors). Tissue was Dounce homogenized, allowing for mechanical separation of nuclei from cells. The nucleic acid stain Hoechst 33342 (5 µM, Life Technologies) was included in the media to facilitate visualization of the nuclei for quantification, but excluded for sorting. Samples were washed, resuspended in nuclei storage buffer (sucrose, MgCl2 5 mM, and TrisCl 10 mM) and filtered. Solutions and samples were kept cold throughout the protocol. For RNA-seq experiments, tools and solutions were made RNAse-free and RNAse inhibitors were used.
Library preparation followed the Smart-seq2 protocol. The Nextera XT kit was used for sample preparation following all transcriptome amplifications. Single-nuclei and amplified bulk samples were measured by Picogreen (LifeTech) and normalized so that samples were at a concentration of 0.3 ng/µl. Samples were first subjected to a tagmentation reaction, indexed, and PCR amplified. Libraries were then mixed in 48-sample pools and purified with magnetic beads (AMPure). Quality control checks for the library preparations included electrophoresis (Agilent Technologies 2100 Bioanalyzer). Samples were sequenced in the Salk Institute Next Generation Sequencing Core on an Illumina HiSeq 2500 high-throughput sequencing system with single-end 50bp reads.

treatment_protocol: Mice were exposed to the A context for 15 min and returned to the homecage for 4 hr. They were then either exposed to the A to C context for 15 minutes and returned to the homecage for an additional 1hr prior to sacrifice.Dimensions of the novel environment (NE) cage were 54" x 34" base, 12" height. The NE included huts and tunnels that the animal was not previously exposed to. NE exposures were performed between 7:00 am and 11:00 am during light cycle. Animals did not undergo any special treatment prior to NE exposure.

tag: strain

tag: gender

value: Female

tag: mousingle number

tag: exposure

value: A>A

value: hippocampus

value: P

value: C

value: F

value: A

tag: context1 (a,c)

tag: context2 (a,c)

tag: unalignable

tag: alignable

tag: multimap

tag: total reads


title: X021618_95

tag: age


title: X021618_89


title: X021618_94


title: X021618_88


title: X021618_91

value: N


title: X021618_86


title: X021618_90


title: X021618_87


title: X021618_85


title: X021618_80


title: X021618_81


title: X021618_82


title: X021618_83


title: X021618_84


title: X021618_78


title: X021618_79


title: CFLD2

description: total free circulating and exosomal RNA


title: CFLD1

description: total free circulating and exosomal RNA


title: X021618_77


title: X021618_92


title: X021618_93


title: X021618_76


title: X021618_74


title: X021618_75


title: X021618_72


title: X021618_71


title: X021618_73


title: X021618_70


title: X021618_69


title: X021618_68


title: X021618_67


title: X021618_65


title: X021618_66


title: X021618_63


title: X021618_64


title: X021618_62


title: Control C362

value: whole blood

tag: diagnosis

tag: anti-retinal ab bands on wb

tag: age (years)


