title: Lung_Control_Day90_rep1

description:
2232
Gene expression in lung of control rat 90 days post exposure

source_name: Rat, Lung, Control, Day 90, replicate 1


title: Lung_Exposed_Day180_rep3

status: Public on Jan 17 2019

type: RNA

city: Vadoeuvre-lès-Nancy

first: Laëtitia

last: CHEZEAU

address: 1 rue du Morvan

country: France

institute: INRS

description:
2293
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 180 days post exposure

hyb_protocol: 600 ng of Cy3-CTP-labelled cRNA (Specific Activity > 10 pmol Cy3 per µg cRNA) were fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25X Agilent Fragmentation Buffer and 10X Agilent Blocking Agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2X Agilent Hybridization Buffer were added to the fragmentation mixture. The subsequent purified labelled cRNAs were hybridized to Agilent G4853A SurePrint G3 Rat GE 8*60K microarrays (Agilent Technologies) at 65°C overnight (17h) in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Agilent Gene Expression Wash Buffer 1 and 1 min with 37°C Agilent Gene Expression Wash buffer 2.

scan_protocol: Slides were scanned immediately after washing using Agilent high-resolution scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing: Agilent Feature Extraction Software (v 11.0.1.1) was used for background subtraction and data were quantile normalized using the software Solo (http://www-microarrays.u-strasbg.fr/Solo/index.html)

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 180, replicate 3

label_protocol: For each of the 50 samples (5 control and 5 exposed rats per time group), 100 ng of RNA were labelled with Cyanine 3-CTP using Low Input Quick Amp Labelling kits (One-Color Microarray-Based Gene Expression Analysis, version 6.7, Agilent Technologies) and purified (RNeasy Mini kit, QIAGEN) according to the manufacturer's instruction . Dye incorporation and cRNA yield and quality were checked by spectrophotometry (BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyser).

growth_protocol: Accessory lobe of rat lungs were stored in RNA later at -20°C before use

extract_protocol: Total RNA were disrupted using gentleMACS™ Dissociator (Miltenyi Biotech) and extracted from accessory lobe of lungs with Nucleospin® RNA midi kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality was determined by spectrophotometry (A260nm/A280nm > 1.8, BioSpec-nano, Shimadzu) and by capillary electrophoresis using Agilent 2100 Bioanalyser (RIN > 7, Agilent RNA 6000 NanoRNA 6000 Nano® Kit, Santa Clara, CA, USA).

treatment_protocol: 12 week old male F344 rats were exposed by nose-only inhalation 6 hours/day, 5 days/week for 4 weeks to an aerosol of TiO2 P25 nanoparticles (Evonik, 10 mg/m3).

tag: strain

tag: tissue

value: accessory lobe of lung

tag: gender

value: male

tag: age

value: 12 weeks-old


title: Lung_Control_Day28_rep3

description:
2228
Gene expression in lung of control rat 28 days post exposure

source_name: Rat, Lung, Control, Day 28, replicate 3


title: Lung_Exposed_Day90_rep5

description:
2289
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 90 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 90, replicate 5


title: Lung_Exposed_Day28_rep4

description:
2278
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 28 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 28, replicate 4


title: Lung_Exposed_Day90_rep2

description:
2285
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 90 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 90, replicate 2


title: Lung_Control_Day90_rep2

description:
2237
Gene expression in lung of control rat 90 days post exposure

source_name: Rat, Lung, Control, Day 90, replicate 2


title: Lung_Control_Day28_rep4

description:
2297
Gene expression in lung of control rat 28 days post exposure

source_name: Rat, Lung, Control, Day 28, replicate 4


title: Lung_Control_Day28_rep5

description:
2298
Gene expression in lung of control rat 28 days post exposure

source_name: Rat, Lung, Control, Day 28, replicate 5


title: Lung_Control_Day28_rep2

description:
2227
Gene expression in lung of control rat 28 days post exposure

source_name: Rat, Lung, Control, Day 28, replicate 2


title: Lung_Control_Day28_rep1

description:
2223
Gene expression in lung of control rat 28 days post exposure

source_name: Rat, Lung, Control, Day 28, replicate 1


title: Lung_Exposed_Day3_rep3

description:
2269
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 3 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 3, replicate 3


title: Lung_Exposed_Day3_rep5

description:
2271
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 3 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 3, replicate 5


title: Lung_Exposed_Day3_rep4

description:
2270
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 3 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 3, replicate 4


title: F2110

type: SRA

city: Madison

first: Dudley

last: Lamming

state: WI

address: 2500 Overlook Terr

department: Medicine

country: USA

institute: University of Wisconsin-Madison

library_source: transcriptomic

data_processing:
base-calling: bcl2fastq 1.8.2
trimming: skewer-0.1.123
alignment: STAR_2.5.0a
expression: RSEM v1.2.6
differential expression: edgeR 3.10.5 under R 3.2.1
Genome_build: mm10
Supplementary_files_format_and_content: CSV containing RSEM values

molecule: polyA RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Trireagent (Sigma)
stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide Rev. E.

value: liver

tag: diet

value: Control (TD.140711)

value: 9 week-old


title: F7111


title: H828


title: H1315


title: H817


title: H1126


title: F2212


title: F129


title: Lung_Control_Day3_rep1

description:
2212
Gene expression in lung of control rat 3 days post exposure

source_name: Rat, Lung, Control, Day 3, replicate 1


title: Lung_Exposed_Day3_rep2

description:
2263
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 3 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 3, replicate 2


title: Lung_Control_Day3_rep3

description:
2215
Gene expression in lung of control rat 3 days post exposure

source_name: Rat, Lung, Control, Day 3, replicate 3


title: Lung_Control_Day3_rep4

description:
2221
Gene expression in lung of control rat 3 days post exposure

source_name: Rat, Lung, Control, Day 3, replicate 4


title: Lung_Exposed_Day0_rep4

description:
2253
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) immediately after the end of exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 0, replicate 4


title: Lung_Exposed_Day0_rep1

description:
2250
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) immediately after the end of exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 0, replicate 1


title: Lung_Control_Day0_rep2

description:
2202
Gene expression in lung of control rat immediately after the end of exposure

source_name: Rat, Lung, Control, Day 0, replicate 2


title: Lung_Exposed_Day3_rep1

description:
2262
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 3 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 3, replicate 1


title: Lung_Control_Day0_rep1

description:
2201
Gene expression in lung of control rat (exposed to inhaled air) immediately after the end of exposure

source_name: Rat, Lung, Control, Day 0, replicate 1


title: Lung_Control_Day3_rep2

description:
2213
Gene expression in lung of control rat 3 days post exposure

source_name: Rat, Lung, Control, Day 3, replicate 2


title: Lung_Control_Day0_rep5

description:
2206
Gene expression in lung of control rat immediately after the end of exposure

source_name: Rat, Lung, Control, Day 0, replicate 5


title: Lung_Control_Day3_rep5

description:
2222
Gene expression in lung of control rat 3 days post exposure

source_name: Rat, Lung, Control, Day 3, replicate 5


title: Lung_Exposed_Day0_rep2

description:
2251
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) immediately after the end of exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 0, replicate 2


title: Lung_Control_Day0_rep3

description:
2204
Gene expression in lung of control rat immediately after the end of exposure

source_name: Rat, Lung, Control, Day 0, replicate 3


title: Lung_Control_Day0_rep4

description:
2205
Gene expression in lung of control rat immediately after the end of exposure

source_name: Rat, Lung, Control, Day 0, replicate 4


title: Lung_Exposed_Day0_rep3

description:
2252
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) immediately after the end of exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 0, replicate 3


title: Lung_Exposed_Day0_rep5

description:
2254
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) immediately after the end of exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 0, replicate 5


title: IL27_Minicircle_1: mouse_splenocytes_IL27_treated_rep1

city: Cambridge

first: Devan

last: Moodley

state: MA

address: 50 Hampshire St, 8th floor

institute: Surface Oncology

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce expression values using the implementation of the Robust Multiarray Average (RMA) in Expression Console (build 1.4.1.46).

