title: keratinocytes, KLF4i_RNAseq_rep_2

city: La Jolla

first: George

last: Sen

state: California

address: 9452 Medical Center Dr.

department: Dermatology

institute: University of California San Diego

description: RNA_seq_RPKM_data.xlsx, KLF4i_RNAseq.xlsx

data_processing:
Illumina Hiseq 4000 reads were trimmed and filtered using Partek Flow. High quality reads were aligned using STAR.
BAM files were imported into the RNA-seq pipeline of Partek Genomic Suite, version 6.6 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq Transcripts).  Genes with less than 10 reads in every sample were excluded.
Statistics were calculated by ANOVA and differential genes with significant p-values and FDR(<0.05) with a >2 fold change (+/-) were selected as differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content:  RNA_seq_RPKM_data.xlsx, BRD4i_RNAseq.xlsx, KLF4i_RNAseq.xlsx

source_name: Human epidermal keratinocyte

growth_protocol: Primary keratinocytes were grown on culture dishes and maintained in keratinocyte EpiLife medium plus HKGS (Thermo Scientific).

extract_protocol:
RNA was isolated using GeneJET RNA purification kit (Thermo Scientific).
RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: Control (non-targeting), BRD4, and KLF4 siRNA knockdown

value: Neonatal foreskin

value: primary keratinocytes

value: KLF4 knockdown


title: keratinocytes, Input_BRD4_CHIP

status: Public on Apr 03 2020

type: SRA

country: USA

library_source: genomic

data_processing:
Raw ChIP-seq reads were aligned using Bowtie2 and low quality reads and duplicates were filtered out of the data.
HOMER's findPeaks was used for call peaks in individual replicates using Input ChIP-seq as the control sample. Common peaks among replicates were identified using HOMER's mergePeaks function.
Genome_build: hg19
Supplementary_files_format_and_content: BRD4_peaks.xlsx

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
DNA was isolated with Thermo Scientific's GeneJET Gel Extraction kit
ChIP-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: 20 million cells were crosslinked with 2mM DSG and 1% formaldehyde and used to pulldown BRD4.

tag: tissue

tag: cell type

tag: chip antibody


title: keratinocytes, BRD4_CHIP_rep_1

value: BRD4 (Bethyl A301-985A)


title: keratinocytes, BRD4_CHIP_rep_2


title: keratinocytes, BRD4i_RNAseq_rep_2

description: RNA_seq_RPKM_data.xlsx, BRD4i_RNAseq.xlsx

library_source: transcriptomic

molecule: total RNA

tag: genotype

value: BRD4 knockdown


title: keratinocytes, KLF4i_RNAseq_rep_1


title: keratinocytes, CTLi_RNAseq_rep_1

description: RNA_seq_RPKM_data.xlsx, BRD4i_RNAseq.xlsx, KLF4i_RNAseq.xlsx

value: control


title: keratinocytes, BRD4i_RNAseq_rep_1


title: S342: SC_etoh_rep2

status: Public on Apr 04 2020

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

country: China

institute: Fudan Univ, Shanghai, China

data_processing:
Salmon quantification produced count data
DEseq2 differential expression analysis produced p-values and log2 fold change values

molecule: polyA RNA

growth_protocol: Cultured in DMEM supplemented with 10% FBS, and changed to DMEM with 5% charcoal stripped FBS for 24 hours prior to Dex or ethanol treatment

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 100nM Dex or equal volume ethanol for 24 hours

value: scramble

tag: treatment

value: ethanol


title: Wild-type OE Cse4 input

city: Worcester

first: Richard

middle: E

last: Baker

state: MA

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

data_processing:
50-base paired-end Illumina reads were aligned to the S. cerevisiae S288C reference (R64-2-1) using Bowtie version 1.0.0 with command line options -n2 -m1 -X 500.
Duplicate reads (20-89%) were removed using Samtools rmdup (version 0.1.19).
Input alignments were randomly down sampled to 10M alignments each. Peaks were called using MACS (ZHANG et al. 2008) version 2.1.1.20160226 in paired-end mode with default parameters and no additional down sampling.
Genome_build: sacCer3
Supplementary_files_format_and_content: narrowPeak files were generated during peak calling; scores are -10*log10qvalue
Supplementary_files_format_and_content: bedGraph files were generated by MACS during peak calling. Results are expressed as reads per million total reads.

organism: Saccharomyces cerevisiae S288C

source_name: WT-IN-OE

growth_protocol: Cells were grown to logarithmic phase in glucose (endogenous Cse4) or raffinose/galactose (OE Cse4) media for 1.75 hours.

extract_protocol:
Cell suspension was distributed to screw top tubes with glass beads (0.4-0.65 mm diameter) and lysed three times for 40 seconds each, followed by a five-minute rest on ice, and lysed two times for 40 seconds each in an MP Bio FastPrep-24 5G. Lysates were collected, and the chromatin pellets  washed twice in FA lysis buffer, resuspended in FA lysis buffer, sonicated 24 times with repeated 15 seconds on/off at 20% amplitude using a Branson digital sonifer. After 3 minutes of centrifugation (13000 rpm, 4ºC), a portion of the supernatant was saved for input library constucation and the remainder incubated with anti-FLAG® M2 Affinity Gel (Sigma, A2220-5ML) overnight. The beads were washed with FA, FA-HS (500 mM NaCl), RIPA, and TE buffers twice each. The beads were resuspended in 25 mM Tris-HCl pH7.6, 100 mMNaCl, 0.5% SDS), incubated at 65°C overnight, treated with proteinase K (0.5 mg/ml) at 55°C for four hours followed by Phenol/Chloroform extraction and ethanol precipitation.
Following repair using the NEB Pre-PCR Repair Mix (New England Biolabs, M0309), paired-end libraries were prepared using the NEBNext® End Prep (New England Biolabs, E7370) and NEBNext® Multiplex Oligos for Illumina (New England Biolabs, E7335).

treatment_protocol: Cells were treated with formaldehyde (final 1%) for 20 minutes at 30°C followed by the addition of 2.5 M glycine for 10 minutes, then washed twice with 1 X PBS and resuspended in 2 mL FA Lysis Buffer (1 mM EDTA pH8.0, 50 mM HEPES-KOH pH7.5, 140 mM NaCl, 0.1% sodium deoxycholate, 1% Triton X-100) with 1 x protease inhibitors (Sigma) and 1 mM PMSF final concentration.

tag: genotype/variation

tag: sample type

value: sonicated spheroplasts


title: CRISPR E7 clone 2 replicate 3

city: Oxford

first: Ling

last: Felce

state: Select State

address: Botnar Research Centre, Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

data_processing:
Reads were mapped and aligned to mouse genome mm10 carried out using hisat.
Mapped reads converted to binary format and indexed using samtools.
featureCounts used to quantify binary indexed reads against annotated genome.
Example code: $featureCounts" "-T" "4" "-p" "-F" "GTF" "-a" "<annotation file>" "-o" "<output file>featureCount_Dup.txt" "<input file>.bam"
Genome_build: mm10
Supplementary_files_format_and_content: text files include read counts for each sample

organism: Mus musculus

source_name: A20 lymphoma cells

growth_protocol: A20 parental and CRISPR cell lines were grown under standard tissue culture conditions, and three biological replicates were collected from separate passages.

extract_protocol:
RNA was extracted from cells using Rneasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: BALB/c

value: Mutation in Foxp1 exon 7


title: keratinocytes, CTLi_RNAseq_rep_2


title: CRISPR E7 clone 2 replicate 2


title: CRISPR E7 clone 1 replicate 1


title: CRISPR E7 clone 1 replicate 3


title: CRISPR E6 clone 1 replicate 3

value: Mutation in Foxp1 exon 6


title: 85: AtT20_Creb3l1 shRNA

city: Bristol

first: Michael

middle: Paul

last: Greenwood

address: Whitson Street

department: Bristol Medical School / Translational Health Sciences

institute: University of Bristol

data_processing:
Quality control (FastQC)
Adapter Trimming (BBDuk)
Alignment to reference genome (Mus musculus GRCm38.92, STAR)
Read counts (Ensembl Mus musculus GRCm38.92, FeatureCounts)
Differential Expression Analysis (DESeq2)
Genome_build: Mus musculus GRCm38.92
Supplementary_files_format_and_content: Raw reads gzipped in .fastq.gz format. Raw counts as generated by FeatureCounts

source_name: Pituitary tumour

growth_protocol: AtT20/D16v-F2 cells (Sigma; 94050406) were cultured in DMEM (Sigma; D6546) supplemented with 10 % (v/v) heat-inactivated fetal bovine serum (Gibco), 2 mM L-glutamine and 100 unit/ml of penicillin-streptomycin. Cells were incubated at 37 °C in a humidified incubator with 5 % (v/v) CO2.

extract_protocol:
QIAzol Lysis Reagent (Qiagen) followed by Direct-zol RNA extraction kit (Zymo research).
Illumina TruSeq mRNA kit

value: mouse corticotroph cell line

tag: cell line

value: AtT20/D16v-F2 cells

value: Creb3l1 shRNA


title: 82: AtT20_Creb3l1 shRNA


title: 83: AtT20_Creb3l1 shRNA


title: 11: AtT20_non-targeting shRNA

value: non-targeting control shRNA


title: 12: AtT20_non-targeting shRNA


title: 15: AtT20_non-targeting shRNA


title: 84: AtT20_Creb3l1 shRNA


title: 81: AtT20_Creb3l1 shRNA


title: CRISPR E6 clone 2 replicate 3


title: CRISPR E7 clone 2 replicate 1


title: 14: AtT20_non-targeting shRNA


title: CRISPR E7 clone 1 replicate 2


title: CRISPR E6 clone 2 replicate 2


title: 13: AtT20_non-targeting shRNA


title: CRISPR E6 clone 2 replicate 1


title: A20 parental replicate 2

value: WT


title: CRISPR E6 clone 1 replicate 2


title: CRISPR E6 clone 1 replicate 1


title: A20 parental replicate 3


title: A20 parental replicate 1


title: Th17_KO3 (RNA-seq)

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquistion on the sequencing instrument.
Basecalling was performed with the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing was performed with custom programs based on Picard tools (v2.18.11, http://broadinstitute.github.io/picard/).
The transcriptome analysis was performed using the Tuxedo suite. TopHat2 (v2.1.1, http://genomebiology.com/2013/14/4/R36/abstract) was supplied with reads passing vendor quality filtering (PF reads) and the Ensembl transcript set (Homo sapiens, e87, December 2016) as reference. Tophat2 spliced alignments were run independently for each replicate.
Cufflinks (v2.2.1, http://www.nature.com/nbt/journal/v31/n1/full/nbt.2450.html) was then used to assemble transcripts from spliced read alignments, again using the Ensembl e87 transcriptome as the reference, preventing de novo assembly of transcript models.
Transcriptome sets of all replicates for each sample group were combined with Cuffmerge.
Differential expression was assessed with Cuffdiff v2.2.1 (http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html).
The Bioconductor cummeRbund (http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html) pckage was used in combination with custom R scripts to perform quality assessment and further refine analysis results.
Genome_build: GRCm38 (UCSC mm10)
Supplementary_files_format_and_content: tab-separated value files of FPKM estimates obtained from Cufflinks, enriched with Ensembl transcrit annotation.

source_name: spleen, lymph nodes

extract_protocol:
Total RNA was prepared from 3x10^6 viable WT and NCOR1f/f,Cd4Cre in vitro-generated Th17 cells with QIAshredder, RNaeasy Mini Kit and RNase-Free DNase Set (Qiagen) according to manufacturer's protocol.
RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.

