title: STAT3_TAM_ChIPseq

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

data_processing:
Fastq reads were aligned to human reference genome (hg19) using Bowtie (Langmead et al., 2009) allowing up to 2 mismatches. Only the uniquely mappable reads were used for subsequent analyses. For ChIP-seq data for STAT3, NFKB1, JUN, JUNB and FOS, we used MACS (Zhang et al., 2008) to call peaks with the cutoff P-value < 10-8 in at least one sample, using the parameters “macs2 callpeak --llocal 1000000 -g 2.7e9”.
Genome_build: hg19
Supplementary_files_format_and_content: text file with MACS called peak data

source_name: MCF10A-ER-Src cell

growth_protocol: All cultures were performed at 37°C under 5% CO2. The breast epithelial cell line (MCF-10A-ER-Src) was grown in DMEM/F12 with 5% charcoal-stripped fetal bovine serum (Invitrogen) and supplements(Iliopoulos et al., 2009). Cells were seeded at 1 × 10^6 cells per 10-cm culture dish and cultured overnight. MCF-10A-ER-Src cells were treated by 1 µM 4-hydroxy-tamoxifen for various time points to induce transformation.

extract_protocol:
The ChIP experiments follow the ENCODE protocol, http://genome.ucsc.edu/ENCODE/, using the following antibodies: STAT3 (Cell Signaling, 9131), NFKB1 (Sigma, HPA027305), FOS (Santa Cruz Biotech, SC-7202x), JUN (Santa Cruz Biotech, SC-1694) and JUNB (Santa Cruz Biotech, SC-73). We performed the ChIP experiments, using the non-transformed MCF10A-ER-Src cells and the cells after 12hr of cell transformation.
Library preparation and sequencing were carried out as per ENCODE protocols, and a detailed protocol is available at http://genome.ucsc.edu/ENCODE/

value: Breast

tag: chip target

tag: transformation status

value: transformed


title: STAT3_EtOH_ChIPseq

status: Public on Jun 11 2018

type: SRA

city: Chicago

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: cell line

value: non-transformed


title: P1DPSC1

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

library_source: transcriptomic

data_processing:
Basecalling performed by RTA version 1.18.66.3
Demultiplexing performed by Bcl2fastq version 1.8.4
Adaptor trimming and quality control by Trimmomatic version 0.30
Read alignment performed by STAR version 2.5.1
Transcript quantification performed by RSEM version 1.2.22
Data normalized by median normalization
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file of RSEM values for each single cell

molecule: total RNA

source_name: Patient EPCAM+CD24 positive single cell 1

growth_protocol: HuH-1 and HuH-7 were grown in DMEM medium plus 10% fetal bovine serum and 1% antibiotics. At 80% confluence, the cell were harvested for flow cytometry sorting

extract_protocol:
no RNA extraction step droplet-based single-cell RNA-seq (SMART-seq)
Cells were lysed in ice-cold lysis buffer. SMART-seq protolcol was performed on single or pooled sorted cells following the manufacturere's instructions with some modification. Briefly, whole transcriptome was amplified with the SMART-seq v4 Ultra Low Input RNA kit (Clonetech), purified (Beckman Coulter, A63881) and barcoded (Illumina, FC-131-1096). Finally, libraries were pooled and sequenced on Illumina Hiseq2500.

value: hepatcellular carcinoma

tag: cell surface marker

tag: cell number

tag: cell status

value: single-cell


title: P1TPSC2

source_name: Patient triple positive single cell 2

value: TriplePos


title: NFKB1_TAM_ChIPseq


title: JUN_TAM_ChIPseq

value: JUN


title: P1TNSC3

source_name: Patient triple negative single cell 3

value: TripleNeg


title: NFKB1_EtOH_ChIPseq


title: P1TPSC1

source_name: Patient triple positive single cell 1


title: JUNB_TAM_ChIPseq

value: JUNB


title: JUNB_EtOH_ChIPseq


title: FOS_TAM_ChIPseq

value: FOS


title: FOS_EtOH_ChIPseq


title: JUN_EtOH_ChIPseq


title: P1TNSC2

source_name: Patient triple negative single cell 2


title: Ctrlb_TAM

data_processing:
Raw reads were aligned to GENCODE (Harrow et al., 2012) defined transcripts and then human reference genome (hg19) using Tophat (Langmead et al., 2009) allowing up to 2 mismatches. The gene expression levels were indicated as transcript per million (TPM) values.
Genome_build: hg19
Supplementary_files_format_and_content: text file with TPM for fene expression levels

molecule: polyA RNA

extract_protocol:
RNA was extracted using mRNeasy Mini Kit following the manufacturer’s instruction. We performed RNA-seq experiments for cells before cell transformation, and cells after 24 hrs of cell transformation. For cells with gene knockouts, we performed RNA-seq for cells after 24hrs of cell transformation.
RNA-seq libraries were prepared using TruSeq Ribo Profile Mammalian Kit (Illumina, RPHMR12126) as per manufacturer’s instruction. RNA-seq libraries were sequenced by Harvard Bauer Core Facility using Hiseq 2000.

tag: genotype

value: wildtype


title: STAT3KO_TAM

value: STAT3 KO


title: FOSKOb_TAM

value: FOS KO


title: NFKB1KO_TAM

value: NFKB1 KO


title: JUNBKO_TAM

value: JUNB KO


title: Ctrl_EtOH


title: Ctrl_TAM


title: WAT_array_DKO_rep3

type: RNA

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description: Gadd45a/Ing1 double knockout (DKO) WAT, replicate 3

hyb_protocol: Agilent Hybridisation Oven and SurePrint G3 Mouse GE 8x60K microarrays following the manufacturer's protocol.

scan_protocol: Agilent Scanner G2505C with v.10.7.3.1 Feature Extraction Software at 3 µm resolution.

data_processing:
The raw array data were processed using the Bioconductor package limma v.3.26.9 (https://bioconductor.org/packages/release/bioc/html/limma.html) following the standard workflow for single-channel Agilent arrays (chapter 17.4 of the User’s Guide). Following normexp background correction and quantile inter-sample normalisation, the control and low-signal probes were filtered out, the replicate probes were averaged and the knockout samples were compared against the wildtype samples for differential gene expression (lmFit; eBayes).
log2 signal intensity from limma after background correction, quantile normalisation, removal of control and low-signal probes, and averaging of replicate probes

organism: Mus musculus

label_protocol: Agilent one-color Quick Amp Labeling Kit following the manufacturer's protocol.

extract_protocol: Gonadal WAT was individually collected from 9 male mice per genotype (59-67 day old) and snap-frozen in liquid nitrogen. Total RNA was extracted with Qiazol and an Ultra turrax homogeniser. RNA was further purified using the RNeasy mini kit with on-column DNase digest (Qiagen), quantified with a Thermo NanoDrop and quality tested on Agilent Bioanalyzer. Employing a sub-pooling approach (doi:10.1186/1471-2105-4-26), purified RNA from 3 animals of each genotype was pooled to create 3 biological replicates for microarray expression profiling.

treatment_protocol: Gadd45a deficient mice (Hollander et al. 1999; doi:10.1038/13802) and Ing1 deficient mice (Kichina et al. 2006; doi:10.1038/sj.onc.1209118) were interbred to obtain single-mutant, Gadd45a-/-;Ing1-/- double-mutant (DKO) and wildtype (WT) animals.

tag: strain

value: male gonadal White Adipose Tissue (WAT)


title: WAT_array_Gadd45a-KO_rep2

description: Gadd45a knockout WAT, replicate 2


title: Infected THP-1 by Mycobacterium tuberculosis (H37Rv)

city: Tehran

first: Farzam

last: Vaziri

address: 12th Farvardin Ave, Jomhhoori St

country: Iran

institute: Pasteur Institute of Iran

description:
Test
SAMPLE 3
Test

scan_protocol: RT2 Profiler PCR Array Data Analysis Webportal was applied (https://www.qiagen.com/ir/resources/geneglobe/).

data_processing:
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPLP0, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target ? Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control

label: SYBR Green

source_name: THP-1, infected by Mycobacterium tuberculosis (H37Rv)

extract_protocol: The qRT-PCR was performed by RT² Profiler? PCR Array kit (QIAGEN) which including RT² Profiler? PCR Array Human Cytokines & Chemokines(QIAGEN, Cat.No. PAHS-150Z)according to the manufacturer?s instructions. Quantitative real-time PCR were performed (Light Cycler 96, Roche) with 40cycles at 95 oC for 15 sec and 55oC for 40sec ,72oC for 30sec

tag: cell type

value: human monocytic leukemia

tag: infection

tag: time

value: 1 days


title: Ctrlb_EtOH

value: Breast


title: JUNKO_TAM

value: JUN KO

value: transformed


title: WAT_array_Ing1-KO_rep1

description: Ing1 knockout WAT, replicate 1


title: WAT_array_Gadd45a-KO_rep1

description: Gadd45a knockout WAT, replicate 1


title: single cells from patient

description: droplet-based single-cell RNA-seq with unique molecular identifiers (UMIs).

data_processing:
Basecalling performed by RNA v. 1.12.4.2
Demultiplexing performed by Bcl2fastq v. 2.17
Alingment, tagging, gene and transcript counting performed by Cellranger v. 2.0.1
Data normalized by median normalization
Genome_build: hg19
Supplementary_files_format_and_content: Three filtered matrix files 1) sample barcodes (barcodes.tsv) 2) genes detected (genes.tsv) and 3) count matrix (matrix.mtx)

source_name: hepatocellular carcinoma patient sample

growth_protocol: Human liver cancer cell lines, HuH1 and HuH7 were routinely maintained in DMEM medium plus 10% fetal bovine serum and 1% antibotics. At 80% confluence, the cells were harvested and frozen in liquid nitrogen.

extract_protocol:
no extraction step
Chromium Single Cell platform from 10X Genomics was used to generate gene expression data from single cells. Briefly, frozen cells were thawed at 37°C, washed and were loaded onto the 10XGenomics Chromium Controller machine for Gel Beads-in-Emulsion (GEM) generation. Cells were lysed inside the cell-specific droplets and cDNA libraries were constructed. Illumina libraries were then prepared using the Chromium Single cell 3’ Reagent Kit (V1 chemistry) from 10X Genomics. All samples were pooled and sequenced.

treatment_protocol: For HuH1 and HuH7, at 80% confluence, the cells were harvested and frozen in liquid nitrogen. For primary HCC cells, they were dissociatd from HCC biopsy and frozen in liquid nitrogen.

value: random

value: hepatocellular carcinoma


title: WAT_array_DKO_rep1

description: Gadd45a/Ing1 double knockout (DKO) WAT, replicate 1


title: WAT_array_WT_rep3

description: Wildtype WAT, replicate 3

value: Wildtype


title: WAT_array_Ing1-KO_rep3

description: Ing1 knockout WAT, replicate 3


title: wt_iWAT_ATACseq_rep2

city: New York

first: Yinxin

last: Zhang

state: New York

address: 1230 York Avenue

department: Molecular Genetics

institute: The Rockefeller University/HHMI

data_processing:
Reads were aligned to the mm9 build and Ensemble gene model (NCBIM37) using Bowtie with parameters –X2000 and –m1.
Then we processed the alignments using Samtools and adjusted the read start sites to represent the center of the transposon binding event as previously described: all reads aligning to the + strand were offset by +4 bp, and all reads aligning to the – strand were offset −5 bp.
Reads in two libraries from two individual mouse in each condition were mixed.
After that, we found peaks in ob/ob samples with at least a 3 fold higher signal than fasted conditions using Homer.
Within the above peak region, footprint scores were calculated based Wellington method.
The bedGraph files only use the first 3 steps.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph, wig file were generated using Wellington Footprint method; Scores represent the likelihood of protection by protein at each base pair in ob/ob condition;

source_name: inguinal White Adipose Tissue (iWAT)

extract_protocol:
The fat tissue was minced with blades, dounced in homogenization buffer (20mM Tricine pH7.8, 25mM D-Sucrose, 15mM NaCl, 60mM KCl, 2mM MgCl2, 0.5mM Spermidine), filtered with EMD Millipore Nylon-Net Steriflip™ Vacuum Filter Unit (100um), and centrifuged at 18000g for 5min at 4C. The resulting nuclei pellet was washed once with Tagmentation DNA buffer (10mM Tris pH7.6: acetic acid, 5mM MgCl2, 10% dimethylformamdie) followed by centrifugation at 500g for 5min at 4C.
After resuspension in the same Tagmentation DNA buffer and counting using Trypan Blue, an aliquot contacting 50K nuclei was performed transposition reaction using Nextera DNA Library Preparation Kit (illumina) and processed as descripted.

