title: SR-A1 Knockout_rep1

city: Nanjing

first: jingjing

last: ben

address: Longmian road 101

institute: Nanjing Medical University

description: SR-A1 KO1

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: SR-A1  knockout, lung

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

tag: gender

value: SR-A1 Knockout

tag: protocol

value: LLC cells injected into tail vein

value: lung


title: WT input 2

status: Public on Jun 16 2019

type: SRA

city: Daejeon

first: Hogyu David

last: Seo

address: 291 Daehak-ro

country: South Korea

institute: KAIST

library_source: genomic

data_processing:
Prepared libraries were sequenced on a HiSeq2500 with single-end method (50-bp reads).
ChIP-seq reads were aligned to the S.pombe genome (ASM294v2) using NovoAlign (Novocraft technologies, Malaysia).
Significantly enriched peaks were identified using Homer and mapped reads were quantified using DeepTools and bwtool.
Genome_build: S. pombe EF2 genome assembly; ASM294v2
Supplementary_files_format_and_content: bigWig files of the processed raw files

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: cells

growth_protocol: Grow cells in  YES medium at 30°C

extract_protocol: ChIP-seq libraries for genome-wide sequencing were prepared using 10 ng of input DNA or 1 to 10 ng of eluted ChIP DNA using NEXTflex ChIP-Seq kit, Bioo Scientific (cat.5143).

tag: genotype

tag: genotype/variation

value: wild type


title: WT No-tag control Flag ChIP-seq

tag: antibody

value: FLAG M2 (F1804, Sigma)


title: SR-A1 Knockout_rep2

type: RNA

country: China

description: SR-A1 KO2

molecule: total RNA

organism: Mus musculus

tag: strain

value: female

tag: tissue


title: WT H3K9me2 ChIP-seq 1

value: anti-H3K9me2 (ab1220, Abcam)


title: WT input 1


title: WT H3K9me2 ChIP-seq 2


title: WT Epe1 ChIP-seq 1


title: wild-type_rep2

source_name: wild-type, lung

value: Wild-type


title: microRNA profile of HNT29

city: Guangzhou

first: Mei-Yin

last: Zhang

state: Guangdong

address: 651 Dongfeng East Road

department: State Key Laboratory of Oncology in South China

institute: Sun Yat-sen University Cancer Center

hyb_protocol: The labeled RNAs were hybridized to the array with a 1× hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc., Beijing, China).

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels, EXPression Analyzer and DisplayER (EXPANDER) version 4.1 was used.

organism: Homo sapiens

label_protocol: 2.5 μg of total RNA of nasopharyngeal carcinoma, head-neck tumours and normal controls whole blood was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight.

extract_protocol: Total RNA was extracted using RNA Purification Kit (Norgen Biotek, Thorold, Ontario, Canada).

tag: disease state

value: head-neck tumor

value: whole blood


title: microRNA profile of HNT28


title: microRNA profile of HNT30


title: microRNA profile of HNT26


title: microRNA profile of HNT23


title: microRNA profile of HNT24


title: microRNA profile of HNT19


title: clr4D H3K9me2 ChIP-seq 1

value: lacking Clr4


title: microRNA profile of HNT21


title: microRNA profile of HNT20


title: WT Epe1 ChIP-seq 2


title: microRNA profile of HNT22


title: wild-type_rep1


title: microRNA profile of HNT25


title: HeLa_shCtrl_2nd

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

library_source: transcriptomic

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue < =0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

growth_protocol: The human HeLa cell line was purchased from the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China. Cells were seeded into a petridish (100 mm) at a density of 1 × 105 cells/mL per well, and cultured at 37 ℃with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (Hyclone), penicillin (100 U/ml) and streptomycin (100 g/ml). ZFP36 overexpression plasmid transfection of HeLa cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Transfected cells were harvested after 48 h.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

treatment_protocol: shRNA against human KRT18 transfection of HeLa cells was performed using lipofectAMINE 2000

tag: cell line background

value: HeLa

value: control plasmid


title: microRNA profile of HNT17


title: HeLa_shCtrl_1st


title: microRNA profile of HNT16


title: microRNA profile of HNT27


title: microRNA profile of HNT15


title: microRNA profile of HNT18


title: microRNA profile of HNT11


title: microRNA profile of HNT12


title: microRNA profile of HNT14


title: HeLa_shKRT18_2nd

value: KRT18 knockdown


title: microRNA profile of HNT9


title: microRNA profile of HNT10


title: HeLa_shKRT18_1st


title: Col_0_NaCl3

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

data_processing:
Adaptors were removed and quality values above phred33 were used for analysis (cutadapt version 1.9).
Mapping and alignment was performed using TopHat version 2.1.0 using Bowtie2 (v2.2.6) (reference genome TAIR10), followed by gene counting performed by HTseq-count version 0.6.1.
Values above 10 were used for normalization and gene expression analysis (DESeq2 version 1.10.0).
Genome_build: TAIR10
Supplementary_files_format_and_content: raw expression values

organism: Arabidopsis thaliana

source_name: pre-germinated seedlings

growth_protocol: Cold stratified seeds of wild-type (Col-0) and an allele of camta6 mutant (camta6-5) was sown on 0.25 X MS, agar-solidified medium.

extract_protocol:
RNA was extracted using the ZR Plant RNA MiniPrep™ kit (Zymo Research, USA).
Illumina HiSeq 2500; Illumina TruSeq RNA Library Preparation Kit v2

treatment_protocol: medium was supplemented with 0 (control) or 200 mM NaCl for 16 hours.

value: seedlings

tag: treatment

value: 200 mM NaCl for 16 hrs


title: microRNA profile of HNT13


title: Col_0_NaCl2


title: Col_0_control3

value: control


title: Col_0_control2


title: Col_0_NaCl1


title: microRNA profile of HNT6


title: microRNA profile of HNT8


title: microRNA profile of HNT2


title: microRNA profile of HNT4


title: microRNA profile of NC30

value: normal control


title: microRNA profile of HNT7


title: camta6_5_NaCl1

value: camta6 mutant


title: microRNA profile of HNT1


title: microRNA profile of HNT3


title: camta6_5_control3


title: microRNA profile of HNT5


title: camta6_5_NaCl2


title: Col_0_control1


title: microRNA profile of NC29


title: microRNA profile of NC27


title: microRNA profile of NC26


title: camta6_5_control1


title: microRNA profile of NC28


title: microRNA profile of NC25


title: microRNA profile of NC24


title: microRNA profile of NC23


title: microRNA profile of NC22


title: camta6_5_NaCl3


title: U937 cell line DMSO treated rep3

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

country: USA

institute: Broad Institute

data_processing:
Illumina NextSeq500 at the at the Molecular Biology Core Facilities (Dana-Farber Cancer Institute, Boston, MA, USA).
Quality control tests for the mapped reads were performed using the FASTQC software (www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads were aligned to the GRCh37/hg19 human genes by using Bowtie2 (Tophat2 v2, Kim et al., 2013) with standard parameters. Quality control tests for the aligned reads and for the replicate consistency were performed by using the qualimap v2.2 (Garcia-Alcalde et al., 2012) and the SARTools (Hugo Varet, 2015) pipelines.
Gene level reads were computed using the Feature Counts method implemented in the Bioconductor v3.2 RSubread package (Liao et al., 2014) based on the RefSeq (GRCh37/hg19) GTF gene annotation file.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include genome-wide gene counts values for each sample.

source_name: U937 acute myeloid leukemia cell line

extract_protocol:
RNA was extracted from cells with the RNeasy Kit and on-column DNA digestion (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina 1.9 protocols
Strand-specific mRNA seq libraries were pooled and sequenced on a NextSeq500 instrument with single-end 75bp reads to a depth of 20-30 M reads/sample at the Molecular Biology Core Facilities (Dana-Farber Cancer Institute, Boston, MA, USA).

tag: group

value: DMSO (10 µM, 24h)

tag: cell line


title: U937 cell line BRD3731 treated rep1

value: BRD3731 treated


title: U937 cell line BRD3731 treated rep2


title: camta6_5_control2


title: microRNA profile of NC21


title: U937 cell line DMSO treated rep2


title: Metformin_patient_11_Mtb

city: London

first: Jackie

last: Cliff

address: Keppel Street

department: Immunology and Infection

country: United Kingdom

institute: London School of Hygiene & Tropical Medicine

data_processing:
Alignment: STAR version 2.5.1b
Quantification: HT-seq count version 0.6.1 (f=bam, r=name, s=rev, m=union, i=gene id)
Normalisation: DESeq2 version 1.12.4
Genome_build: Human_g1k_v37
Supplementary_files_format_and_content: read count for each ensembl gene id, un-normalised, un-filtered

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
PBMC were stored in RNAProtect and then total RNA was extracted using the RNeasy Mini Kit  (Qiagen).
TruSeq stranded mRNA library prep kit (Illumina) according to manufacturer's instructions.

treatment_protocol:
Metformin was administered to healthy volunteers, 1000mg twice per day
PBMC were cultured in RPMI in the presence or absence of 5ug Mycobacteium tuberculosis lysate

value: Healthy volunteer

tag: patient id

tag: stimulation

value: MtbLysate

value: metformin

value: Peripheral Blood Mononuclear Cells


title: U937 cell line DMSO treated rep1


title: microRNA profile of NC20


title: Metformin_patient_11_Unstim

value: unstimulated


title: microRNA profile of NC19

value: whole blood


title: Baseline_patient_11_Mtb


title: U937 cell line BRD3731 treated rep3


title: Baseline_patient_11_Unstim


title: Metformin_patient_10_Unstim


title: microRNA profile of NC16


title: microRNA profile of NC18


title: microRNA profile of NC17


title: microRNA profile of NC15


title: microRNA profile of NC14


title: Baseline_patient_10_Mtb


title: Metformin_patient_10_Mtb


title: microRNA profile of NC11


title: microRNA profile of NC9


title: microRNA profile of NC10


title: microRNA profile of NC13


title: Metformin_patient_9_Mtb


title: Baseline_patient_9_Mtb


title: Metformin_patient_9_Unstim


title: microRNA profile of NC8


title: microRNA profile of NC6


title: microRNA profile of NC7


title: Metformin_patient_8_Mtb


title: Metformin_patient_8_Unstim


title: Baseline_patient_8_Mtb


title: Baseline_patient_8_Unstim


title: microRNA profile of NC12


title: Metformin_patient_7_Mtb


title: microRNA profile of NC3


title: microRNA profile of NC5


title: Baseline_patient_7_Unstim


title: microRNA profile of NC2


title: Baseline_patient_7_Mtb


title: microRNA profile of NPC119

value: nasopharyngeal carcinoma


title: Metformin_patient_6_Unstim


title: microRNA profile of NC1


title: Baseline_patient_9_Unstim


title: Baseline_patient_6_Mtb


title: microRNA profile of NPC118


title: Baseline_patient_6_Unstim


title: microRNA profile of NPC115


title: microRNA profile of NPC116


title: microRNA profile of NPC117


title: Metformin_patient_6_Mtb


title: microRNA profile of NC4


title: Metformin_patient_5_Mtb


title: Baseline_patient_10_Unstim


title: Metformin_patient_7_Unstim


title: Baseline_patient_5_Mtb


title: microRNA profile of NPC114


title: Metformin_patient_4_Mtb


title: Baseline_patient_5_Unstim


title: microRNA profile of NPC113


title: Metformin_patient_4_Unstim


title: microRNA profile of NPC111


title: microRNA profile of NPC112


title: microRNA profile of NPC110


title: Metformin_patient_5_Unstim


title: Baseline_patient_4_Mtb


title: microRNA profile of NPC120


title: Metformin_patient_3_Mtb


title: microRNA profile of NPC106


title: microRNA profile of NPC108


title: microRNA profile of NPC109


title: microRNA profile of NPC107


title: Baseline_patient_3_Mtb


title: microRNA profile of NPC105


title: Baseline_patient_3_Unstim


title: microRNA profile of NPC102


title: microRNA profile of NPC104


title: microRNA profile of NPC103


title: Baseline_patient_2_Mtb


title: Metformin_patient_2_Unstim


title: Baseline_patient_2_Unstim


title: microRNA profile of NPC101


title: microRNA profile of NPC100


title: microRNA profile of NPC99


title: Metformin_patient_1_Unstim


title: Baseline_patient_4_Unstim


title: Baseline_patient_1_Mtb


title: Baseline_patient_1_Unstim


title: microRNA profile of NPC95


title: microRNA profile of NPC98


title: Metformin_patient_1_Mtb


title: microRNA profile of NPC97


title: microRNA profile of NPC94


title: Metformin_patient_11

data_processing:
Alignment: STAR, version 2.5.1b
Quantification: HT-seq count, version 0.6.1, f=bam, r=name, s=rev, m=union, i=gene id
Normalization: DESeq2, version 1.12.4
Genome_build: Human_g1k_v37
Supplementary_files_format_and_content: [txt] HT-Seq output, read count for each ensembl gene id, un-normalized, un-filtered

extract_protocol:
Blood samples were stored in PAXgene RNA tubes (Preanalytix) and then total RNA was extracted using the PAXgene blood miRNA kit (Qiagen).  Globin transcripts were depleted using GLOBINclear TM (Invitrogen).
TruSeq stranded mRNA library prep kit (Illumina) according to manufacturer's instructions.