title: X021618_55

tag: tissue


title: X021618_60


title: X021618_61


title: X021618_52


title: X021618_53


title: X021618_57


title: X021618_58


title: X021618_54


title: X021618_56


title: X021618_59


title: X021618_51


title: X021618_50


title: X021618_49


title: X021618_48


title: X021618_47


title: X021618_46


title: X021618_44


title: X021618_45


title: X021618_43


title: X021618_41


title: X021618_40


title: X021618_38


title: X021618_39


title: X021618_37


title: X021618_36


title: X021618_25


title: X021618_24


title: X021618_29


title: X021618_28


title: X021618_33


title: X021618_31


title: X021618_32


title: X021618_23


title: X021618_26


title: X021618_27


title: X021618_30


title: X021618_42


title: RP patient R242

value: Retinitis pigmentosa


title: X021618_19


title: X021618_20


title: X021618_17


title: X021618_21


title: X021618_35


title: X021618_14


title: X021618_16


title: X021618_18


title: X021618_34


title: X021618_12


title: X021618_11


title: X021618_10


title: X021618_08


title: X021618_22


title: X021618_15


title: X021618_13


title: X021618_04


title: X021618_05


title: X021618_07


title: X021618_02


title: X170525_93


title: X170525_96


title: X170525_94


title: X170525_92


title: X170525_90


title: X170525_91


title: X170525_88


title: X170525_83


title: X170525_86


title: X170525_85


title: X170525_89


title: X170525_84


title: X170525_82


title: X170525_87


title: X170525_80


title: X170525_81


title: X021618_09


title: X021618_06


title: X170525_79


title: X170525_78


title: X021618_03


title: X170525_77


title: X170525_76


title: X170525_75


title: X170525_95


title: X021618_01


title: X170525_74


title: X170525_73


title: X170525_71


title: X170525_68


title: X170525_69


title: X170525_72


title: X170525_70


title: X170525_67


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title: X170525_59


title: X170525_61


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title: X170525_63


title: X170525_52


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title: X170113_09


title: X170113_12


title: X170113_02


title: X170113_04


title: X161209_48


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title: X161209_34


title: X170113_07


title: X170113_05


title: X161209_29


title: X161209_30


title: X161209_18


title: X170113_13


title: X161209_17


title: X161209_28


title: X170113_15


title: X170113_06


title: X161209_24


title: X161209_16


title: X161209_22


title: X161209_05


title: X161209_23


title: X161209_04


title: X161209_11


title: X161121_47


title: X161209_10


title: X161121_44


title: X161209_06


title: X161121_45


title: X161209_12


title: X161121_43


title: X161121_42


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title: X161121_36


title: X161121_37


title: X161121_48


title: X161121_46


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title: X161121_31


title: X161121_29


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title: X161121_23


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title: X161121_11


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title: X161121_06


title: X161121_08


title: X161121_09


title: X161121_07


title: X161121_04


title: X161121_25


title: X161121_05


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title: X160622_48


title: X161121_01


title: X160622_46


title: X160622_47


title: X161121_03


title: X161121_02


title: X160622_45


title: X160622_44


title: X160622_42


title: X160622_41


title: X160622_43


title: X160622_37


title: X160622_38


title: X160622_34


title: X160622_35


title: X160622_40


title: X160622_39


title: X160622_33


title: X160622_32


title: X160622_31


title: X160622_30


title: X160622_29


title: X160622_27


title: X160622_25


title: X160622_23


title: X160622_24


title: X160622_28


title: X160622_18


title: X160622_21


title: X160622_16


title: X160622_36


title: X160622_22


title: X160622_15


title: X160622_26


title: X160622_19


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title: X160622_14


title: X160622_09


title: X160622_08


title: X160622_06


title: X160622_07


title: X160622_17


title: X160622_20


title: X160622_04


title: X160622_05


title: X160622_03


title: X160622_02


title: X160622_01


title: X160619_48

value: A>C


title: X160619_47


title: X160619_44


title: X160619_45


title: X160619_42


title: X160619_41


title: X160622_13


title: X160619_40


title: X160619_39


title: X160622_10


title: X160619_36


title: X160619_34


title: X160619_33


title: X160619_32


title: X160619_38


title: X160619_31


title: X160619_26


title: X160619_27


title: X160619_28


title: X160619_30


title: X160619_25


title: X160619_23


title: X160619_29


title: X160619_22


title: X160619_21


title: X160619_46


title: X160619_43


title: X160619_20


title: X160619_18


title: X160619_19


title: X160619_17


title: X160619_37


title: X160619_35


title: X160619_16


title: X160619_15


title: X160619_14


title: X160619_12


title: X160619_13


title: X160619_11


title: X160619_10


title: X160619_09


title: X160619_24


title: X160619_06


title: X160619_07


title: X160619_08


title: X160619_05


title: X160619_03


title: X160619_04


title: X160619_01


title: X160619_02


title: X160602_47


title: X160602_46


title: X160602_48


title: X160602_45


title: X160602_43


title: X160602_44


title: X160602_41


title: X160602_42


title: X160602_40


title: X160602_37


title: X160602_36


title: X160602_38


title: X160602_34


title: X160602_35


title: X160602_31


title: X160602_32


title: X160602_33


title: X160602_28


title: X160602_29


title: X160602_30


title: X160602_26


title: X160602_23


title: X160602_27


title: X160602_25


title: X160602_24


title: X160602_22


title: X160602_19


title: X160602_20


title: X160602_18


title: X160602_15


title: X160602_16


title: X160602_21


title: X160602_14


title: X160602_13


title: X160602_11


title: X160602_12


title: X160602_10


title: X160602_39


title: X160602_09


title: X160602_08


title: X160602_07


title: X160602_06


title: X160602_04


title: X160602_01


title: X160512_48


title: X160512_47


title: X160602_03


title: X160512_46


title: X160602_02


title: X160512_45


title: X160602_17


title: X160512_41


title: X160512_39


title: X160512_40


title: X160512_44


title: X160512_38


title: X160512_37


title: X160512_36


title: X160512_33


title: X160512_34


title: X160512_31


title: X160512_32


title: X160512_30


title: X160602_05


title: X160512_29


title: X160512_28


title: X160512_27


title: X160512_25


title: X160512_26


title: X160512_24


title: X160512_23


title: X160512_22


title: X160512_43


title: X160512_18


title: X160512_20


title: X160512_42


title: X160512_35


title: X160512_15


title: X160512_16


title: X160512_13


title: X160512_12


title: X160512_11


title: X160512_09


title: X160512_08


title: X160512_07


title: X160512_06


title: X160512_05


title: X160512_04


title: X160512_03


title: X160512_02


title: X160512_01


title: X160512_17


title: X160512_14


title: X160512_10


title: sick1

city: Newtown

first: Ben

last: Roediger

state: NSW

address: Locked Bag No. 6

institute: Centenary Institute

data_processing:
The raw sequence reads were screened for Illumina adapters, cross-species contamination and low quality bases. The low quality bases, and any possible adapter sequence, were trimmed using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and Cutadapt (Martin, 2011). A minimum quality score of 20 was used, with a minimum length requirement of 50 bp.
The Mus musculus mm10 genome was used to create a BWA (Burrows-Wheeler Aligner) index (Li and Durbin, 2010 PMID: 20080505). The index was used as a reference within the application Deconseq (Schmieder and Edwards, 2011 PMID: 21408061) to remove non-viral Mus musculus sequences as well as bacterial, plant and fungal sequences, thereby enriching for unidentified viral sequence reads.
The sequence reads that passed Quality Control procedures were aligned against the Mus musculus genome (Build version mm10) using Tophat Aligner (Version 2.0.14). The resulting BAM files were used in the downstream analysis. The counts of reads mapping to each known gene were summarized at gene level using the featureCounts v1.4.6-p2 utility of the subread package (http://subread.sourceforge.net/).
The differential gene expression analysis was performed using Biconductor (V3.2) and the limma package (https://bioconductor.org/packages/release/bioc/html/limma.html) (Ritchie et al., 2015 PMID: 25605792). The raw gene count data from the tophat alignment stage was used as input to determine the list of differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: .txt, .csv and .xlsx files of read and gene counts, and differentially expressed genes

source_name: whole kidney

growth_protocol: Mice were housed in specific pathogen-free (SPF) conditions at the Centenary Institute

extract_protocol:
RNA extraction was performed using an RNeasy® Mini Kit (Qiagen) according to the manufacturer's instructions with slight modifications. Briefly, each kidney was snap frozen in liquid nitrogen immediately following organ harvest and then ground manually using a sterile mortar and pestle in liquid nitrogen. The sample was ground to a fine powder and extreme care was taken to ensure it did not thaw. Post-grinding, the fine suspension (tissue + liquid nitrogen) was immediately transferred to liquid nitrogen-cooled, appropriately sized, pre-weighed tubes. The ground tissue from each individual kidney was transferred into multiple tubes and weighed quickly. Lysis buffer was immediately added at this step and homogenization carried out using a 20G needle and syringe. Lysate was passed through the syringe at least 5–10 times to obtain a homogenous lysate. Post-lysis, ethanol was added to the sample, which was then mixed and applied to the RNeasy® column. Total RNA bound to the membrane at this stage. On-column DNase digestion was carried out followed by multiple washes before the RNA was finally eluted. RNA quality was analyzed employing a Nanodrop (Thermo Fisher Scientific) and Bioanalyzer (Agilent Genomics).
RNA libraries were prepared using Illumina's Ribo-zero Gold protocol.

treatment_protocol: Mice were not subject to any experimental procedure. Naturally sick mice were selected from a disease-affected line (Cxcr6gfp/gfp Rag1–/–). Healthy control C57BL/6 mice were used as controls

value: Cxcr6gfp/gfp Rag1-/-

tag: phenotype

value: Inclusion body nephropathy-affected

tag: disease severity

value: moribund


title: healthy1

tag: strain

value: Healthy


title: sick2

value: reduced weight, not moribund


title: WT 3

city: Cambridge

first: Jea Hyun

last: Baek

state: Massachusetts

address: 225 Binney Street

institute: Biogen

data_processing:
Total reads were mapped using the aligner STAR
Genes were quantified with RSEM using OmicSoft Array Studio 10
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include COUNTS for each Sample ...

source_name: kidney

extract_protocol:
Kidneys were removed, flash frozen using liquid nitrogen, and RNA was harvested using Qiagen RNeasy Plus Mini kit. Illumina TruSeq Stranded mRNA  Kit was used with 500 ng of total RNA for the construction of sequencing libraries.
RNAseq library were cleaned up with AMPure XP beads and QC checked with Caliper LabChip GX.

value: kidney

value: 3 months

tag: genotype

value: wild type


title: WT 1


title: cKO 2

value: 2.5 months


title: cKO 1


title: cKO 3


title: cKO 4


title: WT 2


title: WT 4


title: healthy2


title: RPE_2w_rep2

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description: hESC-RPE 14 days, rep2

hyb_protocol: Hybridized in an Affymetrix Hybridization Oven to Affymetrix Gene ST 1.0 Arrays. GeneChips were washed and stained using the Affymetrix Fluidics Station   Hybridized in an Affymetrix Hybridization Oven to Affymetrix Gene ST 1.0 Arrays. GeneChips were washed and stained using the Affymetrix Fluidics Station

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner

data_processing: RMA implemented in Affymetrix Expression Console

source_name: hES-RPE

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: For RPE differentiation, hESCs colonies (Hes1 hES) were picked up using collagenase IV (1 mg/ml; 200 U/mg, Gibco-BRL, Gaithersburg, MD), and cultured using differentiation protocol including treatment with nicotinamide and activinA. After 6-10 weeks in suspension, pigmented clusters were triturated, plated on gelatin (Sigma) coated plates (Corning Incorporated, Corning, NY), and cultured in Knock out medium with 10mM nicotinamide for 3-5 weeks. The RPE cell lines were further propagated using TrypLE Select (Gibco-BRL). The cells were passaged every 2 weeks.

extract_protocol: Extraction of polyA RNA was performed according to the manufacturer's instructions.

treatment_protocol: Hes1 hES differentiation to hES-RPE were differentiated as described (Idelson et al., Cell Stem Cell 2009; PMID: 19796620) using nicotinamide and activinA. After 6-10 weeks in suspension, pigmented clusters were triturated, plated on gelatin (Sigma-Aldrich)-coated plates (Corning Incorporated) and cultured in Knockout medium with 10 mM nicotinamide for 3-5 weeks. Cells were analyzed 5 or 14 days (d5, d14) after splitting.

tag: cell type

value: ES-derived retinal pigment epithelium (RPE) cells


title: RPE_5d_rep2

description: hESC-RPE 5days, rep2


title: RPE_2w_rep3

description: hESC-RPE 14 days, rep3


title: 74_primary_3

city: Toronto

first: Bradly

middle: G.

last: Wouters

state: ON

address: 101 College st West

country: Canada

institute: UHN

description: SAMPLE 18

data_processing: Data was checked for overall quality using R (v2.15.1) with the lumi Bioconductor package. The data was imported into GeneSpring (Agilent), log2 transformed and normalized using a quantile normalization.

source_name: HNSCC derived cell line - primary from tongue

label_protocol: 200 ng of RNA was labelled and amplified using Illumina TotalPrep-96 RNA Amplification kit (Ambion).

growth_protocol: Cells are cultured at 5% CO2  in Modified Eagle Medium F15  supplemented with 10% v/v fetal bovine serum (Gibco).

extract_protocol: Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen inc), following manufacturer’s protocol.

treatment_protocol: 2M cells are plated in 100 mm dish in triplicates for 48 hours at which point the pellets are collected, washed with PBS and flash frozen at -80.