value: wild type

tag: age

value: 10 week old

tag: treatment

value: fed


title: fast_iWAT_ATACseq_rep1

value: fasted for 2 days


title: ob_iWAT_ATACseq_rep2

value: ob/ob


title: fast_iWAT_ATACseq_rep2


title: WAT_array_WT_rep1

description: Wildtype WAT, replicate 1


title: WAT_array_Ing1-KO_rep2

description: Ing1 knockout WAT, replicate 2


title: THP-1

description:
Control
SAMPLE 1
Control

source_name: THP-1, control

value: control


title: Infected THP-1 by Mycobacterium tuberculosis (Rifampine Mono Resistant ,RMR)

description:
Test
SAMPLE 2
Test

source_name: THP-1, infected by Mycobacterium tuberculosis (Rifampine Mono Resistant ,RMR)

value: RMR M.tb


title: WAT_array_Gadd45a-KO_rep3

description: Gadd45a knockout WAT, replicate 3


title: WAT_array_DKO_rep2

description: Gadd45a/Ing1 double knockout (DKO) WAT, replicate 2


title: WAT_array_WT_rep2

description: Wildtype WAT, replicate 2


title: ob_iWAT_ATACseq_rep1


title: Diploid_RNA_Seq_2

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description: processed data file: hybrid_rna_total_per_domain.txt

data_processing:
Standard Illumina base-calling pipeline.
Sequence processing pipeline
TADs were called separately for the haploid and diploid data by applying a cutoff on the insulation parameter calculated every 1Kb on the pooled single-cell Hi-C maps, as described in the paper. RNA-seq sequences of each replicate were mapped to the mm9 genome assembly using Bowtie 2.0. Properly mapped pairs (SAM flag 0x02), first in pair (SAM flag 0x40) and good quality reads (quality above 37) were retained, extended to 150 bps and raw total read coverage was calculated for 50 bps bins. Usage of these raw counts per TAD is described in the Methods section.
Genome_build: mm9
Supplementary_files_format_and_content: Text summary table quantitating raw counts over TADs

source_name: Diploid 129 Cataneus Mus musculus hybrid ESC cell line

extract_protocol:
Strand-specific nuclear RNA-seq library preparation
Ten to 20 million unfixed ESCs (grown in 2i medium without feeder cells) were washed with cold PBS, resuspended in 0.5 ml of cold buffer RLN (50 mM Tris pH 7.5, 140 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 0.4% IGEPAL CA-630) and incubated for 5 min on ice. The samples were spun and the resultant pellets (nuclei) were washed with buffer RLN and subject to RNA isolation using RNeasy Mini Kit (Qiagen) and QIAshredder spin columns (Qiagen) according to the instructions from the manufacturer. The strand-specific RNA-seq libraries were prepared from 200 ng each of nuclear RNA samples using TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) according to manufacturer's instructions.

tag: sample type


title: seeds following 3 d of anaerobic germination, followed by 1 d under aerobic conditions (3dN1dA) Methyl-Seq Replicate 3

city: Bundoora

first: Reena

last: Narsai

address: 5 Ring road

country: Australia

institute: La trobe University

description: De‐hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30°C in the dark for 3 d, the gas was then switched to air for 1 d (3dN1dA). These coleoptiles were immediately extracted and snap frozen.

data_processing:
Quality control was confirmed within the Illumina Hiseq software and all reads passing filter were used for downstream analysis.
Filtered reads were mapped onto the O.sativa genome with the International Rice Genome Sequencing Project 1.0 (IRGSP‐1.0) rice genome sequence (from the RAP‐DB) and analysed as previously for MethylC‐seq data (Lister et al., 2011, 2013) and DMRs were identified in the same manner as previously described for this data type (Secco et al., 2015). Briefly, the frequency of cytosine basecalls at reference cytosine positions in the spiked‐in lambda genome was normalized against the total number of base‐calls at reference positions in the lambda genome (which is unmethylated), enabling the calculation of the bisulphite non‐conversion frequency. If regions of differential methylation were within 200 bases of each other and showed the same direction of change in methylation (hypo‐/hyper‐methylation), these were combined into a block and defined as one DMR.
Genome_build: International Rice Genome Sequencing Project 1.0 (IRGSP‐1.0)
Supplementary_files_format_and_content: tab-delimited text files with results of differential methylation analyses (CNN).

organism: Oryza sativa

source_name: Rice coleoptile

growth_protocol: Rice (Oryza sativa ‘Amaroo’) was de‐hulled, surface sterilised and grown in culture medium [0.5 mm 2‐(N‐morpholine)‐ethanesulphonic acid (MES), 0.4 mm CaSO4, pH 6.5) that was bubbled with air or nitrogen gas (N2) (6–7 L min−1).

extract_protocol:
gDNA was extracted from the seeds/seedlings using the Qiagen DNeasy Plant minikit and 600ng of purified gDNA was used for MethylC-seq library preparation after spiking in 0.5% lambda DNA (N6-methyladenine-free) (New England BioLabs).
MethylC-seq library preparation was carried out as described previously (Urich et al., 2015 - http://www.nature.com/nprot/journal/v10/n3/full/nprot.2014.114.html).

treatment_protocol: For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.

value: coleoptile

value: WT(Oryza sativa cv Amaroo)

value: seeds following 3 d of anaerobic germination, followed by 1 d under aerobic conditions (3dN1dA) Replicate 3

tag: treatment/conditions

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30 C in the dark for 3 d, the gas was then switched to air for 1 d (3dN1dA).


title: seeds following 4 d of anaerobic germination (4dN) Methyl-Seq Replicate 2

description: De‐hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30°C in the dark for 4 d, coleoptiles were immediately extracted and snap frozen.

value: seeds following 4 d of anaerobic germination (4dN) Replicate 2

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30 C in the dark for 4 d.


title: seeds following 4 d of anaerobic germination (4dN) Methyl-Seq Replicate 1

value: seeds following 4 d of anaerobic germination (4dN) Replicate 1


title: seeds following 4 d of anaerobic germination (4dN) Methyl-Seq Replicate 3

value: seeds following 4 d of anaerobic germination (4dN) Replicate 3


title: seeds following 24 h of anaerobic germination (24hN) Methyl-Seq Replicate 3

description: De‐hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30°C in the dark for 24 h, embryos were then immediately extracted and snap frozen.

source_name: Rice germinating embryos

value: germinating embryos

value: seeds following 24 h of anaerobic germination (24hN) Replicate 3

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30 C in the dark for 24 h.


title: Diploid_RNA_Seq_1

value: Diploid 129 Cataneus Mus musculus hybrid ESC cell line


title: seeds following 3 d of anaerobic germination, followed by 1 d under aerobic conditions (3dN1dA) Methyl-Seq Replicate 2

value: seeds following 3 d of anaerobic germination, followed by 1 d under aerobic conditions (3dN1dA) Replicate 2


title: Haploid_RNA_Seq_2

description: processed data file: haploid_rna_total_per_domain.txt

source_name: Haploid H129-3 Mus musculus hybrid ESC cell line


title: seeds following 24 h of anaerobic germination (24hN) Methyl-Seq Replicate 2

value: seeds following 24 h of anaerobic germination (24hN) Replicate 2


title: Haploid_RNA_Seq_1

source_name: Haploid H129-1 Mus musculus hybrid ESC cell line


title: seeds following 3 d of anaerobic germination, followed by 1 d under aerobic conditions (3dN1dA) Methyl-Seq Replicate 1

value: seeds following 3 d of anaerobic germination, followed by 1 d under aerobic conditions (3dN1dA) Replicate 1


title: seeds following 4 d of aerobic germination (4dA) Methyl-Seq Replicate 3

description: De‐hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30°C in the dark for 4 d, coleoptiles were immediately extracted and snap frozen.

value: seeds following 4 d of aerobic germination (4dA) Replicate 3

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30 C in the dark for 4 d.


title: seeds following 4 d of aerobic germination (4dA) Methyl-Seq Replicate 2

value: coleoptile

value: seeds following 4 d of aerobic germination (4dA) Replicate 2


title: seeds following 24 h of anaerobic germination (24hN) Methyl-Seq Replicate 1

value: WT(Oryza sativa cv Amaroo)

value: seeds following 24 h of anaerobic germination (24hN) Replicate 1


title: seeds following 4 d of aerobic germination (4dA) Methyl-Seq Replicate 1

value: seeds following 4 d of aerobic germination (4dA) Replicate 1


title: seeds following 24 h of aerobic germination (24hA) Methyl-Seq Replicate 3

description: De‐hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30°C in the dark for 24 h, embryos were then immediately extracted and snap frozen.

value: seeds following 24 h of aerobic germination (24hA) Replicate 3

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30 C in the dark for 24 h.


title: seeds following 24 h of aerobic germination (24hA) Methyl-Seq Replicate 1

value: seeds following 24 h of aerobic germination (24hA) Replicate 1


title: seeds following 24 h of aerobic germination (24hA) Methyl-Seq Replicate 2

value: germinating embryos

value: seeds following 24 h of aerobic germination (24hA) Replicate 2


title: Tlr7-/- rep2

city: Taipei

first: Yi-Ping

last: Hsueh

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description:
KO-D-2_S15
KO-D-2_S15_R1_001 trimmed (GE) - RPKM

data_processing:
Illumina bcl2fastq2.17 was used to generate fastqs from bcl files
Sequenced reads were trimmed for adaptor sequence,low quality sequences, then mapped to GRCm38.p6 whole genome using CLC Genomics Workbench with parameters: mismatches=2, minimum fraction length =0.9, minimum fraction similarity=0.9, and maximum hits per read = 5.
Hisat2 for raw sequence trimming and mapping, FeatureCount for read counts,
Generalized Linear Model (GLM) and Wald Test were then used to analyzed differential expression of genes and statistical significance.
classic EdgeR and Fisher’s exact test for differential expression and statistical analysis.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Excel files include Raw, TPM, RPKM , fold change and p values for each Sample .
Supplementary_files_format_and_content: Excel files include fold change and p values for each Sample .

source_name: Tlr7-/- _primary cultured neuron

growth_protocol: Mouse cortical and hippocampal mixed neurons were cultured in Neurobasal medium/DMEM (1:1) with B27 supplement

extract_protocol:
Total RNA was  using Trizol reagent according to the manufacturer’s instructions (Invitrogen).
2 ug of total RNA was used for RNA-seq library preparation using the TruSeq Stranded mRNA LT set A/B Sample Prep Kit.

tag: strain background

tag: genotype/variation

tag: day in vitro

value: Div 18

value: cortical and hippocampal mixed neurons


title: Tlr7-/- rep3

description:
KO-F-2_S16
KO-F-2_S16_R1_001 trimmed (GE) - RPKM


title: dry seed 0 h Methyl-Seq Replicate 3

description: Oryza sativa seeds were de-hulled and embryos were immediately extracted and snap frozen.