treatment_protocol: Metformin was administered to healthy volunteers, 1000mg twice per day

value: healthy volunteer

value: Blood


title: Metformin_patient_3_Unstim


title: Baseline_patient_10


title: Baseline_patient_11


title: microRNA profile of NPC93


title: microRNA profile of NPC92


title: microRNA profile of NPC91


title: Metformin_patient_10


title: microRNA profile of NPC96


title: Metformin_patient_9


title: Baseline_patient_9


title: Metformin_patient_2_Mtb


title: Metformin_patient_8


title: microRNA profile of NPC90


title: microRNA profile of NPC87


title: microRNA profile of NPC88


title: microRNA profile of NPC89


title: Baseline_patient_7


title: Metformin_patient_7


title: Baseline_patient_8


title: Metformin_patient_6


title: microRNA profile of NPC86


title: Baseline_patient_6


title: Metformin_patient_5


title: Baseline_patient_5


title: Baseline_patient_4


title: microRNA profile of NPC83


title: microRNA profile of NPC85


title: Baseline_patient_3


title: microRNA profile of NPC84


title: microRNA profile of NPC78


title: microRNA profile of NPC80


title: microRNA profile of NPC79


title: microRNA profile of NPC81


title: microRNA profile of NPC82


title: Metformin_patient_4


title: Baseline_patient_2


title: Metformin_patient_2


title: Metformin_patient_1


title: microRNA profile of NPC77


title: Baseline_patient_1


title: microRNA profile of NPC74


title: microRNA profile of NPC76


title: microRNA profile of NPC73


title: microRNA profile of NPC72


title: cystic organoids

city: Leuven

first: Benoit

last: Cox

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
Raw reads were subjected to quality control
Sequence reads were pre-processed to remove adaptors and filter low-quality reads
high-quality reads were aligned to the mouse reference genome using Tophat
Statistic modeling was performed using the DESeq 1.32.0 package of Bioconductor
Genome_build: mm9
Supplementary_files_format_and_content: .xls, normalized counts generated by the DESeq package

source_name: cystic organoids derived from pituitary

growth_protocol: organoids were cultured with PitOM medium (see reference) and passaged every 10-14 days

extract_protocol:
RNA was isolated using the Rneasy micro kit (Qiagen)
RNA was amplified using the Smart-seq v4 (Takara) and library prep was performed using the NEBNext Ultra DNA Library prep kit (Illumina)

value: cystic organoids derived from pituitary

tag: passages

tag: medium

value: PitOM

tag: murine origin

value: GHCre/iDTR male 10-week old mouse


title: dense organoids

source_name: dense organoids derived from pituitary

value: dense organoids derived from pituitary

value: -/iDTR male 10-week old mouse


title: microRNA profile of NPC70


title: D458J1_resistant_H3_input

city: Boston

first: Pratiti

last: Bandopadhayay

state: Massachusetts

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
Raw data was aligned to the human reference genome Hg19 using Picard tools (http://broadinstitute.github.io/picard/). Raw sequencing data was mapped to the reference genome using bowtie2 version 2.2.1 with parameters -p 4 -k 1.
Peaks were called using MACS version 1.4.2 over an input control. Reads were extended 200-bp and normalized to read-density in units of reads per million mapped reads per bp (rpm/bp).
Genome_build: Hg19
Supplementary_files_format_and_content: BED peak files

extract_protocol: Sensitive and drug-tolerant D425 and D458 were passaged in DMSO or JQ1 (1 µM) for 24 hours. Sheared chromatin from each cell line was subjected to ChIP-sequencing as previously described62 , enriching for H3K27ac (Cell Signaling Technologies, 8173S)), H3K4me3 (Cell Signaling Technologies, 9751S), Histone H3 (Cell Signaling 4499S) and BRD4 (Bethyl, A301-985A100). ChIP libraries were indexed, pooled and sequenced on Illumina Hi-seq-2000 sequencers.

tag: cell type

value: D458 tolerant

tag: ip antibody


title: microRNA profile of NPC71


title: Metformin_patient_3


title: microRNA profile of NPC69


title: D458J2_resistant_H3_input


title: microRNA profile of NPC68


title: D458J1_resistant_H3K27ac


title: D458J1_resistant_H3K4me3


title: D458_sensitive_JQ1_H3K27ac

value: D458 sensitive


title: D458_sensitive_JQ1_H3K4me3


title: microRNA profile of NPC67


title: microRNA profile of NPC66


title: D458_sensitive_JQ1_H3_input


title: microRNA profile of NPC75


title: microRNA profile of NPC63


title: microRNA profile of NPC65


title: microRNA profile of NPC62


title: D458_sensitive_DMSO_H3K27ac

value: DMSO


title: microRNA profile of NPC61


title: D425J3_resistant_H3K27ac

value: D425 tolerant


title: D458_sensitive_DMSO_H3K4me3


title: D425J3_resistant_H3K4me3


title: D458_sensitive_DMSO_H3_input


title: microRNA profile of NPC59


title: microRNA profile of NPC64


title: microRNA profile of NPC58


title: microRNA profile of NPC60


title: microRNA profile of NPC57


title: microRNA profile of NPC56


title: D425J1_resistant_H3K27ac


title: D425J1_resistant_H3K4me3


title: microRNA profile of NPC54


title: microRNA profile of NPC55


title: D425_sensitive_JQ1_H3K27ac

value: D425 sensitive


title: microRNA profile of NPC53


title: D425_sensitive_JQ1_H3K4me3


title: D425J1_resistant_H3_input


title: D425J3_resistant_H3_input


title: microRNA profile of NPC52


title: D425_sensitive_JQ1_H3_input


title: D425_sensitive_DMSO_H3K4me3


title: microRNA profile of NPC50


title: D425_sensitive_DMSO_H3_input


title: microRNA profile of NPC49


title: PMLIV OE_spheres_biological rep 1

city: Heraklion

first: Joseph

last: Papamatheakis

state: Crete

address: Nikolaou Plastira 100

country: Greece

institute: Foundation for Research and Technology - Hellas

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C GeneChip® Human Transcriptome Arrays 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000.

data_processing: The data were analyzed using Transcriptome Analysis Console Software according to Affymetrix' instructions.

label: Biotin

source_name: MDA-MB-231 Breast cancer cells PMLIV OE_spheres

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2005-2009, Affymetrix).Briefly, double-stranded cDNA is synthesized from 10 μg total RNA isolated from MDA-MB-231 cells. An in vitro transcription (IVT) reaction is then done to produce biotin-labeled cRNA from the cDNA. The cRNA is fragmented before hybridization.

growth_protocol: The PMLIV inducible MDA-MB-231 clone was cultured in DMEM (Gibco), supplemented with 10% FBS and Gentamycin in 5% CO2 and at 37oC.MDA-MB-231 spheres were grown in DMEM-F12 1:1 (Gibco) medium containing B27 (1:50) (Gibco) , bFGF (20ng/ml)  (Gibco) , EGF (20ng/ml) (Gibco)  and 0.2% methylcellulose, in ultralow attachment plates.

extract_protocol: Total RNA was extracted from control and PMLIV OE MDA-MB-231 cells using TRIzol reagent according to the manufacturer’s protocol.

treatment_protocol: The tetPMLIV MDA-MB-231 cells cultured in monolayer or sphere conditions were treated with doxycycline (sigma) for 48h to induce PMLIV OE.

value: MDA-MB-231 cell line

tag: phenotype

value: spheres

tag: genotype

value: PMLIV OE


title: PASS4 in DNA, repl 3

city: Macquarie University

first: Anahit

last: Penesyan

state: NSW

address: E8A, Eastern road

country: Australia

institute: Mcquarie University

description: grown in DNA as a sole carbon source, replicte 3

data_processing:
Paired-end RNA sequence files were assessed for quality using FastQC software (Babraham Bioinformatics)
Sequenced reads were trimmed for adaptor sequence and the low-quality sequence, then mapped to the complete genome of PAO1 via EdgePro software
Differential expression calculated using DESeq software
De novo transcript assembly and differential gene expression analysis was performed for PASS4 strain using the Rockhopper 2.03 tool (54, 55) to supplement the data on PASS4 genes absent in PAO1 genome.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Pseudomonas aeruginosa

source_name: Whole cell

growth_protocol: P. aeruginosa strains PAO1 and PASS4 were simultaneously inoculated into 5 ml of LB liquid medium from the frozen stock and grown overnight. Overnight cultures were used to inoculate 15 ml of M9 minimal medium supplemented with either L-Asparagine (20mM) or DNA (1.5 mg/ml) (Salmon sperm DNA, Sigma), both in biological triplicates. Cultures were grown until mid-exponential phase (OD600 = 0.6).

extract_protocol:
RNA was extracted from these cultures using the miRNEasy RNA extraction kit (Qiagen) according to the manufacturer’s protocol. To remove any residual genomic DNA, the samples were treated with DNAse using the TurboDNAse kit (Invitrogen). To remo.ve highly abundant ribosomal RNA from the RNA extracts before sequencing, the samples were treated using RiboZero GN Magnetic rRNA depletion kit (Epicentre); the rRNA depleted samples were purified using RNeasy MinELute Cleanup kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type


title: PMLIV OE_spheres_biological rep 2


title: PMLIV OE_monolayer_biological rep 2

source_name: MDA-MB-231 Breast cancer cells PMLIV OE_monolayer

value: monolayer


title: control_spheres_biological rep 1

source_name: MDA-MB-231 Breast cancer cells control_spheres

value: control


title: PASS4 in DNA, repl 2

description: grown in DNA as a sole carbon source, replicate 2


title: PASS4 in DNA, repl 1

description: grown in DNA as a sole carbon source, replicate 1


title: Patient2-P

city: Shanghai

first: qinyi

last: zhou

address: Yishan Road 600

department: Department of Otolaryngology Head and Neck Surgery

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

description: all expression.txt

data_processing:
Sequence reads were mapped to the human genome (hg19) using TopHat v2.0.11 with the default options with a TopHat transcript index built from Ensembl_GRCh37.
Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file
Genome_build: hg19
Supplementary_files_format_and_content: count file

source_name: adjacent normal tissue sample

growth_protocol: Human papillary thyroid cancer tissue sample and adjacent normal tissue sample were collected from patients who underwent standard surgical procedures from January 2015 to December 2016 at the Department of Neck and Head Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University (P.R. China). All collected tissues were frozen in liquid nitrogen immediately after removal and then stored at -80℃.

extract_protocol:
total RNA of samples were 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

treatment_protocol: The tissue samples were divided into  papillary thyroid cance tissue  group and adjacent normal tissue group

value: adjacent normal tissue


title: control_monolayer_biological rep 1

source_name: MDA-MB-231 Breast cancer cells control_monolayer


title: control_spheres_biological rep 2


title: PASS4 in L-Asp, repl 3

description: grown in L-Asparagine as a sole carbon source, replicate 3


title: PMLIV OE_monolayer_biological rep 1


title: microRNA profile of NPC51

value: nasopharyngeal carcinoma

value: whole blood


title: D425_sensitive_DMSO_H3K27ac


title: control, biological replicate 1

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

country: Germany

institute: RWTH Aachen University

description: wt_280 Avg

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to the manufacturers instructions: hybridization 45°C for 18 hours at 60 rpm; Fluidics Station Program FS_450_0001