value: in vitro-generated Th17 cells

tag: culture time

value: 3 days

value: NCOR1f/f Cd4Cre


title: Th17_WT3 (RNA-seq)

value: wild-type


title: Th17_WT1 (RNA-seq)


title: Th17_WT2 (RNA-seq)


title: Th17_KO1 (RNA-seq)


title: ST486_shKTN1-AS1#1_rep2_day6

type: RNA

city: Groningen

first: Melanie

last: Winkle

state: Groningen

address: Hanzeplein 1

department: Pathology & Medical Biology

country: Netherlands

institute: UMC Groningen

description:
raw data file: US45102948_257236316859_S01_GE2_1200_Jun14_2_3
Gene expression analysis_ST486 cells_KTN1-AS1 low

hyb_protocol: According to manufacturers instructions

scan_protocol: Agilent DNA Microarray Scanner, Agilent Feature Extraction software version 12

data_processing: GeneSpring GX 13.1.1 software (Agilent Technologies); quantile normalization without base line transformation; analyzed as single color experiment

source_name: ST486 cells, shKTN1-AS1 #1, day 6 post-infection

label_protocol: Cy3 or Cy5 labelled using 50-100ng total RNA in combination with the LowInput QuickAmp Labelling Kit, Cyanine 3/5 CTP Dye Pack and RNA Spike-In kit (all Agilent Technologies).

growth_protocol: RPMI-1640 medium supplemented with 100U/ml penicillin, 0.1mg/ml  streptomycin, 2mM ultraglutamine and 10% Fetal Calf Serum (all Cambrex Biosciences, Walkersville, MD, USA), 37⁰C, 5% CO2

extract_protocol: The miRNeasy mini kit (Quiagen) was applied according to manufacturers instructions and including on column DNAse digestion

treatment_protocol: Anti-Myc or non-targeting control shRNAs were infected lentivirally into ST486 cells. Cells were harvested for RNA isolation at day 8 post infection.

value: shKTN1-AS1 #1, day 6 post-infection

value: ST486 Burkitt lymphoma


title: ST486_shControl2_rep2_day6

description:
raw data file: US45102948_257236316859_S01_GE2_1200_Jun14_2_2
Gene expression analysis_ST486 cells_KTN1-AS1 high

source_name: ST486 cells, shControl #2, day 6 post-infection

value: shControl #2, day 6 post-infection


title: ST486_shKTN1-AS1#2_rep2_day6

description:
raw data file: US45102948_257236316859_S01_GE2_1200_Jun14_2_4
Gene expression analysis_ST486 cells_KTN1-AS1 low

source_name: ST486 cells, shKTN1-AS1 #2, day 6 post-infection

value: shKTN1-AS1 #2, day 6 post-infection


title: ST486_shControl2_rep2_day4

source_name: ST486 cells, shControl #2, day 4 post-infection

value: shControl #2, day 4 post-infection


title: ST486_shControl1_rep2_day4

description:
raw data file: US45102948_257236316859_S01_GE2_1200_Jun14_2_1
Gene expression analysis_ST486 cells_KTN1-AS1 high

source_name: ST486 cells, shControl #1, day 4 post-infection

value: shControl #1, day 4 post-infection


title: ST486_shControl#2_rep1_day6

description:
raw data file: US45102948_257236316859_S01_GE2_1200_Jun14_1_2
Gene expression analysis_ST486 cells_KTN1-AS1 high


title: ST486_shKTN1-AS1#2_rep1_day6

description:
raw data file: US45102948_257236316859_S01_GE2_1200_Jun14_1_4
Gene expression analysis_ST486 cells_KTN1-AS1 low


title: ST486_shControl#2_rep1_day4


title: ST486_shKTN1-AS1#2_rep1_day4

source_name: ST486 cells, shKTN1-AS1 #2, day 4 post-infection

value: shKTN1-AS1 #2, day 4 post-infection


title: ST486_shKTN1-AS1#2_rep2_day4


title: ST486_shControl1_rep2_day6

source_name: ST486 cells, shControl #1, day 6 post-infection

value: shControl #1, day 6 post-infection


title: Th17_KO2 (RNA-seq)


title: ST486_shKTN1-AS1#1_rep2_day4

source_name: ST486 cells, shKTN1-AS1 #1, day 4 post-infection

value: shKTN1-AS1 #1, day 4 post-infection


title: ST486_shKTN1-AS1#1_rep1_day4

description:
raw data file: US45102948_257236316859_S01_GE2_1200_Jun14_1_3
Gene expression analysis_ST486 cells_KTN1-AS1 low


title: PC3 cells transfected with miR-205 rep3

city: Atlanta

first: Mengnan

last: Zhang

state: Georgia

address: 315 Ferst Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

hyb_protocol: Chips were hybridized to platform GPL570 platform using Affymetrix HWS KIT and FS450_0004 Protocol.

scan_protocol: Scan on 7G Affymetrix GeneChip scanner.

data_processing: The data were analyzed with Robust Multi-Array Average (RMA) using Affymetrix default analysis.

label: biotin

source_name: mRNA expression data of PC3 cells transfected with miR-205

label_protocol: Total RNA was amplified with Applause 3'-Amplification KIT (NuGen) and labeled with Encor Biotin Module (NuGen).

growth_protocol: Cells were cultured in RPMI 1640 (Mediatech, Manassas, VA) supplemented with 10% FBS (Fetal Bovine Serum; Atlanta Biologicals, Lawrenceville, GA) and 1% antibiotic-antimycotic solution (Mediatech-Cellgro, Manassas, VA).

extract_protocol: Total RNA was extracted from cells using the RNeasy Mini Kit (RNeasy, Qiagen, Germantown, MD).

treatment_protocol: 1 × 105 cells were seeded per well in 6-well plates. For miRNA transfection, cells at exponential phase of growth were transfected with 33 nM Pre-miR miRNA Precursors (Life Technologies, Carlsbad, CA) using Lipofectamine 2000 (Life Technologies, Carlsbad, CA). Pre-miR miRNA Precursor Negative was used as negative control. For siRNA transfection, cells at exponential phase of growth were transfected with 33 nM Silencer Select (Life Technologies, Carlsbad, CA) using Lipofectamine 2000 (Life Technologies, Carlsbad, CA). Silencer Select Negative Control siRNA was used as a negative control. Cells were allowed to grow for 48 hours before RNA extraction.

value: PC3 cells

value: transfected with miR-205


title: PC3 cells transfected with miR-429 rep1

source_name: mRNA expression data of PC3 cells transfected with miR-429

value: transfected with miR-429


title: PC3 cells transfected with miR-429 rep3


title: PC3 cells transfected with miR-203a rep3

source_name: mRNA expression data of PC3 cells transfected with miR-203a

value: transfected with miR-203a


title: PC3 cells transfected with miR-205 rep2


title: ST486_shControl#1_rep1_day6

description:
raw data file: US45102948_257236316859_S01_GE2_1200_Jun14_1_1
Gene expression analysis_ST486 cells_KTN1-AS1 high


title: PC3 cells transfected with miR-205 rep1


title: 92.1BAP1KD_rep2

type: genomic

city: Miami

first: Matthew

middle: G.

last: Field

state: FL

address: 1501 NW 10th Avenue

institute: University of Miami

description: uveal melanoma, cell line

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: ChAMP pipeline in R (2.12.4)

label: Cy5 and Cy3

source_name: 92.1 uveal melanoma cell line

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using QIAamp DNA Mini Kit (Qiagen) according to standard instuctions.

value: BAP1 KD

value: uveal melanoma, cancer cell


title: PC3 cells transfected with miR-203a rep2


title: ST486_shControl#1_rep1_day4


title: SKOV3 cells transfected with miR-429 rep2

source_name: mRNA expression data of SKOV3 cells transfected with miR-429

value: SKOV3 cells


title: SKOV3 cells transfected with miR-429 rep3


title: SKOV3 cells transfected with miR-429 rep1


title: untransfected PC3 cells rep2

source_name: mRNA expression data of untransfected PC3 cells

value: untransfected


title: PC3 cells transfected with miR-203a rep1


title: PC3 cells transfected with miR-NC rep3

source_name: mRNA expression data of PC3 cells transfected with miR-NC

value: transfected with miR-NC


title: SKOV3 cells transfected with miR-203a rep2

source_name: mRNA expression data of SKOV3 cells transfected with miR-203a


title: SKOV3 cells transfected with miR-NC rep2

source_name: mRNA expression data of SKOV3 cells transfected with miR-NC


title: SKOV3 cells transfected with miR-205 rep1

source_name: mRNA expression data of SKOV3 cells transfected with miR-205


title: SKOV3 cells transfected with miR-203a rep1


title: untransfected SKOV3 cells rep3

source_name: mRNA expression data of untransfected SKOV3 cells


title: PC3 cells transfected with miR-NC rep2


title: SKOV3 cells transfected with miR-NC rep1


title: 92.1WT_rep1

description: uveal melanoma, cell line

value: wildtype


title: 92.1BAP1KD_rep1

description: uveal melanoma, cell line


title: PC3 cells transfected with miR-NC rep1


title: Mel202BAP1KD_rep2

description: uveal melanoma, cell line

source_name: Mel202 uveal melanoma cell line


title: ST486_shKTN1-AS1#1_rep1_day6

source_name: ST486 cells, shKTN1-AS1 #1, day 6 post-infection

value: shKTN1-AS1 #1, day 6 post-infection

value: ST486 Burkitt lymphoma


title: HEY cells transfected with miR-429 rep1

source_name: mRNA expression data of HEY cells transfected with miR-429

value: HEY cells


title: untransfected SKOV3 cells rep2


title: untransfected SKOV3 cells rep1


title: SKOV3 cells transfected with miR-205 rep3


title: HEY cells transfected with miR-429 rep3


title: SKOV3 cells transfected with miR-NC rep3


title: HEY cells transfected with miR-429 rep2


title: SKOV3 cells transfected with miR-205 rep2


title: HEY cells transfected with miR-205 rep3

source_name: mRNA expression data of HEY cells transfected with miR-205


title: PC3 cells transfected with miR-429 rep2


title: HEY cells transfected with miR-205 rep1


title: HEY cells transfected with miR-203a rep2

source_name: mRNA expression data of HEY cells transfected with miR-203a


title: HEY cells transfected with miR-NC rep3

source_name: mRNA expression data of HEY cells transfected with miR-NC


title: HEY cells transfected with miR-203a rep3


title: Mel202BAP1KD_rep1

description: uveal melanoma, cell line


title: Mel202WT_rep1

description: uveal melanoma, cell line


title: Sorafenib-resistant HCC patient2

city: Guangzhou

first: Guohui

last: Wan

state: Guangdong

address: 132# Waihuan Dong Road, High Education Mega Center

institute: Sun-yat sen University

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, and then we generated the purpose short read aligner from reference genome hg38 using bowtie-build, then aligned to hg38 whole genome using Tophat v2.1.0 with parameters -p 32 -G genes.gtf -o
Fragments per Kilobase of exon per Megabase of library size (FPKM) were calculated using a cufflinks package protocol from Cole,T et al., Nature Protocol, 2014.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene differential FPKM values for 2 conditions (normal and sorafenib-resistant)

source_name: liver cancer

extract_protocol:
Liver cancer tissue were removed, flash frozen on dry ice, 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: phenotype

value: sorafenib resistant

value: liver cancer

tag: patient diagnosis

value: HCC


title: untransfected HEY cells rep2

source_name: mRNA expression data of untransfected HEY cells


title: Normal HCC patient3

value: sorafenib sensitive


title: HEY cells transfected with miR-203a rep1


title: HEY cells transfected with miR-NC rep1


title: untransfected HEY cells rep3


title: Sorafenib-resistant HCC patient1


title: Sorafenib-resistant HCC patient3


title: untransfected HEY cells rep1


title: C11d34_3

city: Chippendale

first: Darya

middle: Pavlovna

last: Vanichkina

state: New South Wales

address: 32 Queen Street

country: Australia

institute: University of Sydney

description: day34. This is the same iPS line as SAMD00005689, but the passage, neuronal differentiation, and RNA purification are all distinct.