label: biotin

source_name: spleen IL27 treated

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Six-week-old female Balb/c mice housed under SPF conditions

extract_protocol: Total RNA was extracted from splenocytes after mechanical dissociation and ACK lysis, with the RNeasy® Mini Kit (Qiagen, Cat. No: 74104)

treatment_protocol: Mice were injected with 20 μg of either empty vector or linked human IL-27 minicircle DNA (System Biosciences, Palo Alto, CA) in 2 ml 0.9% normal saline via the tail vein over the course of 5 seconds (3 replicates each). Spleens were collected from mice five days after minicircle injection.

value: Balb/c

value: spleen

tag: cell type

value: splenocytes


title: IL27_Minicircle_2: mouse_splenocytes_IL27_treated_rep2


title: IL27_Minicircle_3: mouse_splenocytes_IL27_treated_rep3


title: 10 days diff PLZF siRNA-C RNA-seq

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
Genome_build: hg19
Data received from RNA sequencing were mapped and analyzed by using Genomatix software and the Genomatix Mapper algorithm (Expression Analysis for RNASeq Data, GGATM) (Genomatix Software GmbH, Germany) according to their guidelines.
Normalised gene expression was calculated using following formula (by the software): NE = c * #reads / (#reads * length) where NE is the normalized expression or enrichment value, #reads: the reads (sum of base pairs) of falling into either the transcript or the cluster region, #reads: all mapped reads (in base pairs), length: the transcript or cluster length in base pairs and c a normalization constant set to 10^7.
Differential expression and significance was calculated and corrected for multiple testing using Genomatix's implementation of the DeSeq algorithm (Anders S, Huber W. Genome Biology, 11, R106 (2010)). This was done as pair-wise and transcript-based analyses in a strand-unspecific manner.

organism: Homo sapiens

source_name: Bone marrow derived hMSC

growth_protocol: Cells were cultured according to manufacturer’s instructions (Lonza, CAt.No-PT-2501) using mesenchymal stem cell growth medium (MSCGM) (Lonza MSCGM™: PT-3238) supplemented with one MSCGM™ SingleQuots™ (PT-4105).

extract_protocol:
Total RNA representing the indicated time points were purified from hMSC using RNeasy Plus Mini kit (QIAGEN 74106)
For RNA sequencing, samples were processed using a True Seq RNA Sample preparation kit (Illumina # 15025062) following the manufacturer’s instructions. Samples were multiplexed and sequenced in HiSeq2000

treatment_protocol: Differentiation was induced using StemPro osteogenesis (Gibco A10072-01), differentiation kit as per manufacturer’s instructions.  Cells were harvested at the indicated time points for ChIP, RNA, 4C-seq and protein using appropriate buffers as described below.

value: human Mesenchymal Stem Cells

tag: passages


title: 2 days diff PLZF siRNA-C RNA-seq


title: 2 days diff PLZF siRNA-B RNA-seq


title: 10 days diff PLZF siRNA-B RNA-seq


title: 10 days diff PLZF siRNA-A RNA-seq


title: NaïvePLZF siRNA-C RNA-seq


title: 2 days diff PLZF siRNA-A RNA-seq


title: NaïvePLZF siRNA-B RNA-seq


title: Control_3: mouse_splenocytes_untreated_rep3

source_name: spleen untreated


title: 10 days diff Control siRNA-A RNA-seq


title: Control_2: mouse_splenocytes_untreated_rep2


title: 10 days diff Control siRNA-B RNA-seq


title: 10 days diff Control siRNA-C RNA-seq


title: NaïvePLZF siRNA-A RNA-seq


title: 2 days diff Control siRNA-B RNA-seq


title: 2 days diff Control siRNA-C RNA-seq


title: NaïveControl siRNA-B RNA-seq


title: NaïveControl siRNA-C RNA-seq


title: NaïveControl siRNA-A RNA-seq


title: Input_d10: Input 10 days_ChIP

library_source: genomic

data_processing:
Reads were trimmed for low quality nucleotides and mapped to the hg19 human genome sequence using Bowtie v0.12.7 (Langmead, Trapnell et al., 2009) using the parameters "-S -m 1".
Aligned datasets were filtered for multiple reads at the same position likely to occur from PCR amplification using EaSeq (Lerdrup et al, NSBM 2016, http://easeq.net)
The reads were extended to a DNA fragment size of 300 bp and exported as wig files using EaSeq (Lerdrup et al, NSBM 2016, http://easeq.net)
Genome_build: hg19
Supplementary_files_format_and_content: Fixed-step wig-files generated using  (Lerdrup et al, NSBM 2016, http://easeq.net)
Supplementary_files_format_and_content: Values represent fragments/kilobasepair/Mreads (FPKM)

molecule: genomic DNA

extract_protocol:
Cells were processed for ChIP as previously described with slight modifications (Dietrich, Lerdrup et al., 2012). Briefly, cells were fixed for 10 min in culture media containing 1% formaldehyde and were processed for ChIP as previously described with slight modifications (Dietrich et al., 2012).
ChIP DNA from three parallel ChIPs were pooled or individual ChIPs from three biological replicates were used and 10 ng each was used for making ChIP-seq libraries. The libraries were prepared using “ChIP seq DNA sample preparation kit” from Illumina following manufacturer’s instructions. H3K27ac samples were multiplexed (using NEB kit) and run on HiSeq2000 (Illumina).

tag: chip antibody


title: K4me1_d10: H3K27Me1 10 days_ChIP

value: anti-H3K4me1-Abcam (ab8895)


title: K4me1_d0: H3K27Me1 naïve_ChIP


title: Input_d0: Input naïve_ChIP


title: K27Ac_d0: H3K27Ac naïve_ChIP

value: anti-H3K27ac-Abcam (ab4729)


title: K27Ac_d10: H3K27Ac 10 days_ChIP


title: K27me3_d0: H3K27Me3 naïve_ChIP

value: anti-H3K27me3-Cell Signalling (9733)


title: Control_1: mouse_splenocytes_untreated_rep1


title: K27me3_d10: H3K27Me3 10 days_ChIP


title: 2 days diff Control siRNA-A RNA-seq


title: PLZF_Si_Ud: hMSC-Naïve-PLZF Si-EnP

data_processing:
Library strategy: 4C-seq
The 4C-seq mapping and normalization was carried out using the mapping and normalization strategy (van de Werken et al., 2012a) as previously described (van de Werken et al., 2012b).
4C-seq reads were demultiplexed and the primers sequences without the first restriction enzyme recognition site, were removed from the reads.
Trimmed reads were mapped to a database with in silico digested genomic fragment-ends of the human reference genome build hg19.
The view point, the non-cut fragment-end and the self-ligation fragment-end were discarded.
After linear interpolation of the center of the fragment-ends, the distribution of the blind-fragment reads and the non-blind fragment reads were quantile normalized using R's limma package (Smyth, 2005).
The 4C-seq contact frequencies within the locus of interest were normalized to its library size. The 4C-seq contact frequencies were used to calculate the trimmed mean (10%) with a running window size of 21 fragment-ends.
Since 4C-seq contact frequencies have a PCR amplification bias, we carried out a non-parametric approach by ranking each fragment-end and applying a 2-test on the summed rank position for both samples on each running window.
We determined the sample with the highest contact frequencies per window and corrected for multiple hypothesis testing using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995).
Genome_build: hg19
Supplementary_files_format_and_content: Variable step wiggle files

extract_protocol:
Templates for 4C were prepared as described previously (van de Werken et al., 2012a; van de Werken et al., 2012b). The enzymes used were four base pair cutters DpnII and Csp6I. Osteogenic induced (2 days; preosteoblasts) or naive hMSCs (10   107 cells per group) .
PCR amplification was performed using 3 mg of 4C DNA, and PCR conditions were 98°C (2 min), 98°C (15 s), 58°C (1 min), 72°C (3 min), repeated for 30 cycles and final amplification for 7 min at 72°C using Phusion High Fidelity DNA Polymerase (Thermo Scientific).