tag: source tissue

value: primary from tongue


title: RPE_5d_rep3

description: hESC-RPE 5days, rep3


title: 74_metastasis_2

description: SAMPLE 13

source_name: HNSCC derived cell line -metastatic

value: metastatic


title: 60_primary_1

description: SAMPLE 11

source_name: HNSCC derived cell line - primary from left tonsil

value: primary from left tonsil


title: 74_primary_2

description: SAMPLE 14


title: RPE_5d_rep1

description: hESC-RPE 5days, rep1


title: 74_metastasis_1

description: SAMPLE 16


title: 74_metastasis_3

description: SAMPLE 15


title: 60_primary_2

description: SAMPLE 9


title: 60_metastasis_3

description: SAMPLE 12


title: RPE_2w_rep1

description: hESC-RPE 14 days, rep1


title: 54_primary_2

description: SAMPLE 10

source_name: HNSCC derived cell line - primary from buchal mucosa

value: primary from buchal mucosa


title: Rfa2_WT_16dC_ChIP

city: Beijing

first: Qing

last: Li

address: No.5 Yiheyuan Road Haidian District

department: School of Life Science

country: China

institute: Peking University

data_processing:
After quality control, samples were mapped by bowtie2 with parameters -k 1 -N 1 --very-sensitive --no-mixed
Reads coverage were calculated and normalized to total reads.
Signal enriched regions were called by MACS2 with parameters -t ChIP_file -c input_file -g 12000000 -B --broad
Genome_build: sacCer3
Supplementary_files_format_and_content: bigWig format

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: Yeast cells were grown on YPD at 25°C and were arrested at G1 phase with alpha-factor, and then released into fresh YPD media for 72 min at 16°C.

extract_protocol:
The Rfa2-DNA were isolated with anti-Rfa2 antibody (gift from Dr. Steven Brill’s laboratory).
DNA prepared above were immobilized on MyOne C1 beads (Life Technology). Primers were added by PCR and adaptors by ligation. Then DNA were eluted as ssDNA at 95°C. The ssDNA were amplified by PCR reaction, and the amount of each sample was verified by qPCR. Verified sample DNA were sequenced by Illumina HiSeq generating about 40bp pair-ended reads.

treatment_protocol: Cells were crosslinked with PFA at 25°C 180rpm for 20min, and PFA was quenched by Glycine.

tag: genotype/variation

value: WT

tag: cell cycle stage

value: S phase

tag: release condition

value: YPD, 16 degree C, 72 min

tag: antibody


title: Rfa2_rtt105d_16dC_ChIP


title: Rfa2_rtt105d_16dC_Input


title: 74_primary_1

description: SAMPLE 17


title: Rfa2_WT_16dC_Input


title: 54_primary_3

description: SAMPLE 5


title: 60_primary_3

description: SAMPLE 6


title: 54_metastasis_1

description: SAMPLE 7


title: rtt105d_RPA-eSPAN_S-phase-96-16degreeC

data_processing:
After quality control, samples were mapped by bowtie2 with parameters -k 1 -N 1 --very-sensitive --no-mixed
Following the algorithm of eSPAN (Yu et al., 2014)
Genome_build: sacCer3
Supplementary_files_format_and_content: default wiggle (WIG) format

growth_protocol: Yeast cells were grown on YPD at 25°C and were arrested at G1 phase with alpha-factor, and then released into fresh YPD media containing 0.2 M Hydroxyurea and 400μg/ml BrdU for 45min at 25°C, or released into fresh YPD media containing 400μg/ml BrdU for 72min and 96min at 16°C.

extract_protocol: DNA prepared above were immobilized on MyOne C1 beads (Life Technology). Primers were added by PCR and adaptors by ligation. Then DNA were eluted as ssDNA at 95°C. The ssDNA were amplified by PCR reaction, and the amount of each sample was verified by qPCR. Verified sample DNA were sequenced by Illumina HiSeq generating about 50bp pair-ended reads.

value: YPD, 16 degree C


title: 54_metastasis_4

description: SAMPLE 3


title: WT_RPA-ChIP_S-phase-96-16degreeC


title: rtt105d_RPA-ChIP_S-phase-72-16degreeC


title: rtt105d_BrdU-IP_S-phase-72-16degreeC

value: BrdU (GE Healthcare(Catalog number:RPN202))


title: 1A vs. 1B_251486817140A

city: Miami

first: Tongyu

last: Wikramanayake

state: FL

address: 1600 NW 10th Avenue, RMSB 2023A

department: Dermatology and Cutaneous Surgery

institute: University of Miami Miller School of Medicine

hyb_protocol: Cy3- and Cy5-labeled aRNA probes were diluted in 2xGEx hybridization buffer, and loaded on to the microarrays in the Agilent SureHyb chamber. Constant rotation at 10rpm in the hybridization oven is designed to achieve uniform sample dispersion across the array surface.  Hybridization was done at 65oC for 17 hours.

scan_protocol: After hybridization, the microarray slides were washed under stringent conditions, and scanned at 10µm resolution using a GenePix 4000A scanner (Molecular Devices, San Jose, CA) at 635nm and 532nm wavelength.

data_processing:
The resulting images were analyzed with the software package GenePix Pro 5.1 (Molecular Devices, San Jose, CA).
Quality Control Criteria used by UM DNA Microarray Facility:
a) Features with Signal to Noise Ratio 3 and above for both Cy3 and Cy5,
b) Features with Diameters between 45 and 70 micron,
c) Features which are not flagged as absent or not found,
d) Features with less than 2% of saturated pixels in both Cy3 and Cy5.
Spot intensities for each probe were calculated by subtracting median local background from median local foreground for each spot.  Spot intensities were transformed by taking the base 2 logarithm of each value.  Data extracted from the images were transferred to the software package Acuity 4.0 (Axon Instruments) for normalization and statistical analysis. Each array was normalized for signal intensities across the whole array and locally, using Lowess normalization.

source_name: Mpzl3 null_P1

label_protocol: The aRNA probes were synthesized using theAmino Allyl MessageAmp™ II aRNA Amplification Kit and coupled with Cy3 or Cy5. First, ArrayScript™ RT was used to produce high yields of full-length cDNA.  The second-strand cDNA synthesis has also been optimized to allow maximal conversion of first-strand cDNA into full-length double-stranded cDNA templates. During probe synthesis, amino allyl–modified NTPs are incorporated into aRNA almost as efficiently as unmodified NTPs.  The a RNA probes are then coupled with Cy3 or Cy5, and purified for hybridization.

extract_protocol: Total RNA was extracted from the dorsal skin of mouse pups with TriZol Reagent (Life Technologies, Grand Island, NY) and purified with the RNeasy mini kit (Qiagen, Germantown, MD).

treatment_protocol: Dorsal skin was collected from euthanized Mpzl3 -/- and +/+ littermates that are 1 day old or 9 days old.

value: Mpzl3 null

value: Dorsal skin

source_name: wild typ_P1


title: rtt105d_BrdU-IP_S-phase-96-16degreeC


title: rtt105d_Input_S-phase-72-16degreeC


title: rtt105d_RPA-ChIP_S-phase-96-16degreeC


title: WT_RPA-eSPAN_S-phase-72-16degreeC


title: rtt105d_Input_S-phase-96-16degreeC


title: rtt105d_RPA-eSPAN_S-phase-72-16degreeC


title: 3B vs. 3A_251486817140C

source_name: Mpzl3 null_P9

source_name: wild typ_P9


title: WT_RPA-eSPAN_S-phase-96-16degreeC


title: 54_primary_1

description: SAMPLE 1


title: WT_RPA-ChIP_S-phase-72-16degreeC


title: 60_metastasis_2

description: SAMPLE 8


title: 60_metastasis_1

description: SAMPLE 2


title: WT_BrdU-IP_S-phase-72-16degreeC


title: WT_BrdU-IP_S-phase-96-16degreeC


title: WT_Input_S-phase-96-16degreeC


title: MPG3

first: Tai

last: Wang

address: Nanxincun 20, Xiangshan

institute: Institute of Botany, CAS

data_processing:
Redundant reads and low-quality reads were removed by Trinity kmer filteri.
The filtered dataset was assembled by using SOAPDenovo-Trans and treated as EST evidence. Protein-encoding and non-coding RNA genes were predicted by an evidence-based approach (Liang et al., 2009)
Cuffdiff (v2.1.1) was used to calculate fragments per kilobase of exon per million reads (FPKM) for both lncRNA and protein-coding genes in each sample (Trapnell et al., 2010).
Genome_build: SL2.5
Supplementary_files_format_and_content: xlsx file includes FPKM values for each sample

organism: Solanum lycopersicum

source_name: Mature pollen grain

growth_protocol: The tomato cultivar Heinz 1706 (Solanum lycopersicum) was planted in a climate-controlled chamber under 14-h light/10-h dark at 28°C for 2 weeks, then fully expanded leaves were collected. One-month-old friable callus was generated from tomato hypocotyls on solid Murashige and Skoog medium containing 1 mg/L 2,4-dichlorophenoxyacetic acid and 0.5 mg/L kinetin in a 12-h light/12-h dark cycle at 25°C.