data_processing:
Illumina Casava software used for basecalling.
After read quality control using FastQC (Andrews, 2012), primary alignment to the reference human genome (hg19) was carried out using the Burrows-Wheeler Aligner (Li and Durbin, 2009) version 0.6.2 with default mapping parameters.
Output data was converted to bam format using SAMtools (Li et al., 2009).
The exon_utils.py module of the MISO framework (Katz et al., 2010) was used to extract constitutive exons longer than 1000 nucleotides, and pe_utils.py was used to determine the mate inner distance and mate standard deviation parameters for each dataset (these are provided in the table below).
Tophat (Kim et al., 2013) version 2.0.8 was then used to map reads to the genome and reference transcriptome (GENCODE v. 17 (Harrow et al., 2012)) simultaneously, with the parameters --b2-very-sensitive --read-mismatches 3 --read-gap-length 2 --read-edit-dist 3 --read-realign-edit-dist 0.
All subsequent analyses were conducted using the results of this mapping. Count tables were obtained using the HTSeq (Anders, 2010) framework in union mode, with GENCODE v. 17 as a reference.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file reports gene-level count table for each GENCODE17 annotated gene

source_name: C11-CRL2429 iPS differentiated into neurons d34

growth_protocol: hESC and iPSC were grown in hESC culture medium (80% DMEM F-12, 20% KnockOut-Serum replacement, 2 mM 1-glutamine, 1% non-essential amino acids (NEAA) 0.1 mM 2-mercaptoethanol and between 50-100 ng/ml basic fibroblast growth factor) at 37°C at 5% CO2 at high humidity. Cells were maintained on Mouse embryonic fibroblast feeder layers supplied by the Australian Stem Cell Centre. For experimentation, cells were cultured in feeder-free conditions on Matrigel (BD) in MEF conditioned hESC media. Cells were passaged as previously described before replating at a seeding ratio of between 1:2 and 1:6. hESC media was replaced daily and cells were split at approximately 80% confluence on days 6-7. All work was carried out with informed consent from patients under the approval of the Human Research Ethics Committee (HREC/09/QRCH/103). Embryoid bodies (EBs) were formed by detachment of undifferentiated iPS cells from the MEF monolayer (12,000/cm2) using a P200 pipette. EBs were transferred to a low-attachment plate (Costar) in Knock-Out Serum (KSR) replacement hESC culture medium (80% DMEM -F12 (GIBCO), 20% KnockOut-Serum replacement (GIBCO), 2 mM L-glutamine (GIBCO), 1% non-essential amino acids (NEAA) (GIBCO), 0.1 mM 2-mercaptoethanol at 37°C at 5% CO2 at high humidity. EBs were cultured in the absence of basic fibroblast growth factor (to promote differentiation towards neurectodermal lineage). Medium was changed each day. After four days EBs were resuspended in neural induction medium (DMEM F-12with Glutamax (GIBCO), N2 supplement (GIBCO) and heparin sulfate (R&D)) and supplemented with human FGF8 (Sigma Aldrich) (100 ng/mL) and RA (Retinoic acid) (10 µM) (Sigma Aldrich). After 7 days of incubation in this medium EBs were deposited in plates coated with laminin (Sigma) (2 µg/mL) and fibronectin (BD) (5 µg/mL) in basal medium eagle (BME) media (Invitrogen) supplemented with ITS (Insulin, Transferrin, Selenite) (GIBCO), human FGF8 (100 ng/mL), human FGF4 (Life technologies) (100 ng/mL) and human basic fibroblast growth factor (Invitrogen) (20 ng/mL) and allowed to grow for four days. Medium was changed to DMEM-F12 with human FGF8 (100 ng/mL), WNT1 (Peprotech/Abacus) (50 ng/mL) and WNT3A (50 ng/mL) (R&D) for five days. The next stage of differentiation involved culturing the cells in BME media supplemented with N2, B27 (GIBCO), human BMP4 (R&D), (50 ng/mL), human BMP6 (R&D) (20 ng/mL), human BMP7 (Peprotech/Abacus) (100 ng/mL) and human growth differentiation factor 7 (GDF7) (R&D) (100 ng/mL) for a further eight days. Attached cells were then disaggregated and replated on laminin/fibronectin for another 8 days of growth in BME supplemented with N2, B27, human BMP4 (50 ng/mL), human BMP6 (20 ng/mL), human BMP7 (100 ng/mL), human GDF7 (100 ng/mL), human Sonic hedgehog (R&D) (100 ng/mL), human neurotrophin 3 (R&D), (NT3) (100 ng/mL), jagged1 (JAG1) (R&D) (20 ng/mL) and human brain derived neutrotrophic factor  (BDNF) (100 ng/mL) (R&D).

extract_protocol:
Total RNA was extracted using RNA Spin II isolation columns (Machery Nagel). On column digestion of DNA with RNase free DNase was performed according to the manufacturer’s specifications (Ambion, Austin, TX). RNA samples were subject to RNA integrity analysis using the RNA 6000 Nano total RNA kit (Agilent). All samples recorded a RIN (RNA integrity number) in excess of 8.5 out of 10. Samples were processed according to the TruSeq Stranded Total RNA Sample preparation LS protocol kit (Illumina) as per the manufacturer’s specifications.
Total RNA libraries were prepared for sequencing using standard Illumina protocols in the TruSeq Total Stranded Library Preparation kit. 100 bp PE reads were generated.

value: Cerebellar-like iPS derived neurons

tag: atcc cell line source

value: CCD-1112Sk (ATCC CRL-2429)

tag: gender

value: male


title: SKOV3 cells transfected with miR-203a rep3

value: transfected with miR-203a


title: PBMC total RNA-late convalescent Lyme disease subject 5

city: Valhalla

first: Mary

last: Petzke

state: NY

address: 15 Dana Road

department: Microbiology and Immunology

institute: New York Medical College

description: Gene expression data from PBMCs of subjects with late convalescent (6 months after initiation of antibiotics) Lyme disease

hyb_protocol: cDNA was hybridized to the Affymetrix GeneChip.HG-U219 high-density oligonucleotide array (Affymetrix, Santa Clara, CA).  Following hybridization, arrays were stained with streptavidin-phycoerythrin and washed in an Affymetrix fluidics module using standard Affymetrix protocols.

scan_protocol: The detection and quantitation of target hybridization was performed using a GeneArray Scanner 3000 (Affymetrix).

data_processing: Microarray data were analyzed using GeneSpring GX14.9 software (Agilent Technologies, Santa Clara, CA).  Raw expression values in CEL file format were normalized by robust multi-array analysis (RMA) and quantile normalization, filtered to include only those with intensity values above the 20th percentile, and baseline transformed to the median of all samples.  Statistical analysis was performed using a one-way ANOVA with Benjamini-Hochberg multiple testing correction to reduce false positives.  Differentially expressed transcripts, defined as those having a P-value of <0.05 and a fold change of at least 2 relative to the healthy donor group, were subjected to hierarchical clustering and principal component analysis.  A generic predictive modeling framework was developed and applied to two comparisons:  acute LD (n=28) versus healthy donors (n=21), and acute LD versus 6 month convalescent LD (n=10).  In the first step, the distribution of the gene expression variance across all experimental groups was computed, and genes with variance at or above the 90th percentile were identified. This threshold is a parameter of the framework and can be appropriately set based on the variance distribution in a considered cohort of samples. In the second step, expression data containing the top 10% of variance in each experimental group were subjected to iterations (n = 50) of random forest analysis. An importance value for each gene was generated following each iteration of random forest analysis, and a final importance value for each gene was computed by averaging the importance values across all 50 iterations. Averaged importance values were used to rank all top selected genes. Finally, for each experiment, leave-one-out predictive modeling was performed and tested using incrementally expanding sets of the most significant genes (top 20 through top 2004) to assess the changes of accuracy performance across different sets of predictors.

label_protocol: Between 5 and 20 ng of total RNA from each PBMC sample was used to generate high fidelity cDNA using the Ovation RNA amplification system (NuGEN Technologies, Inc., San Carlos, CA), according to the manufacturer’s protocol.  The amplified cDNA was fragmented to 50-100 nucleotides and labeled with biotin using standard Affymetrix protocols.

growth_protocol: Not applicable; primary human cells were processed immediately after collection from subjects.

extract_protocol: Venous blood was collected directly into BD-Vacutainer CPT tubes (Becton Dickinson, Franklin Lakes, NJ).  Peripheral blood mononuclear cells (PBMCs) were isolated by centrifugation, according to the manufacturer’s protocol, no later than three hours after blood collection.  PBMCs were washed with Hank’s Balanced Salt Solution without calcium, magnesium or phenol red (Gibco-BRL, Grand Island, NY), and RNA was isolated immediately thereafter under RNase-free conditions using the Purescript total RNA isolation kit (Gentra, Minneapolis, MN) or the Ambion ToTALLY RNA isolation kit (Life Technologies, Grand Island, NY), according to the manufacturers’ instructions.  Contaminating DNA was removed using the DNA-free kit (Ambion, Austin, TX).  RNA was eluted in 20 l RNase/DNase-free water and stored at -80°C after the addition of 32 U of RNase inhibitor (Promega, Madison, WI).  RNA integrity was assessed by electrophoresis using an Agilent Bioanalyzer 2100 (Agilent, Palo Alto, CA) prior to cDNA synthesis for microarray hybridization. Samples having an RNA integrity number below 6 were excluded from further analysis.

tag: disease state

value: Late convalescent Lyme disease (6 months following initiation of antibiotic regimen)


title: C11d34_2


title: PBMC total RNA-late convalescent Lyme disease subject 9

source_name: Peripheral blood mononuclear cells (PBMCs)

treatment_protocol: Not applicable; primary human cells were processed immediately after collection from subjects.


title: PBMC total RNA-late convalescent Lyme disease subject 10


title: C11d0_3

description: day0. This is the same iPS line as SAMD00005689, but the passage, neuronal differentiation, and RNA purification are all distinct.

source_name: C11-CRL2429 iPS day 0

value: undifferentiated human iPS cells


title: PBMC total RNA-late convalescent Lyme disease subject 8


title: Mel202WT_rep2

description: uveal melanoma, cell line

value: uveal melanoma, cancer cell


title: C11d0_2


title: PBMC total RNA-late convalescent Lyme disease subject 6


title: Normal HCC patient1


title: PBMC total RNA-late convalescent Lyme disease subject 7


title: PBMC total RNA-late convalescent Lyme disease subject 3


title: PBMC total RNA-late convalescent Lyme disease subject 4


title: PBMC total RNA-early convalescent Lyme disease subject 25

description: Gene expression data from PBMCs of subjects with early convalescent (1 month after initiation of antibiotics) Lyme disease

value: Early convalescent Lyme disease (1 month following initiation of antibiotic regimen)


title: PBMC total RNA-early convalescent Lyme disease subject 27


title: PBMC total RNA-early convalescent Lyme disease subject 24


title: PBMC total RNA-late convalescent Lyme disease subject 1


title: PBMC total RNA-early convalescent Lyme disease subject 26


title: M62K: human ccRCC cell line M62-shAXL

city: Stanford

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

data_processing:
TrimGalore
STAR
RSEM
Genome_build: hg38
Supplementary_files_format_and_content: TPM and fold changes

source_name: tumor

extract_protocol:
Qiagen RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1×106 cancer cells were growth in 100 mm plate 37 ℃, 5% CO2 overnight

value: human clear cell renal cell carcinoma (ccRCC)

tag: cell origin

value: transfected with shAXL


title: C11d34_1


title: W-5-2 [RNA-seq]

