title: W160A Sample #7

city: Cullowhee

first: Jamie

middle: R

last: Wallen

state: North Carolina

address: 111 Memorial Drive

department: Chemistry & Physics

institute: Western Carolina University

description: Sample 22

data_processing:
Sequence data was demultiplexed and adapter sequences were trimmed during primary analysis using Illumina® Real Time Analysis (RTA) software. Resulting raw fastq files were uploaded into CLC Genomics Workbench software v12.0.  All failed reads were filtered from the data set prior to sec-ondary analysis.
Remaining reads were quality trimmed when a) base accuracy decreased below 95% b) two or more ambiguous nucleotides were called sequentially and 3) when a sequence read was less than 15 bp in length or greater than 1000 bp in length.
Retained reads were mapped against a bacteriophage T7 reference genome (NC_001604.1-2) to maintain consistency in position number across the genome using the standard CLC mapping algorithm.
For the first round of samples sequenced (passage zero and samples 1-3 for each polmerase background), variant tables were constructed using the Basic Variant Detection algorithm v2.02 with a specified minimum coverage of 10, minimum count of 2, and frequency threshold of 10%
For the second round of samples sequenced (samples 4-7 for each polmerase background), variant tables were constructed using the Basic Variant Detection algorithm v2.02 with a specified minimum coverage of 100, minimum count of 25, and frequency threshold of 35%
Four variants from the reference genome were consistently found in all T7 data sets, including passage zero (P0). These variants did not represent mutations of interest and were therefore removed from the data set.
Genome_build: NC_001604.1-2
Supplementary_files_format_and_content: Variants were analyzed using CLC Genomics Workbench. All mutations were mapped to specific locations in the T7 genome. A full analysis of all mutations are provided in the SequencingTable_FullAnalysis.xlsx

organism: Escherichia phage T7

source_name: Bacteriophage T7

growth_protocol: Samples were grown in either LB broth or LB agar at 37 degrees C in the presence of 100 ug/mL ampicilin to maintain the pET21b plasmid containing wild-type, 5A7A, or W160A T7 DNA polymerase.

extract_protocol:
Genomic DNA from each purified viral stock was purified by phenol/chloroform extraction.
NEBNext UltraII DNA Library Prep Kit and NEBNext index primers were used to create libraries from viral genomic DNA following manufacturer’s protocol.  AMPure XP beads were used for size selection. Viral genomic libraries were then pooled, denatured, and sequenced using either a MiSeq Reagent Nano v2 300 cycle kit (for passge 0 and samples 1-3 for each polymerase) or v3 600 cycle kit (for samples 4-7 of each polymerase background) according to Illumina protocols.
MiSeq Reagent Nano Kit v2 300 cycle, or v3 600 cycle

treatment_protocol: The stock T7Δ5 virus was serially passaged ten times at a multiplicity of infection (MOI) of 0.001 in E. coli BL21(DE3) cells harboring a pET21b plasmid containing either wild-type, 5A7A, or W160A gp5. For passaging, two mL of an overnight culture of E. coli containing a pET21b gp5 plasmid were added to eighteen mL of LB broth containing ampicillin to give a starting cell OD600 of ~0.4 (~3.2 x 108 cells/mL). Stock T7Δ5 phage was then added to the bacterial cell culture at an MOI of 0.001, and the cultures were allowed to shake at 37C for four hours. After four hours, the cultures were spun at 2,600 RPM for 10 minutes, and the resulting supernatant containing virus (passage one) was tittered and stored at 4C. For each polymerase, this process was repeated for a total of ten passages (passage one virus was subsequently used to infect a fresh culture of cells at a MOI=0.001, and four hours later passage two virus was collected and tittered, etc.). Each passage was stored at 4C after harvest. This process was performed in duplicate in order to provide viral samples for sequencing from two independent experiments.  To prepare for whole-genome sequencing a plaque assay was performed. Seven individual, well-isolated plaques (three from the first viral passaging, four from the second passaging) from each polymerase background passage ten sample were picked and amplified.

tag: sample type

value: W160A Sample

tag: passages

tag: protocol

value: Virus passaged in the presence of W160A T7 DNA polymerase


title: Poplar_G798-T03

status: Public on Jan 01 2020

type: SRA

city: Beijing

first: Huimin

last: Chen

state: Beijing

address: No. 20 Nanxin Village, Xiangshan, Haidian District, Beijing

department: State Key Laboratory of Systematic and Evolutionary Botany

country: China

institute: Institute of Botany, Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Raw reads were filtered to obtain clean reads using NGSToolkit(V2.3.3) and Trimmomatic(V0.36) software
Clean reads were aligned with Populus trichocarpa genome (https://phytozome.jgi.doe.gov/pz/portal.html#!bulk?org=Org_ Ptrichocarpa_er) using the HISAT (V2.0.5) software with default parameters
The reads which mapped to transcripts was quantified by using HTSeq (V2.2.1) package
The differential expression genes(DEGs) were identified using edgeR (V3.16.5) package. The screening criteria are as follows: |log2FC| ≥ 1 and FDR < 0.05
Genome_build: Ptrichocarpa_444_v3.1
Supplementary_files_format_and_content: tab-delimited text files include ht-count values for each Sample

molecule: total RNA

organism: Populus tomentosa

source_name: Root

growth_protocol: P.tomentosa were micro propagated on 5‰ agar-solidified Lloyd & McCown woody plant basal medium (WPM) with 1.5% sucrose and 1mg/L NAA. The growth chamber conditions were set as follows: 24°C, 16h of light per day and photon flux density of approximately 50 μmol m-2 s-1. Micro propagated plants which had the same developmental stage (~10 cm shoot length) were selected and transferred to WPM solution.

extract_protocol:
RNA isolation and extraction were carried out at Biomarker technologies company (Beijing, China) with three biological replicates
Library construction were carried out at Biomarker technologies company (Beijing, China) with three biological replicates

treatment_protocol: Plants were divided into two groups on average and transferred to new WPM solution containing 100μM Fe (Fe-sufficient group) and 0μM Fe (Fe-deficient group), respectively.

tag: tissue

value: Root

tag: group

value: Fe-sufficient

tag: developmental stage

value: Seedling stage


title: PfRrp6-DD-1C-GlcN+_R_rep1_RNA-seq

city: Shanghai

first: Shijun

last: Shen

state: Shanghai

address: 1239 Siping Road, Shanghai, P.R. China

department: Bioninformatics

institute: Tongji University

data_processing:
Low-quality and adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 75 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Hisat2 strand-specific mode (v2.1.0)  with parameters: --rna-strandness RF --dta --no-discordant --no-mixed --no-unal.
The Samtools (v1.9)  was used to transfer the mapping results from sam format to position sorted bam format.
Mapped reads were subsequently assembled into transcripts guided by the PlasmoDB gff annotation files (Pf 3D7 v32) using featureCounts (v1.6.1)  with parameters: -M -p -B -C for all; -s 2 for sense transcripts; -s 1 for antisense transcripts.
The bam files were converted to bigwig files using bamCoverage from the deeptools suite  (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 10 --smoothLength 30 -ignore Pf3D7_API_v3 Pf_M76611
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The raw counts were calculated by featureCounts as described above.

organism: Plasmodium falciparum

source_name: PfRrp6-DD clone line PfRrp6-DD-1C cultured with 5 nM GlcN

growth_protocol: Parasite-infected red blood cells were cultured in T75 flask at 2% hematocrit in the presence of 5% O2 and 5% CO2 (rest N2) in RPMI 1640 supplemented with 25mM Hepes, 50mg/l Hypoxanthine, 0.21% NaHCO3, 0.5% Albumax I and 20mg/l Gentamicin. The vector line was selected and cultured with 2.5nM WR99210. The 5mM GlcN was added in the inducible knock down culture.

extract_protocol:
Highly synchronous parasites were harvested at the ring stage (10 h after invasion), Total RNA was isolated using TRIzol (Life) according to the manufacturer’s manual and further purified using the Direct-zol RNA Kit (ZYMO RESEARCH) for removal of gDNA. Residual gDNA was digested with TURBO DNA-freeTM DNaseI (Ambion) and the RNA was quantified by NanoDrop.
The RNA isolation, mRNA enrichment and library construction were performed as described using 15 cycles of library amplification. The mRNA was enriched by poly(A) selection with the KAPA mRNA Capture Beads (KAPA), and fragmented to about 300–400 nucleotides (nt) in length, then all subsequent steps were performed in accordance with an KAPA Stranded mRNA-Seq Kit Illumina platform (KAPABIOSYSTEMS KK8421-96 libraries).

treatment_protocol: Parasite cultures were synchronized by repeated sorbitol and percoll-sorbitol treatments ((Lambros and Vanderberg, 1979)

tag: development stage

value: Ring

tag: strain

value: Pf 3D7

tag: genotype

tag: host

value: Homo sapiens


title: PfRrp6-DD-1C_T_rep1_RNA-seq

source_name: PfRrp6-DD clone line PfRrp6-DD-1C

value: Trophozoite


title: TX9582

city: Galveston

first: Daniele

last: Swetnam

state: TX

address: 301 University Blvd

department: Experimental Pathology

country: USA

institute: University of Texas Medical Branch

data_processing:
Aptmers and poor quality bases (q< 20) were removedwith Trimmomatic
reads were aligned to the reference (AF196835) with bowtie2 under the sensitive local parameters
a consensus sequence was extracted using the mpileup function in samtools
alignment was repaired by realigning to the new consensus sequence in Bowtie2 under the very sensitive local parameters
reads were sorted by coordinate by the SamSort function of picard tools
Duplicates were removed with the MarkDuplicate function of picard tools
Single nucleotide variants were identified with V-phaser2
Genome_build: AF196835
Supplementary_files_format_and_content: variant caller summary; Each variant entry consists of the following: the reference position (coordinate starts at 1), predicted variant, consensus base, strand-bias p-value, type of variant (Single nucleotide polymorphism (SNP) or Length polymorphism (LP)), frequency of the variant and the profile, where each entry consists of three values: the base, its count in the forward strand, and its count in the reverse strand, separated by Colons.

