title: CON_46_Pax_miRNA


title: Healthy PBMC (Validation) (CHIP_CD14_1)

status: Public on Mar 31 2019

type: SRA

city: Cambridge

first: Paul

last: Blainey

state: Massachusetts

address: 415 Main St

country: USA

institute: Broad Institute

description: Technical Validation - RNA-seq.matrix

library_source: transcriptomic

data_processing:
Bcls were demultiplexed using Illumina bcl2fastq (v2.20.0.422)
Fastqs were aligned to hg19 using STAR
Gene expression matrices were generated using Bowtie2
Genome_build: hg19
Supplementary_files_format_and_content: Matrices are provided as samples (columns) vs. genes (rows)

molecule: total RNA

organism: Homo sapiens

source_name: Healthy PBMC

extract_protocol:
Cells were resuspended in TCL buffer, supplemented with 1 mg/mL proteinase K, and processed through the Smart-seq2 protocol (on a microfluidic device)
Libraries were constructed using the Nextera XT (Illumina) library preparation kit

tag: disease state

value: Healthy

tag: cell type

value: PBMC

tag: cell subset

value: CD14 monocytes


title: CON_45_Pax_miRNA

city: Seattle

first: alison

middle: g

last: paquette

state: WA

address: 401 Terry Avenue N

institute: Institute of Systems Biology

data_processing:
miRNAs were aligned to homo sapien miRNA transcripts with 0 mismatches catalouged by miRbase (V 21) using miRNA pipeline SRNAnalyzer (Wu et al, Nucleic Acids Research, 2017)
miRNA abudances were called calculated using single assignment miRNA mapping using SRNAnalyzer (Wu et al, Nucleic Acids Research, 2017)
Transcripts were filtered so that low expressing samples (mean read count <20), or mostly unexpressed (>50% of samples NA) transcripts were removed prior to preprocessing
Data was normalized using Read Counts Per Million (RPKM)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data matrix reflects RPKM values of final dataset

source_name: Whole Blood

extract_protocol:
Whole blood RNA was isolated from PAXgene tubes using microRNA isolation kit (Qiagen) using TRIsol LS (Invitrogen) following manufacturer’s instructions.
RNA library preparation was performed following the NEB NEBNext Multiplex Small RNA Library Preparation protocol. Briefly, 400 ng of total RNA was used as the input material. The 3’ SR Adapter was ligated to the small RNA, followed by RT primer hybridization to the 3’ SR adapter and then the 5’ SR Adapter was ligated to the opposite end (this strategy prevents formation of adapter-dimers). First stranded synthesis was then performed off the RT primer and the library was enriched by PCR using the following conditions: initial denaturation at 94oC for 30 seconds, followed by 15 cycles of 94oC for 15 seconds, 62oC for 30 seconds and 70oC for 15 seconds, and finally an extension step for 5 minutes at 70oC; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. One ul of the final Small RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size and libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).
Libraries were pooled in equimolar quantities and sequenced on a High Throughput Run Mode flowcell with the V4 sequencing chemistry on an Illumina HiSeq 2500 platform following Illumina’s recommended protocol to generate single-end reads of 50-bases in length.

tag: condition

value: Term Delivery


title: Healthy PBMC (Validation) (BENCH_CD8_2)

description: Technical Validation - RNA-seq.matrix

value: CD8 T cells


title: Healthy PBMC (Ex Vivo) (CD14_DEX_2)

description: Ex Vivo.matrix


title: Healthy PBMC (Validation) (BENCH_CD8_3)

description: Technical Validation - RNA-seq.matrix


title: Vglut2:Ndufs4cKO rep #3

type: RNA

city: Bellaterra

first: Elisenda

last: Sanz

state: Barcelona

address: M1/113 Facultat de Medicina

department: Institut de Neurociencies

country: Spain

institute: Universitat Autonoma de Barcelona

description:
replicate 3
9380251012_G

hyb_protocol: Standard Illumina hyb protocol (58ºC for 16h)

scan_protocol: Standard Illumina scan protocol

data_processing: Data was analyzed for differential expression using the GenomeStudio data analysis software (Illumina). Average normalization, the Illumina custom error model and multiple testing corrections using Benjamini and Hochberg False discovery rate were applied to the analysis.

label: biotin

organism: Mus musculus

source_name: Brainstem

label_protocol: RNA was labelled using Illumina's total Prep kit (Ambion)

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen)

tag: strain

tag: genotype/variation


title: Vglut2:Ndufs4cKO rep #1

description:
replicate 1
9380251012_E


title: Healthy PBMC (Validation) (BENCH_CD8_1)

description: Technical Validation - RNA-seq.matrix


title: Healthy PBMC (Validation) (BENCH_CD4_3)

description: Technical Validation - RNA-seq.matrix

value: CD4 T cells


title: Vglut2:Ndufs4cKO rep #4

description:
replicate 4
9380251012_H


title: CON_44_PAX_miRNA


title: CON_41_Pax_miRNA


title: Vglut2:Ndufs4cCT rep #4

description:
replicate 4
9380251012_D


title: CON_42_Pax_miRNA


title: CON_40_Pax_miRNA


title: CON_8_PAX_miRNA


title: Healthy PBMC (Validation) (BENCH_CD4_2)

description: Technical Validation - RNA-seq.matrix


title: Vglut2:Ndufs4cCT rep #2

description:
replicate 2
9380251012_B


title: Healthy PBMC (Validation) (CHIP_CD14_2)

description: Technical Validation - RNA-seq.matrix


title: SC

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

country: Italy

institute: CNR

description:
pulled-down RNA
X121.SC12
scrambled probes

data_processing:
Library strategy: RNA pull-down (miR-CATCH)
Raw sequences were de-multiplexed using the Illumina pipeline CASAVA v1.8.
Cutadapt v.1.2.1 was used for trimming adapter sequences off the raw reads. Reads with N calls were discarded using FASTX_Toolkit v 0.0.13.1 and only reads with all base calls showing a Phred score higher than 30 were retained for further analysis.
miRExpress v2.1.3 was exploited to identify pre-miRNA sequences (miRBase v.21) allowing at least 95% of sequence identity and a length tolerance range of 4bp for mapping.
Expression values were normalized to reads per million (rpm).
Supplementary_files_format_and_content: Tab-delimited text file including normalized read count per sample.

source_name: A375 cells

growth_protocol: 2 10^6 A375 cells were seeded in 10cm dishes in DMEM HG complete medium.

extract_protocol:
RNA was extracted using miRNEasy MINI Kit (Qiagen), following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 24h, 10^7 A375 cells were harvested and cross-linked with 1% formaldheyde for 10min, then they were subjected to the miR-CATCHv2.0 protocol.

tag: cell line

value: melanoma cell line

tag: protocol


title: Healthy PBMC (Validation) (BENCH_CD19_3)

description: Technical Validation - RNA-seq.matrix

value: B cells


title: CON_39_PAX_miRNA


title: Vglut2:Ndufs4cCT rep.#1

description:
replicate 1
9380251012_A


title: Vglut2:Ndufs4cCT rep#3

description:
replicate 3
9380251012_C


title: Vglut2:Ndufs4cKO rep #2

description:
replicate 2
9380251012_F


title: CON_38_Pax_miRNA


title: CON_35_Pax_miRNA


title: Healthy PBMC (Validation) (BENCH_CD4_1)

description: Technical Validation - RNA-seq.matrix


title: Healthy PBMC (Validation) (BENCH_CD19_2)

description: Technical Validation - RNA-seq.matrix


title: ODD,rep3

description:
pulled-down RNA
X119.ODD12


title: Healthy PBMC (Validation) (BENCH_CD19_1)

description: Technical Validation - RNA-seq.matrix


title: Healthy PBMC (Validation) (BENCH_CD14_3)

description: Technical Validation - RNA-seq.matrix


title: CON_33_PAX_miRNA


title: CON_32_Pax_miRNA


title: Healthy PBMC (Validation) (BENCH_CD14_1)

description: Technical Validation - RNA-seq.matrix


title: ODD,rep2

description:
pulled-down RNA
X117.ODD10


title: CON_34_Pax_miRNA


title: ODD,rep1

description:
pulled-down RNA
X115.ODD9


title: EVEN,rep2

description:
pulled-down RNA
X118.EVEN10


title: CON_26_Pax_miRNA


title: CON_31_Pax_miRNA


title: CON_29_Pax_miRNA


title: CON_22_Pax_miRNA


title: CON_24_Pax_miRNA


title: CON_20_Pax_miRNA


title: CON_19_Pax_miRNA


title: EVEN,rep3

description:
pulled-down RNA
X120.EVEN12


title: EVEN,rep1

description:
pulled-down RNA
X116.EVEN9


title: Healthy PBMC (Validation) (BENCH_CD14_2)

description: Technical Validation - RNA-seq.matrix


title: CON_14_Pax_miRNA


title: Rice_OsCAld5H1-KO-a-9-2-rep3

city: Tsuruoka

first: Yuri

last: Takeda-Kimura

state: Yamagata

address: 1-23 Wakabamachi

department: Faculty of Agriculture

country: Japan

institute: Yamagata University

description:
Gene expression of CRISPR/Cas9-induced OsCAld5H1-knockout rice plants
OsCAld5H1-knockout rice, biological replicate 3

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 4x44K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Processed signal intensities were normalized by the global scaling method.  A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

organism: Oryza sativa

source_name: OsCAld5H1-knockout rice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Rice plants were grown in a growth chamber at 27℃ with a 12h daily photoperiod.

extract_protocol: RNA was prepared using the RNeasy plant mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA).

tag: cultivar

value: Nipponbare

tag: tissue

value: middle position of the second top internode

tag: developmental stage

value: heading stage

tag: generation

tag: genotype


title: CON_17_Pax_miRNA


title: CON_16_Pax_miRNA


title: CON_10_Pax_miRNA


title: Rice_WT_rep3

description:
Gene expression of wild-type rice plants
wild-type rice, biological replicate 3

source_name: wild-type rice

value: wild-type


title: CON_13_Pax_miRNA


title: TC71 + I-73

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

country: Germany

institute: Charité - Universitätsmedizin Berlin

description: Gene expression data of adherent Ewing sarcoma cell line cultured in tissue culture plates and treated for 8 hrs as described in overall design

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays

scan_protocol: Affymetrix GCS 3000 Genechip system, scanner GC30007G, software expression console, version 1.6

data_processing: RMA normalization.

source_name: Ewing sarcoma cell line TC71 + 2 µM I-73

label_protocol: Total RNA (200 ng) was amplified and labeled using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit

growth_protocol: Cell lines were grown in plastic tissue culture plates in a humidified incubator at 37°C in 5% CO2 atmosphere in RPMI 1640 media containing 10% heat-inactivated fetal bovine serum, 1% glutamine, 100 U/ml penicillin, 100 µg/mL streptomysin and 200 mg/dl D-glucose .