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

description: Generation 5 WT control

data_processing:
Illumina for basecalling
Alignments were performed using STAR (version 2.7.0a) with –twopassMode = Basic and –outFilterMultimapNmax = 1  parameters  (Grant et al., 2011)
The read count data were generated from the SAM files by using QoRTs software package (Hartley and Mullikin, 2015) --minMAPQ 25 --dropChrom Pt,Mt
DESeq2 (Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biology 15(12):550 2014) was used for gene count normalization and to identify differentially expressed genes (FDR < 0.05, |log2FC| > 0.5. GTF file TAIR10.37
Genome_build: TAIR 10
Supplementary_files_format_and_content: Text file with GENEID and COUNTS to be used with DESeq2

organism: Arabidopsis thaliana

growth_protocol: Seeds were sown on peat mix in square pots in reach-in chambers at 12hrs daylenght (22 °C, 120-150 μmol/(m^2*s) light)

extract_protocol:
total RNA from each sample was extracted by NucleoSpin RNA Plant kit (Macherey-Nagel, Germany) following manufacturer’s protocol, including genomic DNA removal.
RNA libraries were constructed as described in the TruSeq RNA Sample Preparation v2 Guide.
These libraries were sequenced with the 150-bp paired read option, in Hi-Seq 4000 analyzer (Illumina, USA) at BGI-Tech (Shenzhen, China).

treatment_protocol: Three of each memory, non-memory, and Col-0 wild-type plants from generation 1 and 5 were sequenced. Whole plants at at bolting were flash freezed in liquid nitrogen.  Tissues were ground by motor and pestle in liquid nitrogen

tag: replicate

value: biological rep 2

value: whole rosette

value: Generation 5 WT control


title: PBMC total RNA-late convalescent Lyme disease subject 2


title: M62C: human ccRCC cell line M62 -shSCM

value: transfected with shSCM


title: W-1-3 [RNA-seq]

description: Generation 1 WT control

tag: tissue

value: Generation 1 WT control


title: H7860K: human ccRCC cell line 786-O-shAXL

tag: cell type


title: W-5-1 [RNA-seq]

description: Generation 5 WT control

value: biological rep 1


title: PBMC total RNA-early convalescent Lyme disease subject 23


title: W-1-1 [RNA-seq]

description: Generation 1 WT control


title: h7860C: human ccRCC cell line 786-O-shSCM


title: NM-1-45 [RNA-seq]

description: Generation 1 non-memory line

value: Generation 1 non-memory line


title: TEN_2942_end

city: Zurich

first: Martin

last: Flück

address: Lengghalde 5

department: Balgrist Campus

country: Switzerland

institute: University of Zurich

data_processing:
Raw reads were cleaned by removing adapter sequences and trimming first three and last four bases.
The resulting high-quality reads were aligned to the current genome build (Oar_v3.1.75, Ensembl) using the STAR aligner (v2.3.0e). The resulting mapping rate was 90%. Approximately 55% of the reads corresponded to mRNA.
Counting was performed using the countOverlaps-method from the IRanges package in Bioconductor (v2.13 with R 3.0.2).
Raw signals were expressed as ‘normalized signals’, reflecting the frequency of the individual gene transcripts.
Genome_build: Genome_build: (Oar_v3.1.75, Ensembl) using STAR (v2.3.0e)

organism: Ovis aries

source_name: skeletal muscle

growth_protocol: Infraspinatus muscle was subjected to 2 weeks of tendon release

extract_protocol:
An approximate of 15 mm3 of cryosections was pooled and processed using the RNeasy kit (Qiagen). The quantity and quality of total RNA were evaluated using Qubit® RNA BR Assay Kit (LifeTechnologies, USA) and Agilent RNA 6000 Nano kit with the Agilent 2100 Bioanalyzer instrument (Agilent Technologies Inc., Santa Clara, USA), respectively. RNA sample was accepted for the study when the RIN was ≥7.0.
The Illumina TruSeq® Stranded total RNA protocol with the TruSeq Stranded total RNA Sample Preparation Kit was used to produce library constructs. The library product was generated from 1 µg total RNA subsequent to the removal of ribosomal RNA with human specific probes with the Epicentre Ribo-Zero™ Magnetic Gold Kit and subsequent fragmentation of the enriched RNA. Then first strand cDNA synthesis was carried out using reverse transcriptase and random hexamers, followed by second strand cDNA synthesis with DNA polymerase. During this step the RNA template was removed and double-stranded cDNA was synthetized in the presence of dUTP in place of dTTP. In a next step the 3’ ends of the blunt fragments were adenylated and multiple indexing adapters were ligated to the ends of double strand cDNA. Finally, the cDNA was amplified using PCR in order to both enrich DNA fragments having adapter molecules on both ends and amplify the amount of DNA in the library. Quantification and a quality of generated libraries were determined by qPCR with Illumina adapter specific primers using Roche LightCycler® system (Roche Diagnostics, Basel, Switzerland) and on an Agilent Technologies 2100 Bioanalyzer with DNA-specific chip, respectively.
Diluted libraries (10 nM) were pooled and were further used for cluster generation according to the manufacturer’s recommendations using TruSeq SR Cluster Kit v3-cBot-HS reagents and sequenced with TruSeq SBS Kit v3-HS reagents on Illumina HiSeq 2500 in the high output mode. On average 50’000’000 reads were sequenced per library.

treatment_protocol: Biopsies were collected from infraspinatus muscle before or after tenotomy (PRE, END)

value: infraspinatus muscle

tag: time point

value: two weeks after tendon release

tag: breed

value: Swiss Alpine sheep

tag: age

value: 2 years-old

value: female


title: untransfected PC3 cells rep1

source_name: mRNA expression data of untransfected PC3 cells

value: PC3 cells

tag: treatment

value: untransfected


title: PBMC total RNA-early convalescent Lyme disease subject 19

value: Early convalescent Lyme disease (1 month following initiation of antibiotic regimen)


title: PBMC total RNA-early convalescent Lyme disease subject 16


title: PBMC total RNA-early convalescent Lyme disease subject 22


title: PBMC total RNA-early convalescent Lyme disease subject 17


title: PBMC total RNA-early convalescent Lyme disease subject 20


title: TEN_2942_pre

value: prior to tendon release


title: untransfected PC3 cells rep3


title: PBMC total RNA-early convalescent Lyme disease subject 15


title: PBMC total RNA-early convalescent Lyme disease subject 13


title: PBMC total RNA-early convalescent Lyme disease subject 12


title: PBMC total RNA-early convalescent Lyme disease subject 14


title: PBMC total RNA-early convalescent Lyme disease subject 11


title: NM-1-12 [RNA-seq]

description: Generation 1 non-memory line

tag: sample type


title: NM-1-70 [RNA-seq]

description: Generation 1 non-memory line

value: biological rep 3


title: M-5-3 [RNA-seq]

description: Generation 5 memory line

value: Generation 5 memory line


title: M-5-2 [RNA-seq]

description: Generation 5 memory line

value: biological rep 2

value: whole rosette


title: TEN_2941_pre


title: 92.1WT_rep2

description: uveal melanoma, cell line

source_name: 92.1 uveal melanoma cell line

tag: genotype/variation

value: wildtype

value: uveal melanoma, cancer cell


title: TEN_2941_end


title: TEN_2940_end


title: M-5-1 [RNA-seq]

description: Generation 5 memory line

value: biological rep 1


title: TEN_2940_pre


title: Normal HCC patient2

value: sorafenib sensitive

value: liver cancer

value: HCC


title: M-1-3 [RNA-seq]

description: Generation 1 memory line

value: Generation 1 memory line


title: M-1-27 [RNA-seq]

description: Generation 1 memory line


title: PBMC total RNA-early convalescent Lyme disease subject 5


title: PBMC total RNA-early convalescent Lyme disease subject 6


title: PBMC total RNA-early convalescent Lyme disease subject 8


title: PBMC total RNA-early convalescent Lyme disease subject 4


title: PBMC total RNA-early convalescent Lyme disease subject 7


title: PBMC total RNA-early convalescent Lyme disease subject 9


title: PBMC total RNA-early convalescent Lyme disease subject 3


title: M-1-105 [RNA-seq]

description: Generation 1 memory line


title: HEY cells transfected with miR-205 rep2

tag: cell line

value: HEY cells

value: transfected with miR-205


title: Bone next to empty defect BNED 4c

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description:
Sample_117528
Bone next to empty defect BNED

data_processing:
FastQC version 0.11.3 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to identify features of the raw data that may indicate quality problems
we aligned reads to the reference mRNA transcriptome (rn5) [5] using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.).
FastQC was used for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis
DESeq2 was used for differential expression
we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ 1.5.
Genome_build: rn5
Supplementary_files_format_and_content: raw counts

organism: Rattus norvegicus

source_name: Bone next to empty defect rat 3

extract_protocol:
Tissues were harvested into RNAlater. RNA was harvested using Trizol and subject to on column DNAse treatment. The final RNA product was subject to ammonium acetate precipitation before quality assessment.
TruSeq stranded mRNA kit with 1ug of input and 12 cycles of PCR.
paired end, 100 cycles, stranded Tru-seq poly-A selected mRNA

tag: strain

value: Sprague-Dawley

value: Bone next to empty defect BNED


title: Bone next to empty defect BNED 4d

description:
Sample_117529
Bone next to empty defect BNED

source_name: Bone next to empty defect rat 4


title: PBMC total RNA-Acute Lyme disease subject 28

description: Gene expression data from PBMCs of subjects with acute early disseminated Lyme disease

value: Acute early disseminated Lyme disease


title: PBMC total RNA-early convalescent Lyme disease subject 1

value: Early convalescent Lyme disease (1 month following initiation of antibiotic regimen)


title: Bone next to empty defect BNED 4b

description:
Sample_117527
Bone next to empty defect BNED

source_name: Bone next to empty defect rat 2


title: W-5-3 [RNA-seq]

description: Generation 5 WT control

value: biological rep 3

value: Generation 5 WT control


title: PBMC total RNA-Acute Lyme disease subject 26


title: PBMC total RNA-Acute Lyme disease subject 27


title: PBMC total RNA-Acute Lyme disease subject 25


title: PBMC total RNA-early convalescent Lyme disease subject 18


title: PBMC total RNA-early convalescent Lyme disease subject 2


title: PBMC total RNA-Acute Lyme disease subject 24


title: Bone next to empty defect BNED 4a

description:
Sample_117526
Bone next to empty defect BNED

source_name: Bone next to empty defect rat 1


title: PBMC total RNA-Acute Lyme disease subject 21


title: Bone next to PMMA spacer PMMA 3d

description:
Sample_117525
Bone next to PMMA spacer PMMA

source_name: Bone next to PMMA spacer rat 4

value: Bone next to PMMA spacer PMMA


title: Bone next to PMMA spacer PMMA 3c

description:
Sample_117524
Bone next to PMMA spacer PMMA

source_name: Bone next to PMMA spacer rat 3


title: PBMC total RNA-Acute Lyme disease subject 20


title: PBMC total RNA-Acute Lyme disease subject 18


title: PBMC total RNA-Acute Lyme disease subject 22


title: C11d0_1

value: undifferentiated human iPS cells

value: CCD-1112Sk (ATCC CRL-2429)

value: male


title: PBMC total RNA-Acute Lyme disease subject 19


title: PBMC total RNA-Acute Lyme disease subject 17


title: PBMC total RNA-Acute Lyme disease subject 16


title: PBMC total RNA-Acute Lyme disease subject 14


title: HEY cells transfected with miR-NC rep2

value: transfected with miR-NC


title: Bone next to PMMA spacer PMMA 3a

description:
Sample_117522
Bone next to PMMA spacer PMMA

source_name: Bone next to PMMA spacer rat 1


title: Pre-fibrous non-union PFNU 2d

description:
Sample_117521
Pre-fibrous non-union PFNU

source_name: Non-union from empty osteotomy rat 4

value: Pre-fibrous non-union PFNU


title: Pre-fibrous non-union PFNU 2c

description:
Sample_117520
Pre-fibrous non-union PFNU

source_name: Non-union from empty osteotomy rat 3


title: W-1-4 [RNA-seq]