organism: West Nile virus

source_name: Cyanocitta cristata (Blue Jay)

growth_protocol: virus was isolated from the brain  homogenate  of dead birds by passageing on vero cells

extract_protocol:
RNA was extracted from the supernatant of infected vero cells using the QIAamp Viral RNA Mini kit according to the manufacturer’s recommendations
Libraries were generated with a TruSeq RNA v2 kit (Illumina) according the the manufactures instructions

tag: source tissue

value: dead bird brain homogenate

tag: location

value: USA:TX, Pasadena, Harris Co. (77504)

tag: collection date

tag: molecule subtype

value: viral RNA


title: Poplar_G798-T09

value: Fe-deficient


title: PfRrp6-DD-1C_R_rep2_RNA-seq


title: PfRrp6-DD-1C_R_rep1_RNA-seq


title: SHSY5Y_SOX9-GFP_1112

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

description: SH-SY5Y cell was transfected with pCMV6-SOX9-GFP, and GFP+ cells were sorted

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26
Supplementary_files_format_and_content: tad-delimited, raw counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Neuroblasotma cell line

growth_protocol: Cell lines were culture in DMEM/F-12 medium(Thermo Fisher Scientific) supplemented with 10% fetal bovine serum(Dutscher), 1X L-glutamine(Thermo Fisher Scientific), 1X sodium pyruvate(Thermo Fisher Scientific), and 1X MEM non-essential amino acids(Thermo Fisher Scientific), and maintained in a humidified incubator at 37°C, 5% CO2.

extract_protocol:
Total RNA of harvested cells was extracted by RNeasy Kit (QIAGEN) according to manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: Neuroblasotma cell line

tag: genotype/variation

value: SOX9 overexpression

tag: plasmid


title: TX9589

value: USA:TX, Kingswood (77336)


title: W160A Sample #4

description: Sample 19

library_source: genomic

molecule: genomic DNA

tag: sample type

tag: passages


title: TX9601

source_name: Myiopsitta monachus (Monk Parakeet)

value: USA:TX, Harris Co. (77034)


title: W160A Sample #5

description: Sample 20

value: W160A Sample

tag: protocol


title: 22.NOD2.Jasp

type: RNA

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted txt files were analyzed further using R and the associated BioConductor limma package. Background correction ( normexp) and normalization between arrays  (quantile) was used,control probe were removed. Within-array replicate features were condensed with their average by avereps.

source_name: HeLa NOD2 cells, 4hr, replicate 1

label_protocol: RNA was labeled with the single-color Low Input Quick Amp Labeling Kit (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: HeLa inducible NOD1 or NOD2 cells were grown in DMEM medium supplemented with 10% FBS, 1mM Sodium Pyruvate and 2mM L-Glutamine overnight. To induce NOD1 or NOD2 expression, HeLa NOD1 or NOD2 cells were treated in absence or presence of 0.5 µg/mL or 0.25 µg/mL doxycyclin overnight, respectively.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

treatment_protocol: After doxycycline treatment, medium was replaced with fresh DMEM full medium. Then HeLa NOD1 or NOD2 cells were treated with various stimuli for 4 hrs.

value: HeLa

tag: inducible gene

tag: treatment

value: Jasplanokinolid (0.2 µM)

tag: sample purification

value: ok


title: TX9780

value: USA:TX, Houston (77035)


title: W160A Sample #6

description: Sample 21

value: Virus passaged in the presence of W160A T7 DNA polymerase


title: W160A Sample #3

description: Sample 18


title: Poplar_G798-T02

tag: tissue

value: Root

tag: group

value: Fe-sufficient

tag: developmental stage

value: Seedling stage


title: WT_NF54_S_rep1_RNA-seq

source_name: Pf NF54 clone line

tag: development stage

value: Schizont

tag: strain

value: Pf NF54

tag: genotype

value: wild type

tag: host

value: Homo sapiens


title: TX9364

source_name: Mimus polyglottos (Mocking Bird)

tag: source tissue

value: dead bird brain homogenate

tag: location

value: USA:TX, Kingswood (77339)

tag: collection date

tag: molecule subtype

value: viral RNA


title: TX9587

source_name: Quiscalus mexicanus (Great-Tailed Grackle)

value: USA:TX, Houston (77084)


title: Poplar_G798-T01


title: W160A Sample #1

description: Sample 16

tag: sample type

value: W160A Sample


title: SHSY5Y_SOX9-GFP_1108

tag: cell line

tag: cell type

value: Neuroblasotma cell line

tag: genotype/variation

value: SOX9 overexpression

tag: plasmid


title: W160A Sample #2

description: Sample 17

tag: passages

tag: protocol


title: SHSY5Y_GFP_1112

description: SH-SY5Y cell was transfected with pSUPER-GFP, and GFP+ cells were sorted

value: Control

value: pSUPER-GFP


title: 5A7A Sample #7

description: Sample 15

value: 5A7A Sample

value: Virus passaged in the presence of 5DA,7EA T7 DNA polymerase


title: SHSY5Y_GFP_1108


title: SHSY5Y_SOX9-GFP_1105


title: WT_NF54_R_rep2_RNA-seq

value: Ring


title: WT_NF54_S_rep2_RNA-seq


title: CREB1-GST_rep1

type: protein

city: Bethesda

first: Charles

last: Vinson

state: MD

address: 37 Convent Drive

department: National Cancer Institute

institute: National Institutes of Health

description: CREB1 PBM experiment

hyb_protocol: The double-stranded arrays were blocked with 4% milk for 1 hour and washed with 0.1% Tween-20 in 1x PBS.  Freshly synthesized protein (25 µL) was mixed with 125 µL of protein binding reaction mixture consisting of 4% milk in 1x PBS, 50 ng of salmon testes DNA and 0.2 µg/µL bovine serum albumin and added to double-stranded array.  The protein binding reactions were carried out in hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS.  The protein bound array was incubated with Alexa Fluor 647 conjugated Anti-GST antibody for 1 hour, followed by three washes with 0.05 % Tween-20.  Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 micron resolution. Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 30% PMT (low). The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used. Image spot intensities were quantified using Agilent Feature Extraction.

data_processing: An intensity value was calculated for each 16-mer ETS-CRE motif, SNP, or DNP using the median signal intensity across array probes containing the 16-mer in the same position and orientation along the microarray probe.

molecule: protein

organism: Mus musculus

source_name: CREB1-GST, ETS-CRE DNP design

label_protocol: The proteins were expressed in In-Vitro Translation system (IVT) reactions using PURExpress In Vitro Protein Synthesis Kit (NEB).  For the GABPα-GST and CREB1-GST IVT reactions, 570ng of plasmid was added to 250ul of IVT solution.  For analysis of cooperativity between GABPα-GST and CREB1, 570ng of GABPα-GST plasmid and 66ng of CREB1 plasmid were used in IVT reactions in a final volume of 250ul.  IVT reactions were carried out at 37°C for 2 hours, and then 230ul of the IVT solution was added to the arrays.

extract_protocol: The bZIP DNA binding domains (DBD) of wild type GABPa and CREB1 obtained from Dr. Timothy Hughes, University of Toronto, Canada as a GST construct cloned into a modified pDEST15 MAGIC vector (N-terminal GST) vector.  The CREB1 bZIP domain without GST was expressed from a pT5 plasmid.

treatment_protocol: The single-stranded oligonucleotide microarrays were double-stranded by primer extension as described in Badis et al. Science (2009).

tag: dbd

value: bZIP

tag: protein


title: CREB1-GST_rep2

description: CREB1 PBM experiment


title: SHSY5Y_GFP_1105


title: 5A7A Sample #5

description: Sample 13


title: 5A7A Sample #6

description: Sample 14


title: WT_NF54_R_rep1_RNA-seq

tag: development stage


title: IMR5_SOX9-GFP_1112

description: IMR-5 cell was transfected with pCMV6-SOX9-GFP, and GFP+ cells were sorted


title: WT_NF54_T_rep2_RNA-seq

value: Trophozoite

tag: strain


title: WT_NF54_T_rep1_RNA-seq

value: Pf NF54

tag: genotype


title: 5A7A Sample #4

description: Sample 12


title: IMR5_GFP_1112

description: IMR-5 cell was transfected with pSUPER-GFP, and GFP+ cells were sorted


title: 5A7A Sample #3

description: Sample 11


title: GABPa-GST_CREB1-PT5_rep2

description: GABPa and CREB1 PBM experiment

source_name: GABPa-GST/CREB1-PT5, ETS-CRE DNP design

value: GABPa and CREB1


title: SU5402_late_6h_2

city: BANYULS SUR MER

first: Stephanie

last: Bertrand

address: AVENUE PIERRE FABRE

country: France

institute: CNRS/SU UMR7232

description: SU5402 50µM

data_processing:
The first 50 bases of pass-filter reads were retained, in order to be comparable between the different samples.
These reads were mapped onto the reference transcriptome (https://wwwphp.obs-banyuls.fr/repository/transcriptome_B_lanceolatum/TotalMergeAssembliesGenbankRenomme.fasta.gz) using bwa v0.6.1 29 and the following set of parameters : -l 27 -n 4 -e 4. Only uniquely aligned reads were then retained. The number of reads aligned to each contig was computed using R.
Genome_build: Reference transcriptome constructed using data from Oulion et al (PLoS One. 2012; 7(5): e36554) and the data obtained in this study, available on the following URL : https://wwwphp.obs-banyuls.fr/repository/transcriptome_B_lanceolatum/TotalMergeAssembliesGenbankRenomme.fasta.gz
Supplementary_files_format_and_content: Tabulated text file containing raw read counts in each sample.

organism: Branchiostoma lanceolatum

source_name: Mix of whole embryos

growth_protocol: Embryos were grown in 6cm Petri dishes filled with 6mL of filtered sea water with DMSO or SU5402.