source_name: Rice embryos

tag: tissue

value: embryos

value: dry seed 0 h Replicate 3


title: Tlr7-/- rep1

description:
KO1_div18_S4
KO1_div18_S4_R1_001 trimmed (GE) - RPKM


title: WT rep3

description:
WT3_div18_S3
WT3_div18_S3_R1_001 trimmed (GE) - RPKM

source_name: WT_primary cultured neuron

value: wild type


title: dry seed 0 h Methyl-Seq Replicate 2

value: dry seed 0 h Replicate 2

value: Oryza sativa seeds were de-hulled and embryos were immediately extracted and snap frozen.


title: dry seed 0 h Methyl-Seq Replicate 1

value: dry seed 0 h Replicate 1


title: seeds following 3 d of anaerobic germination, followed by 1 d under aerobic conditions (3dN1dA) Replicate 3

data_processing:
Quality control was confirmed within the Illumina Hiseq software and all reads passing filter were used for downstream analysis.
Filtered reads were mapped onto O.sativa genome with the International Rice Genome Sequencing Project 1.0 (IRGSP‐1.0) rice genome sequence (from the RAP‐DB). The cufflinks package (Trapnell et al., 2012) version 2.2.0 (Bowtie2 v.2.2.0‐beta7 and Tophat v.2.2.0) was used for RNA‐seq analyses.
Genome_build: International Rice Genome Sequencing Project 1.0 (IRGSP‐1.0) and MSU v.7
Supplementary_files_format_and_content: tab-delimited text files showing results from differential expression analyses using Cuffdiff (v. 2.2.0).

extract_protocol:
RNA isolation was carried out using the Sigma Spectrum Plant Total RNA kit.
TruSeq Stranded Total RNA with Ribo‐Zero Plant Sample Prep Kits were used to generate the libraries, according to manufacturer’s instructions (Illumina).
rRNAs removed, random fragmentation, stranded library

value: coleoptile

value: seeds following 3 d of anaerobic germination and 1 d under aerobic conditions (3dN1dA) Replicate 3

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30 C in the dark for 3 d, the gas was then switched to air for 1 d (3dN1dA).


title: K562_CBP30_5uM_2

status: Public on Jun 12 2018

city: Majadahonda

first: Maria

last: Barrero

state: Madrid

address: Crta. Majadahonda-Pozuelo KM 2.2

country: Spain

institute: ISCIII

description:
Isolation of poly A+ RNA from total RNA
CBP30_5uM_2

data_processing:
RNA-seq processing:
RNA-seq analysis was performed with the nextpresso pipeline v1.4, using the following tools:
Read files were quality-checked with FastQC.
Reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 2.2.1
Homo sapiens GRCh37/hg19 transcript annotations from the UCSC Genome Browser were used
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM values obtained with Cuffnorm

source_name: K562 cells

growth_protocol: K562 cells wer grown in RPMI+10%FBS

extract_protocol:
Cells were trypsinized and total RNA was extracted using the RNeasy kit (Qiagen).
From 1 µg of total RNA PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit. Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced for 50 bases in a single-read format (Illumina HiSeq 2000).

treatment_protocol: K562 cells were treated for 48 hours with with 2 µM CBP30, 5μM CBP30 , 2 μM I-CBP112, 5 μM I-CBP112 or vehicle (DMSO). Two biological replicates were used per condition.

tag: cell line

value: 5 μM CBP30


title: wt_iWAT_ATACseq_rep1

value: 10 week old

value: fed


title: seeds following 3 d of anaerobic germination, followed by 1 d under aerobic conditions (3dN1dA) Replicate 2

value: WT(Oryza sativa cv Amaroo)

value: seeds following 3 d of anaerobic germination and 1 d under aerobic conditions (3dN1dA) Replicate 2


title: seeds following 4 d of anaerobic germination (4dN) Replicate 3

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30 C in the dark for 4 d.


title: seeds following 3 d of anaerobic germination, followed by 1 d under aerobic conditions (3dN1dA) Replicate 1

value: seeds following 3 d of anaerobic germination and 1 d under aerobic conditions (3dN1dA) Replicate 1


title: seeds following 4 d of anaerobic germination (4dN) Replicate 2


title: WT rep2

description:
WT2_div18_S2
WT2_div18_S2_R1_001 trimmed (GE) - RPKM

value: Div 18

value: cortical and hippocampal mixed neurons


title: WT rep1

description:
WT1_div18_S1
WT1_div18_S1_R1_001 trimmed (GE) - RPKM


title: seeds following 4 d of anaerobic germination (4dN) Replicate 1


title: seeds following 4 d of aerobic germination (4dA) Replicate 2

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30 C in the dark for 4 d.


title: seeds following 4 d of aerobic germination (4dA) Replicate 3


title: seeds following 3 d of aerobic germination (3dA) Replicate 3

description: De‐hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30°C in the dark for 3 d, coleoptiles were immediately extracted and snap frozen.

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30 C in the dark for 3 d.


title: seeds following 3 d of anaerobic germination (3dN) Replicate 2

description: De‐hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30°C in the dark for 3 d, coleoptiles were immediately extracted and snap frozen.

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30 C in the dark for 3 d.


title: seeds following 4 d of aerobic germination (4dA) Replicate 1


title: seeds following 3 d of anaerobic germination (3dN) Replicate 3


title: seeds following 2 d of anaerobic germination (2dN) Replicate 3

description: De‐hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30°C in the dark for 2 d, coleoptiles were immediately extracted and snap frozen.

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30 C in the dark for 2 d.


title: seeds following 2 d of anaerobic germination (2dN) Replicate 1


title: seeds following 3 d of aerobic germination (3dA) Replicate 2


title: seeds following 24 h of anaerobic germination (24hN) Replicate 3

value: germinating embryos

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30 C in the dark for 24 h.


title: seeds following 2 d of aerobic germination (2dA) Replicate 2

description: De‐hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30°C in the dark for 2 d, coleoptiles were immediately extracted and snap frozen.

value: coleoptile

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30 C in the dark for 2 d.


title: seeds following 3 d of aerobic germination (3dA) Replicate 1


title: seeds following 2 d of aerobic germination (2dA) Replicate 1


title: seeds following 2 d of aerobic germination (2dA) Replicate 3


title: seeds following 24 h of anaerobic germination (24hN) Replicate 2


title: seeds following 24 h of anaerobic germination (24hN) Replicate 1


title: seeds following 24 h of aerobic germination (24hA) Replicate 3

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30 C in the dark for 24 h.


title: MEF_undifferentiated_RNASeq_DKO_rep1

data_processing:
RNA-Seq reads were quality assesed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The reads were aligned to the mm9 genome with TopHat v2.0.9 (https://ccb.jhu.edu/software/tophat) and Bowtie v.2.1.0 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) with a GTF annotation transcript file of Ensemble release 67 and additional parameter: -g 5
The mapped reads were summarized on gene level using htseq-count, HTSeq package v0.5.4 (http://www-huber.embl.de/HTSeq)
Differential expression analysis were performed using the R Bioconductor package DESeq (http://bioconductor.org/packages/release/bioc/html/DESeq.html)
Genome_build: NCBIM37 (mm9)
Supplementary_files_format_and_content: tab-delimited text file with summarised read counts per gene from htseq-count

source_name: Gadd45a-/- Ing1-/- (DKO) MEF cells, replicate 1

growth_protocol: Gadd45a deficient mice (Hollander et al. 1999; doi:10.1038/13802) and Ing1 deficient mice (Kichina et al. 2006; doi:10.1038/sj.onc.1209118) were interbred to obtain single-mutant, Gadd45a-/-;Ing1-/- double-mutant (DKO) and  wildtype (WT) embryos. Mouse embryonic fibroblasts (MEFs) of the four genotypes were isolated from embryonic day E15.5 male embryos and cultured for 4 passages.

extract_protocol:
Total RNA was isolated using the RNeasy mini kit with on-column DNase digest (Qiagen) following the manufacturer's protocol, quantified with a Thermo NanoDrop and quality tested on Agilent Bioanalyzer.
NGS libraries were prepared from 280ng RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina) according to manufacturer’s recommendations and amplified in 12 PCR cycles. Libraries were profiled in a High Sensitivity DNA chip on a 2100 Bioanalyzer and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). The 12 libraries were pooled in equimolar ratio and sequenced in 7 lanes on a HiSeq 2000 Illumina sequencer, single read mode for 51 cycles plus 7 cycles for the index read.

treatment_protocol: Primary cells were grown to 80% confluency at passage 4 for harvesting.

value: MEF

tag: Sex

value: male


title: MEF_undifferentiated_RNASeq_DKO_rep2

source_name: Gadd45a-/- Ing1-/- (DKO) MEF cells, replicate 2


title: MEF_undifferentiated_RNASeq_Ing1-KO_rep3

source_name: Ing1-/- MEF cells, replicate 3


title: seeds following 24 h of aerobic germination (24hA) Replicate 2

value: WT(Oryza sativa cv Amaroo)


title: seeds following 24 h of aerobic germination (24hA) Replicate 1


title: seeds following 12 h of anaerobic germination (12hN) Replicate 3

description: De‐hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30°C in the dark for 12 h, embryos were then immediately extracted and snap frozen.

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30 C in the dark for 12 h.


title: MEF_undifferentiated_RNASeq_Ing1-KO_rep2

source_name: Ing1-/- MEF cells, replicate 2


title: MEF_undifferentiated_RNASeq_Gadd45a-KO_rep3

source_name: Gadd45a-/- MEF cells, replicate 3


title: seeds following 2 d of anaerobic germination (2dN) Replicate 2


title: seeds following 3 d of anaerobic germination (3dN) Replicate 1


title: seeds following 12 h of anaerobic germination (12hN) Replicate 1


title: seeds following 12 h of aerobic germination (12hA) Replicate 3

description: De‐hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30°C in the dark for 12 h, embryos were then immediately extracted and snap frozen.

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30 C in the dark for 12 h.


title: MEF_undifferentiated_RNASeq_DKO_rep3

source_name: Gadd45a-/- Ing1-/- (DKO) MEF cells, replicate 3


title: seeds following 12 h of anaerobic germination (12hN) Replicate 2


title: MEF_undifferentiated_RNASeq_Gadd45a-KO_rep2

source_name: Gadd45a-/- MEF cells, replicate 2


title: MEF_undifferentiated_RNASeq_Ing1-KO_rep1

source_name: Ing1-/- MEF cells, replicate 1


title: MEF_undifferentiated_RNASeq_Gadd45a-KO_rep1

source_name: Gadd45a-/- MEF cells, replicate 1


title: MEF_undifferentiated_RNASeq_WT_rep2

source_name: Wildtype MEF cells, replicate 2

value: Wildtype


title: seeds following 12 h of aerobic germination (12hA) Replicate 1

source_name: Rice germinating embryos


title: MEF_undifferentiated_RNASeq_WT_rep3

source_name: Wildtype MEF cells, replicate 3


title: seeds following 12 h of aerobic germination (12hA) Replicate 2


title: seeds following 3 h of anaerobic germination (3hN) Replicate 2

description: De‐hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30°C in the dark for 3 h, embryos were then immediately extracted and snap frozen.

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30 C in the dark for 3 h.


title: MEF_undifferentiated_RNASeq_WT_rep1

source_name: Wildtype MEF cells, replicate 1


title: seeds following 3 h of aerobic germination (3hA) Replicate 2

description: De‐hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30°C in the dark for 3 h, embryos were then immediately extracted and snap frozen.

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30 C in the dark for 3 h.


title: seeds following 1 h of anaerobic germination (1hN) Replicate 3

description: De‐hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30°C in the dark for 1 h, embryos were then immediately extracted and snap frozen.