tag: view point

value: EnP View point

tag: primers

value: PrimerS-EnP-(illumina+Comp or direct genomic region+genomic)=AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGCTTCTTCTGGTGTGAGATC, PrimerAS-EnP (illumina+genomic)=CAAGCAGAAGACGGCATACGACCCTCAACAAAACAATCACT


title: hMSC_udiff_pr2: hMSC-Naïve-PLZF-Promoter

value: PLZF Promoter view point

value: PrimerS-PLZF-promoter (illumina+Comp or direct genomic region+genomic)=AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTTAGTGAGGGGGCCTAGGATC,PrimerAS-PLZF-promoter(illumina+genomic)= CAAGCAGAAGACGGCATACGAAATGAAGTGGAGACTGAAGG


title: Ud_alt_start: hMSC-Naïve-NNMT-Promoter

value: NNMT Promoter view point

value: PrimerS-NNMT-Promoter-(illumina+Comp or direct genomic region+genomic)=AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTCCACACTTGGTGAGCAGGATC, PrimerAS-NNMT-Promoter ((illumina+genomic)=CAAGCAGAAGACGGCATACGAAAGTTGTTATCCTGGTTTGC


title: hMSC_diff_pr2: hMSC-2ddiff-PLZF Promoter


title: PLZF_Si_2ddiff: hMSC-2ddiff-PLZF Si-EnP


title: 2ddiff: hMSC-2ddiff-EnP (Rep3)


title: hMSC_Ud: hMSC-Naïve-EnP (Rep2)


title: Ud: hMSC-Naïve-EnP (Rep3)


title: hMSC_udiff_pr13: hMSC-Naïve-EnP (Rep1)


title: hMSC_diff_pr13: hMSC-2ddiff-EnP (Rep1)


title: 2ddiff_alt_start: hMSC-2ddiff-NNMT-Promoter

value: PrimerS-NNMT-Promoter-(illumina+Comp or direct genomic region+genomic)=AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTCACACTTGGTGAGCAGGATC, PrimerAS-NNMT-Promoter ((illumina+genomic)=CAAGCAGAAGACGGCATACGAAAGTTGTTATCCTGGTTTGC


title: ST_NR3

city: Lausanne

first: Olaia

last: Naveiras

address: Route cantonale

country: Switzerland

institute: EPFL

data_processing:
Fastq were trimmed for Nextera and Smart adapters
Fastq files were evaluated using FastQC v0.11.2
Sequences were mapped to the Ensembl-91 gene annotation of GRCm81 using STAR v2.5.0b
The number of tags belonging to each gene was then counted using HTSeq v0.6.1 with the following parameters “htseq-count -s no -m union -f bam”
Genome_build: GRCm81.91

source_name: Bone marrow

growth_protocol: LT-HSCs (Lin-ckit+sca1+CD150+CD48-CD34-) and ST-HSCs (Lin-ckit+sca1+CD150+CD48-CD34+) were FACS-sorted and cultured for 2 days. Cultures were maintained in Stemline II (Sigma) supplemented with 100ng/ml SCF (R&D) and 2ng/ml Flt3 (R&D) +/- NR.

extract_protocol:
Total RNAs extracted using the Quick-RNA Microprep Kit (R1050, Zymo Research) following the manufacturer's instructions.
The cDNAs were prepared from 2.5 ng RNA per sample with the "SMART-seq v4 Ultra Low Input RNA Kit for Sequencing" (Clontech), and subsequently processed into sequencing libraries with the Nextera XT kit (Illumina FC-131-1096), following manufacturer’s instructions.

treatment_protocol: NR was added at 1mM and replenished after 24h into the culture media.

tag: cells

value: ST-HSC

tag: treatment

value: Treated with 1mM NR


title: LT_NR2

value: LT-HSC


title: LT_C3

value: Control


title: ST_C3


title: ST_NR1


title: LT_C2


title: ST_C1


title: LT_NR3


title: Control_Si_2ddiff: hMSC-2ddiff-Control Si-EnP


title: Control_Si_Ud: hMSC-Naïve-Control Si-EnP


title: mouse medial cntrl rep 1

city: Boston

first: Benjamin

last: Okaty

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

data_processing:
Illumina CASAVA 1.8.2 for HiSeq 2000 or RTA 2.4.6 for NextSeq500
Sequencing data in FASTQ format were aligned to the mouse genome (mm9) using the RUM pipeline (version 1.11 (Grant et al., 2011)) or to the chicken genome (Galgal5) using the STAR aligner (Dobin et al., 2013).
Genome feature quantification for mouse data was performed with RUM, using RefSeq annotations, and for chicken data with STAR using the Gallus_gallus.Gallus_gallus-5.0.93.gtf annotation file downloaded from Ensembl.org
Genome_build: mm9 for mouse, Galgal5 for chicken
Supplementary_files_format_and_content: counts

source_name: Embryonic brainstem

extract_protocol:
Vestibulospinal neurons were retrogradely labeled for manual cell isolation with tetramethylrhodamine-conjugated dextran amine, acutely dissociated, and manually sorted.
RNA was isolated using the PicoPure RNA Isolation kit (Applied Biosystems), cDNA was synthesized and amplified using Ovation RNA-seq System v2 (Nugen), and RNA-seq libraries were prepared using the Ovation Ultralow DR Multiplex System (Nugen)

value: embryonic day 13.5


title: ST_NR2


title: mouse medial cntrl rep 4


title: mouse medial cntrl rep 3


title: mouse caudal cntrl rep 4

source_name: Embryonic brainstem cells


title: LT_C1


title: hMSC_2ddiff: hMSC-2ddiff-EnP (Rep2)


title: mouse caudal cntrl rep 3


title: mouse cMVST rep 2

source_name: Embryonic brainstem vestibulospinal neurons


title: mouse cMVST rep 3


title: ST_C2


title: mouse cMVST rep 1


title: mouse LVST rep 3


title: mouse LVST rep 4


title: MKFs Kindlin-2 K.O._2

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

description:
mkf_kindlin2_ko_2
matrix_k2.txt

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads of at least 15 nucleotides were cleared for subsequent analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.5.3a with the parameters “--outFilterMismatchNoverLmax 0.1 --alignIntronMax 200000”.
The number of reads aligning to genes was counted with featureCounts 1.6.0 from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.14.1.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files contain DESeq normalized counts.

source_name: mouse kidney fibroblasts (MKF)

extract_protocol:
RNA was isolated using the miRNeasy micro Kit (Qiagen). To avoid contamination by genomic DNA samples were treated by on-column DNase digestion (DNase-Free DNase Set, Qiagen). Total RNA and library integrity were verified on LabChip Gx Touch 24 (Perkin Elmer).
1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech).

tag: genotype/variation

value: Kindlin-2 K.O.