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

data_processing: Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with SST robust multiarray average algorithm (Affymetrix): SST-RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.

label: biotin

source_name: bone marrow, control

label_protocol: Fragmented, biotinylated cDNAs were prepared from 40 ng total RNA using  the NuGen Ovation Pico WTA System 2 Kit according to the manufacturers instructions.

growth_protocol: For the induction of Cre expression and subsequent recombination, poly(dIdC) was injected (i.p.)  three times on alternating days (d1, d3, d5). Mouse bone marrow cells were isolated at day 10.

extract_protocol: Total RNA was isolated from LSK cells with the RNeasy Micro Kit (Qiagen).

treatment_protocol: Bone marrow cells were FACS-sorted to obtain stem and progenitor cells (LSK cells: lin-, Sca1+, cKit+)

tag: genotype/variation

value: Ash2l exon4 fl/fl

value: bone marrow

value: LSK cells:lin-, Sca1+, cKit+


title: microRNA profile of NPC47


title: KO, biological replicate 3

description: ko_301 Avg

source_name: bone marrow, KO

value: Ash2l exon4 fl/fl, MxCre


title: KO, biological replicate 1

description: ko_280 Avg


title: control_monolayer_biological rep 2


title: Patient1-P

description: all expression.txt


title: PASS4 in L-Asp, repl 2

description: grown in L-Asparagine as a sole carbon source, replicate 2

tag: strain


title: KO, biological replicate 2

description: ko_300 Avg

tag: tissue


title: control, biological replicate 2

description: wt_301 Avg


title: control, biological replicate 3

description: wt_322 Avg


title: PAO1 in DNA, repl 3

description: grown in DNA as a sole carbon source, replicate 3


title: microRNA profile of NPC48

tag: disease state


title: Patient2-T

description: all expression.txt

source_name: human papillary thyroid cancer tissue

value: thyroid cancer tissue


title: microRNA profile of NPC45


title: Patient1-T

description: all expression.txt


title: PAO1 in DNA, repl 2


title: PAO1 in DNA, repl 1


title: PAO1 in L-Asp, repl 2


title: PAO1 in L-Asp, repl 3


title: U937 cell line BRD0320 treated rep3

data_processing:
Illumina HiSeq 2000 at the BioMicroCenter from the Massachusetts Institute of Technology (Cambridge, MA, USA).
Quality control tests for the mapped reads were performed using the FASTQC software (www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads were aligned to the GRCh37/hg19 human genes by using Bowtie2 (Tophat2 v2, Kim et al., 2013) with standard parameters. Quality control tests for the aligned reads and for the replicate consistency were performed by using the qualimap v2.2 (Garcia-Alcalde et al., 2012) and the SARTools (Hugo Varet, 2015) pipelines.
Gene level reads were computed using the Feature Counts method implemented in the Bioconductor v3.2 RSubread package (Liao et al., 2014) based on the RefSeq (GRCh37/hg19) GTF gene annotation file.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include genome-wide gene counts values for each sample.

extract_protocol:
RNA was extracted from cells with the RNeasy Kit and on-column DNA digestion (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina 1.9 protocols
Strand-specific mRNA seq libraries were pooled and sequenced on a HiSeq2000 instrument with single-end 40bp reads to a depth of 20-30 M reads/sample at the BioMicroCenter from the Massachusetts Institute of Technology (Cambridge, MA, USA).

value: BRD0320 treated


title: microRNA profile of NPC43


title: microRNA profile of NPC44


title: PAO1 in L-Asp, repl 1

description: grown in L-Asparagine as a sole carbon source, replicate 1


title: PASS4 in L-Asp, repl 1


title: U937 cell line BRD0320 treated rep2


title: U937 cell line BRD0320 treated rep1


title: U937 cell line BRD0705 treated rep3

value: BRD0705 treated


title: SYT7eDelH3AcK27FSK

city: La Jolla

first: Sam

last: Van de Velde

state: CA

address: 10010 North Torrey Pines Road

department: PBL

institute: Salk Institute

data_processing:
genome build: rn6
Reads were aligned to the mouse (mm10) or rat (rn5, rn6) genomes using bowtie2 or STAR
Binding peaks were called using Homer
Homer peak files were converted to BED files using Homer
Co-occupancy of binding sites was performed using Homer (mergePeak command -prefix option)
Super-enhancers were identified based on H3AcK27 occupancy with HOMER (findPeaks –style super –L 0, maximum distance to stitch peaks together: 12.5 kb).

organism: Rattus norvegicus

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
ChIP-seq libraries were constructed with NEBNext ChIPseq library kit (NEB) according to manufacturer's instructions.

value: insulinoma cells

value: CRISPR/CAS9 deletion of intronic SYT7 enhancer

tag: sample treatment

value: 1 hour 10 uM forskolin

tag: chip antibody

value: rabbit anti-H3AcK27 (Abcam ab4729)


title: microRNA profile of NPC42


title: SYT7eDelH3AcK27CON


title: SYT7eDelPolIIFSK

data_processing:
Reads were aligned to the mouse (mm10) or rat (rn5, rn6) genomes using bowtie2 or STAR
Binding peaks were called using Homer
Homer peak files were converted to BED files using Homer
Co-occupancy of binding sites was performed using Homer (mergePeak command -prefix option)
Super-enhancers were identified based on H3AcK27 occupancy with HOMER (findPeaks –style super –L 0, maximum distance to stitch peaks together: 12.5 kb).

source_name: RNA PolII_ChIPseq

value: rabbit anti-RPB1 (Cell Signaling 2629)


title: SYT7eDelPolIICON


title: WTPolIICON


title: U937 cell line BRD0705 treated rep2

tag: group

tag: treatment


title: microRNA profile of NPC41


title: WTH3AcK27FSK

data_processing:
genome build: rn5
Reads were aligned to the mouse (mm10) or rat (rn5, rn6) genomes using bowtie2 or STAR
Binding peaks were called using Homer
Homer peak files were converted to BED files using Homer
Co-occupancy of binding sites was performed using Homer (mergePeak command -prefix option)
Super-enhancers were identified based on H3AcK27 occupancy with HOMER (findPeaks –style super –L 0, maximum distance to stitch peaks together: 12.5 kb).

tag: cell line


title: WTH3AcK27CON


title: U937 cell line BRD0705 treated rep1


title: microRNA profile of NPC38


title: AR42JH3AcK27CONNeuroD1

value: pancreatic cell line


title: U937 cell line DMSO treated rep3

value: control

value: DMSO (10 µM, 24h)


title: AR42JH3AcK27FSKGFP

value: Ad-GFP/1 hour 10 uM forskolin


title: AR42JH3AcK27FSKNeuroD1

value: Ad-NeuroD1/1 hour 10 uM forskolin


title: AR42JH3AcK27CONGFP

value: Ad-GFP


title: U937 cell line DMSO treated rep2


title: U937 cell line DMSO treated rep1


title: AR42JCREBCONGFP

value: 244 anti-CREB rabbit serum


title: microRNA profile of NPC36

value: nasopharyngeal carcinoma

value: whole blood


title: microRNA profile of NPC40


title: microRNA profile of NPC35


title: WTPolIIFSK


title: PDX1FSKPDX1i

value: Ad-PDX1i/1 hour 10 uM forskolin

value: 5538 rabbit anti-PDX1 serum


title: microRNA profile of NPC39


title: HCAECs under OS rep3

city: Ann Arbor

first: Jifeng

state: Michigan

address: 2800 Plymouth Road

department: Internal medicine

institute: University of Michigan

data_processing:
RNA-seq fastq files were aligned to the human genome primary assembly (GRCh38) using the Subread package
Read counts on each gene were determined by featureCounts function in the Subread package using GeneCode human GTF file version 23 (http://www.gencodegenes.org/).
Differential expression analysis between endothelial cells under different types of shear stress were performed using the limma package with the voom transformation.
P values were adjusted by default Benjamini-Hochberg procedure.
We require at least 4 samples have normalized read counts of ≥ 1 rpm (one read count per million aligned reads) to include a gene in the differential expression analysis and other downstream analyses
Genome_build: GRCh38
Supplementary_files_format_and_content: Text files including Ensembl ID, gene symbol, gene type and raw read counts for each Sample

source_name: Coronary artery endothelial cells

growth_protocol: Human primary coronary artery endothelial cells (HCAECs) cultured in MesoEndo Cell Growth Medium, which contains 5% fetal bovine serum (FBS), 10 ng/mL human epidermal growth factor (hEGF), and 6 ng/mL basic fibroblast growth factor (bFGF). Cells were incubated at 37 °C in a standard cell culture incubator.

extract_protocol:
After exposed to LS, OS and ST for 24 hours, ECs were harvested by scraping, and RNA was isolated and purified using RNeasy mini kit and subjected to on-column RNase-free DNase treatment according to product protocol
Double-stranded cDNA was generated from 100 to 150 ng of total RNA using selective priming and prepared for the final library. Samples with RNA Integrity Numbers of 8 were prepared using the EnCore Complete RNA Seq Library System. Final libraries were checked for quality as well as quantity by the BioAnalyzer DNA 1000

treatment_protocol: HCAECs monolayers at confluence in 100-mm tissue culture dishes were exposed to arterial levels of unidirectional LS (15 dyn/cm2), bidirectional OS at 1 Hz cycle (±5 dyn/cm2) by rotating a Teflon cone (0.5° cone angle) with a stepping motor and a computer program, and static culture condition for 24 hours (n=4 for each conditions).

value: primary coronary artery ECs

value: oscillatory shear stress (OS)


title: HCAECs under OS rep4


title: H3AcK27FSKPDX1i

value: insulinoma cells


title: CREBFSKPDX1i


title: H3AcK27FSKUSi2

value: Ad-Usi (non-specific shRNA)/1 hour 10 uM forskolin


title: microRNA profile of NPC34

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels, EXPression Analyzer and DisplayER (EXPANDER) version 4.1 was used.


title: PDX1FSKUSi2

description:
Usi_plus_PDX1--4-GCCAAT_GCCAAT_L004
processed data file:
CREBNeuroD1cobound.bed
CREBNeuroD1PDX1cobound.bed
CREBnoNeuroD1PDX1.bed
CREBPDX1cobound.bed
NeuroD1noCREB.bed
PDX1NeuroD1noCREB.bed
PDX1noCREB.bed


title: microRNA profile of NPC33


title: CREBFSKUSi2


title: microRNA profile of NPC32


title: microRNA profile of NPC37


title: H3AcK27FSKNeuroD1i

value: Ad-NeuroD1i/1 hour 10 uM forskolin

value: rabbit anti-H3AcK27 (Abcam ab4729)


title: H3AcK27CONNeuroD1i


title: microRNA profile of NPC31


title: HCAECs under LS rep4

value: laminar shear stress (LS)


title: HCAECs under LS rep2


title: HCAECs under LS rep3


title: NeuroD1USi

value: Ad-Usi (non-specific shRNA)

value: Goat anti-NeuroD1 (Santa Cruz sc-1086X)


title: CREBFSKUSi


title: CREBFSKNeuroD1i


title: CREBCONNeuroD1i


title: HCAECs under ST rep2

value: static culture (ST)


title: microRNA profile of NPC28


title: H3AcK27FSKUSi


title: CREBCONUSi


title: HCAECs under LS rep1


title: microRNA profile of NPC30


title: HCAECs under ST rep4


title: HCAECs under OS rep2


title: microRNA profile of NPC24


title: microRNA profile of NPC25


title: HCAECs under ST rep1


title: HCAECs under OS rep1


title: hepaFSK_rep2 [RNA-seq]

description:
hepaFSKrep2
processed data file:
mousehepaRNAseqrepeat.xlsx

data_processing:
FASTQ files were aligned against the mouse mm10 or rat rn6 genome builds using Tophat v2.0.9 or STAR
For differential expression analysis, raw read count tables of two biological replicates from control and FSK treated material were generated using Homer(analyzeRepeats.pl with option –raw). Differential expression and adjusted p-values for significance calculated with Homer (getDiffExpression.pl using DESeq2)
Genome_build: mm10 or rn6