extract_protocol:
Embryos were frozen in liquid nitrogen after getting rid of the filtered sea water by centrifugation. Total RNA was extracted using the RNeasy Mini Plus Kit from QIAGEN following manufacturer's instructions. Disruption and homogenization were undertaken using TissueLyzer from QIAGEN.
A library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “Truseq RNA sample preparation low throughput” protocol with some modifications. Briefly, mRNA was purified from 2 µg total RNA using oligo-dT magnetic beads and fragmented using divalent cations at 94°C for 8 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers, then the second strand of the cDNA was synthesized using Polymerase I and RNase H. The next steps of RNA-Seq library preparation were performed in an automated system using SPRIworks Fragment Library System I kit (ref A84801, Beckman Coulter, Inc) with the SPRI-TE instrument (Beckman Coulter, Inc). Briefly, in this system double stranded cDNA fragments were blunted, phosphorylated and ligated to indexed adapter dimers, and fragments in the range of ~200-400 bp were size selected. The automated steps were followed by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 15 cycles (6 hpt libraries) or 12 cycles (3 and 9 hpt libraries); 5 min at 72°C), then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent).

treatment_protocol: Embryos were treated with 0,1% DMSO or 50µM SU5402.

tag: treatment

value: SU5402 50microM

tag: time of treatment

tag: developmental stage


title: WT_3D7-G7_T_rep2_RNA-seq

source_name: Pf 3D7 clone line 3D7-G7

value: Pf 3D7

value: wild type

tag: host

value: Homo sapiens


title: WT_3D7-G7_S_rep1_RNA-seq

value: Schizont


title: WT_3D7-G7_T_rep1_RNA-seq


title: WT_3D7-G7_S_rep2_RNA-seq


title: IMR5_GFP_1108


title: 5A7A Sample #2

description: Sample 10


title: IMR5_SOX9-GFP_1105


title: 5A7A Sample #1

description: Sample 9


title: WT_3D7-G7_R_rep2_RNA-seq


title: GABPa-GST_rep2

description: GABPa PBM experiment

source_name: GABPa-GST, ETS-CRE DNP design

value: GABPa


title: SU5402_late_6h_1

description: SU5402 50µM


title: Wild-type Sample #7

description: Sample 8

value: Wild-type Sample

value: Virus passaged in the presence of wild-type T7 DNA polymerase


title: GABPa-GST_CREB1-PT5_rep1

description: GABPa and CREB1 PBM experiment


title: Ctrl_late_6h_2

description: DMSO 0.1%

value: DMSO 0.1percent


title: GABPa-GST_rep1

description: GABPa PBM experiment


title: Wild-type Sample #6

description: Sample 7


title: WT_3D7-G7_R_rep1_RNA-seq


title: IMR5_SOX9-GFP_1108

value: Neuroblasotma cell line

value: SOX9 overexpression


title: IMR5_GFP_1105

value: Control

value: pSUPER-GFP


title: SU5402_early_6h_2

description: SU5402 50µM


title: Wild-type Sample #5

description: Sample 6


title: Ctrl_late_6h_1

description: DMSO 0.1%


title: Histone H3K122 succinylation ChIPseq

city: Tianjin

first: Xiaodong

last: Zhang

address: 94 Weijin Road

institute: Nankai University

description: the chromatin occupancy of histone H3K122 succinylation and its correlation with HAT1

data_processing:
A total of 5× 10^7 cells were used for each ChIP assays.
Enriched DNA fragments were subjected to library preparation and next-generation sequencing with Annoroad Gene Technology using a Novaseq6000 (Illumina).
Short reads were mapped to the Homo_sapiens.GRCh38.87.chr reference genome using Bowtie2
ChIP peaks were called using model-based analysis of ChIP-seq 14 (MACS 14)
Enrichment heat-maps that surrounded the ChIP peaks were generated using seqMINER
Genome_build: Homo_sapiens.GRCh38.87.chr
Supplementary_files_format_and_content: bigwid files include mapping information

source_name: HepG2 cells

growth_protocol: The HepG2 cells were maintained in Dulbecco's modified Eagle’s medium (DMEM)

extract_protocol:
ChIP assays were performed by using a SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology, USA)
Enriched DNA fragments were subjected to library preparation and next-generation sequencing with Annoroad Gene Technology using a Novaseq6000 (Illumina).

treatment_protocol: ChIP-seq was performed by using the antibody of histone H3K122 succinylation and HAT1

value: HepG2 cells

value: hepatocellular carcinoma

tag: chip antibody

value: Histone H3K122 succinylation (PTMBIO PTM-413)


title: Input DNA


title: Ctrl_early_6h_2

description: DMSO 0.1%


title: WT

city: Hangzhou

first: Haichun

last: Gao

state: Zhejiang Province

address: 866 Yuhangtang Rd

department: Institude of microbiology college of life science

institute: Zhejiang University

data_processing:
Illumina HiSeq 1000 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Shewanella oneidensis MR-1 whole genome using Bowtie2 2.2.4 sofeware.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, sequences of a gene were merged to create one meta-transcript. The number of reads falling in the sequences of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: ASM14616v2
Supplementary_files_format_and_content: the excel file include RPKM values for each Sample

organism: Shewanella oneidensis

source_name: bacteria

extract_protocol:
Centrifugal collection of bacterial liquid, and RNA was harvested using Trizol reagent and RNeasy minikit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: log phage


title: Wild-type Sample #4

description: Sample 5

source_name: Bacteriophage T7

tag: sample type


title: Wild-type Sample #2

description:
Sample 3
Note: No mutations present as compared to passage zero


title: SU5402_early_6h_1

description: SU5402 50µM

value: SU5402 50microM


title: Ctrl_early_6h_1

description: DMSO 0.1%


title: Wild-type Sample #3

description: Sample 4


title: ΔfadR

value: fadR knock out


title: PGAM1 (K99R) rep2

description:
the effect of PGAM1 mutant (K99R) on gene  expression
P2

data_processing:
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina)
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Genome_build: Homo_sapiens.GRCh38.87.chr
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: PANC1 cells depleted endogenous PGAM1 and reconstituted expression of PGAM1 mutant (K99R)

growth_protocol: The PANC1 cells were maintained in Dulbecco's modified Eagle’s medium (DMEM)

extract_protocol:
Total RNA was extracted from the cells
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The PANC1 cells were stably depleted endogenous PGAM1 and reconstituted expression of PGAM1 or PGAM1 mutant (K99R)

tag: cell line

value: pancreatic cancer

tag: gene depletion

value: stably deplete endogenous PGAM1

tag: reconstituted expression


title: HAT1 ChIPseq

tag: cell type

value: HAT1 (Abcam ab194296)


title: PGAM1 (K99R) rep1

description:
the effect of PGAM1 mutant (K99R) on gene  expression
P1

value: reconstituted expression of PGAM1 mutant (K99R)


title: Wild-type Sample #1

description:
Sample 2
Note: No mutations present as compared to passage zero

value: Wild-type Sample

tag: passages


title: 4 hour replicate 3

city: Ottawa

first: Vern

last: Lewis

state: Ontario

address: 1125 Colonel By Drive

department: Neuroscience

country: Canada

institute: Carleton University

description:
4hour_vs_control.DESeq2.csv
eXpress_output
Annotation_File_Trinotate

data_processing:
RNA-seq was performed on RNA extracted from Brain tissue.
Quality trimming and de novo transcriptome assembly was performed using the Trinity assembly suite.
Read alignment was performed using Bowtie2 integrated in to the Trinity suite.
Differential expression analysis was performed using eXpress and DESeq2
Annotation was done using the Trinnotate annotation platform which uses the ref-seq NCBI, and Uniprot databases to run homology searches.
Gene ontology enrichment analysis and co-expression clustering was performed using the David Bioinformatics Resources website, and the MeV: MultiExperiment Viewer data analysis tool.
Supplementary_files_format_and_content: DESeq2 files for each treatment comparison (2h vs. con, 4h vs. con, 24 vs. con). Files are comma delimited and the output consists of log2 fold changes, p-values, and p-adjusted values (FDR).
Supplementary_files_format_and_content: eXpress output is a tab delimited file consisting of fpkm and tpm values for each transcript.
Supplementary_files_format_and_content: Full processed dataset is a tab delimited file which includes output from the trinotate annotation tool, abundance measure from the eXpress tool, and differential expression output from DSeq2. Trinotate output consists of homology search results from both NCBI's refseq database and Uniprots protein database. Also included are pfam, signalP, eggnog, KEGG, and gene ontology annotations, as well as the associated nucleotide and protein sequences. TPM and FPKM are included for all transcripts, as well as , the log2 Fold-change and FDR for all differentially expressed transcripts.

organism: Bombina orientalis

source_name: Whole brain

extract_protocol:
Trizol extraction + isolation with a Qiagen RNease kit
RNA libraries were prepared for sequencing using standard Illumina protocols by The Center for Advanced Genomic (TCAG) at The Hospital for Sick Children's.

tag: tissue

value: Brain

tag: post-training sacrifice timings

value: 4 hours post


title: WT PGAM1 rep3

description:
the effect of PGAM1 on gene expression
C3

source_name: PANC1 cells depleted endogenous PGAM1 and reconstituted expression of PGAM1

value: reconstituted expression of PGAM1


title: Passage zero reference virus

description: Sample 1

value: Passage zero reference virus

value: 0-Our starting virus used for all experiments


title: 4 hour replicate 2


title: 741_WT

city: Munich

first: Mattias

last: Backman

state: Bavaria

address: Feodor-Lynen-Straße 25

department: Genzentrum

institute: Ludwig Maximilian University of Munich

description: ribosomal depletion for mRNA enrichment

data_processing:
HCS 2.2.68/RTA 1.18.66.3 was used for basecalling
STAR was used to align FASTQ reads against Sscrofa11.1 using default parameters
HTSeq was used to generate a counts matrix. Strict intersection mode was used with a minimum aligment score of 10.
DESeq2 was used for calculating differential expression using the default parameters
Genome_build: Sscrofa11.1.91
Supplementary_files_format_and_content: tab delimited text files show non-normalized Counts data in a matrix format as well as DESeq2 results sorted by significance

organism: Sus scrofa

source_name: Liver

growth_protocol: Animals were housed under controlled conditions with daily feeding and free access to water. Diabetic animals were treated with short and long acting insulin during daytime.