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30 C in the dark for 1 h.


title: seeds following 1 h of anaerobic germination (1hN) Replicate 2


title: seeds following 1 h of aerobic germination (1hA) Replicate 3

description: De‐hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30°C in the dark for 1 h, embryos were then immediately extracted and snap frozen.

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30 C in the dark for 1 h.


title: seeds following 1 h of aerobic germination (1hA) Replicate 2


title: batch culture with 10ml pure hexadecane, replicate 3

city: Wageningen

first: Ye

last: Tian

address: Stippeneng 4

department: AFSG

country: Netherlands

institute: Wageningen University

hyb_protocol: For each labelled sample, 600 ng of purified dye-coupled cDNA  was hybridized to the oligo-microarray at 65 ºC for 16 h following the one-colour microarray-based prokaryote analysis FairPlay III labelling protocol (Agilent Technologies, ver.1.3).

scan_protocol: Slides were scanned on an Agilent DNA Microarray Scanner G2505C

data_processing: Outlier spots and spot intensity were extracted with Agilent Feature Extraction software version 10.7.3.1. After background subtraction, mexp and quantile normalization method for within-and inter-array normalization, respectively, were applied using the R-Bioconductor package. Moreover,  the normalized values were used of averaging probes replicates and genes replicates.

organism: Desulfitobacterium hafniense Y51

source_name: batch culture with 10ml pure hexadecane

label_protocol: Five micrograms of total RNA was first reverse-transcribed to cDNA, labelled, and purified using a FairPlay Microarray Labeling Kit according to the one-colour microarray-based prokaryote analysis FairPlay III labelling protocol (Agilent Technologies, ver.1.3).

extract_protocol: Modified version of Macaloid based RNA isolation protocol (Zoetendal et al., 2006: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2006.05056.x/full).

tag: cultivation

value: batch

tag: electron acceptor (concentration)

value: Fumarate (30mM)

tag: electron donor (concentration)

value: Lactate (20mM)

tag: volume


title: river sediment replicate 1

source_name: river sediment

value: sediment

value: irrelvent

value: 30 gram sediment (fresh weight) in 30 ml anoxic, artificial moderately hard freshwater


title: seeds following 1 h of aerobic germination (1hA) Replicate 1

value: germinating embryos

tag: genotype


title: dry seed 0 h Replicate 3

source_name: Rice embryos

value: embryos

value: dry seed 0 h Replicate 3

value: Oryza sativa seeds were de-hulled and embryos were immediately extracted and snap frozen.


title: dry seed 0 h Replicate 2

value: WT(Oryza sativa cv Amaroo)

value: dry seed 0 h Replicate 2


title: batch culture with 10ml pure hexadecane, replicate 2


title: batch culture with 10ml pure hexadecane, replicate 1


title: seeds following 3 h of anaerobic germination (3hN) Replicate 1


title: DCoG cells_1

city: Kyoto

first: Leqian

last: Yu

address: 205 Room, International Science Innovation Building

country: Japan

institute: Kyoto university

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
RNA-seq reads were aligned to the mouse refference genome (hg19) using Tophat software
gene expression level was calculated Cufflink.
Genome_build: hg19
Supplementary_files_format_and_content: txt files reflect FPKM of each gene in Refseq.

source_name: human iPSCs

growth_protocol: human iPSCs 253G1 cultured in mTesR1 medium

extract_protocol:
Total RNA was isolated using the  RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions
The purifed mRNAs were used to construct the cDNA library with the NEB RNA library construct kit. The quality-ensured libraries were used for pair-end deep sequencing on Illumina HiSeq Sequencer.

tag: culture medium

value: mTesR 1

tag: passage

tag: substrates

value: Gelatin nanofiber

tag: cell subtype

value: Domed


title: dry seed 0 h Replicate 1

tag: age

value: dry seed 0 h Replicate 1


title: seeds following 3 h of anaerobic germination (3hN) Replicate 3

tag: treatment/conditions

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30 C in the dark for 3 h.


title: Replicate3_Input_6mA

status: Public on Jun 10 2018

city: yichang

first: chao

last: zhou

address: No.8,daxuelu Street

country: China

institute: CTGU

data_processing:
Library strategy: 6mA IP-Seq
Quality Control: fastqc
Remove low quality data: 6mA-IP-seq raw data's low quality reads were removed from raw data by Trimmomatic.
6mA-IP-seq clean reads were aligned to the rice MSU7.0 reference genome by bowtie
6mA-IP-seq's peaks calling were used with MACS software with default parameters.
6mA_modification.gff was analyzed using the SMRT analysis platform for DNA 6mA modification detection which identifies 6mA-modified bases based on inter-pulse duration ratios in the sequencing data
Genome_build: MSU7.0 rice reference genome;rice MH63 reference genome
Supplementary_files_format_and_content: bed files were generated using MACS software;

organism: Oryza sativa Japonica Group

source_name: Nipponbare

growth_protocol: Seedling were grown in one-half-strength Murashige and Skoog medium under a 16-h-light/8-h-dark cycle at 30°C for 12 days.

extract_protocol:
For 6mA IP-seq, the total genomic DNA was extracted from 12 days of leaves using the DNeasy plant mini kit (Qiagen) with overnight RNase A treatment.
Briefly, 5g genomic DNA extracted from 12 days leaf was sonicated into 200 ~ 400bp and end-repaired, followed by adapter ligation. DNA was denatured at 95 degree for 10 min, and chilled on ice for 10 min. A part of denatured DNA was saved as input. The remaining of DNA was immunoprecipitated with anti-6mA antibody (202-003, Synaptic Systems) overnight at 4 degrees. DNA was eluted by 6mA salt competition. After DNA fragment’s size selection and PCR amplification, the DNA fragments were sequenced with the NextSeq 500.

value: seedling's leaf

tag: cultivar

value: Nipponbare

value: 12 days

tag: chip antibody


title: Replicate1_Input_6mA


title: Replicate3_IP_6mA

value: anti-6mA antibody (ab151, 230, Abcam)


title: Replicate2_Input_6mA


title: Replicate1_IP_6mA

value: anti-6mA antibody (202-003, Synaptic Systems)


title: Replicate2_IP_6mA


title: seeds following 3 h of aerobic germination (3hA) Replicate 1

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30 C in the dark for 3 h.


title: seeds following 3 h of aerobic germination (3hA) Replicate 3

value: germinating embryos


title: seeds following 1 h of anaerobic germination (1hN) Replicate 1

value: De-hulled sterilised seeds were grown in MES culture medium bubbled with nitrogen gas (anaerobic-N) at 30 C in the dark for 1 h.


title: MDCK STK11 Knockdown 1

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

description: Cell Line

data_processing:
Raw sequence reads were pseudo aligned to the Dog transcriptome CanFam3.1 (Ensembl Build 83) using Kallisto (Version 0.42.4, Bray et al. Nat. Biotechnology 2016) runing 100 bootstrap rounds.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: Tab-delimited text files per sample include effectice read counts and transcript per million (TPM) values for each transcript

organism: Canis lupus familiaris

source_name: Madin-Darby canine kidney (MDCK) cells

growth_protocol: Madin-Darby canine kidney (MDCK) cells were cultured using Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (Biochrome, Berlin, Germany) and 1% Penicillin-Streptomycin.

extract_protocol:
Total RNAs were extracted and purified from tetracycline-inducible Lkb1 knockdown MDCK cell line (2 independent experiments per condition), using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNAs quality was checked using a Fragment Analyzer™ (Advanced Analytical Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To generate tetracycline-inducible knockdown MDCK cell lines, MDCK-tTR-KRAB were transduced with shRNAs by the lentivirus-based transduction system (pLVTH) as previously described (Wiznerowicz et al. J virology 2003).

tag: strain

value: MDCK cell line

value: Kidney

tag: knockdown

tag: treatment

value: plus tetracycline

tag: replicate

value: replicate 1

tag: cell type

value: adult epithelial kidney cell


title: MDCK control 2

description: Cell Line

tag: tissue

value: control

value: minus tetracycline

value: replicate 2


title: MDCK control 1

description: Cell Line


title: DMS-MaPseq on E. coli (Ribo-depleted RNA)

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

institute: University of Groningen

description:
Ribo-depleted RNA
Data analysis was performed using RNA Framework (http://www.rnaframework.com).  Processed data files are: 1) WIGGLE track file of Box-plot normalized DMS reactivities (Ecoli_DMS-MaPseq.wig); 2) RC file for analysis with RNA Framework (Ecoli_DMS-MaPseq.rc); 3) RC file's index (index.rci).

data_processing:
Data analysis was performed using RNA Framework (http://www.rnaframework.com).  Processed data files are: 1) WIGGLE track file of Box-plot normalized DMS reactivities (Ecoli_DMS-MaPseq.wig); 2) RC file for analysis with RNA Framework (Ecoli_DMS-MaPseq.rc); 3) RC file's index (index.rci).
Genome_build: U00096.2
Supplementary_files_format_and_content: WIG, RC, RCI

organism: Escherichia coli

growth_protocol: LB medium, 37°C, 300 RPM

extract_protocol:
Each bacteria pellet from a 25 ml culture (OD600 ~0.3) was homogeneously resuspended in 200 µl of Buffer A [10 mM Tris pH 8.0; 20% Sucrose; 100 mM NaCl] supplemented with 200 U SUPERase• In™ RNase Inhibitor, by pipetting. 50 µl of Buffer B [50 mM EDTA; 120 mM Tris pH 8.0] supplemented with 1 µl Ready-Lyse™ Lysozyme Solution (Epicentre, cat. R1810M) were added dropwise, and the vial was gently tilted 5 times to ensure homogenous mixing. The sample was then incubated 1 minute at room temperature. 250 µl of Buffer C [0.5% Tween-20: 0.4% NaDOC; 2 M NaCl; 10 mM EDTA] were immediately added dropwise. The sample was then incubated 5 minutes at room temperature. For each 100 µl of lysate, 1 mL of ice-cold TRIzol was added and sample was incubated at 56°C for 5 minutes. RNA was then extracted following manufacturer instructions.
1 μg of DMS-treated RNA, either total, or rRNA-depleted using Ribo-Zero rRNA Removal Kit (Illumina), was fragmented in the presence of 10 mM MgCl2 at 94°C for 8 minutes. RNA was end-repaired by treatment with 1 U rSAP (NEB) at 37°C for 30 minutes. After heat-inactivating the enzyme at 65°C for 5 minutes, RNA fragments were phosphorylated by treatment with 10 U T4 Polynucleotide kinase (NEB) in the presence of 1 mM final ATP at 37°C for 1 hour. After reaction cleanup on RNA Clean & Concentrator™-5 columns (Zymo Research), 3' and 5' adapters were ligated to RNA fragments using the NEBNext® Small RNA Library Prep Set (NEB). RNA was then heat-denatured at 70°C for 5 minutes and incubated at room temperature for 5 minutes. Reverse transcription was carried out in a final volume of 10 μl, in the presence of 1 mM dNTPs, 10 pmol of SR RT primer (NEBNext® Small RNA Library Prep Set kit), 20 U RNaseOUT™ Recombinant Ribonuclease Inhibitor, and 100 U TGIRT™-III Reverse Transcriptase (InGex), by incubating at 50°C for 5 minutes, followed by 2 hours at 57°C. Template RNA was degraded by adding 1 μl of 5 M NaOH and incubating at 95°C for 3 minutes. After reaction cleanup, cDNA was eluted in 20 μl nuclease-free water, and barcodes were introduced by 15 cycles of PCR in the presence of 25 pmol of each primer, and 25 μl NEBNext® High-Fidelity 2X PCR Master Mix.
DMS-MaPseq

treatment_protocol: A single colony of Escherichia coli strain DH10B was inoculated into 250 ml of LB medium without antibiotics and grown at 37°C with shaking (150 RPM) for approximately 4 hours, until OD600 was ~0.3 (log phase). 25 ml aliquots of bacteria were then pelleted by centrifugation at 1800g for 15 minutes (4°C). After centrifugation, medium was decanted, and cells from each 25 ml of culture were resuspended in 1ml of structure probing buffer [50 mM HEPES-KOH pH7.9; 100 mM NaCl; 3 mM KCl]. DMS was diluted 1:6 in 100% Ethanol to a final concentration of 1.76 M. Diluted DMS was added to bacteria to a final concentration of ~105 mM. Samples were incubated with moderate shaking (800 RPM) at 25°C for 2 minutes, after which reactions were immediately transferred to ice. DTT was added to a final concentration of 0.7 M to quench DMS, and samples were vigorously vortexed for 10 seconds. Bacteria were then pelleted by centrifugation at 10,000g for 30 seconds (4°C), and the supernatant was decanted. Pellets were then washed once with 1 ml Isoamyl alcohol (Sigma Aldrich, cat. W205702) to remove traces of water-insoluble DMS. Bacteria were then pelleted by additional centrifugation at 10,000g for 30 seconds (4°C), supernatant was decanted, and samples were snap-frozen in liquid nitrogen.