extract_protocol:
RNA was extracted from cultured cells or tissue with Trizol/chloroform and cleaned up with Rneasy mini columns (Qiagen)
Libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit

value: Wild-type black6 mice

value: cultured mouse primary hepatocytes

value: 2 hours 10 uM forskolin


title: microRNA profile of NPC22

value: nasopharyngeal carcinoma


title: microRNA profile of NPC23

value: whole blood


title: hepaCON_rep2 [RNA-seq]

description:
hepaCONrep2
processed data file:
mousehepaRNAseqrepeat.xlsx


title: NeuroD1NeuroD1i


title: hepaCON_rep1 [RNA-seq]

description:
hepaCONrep1
processed data file:
mousehepaRNAseqrepeat.xlsx


title: PolIIA485

description:
processed data file:
BRD4inducedRNA.bed, BRD4repressedRNA.bed
PolIIA485_S18

value: 3 hours 10 uM A485

value: rabbit anti-RPB1 (Cell Signaling 2629)


title: H3AcK27A485FSK

value: 3 hours 10 uM A485/1 hour 10 uM forskolin


title: H3AcK27CONUSi


title: PolIIA485FSK

description:
processed data file:
BRD4inducedRNA.bed, BRD4repressedRNA.bed
PolIIA485FSK_S20


title: hepaFSK_rep1 [RNA-seq]

description:
hepaFSKrep1
processed data file:
mousehepaRNAseqrepeat.xlsx


title: NeuroD1FSK

description:
NeuroD1FSK-2-1-CGATGT_CGATGT_L001
processed data file:
CREBNeuroD1cobound.bed
CREBNeuroD1PDX1cobound.bed
CREBnoNeuroD1PDX1.bed
CREBPDX1cobound.bed
NeuroD1noCREB.bed
PDX1NeuroD1noCREB.bed
PDX1noCREB.bed

value: 1 hour 10 uM forskolin


title: microRNA profile of NPC21


title: H3AcK27A485

value: insulinoma cells


title: microRNA profile of NPC20


title: isletCRTC2KO_FSK [RNA-seq]

description:
processed data file:
WTvCRTC2KOisletRNAseq.xlsx

value: CRTC2KO mice

tag: tissue/cell line

value: whole body

value: cultured mouse primary pancreatic islets


title: microRNA profile of NPC29


title: BRD4A485FSK

value: rabbit anti-BRD4 (Bethyl A301-985A)


title: microRNA profile of NPC18


title: isletCRTC2KO_CON [RNA-seq]


title: microRNA profile of NPC19


title: NeuroD1CON

description:
NeuroD1CON-1-1-ATCACG_ATCACG_L001
processed data file:
CREBNeuroD1cobound.bed
CREBNeuroD1PDX1cobound.bed
CREBnoNeuroD1PDX1.bed
CREBPDX1cobound.bed
NeuroD1noCREB.bed
PDX1NeuroD1noCREB.bed
PDX1noCREB.bed


title: microRNA profile of NPC17


title: isletFSK_rep2 [RNA-seq]

description:
isletWTFSKrep2
processed data file:
mouseisletRNAseqrepeats.xlsx


title: isletCON_rep2 [RNA-seq]

description:
isletWTCONrep2
processed data file:
mouseisletRNAseqrepeats.xlsx


title: BRD4FSKrep2


title: microRNA profile of NPC16


title: BRD4CONrep2


title: isletCON_rep1 [RNA-seq]

description:
isletWTCONrep1
processed data file:
mouseisletRNAseqrepeats.xlsx


title: PolIIJQ1CON

description:
processed data file:
BRD4inducedRNA.bed, BRD4repressedRNA.bed
PolIIJQ1_S33

value: 3 hours 1 uM JQ1


title: microRNA profile of NPC14


title: microRNA profile of NPC15


title: PolIIJQ1FSK

description:
processed data file:
BRD4inducedRNA.bed, BRD4repressedRNA.bed
PolIIJQ1FSK_S34

value: 3 hours 1 uM JQ1/1 hour 10 uM forskolin


title: microRNA profile of NPC12


title: BRD4A485


title: microRNA profile of NPC27


title: H3AcK27JQ1FSK

value: rabbit anti-H3AcK27 (Abcam ab4729)


title: PolIICON

description:
processed data file:
BRD4inducedRNA.bed, BRD4repressedRNA.bed
PolIICON_S17


title: Young oocytes (small non-coding RNA)

city: Callaghan

first: Bettina

middle: P

last: Mihalas

address: Level 4 Life Science Building, University Drive

department: Life Sciences

institute: University of Newcastle

description: oocytes

data_processing:
Raw sequence reads obtained from AGRF were processed through CutAdapt (https://cutadapt.readthedocs.io/) [56] and FastQC Babraham Bioinformatics, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to identify and remove adapter sequences, possible contaminates, and poor-quality bases
The remaining reads were scanned and trimmed once a base with a Phred quality score of <20 found
Sequenced reads were then mapped against the Mus musculus reference genome 9 (NCBI37/mm9) (June 2007, NCBI) and the RNAcentral sequence database (August 2017, RNAcentral) (https://rnacentral.org/) using Bowtie and Bowtie 2
Mapped reads were then processed using two personalized perl algorithms. Firstly, sequences were separated into RNA type by querying the RNAcentral database to retrieve the relevant information using the individual accession numbers that each mapped read aligned to. The second algorithm calculated and compiled the number of each unique sncRNA molecule identified in both sample groups.
To assess differential expression of sncRNAs in young and aged oocytes, combined data for both sample groups was imported into R Statistical Software (http://www.R-project.org/) and analyzed using the edgeR package
Reads were normalized by reads per kilobase million (RPKM). A negative binomial exact test was used to determine the differential expression for each individual sncRNA. Results were adjusted for multiple testing by the Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR)
Genome_build: Mus musculus reference genome 9 (NCBI37/mm9) (June 2007, NCBI)
Supplementary_files_format_and_content: Excel files (xlsx). Accession numbers (Accession No) Read numbers (read No), log2 fold change (Log2 FC), and false discovery rate (FDR) of endo-siRNAs and miRNAs identified from RNA-Seq. Counts of ≥ 10 reads were used as a threshold for positive  identification

source_name: GV oocyte

growth_protocol: GV oocytes from  mice between four to six weeks (young) and 14 to 16 months (aged) of age were utilized for the study of aged oocytes and were not hormonally stimulated

extract_protocol:
Small RNAs were purified using the miRNeasy Mini Kit (Cat. # 217004, Venlo, NV, Netherlands) according to the manufacturer’s instructions.
Samples were subjected to Illumina TrueSeq small RNA sample preparation protocol as per the manufacturers’ instructions (Illumina Inc., San Diego, CA, USA) at the Australian Genome Research Facility (AGRF, Brisbane, QLD, Australia). The samples were again analyzed after small RNA library construction to confirm the size of the products

value: C57Bl/6 x CBA F1

tag: Sex

value: female

tag: age

value: 4 to 6 weeks

value: oocytes


title: Aged oocytes (small non-coding RNA)

description: oocytes

value: 14 to 16 months


title: microRNA profile of NPC9

extract_protocol: Total RNA was extracted using RNA Purification Kit (Norgen Biotek, Thorold, Ontario, Canada).

value: nasopharyngeal carcinoma

value: whole blood


title: microRNA profile of NPC10


title: microRNA profile of NPC11


title: H3AcK27JQ1


title: microRNA profile of NPC13


title: isletFSK_rep1 [RNA-seq]

description:
isletWTFSKrep1
processed data file:
mouseisletRNAseqrepeats.xlsx

value: Wild-type black6 mice

value: 2 hours 10 uM forskolin


title: HCAECs under ST rep3

value: primary coronary artery ECs

tag: passages

value: static culture (ST)


title: BRD4JQ1FSK

tag: cell type

value: insulinoma cells


title: PolIIFSK

description:
processed data file:
BRD4inducedRNA.bed, BRD4repressedRNA.bed
PolIIFSK_S19

value: 1 hour 10 uM forskolin

value: rabbit anti-RPB1 (Cell Signaling 2629)


title: PorcineMatureAdipocyte_12hr_PolyIC_stimulation_rep1

city: Sendai

first: Haruki

last: Kitazawa

state: Miyagi

address: 468-1 Aramaki Aza Aoba, Aoba-ku,, Sendai

country: Japan

institute: Tohoku University

description: TLR3 ligation

hyb_protocol: The Gene Expression Hybridization kit (Agilent Technologies) was used for hybridization. In brief, 1650 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Porcine (V2) Gene Expression Microarray, 4x44K  (G2519F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Sus scrofa

source_name: Mature adipocyte, 12hr with PolyIC stimulation, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini spin column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The porcine intramuscular pre-adipocyte (PIP) cell lines (between the 26th and 35th passages) were maintained in Dulbecco’s modified Eagle medium (DMEM, Gibco, Paisley, Scotland, UK) supplemented with 10% fetal calf serum (FCS), 100 mg/ml penicillin, and 100 U/ml streptomycin as a growth medium. PIP cells were plated at density of 2.5×104/cm2 in 6-well cell culture plates (BD Falcon, Tokyo, Japan) and incubated at 37°C in a humidified atmosphere of 5% CO2. The 4-day post-confluent PIP cells were fed with differentiation medium for another 4 more days to yield the differentiated adipocyte. The differentiation medium was DMEM containing 10% FBS, 50 ng/ml insulin (swine, Sigma-Aldrich), 0.25 μM dexamethasone (Sigma-Aldrich), 2 mM octanoate (Wako, Osaka, Japan), 200 μM oleate (Ardorich, Milwaukee, WI, USA), 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol: Total RNA was isolated from the ligand-treated and control PMA cells using PureLink RNA Mini Kit (Life Technology Inc., USA) along with on-column DNase treatment. RNA integrity, quality and quantity were evaluated with microcapillary electrophoresis (2100 Bioanalyzer, Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 Nano kit.

treatment_protocol: The porcine mature adipocyte (PMA) cells were seeded at density of 2.5×104/cm2 in 6 well or 12 well plates (BD Falcon, Tokyo, Japan). The 4-day post-confluent PMA cells were stimulated either with Pam3csk4 @10 ng/ml or Poly(I:C) @ 0.1 µg/ml or LPS @ 0.1 µg/ml at 37° C with 5% CO2 for 12 hours.

tag: agent

value: PolyIC stimulation


title: PorcineMatureAdipocyte_12hr_LPS_stimulation_rep1

description: TLR4 ligation

source_name: Mature adipocyte, 12hr with LPS stimulation, replicate 1

value: LPS stimulation


title: microRNA profile of NPC46


title: PorcineMatureAdipocyte_12hr_Without_stimulation_rep1

description: Control

source_name: Mature adipocyte, 12hr without stimulation, replicate 1


title: KO-D5 3

first: Fasih

middle: Mubtasim

last: Ahsan

address: 185 Cambridge Street, CPZN 6500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description:
afb27cc5-fea4-47d8-b917-1c46c2c548a0
processed data file: GEO_rawcountmatrix.csv

data_processing:
Pre-Processing: Raw sequencing runs were filtered for low quality reads and adapter contamination using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), SeqTK (https://github.com/lh3/seqtk), and Cutadapt (Martin, 2011). rRNA contaminants carried over from the rRNA-depletion library preparation were filtered and removed using BBDuk from the BBTools (v. 38.08) suite (https://jgi.doe.gov/data-and-tools/bbtools/), comparing reads to rRNA species located in the SILVA rRNA database (Quast et al., 2013). Filtered reads were quantified and quasi-mapped to the Mus musculus Gencode M175 (GRCm38.p5) reference transcriptome using the alignment-free transcript level quantifier Salmon v.0.9.18.2 (Harrow et al., 2012; Mudge and Harrow, 2015; Patro et al., 2017). The resulting estimated transcript counts were summarized into normalized gene level transcripts per million (TPM) and estimated count matrices using R (v. 3.4.0) Bioconductor (v. 3.5) package tximport (v. 1.4) (Soneson et al., 2015).
Differential Gene Expression: The resulting sample gene count matrix was normalized and analyzed for differential gene expression using R (v. 3.4.0) Bioconductor (v. 3.5) package DESeq2 v1.16.0 (Huber et al., 2015; Love et al., 2014). Significance testing was performed using the Wald test, testing for the significance of deviance in a full design “Batch + Genotype-Stimulation”, modeling the genotype over time effect at both stimulated and unstimulated timepoints while accounting fo batch variance between stimulation replicates. Resulting P values were adjusted for multiple testing using the Benjamini-Hochberg procedure (Benjamini and Hochberg, 1995). Differentially expressed genes (DEGs) were filtered using an adjusted false discovery rate (FDR) P value < 0.05 and an absolute log2(Fold Change) > 0.5 in either the stimulated or unstimulated paired conditions.
Genome_build: Mus musculus GENCODE M17 (Nov 2017, GRCm38) - Ensembl 92
Supplementary_files_format_and_content: *_salmon_rRNAdepleted.quant.sf.txt: Salmon v0.9.1 quantification output files for each respective sample after quasi-mapping to the GENCODE M17 reference transcriptome. Columns are (in order): (1) Name of transcript from GENCODE M17 reference, (2) Length of the transcript (nt), (3) Effective length of the transcript, correcting for sequencing and GC fragment bias, (4) transcripts per million of the transcript (TPM), and (5) number of estimated reads mapping to each quantified transcript.
Supplementary_files_format_and_content: GEO_rawcountmatrix.csv: Comma-separated text file includes gene counts.