extract_protocol:
RNA isolation with Trizol Reagent (Invitrogen)
Encore complete RNA-Seq Library System (Nugen)

value: WT

tag: Sex

value: female

tag: age

value: 2 years


title: 743_WT

description: ribosomal depletion for mRNA enrichment


title: 738_WT

description: ribosomal depletion for mRNA enrichment


title: PGAM1 (K99R) rep3

description:
the effect of PGAM1 mutant (K99R) on gene  expression
P3


title: 736_WT

description: ribosomal depletion for mRNA enrichment


title: WT PGAM1 rep1

description:
the effect of PGAM1 on gene expression
C1


title: 745_WT

description: ribosomal depletion for mRNA enrichment


title: 739_TG

description: ribosomal depletion for mRNA enrichment

value: MIDY


title: Control replicate 3

description:
2hour_vs_control.DESeq2.csv
4hour_vs_control.DESeq2.csv
24hour_vs_control.DESeq2.csv
eXpress_output
Annotation_File_Trinotate

value: Unmanipulated


title: TMU38_lncRNA

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

data_processing:
Basecalls performed using Illumina CASAVA.
Raw reads from RIP and Input-seq data were mapped to the B73 genome using TopHat (v2.0.12) with the default parameters. The paired-end reads from anti-CENH3 RIP, input and lncRNA data were joined with SeqPrep (https://github.com/jstjohn/SeqPrep) with the parameter “-q 30 -L 25”
The gene expression levels were calculated following procedures and steps with cufflinks. The merged reads with remaining unmerged paired-end reads were used to conduct a BLAST search of the different sequences using the parameter “-e value 1e-5”.
The number of reads for each unit of the different repeat sequences was counted, and the relative enrichments of different sequences between the input and RIP samples were calculated using the ratios normalized by the total reads
Genome_build: Maize B73 RefGen_v4 and Triticum urartu genome
Supplementary_files_format_and_content: TXT files from RNA-seq data contain genes expression level. Merge fasta file.

organism: Triticum urartu

source_name: wheat

growth_protocol: Suitable materials were planted in the greenhouse for resequencing experiments.

extract_protocol:
The leaves were then transferred to liquid nitrogen and ground into a fine powder. The following experiment was carried out using the native ChIP protocol. The chromatin was digested into single nucleosomes using 0.02 U/μl DNase I (RNase-free) at 37°C. Dynabeads Protein A (ThermoFisher, Cat#:10001D) was used for binding the anti-CENH3 antibody. After washing the beads incubated with the antibody and chromatin fragments, the beads were eluted twice at 65°C for 15 min using elution buffer containing 50 mM Tris-HCl (pH = 7.5), 10 mM EDTA, 200 mM NaCl and 1% SDS. The eluted fractions were combined, and Proteinase K (Invitrogen, Cat#: 25530-49) was added to relieve cross-linking at 37°C overnight after which the RNA was extracted using TRIzol reagent, and the residual DNA was removed using RNase-free DNase I (NEB, Cat#: M0303S).
The cDNA libraries of RIP samples were prepared using the standard manual provided in the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Cat#: E7530S).

tag: genotype/variation

value: young leaves


title: Control replicate 1

description:
2hour_vs_control.DESeq2.csv
4hour_vs_control.DESeq2.csv,
24hour_vs_control.DESeq2.csv
eXpress_output
Annotation_File_Trinotate


title: 740_TG

description: ribosomal depletion for mRNA enrichment

tag: genotype


title: Control replicate 2


title: WT PGAM1 rep2

description:
the effect of PGAM1 on gene expression
C2


title: 4 hour replicate 1

description:
4hour_vs_control.DESeq2.csv,
eXpress_output
Annotation_File_Trinotate


title: 744_TG

description: ribosomal depletion for mRNA enrichment


title: 256685210002_b2 - 240_Vasc1_Ho_rep3 vs 240_Vasc1_He_rep3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Are hormone signaling genes misregulated in VASC1.

hyb_protocol: 240_Vasc1_He_rep3 Cy5 / 240_Vasc1_Ho_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Brachypodium distachyon

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: aerial - Media: soil hygrometry: 60% Temperature: 21°C light: 18 hours/day

treatment_protocol: no treatment

value: vasc1 heterozygote

value: vasc1 homozygote


title: 256685210002_b3 - 256_Vasc1_He_rep4 vs 256_Vasc1_Ho_rep4

hyb_protocol: 256_Vasc1_Ho_rep4 Cy5 / 256_Vasc1_He_rep4 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 256685210002_b1 - 240_Vasc1_He_rep3 vs 240_Vasc1_Ho_rep3

hyb_protocol: 240_Vasc1_Ho_rep3 Cy5 / 240_Vasc1_He_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: GBM39 SMC3 ChIP-seq replicate 1

status: Public on Dec 31 2019

city: La Jolla

first: Paul

middle: S

last: Mischel

address: 9500 Gilman Dr.

institute: Ludwig Institute for Cancer Research

description: ChIP DNA

data_processing:
Bowtie2 for mapping, MarkDuplicates from Picard tools v1.119 to remove PCR duplicates, Samtools v1.3.1, MACS2 2.1.2 for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: tdf

growth_protocol: Human prostate cancer cell line PC3, colon cancer cell line COLO320DM and glioblastoma cell line U87 were purchased from ATCC and cultured in DMEM/F12 with 10% FBS. Human glioblastoma GBM39 tumor spheroid was derived from patient tissue, and cultured in DMEM/F12 with GlutaMAX, B27, 20 ng/ml EGF, 20 ng/ml FGF and 5 μg/ml heparin.

extract_protocol:
ATAC-seq: Briefly, 100-500K cell nuclei were extracted by NPB buffer (5% BSA, 0.2% IGEPAL-CA630, 1 mM DTT, EDTA-free protease, in PBS) at 4°C for 10 min. Tagmentation was done in TB buffer (33 mM Tris-acetate pH 7.8, 66 mM K-acetate, 11 mM Mg-acetate, 16% DMF) with Tn5 transposase (Illumina), at 37°C for 30 min. DNA samples were then extracted and DNA libraries were generated by PCR. ChIP-seq: Formaldehyde crosslinked chromatin from 5 million cells per ChIP was sheared to small fragments by Covaris M220 Focused-ultrasonicator. The following antibodies were used for chromatin pull-down in RIPA buffer with protease inhibitor cocktail: anti-H3K27ac (Active Motif 39685, 5 µg), anti-H3K4me1 (Active Motif 39297, 10 µl), anti-CTCF (Abcam ab70303, 5 µg), anti-SMC3 (Abcam ab9263, 5 µg). After capturing by Protein A/G magnetic beads, chromatin was washed 6 times and reverse-crosslinked for 3 hr with RNase A and Proteinase K.
DNA library was constructed by NEBNext Ultra II DNA Library Prep kit for paired-end sequencing.

treatment_protocol: No

value: Human brain tumor


title: GBM39 CTCF ChIP-seq replicate 2

description: ChIP DNA


title: GBM39 SMC3 ChIP-seq replicate 2

description: ChIP DNA


title: GBM39 ChIP-seq input replicate 1

description: ChIP DNA


title: GBM39 ChIP-seq input replicate 2

description: ChIP DNA


title: GBM39 CTCF ChIP-seq replicate 1

description: ChIP DNA


title: 256685210001_b2 - 171_Vasc1_Ho_rep1 vs 171_Vasc1_He_rep1

hyb_protocol: 171_Vasc1_He_rep1 Cy5 / 171_Vasc1_Ho_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 256685210001_b3 - 202_Vasc1_He_rep2 vs 202_Vasc1_Ho_rep2

hyb_protocol: 202_Vasc1_Ho_rep2 Cy5 / 202_Vasc1_He_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 737_TG

description: ribosomal depletion for mRNA enrichment


title: miR-124a Teratoma_2 (mRNA)

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

country: Japan

institute: National cancer center research institute

description: Gene expression in teratoma treated with miR-124a-3p mimic_Rep2

hyb_protocol: Gene Expression Hybridization Kit and Gene Expression Wash Pack (Agilent)

scan_protocol: Agilent SureScan Microarray Scanner System (G4900DA)

data_processing: Intensity values of each scanned feature were quantified using Agilent Feature Extraction software version 11.5.1.1 that performs background subtractions.

source_name: Teratoma treated with miR-124a-3p mimic_Rep2

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies), Cyanine (Cy3)

extract_protocol: Each of the resected teratomas was cut into 2 pieces. Total RNAs were extracted from half of the  teratomas using QIAzol and purified using the QIAGEN miRNeasy Mini Kit, according to the manufacturer’s protocols.

treatment_protocol:
[Teratoma formation protocol]  Teratoma was formed by subcutaneous injection of 1 x 10e6 mESCs into the flank of the mice. Treatment started when the tumors reached a palpable size (≥100 mm3; approximately 10 days after the initial inoculation of mESCs).
In vivo miRNA transfection ( miRNA negative control vs miR-124a mimic) was performed by intratumoral administration of miRNAs: “Atelogen QG” complexes at a final concentration of 15 µg/100 µL. Intratumoral injection of miRNAs was performed once every 3 days until Day 28.