description: Generation 1 WT control

value: whole rosette

value: Generation 1 WT control


title: PBMC total RNA-Acute Lyme disease subject 15


title: PBMC total RNA-Acute Lyme disease subject 12


title: PBMC total RNA-Acute Lyme disease subject 9


title: Medicine-4

city: jilin city

first: guangyu

last: xu

address: Binjiang Road 3999,jilin city,132013

institute: College of Pharmacy, Beihua University

description: Gene expression after 28d in mouse spleen

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 at 60°C for 30 min, and 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.The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and 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). After quantile normalization of the raw data, genes that at least 3 out of 9 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: spleen organization,28d,1000 mg/kg/d,replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 700μL RNA using the RNeasy Mini Kit (Qiagen p/n 74104) according to the manufacturer's instructions, followed by RNAeasy column purification. The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Briefly, the spleen tissue was ground into powders under the frozen condition with liquid nitrogen, and before the liquid nitrogen was volatilized, the liver powder was transferred into a 1.5ml microcentrifuge tube containing Trizol reagent (500mg of the liver tissue per 0.5 ml Trizol reagent). The liver powder in the microcentrifuge tube was drawn and re-injected vigorously several times with a 5 ml disposable syringe until the tissue homogenate was no longer sticky, in favor of the full breaking down of the cells and genomic DNA. The tissue homogenate was left to stand at room temperature for use. According to the ratio of 200ul chloroform per 1mlTrizol reagent, chloroform was added to the homogenate. The mixed solution was oscillated violently for 30sec for evenly mixing and then left to stand at room temperature for 5min. The mixed sample solution was centrifuged at 12000r/m for 15min to obtain the supernatant and the obtained supernatant was carefully transferred to another centrifuge tube, in which it was noticeable not to draw the intermediate phase. 500ul isopropanol was added to the supernatant, which was left to stand at the room temperature for 10min for its precipitation, and then centrifuged at 12000r/m for 15min and the supernatant was discarded to obtain the precipitation. 1Ml of 75% ethanol was added to the precipitation for the wash of RNA by oscillating it with a vortex, which was left to stand at room temperature for 5min and then centrifuged at 7500r/m for 5min to discard the supernatant. Finally, 75% ethanol was added to the precipitation to wash the RNA again, the precipitation solution was centrifuged at 7500r/m for 5min, the supernatant was removed, and the final precipitation was dried at room temperature, in which the RNA precipitation should not be too dried, otherwise it was not easy to dissolve.

treatment_protocol: 240 Eight-week-old male ICR mice (SPF grade), weighing 18~22g, were purchased from Liaoning Changsheng Biotechnology Co., LTD (license number: SCXK (Liao)-2015-0001). Animals were housed individually in cages at 20±1℃and in 40-70% humidity, subjected to 12h light/dark cycle with free access to food and water.ICR mice were randomly divided into control group, Cy model group, Sch A low-dose, middle-dose, and high-dose group. Except those in the control group, mice in the other groups were given 40 mg/kg Cy in intraperitoneal injection for 5d for the establishment of immunodeficiency mice model. On the next day after the modeling, mice in low-, middle- and high-dose Sch A groups were intragastrically given 0.2g/kg/d, 0.4g/kg/d and 1g/kg/d Sch A respectively, and those in the control group and Cy model group were given an equal volume of distilled water in the same way successively for 4 weeks. Changes in the mice’s body weight and general status were regularly observed weekly. The mice’s body weights were measured every week regularly for the observation on changes in their body weights and their general states were also observed at the same time.  we choose best group to do mRNA  expression microarray.

value: ICR

value: spleen


title: PBMC total RNA-Acute Lyme disease subject 13


title: Pre-fibrous non-union PFNU 2b

description:
Sample_117519
Pre-fibrous non-union PFNU

source_name: Non-union from empty osteotomy rat 2


title: PBMC total RNA-Acute Lyme disease subject 10

source_name: Peripheral blood mononuclear cells (PBMCs)


title: Medicine-5


title: PBMC total RNA-Acute Lyme disease subject 11


title: PBMC total RNA-Acute Lyme disease subject 7


title: Medicine-6


title: PBMC total RNA-early convalescent Lyme disease subject 10


title: PBMC total RNA-Acute Lyme disease subject 8


title: Model-3

description: Gene expression after 5d in mouse spleen

source_name: spleen organization,5d,40 mg/kg,replicate 1


title: Model-2


title: Pre-fibrous non-union PFNU 2a

description:
Sample_117518
Pre-fibrous non-union PFNU

source_name: Non-union from empty osteotomy rat 1


title: PBMC total RNA-Acute Lyme disease subject 4


title: PBMC total RNA-Acute Lyme disease subject 6


title: PBMC total RNA-Acute Lyme disease subject 5


title: Induced Membrane IM 1d

description:
Sample_117517
Induced Membrane IM

source_name: PMMA spacer induced membrane rat 4

value: Induced Membrane IM


title: Induced Membrane IM 1c

description:
Sample_117516
Induced Membrane IM

source_name: PMMA spacer induced membrane rat 3

value: Sprague-Dawley


title: PBMC total RNA-Acute Lyme disease subject 23


title: Induced Membrane IM 1b

description:
Sample_117515
Induced Membrane IM

source_name: PMMA spacer induced membrane rat 2


title: PBMC total RNA-early convalescent Lyme disease subject 21


title: Model-1


title: Induced Membrane IM 1a

description:
Sample_117514
Induced Membrane IM

source_name: PMMA spacer induced membrane rat 1


title: PBMC total RNA-Acute Lyme disease subject 1


title: PBMC total RNA-Acute Lyme disease subject 3


title: PBMC total RNA-Healthy control 21

description: Gene expression data from healthy adult PBMCs

value: Healthy control


title: PBMC total RNA-Acute Lyme disease subject 2

value: Acute early disseminated Lyme disease


title: PBMC total RNA-Healthy control 20


title: ShEE10

city: MADISON

first: Changjiu

last: Zhao

state: WI

address: 430 Lincoln Drive

department: Integrative Biology

institute: University of Wisconsin-Madison

data_processing:
Illumina bcl2fastq v2.20
Read trimming with Skewer v0.2.2b -m pe -q 20 -k 15 -l 25
Read alignment with STAR v2.5.3a --runThreadN 10 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM rsem-calculare-expression v1.2.31 --alignments --paired-end --no-bam-output
Differential expression estimation with edgeR v3.28.0
Genome_build: Rnor_6.0;  NCBI:GCA_000001895.4
Supplementary_files_format_and_content: MS Excel differential expression results

source_name: Brain tissue

growth_protocol: microinjection protocol: Juvenile rats (PN21) were securely placed on a stereotaxic apparatus (David Kopf Instruments, Tunjunga, CA, USA) and the cannula (33 gauge) tip was moved to the coordinates of target site. AP=−0.2 mm, ML=± 0.4 mm, and DV=8.0 mm. AAV vectors expressing either rat Oprm1 shRNA (i.e., AAV5-GFP-U6-Oprm1-shRNA) or Scr shRNA (i.e., AAV5-GFP-U6-Scr-shRNA) were injected bilaterally into the MPOA in a volume of 0.5 uL per side.

extract_protocol:
brain collection and total RNA extraction protocol: Rats were lightly anesthetized with isoflurane and decapitated. Brains were dissected and flash frozen in isopentane on dry ice and stored at −80°C. Sections of 200-micron thickness were cut and mounted on gelatin-coated glass slides. MPOA from Bregma −0.24 to −0.72 mm was dissected bilaterally under a dissecting microscope. Total RNA was extracted with the Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad, Hercules, CA, USA). The integrity, purity and concentration of RNA were measured. Purified total RNA was stored at −80°C until processed.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: brain region

value: MPOA-derived brain tissues

tag: developmental stage

value: Adolescence

value: SAS Sprague-Dawley

tag: aav type


title: ShEE6

description: This sample (ShEE6) is an outlier, and excluded from data analysis


title: ShEE11


title: ShEE9


title: PBMC total RNA-Healthy control 19


title: SMMC-7721 hypoxia

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 hg19 whole genome using bowtie v0.12.2 with parameters -p 32 -m 5 --best --strata
peak calling was conducted using MACS v1.4.2 with the parameters --name --format --gsize --tsize --nomodel --shiftsize -S, and then sort out peaks having an FDR<5%
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes m6A abundance of RNAs for sample

source_name: human liver cancer cells

growth_protocol: SMMC-7721 cells were cultured under hypoxia(1% O2) for 48 hours in DMEM(Corning, USA) supplemented 10% FBS(Gibco,South America)

extract_protocol:
total RNAs were harvested from SMMC-7721 cells cultured under hypoxia using Trizol reagent, and then were chemically broken into fragments of ~100 nt. The m6A modification of RNAs were isolated with m6A antibody
Libraries were constructed according to the standard manufacture's instruction(NEB Next Ultra RNA library Prep Kit,illumina)

tag: passages

value: liver cancer

tag: m6a antibody


title: PBMC total RNA-Healthy control 15

tag: disease state


title: PBMC total RNA-Healthy control 14


title: PBMC total RNA-Healthy control 13


title: PBMC total RNA-Healthy control 18


title: PBMC total RNA-Healthy control 12


title: PBMC total RNA-Healthy control 17


title: ShEE3


title: ScrCC10


title: ShEE5


title: PBMC total RNA-Healthy control 16


title: PBMC total RNA-Healthy control 8


title: PBMC total RNA-Healthy control 9


title: ScrCC9


title: PBMC total RNA-Healthy control 5


title: PBMC total RNA-Healthy control 10


title: PBMC total RNA-Healthy control 11


title: PBMC total RNA-Healthy control 6


title: PBMC total RNA-Healthy control 1


title: PBMC total RNA-Healthy control 7


title: ScrCC6


title: ScrCC5


title: CT14

city: London

first: Joerg

last: Albert

address: 332 Grays Inn Rd

department: Ear Institute

institute: University College London

data_processing:
Sequenced reads were mapped to the dm6 Drosophila melanogaster reference genome using Partek Flow software.
Read counts were produced using HTSeq from the bam files generated by Partek Flow.
Normalization of read counts and subsequent statistical analyses were conducted with DESeq2.
Genome_build: dm6
Supplementary_files_format_and_content: The processed_data.xlsx file includes the DESeq2-normalized counts for all samples (columns labeled ct01 to ct18), as well as the results of the statistical comparisons between them.

organism: Drosophila melanogaster

source_name: Second antennal segment

extract_protocol:
Flies were anesthetised on ice, their second antennal segments (which contain the flies' Johnston's organs) were dissected, collected in Lysis Buffer (containing 1% beta-mercaptoethanol, as provided in the Qiagen Rneasy Mini kit) and subsequently placed in storage at -80 degrees Celsius. Samples were removed from the freezer for RNA extractions: These were conducted according to the Qiagen RNeasy Mini kit protocol.
Sample libraries were prepared with a Nextera XT DNA Library Preparation kit (Illumina).