source_name: Day 5 CD40L + IL4 Stimulated KO B cells

growth_protocol: C57BL/6J, Prkaa1fl/fl, CD19-Cre, and Rosa26 lox-STOP-lox EYFP mice (JAX: 000664, 014141, 006785, and 006148) were housed in a pathogen-free animal facility at UCLA. All mouse studies were on mixed-sex mice between 6 and 16 weeks of age with approval from the UCLA Institutional Animal Research Committee. Genotypes for WT (Prkaa1+/+) and Ampk KO (Prkaa1-/-) mice were as follows: Prkaa1wt/wt or Prkaa1fl/fl, respectively, with CD19-Cre+/-, and Rosa26-YFP+/+ or +/- for experiments requiring YFP.

extract_protocol:
At least 10^7 WT and AMPK KO B cells were grown in biological triplicates and RNA purified immediately after isolation, or 24 hours after CD40L/IL-4 stimulation using the RNeasy Mini Kit (Qiagen) and RNase-free DNase (Qiagen) following the manufacturer’s protocols. All samples showed a A260/280 ratio > 1.99. Prior to library preparation, quality control of the RNA was performed using the Advanced Analytical Technologies Fragment Analyzer (Advanced Analytical, Inc.) and analyzed using PROSize 2.0.0.51 software. RNA Quality Numbers (RQNs) were computed per sample between 8.7 and 10, indicating intact total RNA per sample prior to library preparation.
Strand-specific ribosomal RNA (rRNA) depleted RNA-Seq libraries were prepared from 1 µg of total RNA using the KAPA Stranded RNA-Seq Kit with Ribo-Erase (Kapa Biosystems, Roche). Briefly, rRNA was depleted from total RNA samples, the remaining RNA was heat fragmented, and strand-specific cDNA was synthesized using a first strand random priming and second strand dUTP incorporation approach. Fragments were then A-tailed, adapters were ligated, and libraries were amplified using high-fidelity PCR. All libraries were prepared in technical duplicates per sample and resulting raw sequencing reads merged for downstream alignment and analysis. Libraries were paired-end sequenced at 2x150 bp on an Illumina NovaSeq 6000.

treatment_protocol: Red blood cell-lysed mouse spleen cells were enriched for B cells using CD43 negative magnetic selection (Miltenyi). Cells were grown in RPMI supplemented with 10% FBS and 50 μM β-mercaptoethanol. B cells were stimulated with 1 μg/ml αCD40 mAb (BD Pharmingen) and 25 ng/ml IL-4 (R&D Systems). At day 3, αCD40 was washed out and cells replated in media containing only IL-4 until day 5.

value: CD43- splenic B cells

value: CD40L + IL4 Stimulated

tag: timepoint

value: Day 5

tag: mouse age

tag: mouse sex

value: Pooled male and female

tag: rosa26 yfp genotype

value: wt/wt

tag: date of isolation

tag: date of rna isolation

tag: rna concentration

tag: dnase aliquot lot

tag: cd40l aliquot lot

tag: il-4 aliquot lot


title: WT-D5 3

description:
fa728143-238a-4ae2-894e-09b193b72bf7
processed data file: GEO_rawcountmatrix.csv

source_name: Day 5 CD40L + IL4 Stimulated WT B cells

tag: genotype

tag: treatment

value: 11 wks


title: BRD4JQ1

tag: cell line

tag: sample treatment

value: 3 hours 1 uM JQ1

tag: chip antibody

value: rabbit anti-BRD4 (Bethyl A301-985A)


title: D458_Resistant_JQ1_4

description: Gene expression data from D458 resistant cells treated with JQ1

hyb_protocol: standard Affymetrix protocol

scan_protocol: Affymetric scanner 3000 7G

data_processing: RMA normalizition, comparative marker selection through genepattern, gene set enrichment analysis using GSEA

source_name: D458 drug tolerant

label_protocol: standard Affymetrix protocol

growth_protocol: cells grown un ultralow attachment six well plates

extract_protocol: Qiagen Rneasy extraction kit

treatment_protocol: cells treated with DMSO or 1uM JQ1 for 24 hours

tag: cell type

value: D458 drug tolerant


title: microRNA profile of NPC6

tag: disease state

value: nasopharyngeal carcinoma

tag: tissue

value: whole blood


title: D458_Resistant_JQ1_5


title: PorcineMatureAdipocyte_12hr_Pam3csk4_stimulation_rep1

description: TLR2 ligation

source_name: Mature adipocyte, 12hr with Pam3csk4 stimulation, replicate 1

tag: agent

value: Pam3csk4 stimulation


title: BRD4CONrep1

value: insulinoma cells


title: KO-D4 3

description:
a5cf4494-c0e7-44e2-bc5b-67fea3e9384f
processed data file: GEO_rawcountmatrix.csv

source_name: Day 4 CD40L + IL4 Stimulated KO B cells

tag: timepoint

value: Day 4

tag: mouse age

tag: mouse sex


title: BRD4FSKrep1

value: 1 hour 10 uM forskolin


title: WT-D4 3

description:
6369c64f-acc0-42da-9e04-8274a0f25008
processed data file: GEO_rawcountmatrix.csv

source_name: Day 4 CD40L + IL4 Stimulated WT B cells

tag: rosa26 yfp genotype

tag: date of isolation

tag: date of rna isolation


title: D458_Resistant_JQ1_2


title: microRNA profile of NPC5


title: PolIIpS5FSK

description:
processed data file:
CREBtargetspromoterdrivenRNA.bed, CREBtargetgenesinsuperenhancersRNA.bed
PolIIpS5FSK--3-ACTTGA_ACTTGA_L003

source_name: RNA PolIIphosphoCTDS5_ChIPseq

value: rabbit anti-RNA PolII CTD pS5 (Abcam ab5131)


title: microRNA profile of NPC4


title: D458_Resistant_JQ1_1


title: KO-D3 3

description:
090b77e3-52b8-44bc-a2b9-5e5d28cec9f1
processed data file: GEO_rawcountmatrix.csv

source_name: Day 3 CD40L + IL4 Stimulated KO B cells

value: Day 3

tag: rna concentration

tag: dnase aliquot lot

tag: cd40l aliquot lot


title: microRNA profile of NPC7


title: microRNA profile of NPC8


title: PolIIpS5CON

description:
processed data file:
CREBtargetspromoterdrivenRNA.bed, CREBtargetgenesinsuperenhancersRNA.bed
PolIIpS5CON--3-CGATGT_CGATGT_L003


title: D458_Resistant_DMSO_5

description: Gene expression data from D458 resistant cells treated with DMSO


title: microRNA profile of NPC3


title: PolIIpS2FSK

description:
processed data file:
CREBtargetspromoterdrivenRNA.bed, CREBtargetgenesinsuperenhancersRNA.bed
PolIIpS2FSK--3-CAGATC_CAGATC_L003

source_name: RNA PolIIphosphoCTDS2_ChIPseq

value: rabbit anti-RNA PolII CTD pS2 (Abcam ab 5095)


title: WT-D3 3

description:
92e6537f-338c-43da-8a69-2098fc52fcd9
processed data file: GEO_rawcountmatrix.csv

source_name: Day 3 CD40L + IL4 Stimulated WT B cells

value: CD43- splenic B cells

tag: genotype

tag: treatment

value: CD40L + IL4 Stimulated

tag: il-4 aliquot lot


title: PolIIpS2CON

description:
processed data file:
CREBtargetspromoterdrivenRNA.bed, CREBtargetgenesinsuperenhancersRNA.bed
PolIIpS2CON--3-ATCACG_ATCACG_L003

tag: cell line

tag: chip antibody


title: D458_Resistant_DMSO_4

tag: cell type


title: KO-D2 3

description:
23de6ba0-fc6b-418d-8a6c-916be31e80b1
processed data file: GEO_rawcountmatrix.csv

source_name: Day 2 CD40L + IL4 Stimulated KO B cells

value: Day 2

value: Pooled male and female


title: D458_Resistant_JQ1_3


title: microRNA profile of NPC1

tag: disease state

tag: tissue


title: WT-D2 3

description:
6e3e92f2-b289-4ecd-b5e7-ce1b786ebe96
processed data file: GEO_rawcountmatrix.csv

source_name: Day 2 CD40L + IL4 Stimulated WT B cells

tag: timepoint

value: 11 wks

value: wt/wt


title: PolIIACREBFSK

description:
processed data file: FSKupgenesRNA.bed
PolIIACREBFSK_S28

source_name: RNA PolII_ChIPseq

tag: sample treatment

value: Ad-ACREB/1 hour 10 uM forskolin

value: rabbit anti-RPB1 (Cell Signaling 2629)


title: RNA_buffy_HD3_d18_Tcm

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

institute: BIH at Charité

data_processing:
Fastq-files were quality checked with FastQC (Babraham Bioinformatics) and trimmed for residual adapter sequences.
Reads were aligned to the GRCh38 human genome using TopHatR (2.1.0 - Johns Hopkins University, Center for Computational Biology) and Bowtie2
Reads were summarized per gene by sum up all reads mapped to a gene region using Rsamtools.
Raw counts of protein-coding genes were normalized and variancestabilising transformed using the corresponding function of the DESeq2 package (v1.6.3).
Genome_build: iGenome Homo_sapiens/Ensembl/GRCh38
Supplementary_files_format_and_content: Raw counts - tab-deliminated file with reads summerized per gene.
Supplementary_files_format_and_content: Normalized data - tab-deliminated file with normelized and variancestabilising transformed data of protein-coding genes

molecule: polyA RNA

source_name: T lymphocytes

growth_protocol: CMV-specific T lymphocytes were seperated from PBMCs from fresh blood or buffy coats by MACS in a IFNgamm-secretion assay after stimulation with CMV-peptides. Tcm and Tem were seperated from expanded cells by FACS.

extract_protocol:
RNA of the samples were extracted with the All-prep DNA/RNA kit from quiagen according to the manufacturer instructions.
Libraries were constructed using the TrueSeq Kit from Illumina.

treatment_protocol: Samples were expanded under the presence of Rapamycin as indicated in the sample characteristics.