extract_protocol:
Generative cells and sperm cells were isolated from just-germinated pollen cultured in vitro for 20 min and 10-h-cultured pollen tubes(Lu et al., 2015), respectively. For microspore isolation, flowers 7 mm long were excised and anthers 5 mm long were squashed in ice-cold 0.6 M mannitol solution. The released microspore was filtered through a 75-μm nylon mesh and collected by centrifugation at 200 g for 2 min.
Strand-specific sequencing libraries were generated by using the rRNA-depleted RNA and NEBNext Ultra directional RNA library prep kit for Illumina (NEB) following the manufacturer’s recommendations. The libraries were qualified on the Agilent Bioanalyzer 2100 system, sequenced on an Illumina Hiseq 2000 platform, and 100-bp paired-end reads were generated.

value: Mature pollen grain


title: MPG2


title: MPG1


title: WT_Input_S-phase-72-16degreeC


title: rtt105d_RPA-ChIP_S-phase-45-HU_rep2

value: Early S phase

value: 0.2M HU, 25 degree C


title: rtt105d_RPA-eSPAN_S-phase-45-HU_rep1


title: rtt105d_RPA-eSPAN_S-phase-45-HU_rep2


title: rtt105d_RPA-ChIP_S-phase-45-HU_rep1


title: rtt105d_RPA-ChIP_G1-phase_rep1

value: G1 phase


title: SC2

source_name: Sperm cell

value: Sperm cell


title: PI2

source_name: Pistil

value: Pistil


title: PI1


title: MS3

source_name: Microspore

value: Microspore


title: SC1


title: MS2


title: PI3


title: MS1


title: rtt105d_RPA-ChIP_G1-phase_rep2


title: rtt105d_Input_S-phase-45-HU_rep2


title: Leaf3

source_name: Leaf

value: Leaf


title: rtt105d_Input_S-phase-45-HU_rep1


title: Leaf1


title: GC3

source_name: Generative cell

value: Generative cell


title: rtt105d_Input_G1-phase_rep2


title: rtt105d_Input_G1-phase_rep1


title: rtt105d_BrdU-IP_S-phase-45-HU_rep2


title: rtt105d_BrdU-IP_S-phase-45-HU_rep1


title: SC3


title: WT_RPA-eSPAN_S-phase-45-HU_rep2


title: X160512_21

tag: gender

value: Female

tag: mousingle number

tag: exposure

value: hippocampus

value: P

value: C

value: N

value: A

tag: context1 (a,c)

tag: context2 (a,c)

tag: unalignable

tag: alignable

tag: multimap


title: X160512_19

tag: age

tag: tissue

tag: total reads


title: Cal3

source_name: Callus

value: Callus


title: WT_RPA-ChIP_S-phase-45-HU_rep2

value: WT


title: Leaf2


title: Cal2


title: B3: Cold treatment 1 hour rep3

city: Tottori

first: Yuji

last: Yamasaki

address: 1390 Hamasaka

country: Japan

institute: Tottori University

data_processing:
HISeq read sequences were cleaned using Cutadapt 1.2.1 to remove TruSeq adapter sequences and perform quality trimming at cutoff of 30. Reads trimmed to less than 80bp were removed, as were any reads containing ambiguous bases.
FLASH 1.2.2 was then used with the parameters “-m 15 –x 0” to merge read pairs in which the forward and reverse read overlapped by at least 15 bases. Read pairs merged by FLASH were combined with forward reads without paired reversed reads were combined to create a singleton library.
The read count for a gene (of which there are 49,777) as the number of reads mapping to any transcript of that gene, ensuring that a read that maps to multiple transcripts of a gene is only counted once.
Read counts were normalized across samples using the DESeq package (version 1.12) in R/Bioconductor.
Genome_build: Glycine max (c.v. Williams82)
Supplementary_files_format_and_content: Normalized reads count

organism: Glycine max

source_name: Unifoliates

growth_protocol: Seeds were soaked overnight in water at room temperature and then sown in pots (16.5 cm diameter x 11cm tall) containing a potting soil composed of a mixture of peat, perlite, and vermiculite (PRO-MIX BX, Premier Tech Horticulture) at a depth of approximately 2 cm. Seedlings were grown and watered regularly in a plant growth chamber with 18 h light/6 h dark at 20 ◦C. Lighting was 70 to 80 mmolm−2 s−1. Plants were not inoculated with Rhizobium nor were they fertilized for these short-term experiments.

extract_protocol:
All harvested samples were immediately frozen in liquid nitrogen and stored in -80 °C until RNA isolation. RNA from 100 mg of leaf samples pulverized in liquid nitrogen was obtained with the RNeasy Plant Mini kit (Qiagen Cat. No. 74903, http://www1.qiagen.com/). The lysis buffer (RLT) containing GITC with 157 mM β-mercaptoethanol was used for RNA isolation. RNA was treated with DNase (Qiagen Cat. No. 79254) during isolation, was then eluted from column with water, and quantified by absorbance at 260nm.
Illumina RNA TruSeq v2 sample preparation protocol

treatment_protocol: Cold treatment (4 °C) maintained light cycle started at ZT-4h (4 hours after dawn) on the two weeks old plants (between VC and V1).

tag: cultivar

value: Williams82 PI518671

value: Unifoliates

tag: treatment time

value: 1 hour


title: B2: Cold treatment 1 hour rep2


title: B1: Cold treatment 1 hour rep1


title: GC1


title: C2: Cold treatment 24 hour rep2

value: 24 hour


title: C3: Cold treatment 24 hour rep3


title: Cal1


title: WT_RPA-eSPAN_S-phase-45-HU_rep1

tag: genotype/variation

value: Early S phase

value: 0.2M HU, 25 degree C


title: WT_RPA-ChIP_G1-phase_rep1

tag: cell cycle stage

value: G1 phase


title: A3: Cold treatment 0 hour rep3

value: 0 hour


title: GC2

value: Generative cell


title: WT_BrdU-IP_S-phase-45-HU_rep2

value: BrdU (GE Healthcare(Catalog number:RPN202))

tag: release condition


title: Dauer_starved_7

city: Eugene

first: Amy

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

description:
Dauer_F3_24hr
RC-L141_S15_L001

data_processing:
Bowtie version 1.1.2 was used to map reads to the WS210 version of the genome.
Count files were generated with HTSeq using the GTF file used in Maxwell et al., 2012. This file includes features of the WS210 genome in addition to features of WS220 mapped back to WS210.
edgeR exact test was used on normalized count tables for differential expression analysis. Genes with counts per million (CPM) >4 in all libraries were included in the analysis. LC4_49d_Dauer_starved sample was not included in subsequent differential expression analysis because it did not cluster with other starved samples. The other 38 samples were used.
Genome_build: WS210
Supplementary_files_format_and_content: Count files include the sequence identifier for each gene and the number of counts mapping to that gene (not normalized across libraries).

organism: Caenorhabditis elegans

growth_protocol: N2 worms were maintained well fed for at least 3 generations. Gravid adults were hypochlorite treated to obtain emrbyos, which were put in liquid culture under control or dauer-forming conditions. After control, short-term dauer, or long-term dauer, worms were recovered on plated and maintained well fed. F1 and F2 adults were bleached to obtain embryos for the next generations. F3 embryos were set up in liquid cultures as either fed or starved, and these F3 samples were collected for RNA-seq.

extract_protocol:
Total RNA was extracted using TRIzol with minor modifications to the manufacturer's protocol. 1mL of TRIzol was used per sample. Samples were homogenized using 100uL of acid-washed sand.
Libraries were prepared using the NEB Next Ultra Non-directional mRNA-seq Kit.

treatment_protocol: After 18 hr of feeding or 24 hr of starvation as L1 larvae, worms were spun down for collection. Fed worms were washed quickly 3-4X with S-basal to remove bacteria, and starved worms were washed 0-1X. Samples were flash frozen in liquid nitrogen and stored at -80C until RNA extraction.