value: teratomas derived from mESCs

tag: treatment

value: miR-124a-3p mimic


title: 256685210002_b4 - 256_Vasc1_Ho_rep4 vs 256_Vasc1_He_rep4

hyb_protocol: 256_Vasc1_He_rep4 Cy5 / 256_Vasc1_Ho_rep4 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 256685210001_b4 - 202_Vasc1_Ho_rep2 vs 202_Vasc1_He_rep2

hyb_protocol: 202_Vasc1_He_rep2 Cy5 / 202_Vasc1_Ho_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: GBM39 H3K27ac ChIP-seq replicate 2

description: ChIP DNA


title: GBM39 H3K27ac ChIP-seq replicate 1

description: ChIP DNA


title: GBM39 H3K4me1 ChIP-seq replicate 2

description: ChIP DNA


title: 256685210001_b1 - 171_Vasc1_He_rep1 vs 171_Vasc1_Ho_rep1

hyb_protocol: 171_Vasc1_Ho_rep1 Cy5 / 171_Vasc1_He_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Ctrl Teratoma_3 (mRNA)

description: Gene expression in teratoma treated with miRNA negative control_Rep3

source_name: Teratoma treated with miRNA negative control_Rep3

value: miRNA negative control


title: Ctrl Teratoma_2 (mRNA)

description: Gene expression in teratoma treated with miRNA negative control_Rep2

source_name: Teratoma treated with miRNA negative control_Rep2


title: miR-124a Teratoma_3 (mRNA)

description: Gene expression in teratoma treated with miR-124a-3p mimic_Rep3

source_name: Teratoma treated with miR-124a-3p mimic_Rep3


title: JARCyc-2

first: Yibin

last: Pan

address: 3 East Qingchun Road,

institute: Sir Run Run Shaw Hospital

data_processing:
bcl2fastq software were used for basecalling.
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).The steps are: 1) trim Smart-seq2 public primer sequence from the Reads; 2) remove the contaminated reads for adapters; 3) remove the low quality reads; and 4) remove the reads whose N base more than 5% for total bases.
Sequenced reads were mapped to hg38 using Bowtie2 v2.2.3 software.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0. and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from  Trapnell, C. et al., Nat. Biotechnol, 2010.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: JAR cell, Cyclopamine 20μM for 24h

growth_protocol: Human JAR cells were grown in RPMI 1640 medium supplemented with 10% FBS at 37°C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina  was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment with Cyclopamine 20μM for 24h

value: JAR

value: Human Choriocarcinoma


title: miR-124a Teratoma_1 (mRNA)

description: Gene expression in teratoma treated with miR-124a-3p mimic_Rep1

source_name: Teratoma treated with miR-124a-3p mimic_Rep1


title: Ctrl Teratoma_1 (mRNA)

description: Gene expression in teratoma treated with miRNA negative control_Rep1

source_name: Teratoma treated with miRNA negative control_Rep1


title: JARC-3

source_name: JAR cell


title: JARCyc-1


title: JARC-2


title: C 6

first: yihan

last: liu

address: No.10 Xitoutiao, Youanmen, Fengtai District

institute: Capital Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HISAT v2.0.5 with parameters --rna-strandness RF--dta –t –p 4.
Read Count for each gene in each sample is counted by HTSeq, and FPKM (Fragments Per Kilobase Millon Mapped Reads) were then calculated to represent the expression level of genes in each sample.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: peripheral blood leucocyte

extract_protocol:
Leukocyte were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.  NEB Next Ultra Directional RNA LibraryPrep Kit for Illumina （ NEB，Ispawich，USA） was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leukocyte

tag: disease

value: Healthy


title: T1D 1

value: Type 1 Diabetes  Mellitus with family history


title: T1D 6

value: Type 1 Diabetes  Mellitus


title: C 3


title: JARC-1


title: T1D 4


title: C 2


title: T1D 5


title: JARCyc-3


title: T1D 2


title: T1D 3


title: C 4


title: C 5


title: 8mpf_Thyroid

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

data_processing:
The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software (v2.1.0) provided by 10X Genomics with the option ‘--expect-cells’ set to 6000 (all other options were used as per default).
To build the reference for Cell Ranger, zebrafish genome (GRCz10) as well as gene annotation (Ensembl 87) were downloaded from Ensembl and the annotation was filtered with the ‘mkgtf’ command of Cell Ranger (options: ‘--attribute=gene_biotype:protein_coding --attribute=gene_biotype:lincRNA –attribute=gene_biotype:antisense’). Genome sequence and filtered annotation were then used as input to the ‘mkref’ command of Cell Ranger to build the appropriate Cellranger Reference.
Genome_build: Zebrafish GRCz10
Supplementary_files_format_and_content: Matrix with rows as genes and columns as cells.

organism: Danio rerio

source_name: thyroid gland

extract_protocol:
Enzymatic Dissociation
The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer’s instructions to yield 12000 cells. Subsequently, the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system (Zheng et al., 2016). After the gel emulsion bead suspension underwent the reverse transcription reaction, emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles, following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA-seq library preparation - involving fragmentation, dA-Tailing, adapter ligation and indexing PCR – was performed based on the manufacturer’s protocol.

tag: strain

tag: tag

value: Normal


title: 2mpf_Thyroid


title: DB-liver DNA

city: Chengdu

first: Song

last: Yang

address: No.211, Huimin Road, Wenjiang District, Chengdu City, Sichuan Province, P.R.China

institute: Sichuan Agricultural University College of Animal Science and Technology

description: domestic pig

data_processing:
Library strategy: DNA-seq
The paired-end reads were aligned to the reference genome using the BWA version 0.7.15 and SAMtools version 0.1.19 was used to remove the duplication
R packages "cn.mops" version 3.8 was used for calling CNV.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Tab-delimited text files include copy number values.

extract_protocol:
Genomic DNA was extracted from the liver tissue using Qiagen DNeasy Tissue kit (Qiagen, Germany)
DNA libraries were prepared for sequencing using standard Illumina protocols

value: 60 days old

value: Liver

tag: breed name

value: Northeast min pig


title: Leaf rep1

city: yichang

first: chao

last: zhou

address: No.8,daxuelu Street

institute: CTGU

data_processing:
RNA-seq data were first cleaned by removing contaminations and low quality reads by Trimmomatic. The clean data were aligned with Tophat 2.0 (Kim et al., 2013) using the Phytozome Sorghum bicolor (BTx623) genome as the reference under default parameters (Paterson et al., 2009). Then, the gene counts were calculated with Cufflink, and the differentially expressed genes (greater than 2, P value < 0.05) were calculated by Cuffdiff. The up- or down-regulated genes were subjected to GO analysis and KEGG analysis to see which pathways the differential gene function was concentrated on.
Genome_build: sorghum BTx623
Supplementary_files_format_and_content: tab-delimited text files include gene ID, gene locus and FPKM values for each sample.

organism: Sorghum bicolor

source_name: Leaf

growth_protocol: Sorghum bicolor (L.) Hiro-1 were used in this study. Young embryos (about 1-2 mm) were collected from 13-15 day-old plants after flowering, and subsequently inoculated on callus induction medium (CIM) and cultured under sterile and non-light conditions at 25 °C. After 3 weeks, after removing the buds and outer membranes of the immature embryos, three types of callus was excised from the explants, and separately transferred to the new CIM for additional 20 days subculture before being moved into differentiation medium and cultured under condition of 16/8 h of light/dark at 25 °C and 2000 lx of light intensity.

extract_protocol:
Total RNA was isolated from Callus I, Callus II, Callus III and leaves generated from Callus II by using Trizol reagent (Invitrogen). Four RNA samples were then separately subjected to transcriptome analysis using Illumina sequencing with two biological replicates.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Leaf

value: Regenerative leaves from Callus II

value: wild type

tag: phenotype

value: Callus II


title: Leaf rep2


title: Callus III rep1

source_name: Callus

value: Callus

value: 3 weeks callus induced from young embryo,and additional 20 days subculture

value: Callus III


title: Callus II rep1


title: Callus II rep2


title: GBM39 H3K4me1 ChIP-seq replicate 1

description: ChIP DNA

value: Human brain tumor


title: Callus I rep1

value: Callus I


title: Callus I rep2


title: Hep3B: HIF3A-Ctrl1

city: Oulu

first: Jussi-Pekka

middle: Matteus

last: Tolonen

address: Aapistie 7A

department: Faculty of Biochemistry and Molecular Medicine

country: Finland

institute: University of Oulu

hyb_protocol: Biotinylated cRNA was cleaned with a GeneChip Sample Cleanup Module, fragmented to 35 to 200 nt, and hybridized to Affymetrix Human Genome U133 Plus 2.0 Array Chip according to manufacturer's instructions. After washing, the array was stained with streptavidin-phycoerythrin (Molecular Probes), the staining signal was amplified by biotinylated anti-streptavidin (Vector Laboratories) and the array was stained a second time with streptavidin-phycoerthrin.

scan_protocol: The Affymetrix Human Genome U133 Plus 2.0 Array chips were scanned with an Affymetrix Gene Chip Scanner 3000 7G in Biocenter Oulu DNA Analysis Core

data_processing: The data was analyzed using the RMA algorithm with no variance stabilization in the Chipster software

label: biotin

source_name: Hep3B cells, control siRNA treated

label_protocol: Biotin-labeled cRNA was produced using One-cycle cDNA synthesis kit (Affymetrix) and a IVT labeling kit (Affymetrix) according to the Affymetrix GeneChip Expression Analysis Technical Manual and manufacturer's instructions for the kits.

growth_protocol: 300 000 Hep3B cells were plated on 6-well plates and incubated 24 h in normoxia after the first transfection and then 24 h in 1 % hypoxia after the second transfection in EMEM

extract_protocol: Total RNA was extracted by E.Z.N.A. Total RNA kit I (Promega) after washing with PBS.

treatment_protocol: The cells were transfected twice with control siRNA or siRNA targeting a shared HIF3A region using siPORT NeoFX (Ambion) according to manufacturer's instructions. Samples were prepared in triplicate and pooled for each chip.

tag: cell line

value: Human hepatoma, Hep3B

tag: conditions


title: Hep3B: HIF3A-siRNA2

source_name: Hep3B cells, HIF3A siRNA treated


title: C 1

city: Beijing

value: leukocyte

value: Healthy


title: Hep3B: HIF-3a2-Overexpression

source_name: Hep3B cells, HIF-3a2 overexpression plasmid

growth_protocol: 300 000 Hep3B cells were plated on 6-well plates and incubated 24 h in normoxia after transfection and then 24 h in 1 % hypoxia in EMEM

treatment_protocol: The cells were transfected with 1000 ng of HIF-beta overexpression plasmid and 1000 ng of pcDNA3.1/Zeo(-) empty vector or 1000 ng of HIF-3a2 overexpression vector with FuGENE HD (Promega) according to manufacturer's instructions. Samples were prepared in triplicate and pooled for each chip.