extract_protocol: RNA was isolated using the RNeasy RNA isolation kit according to the manufacturer´s instructions

treatment_protocol: Ewing sarcoma cell lines were treated with 2 µM CDK9 inhibitor I-73 or solvent control for 8 hrs at 37 °C, 5% CO2

value: Ewing sarcoma

value: bone (Ewing sarcoma, 22 year old male)

tag: agent

value: CDK9 inhibitor I-73


title: Rice_OsCAld5H1-KO-a-9-2-rep1

description:
Gene expression of CRISPR/Cas9-induced OsCAld5H1-knockout rice plants
OsCAld5H1-knockout rice, biological replicate 1


title: TC71 control

source_name: Ewing sarcoma cell line TC71 + solvent control

value: control


title: CON_18_Pax_miRNA


title: Rice_OsCAld5H1-KO-a-9-2-rep2

description:
Gene expression of CRISPR/Cas9-induced OsCAld5H1-knockout rice plants
OsCAld5H1-knockout rice, biological replicate 2


title: Rice_WT_rep1

description:
Gene expression of wild-type rice plants
wild-type rice, biological replicate 1


title: SKNMC + I-73

source_name: Ewing sarcoma cell line SKNMC+ 2 µM I-73

value: soft tissue (Ewing sarcoma, 14 year old female)

value: SKNMC


title: Rice_WT_rep2

description:
Gene expression of wild-type rice plants
wild-type rice, biological replicate 2


title: CON_1_PAX_miRNA


title: SKNMC control

source_name: Ewing sarcoma cell line SKNMC + solvent control


title: A673 control

source_name: Ewing sarcoma cell line A673 + solvent control

value: soft tissue (Ewing sarcoma, 15 year old female)


title: A673 + I-73

source_name: Ewing sarcoma cell line A673 + 2 µM I-73


title: SW13

city: Hannover

first: Rui

last: Costa

state: Niedersachsen

address: Carl Neuberg Strasse 1

department: Gastroenterology Hepatology and Endocrinology

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing:
Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml’. Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling. For this, all gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be scaled (‘Array i’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  A lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15. Finally, normalized signal intensities were log-transformed for visualization (base 10).
Log-transformed normalized processed signal intensities. Measurements of control features have been removed.

source_name: Immortalized cell line

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: Cells were grown to approx. 90% confluency on 10 cm dishes prior extraction. Maintenance of adherent immortalized cell lines was carried out by culture with Dulbecco´s Modified Eagle Medium (DMEM) supplemented with 10% Fetal Calf Serum (FCS), penicillin/streptomycin (100 U/ml), non-essential amino acids (1X), and L-glutamine (2mM) at 37C and 5% CO2. Suspension cell line Jurkat was cultured with Roswell Park Memorial Institute (RPMI) 1640 medium plus 25 mM HEPES with the same supplements and conditions as adherent cell lines.

extract_protocol: Total RNA was extracted as instructed in the RNeasy Midi kit (Qiagen, Hilden, Germany) guidelines.

value: Epithelial

tag: tissue origin

value: Adrenal Gland/Cortex


title: IMR-90_siGFP_exp3_rep2

city: Palermo

first: Salvatore

last: Feo

address: Viale delle Scienze, Edificio 16

department: Dept. of Biological, Chemical and Pharmaceutical Sciences and Technologies

institute: University of Palermo

hyb_protocol: 1.0 ug of Cy3- or Cy5-labelled cRNA (specific activity >9.0 pmol Cy/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarray 4x44K (Agilent-G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channels PMT set to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters (protocol: GE2-v5_95_Feb07 and Grid: 014850_D_F_20110325) to obtain background subtracted, dye normalized and spatially detrended processed signal intensities

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 labeled cRNA was prepared from 200 ng total RNA using the LowInput QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions (Agilent protocol: G4140-90050_GeneExpression_TwoColor_ver._6.9.1), followed by RNAeasy mini kit column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 spectrophotometer

growth_protocol: Cultivated in DMEM + 10% fetal bovine serum

extract_protocol: Total RNA from siRNA treated cells was extracted using Trizol reagent (Invitrogen) and further purified with RNeasy RNA isolation kit according to manufacturer’s instructions (Qiagen). RNA 6000 Nano LabChip kit (Agilent) was used to determine the concentration, the purity and the integrity of the RNA samples using an Agilent 2100 bioanalyzer. Only samples with a RIN (RNA Integrity Number) > 8.0 were used for analysis.

treatment_protocol: IMR-90 cells were transfected with gene specific siRNA with Lipofectamine 2000 Reagent (Invitrogen), according to manufacturer’s recommendation

value: Fetal lung fibroblast

tag: transfected with

value: GFP siRNA


title: 293T

value: Embryonic Kidney


title: BJ1

value: Fibroblast

value: Skin


title: IMR-90_siDNMT1_exp3_rep2

value: DNMT1 siRNA


title: IMR-90_siDNMT1_exp3_rep1


title: HPMEC

value: HPMEC

value: Endothelial

value: Lung


title: IMR-90_siMAD_exp3_rep1

value: MAD2 siRNA


title: IMR-90_sipRb_exp3_rep2

value: pRb siRNA


title: IMR-90_sipRb_exp3_rep1


title: IMR-90_sipRb_exp2_rep2


title: IMR-90_siDNMT1_exp2_rep1


title: A549


title: Jurkat

value: Jurkat

value: T-lymphocyte

value: Peripherial blood


title: 786-O

value: Prostate


title: SK-N-SH

value: SK-N-SH

value: Epithelial

value: Bone marrow


title: IMR-90_siGFP_exp2_rep1

value: Fetal lung fibroblast

value: GFP siRNA


title: IMR-90_siDNMT1_exp2_rep2


title: IMR-90_sipRb_exp2_rep1


title: IMR-90_siMAD_exp2_rep2


title: IMR-90_siGFP_exp2_rep2


title: EAhy 2

value: EAhy 2

value: Somatic cell hybrid


title: PHH 27.9.2012

value: Hepatocyte

value: liver


title: SKNMC

value: SKNMC

value: Brain, Supra-orbital Area


title: IMR-90_siGFP_exp1_rep2


title: IMR-90_siDNMT1_exp1_rep2

value: DNMT1 siRNA


title: IMR-90_siMAD_exp2_rep1

value: MAD2 siRNA


title: Huh7.5 RNA I

value: Huh7.5 RNA I

value: Liver


title: BA62

type: genomic

city: Norman

first: Jie

last: Deng

state: OK

address: 101 David L Boren Blvd, SRTC 2022

institute: University of  Oklahoma

description: gDNA labeled by Cy5

hyb_protocol: Microarray slides were pre‐hybridized in buffer containing 0.1% SDS, 5xSSC and 1 mg/mL BSA at 50 0C for 90 min, and washed with 0.5xSSC and water. Cy5‐labeled DNA samples were mixed with the same .volume of 2X hybridization buffer (10xSSC, 0.2% SDS, 0.2 mg/mL herring sperm DNA, and 46% formamide), heated at 95 0C for 5 min and then transferred to 68 0C. Samples were applied to pre‐hybridized slides, which were then incubated at 50 0C for 18 h before being washed

scan_protocol: Arrays were and scanned using an Axon GenePix 4000B scanner.

data_processing: For each array, the average signal from quality control probes was calculated and deducted from the signals of all non-QC probes.

molecule: genomic DNA

organism: Shewanella baltica

label_protocol: Resuspend pellets in 4.5uL 100 mM Na2CO3.  Mix with 4.5 uL Cy5, Incubate at 25C for 1.5 hrs, Clean-up with Qiagen Min-Elute PCR purification kit

growth_protocol: Aerobic growth with LB medium.

extract_protocol: According to methods described in Richards E, Reichardt M, & Rogers S (1994) Preparation of Genomic DNA from Plant Tissue. Current Protocols in Molecular Biology eds Ausubel M, Brent R, Kingston RE, Moore DD, Seidman JG, John A. Smith JA, & Struhl K (John Wiley, Hoboken, NJ), pp 2.3.1-2.3.7

treatment_protocol: No treatment


title: BA194

description: gDNA labeled by Cy5


title: BA185

description: gDNA labeled by Cy5


title: IMR-90_siDNMT1_exp1_rep1


title: IMR-90_sipRb_exp1_rep1

value: pRb siRNA


title: BA38

description: gDNA labeled by Cy5


title: BA173A

description: gDNA labeled by Cy5


title: IMR-90_sipRb_exp1_rep2


title: BA37

description: gDNA labeled by Cy5


title: IMR-90_siMAD_exp1_rep1


title: Left lesion

city: Shanghai

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

country: China

institute: Shanghai Jiao Tong University

description: Gene expression data from left lesion.

hyb_protocol: Standard Affymetrix procedures

scan_protocol: GeneChips were scanned by the Affymetrix Scanner 3000.

data_processing: The data were analyzed with Affymetrix GeneChip Command Console version 4.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Brain tissue from GBM patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: histopathological diagnostic

value: :GBM, grade 4

value: Left lesion


title: IMR-90_siMAD_exp1_rep2


title: OS696

description: gDNA labeled by Cy5


title: OS167

description: gDNA labeled by Cy5


title: BA173B

description: gDNA labeled by Cy5


title: Right lesion

description: Gene expression data from right lesion.

value: Right lesion


title: BA196

description: gDNA labeled by Cy5


title: OS189

description: gDNA labeled by Cy5


title: OS187

description: gDNA labeled by Cy5


title: OS697

description: gDNA labeled by Cy5


title: OS681

description: gDNA labeled by Cy5


title: OS250

description: gDNA labeled by Cy5


title: OS678

description: gDNA labeled by Cy5


title: OS652

description: gDNA labeled by Cy5


title: OS690

description: gDNA labeled by Cy5


title: OS252

description: gDNA labeled by Cy5


title: SAMPLE 11: THP1_Echinaforce_rep5

city: Antwerp (Wilrijk)

first: Ken

last: Declerck

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

description: THP1 cells treated with 1% Echinaforce for 48h, replicate5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Expression values were log2 transformed and quantile normalized using the limma R package

source_name: THP1, Echinaforce, 48h, replicate5

label_protocol: Biotinylated cRNA were prepared with the Illumina Totalprep RNA amplification kit (Life technologies)

growth_protocol: THP-1 cells were grown in RPMI-1640 medium supplemented with glutamine, 10 % heat inactivated Fetal Bovine Serum, 50 IU/mL Penicillin, 50 µg/mL Streptomycin, 10 mM HEPES and 0.05 mM β-mercaptoethanol.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) according to the manufacterer's protocol.

treatment_protocol: Cells were treated with 1% Echinaforce® tincture versus ethanol solvent control. Each treatment condition consisted of six biological replicates.

value: monocyte


title: OS650

description: gDNA labeled by Cy5


title: OS710

description: gDNA labeled by Cy5


title: Left perilesion

description: Gene expression data from left perilesion.