value: Canton-S

value: Second antennal segment

value: 25 days old

tag: Sex

value: female


title: CT15

tag: tissue

value: 50 days old

value: male


title: CT10

value: 10 days old


title: CT12


title: CT17


title: CT13


title: CT11


title: CT18


title: CT16


title: PBMC total RNA-Healthy control 2


title: PBMC total RNA-Healthy control 4


title: ST486_shMyc1_rep2

description:
raw data file: US45102948_253973110008_S01_GE2_1200_Jun14_1_2
mRNA and lncRNA expression analysis_ST486 cells_Myc low

source_name: ST486 cells, shMyc1, day 8 post-infection

value: shMyc1, day 8 post-infection

value: ST486 Burkitt lymphoma


title: ST486_shMyc1_rep1


title: ST486_shMyc2_rep1

description:
raw data file: US45102948_253973110008_S01_GE2_1200_Jun14_1_3
mRNA and lncRNA expression analysis_ST486 cells_Myc low

source_name: ST486 cells, shMyc2, day 8 post-infection

value: shMyc2, day 8 post-infection


title: PBMC total RNA-Healthy control 3


title: ST486_shControl_rep2

description:
raw data file: US45102948_253973110008_S01_GE2_1200_Jun14_1_1
mRNA and lncRNA expression analysis_ST486 cells_Myc high

source_name: ST486 cells, shControl, day 8 post-infection

value: shControl, day 8 post-infection


title: ST486_shControl_rep1


title: ScrCC2


title: CT08

value: 5 days old


title: CT09


title: DL193 plate4

city: Cambridge

first: Luyi

address: 415 main st Cambridge

institute: Broad institute

description:
RPI-46_S4
index sorted CTV+ donor-derived cells from recipient mouse bone marrow, FACS value in DL193 sample info.xlsx

data_processing:
gene counting matrix generated using scPipe 1.3.0
reads were aligned using Rsubread 1.29.6
Genome_build: ENSEMBL Homo_sapiens.GRCh38.88
Supplementary_files_format_and_content: gene counting matrix, rows repsent genes and each column is a well

source_name: mouse BM cells

growth_protocol: All mice were bred and maintained under specific pathogen-free conditions, and protocols were approved by the WEHI animal ethics committee (AEC2018.015, AEC2018.006, AEC2014.031). CD45.2 (C57BL/6) and CD45.1 (C57BL/6 Pep3b) male mice aged between 8-16 weeks were used.

extract_protocol:
marrow cells from recipient mice were harvested, made into a single cell suspension, incubated with red cell removal buffer (NH4Cl), and stained with antibodies against cKit, Sca1, Flt3, CD150, CD16/32, CD34, CD11c, CD45.1 and CD45.2 in the first experiment (LC27 & 28), with additional antibodies against CD48, CD11b and  IL7Ra in the second experiment (RPI39, 41, 44 & 46). Viable CTV+ cells were index sorted into wells of 384-well plates containing pre-aliquoted Cel-Seq2 reagents using a BD Aria cell sorter..
For CEL-seq2, Single cells were flow sorted into chilled 384-well PCR plates containing 1.2ul of primer/ERCC mix using a BD FACSAria III flow cytometer. Sorted plates were sealed and immediately frozen upside down at -80C. Then these plates, together with the mRNA mixture plates, were taken from -80C and processed using an adapted Cel-Seq2 protocol with the following variations. We pooled the samples after the first strand synthesis and the second strand synthesis was performed using NEBNext Second Strand Synthesis module. NucleoMag NGS Clean-up and Size select magnetic beads were used for all DNA purification and size selection steps.

treatment_protocol: Bone marrow cells from donor CD45.2 mice were isolated and labelled with Cell Trace Violet (CTV). HSPCs (CD11b-cKit+Sca1+) were sorted and transplanted intravenously into non-irradiated CD45.1 recipient mice. Mice then received either PBS or Flt3L treatment subcutaneously for 3 days. On day 4, recipient BM were isolated.

tag: cell type

value: mouse BM cells

tag: cellular barcode

value: 8bp as in cell_barcode.csv

tag: umi position

value: 6bp after the cell barcode

tag: barcode position

value: R1 first eight base


title: ScrCC1

value: MPOA-derived brain tissues

value: Adolescence

value: SAS Sprague-Dawley


title: DL193 plate3

description:
RPI-44_S3
index sorted CTV+ donor-derived cells from recipient mouse bone marrow, FACS value in DL193 sample info.xlsx


title: CT06

value: Canton-S

value: Second antennal segment

tag: age


title: CT07

value: female


title: DL193 plate2

description:
RPI-41_S2
index sorted CTV+ donor-derived cells from recipient mouse bone marrow, FACS value in DL193 sample info.xlsx


title: CT05

value: male


title: CT01

value: 1 day old


title: CT02


title: CT04


title: DL162 plate2

description:
LC28-SC-pool_S2
index sorted CTV+ donor-derived cells from recipient mouse bone marrow, FACS value in DL162 sample info.xlsx


title: CT03


title: DL193 plate1

description:
RPI-39_S1
index sorted CTV+ donor-derived cells from recipient mouse bone marrow, FACS value in DL193 sample info.xlsx


title: W-6-3 [BiSulfite-seq]

description: Generation 6 WT control

data_processing:
Illumina for basecalling
Raw sequencing reads were quality controlled with FastQC (version 0.11.5), trimmed with TrimGalore! (version 0.4.1) and Cutadapt (version 1.15).
aligned to the TAIR10 reference genome using Bismark (version 0.19.0)33 along with bowtie2 (version 2.3.3.1).
Methylated Cs (COV files) were acquired from Bismark methylation extractor with default parameters
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited file, 1-based genomic coords with <chromosome>  <position>  <strand>  <count methylated>  <count unmethylated>  <C-context> <trinucleotide context> fields

extract_protocol:
genomic DNA extraction using DNeasy Plant kit (Qiagen, Germany).
Genomic DNA Sonicated to 100-300 bp fragments and purified with MiniElute PCR Purification Kit (Qiagen, Germany), incubated at 20 ℃ after add End Repair Mix. Then purified and added a single ‘A’ nucleotide to the 3’ ends of the blunt fragments, purified again and add Methylated Adapter to the 5’ and 3’ ends of each fragment. Then fragments with 300bp-400bp size-range were purified with QIAquick Gel Extraction kit (Qiagen, Germany) and subjected to bisulfite treatment by using Methylation-Gold kit (ZYMO). Followed with PCR and gel purification (350bp-400bp range fragments were selected). Qualified libraries sequenced pair end on the HiSeq X-ten system.

treatment_protocol: Five memory plants, four non-memory plants, and four Col-0 wild-type plants were sequenced were used. Leaves at bolting were flash freezed in liquid nitrogen.  Tissues were ground by motor and pestle in liquid nitrogen.

tag: replicate type

value: biological rep 3

value: rosette leaves

tag: sample type

value: Generation 6 WT control


title: W-6-4 [BiSulfite-seq]

description: Generation 6 WT control

value: biological rep 4


title: W-6-5 [BiSulfite-seq]

description: Generation 6 WT control

value: biological rep 5


title: DL162 plate1

description:
LC27-SC-pool_S1
index sorted CTV+ donor-derived cells from recipient mouse bone marrow, FACS value in DL162 sample info.xlsx

value: mouse BM cells


title: W-6-2 [BiSulfite-seq]

description: Generation 6 WT control

value: biological rep 2


title: W-6-1 [BiSulfite-seq]

description: Generation 6 WT control

value: biological rep 1


title: W-5-4 [BiSulfite-seq]

description: Generation 5 WT control

value: Generation 5 WT control


title: Bone next to PMMA spacer PMMA 3b

description:
Sample_117523
Bone next to PMMA spacer PMMA

source_name: Bone next to PMMA spacer rat 2

value: Sprague-Dawley

value: Bone next to PMMA spacer PMMA


title: wild type replicate 4 of P50

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

description:
control group postnatal day (P) 50
P50-WT5_S16

data_processing:
RNA-seq reads were preprocessed by trimming the adaptor sequences, filtering low-quality reads (Phred Score <=20 [Phred]) and eliminating short reads (length <= 20 bps) using software package FASTX-toolkit [http://hannonlab.cshl.edu/fastx_toolkit/].
STAR (v2.5.3a) was used for alignment of the reads to the reference genome and to generate gene-level read counts.
R package DESeq2 was used for data normalization and differentially expressed gene identification for each pair-wise comparison
Genome_build: Mus musculus reference genome version GRCm38.p5
Supplementary_files_format_and_content: In excel file format, including Raw read counts data; Normalized read counts data; Alignment summary; DEGs

source_name: Cortical tissue

growth_protocol: Mice cortical ECs (cECs) were isolated by incubation with CD31-coated magnetic microbeads (130-097-418, Miltenyi Biotec) and placed in the magnetic MACS separator for positive selection. Then cECs were cultured in an endothelial cell culture medium (MV2, PromoCell) replaced 24 hrs post-seeding and every 48 hrs until appropriate level of confluence is reached (30-40% for ICC; 90-100% for matrigel experiments). ECs were isolated as above, but with additional steps to deplete myelin (Myelin removal beads II, Miltenyi Biotec) and CD45-positive cells (CD45 microbeads, 130-052-  301, Miltenyi Biotec) to obtain a pure CD31-positive cell suspension. Cell suspensions from two animals were pooled in one biological replicate.

extract_protocol:
RNA was acutely extracted using this suspension (E.Z.N.A. HP Total RNA kit, OMEGA bio-tek), with additional DNase step (E1091, OMEGA bio-tek) following the manufacturer’s protocol. Total cEC RNA was extracted as for RNA sequencing. RNA was converted to cDNA  using the High-Capacity cDNA Reverse Transcription kit (Life Technologies) with 200-500 ng  starting material per reaction. qPCR was performed using an ABI Prism 7000 Sequence Detection  System with SYBR Advantage qPCR Premix (Cedarlane). Amplicons were separated by agarose  gel (1%) electrophoresis. Primers used were: 5′-CAACGCTACCACGAGGACATT-3′ (forward)  and 5′-CTCCTGCAAAGAAAAGCTCTGG-3′ (reverse) for eNOS; 5'-  CTGCCAGTCCGAAAATGGAAC-3' (forward) and 5'-CTTCATCCACCGGGGCTATC-3'  (reverse) for CD31; 5'-CTCATGTCTGAACTCAAGATCC-3' (forward) and 5'-  CCAGAATCCTCTTCCATGCTCA-3' (reverse) for VEGFR2; 5'-  GGCAAATTCAACGGCACAGT-3' (forward) and 5'-AGATGGTGATGGGCTTCCC-3'  (reverse) for GAPDH. A no reverse transcriptase control (NRT) was used by carrying out the  reverse transcription step of the qRT-PCR experiment in the absence of reverse transcriptase in  order to assess the amount of DNA contamination present in an RNA preparation.
RNA-Seq Libraries were generated using the TruSeq strand mRNA kit (Illumina). The RNA-Seq libraries were quantified by Qbit and qPCR according to the Illumina Sequencing Library qPCR Quantification Guide and the quality of the libraries was evaluated on Agilent Bioanalyzer 2100 using the Agilent DNA-100 chip. The RNA-Seq library sequencing was performed using Illumina Next-Seq500.

treatment_protocol: Males 16p11.2df/+ (Jackson laboratory, stock #013128; mixed B6/129 background) were crossed with WT females of the same background (Jackson laboratory, stock #101043) to obtain hemizygous 16p11.2df/+ offspring and WT littermates. Conditional Cdh5- Cretg/+;16p11.2flox/+ mutants (i.e. ‘16p11.2DEC’; mixed B6/129 background) and littermate controls were obtained from breeding between Cdh5-Cretg/+ males (Jackson laboratory, stock #006137, B6 background) and 16p11.2flox/+ females (Jackson laboratory, stock #025330; 129 background). As recommended by Jackson Laboratory to improve 16p11.2df/+ pup survival, breeding cages (both constitutive and conditional mutants) were supplemented with breeding chow (#2019, Envigo Teklad) and DietGel (#76A, ClearH2O) up to weaning age. To assess astrocyte coverage/number in 16p11.2 hemizygous mice, 16p11.2df/+ males were crossed with Aldh1l1-eGFP (BAC) females (Jackson laboratory, stock #026033; B6 background).