title: Callus III rep2


title: Set2_mESC_Day0 (miRNA)

description: miRNA expression in undifferntiated mESCs

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Agilent SureScan Microarray Scanner System (G4900DA).

source_name: Embryonic stem cells

label_protocol: The miRNA Complete Labeling and Hyb Kit (Agilent Technologies), Cyanine 3 (Cy3)

growth_protocol: The mESC line (129/SVEV) was cultured on a gelatin-coated dish under feeder-free conditions, in a serum-free N2B27 medium, supplemented with MEK inhibitor PD0325901 (1 μM), GSK3 inhibitor CHIR99021 (3 μM) (both from Selleckchem), and 1,000 U/ml LIF (Millipore). Fresh medium was replaced daily.

extract_protocol: Cells were harvested at 6 different time points (Day 0, 2, 3, 4, 5 and 6) from 2 independent experiments during the differentiation of mESCs into endoderm. Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols, followed by DNase treatment using TURBO DNA-free kit (Ambion). Total RNA was quantified using a NanoDrop 1000 spectrophotometer (Thermo Scientific), and the integrity of the RNA was evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Mouse ESCs were seeded on gelatin-coated dish at cell density of 10,000 cells/cm2 and cultured in basal chemical defined medium (CDM), consisting of 50% Dulbecco's modified Eagle's medium (DMEM), 50% Advanced DMEM/F12, 0.2% bovine serum albumin (BSA; Sigma) , 1% GlutaMAX, 1% Penicillin-Streptomycin, 0.55mM ascorbic acid (Sigma) and 0.11 mM beta-mercaptoethanol. After 2 days of initial culture, differentiation of endoderm was induced in CDM supplemented with 50 ng/ml Activin A (S&D System), 200 ng/ml Noggin (Prepotech) and 5 μM of CHIR99021. Endoderm induction medium was replenished daily and the differentiation was carried out for a total of 4 days.

value: Undifferentiated mESCs

tag: time


title: Set2_CDM_Day2 (miRNA)

description: miRNA expression in mESCs cultured in chemical define medium for 2 days (NO induction)

tag: cell type

value: mESCs_without ActA-NG-CHIR_2 days


title: Hep3B: HIF3A-siRNA1


title: Set2_Endoderm_D3 (miRNA)

description: miRNA expression in induced endoderm_1 days (ActA-NG-CHIR)

value: Induced DE_with ActA-NG-CHIR_ 1 day


title: Set1_Endoderm_D6 (miRNA)

description: miRNA expression in induced endoderm_4 days (ActA-NG-CHIR)

value: Induced DE_with ActA-NG-CHIR_ 4 days


title: Set2_Endoderm_D6 (miRNA)


title: Set1_Endoderm_D5 (miRNA)

description: miRNA expression in induced endoderm_3 days (ActA-NG-CHIR)

value: Induced DE_with ActA-NG-CHIR_ 3 days


title: Set2_Endoderm_D5 (miRNA)


title: Set1_Endoderm_D4 (miRNA)

description: miRNA expression in induced endoderm_2 days (ActA-NG-CHIR)

value: Induced DE_with ActA-NG-CHIR_ 2 days


title: Hep3B: HIF3A-Ctrl2


title: Set1_mESC_Day0 (miRNA)


title: Set1_CDM_Day2 (miRNA)


title: Set2_Endoderm_D4 (miRNA)


title: Set1_Endoderm_D3 (miRNA)


title: LD cells from WT, biological rep5

city: Seoul

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

department: Biotechnology

country: South Korea

institute: Korea University

description: Gene expression data from WT LD cells at day 3

hyb_protocol: Fragmented and labeled 5 ug of cRNA were hybridized for 16 hr at 45 ℃ on GeneChip Yeast 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The microarray data were normalized by Robust Multiarray Average (RMA) using Affymetrix Expression Console Software

label: Biotin

organism: Saccharomyces cerevisiae

source_name: WT LD cells at day 3

label_protocol: Biotinylated cRNA were prepared according to the manufacurer's protocol (Affymetrix GeneChip Yeast 2.0 array protocol) using 100 ng of purified total RNA.

growth_protocol: Yeast cells were grown in YPD media containing 2% glucose at 30℃ with shaking

extract_protocol: Yeast cells were extracted using TRIzol reagent and treated with DNase1 to remove genomic DNA contamination. The RNA was finally purified using RNeasy Mini kit(Qiagen).

treatment_protocol: There is no additional treatment for cells

value: WT

tag: cell density

value: LD


title: LD cells from WT, biological rep3


title: LD cells from WT, biological rep2


title: Hep3B: HIF-3a2-Ctrl

source_name: Hep3B cells, empty pcDNA3.1


title: OsTMF-OE_cold_rep2

city: wuhan

first: Yan

last: Xu

address: No. 1, Shizishan street

institute: Huazhong agricultural university

description: Gene expression data from OE-29 seedlings under cold stress conditions

hyb_protocol: cRNA were hybridized for 16 hr at 45℃ on Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Gcos1.4 (GeneChip Operating Software) referring to Affymetrix Statistical Algorithms Description Document.

organism: Oryza sativa

source_name: 4-leaf stage OE-29 seedlings under cold stress conditions

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol .

growth_protocol: Rice seedlings grew in potting soil until they went into 4-leaf stage.

extract_protocol: TRIzol Reagent extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: the 4-leaf stage seedlings were moved to artificial chamber at a constant 4℃ with 14 hours/10 hours of light/darkness, we took the samples before treatment and after 24 h of treatment.

tag: cultivar

value: zhonghua 11

tag: tissue

value: shoots and leaves

tag: developmental stage

value: 4-leaf stage

value: OsTMF overexpression

value: cold stress for 24 h


title: OsTMF-OE_cold_rep1

description: Gene expression data from OE-24 seedlings under cold stress conditions

source_name: 4-leaf stage OE-24 seedlings under cold stress conditions


title: OsTMF-OE_normal_rep2

description: Gene expression data from OE-29 seedlings under normal growth conditions

source_name: 4-leaf stage OE-29 seedlings under normal growth conditions

value: normal


title: HD cells from WT, biological rep4

description: Gene expression data from WT HD cells at day 3

source_name: WT HD cells at day 3

value: HD


title: LD cells from WT, biological rep1


title: HD cells from WT, biological rep3


title: LD cells from WT, biological rep4


title: HD cells from WT, biological rep5


title: LD cells from rho0, biological rep3

description: Gene expression data from Rho0 LD cells at day 3

source_name: Rho0 LD cells at day 3


title: LD cells from rho0, biological rep4


title: HD cells from WT, biological rep1


title: HD cells from WT, biological rep2


title: HCC4006 cells, gefitinib resistant, TGFBR inhibitor treated, rep1

city: Burjassot

first: Julian

last: Carretero

state: Valencia

address: Ave. Vicent Andres Estelles s/n

department: Physiology

country: Spain

institute: University of Valencia

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genepattern's IlluminaExpressionFileCreator

source_name: HCC4006 cell line

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Gefitinib resistant, TGFBR inhibitor treated (6 months)


title: OsTMF-OE_normal_rep1

description: Gene expression data from OE-24 seedlings under normal growth conditions

source_name: 4-leaf stage OE-24 seedlings under normal growth conditions


title: ZH11_cold_rep2

description: Gene expression data from ZH11 seedlings under cold stress conditions

source_name: 4-leaf stage ZH11 seedlings under cold stress conditions

value: wild-type


title: HCC4006 cells, gefitinib resistant, TGFBR inhibitor treated, rep2

description: replicate 2


title: LD cells from rho0, biological rep2


title: ZH11_normal_rep2

description: Gene expression data from ZH11 seedlings under normal growth conditions

source_name: 4-leaf stage ZH11 seedlings under normal growth conditions


title: HCC4006 cells, gefitinib resistant, TGFBR inhibitor treated, rep3

description: replicate 3


title: LD cells from rho0, biological rep5


title: LD cells from rho0, biological rep1


title: HCC4006 cells, gefitinib resistant, rep 3

description: replicate 3

value: Gefitinib resistant (6 months)


title: ZH11_cold_rep1


title: HCC4006 cells, gefitinib resistant, rep 2

description: replicate 2


title: ZH11_normal_rep1


title: HCC4006 cells, gefitinib resistant, rep 1

description: replicate 1


title: HCC4006 cells, parental, rep2

description: replicate 2

value: parental


title: HCC4006 cells, parental, rep3

description: replicate 3


title: BT474-Var1A

description: Isolation of total RNA, 100 ng RNA for analysis

scan_protocol: Agilent SureScan G4900DA

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

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: BT474 cell lines were cultured in RPMI-1640 (Nissui Pharmaceutical, Tokyo, Japan) supplemented with 10% heat-inactivated FBS at 37 °C in 5% CO2.

extract_protocol: Total RNA was extracted using QIAzol and the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and a Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, Calif.).

treatment_protocol: BT474 cell lines  transfected with emtpy pcDNA3.1 were named as MOCK , BT474 transfected with pcDNA3.1-NR2F1-AS1variant1 were named as BT474-Var1, BT474 transfected with pcDNA3.1-NR2F1-AS1variant4 were named as BT474-Var4. All cell types were maintained in RPMI-1640 (Nissui Pharmaceutical, Tokyo, Japan) supplemented with 10% heat-inactivated FBS at 37 °C in 5% CO2.

tag: transfection


title: MCF7-miR1285-5p-treated

city: Tokyo

first: AI

last: Mitsuhashi

institute: National Cancer Center Research Institute

description: Total RNA extracted form cancer cells, and 100 ng of RNA for analysis

source_name: MCF-7 breast cancer cells transfected with miR-1285-5p mimic.