title: DMS-MaPseq on E. coli (Total RNA)

description:
Total RNA
Data analysis was performed using RNA Framework (http://www.rnaframework.com).  Processed data files are: 1) WIGGLE track file of Box-plot normalized DMS reactivities (Ecoli_DMS-MaPseq.wig); 2) RC file for analysis with RNA Framework (Ecoli_DMS-MaPseq.rc); 3) RC file's index (index.rci).


title: Kidney_STK11_KD_rep1

hyb_protocol: cDNAs were generated and hybridized on GeneChip® Mouse Transcriptome Assay 1.0 (Affymetrix) according to the Affymetrix protocol.

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 7G using AGCC.

data_processing:
Raw data from CEL files were RMA normalized and summariezd to transcript clusters using the R Bioconductor package olifa
MTA-1_0.na36.mm10.transcript.csv

label: Biotin

source_name: Kidney

label_protocol: Sense target cDNA was prepared from 500 ng total RNA using the Ambion WT Expression kit; the cDNAs were fragmented and labeled with the Affymetrix Terminal labeling and Controls kit according to the manufacturers protocol.

growth_protocol: Mice were housed in a specific pathogen-free facility, fed ad libitum and housed at constant ambient temperature in a 12-hour day/night cycle. Breeding and genotyping were done according to standard procedures. Lkb1flox/flox mice (mixed genetic background) were purchased from The Jackson Laboratories (STOCK Stk11tm1.1Sjm/J, stock number: 014143) and were crossed to KspCre mice (B6.Cg-Tg(Cdh16-cre)91lgr/J; C57Bl/6N background)1  to generate a tubule-specific Lkb1 knockout (further referred to as Lkb1Δtub). Lkb1flox/+ and Lkb1flox/flox littermates that do not bear KspCre transgene were used as controls.

extract_protocol: Total RNAs were extracted and purified from 5-week old control and Lkb1Δtub kidneys (5 mice per genotype), using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

value: whole Kidney

value: 5 weeks

tag: condition

value: Stk11 Knockdown


title: K56 rep1

city: Austin

first: Muyoung

last: Lee

state: TX

address: 2506 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Illumina NextSeq 500 sequencer was used to carry out RNA sequencing.
Reads were aligned by STAR 2.4.2a to KPHS 11286 GCA_000240185.2_ASM24018v2 genome assembly.
Number of reads were counted by featureCounts.
Genome_build: GCA_000240185.2_ASM24018v2 (K. pneumoniae HS11286 genome downloaded from NCBI was used.)
Supplementary_files_format_and_content: Read counts from featureCounts for each sample.

organism: Klebsiella pneumoniae

source_name: clinical isolate

growth_protocol: K. pneumoniae K26, K56 and K26M strains were grown in 5 ml of LB broth for three hours.

extract_protocol:
RNA was isolated by growing the isolates to the logarithmic phase in high osmolarity LB broth at 37°C and extracting the RNA using RNeasy® mini kit (Qiagen GmbH, Hilden, Germany).  On-column DNA digestion was carried out using RNase-free DNase Kit (Invitrogen, Carlsbad, CA, USA). RNA concentration was measured using a NanodropTM spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA).
Library preparation was carried out using TruSeq Stranded total RNA Library Preparation Kit (Illumina, San Diego, CA, USA). Illumina NextSeq 500 sequencer (Illumina, San Diego, CA, USA) was used to carry out RNA sequencing.

tag: susceptibility

value: meropenem-resistant


title: K26 rep2

value: meropenem-susceptible


title: K26 rep1


title: Kidney_WT_rep5

value: replicate 5

value: wildtype


title: K56 rep2


title: U87mg 2-hour, replicate 1

status: Public on Jun 09 2018

city: Durham

first: Johnathan

middle: G

last: Lyon

state: NC

address: 1427 FCIEMAS BOX 90281

department: Biomedical Engineering

institute: Duke University

data_processing:
FASTQC Toolkit 2.0.0 Minimum Read Length 32
FASTQC Toolkit 2.0.0 Adapter Trimming (Stringency: 0.8; 5': GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG; 3': AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT; Trim Ns: True)
FASTQC Toolkit 2.0.0 Base Trimming (Trim reads at 5': 13; Trim reads at 3': 10)
FASTQC Toolkit 2.0.0 Quality Trimming (Trim the 3': 20)
FASTQC Toolkit 2.0.0 Poly A/T (5', 3': 4)
FASTQC Toolkit 2.0.0 Read Filtering (minimum quality: 5; only keep passing: true)
pseudo-alignment with Kallisto v0.43.0 (gencode v24 transcripts GRCh38.p5, 100 bootstrap samples, single-end mode, average fragment length and standard deviation obtained for each sample during quality control)
differential expression using Sleuth v0.28.1 in R v3.2.1
individual sleuth outputs merged into consolidated tsv file and log2 fold changes (using mean across samples for each condition for each transcript) calculated using python script
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: All the following in this subsection pertains to the fields found in consolidated_sleuth_output.tsv
transcript_id: Ensembl transcript accession id
name: Ensembl transcript or gene name
type: Ensembl transcript biotype
chromosome_name: Ensemble chromosome name
description: Ensembl transcript description
(SAMPLENAME)_counts: estimated counts for a given sample, SAMPLENAME (output from Kallisto)
(SAMPLENAME)_tpm: transcripts per million of the transcript for a given sample, SAMPLENAME (output from Kallisto)
(CONDITIONPAIR)_lfc: Log2 fold-change from the comparison of the CONDITIONPAIR for the given transcript. E.g., D0_D8_lfc reports the Log2 fold change of the mean of the tpm for a given transcript from the D0 samples (D0.0, D0.1, D0.2) to D8 samples (D8.0, D8.1, D8.2)
(CONDITIONPAIR)_pval: p-value from the comparison of the CONDITIONPAIR for the given transcript (Sleuth output)
(CONDITIONPAIR)_qval: False-discovery rate adjusted p-value using Benjamin-Hochberg (Sleuth output)

source_name: U87mg 2-hour

growth_protocol: All cells were maintained at 37ºC with 5% CO2 in Dulbecco’s Modified Eagle Medium (cellgro 15-017CV) with 10% fetal bovine serum (Gemini 900-108), 1% L-Glutamine (Lonza 17-605F), 1% Non-essential amino acids (cellgro 25-025-CI), and 1% penicillin-streptomycin (Corning 30-001-CI).  Cells were passaged before confluence using 0.25% Trypsin-EDTA (gibco 25200-056).

extract_protocol:
Electrotaxis channels were scraped and the cells and Matrigel collected into 600 μL of cell recovery solution (BD, now Corning 354253) and kept on ice for 30 min. Technical replices (n=3) were pooled and centrifuged for 5 min at 800xg, supernatant removed and stored at -80ºC. RNA was extracted using a RNeasy Micro Plus Kit (Qiagen 74034). Purity and yield was assessed on a Nanodrop 2000 (Thermo-Fisher). RNA integrity was assessed with an Agilent Bioanalyzer RNA 6000 Nanokit on an Agilent Bioanalyzer 2100.
Library preparation was done with a TruSeq Stranded mRNA Sample Preparation Guide LT with polyA tail pull-down. Library was validated with an Agilent DNA 1000 kit after fragmentation and addition of adapters. Samples were cleaned with AMPure XP beads and normalized with fluorimetric quantification to 10nM using a Qubit 2.0 Fluorometer using Qubit Broad Range (ThermoFisher Q32850) and High Sensitivity (ThermoFisher Q32854) kits.

treatment_protocol: Spheroidal aggregates of 700K and 1.4M cells were combined and embedded in 1:1 cellular media to Growth-Factor-Reduced Matrigel (Corning #354230), 30 uL total volume, and allowed to gel in a 200 um high by 5 mm wide by 15 mm long, channel for 24h. After which time, cells were exposed to 0, 2, or 8 hours of continuous direct current electrical field equivalent to 250 V/m.

tag: cell line

value: glioblastoma

value: electric field exposure

tag: time

value: 2 hr


title: U87mg 8-hour, replicate 0

source_name: U87mg 8-hour

value: 8 hr


title: U87mg 2-hour, replicate 0


title: U87mg 8-hour, replicate 1


title: U87mg 0-hour, replicate 1

source_name: U87mg 0-hour

value: 0 hr


title: U87mg 2-hour, replicate 2


title: DAOY 2-hour, replicate 2

source_name: DAOY 2-hour

value: DAOY

value: desmoplastic cerebellar medulloblastoma


title: DAOY 8-hour, replicate 1

source_name: DAOY 8-hour


title: U87mg 0-hour, replicate 2

value: control


title: DAOY 8-hour, replicate 0


title: U87mg 0-hour, replicate 0


title: Kidney_WT_rep4

value: replicate 4


title: Kidney_WT_rep3

value: replicate 3


title: DAOY 2-hour, replicate 1


title: Kidney_STK11_KD_rep5

value: whole Kidney


title: DAOY 0-hour, replicate 2

source_name: DAOY 0-hour


title: Kidney_WT_rep1

value: replicate 1

value: 5 weeks


title: Kidney_STK11_KD_rep3

value: Stk11 Knockdown


title: Kidney_STK11_KD_rep2

value: replicate 2


title: Kidney_WT_rep2


title: Kidney_STK11_KD_rep4


title: DAOY 2-hour, replicate 0


title: U87mg 8-hour, replicate 2


title: DAOY 8-hour, replicate 2


title: DAOY 0-hour, replicate 1


title: DAOY 0-hour, replicate 0


title: WT Htt_3

city: St. Louis

first: Hiroko

last: Yano

address: 660 South Euclid Avenue

department: Neurological Surgery

institute: Washington University School of Medicine

description:
27_1_wt_htt_expressing_mouse_cortical_neurons.CCATCAT
One library was produced for this sample and sequenced in two lanes to increase sequencing depth, creating technical replicates. The two fastq files were merged into a single aligned bam file.