value: mouse kidney fibroblasts (MKF)


title: LT_NR1


title: mouse medial cntrl rep 2


title: MKFs Kindlin-2 K.O._1

description:
mkf_kindlin2_ko_1
matrix_k2.txt


title: MEFs Actg1 full locus deletion_1

description:
mef_actg1_ld_1
matrix_actg1.txt

source_name: mouse embryonic fibroblasts (MEF)

value: Actg1 full locus deletion

value: mouse embryonic fibroblasts (MEF)


title: MKFs Kindlin-2 floxed_1

description:
mkf_kindlin2_flox_1
matrix_k2.txt

value: Kindlin-2 floxed


title: MKFs Kindlin-2 floxed_2

description:
mkf_kindlin2_flox_2
matrix_k2.txt


title: MEFs Actg1 full locus deletion_2

description:
mef_actg1_ld_2
matrix_actg1.txt


title: Ring1B_d10: RING1B 10 days_ChIP

value: human Mesenchymal Stem Cells

value: anti-RNF2 (NAST)RRID:AB_2755047


title: Ring1B_d0: RING1B naïve_ChIP

value: anti-RNF2 (NAST) RRID:AB_2755047


title: MEFs wt_1

description:
mef_wt_1
matrix_actg1.txt

value: wt


title: ESCs Actb full locus deletion_2

description:
esc_actb_ld_2
matrix_actb.txt

source_name: mouse embryonic stem cells (ESC)

value: Actb full locus deletion

value: mouse embryonic stem cells (ESC)


title: MEFs Actg1 K.O._1

description:
mef_actg1_ko_1
matrix_actg1.txt

value: Actg1 K.O.


title: ESCs Actb K.O._2

description:
esc_actb_ko_2
matrix_actb.txt

value: Actb K.O.


title: Suz12_d10: SUZ12 days_ChIP

value: anti-SUZ12-Cell Signalling (3737)


title: MEFs wt_2

description:
mef_wt_2
matrix_actg1.txt


title: mouse LVST rep 6


title: mouse LVST rep 5


title: PLZF_d0: PLZF naïve_ChIP

value: anti PLZF-SantaCruz (sc-22839)


title: ESCs wt_2

description:
esc_wt_2
matrix_actb.txt


title: PLZF_d10: PLZF 10 days_ChIP


title: Suz12_d0: SUZ12 naïve_ChIP


title: IgG_d10: IgG 10 days_ChIP


title: K4me3_d0: H3K4Me3 naïve_ChIP

value: anti-H3K4me3-Cell Signalling(9751)


title: ESCs wt_1

description:
esc_wt_1
matrix_actb.txt


title: IgG_d0: IgG naïve_ChIP


title: MEFs Actg1 K.O._2

description:
mef_actg1_ko_2
matrix_actg1.txt


title: 1 µM JQ1 GATA2 INPUT Replicate 2

first: Lewis

last: Chaytor

address: Hutchison/MRC Research Centre, Cambridge biomedical campus

department: Department of Oncology

country: United Kingdom

institute: Cambridge University

data_processing:
ChIP-seq reads were aligned to the human genome (hg38) using bowtie2 with default perameters
Non-uniquely aligned reads and aligned reads with more than two mismatches were removed
Potential PCR duplicates were removed using Picard Mark Duplicate
Regions of genomic enrichment were identified using MACS2 with default settings. FDR for peak calling was set as q < 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak files generated by MACS2

source_name: VCaP cell line

growth_protocol: VCaP cells were cultured in steroid depleted conditions for a total time of 72 hours. Prior to harvest, cells were treated with a DMSO control or 1 µM JQ1 for 24 hours.

extract_protocol:
Cells with fixed with 1% formaldehyde and lysed to extract chromatin. Chromatin was sheared using sonication. DNA-protien complexes were immunoprecipitatied using an anti-GATA2 antibody (Sigma, HPA005633)
Indexed libraries were prepared from 5 ng of ChIP DNA with TruSeq ChIP Sample Prep Kit (Illumina) according to the manufacturer’s instructions. Libraries were quantified using the Tape Station 2200 (Agilent Technologies) and Qubit Fluorometer 1.0 (Invitrogen Co., Carlsbad, CA). Libraries were pooled such that each index-tagged sample was present in equimolar amounts, with final concentration of the pooled samples of 2nM. The pooled samples were subject to cluster generation and sequencing using an Illumina NextSeq 500 System (Illumina) in a 1x75 single-end format

value: Human castrate-resistant prostate cancer cell line

tag: cell line

value: VCaP


title: ESCs Actb full locus deletion_1

description:
esc_actb_ld_1
matrix_actb.txt


title: Non-treated GATA2 INPUT Replicate 2


title: K4me3_d10: H3K4Me3 10 days_ChIP


title: ESCs Actb K.O._1

description:
esc_actb_ko_1
matrix_actb.txt


title: 1 µM JQ1 GATA2 ChIP Replicate 2

value: GATA2 antibody (Sigma, HPA005633)


title: Non-treated GATA2 ChIP Replicate 2


title: 1 µM JQ1 GATA2 INPUT Replicate 1


title: 1 µM JQ1 GATA2 ChIP Replicate 1


title: mouse caudal cntrl rep 2

value: embryonic day 13.5


title: Non-treated GATA2 ChIP Replicate 1


title: mouse caudal cntrl rep 1


title: K27Ac_d3_siPLZF_3: H3K27Ac PLZFSi Ost diff_ChIP replicate 3

value: anti-H3K27ac-Abcam (ab4729)


title: Non-treated GATA2 INPUT Replicate 1


title: K27Ac_d3_siPLZF_2: H3K27Ac PLZFSi Ost diff_ChIP replicate 2


title: mouse LVST rep 1


title: mouse LVST rep 2


title: Normal EPCAM Cells 4

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genespring GX 11.0 software (Agilent Tech Inc., Santa Clara, CA, USA).

source_name: kidney tissue specimens

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

growth_protocol: Tumor (ccRCC) and normal (N) kidney tissue specimens were immediately placed in a Petri dish with phosphate-buffered saline (PBS) 1x and cut into small pieces of about 1 mm3. Each small piece of tissue was placed on the surface of the Petri dish with Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen, Life Technologies, Monza, Italy) supplemented with 10% fetal bovine serum (FBS, Sigma-Aldrich, Milan, Italy) and 1% penicillin-streptomycin-L-glutamine (Sigma-Aldrich, Milan, Italy ).  Kidney epithelial tubular and neoplastic cells were isolated with EpCAM (CD326) Ab-conjugated magnetic microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) under the effect of a magnetic field generated by the Mini MACS Separation Unit (Miltenyi Biotec)

extract_protocol: RNA was extracted with QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit.

tag: phenotype

value: Normal


title: K27Ac_d3_siPLZF_1: H3K27Ac PLZFSi Ost diff_ChIP replicate 1

value: human Mesenchymal Stem Cells


title: Normal EPCAM Cells 5


title: Normal EPCAM Cells 3


title: Normal EPCAM Cells 6


title: Tum EPCAM Cells 4

value: Tumoral


title: CENH3_InputSeq_Gossypium_hirsutum

city: Fuzhou

first: Zhiliang

last: Zhang

address: Shangxiadian

country: China

institute: Fujian Agriculture and Forestry University

description: processed data file: TM_1_CHIp.uniq.sort-W200-G400-islands-summary-FDR0.01.txt

data_processing:
Remove PCR duplication and low quality reads using FastUniq and Trimmomatic.
Read mapping using Bowtie2 (reads with mapping quality ≥ 30 and uniquely mapped locus were retained and used for further analysis).
Map the position of centromere regions (the CenH3 binding sites) using SICER (200-bp windows, a required fold change/control ≥5, FDR<0.01, and allowed 400-bp gaps).
Genome_build: TM-1 V2.1; Hai7124 V1.1
Supplementary_files_format_and_content: *_CHIp.uniq.sort-W200-G400-islands-summary-FDR0.01.txt: Tab-delimited text files were generated using SICER include regions and its FDR.

organism: Gossypium hirsutum

source_name: leaf

extract_protocol:
Lysates were clarified from enzyme (MNase) nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).

value: leaf

value: 4 weeks after planting


title: Tum EPCAM Cells 1


title: Tum EPCAM Cells 5


title: Normal EPCAM Cells 1


title: Normal EPCAM Cells 2


title: Tum EPCAM Cells 2


title: Tum EPCAM Cells 3


title: K27Ac_d0_siPLZF_3: H3K27Ac PLZFSi naïve_ChIP replicate 3


title: CENH3_ChIPSeq_Gossypium_hirsutum

value: CENH3 (AbMax Biotechnology Co., Ltd.)