value: Cortical endothelial cells

value: control group

value: postnatal day (P) 50


title: wild type replicate 3 of P50

description:
control group postnatal day (P) 50
P50-WT4_S15


title: wild type replicate 2 of P50

description:
control group postnatal day (P) 50
P50-WT3_S14


title: W-5-3 [BiSulfite-seq]

description: Generation 5 WT control


title: wild type replicate 1 of P50

description:
control group postnatal day (P) 50
P50-WT2_S13


title: W-5-2 [BiSulfite-seq]

description: Generation 5 WT control


title: W-5-5 [BiSulfite-seq]

description: Generation 5 WT control


title: W-5-1 [BiSulfite-seq]

description: Generation 5 WT control


title: W-4-5 [BiSulfite-seq]

description: Generation 4 WT control

value: Generation 4 WT control


title: MAF 8

city: Bethesda

first: Sivaranjani

last: Namasivayam

state: Maryland

address: 33 North Drive

institute: National Institutes of Health

description: Gene expression data from blood of a patient with M. africanum infection

hyb_protocol: Microarray hybridization was performed using human Affymetrix Clariom D (Applied Biosystem Inc., Foster Coty, USA).

scan_protocol: Per Affymetrix protocol.

data_processing: Microarray gene expression data was analyzed using the Partek Genomics Suite 7.0.1 (Partek Ink. St. Louis, MO, USA). Raw data were normalized using the robust multi-array average (RMA) approach.

source_name: Blood from a patient with M. africanum infection

label_protocol: Per Affymetrix protocol.

extract_protocol: RNA was isolated from peripheral blood collected in PAXgene blood RNA tubes (PreAnalytiX, Hombrechtikon, Switzerland) using a QIAamp RNA Blood extraction Kit (QIAGEN Inc., Germantown, USA).

value: Blood

tag: disease status

value: M. africanum infection


title: MAF 5


title: 16p11.2 df/+ mutants replicate 4 of P50

description:
autism spectrum disorders model postnatal day (P) 50
P50-Mut4_S6

value: autism spectrum disorders model


title: W-4-4 [BiSulfite-seq]

description: Generation 4 WT control

value: rosette leaves


title: MAF 7


title: MAF 2


title: MAF 6


title: wild type replicate 4 of P14

description:
control group postnatal day (P) 14
P14-WT4_S8

value: postnatal day (P) 14


title: MAF 9


title: 16p11.2 df/+ mutants replicate 1 of P50

description:
autism spectrum disorders model postnatal day (P) 50
P50-Mut1_S2


title: 16p11.2 df/+ mutants replicate 3 of P50

description:
autism spectrum disorders model postnatal day (P) 50
P50-Mut3_S5


title: 16p11.2 df/+ mutants replicate 2 of P50

description:
autism spectrum disorders model postnatal day (P) 50
P50-Mut2_S4


title: MAF 4


title: MTB 7

description: Gene expression data from blood of a patient with M. tuberculosis infection

source_name: Blood from a patient with M. tuberculosis infection

value: M. tuberculosis infection


title: W-4-3 [BiSulfite-seq]

description: Generation 4 WT control

value: biological rep 3


title: MAF 3


title: MTB 6


title: MAF 10


title: MAF 1


title: MTB 8


title: MTB 10


title: MTB 4


title: MTB 5


title: wild type replicate 3 of P14

description:
control group postnatal day (P) 14
P14-WT3_S7


title: W-4-2 [BiSulfite-seq]

description: Generation 4 WT control


title: MTB 9


title: MTB 1


title: W-3-5 [BiSulfite-seq]

description: Generation 3 WT control

value: biological rep 5

value: Generation 3 WT control


title: wild type replicate 2 of P14

description:
control group postnatal day (P) 14
P14-WT2_S3


title: Healthy 10

description: Gene expression data from blood of an healthy subject

source_name: Blood from a healthy subject

value: Healthy


title: W-3-3 [BiSulfite-seq]

description: Generation 3 WT control


title: 16p11.2 df/+ mutants replicate 2 of P14

description:
autism spectrum disorders model postnatal day (P) 14
P14-Mut3_S10


title: 16p11.2 df/+ mutants replicate 3 of P14

description:
autism spectrum disorders model postnatal day (P) 14
P14-Mut4_S11


title: 16p11.2 df/+ mutants replicate 1 of P14

description:
Autism spectrum disorders model postnatal day (P) 14
P14-Mut2_S9


title: muscle_WT_2

first: Wen

last: Luo

address: Wushan

institute: South China Agricultural University

data_processing:
BGI SOAPnuke software used for trimming and filtering.
Sequenced reads were mapped to gga5 whole genome using HISAT2 v2.0.4 with parameters --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Gene expression analysis step 1: sequenced reads were then mapped to GRCm38 whole genome using Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression analysis step 2: Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using RSEM v1.2.12.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: wild type mice gastrocnemius

extract_protocol:
Total RNA of the proliferating myoblasts or differentiated myotubes were harvested using Trizol reagent according to the manufacturer’s direction.
RNA libraries were prepared for sequencing using standard BGI protocols

tag: strain

value: skeletal muscle

value: 9 week

tag: genotype

value: wild type


title: muscle_WT_1


title: Healthy 9


title: muscle_KO_3

source_name: tmem184-/- mice gastrocnemius


title: muscle_WT_3


title: Healthy 8


title: W-3-1 [BiSulfite-seq]

description: Generation 3 WT control

value: biological rep 1


title: muscle_KO_2

source_name: tmem183-/- mice gastrocnemius


title: MTB 2


title: muscle_KO_1

source_name: tmem182-/- mice gastrocnemius


title: Healthy 6


title: 6h_TMG_Rep3b

city: Boston

first: Zhi-Wei

last: Tan

state: Massachusetts

address: Dept. of Microbiology, Harvard Medical School HIM, Room 1018D, 4 Blackfan Circle Boston, MA 02115

institute: Harvard University

data_processing:
Basecalls were performed by sequencing facility, biopolymers in Harvard
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg19 whole genome using Star Align with the following configurations: --runMode alignReads \  --genomeDir hg19_genome \  --readFilesIn files_R1, files_R2 \  --twopassMode Basic \  --sjdbOverhang 74 \  --outFileNamePrefix $HOME/RNA-seq/6h_T_c \  --outSAMtype BAM SortedByCoordinate \  --outFilterMultimapNmax 20 \  --outFilterMismatchNmax 999 \  --outFilterMismatchNoverLmax 0.04 \  --alignIntronMin 70 \  --alignIntronMax 500000 \  --alignMatesGapMax 500000 \  --alignSJoverhangMin 8 \  --alignSJDBoverhangMin 1 \  --outSAMstrandField intronMotif \  --outFilterType BySJout
After mapping, junction spanning reads were input into custom software to generate exon coordinate and classification information (see Boutz et al., Genes Dev). Mapped reads generated from Star Aligner were assigned to the generated gff and counted, and processed by DEXSeq to provide exon counts. DIfferential expression at the non-overlapping exon part level comparing DMSO/OSMI2 or DMSO/TMG was performed using standard DEXseq differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including exon parts genomic coordinates and differential expression analysis by DEXseq

source_name: Human embryonic kidney

growth_protocol: HEK293T cells grown on 6 well plates to around 80% confluence. Media changed fresh for 3 h befor treatment. Treated with DMSO or compounds for indicated time point.

extract_protocol:
HEK293T cells were scrapped, flash frozen on dry ice, and RNA was harvested using Trizol reagent or Rneasy plus kit.. Illumina TruSeq Stranded mRNA Library Preparation Kit Set A (Cat#RS-122-2101) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard illumina methods

treatment_protocol: Treated with 10 uM OSMI-2 (OGT inhibitor) or 5 uM TMG (OGA/MGEA5 inhibitor)

tag: cell line

tag: treatment

value: OGA/MGEA5 inhibitor


title: ST486_shMyc2_rep2

city: Groningen

first: Melanie

last: Winkle

address: Hanzeplein 1

institute: UMC Groningen

description:
raw data file: US45102948_253973110008_S01_GE2_1200_Jun14_1_3
mRNA and lncRNA expression analysis_ST486 cells_Myc low

data_processing: GeneSpring GX 13.1.1 software (Agilent Technologies); quantile normalization without base line transformation; analyzed as single color experiment

extract_protocol: The miRNeasy mini kit (Quiagen) was applied according to manufacturers instructions and including on column DNAse digestion

value: shMyc2, day 8 post-infection

value: ST486 Burkitt lymphoma


title: Healthy 1

value: Blood


title: W-3-2 [BiSulfite-seq]

description: Generation 3 WT control

value: biological rep 2


title: W-2-5 [BiSulfite-seq]

description: Generation 2 WT control

value: Generation 2 WT control


title: BX795GFP1

city: Fuzhou

first: Yajuan

last: Fu

state: Fujian

address: Fujian Normal University,Qishan Campus, No.1 Keji Road, Shangjie, Minhou

department: Biomedical Research Center of South China

institute: Fujian Normal University

data_processing:
Bowtie2 (version:2.2.5, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus_musculus reference genome (Mus musculus GRCm38.p5) using bowtie2
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) using RNA-seq by Expectation Maximization (RSEM) (version:1.2.12, default parameters).
For the identification of differentially expressed genes (DEGs), we used PossionDis, which is developed by BGI Genomics, implementing the passion distribution method
A false discovery rate (FDR) cutoff of 0.001 and a log-fold change (LogFC) threshold of 2 were implemented to filter the significantly different genes. The genes with logFC ≥ 2 and logFC ≤ -2 with FDR ≤ 0.001 between two treatment conditions were determined to be up-regulated and down-regulated genes. DEGs was used for GO enrichment analysis by culsterProfiler (R version: 3.4.4 , culsterProfiler version: 3.6.0)
Genome_build: Mus_musculus reference genome (Mus musculus GRCm38.p5)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: mouse fibroblast cells

extract_protocol:
L929 cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
cDNA library construction and sequencing were performed by BGI Genomics (BGI-SHENZHEN, China) using BGISEQ-500 platform

treatment_protocol: L929 cells were pretreated with DMSO or 0.5 uM BX795 for one hour, then transfected with pEGFP-N1 plasmid for 6 hours.

value: subcutaneous connective tissue; areolar and adipose

value: fibroblast

tag: agent


title: W-2-4 [BiSulfite-seq]

description: Generation 2 WT control

value: biological rep 4

value: rosette leaves


title: 6h_TMG_Rep1b


title: W-2-3 [BiSulfite-seq]

description: Generation 2 WT control

value: biological rep 3


title: Th1_KO2 (RNA-seq)

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

institute: Medical University of Vienna

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquistion on the sequencing instrument.
Basecalling was performed with the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing was performed with custom programs based on Picard tools (v2.18.11, http://broadinstitute.github.io/picard/).
The transcriptome analysis was performed using the Tuxedo suite. TopHat2 (v2.1.1, http://genomebiology.com/2013/14/4/R36/abstract) was supplied with reads passing vendor quality filtering (PF reads) and the Ensembl transcript set (Homo sapiens, e87, December 2016) as reference. Tophat2 spliced alignments were run independently for each replicate.
Cufflinks (v2.2.1, http://www.nature.com/nbt/journal/v31/n1/full/nbt.2450.html) was then used to assemble transcripts from spliced read alignments, again using the Ensembl e87 transcriptome as the reference, preventing de novo assembly of transcript models.
Transcriptome sets of all replicates for each sample group were combined with Cuffmerge.
Differential expression was assessed with Cuffdiff v2.2.1 (http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html).
The Bioconductor cummeRbund (http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html) pckage was used in combination with custom R scripts to perform quality assessment and further refine analysis results.
Genome_build: GRCm38 (UCSC mm10)
Supplementary_files_format_and_content: tab-separated value files of FPKM estimates obtained from Cufflinks, enriched with Ensembl transcrit annotation.