value: Left perilesion


title: SAMPLE 12: THP1_Echinaforce_rep6

description: THP1 cells treated with 1% Echinaforce for 48h, replicate6

source_name: THP1, Echinaforce, 48h, replicate6


title: BA175

description: gDNA labeled by Cy5


title: OS638

description: gDNA labeled by Cy5


title: OS286

description: gDNA labeled by Cy5


title: OS625

description: gDNA labeled by Cy5


title: SH5Y

value: Epithelial

value: Bone marrow


title: OS641

description: gDNA labeled by Cy5


title: SAMPLE 10: THP1_Echinaforce_rep4

description: THP1 cells treated with 1% Echinaforce for 48h, replicate4

source_name: THP1, Echinaforce, 48h, replicate4


title: OS288

description: gDNA labeled by Cy5


title: IMR-90_siGFP_exp1_rep1

value: Fetal lung fibroblast

value: GFP siRNA


title: SAMPLE 7: THP1_Echinaforce_rep1

description: THP1 cells treated with 1% Echinaforce for 48h, replicate1

source_name: THP1, Echinaforce, 48h, replicate1


title: OS631

description: gDNA labeled by Cy5


title: SAMPLE 3: THP1_EtOH_rep3

description: THP1 cells treated with ethanol for 48h, replicate3

source_name: THP1, EtOH, 48h, replicate3


title: SAMPLE 8: THP1_Echinaforce_rep2

description: THP1 cells treated with 1% Echinaforce for 48h, replicate2

source_name: THP1, Echinaforce, 48h, replicate2


title: OS645

description: gDNA labeled by Cy5


title: OS628

description: gDNA labeled by Cy5


title: SAMPLE 6: THP1_EtOH_rep6

description: THP1 cells treated with ethanol for 48h, replicate6

source_name: THP1, EtOH, 48h, replicate6


title: SAMPLE 9: THP1_Echinaforce_rep3

description: THP1 cells treated with 1% Echinaforce for 48h, replicate3

source_name: THP1, Echinaforce, 48h, replicate3


title: SAMPLE 5: THP1_EtOH_rep5

description: THP1 cells treated with ethanol for 48h, replicate5

source_name: THP1, EtOH, 48h, replicate5


title: BA170

description: gDNA labeled by Cy5


title: Rx3+/+;PV:tdT rep 3

city: New York

first: Joriene

middle: C

last: de Nooij

state: NY

address: 650 West 168th Street

department: Neurology

institute: Columbia University

data_processing:
RNA-seq data was mapped by OLego v1.1.5 (Wu et al., 2013) to the reference genome (mm10) and a comprehensive database of exon junctions was provided for read mapping.  Only reads unambiguously mapped to the genome or exon junctions were used for downstream analysis. Gene expression was quantified using the Quantas pipeline as we described previously (Yan et al., 2015). Differential expression was evaluated by edgeR (Robinson et al., 2010), as part of the Quantas pipeline.  Differentially expressed transcripts were identified based on the following criteria: benjamini FDR <0.03, |log2(fold change)|≥2, and reads per kilo million (RPKM) >1 in at least one of the compared conditions.
Genome_build: mm10
Supplementary_files_format_and_content: Excel

source_name: DRG

extract_protocol:
DRG from neonates (both sexes) were dissected in ice-cold Hank’s balanced salt solution (HBBS) and dissociated by enzymatic digestion (Papain, Collagenase IV, Dispase type II; Worthington Biochemical Corporation) and mechanical trituration, essentially as described (Malin et al., 2007). Cell suspensions were passed through 35 mm gauze filters to clear suspension from remaining cellular aggregates. Fluorescently labeled neuronal subsets were isolated through Fluorescent Activated Cell Sorting (FACS) using a Beckman Coulter Altra Hypersort (Becton-Dickinson). Neurons were sorted at 12-13 psi using a 100 mm nozzle and collected in lysis buffer (Agilent) and stored at -80oC until processed. Total RNA was extracted from all neuronal samples (Absolutely RNA nanoprep kit; Agilent Technologies) and RNA integrity was assessed by Bioanalyzer (quality threshold was set at RIN>8). Amplified cDNA was generated using the Ovation RNA-Seq System V2 kit (NuGen). cDNA Sample quality and fragmentation was measured by Bioanalyzer (DNA1000 chip).
Library preparation and single-end RNA sequencing was performed at the JP Sulzberger Columbia Genome Center (25-30 million reads/sample). See https://systemsbiology.columbia.edu/genome-center for details. Briefly, we use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

value: C57/Sv129 mixed back ground

tag: number of animals contributing to sample

value: DRG

value: Proprioceptors and RA-LTMRs


title: Rx3+/+;PV:tdT rep 2

tag: cell type


title: Rx3-/-;PV:tdT rep 3

value: RA-LTMRs


title: Rx3+/+;PV:tdT rep 1


title: Rx3-/-;PV:tdT rep 1


title: Rx3-/-;PV:tdT rep 2


title: OS193

description: gDNA labeled by Cy5


title: OS225

description: gDNA labeled by Cy5


title: SAMPLE 2: THP1_EtOH_rep2

description: THP1 cells treated with ethanol for 48h, replicate2

source_name: THP1, EtOH, 48h, replicate2


title: OS230

description: gDNA labeled by Cy5


title: OS190

description: gDNA labeled by Cy5


title: C.2N

city: Tokushima city

first: Koichiro

last: Kajiura

department: Department of Thoraci,Endocrine Surgery and Oncology

institute: Institute of Biomedical Sciences, Tokushima University Graduate School

description: Normal, DNA methylation

hyb_protocol: bisulfite convered DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illuminascanner setting

data_processing: GenomeStudio V2011.1

label: Cy5 and Cy3

source_name: human thymus

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from thymic or normal thymus samples using QIAamp® DNA Mini kit according to standard instructions.

value: normal thymus

tag: age

tag: gender

value: M

tag: brinkman index

tag: tnm factor

tag: Stage


title: SAMPLE 1: THP1_EtOH_rep1

description: THP1 cells treated with ethanol for 48h, replicate1

source_name: THP1, EtOH, 48h, replicate1

tag: cell line


title: A.24T

description: A thymoma, DNA methylation

value: type A thymoma


title: OS117

description: gDNA labeled by Cy5

tag: strain


title: TrkC-GFP rep3

tag: tissue

value: Proprioceptors and SA-LTMRs

value: TrkC-GFP


title: A.19T

description: A thymoma, DNA methylation


title: OS183

description: gDNA labeled by Cy5


title: OS106

description: gDNA labeled by Cy5


title: OS110

description: gDNA labeled by Cy5


title: TrkC-GFP rep2

tag: developmental stage


title: TrkC-GFP rep1


title: AB1Lysates_20min_rep1

city: Chongqing

first: zichen

last: yang

address: Gaotanyan

institute: Army Medical University (Third Military Medical University)

data_processing:
The sequenced libraries were mapped against predicted  transcripts from the Acinetobacter baumannii ATCC  17978 genome using TopHat v2.0.4
The transcript  abundance (FPKM, Fragments Per Kilobase of exon per  Million fragments mapped) and significant changes in  transcript expression were estimated using Cufflinks  v2.0.2
Transcripts with p-values less than 0.05,  determined using CuffDiff
Genome_build: NC_021316.1 and NZ_CP018664.1 were used as the reference genomes

organism: Acinetobacter phage AB1

source_name: AB1 lysates, 20min, replicate 1

growth_protocol: AB1with or wihout phage infection was grown in Luria-Bertani (LB) broth medium aerobically.

extract_protocol:
Total RNA was isolated using SV Total RNA Isolation System (Promega) according to the manufacturer’s instructions and   checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer   2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further   purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and   RNase-Free DNase Set    (Cat#79254, QIAGEN, GmBH, Germany).
Barcoded sequencing libraries
Pooled libraries were enriched for the exome using hybridization (TruSeq Exome Enrichment Kit, Illumina), quantified using quantitative PCR and pooled in 1:1 ratio for pairedend sequencing on a HiSeq2500 (Illumina)

treatment_protocol: Bacterial culture were infected with phage Abp1 at MOI of 10 for 5min, 10min, 20min.The uninfected samples served as reference.

tag: treatment

value: without phage infection control 20min


title: OX-yedQ-2

city: Hong Kong

first: Xin

address: To Yuen Building

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

data_processing:
Bacterial RNA-seq reads were mapped to the Pseudomonas syringae pv. syringae B728a genome by using tophat2 (2.1.1), with two mismatches allowed
Only the uniquely mapped reads were kept for the subsequent analyses.
The gene differential expression analysis was performed using cufflinks(2.2.1)
Genome_build: Pseudomonas syringae pv. syringae B728a
Supplementary_files_format_and_content: xls file containing comparisons between OX-yhjH and OX-yedQ

organism: Pseudomonas syringae pv. syringae B728a

source_name: liquid culture in NYGB medium

growth_protocol: grow until mid-log phase in NYGB, 28 °C

extract_protocol:
To test the effect of high c-di-GMP level in Psy B728a on the transcriptome, cells were recovered and cultured to early stationary (OD600 ~ 2) in NYGB medium consisting of 8 g nutrient broth, 10 g glucose and 5 g yeast extract each liter. Cells were mixed with bacterial RNA Protect Reagent (Qiagen) to keep intact RNA. Total RNA was purified using RNeasy Mini Kit (Qiagen). RNase-free DNase Set (Qiagen) was applied to remove DNA contaminant through on-column DNase digestion. Second DNA removal step was applied using Ambion™ TURBO DNA-free Kit. rRNA was depleted using Ribo-Zero rRNA removal Kit (Illumina). The integrity and concentration of total RNA and DNA contamination were examined by Agilent TapeStation System (Agilent Technologies) and Qubit® 2.0 Fluorometer (Invitrogen). Reverse transcription to cDNA was done using NEBNext RNA first and second strand synthesis module (NEB). Analysis of gene expression was carried out via Illumina RNA-Seq. Libraries were produced using an Illumina TruSeq Stranded messenger RNA Sample Prep Kit. The libraries were sequenced using Illumina HiSeq 2500 platform with a paired-end protocol and read lengths of 100 nt.
TruSeq RNA sample prep kit protocol (Illumina)

tag: genotype/variation

value: over-expressing yedQ gene

value: whole organism


title: C.4

description: A thymoma, DNA methylation


title: OS109

description: gDNA labeled by Cy5


title: OS107

description: gDNA labeled by Cy5


title: OS155

description: gDNA labeled by Cy5


title: B3.23T

description: B3 thymoma, DNA methylation

value: B3 thymoma


title: OS195

description: gDNA labeled by Cy5


title: OS185

description: gDNA labeled by Cy5


title: AB1Lysates_20min_rep3

source_name: AB1 lysates, 20min, replicate 3


title: B3.20T

description: B3 thymoma, DNA methylation


title: AB1Lysates_20min_rep2

source_name: AB1 lysates, 20min, replicate 2


title: OS223

description: gDNA labeled by Cy5


title: AB1Lysates_10min_rep3

source_name: AB1 lysates, 10min, replicate 3

value: without phage infection control 10min


title: B3.18T

description: B3 thymoma, DNA methylation


title: OX-yhjH-3

value: over-expressing yhjH gene


title: AB1Lysates_5min_rep2

source_name: AB1 lysates, 5min, replicate 2

value: without phage infection control 5min


title: AB1Lysates_10min_rep2

source_name: AB1 lysates, 10min, replicate 2


title: B3.14T

description: B3 thymoma, DNA methylation


title: OX-yedQ-1


title: AB1Lysates_10min_rep1

source_name: AB1 lysates, 10min, replicate 1


title: AB1Lysates_5min_rep3

source_name: AB1 lysates, 5min, replicate 3


title: SAMPLE 4: THP1_EtOH_rep4

description: THP1 cells treated with ethanol for 48h, replicate4

source_name: THP1, EtOH, 48h, replicate4

value: monocyte


title: B3.11

description: B3 thymoma, DNA methylation


title: OS700

description: gDNA labeled by Cy5


title: OX-yhjH-2


title: OX-yhjH-1


title: OX-yedQ-3


title: AB1Lysates_5min_rep1

source_name: AB1 lysates, 5min, replicate 1


title: C.7

description: TC, DNA methylation

value: squamous cell carcinoma


title: Sample_97L_P_SRC_3

status: Public on Mar 30 2019

city: Xi 'an

first: Xia

last: Liao

state: Shaanxi

address: 277# West Yanta Road

institute: Department of nutrition

data_processing:
Trimmomatic 0.36 software used for filtering.
Using the Trimmomatic software to control the quality and remove the linker. Based on this, the low-quality base and the N-base are filtered out, and finally high-quality clean reads are obtained.
Hisat2 2.2.1.0 software used for alignment.
The clean reads are compared to the reference genome of the species using hisat2, and the software parameters are default parameters, and the sample is evaluated by the genomic alignment ratio.
Genome_build: Homo sapiens (assembly GRCh38.p12)
Supplementary_files_format_and_content: Excel  files include gene expression for each Sample