tag: strain

tag: developmental stage

value: L1 larvae

tag: fed or starved

value: starved

tag: ancestral conditions

value: long-term dauer

tag: batch


title: Dauer_starved_6

description:
Dauer_F3_24hr
RC-L139_S13_L001


title: WT_BrdU-IP_S-phase-45-HU_rep1

tag: antibody


title: Dauer_starved_4

description:
Dauer_F3_24hr
RC-L137_S11_L001


title: Dauer_starved_2

description:
Dauer_F3_24hr
RC-L135_S9_L001


title: C1: Cold treatment 24 hour rep1


title: WT_RPA-ChIP_S-phase-45-HU_rep1


title: A2: Cold treatment 0 hour rep2


title: A1: Cold treatment 0 hour rep1


title: WT_RPA-ChIP_G1-phase_rep2


title: WT_Input_S-phase-45-HU_rep2


title: WT_Input_S-phase-45-HU_rep1


title: Dauer_starved_16

description:
Dauer_F3_24hr
RC-L148_S22_L001

value: short-term dauer


title: G-13063 cell line neurospheres TEAD1 KO replicate 2

city: NEW YORK

first: NADEJDA

last: TSANKOVA

state: NEW YORK

address: 1425 MADISON AVENUE 9TH FLOOR

department: PATHOLOGY

institute: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI

data_processing:
ATAC-seq
Primary data analysis involved read mapping via bowtie2 (VN:2.1.0) disallowing multiple read mapping
Duplicate read removal and peak calling were done via MACS2 with parameters “-g dm –nomodel –shiftsize 100 extsize 200”.
Genome_build: GRCh37
Supplementary_files_format_and_content: counts.txt
RNA-seq
Samples were run on the HiSeq2500 System, and base calling and Q-scoring was performed with Illumina’s Real-Time Analysis (RTA) version 1.18.64. bcl2fastq 1.8.3 was used to demulitplex and convert files to the fastq format
Read alignment was done using STAR v 2.5.2b with default parameters.
Gene counts were obtained using the featureCount utility of the subread package V. 1.5.0.
Differential expression analysis on the RNAseq data was performed using the DESeq2 R package V. 1.14.1
In summary, Illumina sequencer output FASTQ files for each sample were subjected to a quality control assessment using the FASTQC package. RNAseq reads were aligned to the human genome (GENCODE GRCh38) using STAR with default settings. Gene counts were obtained using the featureCount utility of the subread package. Differential expression analysis on the RNAseq data was performed using the DESeq2 R package, which models the data with a negative binomial distribution and uses Empirical Bayes shrinkage for 5 dispersion and fold-change estimation. Gene set enrichment analysis was done utilizing the HOMER tool. The gene background set for the enrichment analysis was defined as the set of genes passing the independent filtering low expression threshold by DESeq2. All RNAseq tests were FDR adjusted for multiple testing correction.
Genome_build: Genome Reference Consortium Human Build 38 (GRCh38)
Supplementary_files_format_and_content: Microsoft Excel file containing normalized abundance measurements as outputs from DESeq2 R package.

source_name: Gliomaspheres from glioblastoma 13063 derived cell line

growth_protocol: GBM derived cells lines were grown on laminin-coated plates, except when gliomaspheres were grown (low-adherence conditions), and Neurosphere media supplemented with EGF (10ng/ml) and bFGF (10ng/ml).

extract_protocol:
GBM derived cell lines and gliomaspheres were resuspended in Trizol reagent (15596-026, Life Technologies) and flash-frozen. Total RNA was obtained following manufacturer’s protocol, including a DNAse digestion step (Zymo Research). cDNA was generated using Clontech SMART-seq v4 (634888). Briefly, 10ng of RNA were converted to cDNA by introducing 3’ SMART-Seq CDS Primer II A and the SMART-Seq v4 Oligonucleotide. cDNA was subsequently amplified in 8 cycles by LD PCR and purified by Agencourt AMPure XP Kit (Beckman Coulter A63880).
Libraries were prepared using Nextera XT (FC-131-1024). Briefly, 1ng of pre-amplified cDNA was tagmented for 5 mins and subsequently amplified adding Index1 (i7) and Index2 (i5) adapters for 12 cycles. Libraries were then cleaned up using AMPure XP and pooled in equimolar conditions. Regular QC assays were applied before sequencing.

treatment_protocol: Cell lines were washed with 1X PBS and dettach from the plates with Accutase and washed again with 1X PBS before being resuspended in Trizol.

value: TEAD1 KO

tag: gbm classification

value: Glioblastoma "mesenchymal" "proneural" EGFR wildtype

tag: gestational stage


title: WT_Input_G1-phase_rep1

value: WT


title: Dauer_starved_14

description:
Dauer_F3_24hr
RC-L146_S20_L001


title: G-13063 cell line neurospheres TEAD1 KO replicate 3


title: Ctl_starved_7

description:
Ctl_F3_24hr
RC-L142_S16_L001

value: control


title: WT_Input_G1-phase_rep2


title: G-13063 cell line neurospheres TEAD1 KO replicate 1


title: Dauer_starved_13

description:
Dauer_F3_24hr
RC-L144_S18_L001


title: G-13063 cell line neurospheres SHAM replicate 2

value: SHAM


title: Dauer_starved_10

description:
Dauer_F3_24hr
RC-L143_S17_L001


title: Ctl_starved_6

description:
Ctl_F3_24hr
RC-L140_S14_L001


title: G-13063 cell line neurospheres SHAM replicate 1


title: G-13063 cell line neurospheres SHAM replicate 3


title: G-16302 cell line TEAD4 KO

source_name: G-16302 Glioblastoma derived cell line

value: TEAD4 KO

value: Glioblastoma "mesenchymal" EGFR wildtype


title: Ctl_starved_2

description:
Ctl_F3_24hr
RC-L136_S10_L001


title: Ctl_starved_4_10

description:
Ctl_F3_24hr
RC-L138_S12_L001


title: Ctl_starved_16

description:
Ctl_F3_24hr
RC-L149_S23_L001


title: Ctl_starved_14

description:
Ctl_F3_24hr
RC-L147_S21_L001


title: Ctl_starved_13

description:
Ctl_F3_24hr
RC-L145_S19_L001


title: G-13063 cell line TEAD4 KO

source_name: G-13063 Glioblastoma derived cell line


title: G-13306 cell line TEAD4 KO

source_name: G-13306 Glioblastoma derived cell line

value: Glioblastoma "proneural" EGFR wildtype


title: G-12746 cell line TEAD4 KO

source_name: G-12746 Glioblastoma derived cell line

value: Glioblastoma "classical" EGFR increased copy number


title: G-16302 cell line TEAD1 KO


title: LC6_Dauer_starved

description:
LC6_Dauer_24hr
RC-L8_S17_L004

source_name: short-term dauer_starved_24hr


title: LC6_Ctrl_starved

description:
LC6_Ctrl_24hr
RC-L7_S16_L004


title: G-13306 cell line TEAD1 KO


title: G-13063 cell line TEAD1 KO


title: G-12746 cell line TEAD1 KO


title: LC4_49d_Dauer_starved

description:
LC4_49d_Dauer_24hr
RC-L6_S15_L004

source_name: long-term dauer_starved_24hr


title: LC4_49d_Dauer_fed

description:
LC4_49d_Dauer_18hr
RC-L5_S14_L004

source_name: long-term dauer_fed_18hr

value: fed


title: G-16302 cell line SHAM


title: LC3_49d_Dauer_starved

description:
LC3_49d_Dauer_24hr
RC-L4_S13_L004


title: Leptin (100nM) Treated 2

city: Durham

first: Jonathan

middle: D.

last: Douros

state: NC

address: 300 N. Duke St.

department: Duke Molecular Physiology Inst.

institute: Duke University

description: Leptin treated, sample 2

data_processing:
Illumina Casava used for basecalling.
Sequenced reads were trimmed for adaptor sequence, O niloticus  whole genome using bowtie2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated and used for differential gene expression in CuffDiff.
Genome_build: Oreochromis_niloticus.Orenil1.0.dna.toplevel.fa.gz
Supplementary_files_format_and_content: Cuffdiff output file provided (q1 = control, q2 = leptin-treated)

organism: Oreochromis mossambicus

source_name: Pituitary Rostral Pars Distalis

growth_protocol: The pituitary was removed and the RPD was dissected and placed individually in wells of a 96-well plate containing Modified Kreb’s bicarbonate Ringer (320 mOsmolal) solution with addition of glucose (5 mM), L-glutamine (2.05 mM), and Eagles MEM (Gibco, Grand Island, NY) whereby pH of the media was adjusted to 7.4. Tissues were incubated at 24ºC in a humidified environment containing  95%O2/5%CO2 at 60 revolutions per minute.

extract_protocol:
Pituitary rostral pars distalis were 5s pulse sonication on ice
Pituitary mRNA (10 μg) was submitted to the North Carolina State University Genomic Sciences Laboratory (Raleigh, NC) for Illumina cDNA library construction. The cDNA was synthesized using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and tagged with a 5’, four-nucleotide barcode. Illumina cDNA libraries (n = 3) were prepared for each treatment (control or leptin).