source_name: spleen, lymph nodes

extract_protocol:
Total RNA was prepared from 3x10^6 viable WT and NCOR1f/f,Cd4Cre in vitro-generated Th1 cells with QIAshredder, RNaeasy Mini Kit and RNase-Free DNase Set (Qiagen) according to manufacturer's protocol.
RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.

value: in vitro-generated Th1 cells

tag: culture time

value: 3 days

value: NCOR1f/f Cd4Cre


title: 6h_DMSO_Rep3b

value: DMSO


title: Th1_KO3 (RNA-seq)


title: W-2-2 [BiSulfite-seq]

description: Generation 2 WT control


title: BX7953


title: Th1_KO1 (RNA-seq)


title: BX7952


title: W-2-1 [BiSulfite-seq]

description: Generation 2 WT control


title: Th1_WT3 (RNA-seq)

value: wild-type


title: BX7951


title: BX795GFP3


title: MTB 3

value: M. tuberculosis infection


title: 6h_DMSO_Rep1b


title: 6h_DMSO_Rep2b


title: GFP3

value: GFP


title: M-6-4 [BiSulfite-seq]

description: Generation 6 memory line

value: Generation 6 memory line


title: M-6-3 [BiSulfite-seq]

description: Generation 6 memory line


title: 6h_TMG_Rep2b

value: OGA/MGEA5 inhibitor


title: 2h_TMG_Rep3b


title: 2h_TMG_Rep2b


title: Th1_WT1 (RNA-seq)


title: GFP2


title: M-6-1 [BiSulfite-seq]

description: Generation 6 memory line

value: biological rep 1


title: naive_CD4_KO2 (RNA-seq)

extract_protocol:
Total RNA was prepared from 3x10^6 viable FACS-purified WT and NCOR1f/f,Cd4Cre naive CD4+ T cells (CD25-CD44loCD62L+) with QIAshredder, RNaeasy Mini Kit and RNase-Free DNase Set (Qiagen) according to manufacturer's protocol.
RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.

value: naive CD4+ T cells


title: DMSO3


title: 2h_DMSO_Rep3b


title: naive_CD4_KO1 (RNA-seq)


title: 2h_TMG_Rep1b


title: Healthy 3

value: Blood

value: Healthy


title: M-6-2 [BiSulfite-seq]

description: Generation 6 memory line

value: biological rep 2


title: DMSO2

value: subcutaneous connective tissue; areolar and adipose

value: fibroblast


title: 2h_DMSO_Rep2b


title: M-5-3 [BiSulfite-seq]

description: Generation 5 memory line

value: biological rep 3

value: rosette leaves

value: Generation 5 memory line


title: DMSO1


title: Healthy 7


title: naive_CD4_WT3 (RNA-seq)


title: 2h_DMSO_Rep1b


title: naive_CD4_KO3 (RNA-seq)

value: NCOR1f/f Cd4Cre


title: naive_CD4_WT2 (RNA-seq)


title: M-5-2 [BiSulfite-seq]

description: Generation 5 memory line


title: naive_CD4_WT1 (RNA-seq)


title: 6h_OSMI2_Rep2a

value: OGT inhibitor


title: M-5-4 [BiSulfite-seq]

description: Generation 5 memory line

value: biological rep 4


title: input (ChIP-seq)

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquistion on the sequencing instrument.
Basecalling was performed with the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing was performed with custom programs based on Picard tools (v2.18.11, http://broadinstitute.github.io/picard/).
NGS reads passing vendor quality filtering were aligned with Bowtie2 (version 2.2.5) to teh UCSC mm10 flavour of the GRCm38 assembly.
The MACS2 program (2.1.2, http://www.ncbi.nlm.nih.gov/pubmed/18798982) was used for peak calling and signal track generation.
Bioconductor DiffBind (2.12.10, http://www.ncbi.nlm.nih.gov/pubmed/22217937) was used in a differntual binding analysis.
Genome_build: GRCm38 (UCSC mm10)
Supplementary_files_format_and_content: tab-separated value peak list obtained by MACS2.

source_name: mixed tissue

extract_protocol: WT and NCOR1f/f,Cd4Cre naive CD4+ T cell samples were prepared according to the ChIPmentation protocol (doi:10.1038/nmeth.3542, doi:10.1186/s12864-018-5299-0) by using a NCOR1 antibody from Cell Signaling Technology (#5948S).

value: wild-type

tag: chip antibody


title: M-5-1 [BiSulfite-seq]

description: Generation 5 memory line


title: M-4-5 [BiSulfite-seq]

description: Generation 4 memory line

value: biological rep 5

value: Generation 4 memory line


title: ScrCC7

source_name: Brain tissue

tag: brain region

value: MPOA-derived brain tissues

tag: developmental stage

value: Adolescence

value: SAS Sprague-Dawley

tag: aav type


title: naive_CD4_NCOR1_KO1 (ChIP-seq)

tag: cell type

value: naive CD4+ T cells

value: NCOR1 antibody (Cell Signaling Technology, #5948S)


title: 6h_DMSO_Rep3a

value: DMSO


title: M-4-4 [BiSulfite-seq]

description: Generation 4 memory line

tag: tissue


title: Chicken DM-2

city: Guangzhou

description: chicken primary myoblasts induced to differentiation for 4 days by culturing the cells in differentiation medium

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 gga5 whole genome using HISAT with default parameters.
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using HTSeq.
Genome_build: gga5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Gallus gallus

source_name: chicken embryo myoblast

growth_protocol: chicken primary myoblasts were growed in growth medium containing RPMI-1640, 15% FBS and 2% pen/srep

extract_protocol:
Total RNA of the proliferating myoblasts or differentiated myotubes were harvested using Trizol reagent according to the manufacturer’s direction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: chicken primary myoblasts were induced to differentiation by culturing in differentiation medium (RPMI-1640, 2% horse serum and 2% pen/strep)

value: chicken embryo skeletal muscle derived myotubes

value: differentiated myotube

tag: passages


title: Chicken DM-1


title: Chicken DM-3


title: 6h_DMSO_Rep2a


title: Chicken GM-3

description: chicken primary myoblasts cultured in growth medium

value: chicken embryo skeletal muscle derived myoblasts

value: proliferating myoblast


title: W-3-4 [BiSulfite-seq]

description: Generation 3 WT control

value: rosette leaves

value: Generation 3 WT control


title: 16p11.2 df/+ mutants replicate 4 of P14

description:
autism spectrum disorders model postnatal day (P) 14
P14-Mut5_S12

value: Cortical endothelial cells

tag: disease state

value: autism spectrum disorders model

tag: age

value: postnatal day (P) 14


title: 6h_OSMI2_Rep3a

value: OGT inhibitor


title: Chicken GM-2


title: M-4-3 [BiSulfite-seq]

description: Generation 4 memory line

tag: replicate type

value: biological rep 3

tag: sample type

value: Generation 4 memory line


title: naive_CD4_NCOR1_WT2 (ChIP-seq)

tag: strain

value: wild-type


title: Chicken GM-1


title: naive_CD4_NCOR1_KO2 (ChIP-seq)

tag: genotype

value: NCOR1f/f Cd4Cre


title: M-4-1 [BiSulfite-seq]

description: Generation 4 memory line

value: biological rep 1


title: Chicken PM-2

description: chicken primary myoblasts that have just completed serial plating

value: primary myoblast


title: 2h_OSMI2_Rep3a

tag: cell line


title: naive_CD4_NCOR1_WT1 (ChIP-seq)

value: naive CD4+ T cells

value: NCOR1 antibody (Cell Signaling Technology, #5948S)


title: 2h_OSMI2_Rep2a

tag: treatment


title: Leaf, S2D2

city: Cordoba

first: Victor

middle: Manuel

last: Guerrero-Sanchez

state: Spain

address: Medina Azahara

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Cordoba

data_processing:
Sequenced reads were trimmed for adaptor sequence
Ambigous nucleotides and low quality sequences (first 12 bp of each read) were removed using Cutadapt v1.9
The trimmed reads were mapped to the Quercus ilex transcriptome using RSEM
Genome_build: qilextranscriptomeV3a.fa
Supplementary_files_format_and_content: tab-delimited text files include the quantification values for each Sample

organism: Quercus ilex

source_name: Leaf

growth_protocol: Germinated acorns as previously reported in Simova-Stoilova et al. 2015

extract_protocol:
Leaves were taken from the biological replicates and total mRNA was extracted according to Echevarria-Zomeno et al. 2012
Illumina's TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Drought was imposed by water withholding for 25 days

value: 6 months

tag: stress

value: Drought (irrigation withdrawal)

tag: time

value: 25 days

value: Leaf


title: Chicken PM-3

value: chicken embryo skeletal muscle derived myoblasts


title: 2h_OSMI2_Rep1a


title: Chicken PM-1


title: M-5-5 [BiSulfite-seq]

description: Generation 5 memory line

value: biological rep 5

value: rosette leaves

value: Generation 5 memory line


title: Leaf, S2D1


title: Leaf, S2D3


title: M-4-2 [BiSulfite-seq]

description: Generation 4 memory line

value: biological rep 2


title: 2h_DMSO_Rep3a

value: DMSO


title: M-3-4 [BiSulfite-seq]

description: Generation 3 memory line

value: biological rep 4

value: Generation 3 memory line


title: M-3-3 [BiSulfite-seq]

description: Generation 3 memory line

value: biological rep 3


title: Leaf, S2C3

value: Control (well watered)


title: 2h_DMSO_Rep2a


title: M-3-5 [BiSulfite-seq]

description: Generation 3 memory line


title: Normal_CSF_03

first: Gang

last: Wang

address: 1023 Guangzhou Avenue North

department: Neurosurgery

institute: Nanfang Hospital of Southern Medical University

description: miRNA expression in cerebrospinal fluid with Normal patients

hyb_protocol: Samples were labeled and hybridized with Agilent's miRNA Complete Labeling and Hyb Kit (P/N 5190-0456).

scan_protocol: Chips were scanned with Agilent Scan Control Software. For 8x60k chips, AgilentG3_miRNA mode (of resolution 3 microns) was selected.

data_processing: Data from scanning was analyzed using Agilent Feature Extraction(AFE) Software (version 10.7.1.1).

source_name: cerebrospinal fluid

extract_protocol: With informed consent of each patient, 10ml cerebrospinal fluid was attained from lumbar puncture while following aseptic principles, and then quickly stored in a condition of -80°C. Then total RNA was extracted using miRNeasy Mini Kit (Qiagen, P/N 217004), after which quality check was performed with NanoDrop ND-2000 and Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, US).

value: cerebrospinal fluid

tag: disease

value: normal


title: Leaf, S2C2


title: M-3-2 [BiSulfite-seq]

description: Generation 3 memory line


title: 2h_DMSO_Rep1a


title: M-3-1 [BiSulfite-seq]

description: Generation 3 memory line

value: biological rep 1


title: Leaf, S2C1

value: 6 months


title: M-2-5 [BiSulfite-seq]

description: Generation 2 memory line

value: Generation 2 memory line


title: Leaf, S1D3

value: Drought (irrigation withdrawal)

value: 20 days


title: M-2-3 [BiSulfite-seq]

description: Generation 2 memory line


title: Leaf, S1D2

value: Leaf


title: Leaf, S1D1


title: Healthy 5

value: Blood

tag: disease status

value: Healthy


title: Normal_CSF_01

label_protocol: Samples were labeled and hybridized with Agilent's miRNA Complete Labeling and Hyb Kit (P/N 5190-0456).


title: MMD_CSF_02

description: miRNA expression in cerebrospinal fluid with moyamoya disease

value: moyamoya


title: M-2-1 [BiSulfite-seq]

description: Generation 2 memory line

value: rosette leaves


title: Leaf, S1C3


title: MMD_CSF_01


title: Normal_CSF_02


title: Leaf, S1C1