source_name: liver

growth_protocol: All cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM; GIBCO, Grand Island, NY, USA) and supplemented with 10% fetal bovine serum (FBS; GIBCO) at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Take an appropriate amount of cell sample, and RNA was harvested using mirVana™ miRNA ISOlation Kit and Ambion-1561. Illumina TruSeq Stranded mRNA LTSample Prep Kit was used with  total RNA for the construction of sequencing libraries.
After extracting total RNA from the sample and digesting the DNA with DNase, enrich the eukaryotic mRNA with magnetic beads with Oligo (dT) (if the prokaryote, remove the rRNA by the kit to enrich the mRNA); add the interrupting reagent The mRNA was broken into short fragments, and the broken mRNA was used as a template. A six-base random primer was used to synthesize a strand cDNA, and then a two-stranded reaction system was synthesized to synthesize a double-stranded cDNA, and the double-stranded cDNA was purified using a kit; The double-stranded cDNA was further ligated to the end, the A tail was added and the sequencing linker was ligated, and then the fragment size was selected, and finally PCR amplification was performed. The constructed library was tested with the Agilent 2100 Bioanalyzer and the Illumina HiSeqTM 2500 or Illumina HiSeq X Ten was used. The sequencer is sequenced to generate double-ended data of 125 bp or 150 bp. After passing the quality test, sequencing was performed using an Illumina sequencer.

treatment_protocol: MHCC97L and Hep3B cells were grown in T25 flasks and treated with saracatinib (2 μmol/L and 1 μmol/L) followed by the addition of increasingly higher concentrations of saracatinib until the MHCC97L cells became stably resistant to 4 μmol/L saracatinib and the Hep3B cells became stably resistant to 2 μmol/L saracatinib. These resistant cells were re-named MHCC97L-SRC and Hep3B-SRC. Oxaliplatin-resistant HCC cell lines were generated as previously described. MHCC97L cells that were stably resistant to 2 μmol/L oxaliplatin were re-named MHCC97L-OXA, and Hep3B cells that were stably resistant to 1 μmol/L oxaliplatin were re-named Hep3B-OXA.

value: hepatoma carcinoma cell

value: liver

value: saracatinib


title: Sample_97L_2


title: Sample_97L_P_AC_1

value: oxaliplatin


title: Sample_97L_P_SRC_2


title: Sample_97L_3


title: Sample_97L_P_AC_3


title: C.16T

description: TC, DNA methylation

value: M


title: Sample_97L_P_AC_2


title: B3.10

description: B3 thymoma, DNA methylation


title: C.2

description: TC, DNA methylation


title: Sample_97L_P_SRC_1


title: B3.9

description: B3 thymoma, DNA methylation


title: B3.12

description: B3 thymoma, DNA methylation


title: C.3

description: TC, DNA methylation


title: C.8

description: TC, DNA methylation


title: C.5

description: TC, DNA methylation


title: Sample_97L_1


title: HomeCage, dVenus+, MouseNr 17 [HC_G17]

city: Rotterdam

first: Steven

last: Kushner

state: Zuid Holland

address: Dr. Molewaterplein 40

department: Psychiatry

country: Netherlands

institute: Erasmus MC

data_processing:
base-calling: Illumina bcl2fastq
alignment: tophat2 version 2.0.13 [Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013 Apr 25;14(4):R36]
fragment counts: htseq-count version 0.6.0 [Anders S, Pyl PT, Huber W (2015) HTSeq - a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015 Jan 15;31(2):166-9]
Genome_build: mm10
Supplementary_files_format_and_content: htseq counts: Output from the htseq program, tab delimited text, no header, 2 columns: gene name and count, one line per gene and 5 lines with summary information at the end of each file. Summary lines start with "__"
Supplementary_files_format_and_content: counts matrix: tab delimited text file with one column per sample and one row per gene. Row and column names are included. Only the genes taken into account in the differential expression analyses are included.

source_name: HomeCage, dVenus+

extract_protocol:
full-length cDNA synthesis from cell lysate from 10 cells, according to the SmartSeq2 method [Picelli S, Bjorklund AK, Faridani OR, Sagasser S, Winberg G, Sandberg R. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods 10, 1096-1098 (2013)]
Illumina Nextera XT, using 500pg of cDNA

tag: mouse id

value: MouseNr 17

tag: sampleID

value: HomeCage

value: Hippocampal Dentate Gyrus granule neurons

value: dVenus+


title: HomeCage, dVenus+, MouseNr 16 [HC_G16]

value: MouseNr 16


title: Mouse brain CPZ-5 [mRNA]

city: Daejeon

first: Yun Hee

last: Kang

address: 77 Gyeryong-ro 771 beon-gil, Jung-gu

department: Eulji Biomedical Science Research Institute

country: South Korea

institute: Eulji University School of Mdicine

description:
CPZ-5
180209_2_CPZ_5_mouse_RNA_(MoGene-2_0-st).CEL

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16 hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). After importing CEL files, the data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Power Tools (APT). We exported the result with gene level RMA analysis and performed the differentially expressed gene (DEG) analysis.

label: Biotin

source_name: CPZ-feeding mouse brain

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

extract_protocol: RNA was harvested using Trizol reagent (Invitrogen). cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer.

treatment_protocol: Mice were given a diet containing 0.2% cuprizone for 6 weeks.

tag: strain/background

value: Cerebellum

tag: Sex

value: Male

value: Cuprizone


title: Mouse brain control [mRNA]

description:
Control
180209_1_Control_mouse_RNA_(MoGene-2_0-st).CEL

source_name: Normal mouse brain

value: Control


title: HomeCage, dVenus-, MouseNr 17 [HC_NG17]

source_name: HomeCage, dVenus-

value: dVenus-


title: Non Shock, dVenus+, MouseNr 21 [NS_G21]

source_name: Non Shock, dVenus+

value: MouseNr 21

value: Non Shock


title: Non Shock, dVenus+, MouseNr 19 [NS_G19]

value: MouseNr 19


title: Non Shock, dVenus-, MouseNr 21 [NS_NG21]

source_name: Non Shock, dVenus-


title: Non Shock, dVenus+, MouseNr 18 [NS_G18]

value: MouseNr 18


title: Non Shock, dVenus-, MouseNr 18 [NS_NG18]


title: HomeCage, dVenus-, MouseNr 16 [HC_NG16]


title: HomeCage, dVenus-, MouseNr 15 [HC_NG15]

value: MouseNr 15


title: Non Shock, dVenus-, MouseNr 20 [NS_NG20]

value: MouseNr 20


title: Non Shock, dVenus+, MouseNr 20 [NS_G20]


title: Fear Conditioned, dVenus-, MouseNr 09 [NG09]

source_name: Fear Conditioned, dVenus-

value: MouseNr 09

value: Fear Conditioned


title: Fear Conditioned, dVenus-, MouseNr 10 [NG10]

value: MouseNr 10


title: Fear Conditioned, dVenus-, MouseNr 12 [NG12]

value: MouseNr 12

value: Hippocampal Dentate Gyrus granule neurons


title: Non Shock, dVenus-, MouseNr 19 [NS_NG19]


title: Fear Conditioned, dVenus-, MouseNr 13 [NG13]

value: MouseNr 13


title: Fear Conditioned, dVenus-, MouseNr 14 [NG14]

value: MouseNr 14


title: Fear Conditioned, dVenus+, MouseNr 09 [G09]

source_name: Fear Conditioned, dVenus+

value: dVenus+


title: C.6

description: TC, DNA methylation

source_name: human thymus

value: squamous cell carcinoma

value: M


title: C.17T

description: NET, DNA methylation

value: neuroendocrine tumor


title: C.13T

description: NET, DNA methylation


title: C.1

description: NET, DNA methylation


title: Fear Conditioned, dVenus+, MouseNr 14 [G14]


title: Fear Conditioned, dVenus+, MouseNr 12 [G12]


title: Fear Conditioned, dVenus+, MouseNr 11 [G11]

value: MouseNr 11


title: Fear Conditioned, dVenus+, MouseNr 10 [G10]


title: Fear Conditioned, dVenus-, MouseNr 04 [NG04]

value: MouseNr 04

value: dVenus-


title: Fear Conditioned, dVenus-, MouseNr 07 [NG07]

value: MouseNr 07


title: Fear Conditioned, dVenus-, MouseNr 06 [NG06]

value: MouseNr 06


title: Fear Conditioned, dVenus+, MouseNr 04 [G04]


title: Fear Conditioned, dVenus-, MouseNr 01 [NG01]

description: I15-1044-05-Non_Green1_GGACTCCT-CTCTCTAT_L001

value: MouseNr 01


title: Fear Conditioned, dVenus+, MouseNr 06 [G06]


title: Fear Conditioned, dVenus-, MouseNr 03 [NG03]

description: I15-1044-08-Non_Green4_CGTACTAG-TATCCTCT_L001

value: MouseNr 03


title: Fear Conditioned, dVenus+, MouseNr 01 [G01]

description: I15-1044-01-Green1_TAAGGCGA-GCGTAAGA_L001

value: Fear Conditioned


title: Fear Conditioned, dVenus+, MouseNr 13 [G13]


title: Fear Conditioned, dVenus+, MouseNr 05 [G05]

value: MouseNr 05


title: Fear Conditioned, dVenus+, MouseNr 03 [G03]

description: I15-1044-04-Green4_TCCTGAGC-CTCTCTAT_L001


title: W813_str: STR_WT_delControl

city: Boston

first: Michael

last: Talkowski

state: MA

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description: TruSeq Protocol