growth_protocol: Breast cancer cells were cultured with RPMI1640 medium supplemented with 10% heat-inactivated fetal bovine serum  for two days at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the miRNeasy Kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Breast cancer cells were transfected with mimic(miR-1285-5p/negative control), then incubated with RPMI1640 medium supplemented with 10% heat-inactivated fetal bovine serum  for two days at 37 ºC in a humidified incubator with 5% CO2.

value: Human breast cancer cell line


title: BT474-Var4A


title: HCC1937-miR1285-5p-treated

source_name: Breast cancer cells, HCC1937, overexpression of miR-1285-5p


title: HCC1954NC

source_name: HCC1954 breast cancer cells, control.


title: MOCKB

value: emtpy pcDNA3.1


title: BT474-Var4B


title: M231-miR1285-5p-treated

source_name: MDA-MB-231 breast cancer cells transfected with miR-1285-5p mimic.


title: HCC4006 cells, parental, rep1

description: replicate 1


title: post_subject40

city: Tokushima

first: Kensei

last: Nishida

state: Tokushima

address: 3-18-15 Kuramoto-cho

institute: Tokushima University Graduate school

hyb_protocol: Hybridizations were performed using GE Hybridization Kit (P/N 5188-5242) and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) as following Agilent's protocol. The fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4858A) for 17 hours at 65C in a rotating Agilent hybridization oven.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner (P/N G2600D).

data_processing: Data extracted using Agilent's Feature Extraction software. Raw data output was imported into Genespring GX14.9 (Agilent) and normalized each chip to the 75th percentile of all measurements (per chip normalization).

source_name: whole blood from athlete, post-intervention

label_protocol: Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis’ Protocol. These protocols are available for download from Agilent's DNA Microarray Manuals website. For microarray analysis, total RNA (150 ng) was used for amplification and labeling of complementary RNA (cRNA) using a Low RNA Input Liner Amplification Kit PLUS and a succinimide-containing fluorescent dye (Cy3)-CTP according to the manufacturer’s protocol (Agilent).

extract_protocol: The total RNA from whole blood was extracted using PAXgene according to the manufacturer's protocol (QIAGEN).

treatment_protocol: Dairy intake of Lactobacillus gasseri CP2305 strain for 12 weeks

tag: gender

value: male

value: peripheral blood leukocytes


title: post_subject44

value: placebo


title: MCF7NC

source_name: MCF-7 breast cancer cells, control.


title: HCC1937NC

source_name: Breast cancer cells, HCC1937, control


title: M231NC

source_name: MDA-MB-231 breast cancer cells, control.


title: BT474-Var1B


title: post_subject43


title: post_subject41


title: MOCKA


title: HCC1954-miR1285-5p-treated

source_name: HCC1954 breast cancer cells transfected with miR-1285-5p mimic.


title: post_subject39


title: post_subject42


title: post_subject37


title: post_subject35


title: post_subject38


title: post_subject36


title: post_subject34


title: AR-KO-2 R1881

city: Baltimore

first: Yezi

last: Zhu

address: 600 N. Wolfe Street

institute: Johns Hopkins University

description: rRNA depleted

data_processing:
Illumina for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Prostate cancer cells

growth_protocol: Parental LNCaP95 cells and AR-KO clone 1 and clone 2 cells (AR-KO-1, AR-KO-2) were maintained in androgen-depleted charcoal stripped serum medium for 72 hrs

extract_protocol:
Total RNA was harvested using Trizol reagent/RNeasy total RNA prep kit. The quality of the RNA were verified by Qubit 3 and Bioanalyzer before construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Parental LNCaP95 cells and Ar-KO clones were treated with 1nM R1881 for 24hrs.

value: Prostate cancer cell line

tag: genotype

value: AR-KO


title: AR-KO-2 EtOH

description: rRNA depleted


title: post_subject31

tag: treatment


title: AR-KO-1 R1881

description: rRNA depleted


title: post_subject33


title: AR-KO-1 EtOH

description: rRNA depleted


title: post_subject22


title: post_subject27


title: post_subject28


title: post_subject26


title: post_subject24


title: post_subject25


title: post_subject23


title: post_subject29


title: post_subject19


title: post_subject20


title: LNCaP95 R1881

description: rRNA depleted

value: wild type


title: post_subject18


title: post_subject17


title: post_subject21


title: LNCaP95 EtOH

description: rRNA depleted


title: RNA-seq_VCaP_siNON_EtOH_rep4

city: Kuopio

first: Einari

middle: A

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

institute: University of Eastern Finland

description: RNA-seq sample

data_processing:
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
For ChIP-seq, reads were aligned against human genome hg19 with Bowtie software (version 0.12.9) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19. Peak calling was done in HOMER (version 4.10.3) using findPeaks command and approppriate input as a control. Two replicates were compared with each other using bedTools (intersectBed) and only those binding sites found in both replicates were used for further analysis.
For RNA-seq, raw reads were trimmed using trimmomatic (v. 0.33; parameters LEADING:5 TRAILING:5 MINLEN:36) and poly-A tails were removed using HOMER (homerTools trim -3 AAAAAAAA -mis 1 -min 36). Contaminants reported in iGENOME hg19 were removed using bowtie2 and remaining reads were mapped to human hg19 transcriptome and genome with tophat2. Differential expression of genes was analyzed using edgeR and expression values (FPKM) from combined replicates using HOMER.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq, the genomic intervals of BCOR binding sites that were common to two replicates are given in bed format. For AR and H2AK119ub, signal tracks are given in tdf format.
Supplementary_files_format_and_content: For RNA-seq, the table with results from differential gene expression analysis (siNON vs siBCOR and EtOH vs R1881) and expression (FPKM) is given as a tab delimited text file.

source_name: VCaP cells

growth_protocol: VCaP cells were maintained in DMEM (Gibco, Invitrogen, 41965-039) supplemented with 10% Defined FBS (Hyclone, SH30070.03), 100U/ml penicillin and 100 ug/ml streptomycin. Before hormone treatments, cells were kept on DMEM supplemented with 2.5% charcoal-treated FBS (steroid-depleted medium).

extract_protocol:
For ChIP-seq, VCaP cells were silenced using siRNA transfection for three days when indicate, grown on steroid-depleted medium for two days and treated for 1h with R1881 (10nM) or equal volume of vehicle (ethanol). Samples were fixed for 10 min. in room temperature with 1% (v/v) formaldehyde, fragmented to 200-400bp fragments by sonication (Bioruptor, Diagenode), chromatin immunoprecipitation was done using rabbit polyclonal anti-BCOR antibody (A310-672A, Bethyl Laboratories), rabbit antiserum against AR or anti-H2AK119ub antibody (#8240, Cell Signaling Technology). Two biological replicates of each condition were sequenced using Illumina HiSeq 2000 or NextSeq500 at EMBL GeneCore (Heidelberg, Germany).
For RNA-seq, VCaP cells were transfected with siRNA against BCOR (siBCOR, 20mM, Dharmacon, ON-TARGETplus SMARTpool, L-004584-01-0005) or control siRNA (siNON, Dharmacon, non-targeting pool) using Lipofectamine RNAiMAX (Invitrogen). After three days, medium was changed to steroid-depleted medium for 32h, followed by treatment with dihydrotestosterone (DHT, 100nM) or equal volume of vehicle (ethanol) for 16h. RNA was extracted using RNease Plus Mini kit (Qiagen) and mRNA using NEBNext Poly(a) mRNA Magnetic Isolation Module (New England Biolabs). Libraries were prepared using NEBNext Ultra II kit (New England Biolabs) and sequenced with HiSeq 2000 at EMBL GeneCore (Heidelberg, Germany).
Library preparation was done using NEBNext Ultra II kit (New England Biolabs) and sequenced using Illumina HiSeq 2000 or NextSeq 500 at EMBL GeneCore (Heidelberg, Germany).

treatment_protocol: See samples.

tag: treatment 1

value: siNON transfection, 72h

tag: treatment 2

value: steroid-depleted medium 32h

tag: treatment 3

value: ethanol, 16h


title: RNA-seq_VCaP_siNON_EtOH_rep3

description: RNA-seq sample


title: RNA-seq_VCaP_siNON_EtOH_rep1

description: RNA-seq sample


title: RNA-seq_VCaP_siNON_EtOH_rep2

description: RNA-seq sample


title: RNA-seq_VCaP_siNON_DHT_rep4

description: RNA-seq sample

value: dihydrotestosterone, 100nM, 16h


title: RNA-seq_VCaP_siNON_DHT_rep3

description: RNA-seq sample


title: RNA-seq_VCaP_siNON_DHT_rep1

description: RNA-seq sample


title: RNA-seq_VCaP_siNON_DHT_rep2

description: RNA-seq sample


title: post_subject15


title: post_subject14


title: post_subject12


title: RNA-seq_VCaP_siBCOR_EtOH_rep3

description: RNA-seq sample

value: siBCOR transfection, 72h


title: RNA-seq_VCaP_siBCOR_EtOH_rep2

description: RNA-seq sample


title: post_subject10


title: post_subject9


title: post_subject7


title: RNA-seq_VCaP_siBCOR_EtOH_rep1

description: RNA-seq sample


title: post_subject13


title: post_subject16


title: post_subject8


title: RNA-seq_VCaP_siBCOR_DHT_rep4

description: RNA-seq sample


title: post_subject11


title: post_subject32


title: post_subject6


title: post_subject5


title: RNA-seq_VCaP_siBCOR_DHT_rep3

description: RNA-seq sample


title: RNA-seq_VCaP_siBCOR_EtOH_rep4

description: RNA-seq sample


title: RNA-seq_VCaP_siBCOR_DHT_rep2

description: RNA-seq sample


title: RNA-seq_VCaP_siBCOR_DHT_rep1

description: RNA-seq sample


title: ChIP-seq_VCaP_BCOR_R1881-1h_rep2

description:
ChIP-seq sample
VCaP_BCOR_R1881-1h.bed

value: steroid-depleted medium, 72h

tag: chip antibody

value: rabbit polyclonal anti-BCOR antibody (A310-672A, Bethyl Laboratories)