tag: blood source

value: buffy coats

value: expanded CMV-specific Tcm

tag: day

value: day 18

tag: rapamycin

value: no


title: RNA_buffy_HD3_d18R_Tcm

value: yes


title: RNA_buffy_HD3_d18R

value: expanded CMV-specific T lymphocytes


title: WT-D1 3

description:
3af965da-1734-46d4-b4a6-42bc9e580fc3
processed data file: GEO_rawcountmatrix.csv

source_name: Day 1 CD40L + IL4 Stimulated WT B cells

value: Day 1

tag: mouse age

tag: mouse sex

tag: rosa26 yfp genotype

tag: date of isolation

tag: date of rna isolation


title: D458_Resistant_DMSO_2

value: D458 drug tolerant


title: PolIIACREBCON

description:
processed data file: FSKupgenesRNA.bed
PolIIACREBCON_S27

value: insulinoma cells

value: Ad-ACREB


title: PolIIGFPFSK

description:
processed data file: FSKupgenesRNA.bed
PolIIGFPFSK_S26

value: Ad-GFP/1 hour 10 uM forskolin


title: KO-D0 3

description:
cffd4898-1c37-42f6-a060-4a44bdf28b45
processed data file: GEO_rawcountmatrix.csv

source_name: KO WT B cells

value: CD43- splenic B cells

tag: genotype

tag: treatment

value: Naive

value: Day 0

tag: rna concentration

tag: dnase aliquot lot

tag: cd40l aliquot lot


title: RNA_buffy_HD3_d18

tag: cell type


title: PolIIGFPCON

description:
processed data file: FSKupgenesRNA.bed
PolIIGFPCON_S25

tag: cell line

value: Ad-GFP

tag: chip antibody


title: D458_Sensitive_JQ1_3

description: Gene expression data from D458 sensitive cells treated with JQ1

value: D458 sensitive


title: D458_Sensitive_JQ1_4


title: AR42JCREBCONNeuroD1

value: pancreatic cell line

tag: sample treatment

value: 244 anti-CREB rabbit serum


title: RNA_buffy_HD3_Tem

tag: blood source

value: buffy coats

value: Tem

value: day 0


title: D458_Resistant_DMSO_3


title: D458_Sensitive_JQ1_5


title: WT-D0 3

description:
6c2a0bbb-6f4a-4306-bd60-be7bf7e0a0d3
processed data file: GEO_rawcountmatrix.csv

source_name: Naïve WT B cells

tag: timepoint

value: 11 wks

value: Pooled male and female

value: wt/wt

tag: il-4 aliquot lot


title: BRD4FSKACREB

value: Ad-ACREB/1 hour 10 uM forskolin

value: rabbit anti-BRD4 (Bethyl A301-985A)


title: KO-D1 3

description:
be45eb24-72a9-4964-8da8-7ab6468830bf
processed data file: GEO_rawcountmatrix.csv

source_name: Day 1 CD40L + IL4 Stimulated KO B cells

value: CD40L + IL4 Stimulated

value: Day 1

tag: mouse age


title: D458_Resistant_DMSO_1

value: D458 drug tolerant


title: KO-D5 2

description:
3601ad00-e2f3-4e38-9d1c-644b7d943cd3
processed data file: GEO_rawcountmatrix.csv

source_name: Day 5 CD40L + IL4 Stimulated KO B cells

value: CD43- splenic B cells

value: Day 5

value: 10 wks

tag: mouse sex

value: Female


title: BRD4CONACREB

value: insulinoma cells

value: Ad-ACREB


title: RNA_buffy_HD2_d18R_Tcm

value: buffy coats

value: expanded CMV-specific Tcm

tag: day

value: day 18

tag: rapamycin

value: yes


title: microRNA profile of NPC2

first: Mei-Yin

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

tag: disease state

value: nasopharyngeal carcinoma

tag: tissue

value: whole blood


title: RNA_buffy_HD3_Tcm

value: Tcm

value: day 0

value: no


title: RNA_buffy_HD2_d18_Tcm


title: WT-D5 2

description:
5af7ea84-9001-4ebb-be79-019d681a3396
processed data file: GEO_rawcountmatrix.csv

source_name: Day 5 CD40L + IL4 Stimulated WT B cells

tag: genotype

tag: treatment

value: CD40L + IL4 Stimulated

value: 14 wks

tag: rosa26 yfp genotype

value: wt/wt

tag: date of isolation

tag: date of rna isolation


title: BRD4CONGFP

tag: cell line

tag: cell type

value: Ad-GFP

value: rabbit anti-BRD4 (Bethyl A301-985A)


title: RNA_buffy_HD2_d18R

value: expanded CMV-specific T lymphocytes


title: BRD4FSKGFP

value: insulinoma cells

tag: sample treatment

value: Ad-GFP/1 hour 10 uM forskolin

tag: chip antibody


title: WT-D4 2

description:
f1a9bf3a-2e16-4bbd-9b0e-311f746925af
processed data file: GEO_rawcountmatrix.csv

value: CD43- splenic B cells

tag: timepoint

value: Day 4

value: Female

tag: rna concentration

tag: dnase aliquot lot

tag: cd40l aliquot lot


title: H3AcK27FSKACREB

value: Ad-ACREB/1 hour 10 uM forskolin

value: rabbit anti-H3AcK27 (Abcam ab4729)


title: KO-D4 2

description:
dd69753c-3b8b-4fac-bea7-535b3474403a
processed data file: GEO_rawcountmatrix.csv

tag: mouse age

value: 10 wks

tag: mouse sex

tag: il-4 aliquot lot


title: H3AcK2CONACREB

value: Ad-ACREB


title: D458_Sensitive_DMSO_4

description: Gene expression data from D458 sensitive cells treated with DMSO

value: D458 sensitive


title: D458_Sensitive_DMSO_3


title: microRNA profile of NPC26

tag: disease state

value: nasopharyngeal carcinoma

tag: tissue

value: whole blood


title: RNA_buffy_HD2_Tem

tag: blood source

value: buffy coats

value: Tem

tag: day

value: day 0

tag: rapamycin

value: no


title: KO-D3 2

description:
f0a38c48-7f1e-419e-8da6-9c21a9054377
processed data file: GEO_rawcountmatrix.csv

tag: genotype

tag: treatment

value: CD40L + IL4 Stimulated

value: Day 3

tag: rosa26 yfp genotype

value: wt/wt

tag: date of isolation

tag: date of rna isolation


title: H3AcK27FSKGFP

tag: cell line

tag: cell type

value: insulinoma cells

tag: sample treatment

value: Ad-GFP/1 hour 10 uM forskolin

tag: chip antibody


title: WT-D3 2

description:
6ef36835-cc63-4fec-9edf-53d95ba61f4d
processed data file: GEO_rawcountmatrix.csv

value: CD43- splenic B cells

tag: timepoint

tag: mouse age

value: 14 wks

value: Female

tag: rna concentration

tag: dnase aliquot lot

tag: cd40l aliquot lot


title: D458_Sensitive_DMSO_5


title: KO-D2 2

description:
d7426fba-eaf5-4bf3-93dc-bde8d5c60796
processed data file: GEO_rawcountmatrix.csv

value: Day 2

value: 10 wks

tag: mouse sex

tag: il-4 aliquot lot


title: RNA_buffy_HD1_d18R_Tcm

tag: blood source

value: expanded CMV-specific Tcm

tag: day

value: day 18

tag: rapamycin

value: yes


title: RNA_buffy_HD1_d18R

value: buffy coats

value: expanded CMV-specific T lymphocytes


title: H3AcK2CONGFP

value: Ad-GFP

value: rabbit anti-H3AcK27 (Abcam ab4729)


title: RNA_buffy_HD2_Tcm

value: Tcm

value: day 0

value: no


title: D458_Sensitive_DMSO_1

value: D458 sensitive


title: CREBFSKACREB

value: insulinoma cells

value: Ad-ACREB/1 hour 10 uM forskolin

value: 244 anti-CREB rabbit serum


title: hepaFSKCRTC2

data_processing:
genome build: mm10
Reads were aligned to the mouse (mm10) or rat (rn5, rn6) genomes using bowtie2 or STAR
Binding peaks were called using Homer
Homer peak files were converted to BED files using Homer
Co-occupancy of binding sites was performed using Homer (mergePeak command -prefix option)
Super-enhancers were identified based on H3AcK27 occupancy with HOMER (findPeaks –style super –L 0, maximum distance to stitch peaks together: 12.5 kb).

value: cultured mouse primary hepatocytes

value: 1 hour 10 uM forskolin

value: 6865 anti-CRTC2 rabbit serum


title: RNA_buffy_HD1_d18


title: hepaCONH3AcK27


title: WT-D2 2

description:
55d2e13e-922a-4b6b-b035-24139b29b11f
processed data file: GEO_rawcountmatrix.csv

value: CD43- splenic B cells

tag: genotype

tag: treatment

value: CD40L + IL4 Stimulated

value: Day 2

value: 14 wks

value: Female

tag: rosa26 yfp genotype

value: wt/het


title: D458_Sensitive_DMSO_2


title: hepaCONCRTC2


title: D458_Sensitive_JQ1_1


title: KO-D1 2

description:
9d4b8ae3-84e3-4b57-8c35-5f69af812844
processed data file: GEO_rawcountmatrix.csv

value: Day 1

value: 10 wks

value: wt/wt

tag: date of isolation

tag: date of rna isolation


title: CREBCONACREB

tag: cell line

tag: cell type

tag: sample treatment

value: Ad-ACREB


title: RNA_buffy_HD1_Tem

value: buffy coats

value: Tem

value: day 0

value: no


title: D458_Sensitive_JQ1_2

value: D458 sensitive


title: hepaFSKH3AcK27

value: cultured mouse primary hepatocytes

value: 1 hour 10 uM forskolin

tag: chip antibody

value: rabbit anti-H3AcK27 (Abcam ab4729)


title: hepaFSKCREB

value: 244 anti-CREB rabbit serum


title: WT-D1 2

description:
e037c860-a6ce-4089-99cf-5cbdbf75ffaf
processed data file: GEO_rawcountmatrix.csv

value: CD43- splenic B cells

value: CD40L + IL4 Stimulated

tag: timepoint

tag: mouse age

tag: rna concentration


title: CREBFSKGFP

value: insulinoma cells

value: Ad-GFP/1 hour 10 uM forskolin


title: KO-D0 2

description:
43ff8864-10ab-4914-8aa1-ca897906e40b
processed data file: GEO_rawcountmatrix.csv

value: Naive

value: Day 0

tag: mouse sex

value: Female

tag: dnase aliquot lot

tag: cd40l aliquot lot


title: RNA_buffy_HD1_Tcm

tag: blood source

value: Tcm

tag: day


title: CREBCONGFP

value: Ad-GFP


title: RNA_fresh_HD3R

value: fresh

value: expanded CMV-specific T lymphocytes

value: day 21

tag: rapamycin

value: yes


title: hepaCONCREB

value: cultured mouse primary hepatocytes


title: hepaCONinput

source_name: inputDNACON


title: RNA_fresh_HD3

value: no


title: KO-D5 1

description:
d25c7359-098c-4504-96b9-aeaba48795d2
processed data file: GEO_rawcountmatrix.csv

tag: genotype

tag: treatment

value: Day 5

value: 8 wks

value: Male

value: wt/het

tag: il-4 aliquot lot


title: CBPFSK

value: insulinoma cells

value: 1 hour 10 uM forskolin

value: 5613 anti-CBP rabbit serum


title: RNA_fresh_HD2R


title: WT-D0 2

description:
b0197d77-c63d-45d8-81ce-773b12bd2c67
processed data file: GEO_rawcountmatrix.csv

value: CD43- splenic B cells

value: Naive

value: Day 0

value: 14 wks

tag: rosa26 yfp genotype

tag: date of isolation

tag: date of rna isolation


title: hepaFSKinput

source_name: inputDNAFSK

tag: cell type


title: CBPCON

tag: cell line

tag: chip antibody


title: isletCONH3AcK27

value: cultured mouse primary pancreatic islets

value: rabbit anti-H3AcK27 (Abcam ab4729)


title: CRTC2FSK

tag: sample treatment

value: 6865 anti-CRTC2 rabbit serum


title: CRTC2CON


title: H3AcK27FSKrep4

description:
processed data file:
H3AcK27FSKrep4_S26
INS1inducibleenhancers.bed
INS1noninducibleenhancers.bed
HAcKoverCREB4000differential.xlsx


title: isletFSKCRTC2


title: KO-D4 1

description:
78ee0948-3c1c-4d3f-9db6-1ff8d2df0537
processed data file: GEO_rawcountmatrix.csv

source_name: Day 4 CD40L + IL4 Stimulated KO B cells

value: CD40L + IL4 Stimulated

tag: timepoint

value: Day 4

tag: mouse age

tag: rna concentration


title: WT-D4 1

description:
8824bbd0-b0d7-48ec-a692-7885bbd2510a
processed data file: GEO_rawcountmatrix.csv