data_processing:
Quality of sequence reads was assessed by fastQC (version 0.10.1) [Andrews, S. FastQC A Quality Control tool for High Throughput Sequence Data. bioinformatics.babraham.ac.uk projects/fastqc/, doi: citeulike-article-id:11583827].
Gene-based counts for all libraries were generated relying on the Ensembl mouse gene annotation, GRCm38 (v83),
Sequence reads were aligned to the mouse reference genome GRCm38 (v83) using STAR (version 2.4.2a, (citation)) with parameters “--outSAMunmapped Within   --outFilterMultimapNmax 1   --outFilterMismatchNoverLmax 0.1   --alignIntronMin 21   --alignIntronMax 0   --alignEndsType Local   --quantMode GeneCounts      --twopassMode Basic”.
Quality of alignments was assessed by custom scripts utilizing Picard Tools and SamTools.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text file of normalized counts for each sample & gene

source_name: Striatum

extract_protocol:
Illumina’s TruSeq stranded mRNA protocol
Libraries were multiplexed, pooled and sequenced on Illumina HiSeq 2500

value: F

tag: genotype

value: WT

value: Striatum


title: W814_str: STR_WT_delControl

description: TruSeq Protocol


title: W808_str: STR_WT_delControl

description: TruSeq Protocol


title: W815_str: STR_WT_delControl

description: TruSeq Protocol


title: Fear Conditioned, dVenus-, MouseNr 05 [NG05]

value: Hippocampal Dentate Gyrus granule neurons

tag: cell type


title: W806_str: STR_WT_delControl

description: TruSeq Protocol

tag: age


title: D809_str: STR_DEL

description: TruSeq Protocol

tag: gender

value: 16p11.2 Deletion


title: W816_str: STR_WT_delControl

description: TruSeq Protocol


title: D810_str: STR_DEL

description: TruSeq Protocol


title: D811_str: STR_DEL

description: TruSeq Protocol


title: D812_str: STR_DEL

description: TruSeq Protocol


title: W807_str: STR_WT_delControl

description: TruSeq Protocol


title: W805_str: STR_WT_delControl

description: TruSeq Protocol


title: D802_str: STR_DEL

description: TruSeq Protocol


title: D803_str: STR_DEL

description: TruSeq Protocol


title: D804_str: STR_DEL

description: TruSeq Protocol


title: D801_str: STR_DEL

description: TruSeq Protocol


title: W816_ctx: CTX_WT_delControl

description: TruSeq Protocol

source_name: Cortex

value: Cortex


title: W814_ctx: CTX_WT_delControl

description: TruSeq Protocol


title: W813_ctx: CTX_WT_delControl

description: TruSeq Protocol


title: W807_ctx: CTX_WT_delControl

description: TruSeq Protocol

value: M


title: W808_ctx: CTX_WT_delControl

description: TruSeq Protocol


title: D812_ctx: CTX_DEL

description: TruSeq Protocol


title: W806_ctx: CTX_WT_delControl

description: TruSeq Protocol


title: W815_ctx: CTX_WT_delControl

description: TruSeq Protocol


title: W805_ctx: CTX_WT_delControl

description: TruSeq Protocol


title: D811_ctx: CTX_DEL

description: TruSeq Protocol


title: D802_ctx: CTX_DEL

description: TruSeq Protocol


title: W807_cereb: CBM_WT_delControl

description: TruSeq Protocol

source_name: Cerebellum

value: Cerebellum


title: W806_cereb: CBM_WT_delControl

description: TruSeq Protocol


title: D811_cereb: CBM_DEL

description: TruSeq Protocol


title: D809_ctx: CTX_DEL

description: TruSeq Protocol


title: W816_cereb: CBM_WT_delControl

description: TruSeq Protocol


title: D804_ctx: CTX_DEL

description: TruSeq Protocol


title: D810_ctx: CTX_DEL

description: TruSeq Protocol


title: W815_cereb: CBM_WT_delControl

description: TruSeq Protocol


title: D803_ctx: CTX_DEL

description: TruSeq Protocol


title: W814_cereb: CBM_WT_delControl

description: TruSeq Protocol


title: D801_ctx: CTX_DEL

description: TruSeq Protocol


title: W808_cereb: CBM_WT_delControl

description: TruSeq Protocol


title: W813_cereb: CBM_WT_delControl

description: TruSeq Protocol


title: D809_cereb: CBM_DEL

description: TruSeq Protocol


title: D812_cereb: CBM_DEL

description: TruSeq Protocol


title: D810_cereb: CBM_DEL

description: TruSeq Protocol


title: D802_cereb: CBM_DEL

description: TruSeq Protocol


title: D801_cereb: CBM_DEL

description: TruSeq Protocol


title: D804_cereb: CBM_DEL

description: TruSeq Protocol


title: W805_cereb: CBM_WT_delControl

description: TruSeq Protocol


title: Fear Conditioned, dVenus+, MouseNr 07 [G07]

value: dVenus+


title: D803_cereb: CBM_DEL

description: TruSeq Protocol


title: Zn deficient root-rep1

city: Hangzhou

first: Houqing

last: Zeng

address: NO.2318, Yuhangtang Rd, Yuhang District

institute: Hangzhou Normal University

description:
ZDR_1 FPKM
prorcessed data file: FPKM value of ZDR and ZSR samples.xlsx

data_processing:
The initial base calling and quality filtering of the reads generated with the Illumina analysis pipeline (Fastq format) were performed using a custom Perl script and the default parameters of the Illumina pipeline (http://www.illumina.com). Additional filtering for poor-quality bases was performed using the FASTX-toolkit available in the FastQC software package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)..
To facilitate the read mapping, the Glycine max reference genome (Gmax2.0 version) was indexed by Bowtie2 (http://www.phytozome.net). The read mapping was performed using the Tophat software package.
Tophat allows multiple alignments per read (up to 40) and a maximum of two mismatches when mapping the reads to the reference genome.
The reads were first mapped directly to the genome using indexing and then the unmapped reads were used to identify novel splicing events. The aligned read files were processed by Cufflinks to measure the relative abundances of the transcripts by using the normalized RNA-seq fragement counts.
The estimated gene abundance was measured in terms of the fragments per kilobase of transcript per million mapped reads (FPKM). The differentially expressed genes (DEGs) between the two sets of samples were identified using Cuffdiff. Only the genes with a log2 fold change ≥1 or ≤−1, and a p-value ≤0.05 were considered as significantly DEGs.
Genome_build: the Glycine max reference genome (Gmax2.0 version)
Supplementary_files_format_and_content: one excel file includes FPKM values for each sample

organism: Glycine max

source_name: Zn deficient root

growth_protocol: Soybean (Glycine max var. Williams 82) seeds were soaked in sterilized water for 4 hours, and then incubated at room temperature in the dark between two layers of moistened filter paper. Four days later, seedlings were grown hydroponically in a 10 L tank filled with half-strength modified Hoagland nutrient solution containing 2.5 mM Ca(NO3)2, 2.5 mM KNO3, 0.5 mM KH2PO4, 1.25 mM MgSO4, 10.0 μM Fe-EDTA, 3.4 μM MnSO4, 0.16 μM CuSO4, 0.38 μM ZnSO4, 23.0 μM H3BO3, 0.25 μM Na2MoO4, with pH adjusted to 5.6. Nutrient solution was changed every two days. Plants were grown in a growth chamber with a photoperiod set at 16-h-light/8-h-dark at 26/22 ◦C and light intensity set at 150 μmol m-2 s-1.

extract_protocol:
Roots and leaves of soybean seedlings were separately sampled after treatment of Zn deficiency for 12 days, frozen in liquid nitrogen and stored at -80°C until RNA preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 8 days of cultivation, soybean seedlings with the first trifoliate true leaves fully expanded were transferred into Zn-sufficient (0.38 μM ZnSO4) or Zn-deficient (0 μM ZnSO4) nutrient solutions.

value: Williams 82

value: the whole root system

value: 20 days after germination

value: without zinc element in the nutrient solution


title: Zn sufficient root-rep2

description:
ZSR_2 FPKM
prorcessed data file: FPKM value of ZDR and ZSR samples.xlsx

source_name: Zn sufficient root

value: with zinc element in the nutrient solution


title: Zn deficient root-rep2

description:
ZDR_2 FPKM
prorcessed data file: FPKM value of ZDR and ZSR samples.xlsx


title: Zn sufficient leaf-rep2

description:
ZSL_2 FPKM
prorcessed data file: FPKM value of ZDL and ZSL samples.xlsx

source_name: Zn sufficient leaf

value: first trifoliate true leaf


title: Zn deficient leaf-rep2

description:
ZDL_2 FPKM
prorcessed data file: FPKM value of ZDL and ZSL samples.xlsx

source_name: Zn deficient leaf


title: Zn sufficient root-rep1

description:
ZSR_1 FPKM
prorcessed data file: FPKM value of ZDR and ZSR samples.xlsx


title: AM3: molecular signal added

city: Yangling

first: HUI

last: TIAN

institute: Northwest A&F University

data_processing:
Sequences obtained for each of the six libraries were imported and individually processed using RSEMversion 1.3.0 (Li and Dewey 2011). Sequencing coverage was estimated according to the RSEM algorithm by dividing the total number of ac- quired sequence bases per condition by the number of refer- ence bases. For quality filtering, a trimming step was per- formed on raw reads with the following conditions: (1) remov- ing reads containing adapters; (2) removing reads containing more than 10% of unknown nucleotides; and (3) removing low-quality reads containing more than 50% of low-quality (Q-value ? 20) bases. High-quality reads were then mapped against the wheat reference transcriptome BEnsembl release 30 IWGSC1.0^ (http://archive.plants.ensembl.org/Triticum_ aestivum/Info/Index) using the following mapping parameters: maximum read mismatch, 2; distance between mate-pair reads, 50 bp; and error of distance between mate- pair reads, ± 80 bp. To pick out RNA sequences belonging to R. irregularis, reads were also mapped against the genome of R. irregularis (https://genome.jgi.doe.gov/Rhiir2_1/Rhiir2_1. home.html). The reconstruction of transcripts was carried out with software Cufflinks, which, together with TopHat2, allows biologists to identify new genes (Trapnell et al. 2012). All of the reconstructed transcripts were aligned to the reference genome and were divided into 12 categories by using Cuffcompare
Gene abundances were quantified by the software RSEM, and gene expression levels were normalized by using the FPKM (fragments per kilobase of transcript per million mapped reads) method (Li and Dewey 2011). To iden- tify differentially expressed genes (DEGs) across treatments, the edgeR package (http://www.r-project.org/) was used. We identified genes with a fold change ? 2 and a false discovery rate (FDR) < 0.05 in a comparison as significant DEGs.
Genome_build: Ensembl release 30 IWGSC1.0
Supplementary_files_format_and_content: txt file. Gene expression level of each genes

organism: Triticum aestivum

source_name: roots, arbuscular mycorrhizal inoculation treatment (AMI)

growth_protocol: Seeds of wheat (T. aestivum L., Cultivar: Chinese spring) were  surface-sterilized with 1% NaClO for 10 min, rinsed with  deionized water, and then pre-germinated onmoist filter paper  in the dark at 25 °C for 24 h. The pre-germinated wheat seeds  were planted into pots (20.5 cm in diameter and 14.5 cm high)  filled with approximately 2.5 L of steam-sterilized soil-quartz  sand mixture (1:3) (v/v). The soil was clay loam and was clas-  sified as a Eum-Orthic Anthrosol (FAO Soil Classification,  Gong et al. 2003).