title: post_subject1


title: post_subject2


title: pre_subject44

source_name: whole blood from athlete, pre-intervention


title: post_subject3


title: pre_subject43


title: ChIP-seq_VCaP_BCOR_R1881-1h_rep1

description:
ChIP-seq sample
VCaP_BCOR_R1881-1h.bed


title: ChIP-seq_VCaP_BCOR_EtOH_rep2

description:
ChIP-seq sample
VCaP_BCOR_EtOH.bed

value: ethanol, 1h


title: HT-29_shMLKL_DMSO

first: Jae whan

last: Song

address: Yonsei-ro 50

department: Department of Biochemistry

institute: College of Life Science and Biotechnology

data_processing:
Preprocessed reads were matched to reference genome sequence using TopHat program (version 2.0.13) and then aligned reads were generated.
Cufflinks program (version 2.2.1) was used for transcript assambly
Expression levels were normalized with length of transcript and depth of coverage.
Expression profile data was exported by normalized FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values.
Differentially expressed transcripts included in the groups were selected through statistical verification.
In case that the genomic information was known, functional annotation and gene-set enrichment analysis were performed on the basis of GO and KEGG database.
Using STAR 2.4.0f1, GATK 2015.1-3.4.0-1-ga5ca3fc, variant calling was performed.
Fusion genes were predicted using defuse program (version deFuse 0.6.2).
Genome_build: UCSC hg19

growth_protocol: HT-29 cells were maintained in RPMI in 5% CO2 at 37°C

extract_protocol:
HT-29 cells were lysed with ice cooled trizol reagent and total RNAs were isolated.
In order to construct cDNA libraries with the TruSeq Stranded mRNA LT Sample Prep Kit, 1ug of total RNA was used. The protocol consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100nt paired-end sequencing by Illumina HiSeq2000. The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using an Agilent Technologies 2100 Bioanalyzer

treatment_protocol: Sample 2 and Sample 4 were treated with 20 ng/mL TNFa + 2 µM BV6 + 30 µM zVAD-fmk (TBZ)

value: human colorectal adenocarcinoma

tag: gene knockdown

value: MLKL knockdown using lentivirus

tag: chemical/cytokine treatment

value: DMSO


title: HT-29_DMSO

tag: cell line


title: ChIP-seq_VCaP_BCOR_EtOH_rep1

description:
ChIP-seq sample
VCaP_BCOR_EtOH.bed


title: HT-29_shMLKL_TBZ 12h

value: TNFa + BV6 + zVaD-fmk (TBZ) - 12h


title: pre_subject42

value: male

value: peripheral blood leukocytes


title: post_subject4

value: placebo


title: AR_PCOS_hESC_ChIPSeq

city: Swansea

first: Marcos

last: Quintela

address: Singleton Park

country: United Kingdom

institute: Swansea University

data_processing:
ChIP-Seq reads were aligned to the genome hg19 using the BWA algorithm with default settings.
Data were filtered so that only reads that pass Illumina's purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in subsequent analysis. Additionally, duplicate reads were removed.
Peaks were called using MACS2 by simple thresholding of BAR files.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files show the fragment density for 32-nt bins along the genome ('signal map') in an indexed binary format.

source_name: Human endometrial stromal cells (hESC)

growth_protocol: hESC cells were plated into 35 mm FluoroDish dishes and maintained in DMEM/F12 media (10% FBS, 1% P/S, 1 mM sodium pyruvate, 1 mM sodium bicarbonate)

extract_protocol:
Lysates were clarified from sonicated nuclei and AR-DNA complexes were isolated with antibody as per manufacturers instructions (Chromatrap® Pro-A kit).
Isolated DNA was sent to Active Motif® for library construction. AM prepared the libraries according to Illumina's instructions accompanying the True-Seq ChIP Library Preparation Kit (IP-202-1012, Illumina®).

treatment_protocol: Confluent monolayers of hESC were treated with DHT (1xE-08M) for 72h.

tag: disease state

value: Polycystic ovary syndrome

value: endometrial stromal cells

tag: antibody

value: anti-AR antibody

value: DHT


title: pre_subject41

tag: cell type


title: HT-29_TBZ 4h

value: TNFa + BV6 + zVaD-fmk (TBZ) - 4h


title: pre_subject35


title: pre_subject30


title: pre_subject33


title: pre_subject31


title: pre_subject38


title: pre_subject39


title: pre_subject34


title: pre_subject32


title: pre_subject36


title: post_subject30


title: pre_subject40


title: pre_subject37


title: pre_subject29


title: pre_subject27


title: pre_subject28


title: pre_subject25


title: pre_subject24


title: pre_subject22


title: pre_subject23


title: pre_subject20


title: grapevine_168hpt_Beauveria treatment_rep3

city: Geisenheim

first: Yvonne

last: Rondot

address: Von-Lade-Str. 1

department: Department of Crop Protection

institute: Geisenheim University

description: Gene expression of grapevine in response to Beauveria bassiana treatment

hyb_protocol: Following fragmentation, 12 µg aRNA were hybridized to Affymetrix GeneChip Vitis vinifera Genome Arrays for 16 h at 45° C and 60 rpm in a GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.1.3 software

data_processing: Summarized probe set signals in log2 scale were background-adjusted, quantile normalized and log-transformed by using the robust multi-chip average (RMA) algorithm with the Affymetrix GeneChip Expression Console v1.4 Software.

organism: Vitis vinifera

source_name: grapevine leaves 168 h after treatment with Beauveria bassiana

label_protocol: 250 ng of total RNA were reverse transcribed into double-stranded copy DNA (cDNA) followed by an in vitro transcription generating biotin-labeled amplified RNA (aRNA).

growth_protocol: Grapevine plants were cultivated in a greenhouse chamber at an average temperature of 24:22°C day:night with a photoperiod of 12 hours.

extract_protocol: Total RNA was extracted from individual leaves using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, Steinheim, Germany) following the manufacturer’s protocol

treatment_protocol: Grapevine plants were treated with a B. bassiana conidia suspension or sterile 1/8 concentrated Ringer’s solution containing 0.02% Tween 80 as a control. 24 and 168 hours post treatment (hpt) one leaf of each grapevine plant was carefully cut at its base from the plant and was immediately shock-frozen in liquid nitrogen before storage at -80°C prior to RNA extraction.

value: grapevine leaves

tag: timepoint

value: 168 hpt

value: B. bassiana conidia syspension


title: grapevine_168hpt_Beauveria treatment_rep2

tag: tissue


title: pre_subject26


title: grapevine_168hpt_Beauveria treatment_rep1


title: pre_subject18


title: grapevine_24hpt_Beauveria treatment_rep3

source_name: grapevine leaves 24 h after treatment with Beauveria bassiana

value: 24 hpt


title: pre_subject16


title: pre_subject17


title: grapevine_168hpt_contol_rep2

description: Gene expression of grapevine in response to control treatment

source_name: grapevine leaves 168 h after control treatment

value: control


title: grapevine_168hpt_contol_rep1


title: grapevine_168hpt_contol_rep3


title: pre_subject19


title: grapevine_24hpt_Beauveria treatment_rep1


title: pre_subject15


title: grapevine_24hpt_Beauveria treatment_rep2


title: pre_subject13


title: pre_subject12


title: pre_subject14


title: pre_subject11


title: pre_subject10


title: grapevine_24hpt_contol_rep2

source_name: grapevine leaves 24 h after control treatment


title: grapevine_24hpt_contol_rep1


title: grapevine_24hpt_contol_rep3


title: pre_subject6


title: pre_subject4


title: pre_subject7


title: pre_subject8


title: pre_subject5


title: pre_subject3


title: pre_subject9


title: pre_subject2


title: Trem2_KO_5XFAD_Hip

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v2.1.0)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v2.1.0)
barcode processing, Cell Ranger Single Cell Software Suite (v2.1.0)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v2.1.0)
alignment, Cell Ranger Single Cell Software Suite (v2.1.0)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: Isolated single nuclei from brain of Trem2 KO 5XFAD mice

extract_protocol:
Mice were aged to 15 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1000 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer.
Isolated single nuclei were subjected to droplet-based 3’ end massively parallel single-cell RNA sequencing using Chromium Single Cell 3’ Reagent Kits as per manufacturer’s instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer.

tag: strain

tag: mouse genotype

value: Trem2-/- 5XFAD

value: nuclei of brain

tag: age

value: 15 months


title: pre_subject1

tag: gender


title: WT_5XFAD_Hip

source_name: Isolated single nuclei from brain of 5XFAD mice


title: Brain, Repo-GAL4 R1

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

hyb_protocol: Done according to Affymetrix protocols

scan_protocol: Scanned on Affymetrix GCS 3000 scanner

data_processing: Processed Expression Console using GMT normalization

organism: Drosophila melanogaster

source_name: Whole Brain

label_protocol: Used WT amplification and Labeling kit (Life Technologies) according to Affymetrix protocols

growth_protocol: All flies were raised at 25deg in a humidity controled biochamber. Approximately 3-5 day old flies were used for expression studies.

extract_protocol: TRI reagent and Directzol miniPrep for total RNA

treatment_protocol: Total RNA was isolated from control (repo>36303-emptyvector-RNAi) and gliopathic seizure lines by removing 15-25 fly heads per genotype and homogenizing in TRI Reagent (Applied Biosystems) and followed by RNA purification with Directzol RNA MiniPrep Plus (Zymo Research Corp) according to the manufacturer’s instructions. Purity and concentration was verified using NanoDrop spectrophotometer (ThermoFisher Scientific) and Qubit (ThermoFisher Scientific). RNA integrity was measured using a Bioanalyzer (Agilent). mRNA from the gliopathic seizure flies was pooled into a single group by adding equal amounts of mRNA from each sample. Samples were run on a GeneChip Drosophila Gene 1.0 ST Array (ThermoFisher Scientific, #902155).

value: Brain

tag: genotype

value: Control