treatment_protocol: Following a 2-h preincubation, the media was replaced with  fresh control or experimental media containing recombinant tilapia Leptin A

tag: treatment

value: Leptin

value: Pituitary Rostral Pars Distalis


title: Leptin (100nM) Treated 3

description: Leptin treated, sample 3


title: G-13306 cell line SHAM


title: LC3_49d_Dauer_fed

description:
LC3_49d_Dauer_18hr
RC-L3_S12_L004


title: Leptin (100nM) Treated 1

description: Leptin treated, sample 1


title: LC3_40d_Dauer_starved

description:
LC3_40d_Dauer_24hr
RC-L2_S11_L004


title: LC3_40d_Dauer_fed

description:
LC3_40d_Dauer_18hr
RC-L1_S10_L004


title: G-12746 cell line SHAM


title: Control (PBS) Treated 2

description: Control group, sample 2

value: Control


title: EGFR+ cells from F-10929

description: F2 E+

source_name: Germinal Matrix

extract_protocol:
EGFR+ and EGFR– cell populations were directly isolated from fresh GM and GBM tissues using FACS, without any prior culturing.  Upon FACS isolation, cells were collected in 1xPBS and tagmented with Tn5 enzyme (Illumina, FC-121-1030) for 50min and consequently frozen until library construction.
DNA was amplified with Custom Nextera PCR Primers cointaining barcodes for 9-14 PCR cycles (NEBNext High-Fidelity 2x PCR Master Mix (New England Labs Cat #M0541). Amplicons were run and extracted from agarose gels with a size selection for 150-700bp fragments in order to optimize yield.

treatment_protocol: Tissues were in PIPES solution for a variable time from 1-3hours since the extraction from the patient to the tissue processing. The time from tissue dissociation to FACS isolation was approximately 3 hours.

tag: cell type

value: EGFR+ cells

value: 20 gestational weeks


title: LC14_Dauer_starved

description:
LC14_Dauer_24hr
RC-L24_S33_L005

value: L1 larvae

value: starved


title: G-13063 cell line SHAM


title: Control (PBS) Treated 3

description: Control group, sample 3

tag: tissue


title: LC14_Dauer_fed

description:
LC14_Dauer_18hr
RC-L23_S32_L005

source_name: short-term dauer_fed_18hr

value: short-term dauer


title: EGFR- cells from F-12437

description: F3 E-

growth_protocol: EGFR+ and EGFR– cell populations were directly isolated from fresh GM and GBM tissues using FACS, without any prior culturing.

value: EGFR- cells

value: 19 gestational weeks


title: EGFR+ cells from F-12266

description: F1 E+

value: 22 gestational weeks


title: Control (PBS) Treated 1

description: Control group, sample 1


title: LC14_Ctrl_fed

description:
LC14_Ctrl_18hr
RC-L21_S30_L005

value: control


title: LC14_Ctrl_starved

description:
LC14_Ctrl_24hr
RC-L22_S31_L005


title: EGFR- cells from F-10929

description: F2 E-


title: EGFR+ cells from F-12437

description: F3 E+


title: LC13_Dauer_fed

description:
LC13_Dauer_18hr
RC-L19_S28_L005


title: LC13_Dauer_starved

description:
LC13_Dauer_24hr
RC-L20_S29_L005


title: EGFR- cells from F-12266

description: F1 E-


title: EGFR+ cells from G-11074

description: G1 E+

source_name: Glioblastoma

value: Glioblastoma "classical" EGFR amplification/EGFR vIII mutation


title: EGFR+ cells from G-12396

description: G2 E+

value: Glioblastoma "classical" EGFR amplification


title: LC12_Dauer_starved

description:
LC12_Dauer_24hr
RC-L18_S27_L005


title: EGFR+ cells from G-9259

description: 59 EGFRP


title: LC12_Ctrl_starved

description:
LC12_Ctrl_24hr
RC-L16_S25_L005


title: EGFR+ cells from G-9217

description: 17 EGFRP


title: EGFR- cells from G-11821

description: RG3 E-


title: Ortigueira, haemocytes, 90 days, Bonamia, sample 11

city: LUGO

first: Belen

middle: G

last: Pardo

state: LUGO

address: Avda. Carballo Calero s/n

department: Zoology, Genetics and Physical Anthropology

country: Spain

institute: University of Santiago de Compostela

description:
L2T3B-11
Ortigueira, gene expression at 90 days after Bonamia ostreae infection sample11

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to turbot custom Oligo Microarrays (G2509F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565B) using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Extended dynamic range implemented in the Agilent software was applied to avoid saturation in the highest intensity range. The Agilent feature extraction was used as raw data for further preprocessing. The processed signal (gProcessed-Signal) value was chosen for the statistical analysis.

organism: Ostrea edulis

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA  of each strain and time using the Low Input Quick Amp Labeling Kit, One-Color (Cy3) (Agilent Technologies, USA)  according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Haemolymph samples were taken at three different times after the challenge (1, 30 and 90 days post-challenge, dpc); as much haemolymph as possible (from 0.2 ml to 1.5 ml) was withdrawn from the adductor muscle of each oyster with a 21 gauge needle screwed to a 2 ml cold syringe. Immediately the haemolymph was poured into a cold vial and kept in crushed ice to avoid haemocyte clumping. Haemolymph samples were centrifuged (800 g, 10 min, 4ºC) and the cell fractions (pellets) were resuspended in RNA later and stored at -20ºC after one night at 4ºC until RNA extraction. RNA was individually extracted by RNeasy Mini Kit (Qiagen, Germany) following the manufacturer's instructions with slight modifications, including two additional RPE washes and the optional DNase digestion.

treatment_protocol: The challenge was performed by individually immersing oysters in beakers containing an aerated suspension of 300,000 B. ostreae cells in filtered seawater for 24 h at the Centro de Investigacións Mariñas. The B. ostreae cells for the challenge were isolated from heavily infected oysters collected in Lough Foyle (Ireland), following the procedure described by Mialhe et al. (1988). After challenge, oysters were kept in tanks with running, filtered (1 µm) seawater plus continuous (pumped) supply of mixed cultured algae until the end of the experiment.

value: Ortigueira

tag: phenotype

value: long-term affected (AS); tolerant

value: haemocyte cells

tag: challenged with

value: B. ostreae cells

tag: sampling time point

value: 90 day


title: EGFR- cells from G-12396

description: G2 E-


title: LC12_Ctrl_fed

description:
LC12_Ctrl_18hr
RC-L15_S24_L005

value: fed


title: Ortigueira, haemocytes, 90 days, Bonamia, sample 10

description:
L2T3B-10
Ortigueira, gene expression at 90 days after Bonamia ostreae infection sample10


title: LC11_Dauer_fed

description:
LC11_Dauer_18hr
RC-L13_S22_L005


title: Ortigueira, haemocytes, 90 days, Bonamia, sample 12

description:
L2T3B-12
Ortigueira, gene expression at 90 days after Bonamia ostreae infection sample12


title: Ortigueira, haemocytes, 90 days, Bonamia, sample 13

description:
L2T3B-13
Ortigueira, gene expression at 90 days after Bonamia ostreae infection sample13


title: LC11_Dauer_starved

description:
LC11_Dauer_24hr
RC-L14_S23_L005


title: Ortigueira, haemocytes, 90 days, Bonamia, sample 15

description:
L2T3B-15
Ortigueira, gene expression at 90 days after Bonamia ostreae infection sample15


title: EGFR- cells from G-11074

description: G1 E-


title: LC11_Ctrl_starved

description:
LC11_Ctrl_24hr
RC-L12_S21_L004


title: 54_metastasis_2

description: SAMPLE 4

source_name: HNSCC derived cell line -metastatic

tag: source tissue

value: metastatic


title: Ortigueira, haemocytes, 30 days, Bonamia, sample 18

description:
L2T2B-18
Ortigueira, gene expression at 30 days after Bonamia ostreae infection sample 18

value: 30 day


title: Ortigueira, haemocytes, 30 days, Bonamia, sample 16

description:
L2T2B-16
Ortigueira, gene expression at 30 days after Bonamia ostreae infection sample 16


title: LC12_Dauer_fed

description:
LC12_Dauer_18hr
RC-L17_S26_L005

value: L1 larvae


title: LC11_Ctrl_fed

description:
LC11_Ctrl_18hr
RC-L11_S20_L004


title: LC10_Ctrl_starved

description:
LC10_Ctrl_24hr
RC-L10_S19_L004

value: starved


title: LC10_Ctrl_fed

description:
LC10_Ctrl_18hr
RC-L9_S18_L004


title: 96hW Larval Head Replicate 3 RNA-Seq

first: Robert

last: Lowe

address: 4 Newark Street

institute: QMUL

data_processing:
Transcripts were quantitated using Kallisto tool (https://pachterlab.github.io/kallisto/). Default parameters were used except for bootstrapping which was set to 100 and reads set to stranded
Genome_build: Amel_4.5
Supplementary_files_format_and_content: Transcript ID, Transcript Length, Effective Length, Estimated Read Counts, Transcripts Per Million

organism: Apis mellifera

source_name: Larval Head

extract_protocol:
Larval head RNA was isolated using TRIzol (ThermoFisher, 15596018), followed by RNA Clean & Concentrator kit (Zymo Reasearch, R1015).
Polyadenylated mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490). Libraries were constructed with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420). Library quality was verified by running an Agilent High Sensitivity DNA chip (Agilent, 5067-4626) on a 2100 Bioanalyzer (Agilent Genomics).