extract_protocol: Six independent comple- mentary DNA (cDNA) libraries corresponding to the three biological replicates for each treatment were constructed. cDNA library quality and fragment length were verified using an Agilent 2100 bioanalyzer and real-time PCR. Fragment length distributions were within the expected ranges accord- ing to the CLC Sequence Viewer software, and the average read length was 150 bp. The resulting cDNA libraries were sequenced in a paired-end system (2 × 150 bp) with the Illumina HiSeq PE150 system. Samples were individually la- beled for library construction and were simultaneously run in one lane.

treatment_protocol: Total RNA was extracted from approximately 100 mg of wheat root of three biological replicates of the two treatments using the RNeasy Plant Mini Kit (Qiagen, USA) according to the manufacturer?s instructions. The concentration and quality of the total RNA were estimated using a NanoDrop Spectrometer (Thermo; USA) and verified using agarose gel electrophoresis and an Agilent 2100 bioanalyzer (Agilent, USA).

value: roots


title: AM2: molecular signal added


title: AM1: molecular signal added


title: Zn deficient leaf-rep1

description:
ZDL_1 FPKM
prorcessed data file: FPKM value of ZDL and ZSL samples.xlsx


title: NM3: no molecular signal added

source_name: roots, non-mycorrhizal treatment (NM)


title: NM2: no molecular signal added


title: NM1: no molecular signal added


title: #947 B1KO bone marrow derived macrophage

city: Sendai

first: Kazuhiko

last: Igarashi

address: Seiryo 2-1

institute: Tohoku University

description: Gene expression bone marrow derived macrophage from Bach1 KO mouse

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (Agilent-028005) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107_Sep9 and Grid: 028005_D_F_20101029) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Total RNA was amplified with an Amino Allyl MessageAmpII aRNA Amplification Kit (Ambion) and was labeled with indocarbocyanine through the use of a CyDye post-labeling Reactive Dye Pack (Amersham).

extract_protocol: RNA was isolated with an RNeasy micro kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: Differentiation media composition is as follows: RPMI 1640  supplemented with 10% heat-inactivated fetal bovine serum (FBS), 100 U/ml penicillin, 100 mg/ml streptomycin, and 10 ng/mL granulocyte/macrophage colony stimulating factor (GM-CSF). Cultures were maintained in a chamber at 37°C in 5% CO2 for 5 days.

value: Bach1 KO

value: bone marrow

value: macrophage

value: male


title: #2 WT bone marrow derived macrophage

description: Gene expression bone marrow derived macrophage from WT mouse

source_name: #2 WT bone marrow derived macrophage

value: wildtype


title: #3 WT bone marrow derived macrophage

source_name: #3 WT bone marrow derived macrophage

value: female


title: LTH-25°C-rep2

city: Guangzhou

first: Junliang

last: Zhao

address: 29 Jinying Road, Tianhe District

institute: Guangdong Academy of Agricultural Science

data_processing:
We use Tophat v2.0.12 and default options for read aligning.
The genome used for read alignment is "MSU Rice Genome Annotation Project Release 7". http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/
We used RPKM to normalized and calculate gene expression value according to the following reference: Wagner, G.P., Kin, K. & Lynch, V.J. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory in Biosciences 131, 281-285 (2012). PMID: 22872506
Genome_build: MSU Rice Genome Annotation Project Release 7
Supplementary_files_format_and_content: TPM

organism: Oryza sativa Japonica Group

source_name: stems and leaves

extract_protocol:
The overground part of the seedings were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext Ultra™ RNA Library Prep Kit for Illumina (#E7530L, NEB, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Lijiangxintuanheigu (LTH)

value: stems and leaves

value: two-weeks old seedings

tag: temperature

tag: treatment duration


title: AD-3

city: Changsha

first: Weijun

last: Peng

address: No.139 Middle Renmin Road

department: The Second Xiangya Hospital

institute: Central South University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide.

scan_protocol: Slides were scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

organism: Rattus norvegicus

source_name: hippocampal tissue

label_protocol: Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

treatment_protocol: In this experiment, we utilized an intracerebroventricular(ICV) injection of Aβ1–42 oligomers into the cerebral ventricles of the animals to induce a validated AD model. For the sham group, the vehicle was injected bilaterally into the lateral ventricles through a stainless steel cannula.

value: SD


title: Sham-2


title: Sham-3


title: Sham-1


title: AD-2


title: LTH-13°C-rep2


title: LTH-25°C-rep1


title: Zn sufficient leaf-rep1

description:
ZSL_1 FPKM
prorcessed data file: FPKM value of ZDL and ZSL samples.xlsx

value: Williams 82


title: #1 WT bone marrow derived macrophage

source_name: #1 WT bone marrow derived macrophage


title: #949 B1KO bone marrow derived macrophage


title: AD-1


title: LTH-11°C-rep2


title: #948 B1KO bone marrow derived macrophage


title: A549-anti-Myocardin

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: Ensemble Human GRCh38.p12
Supplementary_files_format_and_content: bed files were generated using macs14

source_name: human lung cancer cell line A549

growth_protocol: DMEM medium supplementaed by 10% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: MYOCD overexpression

tag: chip antibody

value: anti-Myocardin

tag: cell line


title: Wild type

description: WT

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Ensemble Human GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Cells were rinsed by PBS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: lung

value: Wild type


title: MYOCD-/-

description: MYOCD-

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 BDGP5 genome using TopHat v2.0.10 with default parameters
Cufflinks v2.2.1 was run for relative quantitation of genes expression and differential expression analysis.
Genome_build: Ensemble Human GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

treatment_protocol: Dox treatment for 72 h

value: MYOCD Knockdown


title: Fear Conditioned, dVenus-, MouseNr 11 [NG11]

source_name: Fear Conditioned, dVenus-

tag: strain

value: MouseNr 11

value: Fear Conditioned

value: Hippocampal Dentate Gyrus granule neurons

value: dVenus-


title: A549-IgG

value: IgG


title: PK220K.H3K4me2_ChIPSeq

city: Kyoto

first: Takuyo

last: Kanayama

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Department of Pediatrics

institute: Kyoto Prefectural University of Medicine

data_processing:
Duplicate reads were removed from raw fastq files using the sort command, and adapter sequences were removed using the awk language.
Trimmed fastq files were then mapped to the mouse genome using Burrows-Wheeler Aligner (ver. 0.7.12-r1039, BWA-MEM algorithm) wih the default parameters.
After removing duplicate reads from mapped reads using Picard (ver. 2.18.16-0), peak calling was performed using MACS2 (ver. 2.1.1.20160309) with the default parameters.
Finally, motif analysis was conducted using MEME-ChIP (ver. 4.11.4) with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing peak information

source_name: pro-B cell

growth_protocol: RPMI-1640 medium supplemented with 10% FBS, penicillin (100 U/ml), streptomycin (10 mg/ml), and 20% of the supernatant in which the WEHI-3 were cultured, at 37℃ in a 5% CO2 humidified atmosphere.

extract_protocol:
ChIP was carried out using the Simple ChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology Inc., Danvers, MA) according to the manufacturer’s instructions.
SMARTer® ThruPLEX® Tag-seq Kit (Clontech)

treatment_protocol: with or without 500 ng/mL of doxyxycline

value: BALB/c

value: H3K4me2 monoclonal antibody (Active Motif)


title: WT

description: WT


title: Input.PK220


title: MYOCD overexpression

description: MYOCD


title: Input.PAX5N


title: LTH-13°C-rep1

value: Lijiangxintuanheigu (LTH)

tag: developmental stage


title: LTH-11°C-rep1

value: stems and leaves


title: QSC_1

first: Tom

last: Cheung

address: Clear Water Bay, Kowloon

department: Division of Life Science

institute: Hong Kong University of Science and Technology

description:
Freshly isolated MuSCs from skeletal muscle(CD31-CD45-Sca1-Vcam1+ITGA7+), bulk RNA-seq was performed using Smart-seq2
bulk-rna.tsv

data_processing:
Raw sequencing data was processed by Cell Ranger 2.1.0 (10X Genomics) to generate a gene-cell expression matrix, in which sequencing reads were mapped to mm10 using STAR aligner (version 2.5.1b), cells were demultiplexed by cell barcodes and gene abundance was quantified by corresponding  UMI-tag error-corrected by Hamming distance.
Further data analysis was carried out in R (version 3.4.3) using Seurat (version 2.2). “Cells” that fit any of the following criteria were filtered out: <350 or >9000 UMIs, <350 or >4000 expressed genes, or >20% UMIs mapped to mitochondria.
* Bulk RNA-seq data were aligned using Hisat2 (version 2.1.0) and converted to BAM format using Samtools (version 1.3.1).  StringTie was used with the -e option to quantify gene expression levels according to the reference transcripts.
* Table counts were also produced using the -B option for Ballgown (version 2.2.0) under R (version 3.3.1).  Genes whose mean FPKM levels across all samples is less than 1 were removed.  Then, only genes which have an FPKM of at least 5 in at least one sample was kept.
* Principle Component Analysis using the prcomp () function was used with both centering and scaling set to TRUE.
Genome_build: mm10
Supplementary_files_format_and_content: For single cells, comma-separated values text files include UMI counts for each cell.  For bulk RNA-Seq, table of genes by samples of FPKM values, as calculated using StringTie.

molecule: polyA RNA

source_name: Skeletal muscle

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina  protocols. Briefly, RNA were isolated using Macherey-Nagel Nucleospin RNA XS. 1st strand cDNA synthesis & pre-Amplification was performed using Smart-seq2. Library was prepared using NuGen Ovation Ultra Low system.

value: Quiescent muscle stem cell

value: 2 months old

value: wild type


title: VCAM_Neg_Differentiate_2

description:
Freshly isolated cells from skeletal muscle(CD31-CD45-Sca1-Vcam1-ITGA7+) were cultured and allowed for differentiation before harvesting, bulk RNA-seq was performed using Smart-seq2
bulk-rna.tsv


title: Uninjured_WT_1

description: 3'-droplet-based single-cell RNA-seq

data_processing:
Raw sequencing data was processed by Cell Ranger 2.2.0 (10X Genomics) with mouse transcriptome reference 2.1.0  to generate a gene-cell expression matrices, in which sequencing reads were mapped to mm10 using STAR aligner (version 2.5.1b), cells were demultiplexed by cell barcodes and gene abundance was quantified by corresponding  UMI-tag error-corrected by Hamming distance.
Further data analysis was carried out in R (version 3.5.1) using Seurat (version 2.3.4) with canonical correlation analysis (CCA) for data integration. “Cells” that fit any of the following criteria were filtered out: <500 or >9000 UMIs, <500 or >4000 expressed genes, or >15% UMIs mapped to mitochondria.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated values text files include UMI counts for each cell.

extract_protocol:
Hindlimb skeletal muscles were dissected and dissociated mechanically and enzymatically to yield a mononuclear cell suspension. Cells were loaded onto 10X Chromium platform and Chromium Single Cell Gene Expression Solution was used for generating 3'-droplet-based RNA-seq libraries.
Single-cell RNA-seq libraries were prepared for sequencing using 10X Chromium Single Cell Gene Expression Solution.