title: K27Ac_d3_ctrl_3: H3K27Ac ControlSi Ost diff_ChIP replicate 3


title: K27Ac_d0_siPLZF_2: H3K27Ac PLZFSi naïve_ChIP replicate 2


title: K27Ac_d3_ctrl_2: H3K27Ac ControlSi Ost diff_ChIP replicate 2


title: K27Ac_d0_siPLZF_1: H3K27Ac PLZFSi naïve_ChIP replicate 1


title: K27Ac_d3_ctrl_1: H3K27Ac ControlSi Ost diff_ChIP replicate 1


title: PCNSL24

city: Kyoto

first: Ryuya

last: Yamanaka

address: 465 Kajii-cho, Kamigyoku

country: Japan

institute: Kyoto Prefectural University of Medicine

description: miRNA expression data from PCNSL

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on GeneChip miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: PCNSL tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: primary central nervous system lymphomas

value: Female


title: PCNSL25

description: miRNA expression data from PCNSL


title: PCNSL27

description: miRNA expression data from PCNSL

value: Male


title: PCNSL19

description: miRNA expression data from PCNSL


title: PCNSL23

description: miRNA expression data from PCNSL


title: PCNSL26

description: miRNA expression data from PCNSL


title: diabetic animal, biological rep 6 (STZ-diabetic study)

city: Mannheim

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
Gene expression data from adult C57Bl6/J mice 6 weeks after STZ diabetes induction
DC_6W_1143

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Whole retina from diabetic animals @6 weeks

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

growth_protocol: Diabetes was induced by intra peritoneal injection of streptozotocin (160 mg/kg/bodyweight; Sigma) in 8-week-old outbred male C57BL6/J mice weighing 24-26 g. 7 days after injection, stable hyperglycemia was confirmed (blood glucose >15 mM). Non-diabetic animals served as controls. Body weight and blood glucose values were monitored at regular intervals. Animals were housed with a 12-/12-h light/dark cycle with ad libitum access to standard rodent chow. Termination occured at 6 weeks.

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

treatment_protocol: Enucleated Eyes were snap frozen in liquid nitrogen and stored at -80°C till further preparation. Extraction of the retina was performed at 0°C and immediately suspended in Trizol.

tag: background strain

value: Whole retina

tag: disease state

value: diabetic

tag: streptozotocin

value: yes


title: PCNSL20

description: miRNA expression data from PCNSL

tag: tissue


title: K27Ac_d0_ctrl_3: H3K27Ac ControlSi naïve_ChIP replicate 3


title: diabetic animal, biological rep 4 (STZ-diabetic study)

description:
Gene expression data from adult C57Bl6/J mice 6 weeks after STZ diabetes induction
DC_6W_1105


title: K27Ac_d0_ctrl_2: H3K27Ac ControlSi naïve_ChIP replicate 2


title: PCNSL17

description: miRNA expression data from PCNSL

tag: gender


title: PCNSL21

description: miRNA expression data from PCNSL

tag: age


title: PCNSL22

description: miRNA expression data from PCNSL


title: diabetic animal, biological rep 5 (STZ-diabetic study)

description:
Gene expression data from adult C57Bl6/J mice 6 weeks after STZ diabetes induction
DC_6W_1141


title: PCNSL18

description: miRNA expression data from PCNSL


title: PCNSL16

description: miRNA expression data from PCNSL


title: diabetic animal, biological rep 3 (STZ-diabetic study)

description:
Gene expression data from adult C57Bl6/J mice 6 weeks after STZ diabetes induction
DC_6W_1101


title: PCNSL15

description: miRNA expression data from PCNSL


title: K27Ac_d0_ctrl_1: H3K27Ac ControlSi naïve_ChIP replicate 1


title: diabetic animal, biological rep 2 (STZ-diabetic study)

description:
Gene expression data from adult C57Bl6/J mice 6 weeks after STZ diabetes induction
DC_6W_1097


title: PCNSL14

description: miRNA expression data from PCNSL


title: PCNSL13

description: miRNA expression data from PCNSL


title: GZ27_C9_LNCaP95_drug_500_nM_3

city: boston

first: giorgia

last: zadra

address: 450 Brookline ave

department: Oncologic pathology

institute: DFCI

data_processing:
ALIGNMENT. Data were aligned against the hg19 genome, available at ftp://ftp.ensembl.org/pub/release-75/fasta/ homo_sapiens/dna/.Alignments were performed with STAR aligner (version 2.3.1z4), which is specifically designed for RNA-Seq experiments, which may include multiple splice forms and fusion transcripts. BAM files were generated.
PROCESSING of BAM files.  1) Generation of *.sort.bam. These BAM files were sorted by genomic coordinates. 2) Generation of  *.sort.primary.bam. To obtain these BAM files we filtered the sorted BAM files to retain only “primary” alignments. The aligner scored  the quality of the alignment and marked some reads as secondary. Thus, the primary-filtered files retain only the most high-quality reads for downstream analysis.
RNA-Seq QC.RNA-Seq quality metrics were produced by the Broad Institute’s RNA-SeQC tool
READ QUANTIFICATION. For this analysis, reads and differential expression analysis are treated at the gene level. For this task we used  featureCounts software, which produces integer counts for all genes in the supplied genome annotation file (GTF format).
READ NORMALIZATION. DESeq normalization method as part of DESeq package  was used
DIFFERENTIAL EXPRESSION TESTING. For differential expression testing, DESeq software was used
Genome_build: hg19
Supplementary_files_format_and_content: normalized count matrix table.  This file contains raw counts that have been normalized to account for technical differences between samples, using the method included in DESeq package.  Only primary alignments were retained thus the file is called " normalized_count_matrix.sort.primary.counts".

source_name: LNCaP95-drug 500 nM

growth_protocol: PCa cells were plated for 36-48 hr, after they reached confluence of around 30%. AT that point, medium was changed and drug or vehicle added for 6 days

extract_protocol:
At the end of the treatment, cells and conditioned medium were collected, pelleted down, washed, and stored at -80. RNA extraction was performed using RNeasy Plus MiniKit (Qiagen).
mRNA was isolated from 100 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module, which was then reverse transcribed and library prepped using the NEBNext Ultra Directional RNA Library Prep kit for Illumina. The resulting libraries were run on the bioanalyzer on a High Sensitivity DNA chip to check the library size distribution. The concentration of the library was determined using the DNA High Sensitivity Qubit assay, and a final functional library concentration was determined through qPCR using Illumina adaptor-specific primers with the KAPA SYBR FAST Universal qPCR kit (Sigma-Aldrich). All indexed libraries were normalized to 2 nM and pooled at equal volumes for sequencing. The library pools were denatured and diluted to a loading concentration of 2 pM for Paired End 75 cycle sequencing on a high-throughput flowcell on the NextSeq500 sequencer.

treatment_protocol: PCa cells were treated with DMSO, IPI-9119 (0.1uM),  IPI-9119 (0.5uM) for 6 days, without medium replacement

value: prostate cancer cell line

tag: androgen status

value: Castration resistant

tag: treated with

value: 500nM FASN inhibitor IPI-9119 for 6 days


title: diabetic animal, biological rep 1 (STZ-diabetic study)

description:
Gene expression data from adult C57Bl6/J mice 6 weeks after STZ diabetes induction
DC_6W_1096


title: GZ26_C8_LNCaP95_drug_500_nM_2

tag: cell type


title: GZ25_C7_LNCaP95_drug_500_nM_1


title: PCNSL12

description: miRNA expression data from PCNSL


title: PCNSL10

description: miRNA expression data from PCNSL


title: PCNSL11

description: miRNA expression data from PCNSL


title: normal control, biological rep 6 (STZ-diabetic study)

description:
Gene expression data from normal control C57Bl6/J mice after 6 weeks
NC_6W_1176

source_name: Whole retina from normoglycemic animals @6 weeks

value: normoglycemic

value: no


title: Bulk_WNV (+Ab) WNV_Ab_3

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description:
Bulk_WNV (+Ab)
Interferon signaling-competent
allnormalized_deseq_counts+1.txt