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultipler written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text MS Excel format

source_name: WT Htt

extract_protocol:
Primary cortical neurons were prepared from mouse embryos (E16) and transduced with lentivirus expressing wild-type or mutant Htt (exon 1) or control vector at days culture in vitro (DIV) 5.  RNA was harvested at DIV 10.
Ribo-Zero

value: Swiss Webster

tag: cell type (days culture in vitro; div)

value: Primary cortical neurons (DIV 10)

tag: lentivirus infected

value: Htt-25Q exon1


title: Control vector_4

description:
27_1_control_mouse_cortical_neurons.GGCAGCG
One library was produced for this sample and sequenced in two lanes to increase sequencing depth, creating technical replicates. The two fastq files were merged into a single aligned bam file.

source_name: Control vector

value: Empty vector


title: WT Htt_4

description:
27_wt_htt_expressing_mouse_cortical_neurons.CTTGGAA
One library was produced for this sample and sequenced in two lanes to increase sequencing depth, creating technical replicates. The two fastq files were merged into a single aligned bam file.


title: Mut Htt_4

description:
27_1_mut_htt_expressing_mouse_cortical_neurons.TAACAAG
One library was produced for this sample and sequenced in two lanes to increase sequencing depth, creating technical replicates. The two fastq files were merged into a single aligned bam file.

source_name: Mut Htt

value: Htt-72Q exon1


title: Mut Htt_2

description:
24_mut_htt_expressing_mouse_cortical_neurons.TACTCTA
One library was produced for this sample and sequenced in two lanes to increase sequencing depth, creating technical replicates. The two fastq files were merged into a single aligned bam file.


title: Control vector_3

description:
26_control_mouse_cortical_neurons.AGACTGA
One library was produced for this sample and sequenced in two lanes to increase sequencing depth, creating technical replicates. The two fastq files were merged into a single aligned bam file.


title: Control vector_2

description: 24_control_mouse_cortical_neurons.CACCTCCOne library was produced for this sample and sequenced in two lanes to increase sequencing depth, creating technical replicates. The two fastq files were merged into a single aligned bam file.

value: Control vector


title: Control vector_1

description:
22_control_mouse_cortical_neurons.TGAGGTT
One library was produced for this sample and sequenced in two lanes to increase sequencing depth, creating technical replicates. The two fastq files were merged into a single aligned bam file.


title: WT Htt_1

description:
22_wt_htt_expressing_mouse_cortical_neurons.GCTTAGA
One library was produced for this sample and sequenced in two lanes to increase sequencing depth, creating technical replicates. The two fastq files were merged into a single aligned bam file.


title: WT Htt_2

description:
24_wt_htt_expressing_mouse_cortical_neurons.ATCGAGC
One library was produced for this sample and sequenced in two lanes to increase sequencing depth, creating technical replicates. The two fastq files were merged into a single aligned bam file.


title: cult.ISP_cKO_2

first: Dinah

middle: S.

last: Singer

address: Building 10, Room 4B-17

department: Division of Cancer Biology

data_processing:
RNA-seq reads were aligned to mouse reference genome (mm10) with STAR aligner. Raw read counts were obtained using htseq-count.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts of sequencing reads for each sample

source_name: ISP thymocytes after culture

extract_protocol:
The cell pellets were extracted using the Rneasy Plus Micro kit (Qiagen 74034)
RNA libraries were prepared for sequencing using Clontech SMARTer Ultra Low Input RNA Kit + Nextera XT DNA library

treatment_protocol: The thymocytes were purified by Flow cytometry based on the expression of  CD4, CD8, CD69 and TCRb cell surface markers. After culture, the thymocytes were purified on MACS Miltenyi Microbeads (130-049-201)

tag: tissue/cell type

value: Thymocytes

tag: genotype

value: Brd4 F/- LCK-cre+

tag: phenotype

value: BRD4 cKO

value: OverNight Culture


title: Input_WT

source_name: ISP thymocytes before culture

value: Thymus

value: BRD4 F/+ LCK-cre-

value: BRD4 WT

value: none_input before culture


title: Mut Htt_3

description:
26_mut_htt_expressing_mouse_cortical_neurons.CCGATTA
One library was produced for this sample and sequenced in two lanes to increase sequencing depth, creating technical replicates. The two fastq files were merged into a single aligned bam file.


title: cult.ISP_cKO_1


title: Input_cKO_2


title: CD8_WT_3

source_name: CD8 thymocytes


title: CD8_cKO_2


title: cult.DP_cKO_2

source_name: DP thymocytes after culture


title: CD4_cKO_3

source_name: CD4 thymocytes


title: CD8_cKO_3


title: CD8_WT_2


title: CD4_cKO_2


title: Mut Htt_1

description:
22_mut_htt_expressing_mouse_cortical_neurons.ATGACAG
One library was produced for this sample and sequenced in two lanes to increase sequencing depth, creating technical replicates. The two fastq files were merged into a single aligned bam file.


title: CD8_WT_1


title: CD4_cKO_1


title: cult.DP_cKO_1


title: Input_cKO_1


title: CD4_WT_3


title: CD4_WT_2


title: CD4_WT_1


title: DP_cKO_3

source_name: DP thymocytes


title: CD8_cKO_1


title: DP_cKO_1


title: cult.DP_WT


title: DP_WT_2


title: DP_WT_1


title: DP_WT_3


title: ISP_cKO_2

source_name: ISP thymocytes


title: ISP_cKO_3


title: ISP_WT_3


title: ISP_cKO_1


title: DN_cKO_3

source_name: DN thymocytes


title: DN_WT_3


title: ISP_WT_1


title: DN_cKO_1


title: DN_WT_2


title: WT Htt_control RNAi_4

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultipler written in python
The fastq file was aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text MS Excel format

source_name: WT Htt_control RNAi

extract_protocol:
Primary cortical neurons were prepared from mouse embryos (E16) and co-transduced with Htt (exon1)-expressing lentivirus and Twist1 shRNA- or control luciferase shRNA-expressing lentivirus at days culture in vitro (DIV) 5.  RNA was harvested at DIV 10.
Ribo-Zero

tag: cell  type (days culture in vitro; div)

value: Htt-25Q exon1 and luciferase shRNA


title: ISP_WT_2


title: DN_WT_1


title: Mut Htt_Twist1 RNAi #2_4

source_name: Mut Htt_Twist1 RNAi #2

value: Htt-72Q exon1 and Twist1 shRNA #2


title: Mut Htt_Twist1 RNAi #1_4

source_name: Mut Htt_Twist1 RNAi #1

value: Htt-72Q exon1 and Twist1 shRNA #1


title: Mut Htt_control RNAi_4

source_name: Mut Htt_control RNAi

value: Swiss Webster

value: Htt-72Q exon1 and luciferase shRNA


title: DP_cKO_2


title: Mut Htt_Twist1 RNAi #2_3

value: Primary cortical neurons (DIV 10)


title: Mut Htt_Twist1 RNAi #1_3


title: DN_cKO_2


title: Mut Htt_Twist1 RNAi #2_2


title: Mut Htt_control RNAi_2


title: WT SC, biological rep 2

city: Guelph

first: Dr. Tami

middle: A.

last: Martino

state: Ontario

address: 50 Stone Road E

department: Centre for Cardiovascular Investigations, Department of Biomedical Science

country: Canada

institute: University of Guelph

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix GeneChip Mouse Gene 2.0 ST array,  according to manufacturer's instructions. GeneChips were washed and stained on the GeneAltas platform.

scan_protocol: GeneChips were scanned on the GeneAltas platform.

data_processing: The data were analyzed with GeneSpring GX Software v. 14.8 using default Affymetrix settings.

label: biotin

source_name: WT - SC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA

growth_protocol: The mice were collected at 32 weeks of age (24 weeks on HFD or SC), 7 hours after lights on.

extract_protocol: Total RNA was extracted using the Trizol method according to the manufacturer's instructions.

treatment_protocol: The hearts were collected and snap frozen in liquid nitrogen and stored at -80°C.

tag: strain background

tag: genotype/variation

value: wild type

tag: diet

value: Standard Chow (SC) for 24 wks

tag: time point

value: ZT07; 7 hrs into the light phase

value: myocardium


title: Mut Htt_Twist1 RNAi #1_2

tag: strain


title: WT SC, biological rep 4


title: WT SC, biological rep 1


title: WT HFD, biological rep 4

source_name: WT - HFD

value: High-Fat (HFD) for 24 wks


title: WT SC, biological rep 3


title: WT Htt_control RNAi_2


title: Mut Htt_Twist1 RNAi #2_1


title: WT Htt_control RNAi_1


title: Mut Htt_control RNAi_1


title: WT Htt_control RNAi_3


title: WT HFD, biological rep 1


title: Mut Htt_control RNAi_3


title: Biofilm 72h [S14_13B2_72]

first: Anne

middle: de

last: Jong

institute: university of Groningen

data_processing:
mapping of reads was done using: bowtie2 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Bacillus cereus ATCC14579 | version NC_004722.1  GI:30018278 | 09-APR-2015
Supplementary_files_format_and_content: Tab delimited text file

organism: Bacillus cereus ATCC 14579

source_name: Cell culture

growth_protocol: Cells were grown as standing cultures in TY medium in 24-well plates, 1 ml/well, at 28ºC

extract_protocol:
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
cDNA library was prepared by employing a ScriptSeqtm Complete Kit for Bacteria

treatment_protocol: Planktonic cells were collected at 24h and biofilm cells at 24, 48 and 72 h. Planktonic cells were colected without disturbing submerged biofilm, taking only the 25% upper part of the medium of each well of a 24-well plate. From the same cultures, the medium was completely retired and the ring-shape biofilm was collected with a cotton swab and suspended in TY medium. Samples were inmediately centrifuged for 10 secs. at max. speed, the supernantant was discarded and tubes were inmediately freezed in liquid nitrogen.

tag: cell type

value: biofilm cells


title: Biofilm 72h [S13_13B1_72]


title: Biofilm 72h [S12_1B2_72]


title: Clock SC, biological rep 3

source_name: Clock - SC

value: Transgenic Clock delta 19/delta 19

tag: tissue


title: WT HFD, biological rep 2


title: Clock SC, biological rep 2


title: WT HFD, biological rep 3


title: Clock HFD, biological rep 2

source_name: Clock - HFD


title: Clock HFD, biological rep 1


title: Mut Htt_Twist1 RNAi #1_1


title: sma1-1 Rep 2

city: Lincoln

first: Chi

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

description: small RNA

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to TAIR10 whole genome using bowtie bowtie -v 0 -S -a --best --strata
Genome_build: TAIR10
Supplementary_files_format_and_content: Space-delimited plain text files: the first column is for MicroRNA gene IDs and the second column for reads counts

organism: Arabidopsis thaliana

source_name: sma1-1, inflorescence

growth_protocol: 16 hour light; 8 hour dark;  at 22 oC

extract_protocol:
Flower inflorescences were collected and total RNA was extracted by Trizol. Illumina TruSeq Small RNA Sample Prep Kits was used with 1 ug of total RNA for the construction of sequencing libraries.
Illumina small RNA library protocol

tag: ecotype

value: Columbia (Col)

value: inflorescence


title: Clock HFD, biological rep 4


title: Clock SC, biological rep 1


title: Biofilm 48h [S09_1B1_48]


title: Biofilm 48h [S10_1B2_48]


title: lsr2 mutant - 18 h - sample 2

city: HAMILTON

first: Marie

last: Elliot

state: ON

address: 1280 Main Street West

institute: McMaster University

description: T3_RNA-seq_wt_vs_lsr2mutant_Rockhopper analysis.csv

data_processing:
Raw sequencing reads were trimmed to remove low-quality 3’ ends using PrinSeq
Trimmed reads were checked for quality using FastQC
Reads were aligned to the S. venezuelae ATCC 10712 genome sequence using Bowtie2
Genome_build: S. venezuelae ATCC 10712 genome sequence
Supplementary_files_format_and_content: Resultant SAM files were converted to BAM format, sorted by genomic position and indexed to create bai files. The BAM files were analyzed using Rockhopper (Tjaden, 2015)