value: Skeletal muscle


title: VCAM_Neg_Differentiate_3


title: QSC_2


title: Uninjured_WT_2

description: 3'-droplet-based single-cell RNA-seq


title: VCAM_Neg_Proliferate_1

description:
Freshly isolated cells from skeletal muscle(CD31-CD45-Sca1-Vcam1-ITGA7+) were cultured for three days before harvesting, bulk RNA-seq was performed using Smart-seq2
bulk-rna.tsv


title: PAX5N.H3K4me2_ChIPSeq


title: VCAM_Neg_Fresh_3

description:
Freshly isolated cells from skeletal muscle(CD31-CD45-Sca1-Vcam1-ITGA7+), bulk RNA-seq was performed using Smart-seq2
bulk-rna.tsv


title: VCAM_Neg_Fresh_1


title: iPS-derived cardiomyocytes [CM14_3_S15]

city: San Francisco

first: Todd

last: McDevitt

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

data_processing:
Demultiplexed with bcl2fastq (v2.20.0)
Aligned with tophat2 ( v2.1.1)
Counted with featureCounts (v1.6.2)
Genome_build: hg19
Supplementary_files_format_and_content: Comma separated value files containing unnormalized counts

source_name: iPS-derived cardiomyocytes

growth_protocol: Stromal cells (samples 1-7) were grown on gelatin-coated plates and passaged every 4-5 days, up to passage 10.

extract_protocol:
Stromal cells were lysed with Trizol for RNA extraction with the Direct-zol RNA Miniprep kit. RNA was collected at 70% confluency and fed exactly 24h prior to collection.
Libraries were created with the SMARTer Stranded Total RNA Sample Prep Kit from Takara Bio (Kusatsu, JP) and sequenced on the Illumina NextSeq 500 (Illumina) to a minimum depth of 25 million reads

treatment_protocol: no treatments

value: iPS-derived cardiomyocytes

tag: sample info

value: WTC11-GCaMP6f hiPSCs


title: iPS-derived embryoid body outgrowth cells [EBFib_1_S2]

value: WTC11 hiPSCs


title: iPS-derived embryoid body outgrowth cells [EBFib_3_S10]


title: VCAM_Neg_Differentiate_1


title: VCAM_Neg_Proliferate_3


title: VCAM_Neg_Proliferate_2


title: iPS-derived teratoma outgrowth cells [TeraFib_3_S5]

source_name: iPS-derived teratoma outgrowth cells

value: iPS-derived teratoma outgrowth cells


title: Bone marrow-derived mesenchymal stromal cells [MSC_Adh_1_S4]

value: Primary (Rooster Bio)


title: HomeCage, dVenus+, MouseNr 15 [HC_G15]

source_name: HomeCage, dVenus+

tag: mouse id

value: MouseNr 15

tag: treatment

value: HomeCage

value: dVenus+


title: iPS-derived teratoma outgrowth cells [TeraFib_2_S4]


title: VCAM_Neg_Fresh_2


title: iPS-derived cardiomyocytes [CM14_1_S13]


title: iPS-derived cardiomyocytes [CM14_2_S14]


title: iPS-derived teratoma outgrowth cells [TeraFib_1_S4]


title: iPS-derived embryoid body outgrowth cells [EBFib_2_S3]


title: Human dermal fibroblasts [HDF_1_S1]

source_name: Human dermal fibroblasts

value: Human dermal fibroblasts

value: Primary (Cell Applications)


title: Bone marrow-derived mesenchymal stromal cells [MSC_Adh_2_S11]


title: Human dermal fibroblasts [HDF_3_S2]


title: Identification of miR-490-3p target genes in HCT116

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

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

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: mock

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

value: colorectal cancer

tag: transfection

value: no transfection

source_name: miR-490-3p transfected cell line


title: Identification of si-GINS1_2 target genes in MDA-MB-231

value: breast cancer

source_name: si-GINS1_2 transfected cell line


title: Identification ofmiR-139-5p target genes in 786-O

value: renal cancer

source_name: miR-139-5p transfected cell line


title: Human dermal fibroblasts [HDF_2_S1]


title: Identification of miR-490-5p target genes in HCT116

source_name: miR-490-5p transfected cell line


title: Identification ofmiR-139-3p target genes in A498

source_name: miR-139-3p transfected cell line


title: Fetal human cardiac fibroblasts [fHCF3_S2]

source_name: Fetal human cardiac fibroblasts

value: Fetal human cardiac fibroblasts


title: Identification of si-GINS1_1 target genes in MDA-MB-231

source_name: si-GINS1_1 transfected cell line


title: GSC2_6hr_3 μM clofoctol_replicate 3

city: beijing

first: Yan

last: Hu

state: beijing

address: dongdan san tiao No 5

department: Department of Molecular Biology and Biochemistry

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

description: Gene expression after treatment with  3 μM clofoctol

hyb_protocol: The labelled cRNA was purified with an RNeasy Mini Kit (Qiagen), and 1.65 μg RNA was used for hybridization on the Genechip Agilent Human lncRNA 4*180 K array (Agilent Technologies).

scan_protocol: The slides were scanned in an Agilent Microarray Scanner (Agilent Technologies) under the default settings.

data_processing: The scanned images were analyzed by Quantile algorithm (Gene Spring Software 11.0, Agilent Technologies).

source_name: GSC2_6hr_3 μM clofoctol

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

growth_protocol: Cell was cultured in serum-free stem cell medium (SFM) (Neurobasal (Gibco) containing 20 ng/ml basic fibroblast growth factor (bFGF; catalog 100-18B-50UG;  Peprotech), 20 ng/ml epidermal growth factor (EGF; catalog AF-100-15-100UG; Peprotech), 10 μg/ml heparin (catalog 9041-08-1; Sigma), 2% B27 (Gibco) and 2 mmol/l L-glutamine (catalog SH30034.01; HyClone).

extract_protocol: Total RNA from GSC2 cells was extracted using TRIzol reagent (Life Technologies). The RNA integrity was measured at an Agilent Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA). The qualified total RNA was further purified (RNeasy Mini Kit, Qiagen, Hilden, Germany). Total RNA was amplified and labelled with a Low Input Quick Amp Labelling Kit (Agilent Technologies), per the manufacturer’s instructions.

treatment_protocol: GSC2 cells were digested with Accutase (catalog A6964; Sigma) and resuspended into 10 ml SFM, with approximately 106 cells per 10 cm2 dish. Cells were treated with 3 μM or 10 μM clofoctol for 6 h, and collected for mRNA assays in 1 ml TRIzol reagent (Ambion).

tag: tissue source

value: Glioblastoma

value: Glioma stem cells

value: 3 μM clofoctol


title: GSC2_6hr_10 μM clofoctol_replicate 1

description: Gene expression after treatment with  10 μM clofoctol

source_name: GSC2_6hr_10 μM clofoctol

value: 10 μM clofoctol


title: Identification ofmiR-139-3p target genes in 786-O


title: Identification ofmiR-139-5p target genes in A498


title: Adult human cardiac fibroblasts [HCF_1_S1]

source_name: Adult human cardiac fibroblasts

value: Adult human cardiac fibroblasts

value: Primary (PromoCell)


title: GSC2_6hr_10 μM clofoctol_replicate 2


title: Fetal human cardiac fibroblasts [fHCF2_S1]


title: GSC2_6hr_1‰ DMSO_replicate 2

description: Gene expression after treatment with 1‰ DMSO

source_name: GSC2_6hr_1‰ DMSO

value: 1‰ DMSO


title: GSC2_6hr_3 μM clofoctol_replicate 1


title: GSC2_6hr_1‰ DMSO_replicate 1


title: GSC2_6hr_10 μM clofoctol_replicate 3


title: GSC2_6hr_3 μM clofoctol_replicate 2


title: GSC2_6hr_1‰ DMSO_replicate 3


title: Adult human cardiac fibroblasts [HCF_3_S9]


title: UOCB1: RNAseq

city: MEMPHIS

first: John

last: Diedrich

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

data_processing:
Peaks were called using MACS2 peak caller
ATACseq an RNAseq reads were aligned to the hg19 human genome using Bowtie2
Genome_build: hg19

growth_protocol: Leukemia cells were routinely generated by culturing (typically 20–30 × 106 cells into a T75 flask) in RPMI1640 +10%FBS+1%P/S  and 10,000 cells were used for ATAC transposition

extract_protocol:
DNA was transposed using the FAST-ATAC protocol and mini-elute reaction cleanup kit was used to isolate the transposed DNA
Library was constructed using illumina barcodes and SPRI bead size selection

value: Human-Derived ALL Cell Line


title: ChIPSeq WT FO B cells IRF8 rep2

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: WT IRF8, rep2

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 1.1.2 or Tophat 2.1.1
Aligned reads are converted to bam format using samtools. MACS was used to call peaks for ChIP-Seq data. HOMER is used to perform super-enhancer analysis. RPKM model (reads per kilobase per million reads) was used to normalize gene expression values for RNA-Seq data.
Genome_build: mm10

source_name: Spleen and lymph nodes

growth_protocol: FO B cells were isolated from spleen and peripheral lymph nodes by standard negative selection method. Cells were cultured in RPMI 1640 medium containing 10% fetal bovine serum.

extract_protocol:
For ChIP-Seq, and cross-linked with 1% formaldehyde (methanol-free, Pierce, Rockford, IL) at room temperature for 10 min. After sonication, fragmented chromatin equivalent to 10 million cells was immunoprecipitated with control rabbit IgG or indicated antibodies and Magna ChIPTM Protein A+G Magnetic Beads (Millipore, Billerica MA). ChIP-Seq DNA libraries were prepared using KAPA LTP Library Preparation Kit (Kapa Biosystems, Wilmington, MA) and indexed primers (BIOO Scientific, Austin, TX), and the libraries were then sequenced. For RNA-Seq, KAPA Stranded RNA-Seq Library Preparation Kit (KAPA Biosystems, Wilmington, MA), and each library was indexed using barcoded primers (BIOO Scientific, Austin, TX). Barcoded PCR products were purified on 2% E-Gel, 250-400 bp fragments were purified, quantified on Qbit (Invitrogen), mixed, and sequenced on HiSeq2000 platform.
PCR products were barcoded (indexed) and sequenced on HiSeq 2000 platform.

treatment_protocol: Cells were stimulated with anti-IgM (F(ab’)2) (10 ug/ml), CD40 (2 ug/ml), IL-4 (10 ng/ml), and IL-5 (10 ng/ml) for 2 days.