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
The genome index was built by combining both the genomes, and alignments were carried out for the combined genomes.
STAR v2.5.2b  was used with default parameters to map reads and obtain reads per gene counts (–quantMode Gene Counts)
Genes that were not expressed in any cell were filtered out. The isOutlier function from scran was used to remove cells that had a library size and number of detected genes greater than 3 median absolute deviations lower than the median values or those with percentage of mitochondrial genes that were 3 median absolute deviations higher than the median value
The normalized expression values were obtained using the calculateCPM function in the scater library
Genome_build: GRCm38.p5 Release M16
Genome_build: WNV isolate Texas 2002-HC (GenBank accession number: DQ176637.1) from ViPR
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: Murine fibroblast L929 cell line

growth_protocol: Murine fibroblast L929 cells were obtained from ATCC and grown at 37°C with 5% CO2 in DMEM (Corning) supplemented with 10% heat-inactivated FBS, 2mM L-glutamine (Corning), 25 mM HEPES buffer (Corning), 1mM sodium pyruvate (Corning), MEM nonessential amino acids (Corning) and antibiotics/antimycotics (Corning)

extract_protocol:
Cells were trypsinized and stained for single-cell sorting at 24 hr post-infection. Single viable cells were sorted into skirted 96-well PCR plates containing 10 µL RLT buffer (Qiagen) with 2-betamercaptoethanol (1:100) per well using a BSL-3 level BD Aria II flow cytometer. For bulk samples, 50,000 viable cells were sorted into 100 µL RLT buffer (Qiagen) with 2-betamercaptoethanol (1:100) at 24 hr post-infection for each condition.
SMART-Seq v4 Ultra Low Input RNA Kit (Takara) was used for cDNA preparation. The protocol was modified to include a WNV-specific viral primer during the RT step. WNV SC primer (5’ – AAGCAGTGGTATCAACGCAGAGTACGGGTCAGCACGTTTGTCATTG – 3’) targets the positive-sense envelope protein (E) gene (74) and contains the 5' 25-nucleotide ISPCR universal anchor sequence (underlined) from the Smart-seq2 protocol for downstream amplification alongside 3’ SMART-Seq CDS Primer II A-primed transcripts. Similar to 3’ SMART-Seq CDS Primer II A, 1 µL of WNV SC primer (12 µM) was added to the RT reaction for all samples. Other WNV-specific primer sequences and concentrations were evaluated. The scRNA-seq protocol was optimized to ensure high sensitivity for WNV RNA detection and to mitigate the formation of primer dimers or template-switching oligo (TSO) concatemers observed at high concentrations or with other primer sequences. During template switching, the RT product is extended with a sequence complementary to the TSO due to the addition of 2-5 untemplated nucleotides and the capacity of the RT enzyme to switch templates just as described in Smart-seq2. PCR is performed using PCR Primer II A (the ISPCR universal anchor sequence) for concurrent amplification of both host and viral cDNA. Following PCR amplification, cDNA quantification is performed for each sample, and cDNA quality assessment is accomplished using an Agilent 2100 Bioanalyzer. For library preparation, amplified cDNA is fragmented and appended with dual-indexed barcodes using Illumina Nextera XT DNA Library Prep kits. Sequencing was performed using 101-bp single end reads on an Illumina HiSeq 3000.

treatment_protocol: L929 cells were plated to 70-80% confluent and infected with WNV-TX at a MOI of 1. Following a 1 hr virus adsorption period at 37°C, cells were washed once with complete DMEM (cDMEM) and subsequently incubated for 24 hr with cDMEM or cDMEM supplemented with WNV E16 neutralizing antibody (5 µg/mL).

tag: condition

value: WNV(+Ab)

tag: quanta

value: Bulk


title: Bulk_WNV (+Ab) WNV_Ab_2


title: PCNSL9

description: miRNA expression data from PCNSL


title: Bulk_WNV (+Ab) WNV_ab_1


title: normal control, biological rep 5 (STZ-diabetic study)

description:
Gene expression data from normal control C57Bl6/J mice after 6 weeks
NC_6W_1175


title: PCNSL8

description: miRNA expression data from PCNSL


title: PCNSL3

description: miRNA expression data from PCNSL


title: PCNSL7

description: miRNA expression data from PCNSL


title: PCNSL2

description: miRNA expression data from PCNSL


title: PCNSL4

description: miRNA expression data from PCNSL


title: Bulk_WNV WNV_3

description:
Bulk_WNV
Interferon signaling-competent
allnormalized_deseq_counts+1.txt

value: WNV


title: PCNSL6

description: miRNA expression data from PCNSL


title: normal control, biological rep 4 (STZ-diabetic study)

description:
Gene expression data from normal control C57Bl6/J mice after 6 weeks
NC_6W_1174


title: PCNSL5

description: miRNA expression data from PCNSL


title: Bulk_WNV WNV_2


title: normal control, biological rep 2 (STZ-diabetic study)

description:
Gene expression data from normal control C57Bl6/J mice after 6 weeks
NC_6W_1172


title: Bulk_WNV WNV_1


title: Bulk_Mock Bulk_Mock_2

description:
Bulk_Mock
Interferon signaling-competent
allnormalized_deseq_counts+1.txt

value: Mock


title: Bulk_Mock Bulk_Mock_1


title: Bulk_Mock Bulk_Mock_3


title: normal control, biological rep 3 (STZ-diabetic study)

description:
Gene expression data from normal control C57Bl6/J mice after 6 weeks
NC_6W_1173


title: normal control, biological rep 1 (STZ-diabetic study)

description:
Gene expression data from normal control C57Bl6/J mice after 6 weeks
NC_6W_1171


title: GZ21_C3_LNCaP95_DMSO_3

value: DMSO for 6 days


title: GZ24_C6_LNCaP95_drug_100_nM_3

source_name: LNCaP95-drug 100 nM

value: 100nM FASN inhibitor IPI-9119 for 6 days


title: GZ22_C4_LNCaP95_drug_100_nM_1


title: GZ19_C1_LNCaP95_DMSO_1


title: SingleCell_Mock Mock_9

description:
SingleCell_Mock
Interferon signaling-competent
STAR_log2cpm_qc_withWNV.txt

value: SingleCell


title: SingleCell_Mock Mock_8


title: GZ20_C2_LNCaP95_DMSO_2


title: SingleCell_Mock Mock_7


title: GZ23_C5_LNCaP95_drug_100_nM_2


title: GZ17_B8_22Rv1_drug_500_nM_2

source_name: 22Rv1-drug 500 nM


title: GZ18_B9_22Rv1_drug_500_nM_3


title: SingleCell_Mock Mock_5


title: PCNSL1

description: miRNA expression data from PCNSL

value: primary central nervous system lymphomas


title: SingleCell_Mock Mock_47


title: SingleCell_Mock Mock_43


title: GZ16_B7_22Rv1_drug_500_nM_1


title: GZ15_B6_22Rv1_drug_100_nM_3

source_name: 22Rv1-drug 100 nM


title: SingleCell_Mock Mock_4


title: SingleCell_Mock Mock_38


title: SingleCell_Mock Mock_40


title: SingleCell_Mock Mock_36


title: Day 3 Bcl3−/− 3

city: Glasgow

first: Hussain

last: Jaffery

state: Scotland

address: 120 University Place

department: Institute of Infection Immunity and Inflammation

institute: University of Glasgow

data_processing:
Quality assessment - FastQC
Read trimming - Trim Galore!, default settings
Read alignment - TopHat2, default settings
Read counting - HTSeq
Differential expression - DESeq2, significance: P < 0.05
Abundance calculation - Cufflinks
Genome_build: C57BL/6J mouse genome GRCm38/mm10
Supplementary_files_format_and_content: A count matrix and a normalised FPKM matrix per sample are included as csv files. An xlsx spreadsheet combining statistically significantly differentially expressed genes in any relavent comparison is included.