organism: Streptomyces venezuelae

source_name: Liquid culture-grown bacteria

growth_protocol: S. venezuelae grown for 8, 12 or 18 h in liquid MYM medium

extract_protocol:
RNA was extracted as per Moody et al. (2013) BMC Genomics
NEBNext Ultra Directional RNA Library Prep Kit

tag: developmental stage

value: late in development (18h) (fragmentation/sporulation stage)

value: lsr2 mutant


title: sma1-1 Rep 1

last: Zhang

description: small RNA


title: Biofilm 24h [S08_13B2_24]


title: Biofilm 72h [S11_1B1_72]


title: WT  (Col) Rep1

description: small RNA

source_name: WT, inflorescence

value: WT (Col)


title: lsr2 mutant - 18 h - sample 1


title: Wild type - 18 h - sample 2


title: Wild type - 18 h - sample 1


title: lsr2 mutant - 12 h - sample 2

description: T2_RNA-seq_wt_vs_lsr2mutant_Rockhopper analysis.csv

value: mid development (12h) (early mycelial fragmentation)


title: Biofilm 24h [S06_11B2_24]


title: Biofilm 24h [S05_11B1_24]


title: lsr2 mutant - 12 h - sample 1


title: Wild type - 12 h - sample 2


title: Biofilm 24h [S04_1B2_24]


title: Wild type - 12 h - sample 1


title: lsr2 mutant - 8h - sample 1

description: T1_RNA-seq_wt_vs_lsr2mutant_Rockhopper analysis.csv

value: early development (8h) (vegetative growth)


title: Biofilm 24h [S03_1B1_24]


title: Control (no FLAG-tag) - sample 2

description: Immunoprecipitated DNA

data_processing:
Reads in the fastq files were first checked for quality using FastQC
Reads were then aligned to the S. venezuelae ATCC 10712 genome using Bowtie2 (Langmead et al., 2009).
Resultant SAM files were converted to BAM format, sorted by genomic position and indexed to create bai files
Genome_build: S. venezuelae ATCC 10712
Supplementary_files_format_and_content: Resultant SAM files were converted to BAM format, sorted by genomic position and indexed to create bai files. BAM files were analyzed using DiffBind

source_name: Liquid-grown bacteria

extract_protocol:
Immunoprecipitation was carried out as described in Bush et al. (Bush et al., 2013), using Anti-FLAG (DYKDDDDK) affinity gel (BioTools)
NEBNext Ultra DNA Library Prep Kit was used for library preparation, starting with 10 ng of the sheared ChIP DNA and including a double-AMPure bead (Beckman Coulter) size selection

value: Late development (18h - mycelial fragmentation/sporulation)

value: Lsr2 - untagged (negative control)


title: Clock SC, biological rep 4


title: Biofilm 24h [S07_13B1_24]


title: WT  (Col) Rep2

description: small RNA


title: Wild type - 8 h - sample 2


title: Control (no FLAG-tag) - sample 1

description: Immunoprecipitated DNA


title: lsr2 mutant - 8 h - sample 2


title: Planktonic 24h [S02_1P2_24]

value: Planktonic cells


title: PANC-1 - control

city: Nanning

first: Qiao

address: Shuangyong road, qingxiu district，nanning

institute: First Affiliated Hospital of Guangxi Medical University

description: O

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R

data_processing: Extract data using Agilent Feature Extraction software.Feature Extraction (FE) is the process by which information from probe features is extracted from microarray scan data.

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: The human pancreatic cancer cell line PANC-1 was cultured in complete Dulbecco’s modified Eagle’s medium (DMEM).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: The PANC-1 cells treated with 100 µM chloroquine diphosphate were preferred as the autophagy-inhibited group(group A), and cells cultured by DMEM were selected as the control group(group O)

tag: cell line

tag: treatment

value: control


title: Wild type - 8 h - sample 1

value: wild type


title: Planktonic 24h [S01_1P1_24]


title: PANC-1 - chloroquine diphosphate

description: A

value: 100 µM chloroquine diphosphate for 12 hour


title: Lsr2-FLAG - sample 2

description: Immunoprecipitated DNA

value: Lsr2-FLAG tag


title: Lsr2-FLAG - sample 1

description: Immunoprecipitated DNA


title: Clock HFD, biological rep 3

value: High-Fat (HFD) for 24 wks

value: ZT07; 7 hrs into the light phase

value: myocardium


title: Rad_CD24Pos_3

status: Public on Jun 08 2018

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

description:
H_tdT_CD24pos_S7
FPKM.refGTF_Rad_CD24Pos_3

data_processing:
Read alignment and mapping done with TopHat2, version 2.1.0
Gene and transcript level computation done with StringTie, Version 1.3.4
Normalized abundance measurements generated by Ballgown, Release 3.6
Genome_build: mm9
Supplementary_files_format_and_content: CD24_gene_expression.fpkm_table containing normalized gene expression levels outputted by Ballgown

extract_protocol:
RNA extraction was performed using Qiagen RNeasy Plus Micro kit.
Illumina TruSeq RNA Library Prep kit v2

treatment_protocol: Paneth cells (tdT+CD24+) and derivative (tdT+CD24-) cells were FACS-sorted from irradiated (5 days after radiation) and non-irradiated 8-14 week old Lyz1CreER; R26R-tdT mice with one dose of tamoxifen administration

value: Lyz1CreER; R26R-tdT

tag: age

value: 8-14 week old

tag: mouse condition

value: irradiated (5 days after radiation)

value: Paneth cells (tdT+CD24+)


title: NoRad_CD24Pos_2

description:
C_tdT_CD24pos_S2
FPKM.refGTF_NoRad_CD24Pos_2

value: non-irradiated


title: NoRad_CD24Pos_1

description:
B_tdT_CD24pos_S1
FPKM.refGTF_NoRad_CD24Pos_1


title: Rad_CD24Pos_1

description:
D_Rad_tdT_CD24pos_S3
FPKM.refGTF_Rad_CD24Pos_1


title: Rad_CD24Pos_2

description:
F_tdT_CD24pos_S5
FPKM.refGTF_Rad_CD24Pos_2


title: Rad_CD24Neg_1

description:
E_tdT_CD24neg_S4
FPKM.refGTF_Rad_CD24Neg_1

value: derivative (tdT+CD24-) cells


title: RNAseq stimulated CD8_actinomycin

city: San Francisco

first: Adam

middle: Jacob

last: Litterman

state: CA

address: 513 Parnassus Avenue, UCSF Box 0414, HSE-201

department: Microbiology and Immunology

institute: UCSF

description:
oligo-dT selected RNA
protocol was as described until elution from oligo-dT beads, then poly-A RNA was prepared using Illumina TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions
All_genes_RNAseq.csv

data_processing:
For GCLiPP raw reads were demultiplexed by a custom script and linker trimmed with fastx_trimmer
Linker dimer reads were discarded and one uniquely aligning read with a given di-nucleotide randomer in the 3' RNA linker was kept for further analysis to remove PCR duplicates
GCliPP reads were aligned to mm10 using bowtie2
Peaks were called with in house perl scripts that convolved a normal distribution against observed read distribution at each nucleotide and looked of local maxima of correlation
RNAseq was aligned to mm10 with STAR
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, reads per million at each location in the genome; bed, location of called peaks and voids of GCLiPP read density; csv, per gene expression data from RNAseq

source_name: CD8 T cells

growth_protocol: Mouse T cells were grown on plates coated with anti-CD3 and anti-CD28 antibodies and the indicated cytokines for 5 days

extract_protocol:
Cells were lysed by re-suspension in PXL buffer without SDS. Cell debris were pelleted and supernatants were biotinylated with EZ-Link-NHS-SS-Biotin. Poly-A RNA was enriched by pulldown with oligo-dT beads. RNPs were captured with M-280 Streptavidin dynabeads and RNAs were digested with RNAse T1
Linkers were ligated on while RNPs were immobilized on M-280 beads and released by proteinase K digestion, size selected by TBE-Urea PAGE gel, gel extracted, reverse transcribed and used for cDNA amplification

treatment_protocol: Four hours before harvest cells were re-plated in fresh medium (resting) or re-stimulated with PMA/Ionomycin (stimulated). Cells were crosslinked with 8000 mJ high energy (254 nM) UV light

value: CD8 T cells

tag: culture conditions

tag: restimulation

value: PMA/Ionomycin


title: RNAseq resting Th2_actinomycin

source_name: CD4 T cells

value: CD4 T cells

value: IL-4, anti-Ifn-gamma, IL-2


title: RNAseq stimulated Th2_actinomycin


title: RNAseq resting CD8_actinomycin


title: PANC-1 - chloroquine diphosphate

description: A

treatment_protocol: The PANC-1 cells treated with 100 µM chloroquine diphosphate were preferred as the autophagy-inhibited group (group A), and cells cultured by DMEM were selected as the control group(group O)


title: Rad_CD24Neg_2

description:
G_tdT_CD24neg_S6
FPKM.refGTF_Rad_CD24Neg_2


title: Rad_CD24Neg_3

description:
I_tdT_CD24neg_S8
FPKM.refGTF_Rad_CD24_Neg_3


title: Recurrence glioblastoma tissue from patient 2

city: nanjing

first: chen

last: wanghao

state: jiangsu

address: Ding Jiaqiao 87th

department: School of Medicine

institute: southeast university

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: The lncRNA+mRNA array data were analyzed for data summarization, quantile normalization and quality control by using the GeneSpring software V11.5 (Agilent). Only Cy5 data were analyzed.

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: astrocytes acquired from the peripheral area of edema in tumor tissues from recurrence glioblastoma patients

tag: subject status

value: Recurrence glioblastoma (GBM) patient

tag: ID

value: Patient 2

tag: gender

value: male

tag: smoking

value: never-smoking

tag: tissue type

value: Cancer tissue


title: astrocytes acquired from the peripheral area of edema in tumor tissues from patient 3

value: astrocytes required from the area of edema in Recurrence glioblastoma (GBM) patient

value: Patient 3

value: female

value: Peritumoral  tissue


title: Recurrence glioblastoma tissue from patient 1

value: Patient 1

value: quit smoking more than ten years.


title: astrocytes acquired from the peripheral area of edema in tumor tissues from patient 1


title: Glioblastoma tissue from patient 3

source_name: Glioblastoma tissue from patient 3

value: glioblastoma (GBM) patient


title: Glioblastoma tissue from patient 2

source_name: Glioblastoma tissue from patient 2


title: PANC-1 - control

description: O

value: control


title: astrocytes acquired from the peripheral area of edema in tumor tissues from patient 2


title: DDX5-eCLIP-repC

city: Berkeley

first: Yeon

address: 1 Barker Hall

institute: UC Berkeley

data_processing:
Library strategy: eCLIP-seq
eCLIP sequencing reads were processed, quality-filtered, collapsed to eliminate PCR duplicates, then random barcodes from the adapters were removed before mapping to the hg19 genome. The reads were pre-processed prior to mapping using FASTX-Toolkit (v0.0.13) (http://hannonlab.cshl.edu/fastx_toolkit). Reads were quality filtered based on quality score (fastq_quality_filter -q 25 -p 80), and PCR duplicates were collapsed (fastx_collapser). The adapter sequences were then trimmed using fastx_clipper. 2nd round of clipping was performed to ensure trimming off the 3’ adapters on read 2 as described previously (Van Nostrand et al. 2016) and random-mer sequence were trimmed. Any reads less than 15 nt were discarded, and only reads 2, the read that is enriched for termination at the crosslinking site, were considered for mapping. Only uniquely mapped reads were used for the further analysis. The reads were mapped to hg19 using STAR (v2.5.2) using the following parameters: --outFilterMultimapNmax 1 -- quantMode TranscriptomeSAM GeneCounts --outReadsUnmapped fastx --outSAMtype BAM SortedByCoordinate. Uniquely mapped reads were filtered using samtools (samtools view –bq 1), then used for cluster identification using pyCRAC (v1.2.2.1) (Webb et al. 2014). eCLIP clusters were generated using at least 5 overlapping, unique cDNA reads generated after removal of PCR duplicates (pyClusterReads.py --cic=5 --mutsfreq=20). De novo motif for hnRNPA1 and DDX5 were determined using pyMotif tool from the pyCRAC package with the following options: --n 100 -r 50 --k_min=4 --k_max=8. Z-score are calculated to indicate overrepresentation of the k- mer sequence in the experimental data compared against k-mers from reads randomly distributed over the same genomic features. pyCalculateFDRs were used to filter out statistically significant clusters over the regions with a read coverage of at least 5 (--min=5) and FDR <0.05.