tag: antibody

value: anti-IRF8 (Cell Signaling Technology, clone D20D8)


title: ChIPSeq WT FO B cells PU.1 rep2

description: WT PU.1, rep2

value: Anti-PU.1 (Santa Cruz, sc-390405x)


title: ChIPSeq WT FO B cells H3K27ac rep1

description: WT H3K27ac, rep1

value: anti-H3K27Ac (Abcam)


title: ChIPSeq WT FO B cells H3K27ac rep2

description: WT H3K27ac, rep2


title: ChIPSeq WT FO B cells IgG

description: IgG control

value: rabbit IgG (Santa Cruz)


title: ChIPSeq WT FO B cells PU.1 rep1

description: WT PU.1, rep1


title: Adult human cardiac fibroblasts [aHCF3_S5]

tag: cell type

value: Primary (Cell Applications)


title: RNASeq FO B cells DKO rep2

description: DKO, rep2


title: RS4;11: RNAseq


title: RNASeq FO B cells WT rep2

description: WT, rep2


title: RNASeq FO B cells WT rep1

description: WT, rep1


title: RNASeq FO B cells DKO rep1

description: DKO, rep1


title: Adult human cardiac fibroblasts [aHCF2_S4]


title: REH: RNAseq

source_name: REH

value: REH


title: PTEN-cKO rep2

first: Jun

last: Wang

address: 20 Dongdajie

institute: Beijing Institute of Lifeomics

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the sequences of vertebrata rRNA using Bowtie with parameters -m 0 -x 1000 -s 40 -l 32 -v 5 -r 2 -p 3
The reads mapped to rRNA were filterred in the following analysis using an in-house manuscript.Then the left reads were mapped to mouse whole genome(mm10) using Tophat with parameters --phred64-quals -p 6 --segment-length 30 --segment-mismatches 2 -r 20 --library-type fr-firststrand
The raw count of each sample was generated by HTSeq and a differencial expression analysis was performed by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and RPKM values for each Sample

source_name: Brain endothelial cells

extract_protocol: Brains of 4-week-old SP-A-Cre;PTENfl/+;EYFP+/- and SP-A-Cre;PTENfl/fl; EYFP+/- mice were dissected and digested. Endothelial cells were sorted with an Aria III sorter (BD). Total RNA was harvested using Trizol reagent.

tag: age

value: post natal day 28

tag: genotype/variation

value: PTEN-/-


title: Nalm6: RNAseq


title: SEM: RNAseq

source_name: SEM

value: SEM


title: PTEN-cKO rep1


title: Adult human cardiac fibroblasts [HCF_2_S8]


title: Adult human cardiac fibroblasts [aHCF1_S3]


title: ChIPSeq WT FO B cells IRF8 rep1

description: WT IRF8, rep1


title: UOCB1: ATACseq


title: SUPB15: ATACseq


title: TMCC2_guide2_Rep2_RNA

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh37/hg19) using STAR using a basic two-pass alignment strategy. Aligned reads were filtered for those reads that were uniquely mapping using the --outFilterMultimapNmax 1 flag.
Gene quantifications for Gencode v19 were summarized using the --quantMode GeneCounts parameter in STAR.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression counts for hg19 / Gencode v19 annotations

growth_protocol: HUDEP-2 cells were cultured in StemSpan SFEM supplemented with hSCF (50 ng/ml), erythropoietin (3 IU/ml), dexamethasone (10-6 M) and doxycycline (1 μg/ml), lentivirally infected and then differetiated in erythroid differentiation media (IMDM, 2% human AB plasma, 3% human AB serum, 1 mg/mL Holo-human transferrin, 3 IU/mL heparin,10 μg/mL insulin and 3 IU/mL erythropoietin) for 72 h followed by RNA extraction and RNA-seq

extract_protocol:
Qiagen RCL lysis buffer supplemented with beta-mercaptoethanol
Smart-seq2; Nextera-based indexing

treatment_protocol: CRISPRi nontargeting vs. guide RNAs targeting a TMCC2 enhancer

tag: grna treatment

value: CCATCCTTCAGAGTAAACAG

tag: grna annotation

value: TMCC2 enhancer - gRNA 2


title: TMCC2_guide1_Rep2_RNA

value: GTCGTGCTGCAGGTGAAGTG

value: TMCC2 enhancer - gRNA 1


title: Non_targeting_Rep3_RNA

value: ATCGCGAGGACCCGTTCCGCC

value: Non-targeting


title: TMCC2_guide1_Rep1_RNA


title: SEM: ATACseq


title: RS4;11: ATACseq


title: Non_targeting_Rep2_RNA


title: REH: ATACseq


title: Nalm6: ATACseq


title: WT rep2

value: wild type


title: Non_targeting_Rep1_RNA


title: 17-0138_N4Pos

city: Columbus

first: Dean

last: Lee

state: Ohio

address: 700 Children’s Drive

department: Hematology & Oncology

institute: Nationwide Children’s Hospital

description:
processed data file: AllData_N_E_StimVsUnstim_170515_RNASeq_TruSeqStranded_CHAKRAVARTI_Results.xlsx
processed data file: AllData_NvsE_170515_RNASeq_TruSeqStranded_CHAKRAVARTI_Results.xlsx
processed data file: AllData_Overprocessed data file: All_170515_RNASeq_TruSeqStranded_CHAKRAVARTI_Results.xlsx

data_processing:
Each sample was aligned to the GRCh38.p9 assembly of the Homo sapiens reference from NCBI (http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.35/) using version 2.5.2b of the RNA-Seq aligner STAR.
Features were identified from the GFF file that came with the assembly from NCBI.
Feature coverage counts were calculated using version 0.6.1p1 of HTSeq -count.
Differentially expressed features were calculated using DESeq2.
Genome_build: human NCBI GRCh38.p9
Supplementary_files_format_and_content: Excel spreadsheets containing normalized read counts for each sample and differential expression data for each feature. File AllData_N_E_StimVsUnstim_170515_RNASeq_TruSeqStranded_CHAKRAVARTI_Results.xlsx contains "N+ vs. N-" & "E+ vs. E-" comparisons. File AllData_NvsE_170515_RNASeq_TruSeqStranded_CHAKRAVARTI_Results.xlsx contains "N+ vs. E+" & "N- vs. E-" comparisons. File AllData_Overall_170515_RNASeq_TruSeqStranded_CHAKRAVARTI_Results.xlsx contains the "Allstim(N+,E+,Pooled) vs. AllUnstim(N-,E-)" comparison.

source_name: Norm_17-0138_N4Pos- Naïve NK cells, Donor 4, yes IL-21

extract_protocol:
Total RNA was prepared using the Total RNA Purification Plus Kit (Norgen Biotek, Ontario, ON, Canada). rRNA was removed from 800ng with TruSeq Stranded Total RNA with Ribo-Zero Gold  kit (Illumina, CA).
Libraries were constructed from first strand cDNA using TruSeq Stranded Total RNA with Ribo-Zero Gold removal kit (Illumina, CA).

value: Naive NK cells

tag: donor

tag: disease status

value: Healthy


title: 17-0137_N4Neg

source_name: Norm_17-0137_N4Neg- Naïve NK cells, Donor 4, no IL-21


title: Donor3_P8_Rep4_RNA

source_name: CD34+ hematopoietic cells

growth_protocol: CD34+ hematopoietic cells were cultured in IMDM supplemented with Erytrhopoietin, SCF, IL-3 as described by Hu et al. (Blood 2013)

tag: population


title: Donor3_P7_Rep4_RNA


title: Donor3_P8_Rep3_RNA


title: 697: RNAseq

tag: tissue

value: Human-Derived ALL Cell Line

tag: cell line


title: 17-0136_N3Pos

source_name: Norm_17-0136_N3Pos- Naïve NK cells, Donor 3, yes IL-21


title: WT rep1

tag: strain


title: Donor3_P7_Rep3_RNA


title: 17-0135_N3Neg

source_name: Norm_17-0135_N3Neg- Naïve NK cells, Donor 3, no IL-21


title: Donor3_P6_Rep4_RNA


title: 17-0132_E4Pos

source_name: Norm_17-0132_E4Pos- Expanded NK cells, Donor 4, yes IL-21

value: Expanded NK cells


title: 697: ATACseq


title: Donor3_P6_Rep3_RNA


title: 17-0131_E4Neg

source_name: Norm_17-0131_E4Neg- Expanded NK cells, Donor 4, no IL-21


title: 17-0130_E3Pos

source_name: Norm_17-0130_E3Pos- Expanded NK cells, Donor 3, yes IL-21


title: Donor3_P5_Rep3_RNA


title: 17-0129_E3Neg

source_name: Norm_17-0129_E3Neg- Expanded NK cells, Donor 3, no IL-21


title: Donor3_P4_Rep3_RNA


title: Donor3_P3_Rep3_RNA


title: 17-0127_E2Neg

source_name: Norm_17-0127_E2Neg- Expanded NK cells, Donor 2, no IL-21


title: 17-0128_E2Pos

source_name: Norm_17-0128_E2Pos- Expanded NK cells, Donor 2, yes IL-21


title: Mutant_3

first: Sahar

last: Nissim

address: 77 Ave Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

description:
PolyA RNA
processed data file: diff_exp_deseq2_gene.txt

data_processing:
Paired end reads were aligned using Star v2.3 to the zebrafish genome (Zv9). The mapped reads were counted using HTSeq-count (v0.6.0) and gene models from Ensembl transcriptome. Analysis of differential gene expression was performed using DESeq2. Orthology to human genes was determined using Ensembl and supplemented by performing BLAST. GSEA was performed using normalized counts.
Genome_build: Zv9
Supplementary_files_format_and_content: diff_exp_deseq2_gene.txt: Tab-delimited text file; differential expression table that includes DESeq2 normalized data, statistics, and human orthologs.

organism: Danio rerio

source_name: Whole fish

extract_protocol:
RNA was extracted using TRIzol reagent (Life Technologies) from wild-type and mutant larval zebrafish at 3 weeks post-fertilization according to the manufacturer's instructions. RNA quality was checked by Agilent Bioanalyzer. Sequencing was performed after library construction on an Illumina HiSeq.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Tubingen

value: Homozygous rabl3-TR41 mutant

value: Whole fish

value: 3 weeks post-fertilization


title: Donor3_P2_Rep3_RNA


title: Cortex-rTg4510-Dox-3

city: Gainesville

first: Jose

middle: F

last: Abisambra

state: FL

address: 1275 Center Dr

department: Department of Neuroscience & Center for Translational Research in Neurodegenerative Research

institute: University of Florida

description:
rTg4510 Dox 3
Tg(Camk2a-tTA)1Mmay Tg(tetO-MAPT*P301L)4510Kha/J fed doxycycline feed to suppress transgenic tau expression. Expresses human 0N4R P301L tau at approx 5-8x endongenous murine tau levels.

hyb_protocol: Commercially analyzed by ThermoFisher

scan_protocol: Commercially analyzed by ThermoFisher

data_processing: Signal intensities were calculated using SST-RMA and are reported on the log 2 scale. Transcript clusters were annotated to gene symbols using NetAffx annotation files (Release 36).

source_name: Brain cortex in rTg4510 mouse, Doxycycline (200ppm) feed

label_protocol: Commercially analyzed by ThermoFisher

growth_protocol: Standard housing in a 14 hr light/10 hr dark cycle at a constant temperature (23°C±2°C) with food and water available ad libitum

extract_protocol: Trizol extraction according to manufacturer's instructions from LN2 frozen brain samples.

treatment_protocol: Either normal feed or feed treated with Doxycycline (200ppm) for 35d

tag: Sex

value: F

value: Doxycycline (200ppm) for 35d

value: brain cortex


title: Donor3_P5_Rep4_RNA