source_name: Neonatal Calvarial Osteoblasts

growth_protocol: Neonatal mouse pups (P3-P5) were euthanised with a minimally lethal dose of pentobarbital. To avoid cell loss, pups were immediately decapitated into a petri dish in a Cat II biological safety cabinet. Dissection of the calvariae was conducted by inserting forceps in through the posterior occipital bone, pinning it and clipping the skin behind the ear using curved scissors. The skin was subsequently peeled from the back of the skull toward the nasal bone, revealing the calvarium. Cutting along the edges of the calvarial parietal bones allowed their separation and removal. After scraping off any loose connective tissue and multiple washes with DPBS, one or up to three calvariae were distributed into 50-mL tubes to comprise a single biological replicate. The calvariae were digested with 3 mL of a 2 mg mL‑1 (≥125 U mL‑1) in minimum essential medium α (MEMα) collagenase II solution (Gibco; 17101-015), with shaking at ~200 rpm for 20 min at 37°C, and the supernatant was subsequently discarded. Another digestion with 3 mL of collagenase II was conducted with shaking at ~200 rpm for 30 min at 37°C, and the supernatant was collected. The calvariae were then washed with 5 mL of DPBS, which was also collected. A digestion was initiated with 2 mL of 4 mM EDTA (Ethylenediaminetetraacetic acid) solution for 10 min, at 37°C, and the supernatant and subsequent DPBS wash was collected. The calvariae were further digested with 3 mL of collagenase II solution as before, and the supernatant and the following DPBS wash were collected. Collected supernatant fractions were combined and centrifuged for 5 min at 400 g. Cells were re-suspended in complete culture medium (MEMα supplemented with 10% filtered FBS, 100 U mL‑1 penicillin, 100 µg mL‑1 streptomycin, 1.25 µg mL‑1 amphotericin B, 2 mM L‑glutamine) and medium was replenished next day. Cells were expanded to ~80‑90% sub-confluency in T‑75 flasks for 3 days following isolation.

extract_protocol:
Cells were removed from incubation and culture medium was gently aspirated from 6-well plates. Cells in each well were gently washed thrice with ≥1 mL sterile DPBS pre‑warmed to 37°C. Cells were instantaneously lysed using either 700 μL of QIAzol Lysis Reagent (QIAGEN; 79306) containing 1% 2‑mercaptoethanol and stored at -80°C until required. Samples were retrieved for RNA purification, performed as per standard manufacturer instructions using the miRNeasy Mini Kit (QIAGEN; 217004). The concentration of purified RNA was determined using a NanoDrop 2000 Spectrophotometer (Thermo-Fisher Scientific), and quality assessment criterion was set as ~2.0 for the 260 nm to 280 nm absorbance wavelength ratio. Concentrations of all comparable samples were normalised with respect to the least concentrated sample for downstream use.
For cDNA synthesis, the SMART-seq v4 Ultra Low Input RNA Kit for Sequencing was used (Clontech Laboratories Inc.; 634891). Select samples of purified osteoblast RNA were utilised. 10 ng of input RNA was used per sample to synthesise the first strand of cDNA, followed by long-distance PCR amplification of template in 7-8 cycles. cDNA was purified into ~16 uL using the Agencourt AMPure XP Kit (Beckman Coulter; A63880). 10 μL of cDNA amplicons were subjected to 20 cycles of 30 s shearing fragmentation and 30 s cooling at 4°C, using the Diagenode Bioruptor Pico sonication system. 1 μL cDNA aliquots per sample were used for quantitative validation with the Agilent 2100 Bioanalyzer and the High Sensitivity DNA Kit (Agilent; 5067-4626). Fragment lengths ranged between 200 and 1000 bp, and mean fragment size was ~500 bp. 9 μL of sample was used for library preparation. Library preparation was conducted using the Low Input Library Prep Kit HT (Clontech Laboratories Inc.; 634900). The steps of template preparation, library synthesis, library amplification with indices and library purification were all carried out as per instructions. Library quantification was conducted using the Qubit 3 Fluorometer (ThermoFisher Scientific). Libraries with multiple indices were pooled and dispatched for sequencing. Sequencing of prepared sample libraries was conducted on the Illumina HiSeq 4000 System. An effective per sample read-depth of ~36.3 million was achieved with 75 bp paired-end reads.

treatment_protocol: Cells were seeded at 1.25 104 cells well 1 into 12-well plates (~3.3 103 cells cm 2) or 2.5 104 cells well 1 into 6 well plates (~2.6 103 cells cm 2) and allowed to reach up to 100% confluency for an additional 3 days. Osteogenic medium (complete culture medium as above) was supplemented with filter-sterilised 50 µg mL 1 ascorbic acid and 2 mM β glycerophosphate, as determined to be optimal by comparative studies, and introduced to initiate osteoblast differentiation (day 0). Cell lysate collection for RNA was conducted at days 1 and 3.

tag: strain

tag: genotype

value: Bcl3 knockout

value: osteoblast

tag: differentiation time

value: 3 days

value: 50 μg/mL L-ascorbic acid & 2 mM β-glycerophospate


title: Day 3 Bcl3−/− 1

tag: treatment


title: GZ14_B5_22Rv1_drug_100_nM_2

tag: cell line

value: prostate cancer cell line


title: SingleCell_Mock Mock_34


title: SingleCell_Mock Mock_32


title: GZ13_B4_22Rv1_drug_100_nM_1

value: Castration resistant


title: Day 3 WT 3

value: Wild-type


title: SingleCell_Mock Mock_30


title: SingleCell_Mock Mock_3


title: SingleCell_Mock Mock_29


title: GZ12_B3_22Rv1_DMSO_3


title: GZ11_B2_22Rv1_DMSO_2


title: SingleCell_Mock Mock_28


title: SingleCell_Mock Mock_25


title: Day 3 WT 2


title: Day 1 Bcl3−/− 2

value: 1 day


title: Day 1 Bcl3−/− 3


title: SingleCell_Mock Mock_26


title: GZ10_B1_22Rv1_DMSO_1


title: SingleCell_Mock Mock_21


title: Day 3 Bcl3−/− 2


title: Day 3 WT 1


title: SingleCell_Mock Mock_22


title: Day 1 Bcl3−/− 1


title: SingleCell_Mock Mock_20


title: SingleCell_Mock Mock_2


title: SingleCell_Mock Mock_17


title: Day 1 WT 3


title: GZ7_A7_LNCaP_drug_500_nM_1

source_name: LNCaP-drug 500 nM

value: LNCaP

value: androgen sensitive

value: 500nM FASN inhibitor IPI-9119 for 6 days


title: Day 1 WT 2


title: GZ6_A6_LNCaP_drug_100_nM_3

source_name: LNCaP-drug 100 nM


title: Day 1 WT 1


title: SingleCell_Mock Mock_14


title: SingleCell_WNV (+Ab) InfectedwAb_9

description:
SingleCell_WNV (+Ab)
Interferon signaling-competent
STAR_log2cpm_qc_withWNV.txt

value: WNV(+Ab)


title: SingleCell_WNV (+Ab) InfectedwAb_8


title: GZ9_A9_LNCaP_drug_500_nM_3


title: GZ5_A5_LNCaP_drug_100_nM_2


title: SingleCell_WNV (+Ab) InfectedwAb_6


title: SingleCell_WNV (+Ab) InfectedwAb_7


title: GZ4_A4_LNCaP_drug_100_nM_1


title: Conditional Knockout Rep. 3 (Esr1fl/fl;Nkx2-1-Cre)

city: San Francisco

first: Holly

middle: A

last: Ingraham

state: CA

address: 1550 4th Street, 284F

department: Cellular and Molecular Pharmacology

institute: University of California, San Francisco

data_processing:
Samples were sequenced and demultiplexed by the UCSF Center for Advanced Technology
Sequenced reads were mapped to mm9 whole genome using TopHat v2.1.0
Reads that aligned to exons were quantified using htseq-count v0.6 and the mm9 gene model
Differential gene expression was determined using DESeq2 v1.14.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include number of exon-aligned reads for the given genes

source_name: Arcuate nucleus

growth_protocol: Mice were raised under standard housing conditions with ad lib access to food and water

extract_protocol:
The CNS was rapidly dissected and a 2 mm coronal section containing the hypothalamus was isolated. The arcuate nucleus was manually microdissected from the tissue block, and RNA was prepared using the Invitrogen Pure Link RNA Mini kit (Cat#12183018A). The Nugen Ovation RNA-Seq System V2 Sample Prep Kit (Cat#7102) was used with 50 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using manufacturers protocol.