value: Larval Head

tag: caste


title: 96hW Larval Head Replicate 2 RNA-Seq


title: Ortigueira, haemocytes, 90 days, control

description:
L2T3C
Ortigueira, gene expresion control after 90 days

value: none (non-challenged control)


title: 96hW Larval Head Replicate 1 RNA-Seq


title: Ortigueira, haemocytes, 30 days, Bonamia, sample 5

description:
L2T2B-5
Ortigueira, gene expression at 30 days after Bonamia ostreae infection sample 5


title: Ortigueira, haemocytes, 30 days, control

description:
L2T2C
Ortigueira, gene expresion control after 30 days

source_name: Ortigueira_haemocyte cells_30 days_ control


title: Ortigueira, haemocytes, 1 day, Bonamia, sample 17

description:
L2T1B-17
Ortigueira, gene expression at 1 day after Bonamia ostreae infection sample 17

value: 1 day


title: 96hW Larval Head Replicate 4 RNA-Seq


title: Ortigueira, haemocytes, 30 days, Bonamia, sample 17

description:
L2T2B-17
Ortigueira, gene expression at 30 days after Bonamia ostreae infection sample 17


title: 96hQ Larval Head Replicate 4 RNA-Seq


title: Ortigueira, haemocytes, 1 day, Bonamia, sample 2

description:
L2T1B-2
Ortigueira, gene expression at 1 day after Bonamia ostreae infection sample 2


title: Ortigueira, haemocytes, 1 day, Bonamia, sample 5

description:
L2T1B-5
Ortigueira, gene expression at 1 day after Bonamia ostreae infection sample 5


title: Erlotinib-induced senescence, biological rep3

first: Xiao-Fan

address: 308 Research Drive

department: Pharmacology and Cancer Biology

description: Gene expression data from Senescent NHBE cells treated with Erlotinib

data_processing:
Microarray Analysis was been conducted by Duke Microarray Core facility
The data were analyzed with Partek Genomic Suite

source_name: Normal Human Bronchial Epithelial Cells

growth_protocol: Cells were grown in BEGM Bronchial Epithelial Cell Growth Medium (LONZA)

extract_protocol: total RNAs were isolated using Rneasy mini kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Erlotinib has been added inside the medium 1uM for 20 hours.

value: epithelial lining of airways above bifurcation of the lungs

tag: gender

value: Male

tag: age


title: Ortigueira, haemocytes, 1 day, Bonamia, sample 6

description:
L2T1B-6
Ortigueira, gene expression at 1 day after Bonamia ostreae infection sample 6

tag: strain


title: Ortigueira, haemocytes, 1 day, control

description:
L2T1C
Ortigueira, gene expresion control after 1 day


title: Erlotinib-induced quiescence, biological rep3

description: Gene expression data from Quiescent NHBE cells treated with Erlotinib

hyb_protocol: Microarray Analysis was been conducted by Duke Microarray Core facility


title: Proliferating cells, biological rep3

description: Gene expression data from NHBE cells treated with DMSO

scan_protocol: Microarray Analysis was been conducted by Duke Microarray Core facility


title: Ortigueira, haemocytes, 1 day, Bonamia, sample 22

description:
L2T1B-22
Ortigueira, gene expression at 1 day after Bonamia ostreae infection sample 22


title: Erlotinib-induced senescence, biological rep1

label_protocol: Microarray Analysis was been conducted by Duke Microarray Core facility


title: Erlotinib-induced senescence, biological rep2


title: Ortigueira, haemocytes, 30 days, Bonamia, sample 6

description:
L2T2B-6
Ortigueira, gene expression at 30 days after Bonamia ostreae infection sample 6


title: 96hQ Larval Head Replicate 3 RNA-Seq


title: Erlotinib-induced quiescence, biological rep2


title: Erlotinib-induced quiescence, biological rep1


title: rna_blue_rep2

city: Wako

first: tomoya

last: fujita

state: Saitama

address: 2-1, Hirosawa

department: Cluster for Pioneering Research

institute: RIKEN

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: tair10
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

organism: Arabidopsis thaliana

extract_protocol: RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling) or TruSeq (illumina) (for mRNA-seq)

value: blue light condition


title: PC9 HCI-2509 rep2

city: Cologne

first: Iris

middle: Felicitas

last: Macheleidt

address: Kerpenerstr. 63

department: Institute for Pathology

country: Germany

institute: University Hopsital Cologne

description: Gene expression data from PC9 NSCLC cells treated with 2µM HCI-2509

hyb_protocol: 4.1µg of biotinylated cDNA were hybridized for 16 hr at 45C on a huGene 2.0 St Array Chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner G3000 7G

data_processing: The data were analyzed with Affymetrix ® Transcriptome Analysis Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: PC9 cells treated with 2µM HCI-2509

label_protocol: Biotinylated cDNA was prepared according the manufacturer´s protocol of Applause® WT-Amp ST System (NuGene®; San Carlos, USA) using 100ng of total RNA

growth_protocol: PC9 cells were cultured in DMEM media supplemented with 10% FCS. Cells were seeded out at a density of 2 x 10^6.

extract_protocol: RNA was exctraced using the automated isolation kit AS-1280 (Promega) in the Maxwell-16 (Promega) according to the manufacturer´s protocol.

treatment_protocol: 24hours post plating medium was changed to one containng 2µM HCI-2509. After 48hours, cells were harvested to isolate total RNA

value: Lung


title: PC9 HCI-2509 rep1


title: PC9 HCI-2509 rep3


title: 96hQ Larval Head Replicate 2 RNA-Seq


title: Proliferating cells, biological rep1


title: Limfjord, haemocytes, 90 days, Bonamia, sample 21

description:
L1T3B-21
Limfjord, gene expression at 90 days after Bonamia ostreae infection sample 21

value: Limfjord

value: naïve (NS)


title: PC9 Untreated rep3

description: Gene expression data from PC9 NSCLC cells

source_name: Untreated PC9 cells


title: rna_dark_rep2

value: dark condition


title: 96hQ Larval Head Replicate 1 RNA-Seq


title: rna_dark_rep1


title: Limfjord, haemocytes, 90 days, Bonamia, sample 15

description:
L1T3B-15
Limfjord, gene expression at 90 days after Bonamia ostreae infection sample 15

value: haemocyte cells

value: B. ostreae cells


title: 96hW Input DNA

data_processing:
Reads were mapped to the apis mellifera genome using bowtie2 (v2.2.8)
Reads were extended to 250bp in length and counted in 100bp windows spaced every 50bp. Creating a series of overlapping windows. Each window was then extended to 5kbp and the total number of input reads were counted.
A enrichment value for each 100bp window was calculated by dividing the total number of reads by the averaged backround count and multiplying by the fraction of mapped reads in input divided by ChIP.
Genome_build: Amel_4.5
Supplementary_files_format_and_content: Reference Name,Start Position of Window, End Position of Window, Enrichment Value

extract_protocol:
Extracts from sonicated nuclei were cleared by centrifugation (20000×g; 10 min), histone-DNA complexes were concentrated using an Amicon centrifugal filter (Millipore) and split into 50 μl aliquots. Each aliquot was diluted ten-fold with ChIP dilution buffer (0.01% SDS; 1.1% Triton X-100; 1.2 mM EDTA; 16.7 mM Tris-HCl pH 8.0; 167 mM NaCl; protease inhibitors cocktail) and histone-DNA complexes were immunoprecipitated with antibodies overnight.
Libraries were prepared with the NEBNext Ultra II Library Prep Kit for Illumina (NEB, E7645S) according to the manufacturer’s protocol. Insert sizes were selected for 250 bp with NEBNext Sample Purification Beads (NEB, E7104S).  Libraries were PCR amplified using NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (NEB, E7335S). The number of PCR cycles was selected based on the amount of input DNA. Library quality was verified by running an Agilent High Sensitivity DNA chip (Agilent, 5067-4626) on a 2100 Bioanalyzer (Agilent Genomics).