source_name: Myeloid leukemia cell line

growth_protocol: Human K562 cells (American Type Culture Collection, Manassas, VA, USA) were maintained at 37◦C in RPMI media, supplemented with 15% FBS, 1 mM sodium pyruvate (Gibco, Life Technologies), and 1X nonessential amino acids (Gibco, Life Technologies).

extract_protocol:
eCLIP was performed as previously described (Van Nostrand et al. 2016) with the exception of using nuclear extract prepared from K562 cells instead of whole cell extract, with the following antibodies: monoclonal anti-hnRNPA1 antibody, clone 9H10 (Sigma-Aldrich Cat# R4528 RRID:AB_261962), monoclonal anti-hnRNPA1 antibody, clone 4B10 (Sigma-Aldrich Cat# R9778 RRID:AB_477477), and polyclonal anti-DDX5 antibody (Abcam Cat# ab21696 RRID:AB_446484).
eCLIP was performed as previously described (Van Nostrand et al. 2016)

value: human myeloid leukemia cell line


title: DDX5-eCLIP-noUV-control


title: hnRNPA1-eCLIP-repC


title: DDX5-eCLIP-input-control


title: DDX5-eCLIP-repA


title: hnRNPA1-eCLIP-input-control


title: DDX5-eCLIP-repB


title: hnRNPA1-eCLIP-repA


title: hnRNPA1-eCLIP-noUV-control


title: Glioblastoma tissue from patient 1

source_name: Glioblastoma tissue from patient 1


title: Recurrence glioblastoma tissue from patient 3


title: hnRNPA1-eCLIP-repB


title: Control miRNA mimic-transfected MLE-12 cells_rep3

city: Madison

first: Tadashi

last: Maemura

state: Wisconsin

address: 575 Science Drive

institute: Influenza Research Institute

hyb_protocol: Six hundred nanograms of Cy3-labelled cRNA was fragmented and hybridized on the Agilent SurePrint G3 Mouse GE microarray 8×60 K.

scan_protocol: The microarray slides were scanned using an Agilent High-Resolution Microarray Scanner (Agilent Technologies), and image data were processed by using Agilent Feature Extraction software ver. 10.7.3.1.

data_processing: For the analysis of the mRNA arrays, we used the Bioconductor and the Limma package. First, we read the signals extracted from the array images, and adjusted the signal to account for local background noise. We normalized the signal between the arrays by using the quantile method, and filtered the probes that were expressed at similar levels as the background signal (i.e., < 10% higher), and that were absent from at least 3 arrays. Next, we fitted a linear model to the expression of each gene to estimate the significance of its differential expression between the test conditions. Finally, we calculated all statistical variables using empirical Bayes, and used the Benjamini-Hochberg correction to adjust the p-values to account for multiple comparisons. We considered results significant if the log fold-change was 0.6 lower than that in the control miRNA-transfected MLE-12 cell group, and the adjusted p-values were < 0.05.

source_name: MLE-12 cells transfected with Control miRNA mimic, replicate 3

label_protocol: One hundred nanograms of total RNA was used for microarray by using a Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) according to the manufacturer’s instructions.

growth_protocol: MLE-12 cells were maintained in DMEM/F-12 medium supplemented with 0.005 mg/ml insulin, 0.01 mg/ml transferrin, 30 nM sodium selenite, 10 nM hydrocortisone, 10 nM beta-estradiol, 10 mM HEPES, 2 mM L-glutamine, and 2% FCS. MILE SVEN 1 (MS1) cells were maintained in Dulbecco’s modified Eagle medium supplemented with 5% FCS. All cells were cultured at 37°C and 5% CO2.

extract_protocol: The total RNA from the exosomes was isolated by using the miRNeasy Mini Kit (QIAGEN). Isolated total RNA integrity was evaluated by using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and by examining 28S/18S ribosomal RNA bands with an Agilent 2100 bioanalyzer (Agilent Technologies) according to the manufacturer’s instructions.

treatment_protocol: Approximately 4 × 105 MLE-12 cells were transfected twice with 5 pmol of the miRNA mimic by using the Lipofectamine RNAiMAX Reagent (Thermo Fisher Scientific) with a 24-h interval between transfections according to the manufacturer’s instructions. Twenty-four hours after the second transfection, the transfected cells were infected with PR8 at an MOI of 2. Total RNA was isolated 12 hours after infection.

tag: stimulant

tag: transfection

value: Control miRNA mimic


title: Control miRNA mimic-transfected MLE-12 cells_rep2

source_name: MLE-12 cells transfected with Control miRNA mimic, replicate 2


title: Control miRNA mimic-transfected MLE-12 cells_rep1

source_name: MLE-12 cells transfected with Control miRNA mimic, replicate 1


title: Lung_P40_control_5

city: Großhansdorf

first: Espen

middle: E

last: Groth

address: Wöhrendamm 80

department: Department of Pulmonology

institute: LungenClinic Grosshansdorf

hyb_protocol: Samples were hybridized to Mouse GeneChip 2.0 ST arrays (Affymetrix). Hybridized arrays were washed and stained using the GeneChip Hybridization Wash and Stain Kit with a Fluidics Station 450 (Affymetrix) according to manufacturer's instructions.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G at standard settings (Affymetrix GeneChip Command Console).

data_processing:
RMA expression value calculated with Affymetrix' Expression Console software (gene-level, default settings).
CEL-files were imported to the Expression Console software (Affymetrix). For background correction, normalization and summarization we used the RMA workflow (gene-level) at standard settings. Transcription sets were annoted within the software using the transcription set annotation data available from Affymetrix (release 36).

source_name: P40 control mouse, born of control dam

label_protocol: 100 ng of RNA per sample were amplified, transcribed to terminal single-strand cDNA and labeled with the Ambion WT Expression Kit (Life Technologies), follwing the manufacturer's standard protocol.

growth_protocol: Pregnant dams were sacrificed by intraperitoneal (i.p.) injection of thiopental (200mg/kg), fetuses were retrieved and fetus lungs dissected. Animals at P40 underwent deep anesthesia (thiopental 70mg/kg i.p.) and muscle relaxation (pancuronium 1mg/kg i.p.) before subsequent lung function assessment. Animals were exsanguinated via the abdominal aorta and right lungs were collected. Fetal and adult lungs were snap frozen with liquid nitrogen and stored at -80 °C until RNA extraction.

extract_protocol: Total RNA was isolated from lung samples with the Rneasy Mini Kit (Qiagen), according to the manufacturer's instructions.

value: lung

tag: study group

tag: lung developmental stage

value: Readily alveolarized


title: Lung_P40_exposed_2

source_name: P40 PM2.5-exposed mouse, born of PM2.5-exposed dam

tag: tissue

value: exposed


title: mmu-miR-483-3p mimic-transfected MLE-12 cells_rep2

source_name: MLE-12 cells transfected with mmu-miR-483-3p mimic, replicate 2

value: mmu-miR-483-3p mimic


title: Lung_P40_control_3

tag: developmental stage


title: mmu-miR-483-3p mimic-transfected MLE-12 cells_rep3

source_name: MLE-12 cells transfected with mmu-miR-483-3p mimic, replicate 3

tag: cell line


title: Lung_P40_exposed_3


title: Lung_P40_control_1


title: mmu-miR-483-3p mimic-transfected MLE-12 cells_rep1

source_name: MLE-12 cells transfected with mmu-miR-483-3p mimic, replicate 1


title: Lung_P40_exposed_1


title: Lung_P40_control_2


title: Lung_P40_exposed_5


title: Lung_E18.5_exposed_4

source_name: E18.5 fetus from PM2.5-exposed dam

value: Saccular Stage


title: Lung_E18.5_exposed_3


title: Lung_E18.5_exposed_2


title: Lung_P40_control_4


title: Lung_P40_exposed_4


title: Lung_E18.5_exposed_1


title: Lung_E14.5_exposed_2

source_name: E14.5 fetus from PM2.5-exposed dam

value: Pseudoglandular stage


title: Lung_E18.5_control_2

source_name: E18.5 fetus from control dam


title: Lung_E14.5_exposed_1


title: Lung_E18.5_control_1


title: Lung_E18.5_control_4


title: Lung_E18.5_control_3


title: Lung_E14.5_exposed_4


title: Lung_E14.5_control_4

source_name: E14.5 fetus from control dam


title: Lung_E14.5_exposed_3


title: Lung_E14.5_control_3


title: Lung_E14.5_control_1


title: Mst1/2-KO CD8- Dendritic cells_replicate 4

city: Memphis

first: Jiyang

last: Yu

state: TN

address: 262 Danny Thomas Place, MS 1135

department: Computational Biology

institute: St. Jude Children's Research Hospital

hyb_protocol: Six micrograms (6 ug) of cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Mouse Gene 2.0 ST GeneChip array.

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

data_processing:
Signals were summarized using the Robust Multichip Algorithm (RMA) using Partek Genomics Suite software v6.6 (Partek, Inc). The data from each experiment was summarized as two independent groups.
Performed batch effects removal after combining all together

source_name: CD8- Dendritic cells

label_protocol: One to five nanograms (1-5 ng) of total RNA were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Cells were freshly sorted from spleen of mice by FACS

extract_protocol: RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted DCs were lysed with lysis buffer from Rneasy Micro kit from Qiagen

tag: expid

tag: strain

tag: genotype/variation

tag: cell type

value: CD8- Dendritic cells

tag: group


title: Mst1/2-KO CD8- Dendritic cells_replicate 2


title: Mst1/2-KO total Dendritic cells_replicate 2

source_name: Total Dendritic cells

value: Total Dendritic cells


title: Mst1/2-KO CD8+ Dendritic cells_replicate 4

source_name: CD8+ Dendritic cells

value: CD8+ Dendritic cells


title: WT CD8- Dendritic cells_replicate 2

value: WT


title: Lung_E14.5_control_2


title: Mst1/2-KO CD8- Dendritic cells_replicate 1


title: WT CD8- Dendritic cells_replicate 4


title: WT CD8- Dendritic cells_replicate 1


title: Rag1-ko dendritic cells, non-stimulated, Expt2_replicate 1

source_name: Total Dendritic cells, non-stimulated

tag: stimulatation

value: non-stimulated

value: totalDC


title: WT CD8+ Dendritic cells_replicate 1


title: WT total Dendritic cells_replicate 3


title: Mst1/2-KO CD8- Dendritic cells_replicate 3


title: Mst1/2-KO total Dendritic cells_replicate 1


title: WT total Dendritic cells_replicate 2


title: Mst1/2-KO total Dendritic cells_replicate 3


title: WT total Dendritic cells_replicate 4


title: Mst1/2-KO CD8+ Dendritic cells_replicate 1


title: Mst1/2-KO CD8+ Dendritic cells_replicate 3


title: WT total Dendritic cells_replicate 1


title: Mst1/2-KO CD8+ Dendritic cells_replicate 2


title: WT CD8- Dendritic cells_replicate 3


title: WT CD8+ Dendritic cells_replicate 2