source_name: Day 4 CD40L + IL4 Stimulated WT B cells

tag: mouse sex

value: wt/wt

tag: dnase aliquot lot

tag: cd40l aliquot lot


title: RNA_fresh_HD1

tag: blood source

value: fresh

value: expanded CMV-specific T lymphocytes

tag: day

value: day 21

tag: rapamycin

value: no


title: isletCONCRTC2


title: H3AcK27CONrep4

description:
H3AcK27CONrep4_S25
processed data file:
INS1inducibleenhancers.bed
INS1noninducibleenhancers.bed
HAcKoverCREB4000differential.xlsx

value: insulinoma cells


title: KO-D3 1

description:
2685dbb6-6374-40fa-b9fa-3d85f39e8f60
processed data file: GEO_rawcountmatrix.csv

source_name: Day 3 CD40L + IL4 Stimulated KO B cells

tag: genotype

tag: treatment

value: Day 3

value: 8 wks

value: Male

value: wt/het

tag: il-4 aliquot lot


title: isletFSKCREB

value: 1 hour 10 uM forskolin

value: 244 anti-CREB rabbit serum


title: H3AcK27FSKrep3

description:
H3AcK27FSKrep3-3-2-TTAGGC_TTAGGC_L002
processed data file:
INS1inducibleenhancers.bed
INS1noninducibleenhancers.bed
HAcKoverCREB4000differential.xlsx


title: KO-D2 1

description:
83aef023-562c-48b3-b4a6-403fd99c807b
processed data file: GEO_rawcountmatrix.csv

value: CD43- splenic B cells

value: Day 2

tag: rosa26 yfp genotype

tag: date of isolation

tag: date of rna isolation


title: D333A-2

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Base calls from Illumina HiSeq 4000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (version: Schizosaccharomyces_pombe.ASM294v2.28) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Genome_build: Schizosaccharomyces_pombe.ASM294v2.28.dna.genome.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/OLD/20150909/Schizosaccharomyces_pombe.ASM294v2.28.dna.genome.fa.gz)
Supplementary_files_format_and_content: Matrix file for raw HTSeq counts; individual files for DESeq2 for comparison of each mutant with WT

growth_protocol: log phase cultures, 30ºC, YES medium

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina HiSeq 4000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).

tag: lab strain number

tag: growth conditions

value: log phase culture, YES medium

tag: developmental stage

value: vegetative growth


title: isletFSKH3AcK27

tag: cell type

value: cultured mouse primary pancreatic islets

tag: sample treatment

tag: chip antibody

value: rabbit anti-H3AcK27 (Abcam ab4729)


title: WT-D3 1

description:
534db4a3-de00-4959-b179-2ec734ba0aa9
processed data file: GEO_rawcountmatrix.csv

value: CD40L + IL4 Stimulated

tag: timepoint

tag: mouse age

value: 14 wks

tag: mouse sex

value: wt/wt

tag: rna concentration

tag: dnase aliquot lot


title: RNA_fresh_HD2

tag: blood source

value: fresh

value: expanded CMV-specific T lymphocytes

tag: day

value: day 21

tag: rapamycin

value: no


title: D333A-1


title: D333A-3


title: WT-D2 1

description:
124188c1-8a36-49d0-a042-17d8a8307e1f
processed data file: GEO_rawcountmatrix.csv

tag: genotype

tag: treatment

value: Male

tag: rosa26 yfp genotype

tag: cd40l aliquot lot

tag: il-4 aliquot lot


title: isletCONinput


title: aps1-3

tag: lab strain number

tag: growth conditions

tag: developmental stage


title: H3AcK27CONrep3

description:
H3AcK27CONrep3-5-1-ACAGTG_ACAGTG_L001
processed data file:
INS1inducibleenhancers.bed
INS1noninducibleenhancers.bed
HAcKoverCREB4000differential.xlsx

tag: cell line

tag: cell type

value: insulinoma cells

tag: chip antibody


title: RNA_fresh_HD1R

value: yes


title: isletFSKinput


title: WT-D5 1

description:
3eda413d-880a-4091-b299-3167b282dba6
processed data file: GEO_rawcountmatrix.csv

tag: timepoint

value: Day 5

tag: mouse age

tag: mouse sex

tag: date of isolation

tag: date of rna isolation


title: H3AcK27CONrep2

description:
H3AcK27CONrep2_S17
processed data file:
INS1inducibleenhancers.bed
INS1noninducibleenhancers.bed
HAcKoverCREB4000differential.xlsx


title: isletCONCREB

value: 244 anti-CREB rabbit serum


title: WT-D1 1

description:
509e52f7-a061-4bdb-bed5-405202883ac2
processed data file: GEO_rawcountmatrix.csv

value: CD43- splenic B cells

value: Day 1

tag: rna concentration

tag: dnase aliquot lot


title: KO-D1 1

description:
5a62fe5a-1db2-4b7f-9c07-4fc3571e31af
processed data file: GEO_rawcountmatrix.csv

tag: genotype

tag: treatment

value: 8 wks

value: wt/het


title: H3AcK27FSKrep2

description:
H3AcK27FSKrep2_S19
processed data file:
INS1inducibleenhancers.bed
INS1noninducibleenhancers.bed
HAcKoverCREB4000differential.xlsx

tag: sample treatment

value: 1 hour 10 uM forskolin

value: rabbit anti-H3AcK27 (Abcam ab4729)


title: aps1-2

value: log phase culture, YES medium

value: vegetative growth


title: H3AcK27FSKrep1

description:
H3AcK27FSKrep1-A009_L005
processed data file:
INS1inducibleenhancers.bed
INS1noninducibleenhancers.bed
HAcKoverCREB4000differential.xlsx


title: aps1-1


title: WT-D0 1

description:
cf564b97-9794-40a1-9820-51de2c68fab2
processed data file: GEO_rawcountmatrix.csv

value: Naive

value: Day 0

value: 14 wks

tag: rosa26 yfp genotype

value: wt/wt

tag: cd40l aliquot lot

tag: il-4 aliquot lot


title: H3AcK27CONrep1

description:
H3AcK27CONrep1-A004_L005
processed data file:
INS1inducibleenhancers.bed
INS1noninducibleenhancers.bed
HAcKoverCREB4000differential.xlsx


title: AR42JNeuroD1FSK [RNA-seq]

description:
AR42JNeuroD1FSK_S4_L001_R1_001.fastq.gz
processed data file:
AR42JGFPvNeuroD1RNAseq.xlsx

tag: tissue/cell line

value: pancreatic cell line

value: 2 hours 10 uM forskolin


title: CREBFSKrep4

tag: cell line

value: insulinoma cells


title: CREBCONrep4

tag: cell type


title: AR42JNeuroD1CON [RNA-seq]

description:
AR42JNeuroD1CON_S3_L001_R1_001.fastq.gz
processed data file:
AR42JGFPvNeuroD1RNAseq.xlsx


title: CREBCONrep3

tag: chip antibody


title: CREBFSKrep3


title: AR42JGFPCON [RNA-seq]

description:
AR42JGFPCON_S1_L001_R1_001.fastq.gz
processed data file:
AR42JGFPvNeuroD1RNAseq.xlsx


title: asp1-H397A ssu72-C13S aps1∆ [C13S_H397A_aps1-2]

description:
C13S_H397A_aps1-2
Stranded polyA+ RNA Seq
processed data: RawCounts.txt
processed data: DESeq2_C13S_H397A_aps1_by_WT_analysis.xlsx

data_processing:
Base calls from Illumina HiSeq 4000 (FASTQ files).
Each replicate processed separately.
The FASTQ files were mapped to the S. pombe genome (version: Schizosaccharomyces_pombe.ASM294v2.28) using HISAT2_2.1.0. ERCC Spike in controls were sequenced but not included for data analysis.
Resulting SAM files were converted to BAM files using Samtools.
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’).
Differential gene expression and fold change analysis was performed in DESeq2.
Genome_build: Schizosaccharomyces_pombe.ASM294v2.28.dna.genome.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/OLD/20150909/Schizosaccharomyces_pombe.ASM294v2.28.dna.genome.fa.gz)
Supplementary_files_format_and_content: RawCounts.txt: Matrix file for raw HTSeq counts.
Supplementary_files_format_and_content: *.xlsx: Individual files for DESeq2 for comparison of each mutant with WT.

source_name: asp1-H397A ssu72-C13S aps1∆

growth_protocol: Log phase cultures, 30ºC, YES medium.

extract_protocol:
Hot acid phenol RNA purification protocol.
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturer's protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina HiSeq 4000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).

tag: lab strain number

tag: genotype/variation

value: asp1-H397A ssu72-C13S aps1<delta>

tag: growth conditions

tag: growth stage


title: CREBFSKrep2

value: 244 anti-CREB rabbit serum


title: asp1-H397A ssu72-C13S aps1∆ [C13S_H397A_aps1-3]

description:
C13S_H397A_aps1-3
Stranded polyA+ RNA Seq
processed data: RawCounts.txt
processed data: DESeq2_C13S_H397A_aps1_by_WT_analysis.xlsx


title: INS1A485FSK [RNA-seq]

description:
INS1A485FSK
processed data file:
INS1JQ1A485FSKRNAseq.xlsx

value: 4 hours 10uM A485/2 hours 10 uM forskolin


title: asp1-H397A ssu72-C13S aps1∆ [C13S_H397A_aps1-1]

description:
C13S_H397A_aps1-1
Stranded polyA+ RNA Seq
processed data: RawCounts.txt
processed data: DESeq2_C13S_H397A_aps1_by_WT_analysis.xlsx


title: INS1JQ1FSK [RNA-seq]

description:
INS1JQ1FSK
processed data file:
INS1JQ1A485FSKRNAseq.xlsx

value: 4 hours 1uM JQ1/2 hours 10 uM forskolin


title: KO-D0 1

description:
a1b84580-3438-439a-bf0b-49de54abfa73
processed data file: GEO_rawcountmatrix.csv

value: CD43- splenic B cells

tag: timepoint

tag: mouse age

value: 8 wks

tag: mouse sex

value: Male

tag: date of isolation

tag: date of rna isolation


title: CREBCONrep2


title: asp1-H397A [H397A-3]

description:
H397A-3
Stranded polyA+ RNA Seq
processed data: RawCounts.txt
processed data: DESeq2_H397A_by_WT_analysis.xlsx


title: CREBFSKrep1

description:
CREBFSKrep1-A006-5_L005
processed data file:
INS1inducibleenhancers.bed
INS1noninducibleenhancers.bed
HAcKoverCREB4000differential.xlsx
CREBNeuroD1cobound.bed
CREBNeuroD1PDX1cobound.bed
CREBnoNeuroD1PDX1.bed
CREBPDX1cobound.bed
NeuroD1noCREB.bed
PDX1NeuroD1noCREB.bed
PDX1noCREB.bed

tag: sample treatment

value: 1 hour 10 uM forskolin


title: asp1-H397A [H397A-2]

description:
H397A-2
Stranded polyA+ RNA Seq
processed data: RawCounts.txt
processed data: DESeq2_H397A_by_WT_analysis.xlsx

value: log phase culture, YES medium


title: INS1FSK [RNA-seq]

description:
INS1FSK
processed data file:
INS1JQ1A485FSKRNAseq.xlsx

tag: treatment


title: INS1CON [RNA-seq]

description:
INS1CON
processed data file:
INS1JQ1A485FSKRNAseq.xlsx


title: AR42JGFPFSK [RNA-seq]

description:
AR42JGFPFSK_S2_L001_R1_001.fastq.gz
processed data file:
AR42JGFPvNeuroD1RNAseq.xlsx


title: BMDM KO CM2

city: Durham

first: LUIGI

last: RACIOPPI

state: North Carolina

address: La Salle, GSRB1 2006

department: Medicine

institute: Duke University

description: BMDM generated in regular macrophage differentiation medium in the presence of 20% of tumor conditioned medium

hyb_protocol: Hybridization targets were prepared with the Affymetrix WT Plus Kit (Affymetrix, Santa Clara, CA) and Affymetrix GeneChip WT Terminal Labeling Kit (included with Affy WT Plus) from total RNA

scan_protocol: Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA)

data_processing:
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console

source_name: BMDM KO CM

label_protocol: GeneChip WT Terminal Labeling Kit (Part Number 900670, 900671)

growth_protocol: BM cells were cultured for 5 days in Corning® Costar® Ultra-Low attachment multi-well plates (Sigma). To establish the purity of BMDM, cells were double-stained with anti-CD11b and anti-F4/80 antibodies. Based on this analysis, more than 95% of cells co-expressed these markers, which is a characteristic of macrophages. In the same experiments, tumor-conditioned medium (20% v/v) was added to differentiation medium.