tag: chip antibody


title: Limfjord, haemocytes, 90 days, Bonamia, sample 9

description:
L1T3B-9
Limfjord, gene expression at 90 days after Bonamia ostreae infection sample 9

value: 90 day


title: Limfjord, haemocytes, 90 days, Bonamia, sample 7

description:
L1T3B-7
Limfjord, gene expression at 90 days after Bonamia ostreae infection sample 7


title: rna_blue_rep1


title: ribo_dark_rep2

data_processing:
Library strategy: Ribo-Seq
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: tair10
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

extract_protocol:
Rnase I footprinting, ribosome pelleting, RNA extraction
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling) or TruSeq (illumina) (for mRNA-seq)


title: ribo_dark_rep1


title: Proliferating cells, biological rep2


title: Whole_Brain_Wild_Type_Young_Mice_Rep4

city: NICE

first: Laurent

last: SUISSA

state: (State)

address: 28, Avenue de Valombrose

country: France

institute: Faculté de Médecine

hyb_protocol: Labelled cRNA probes (400 ng) were hybridized on 8 x 60K high-density SurePrint G3 gene mouse GE 8 x 60K Agilent microarrays.

scan_protocol: standard Agilent protocol

data_processing:
standard Agilent protocol
Normalization of microarray data was performed using the Limma package (http://www.bioconductor.org). Interslide normalization was performed using the quantile methods.

source_name: Whole Brain Wild Type Young Mice Replicate4

label_protocol: Cy3 dye using the Low RNA Input QuickAmp Kit (Agilent), as recommended by the supplier.

extract_protocol: RNA was isolated with a RNeasy kit (Qiagen, Courtaboeuf, France) from freshly removed mouse brain tissue according to the manufacturer’s protocol.

value: Whole brain

value: male

value: 4 months


title: Whole_Brain_Wild_Type_Young_Mice_Rep2

source_name: Whole Brain Wild Type Young Mice Replicate2


title: PC9 Untreated rep2


title: 96hW H3K27ac Replicate 2 ChIP-Seq

city: London


title: ribo_blue_rep1


title: 96hW H3K36me3 Replicate 1 ChIP-Seq


title: 96hQ Input DNA


title: 96hW H3K27ac Replicate 1 ChIP-Seq


title: PC9 Untreated rep1


title: P4_7_9

city: Hong Kong

first: Chee Kent

last: Lim

address: Kowloon Tong

department: School of Energy and Environment

country: Hong Kong

institute: City University of Hong Kong

description:
Itaconic acid-producing phaR mutant strain.
AM1_TPM_250718.txt

data_processing:
Quality control (QC) of raw reads was performed using illumina-utils v2.0.2 (Eren et al. (2013) PloS One 8: e66643) and FastQC v0.11.5 (Andrews, S. (2010). FastQC: a quality control tool for high throughput sequence data).
Reads were pseudo-aligned using kallisto v0.43.1 (Bray et al. (2016) Nature biotechnology 34: 525) with 100 bootstraps per sample.
Differential analysis of RNA-Seq data was conducted in sleuth v0.29.0 (Pimentel et al. (2017) Nature methods 14: 687) integrating the bootstraps from the pseudo-alignment.
Genome_build: GCF_000022685.1 (ASM2268v1)
Supplementary_files_format_and_content: AM1_TPM_250718.txt: Tab-delimited text file includes transcripts per million (TPM) values for each sample.

organism: Methylorubrum extorquens

source_name: whole cell

growth_protocol: Cultures were grown aerobically in minimal media adapted from Mokhtari-Hosseini et al. (Bioresource Technology (2009) 100: 2436-43) supplemented with 240 mM methanol for 96 hours at 30 oC.

extract_protocol:
RNA was extracted from biomass using RNeasy kit (Qiagen) after cell lysis with lysozyme (Sigma-Aldrich) for 10 min and followed by homogenization with autoclaved 0.1 mm zirconia-silica beads (BioSpec) for 5 min. For gDNA contamination removal, DNA digestion with DNase (Qiagen) was performed thrice.
Ribosomal RNA removal in RNA samples was done using Ribo-Zero Magnetic Kit (Illumina) and rRNA-depleted RNA samples were used as template to create cDNA libraries containing 250~300 bp inserts with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs).

tag: strain/background

tag: genotype/variation

value: phaR mutant strain with pTE101a-CAD plasmid


title: Limfjord, haemocytes, 90 days, control

description:
L1T3C
Limfjord, gene expresion control after 90 days


title: 96hW H3K4me3 Replicate 2 ChIP-Seq

value: Larval Head


title: P4_4_6


title: 96hW H3K36me3 Replicate 2 ChIP-Seq


title: Limfjord, haemocytes, 30 days, Bonamia, sample 20

description:
L1T2B-20
Limfjord, gene expression at 30 days after Bonamia ostreae infection sample 20

value: 30 day


title: Limfjord, haemocytes, 30 days, Bonamia, sample 14

description:
L1T2B-14
Limfjord, gene expression at 30 days after Bonamia ostreae infection sample 14


title: Limfjord, haemocytes, 90 days, Bonamia, sample 6

description:
L1T3B-6
Limfjord, gene expression at 90 days after Bonamia ostreae infection sample 6


title: 96hW H3K4me3 Replicate 1 ChIP-Seq


title: Whole_Brain_Wild_Type_Old_Mice_Rep4

source_name: Whole Brain Wild Type Old Mice Replicate4

value: 18 months


title: P4_1_3


title: Limfjord, haemocytes, 30 days, Bonamia, sample 115

description:
L1T2B-115
Limfjord, gene expression at 30 days after Bonamia ostreae infection sample 115


title: Limfjord, haemocytes, 30 days, Bonamia, sample 5

description:
L1T2B-5
Limfjord, gene expression at 30 days after Bonamia ostreae infection sample 5


title: Whole_Brain_Wild_Type_Young_Mice_Rep3

source_name: Whole Brain Wild Type Young Mice Replicate3


title: 96hQ H3K36me3 Replicate 2 ChIP-Seq


title: Limfjord, haemocytes, 30 days, Bonamia, sample 4

description:
L1T2B-4
Limfjord, gene expression at 30 days after Bonamia ostreae infection sample 4


title: 96hQ H3K36me3 Replicate 1 ChIP-Seq


title: P2_4_6

description:
Itaconic acid-producing wildtype strain.
AM1_TPM_250718.txt

value: wildtype strain with pTE101a-CAD plasmid


title: Limfjord, haemocytes, 30 days, control

description:
L1T2C
Limfjord, gene expresion control after 30 days

value: none (non-challenged control)


title: Whole_Brain_Wild_Type_Young_Mice_Rep1

source_name: Whole Brain Wild Type Young Mice Replicate1


title: Whole_Brain_Wild_Type_Old_Mice_Rep2

source_name: Whole Brain Wild Type Old Mice Replicate2


title: 96hQ H3K27ac Replicate 2 ChIP-Seq


title: Whole_Brain_SLC5A8_Deficient_Young_Mice_Rep4

source_name: Whole Brain SLC5A8 Deficient Young Mice Replicate4


title: Whole_Brain_SLC5A8_Deficient_Young_Mice_Rep3

source_name: Whole Brain SLC5A8 Deficient Young Mice Replicate3


title: Limfjord, haemocytes, 1 day, Bonamia, sample 17

description:
L1T1B-17
Limfjord, gene expression at 1 day after Bonamia ostreae infection sample 17

source_name: Limfjord_haemocyte cells_1 day_Bonamia

value: 1 day


title: Whole_Brain_Wild_Type_Old_Mice_Rep1

source_name: Whole Brain Wild Type Old Mice Replicate1


title: 96hQ H3K27ac Replicate 1 ChIP-Seq


title: P1_7_9

description:
Wildtype strain with control plasmid.
AM1_TPM_250718.txt

value: wildtype strain with pTE101 plasmid


title: Whole_Brain_Wild_Type_Old_Mice_Rep3

source_name: Whole Brain Wild Type Old Mice Replicate3


title: P1_4_6