extract_protocol: Qiagen Mini Kit Extraction with on-column Dnase treatment followed by Affymatrix WT plus (according to manufacture instructions). Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). and

treatment_protocol: 30% L929-conditioned medium in the presence or absence of 20% of E0771-conditioned medium (CM and RM, respectively)

value: BMDM

tag: genotype

value: Camkk2 -/-

tag: culture condition

value: CM


title: BMDM KO CM4


title: ssu72-C13S [C13S-3]

description:
C13S-3
Stranded polyA+ RNA Seq
processed data: RawCounts.txt
processed data: DESeq2_C13S_by_WT_analysis.xlsx

value: vegetative growth


title: BMDM KO CM3


title: BMDM WT CM2

source_name: BMDM WT CM

value: Camkk2 +/+


title: Dam-/Dcm-_SMRT-seq

first: Eric

last: Greer

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

institute: Boston Children's Hospital/Harvard Medical School

description: Sample 2

data_processing:
Library strategy: SMRT-seq
Adapter dimers were filtered and we got 104179 and 105252 reads respectively for sample 1 and sample2
The filtered reads were mapped to MG1655 genome build using cmph5tools and reached over 150X average coverage.
The variants were detected, producing GFF and VCF track
IPD ratios were calculated, generating modifications.csv and modifications.gff
High IPD ratios in the locations represent putatitve modification
Genome_build: ASM584v2
Supplementary_files_format_and_content: gff file

organism: Escherichia coli

source_name: Bacteria

extract_protocol:
We used the Invitrogen PureLink Genomic DNA Mini kit following the manufacturer’s instructions for isolation of gDNA from gram-negative bacteria.
To examine adenine and cytosine methylation across the 5 Mb E. coli genome strain K12 substrain MG1655, SMRTbell library using C2 chemistry for use in a 120-minute movie protocol was conducted

tag: strain

tag: substrain

value: dam-/dcm-


title: BMDM KO CM1

tag: cell type


title: INS-1input

tag: cell line


title: ssu72-C13S [C13S-2]

description:
C13S-2
Stranded polyA+ RNA Seq
processed data: RawCounts.txt
processed data: DESeq2_C13S_by_WT_analysis.xlsx

tag: lab strain number


title: BMDM WT CM1


title: INS1CON_rep2 [RNA-seq]

description:
INS1CONrep2
processed data file:
INS1RNAseqrepeat.xlsx

tag: tissue/cell line


title: BMDM WT CM4


title: INS1FSK_rep1 [RNA-seq]

description:
INS1FSKrep1
processed data file:
INS1RNAseqrepeat.xlsx

value: 2 hours 10 uM forskolin


title: ssu72-C13S [C13S-1]

description:
C13S-1
Stranded polyA+ RNA Seq
processed data: RawCounts.txt
processed data: DESeq2_C13S_by_WT_analysis.xlsx

tag: genotype/variation

tag: growth conditions


title: WT_Ecoli_SMRT-seq

description: Sample 1

value: wild type


title: BMDM KO RM4

description: BMDM generated in regular macrophage differentiation medium

source_name: BMDM KO RM

value: RM


title: CREBCONrep1

value: insulinoma cells

tag: chip antibody

value: 244 anti-CREB rabbit serum


title: asp1-H397A [H397A-1]

description:
H397A-1
Stranded polyA+ RNA Seq
processed data: RawCounts.txt
processed data: DESeq2_H397A_by_WT_analysis.xlsx

tag: growth stage


title: BMDM WT CM3


title: WT [WT-3]

description:
WT-3
Stranded polyA+ RNA Seq
processed data: RawCounts.txt
processed data: DESeq2_C13S_by_WT_analysis.xlsx; DESeq2_H397A_by_WT_analysis.xlsx; DESeq2_C13S_H397A_aps1_by_WT_analysis.xlsx

source_name: WT

value: JS 77

value: WT


title: BMDM KO RM3


title: WT [WT-2]

description:
WT-2
Stranded polyA+ RNA Seq
processed data: RawCounts.txt
processed data: DESeq2_C13S_by_WT_analysis.xlsx; DESeq2_H397A_by_WT_analysis.xlsx; DESeq2_C13S_H397A_aps1_by_WT_analysis.xlsx


title: Curcumin_treated_2

city: Hyderabad

first: Anand

last: Srivastava

state: India

address: Survey No 37/4,  Gowalidoodi  Area ,   Gopanpally

country: India

institute: National Institute of Animal Biotechnology (NIAB)

description: Gene expression of curcumin treated cells after 24hr

data_processing:
Adaters were removed using Cutadapt, raw read data was run through quality control metrics using FastQC.
Sequence reads were aligned to the Bos taurus genome (UMD3.1 build, Ensembl.org), Theileria annulata genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/225/GCF_000003225.3_ASM322v1/GCF_00  0003225.3_ASM322v1_genomic.fna.gz) using HISAT2.
Cufflinks was used to estimate and calculate transcript abundance. It results in normalized read count in the form of FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values.
Cuffdiff was used to calculate the differentially expressed transcripts and categorize them into UP, Down and Neutrally regulated based on the log2fold change values.

organism:
Theileria annulata
Bos taurus

source_name: Theileria infected bovine leucocytes

growth_protocol: Cells cultured in RPMI media- 1640  supplemented with 10% fetal bovine serum, 2 mM L- glutamine, 25 mM HEPES, 0.1% PenStrep at 37o C with 5% CO2.

extract_protocol:
RNA isolation from the untreated and curcumin treated bovine leucocytes was performed using Trizol reagent as per standard protocol. The purity and concentration of total RNA extracted was checked using Nanodrop spectrophotometer by using 1 µl of total RNA against nuclease free water as blank to determine the absorbance ratio 260/280 nm. The quality check of the isolated RNA was performed in Agilent 2100 Bioanalyzer. RNA with RNA integrity number (RIN) greater than 7 was used for sequencing.
Sequencing libraries were constructed following NEBNext® Ultra™ Directional RNA Library Prep Kit protocol and were then processed by Illumina HiSeq Paired- end sequencing.

treatment_protocol: Theileria annulata infected bovine leucocytes collected from field were treated with 20 µM of curcumin for 24 hrs. RNA isolated from untreates and treated samples.

value: Theileria infected bovine leucocytes


title: pT2N1: Ulcerative Adenocarcinoma

city: Nantong

first: Shan

last: Kong

state: Jiangsu

address: NO.20, Xisi Road

department: Department of Laboratory Medicine

institute: Affiliated Hospital of Nantong University

data_processing:
For circRNA expression analysis, the reads were to mapped genome using 1.the STAR (58) and DCC (59) was used to identify the cirRNA and to estimate the circRNA expression
TMM (trimmed mean of M-values) was used to normalize the gene expression
Genome_build: hg19
Supplementary_files_format_and_content: txt TMM normalized junction read counts

source_name: greater gastric curvature

extract_protocol:
Total RNA  was extracted with TRIzol® Reagent (Life technologies)
RNA sequencing libraries were prepared from 2μg of total RNA using the TruSeq Kit (Illumina, Inc.) with modifications. Instead of purifying poly-A RNA using poly-dT primer beads, we removed ribosomal RNA using the Ribo-Zero rRNA Removal Kit (Illumina, Inc.). Linear RNA was removed using RNase R (Epicentre, Inc). Poly-T oligo-attached magnetic beads (Illumina, Inc.) were used to remove residual poly-A RNA. All other steps were performed according to the manufacturer's protocols.

tag: tissue

value: stomach

value: Ulcerative Adenocarcinoma


title: INS1FSK_rep2 [RNA-seq]

description:
INS1FSKrep2
processed data file:
INS1RNAseqrepeat.xlsx


title: pT3N3: Ulcerative Adenocarcinoma

source_name: lesser gastric curvature


title: BMDM KO RM2


title: WT [WT-1]

description:
WT-1
Stranded polyA+ RNA Seq
processed data: RawCounts.txt
processed data: DESeq2_C13S_by_WT_analysis.xlsx; DESeq2_H397A_by_WT_analysis.xlsx; DESeq2_C13S_H397A_aps1_by_WT_analysis.xlsx

value: log phase culture, YES medium


title: Untreated_Control_1

description: Gene expression of control cells after 24hr


title: BMDM WT RM4

source_name: BMDM WT RM

value: BMDM


title: BMDM KO RM1

value: Camkk2 -/-


title: BMDM WT RM3


title: pT3N2: Ulcerative Adenocarcinoma


title: INS1CON_rep1 [RNA-seq]

description:
INS1CONrep1
processed data file:
INS1RNAseqrepeat.xlsx


title: BMDM WT RM1


title: BMDM WT RM2


title: 041-9297950056_R01C01

status: Public on Jun 15 2019

type: genomic

city: Wenzhou

first: Xiangnan

last: Chen

address: west load of college 268

institute: Wenzhou Medical University

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
041-9297950056_R01C01_Grn.idat
041-9297950056_R01C01_Red.idat

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).
Genomic gains and losses of 100 kb in length that affected a minimum of 50 and 25 markers, respectively, were initially considered to determine the relevance of duplications and deletions. Breakpoint positions of each CNV were converted to Genome Reference Consortium Human Build 37 patch release 13 (GRCh37.p13).

label: A-DNP, C-Bio

source_name: patient with intellectual disability phenotype

label_protocol: 250 ng of genomic DNA was whole-genome amplified in an overnight reaction at 37℃ using amplification master mix (WG-MSM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Genomic DNA was isolated from whole blood with EDTA by using the QIAamp DNA Mini kit (QIAGEN, Germany), following the manufacturer’s instructions. Purified DNA was eluted with 50–200 μL of DNA elution buffer. Sample concentration and purity were detected using the NanoDrop 2000 UV-Vis spectrophotometer (Thermo Scientific, USA).

treatment_protocol: Individuals were considered for inclusion in the study if they met the following criteria: (1) Intelligence Quotient (IQ) < 70 as measured by the China–Wechsler Intelligence Scale for Children; (2) demonstrated neural developmental defects resulting in mental retardation, motor retardation, language delay, epilepsy, etc.; (3) not pregnant (4)no known nongenetic cause of ID, such as perinatal infection, ischemia, hypoxia, etc.; (5) no family history of ID; (6) no obvious genetic metabolic disease; and (7) availability of biological parents to participate in the study. In total, 64 patients with ID (38 males, 26 females; age range: 3–29 years) were enrolled after screening using the aforementioned criteria.

tag: diagnosis

value: intellectual disability

tag: gender

value: female

value: Peripheral Blood


title: 060-3999238220_R06C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
060-3999238220_R06C02_Grn.idat
060-3999238220_R06C02_Red.idat

value: male


title: 040-8387043026_R04C01

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
040-8387043026_R04C01_Grn.idat
040-8387043026_R04C01_Red.idat


title: 044-5921853135_R05C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
044-5921853135_R05C02_Grn.idat
044-5921853135_R05C02_Red.idat


title: 032-8685016027_R06C01

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
032-8685016027_R06C01_Grn.idat
032-8685016027_R06C01_Red.idat


title: 051-9297950042_R05C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
051-9297950042_R05C02_Grn.idat
051-9297950042_R05C02_Red.idat


title: 031-8685016030_R01C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
031-8685016030_R01C02_Grn.idat
031-8685016030_R01C02_Red.idat


title: 057-3999238197_R02C01

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
057-3999238197_R02C01_Grn.idat
057-3999238197_R02C01_Red.idat


title: 036-9481137112_R05C01

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
036-9481137112_R05C01_Grn.idat
036-9481137112_R05C01_Red.idat


title: 022-6066001037_R06C01

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
022-6066001037_R06C01_Grn.idat
022-6066001037_R06C01_Red.idat


title: 035-9297950037_R03C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
035-9297950037_R03C02_Grn.idat
035-9297950037_R03C02_Red.idat