value: Mixed Background (CD-1, 129P2, C57BL/6)

value: Arcuate nucleus

tag: developmental stage

value: Adult

tag: Sex

value: Female


title: SingleCell_WNV (+Ab) InfectedwAb_5

value: SingleCell


title: Conditional Knockout Rep. 2 (Esr1fl/fl;Nkx2-1-Cre)


title: SingleCell_WNV (+Ab) InfectedwAb_48


title: GZ2_A2_LNCaP_DMSO_2

source_name: LNCaP-DMSO

value: DMSO for 6 days


title: GZ8_A8_LNCaP_drug_500_nM_2


title: Conditional Knockout Rep. 1 (Esr1fl/fl;Nkx2-1-Cre)


title: GZ3_A3_LNCaP_DMSO_3


title: SingleCell_WNV (+Ab) InfectedwAb_47


title: SingleCell_WNV (+Ab) InfectedwAb_46


title: Control Rep. 3 (Esr1fl/fl)


title: SingleCell_Mock Mock_19

value: Mock


title: SingleCell_WNV (+Ab) InfectedwAb_44


title: SingleCell_WNV (+Ab) InfectedwAb_41


title: GZ1_A1_LNCaP_DMSO_1


title: SingleCell_WNV (+Ab) InfectedwAb_4


title: 3 siNFE2L2 SDF-1

city: Krakow

first: Anna

last: Grochot-Przeczek

address: Gronostajowa 7

country: Poland

institute: Jagiellonian University

data_processing:
To detect all human miRs, a library of reference sequences was prepared by identifying the sequences of mature miRNAs within the hairpins deposited in miRBase, version 19 (Kozomara and Griffiths-Jones, 2011).
The Illumina NextSeq platform requires a minimum read length of 75 nucleotides, thus all the small RNAs were extended using specific adapters that were annealed to their 3’ends during library preparation. The removal of adapters was performed in silico on the raw, 75-nucleotide- long Illumina sequence reads using cutadapt software (Martin, 2011).
The resulting sequences of the length of 15-28 nucleotides were subjected to further analysis as potential miRNAs. The sequences were mapped on the prepared reference library using Bowtie v 0.12.7 (Langmead et al., 2009), with the requirement of perfect matching.
Data obtained for each sample was normalized using the RPM (Reads Per Million) normalization according to the formula: RPM = (Nref/Nall) x 106, where: Nref – number of reads mapped to the miRNA reference, Nall – total number of reads mapped in the sample.
Selection of miRNAs deregulated between the analyzed groups was performed using Welch t-test – paired. False discovery rate (FDR) was used to assess the multiple testing errors.
Genome_build: miRBase, version 19
Supplementary_files_format_and_content: xls files include reads for miRNAs for each sample

source_name: aortic endothelial cells

growth_protocol: Human aortic endothelial cells (HAECs) (Gibco) were grown in Endothelial Basal Medium (EBM-2) (Lonza) supplemented with EGM-2MV SingleQuot Kit Supplements & Growth Factors (Lonza) and 10% fetal bovine serum (FBS) (EURx). Transfections of HAECs were performed using 50nM siRNA targeted against human NFE2L2 (Life Technologies, s9493) or mock siRNA (Life Technologies; Negative Control #2) using Lipofectamine™ 2000 Transfection Reagent (Life Technologies) in Opti-MEM I Reduced Serum medium (Life Technologies). At 24 h hours after transfection, medium was changed. All experiments were performed 48h after transfection.

extract_protocol:
Total RNA was isolated by a phenol–chloroform extraction. At 48 hours after transfection, the cells were washed with PBS, scraped with 400 μL of Fenozol (A&A Biotechnology) and vigorously mixed with 100 μL of chloroform. After centrifugation (20 minutes, 10 000g, 4°C), an upper aqueous phase was collected and precipitated with 50% isopropanol overnight. RNA was pelleted by centrifugation (30 minutes, 10 000g, 4°C). After washing twice with ethanol, RNA pellet was dissolved in nuclease-free water.
Small RNA fraction (with length not exceeding 50nt) was subjected to hybridization and ligation with TruSeq Small RNA Library Preparation kit (Illumina Inc.). Subsequently, RNAs were reverse transcribed and sequenced using whole-transcriptome sequencing on the Illumina NextSeq 500 platform. To detect all human miRs, a library of reference sequences was prepared by identifying the sequences of mature miRNAs within the hairpins deposited in miRBase, version 19 (Kozomara and Griffiths-Jones, 2011). The Illumina NextSeq platform requires a minimum read length of 75 nucleotides, thus all the small RNAs were extended using specific adapters that were annealed to their 3’ends during library preparation. The removal of adapters was performed in silico on the raw, 75-nucleotide- long Illumina sequence reads using cutadapt software (Martin, 2011). The resulting sequences of the length of 15-28 nucleotides were subjected to further analysis as potential miRNAs. The sequences were mapped on the prepared reference library using Bowtie v 0.12.7 (Langmead et al., 2009), with the requirement of perfect matching.

treatment_protocol: Serum-starved HAECs were stimulated with 250 ng/mL GDF-15 or 100 ng/mL SDF-1 in EBM-2 medium containing 0.5% FBS for 6h.

tag: knockdown

tag: stimulation

value: primary aortic endothelial cells

tag: passages

tag: donor sex

value: male

tag: donor age


title: SingleCell_WNV (+Ab) InfectedwAb_37


title: SingleCell_WNV (+Ab) InfectedwAb_38


title: Control Rep. 1 (Esr1fl/fl)

tag: tissue


title: 3 siMock SDF-1

value: scrambled


title: SingleCell_WNV (+Ab) InfectedwAb_35


title: SingleCell_WNV (+Ab) InfectedwAb_34


title: 3 siMock GDF-15


title: SingleCell_WNV (+Ab) InfectedwAb_33


title: MPE6

first: Laura

last: Bond

address: 655 Huntington Avenue

department: Genetics and Complex Diseases

institute: Harvard School of Public Health

description:
Exp 3- Relates to Table S1 "RNF213kd"
Piccolis_RNAseq_processed_MPE1_MPE2_MPE5_MPE6
MPE6_S14

data_processing:
Briefly, the RNA was run on a Bioanlayzer (Agilent) to assess RNA quality and quantification. The biological triplicates were pooled at this point.
The library preparation was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina). The samples were sequenced by HiSeq 2500, Rapid Paired-End 100 (RL-PE100) or HiSeq 2500, High Output v4 Paired-End 100 (HI-PE100, Illumina).
All reads were mapped to the UCSC hg19 human reference genome using Tophat2 with multi-read correction, followed by normalization, quantification and differential expression analysis using Cuffdiff.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized abundance measurements for each sample

source_name: K562 leukemia cells

growth_protocol: Cells were diluted to 10^4 cells/ml

extract_protocol:
Total RNA was isolated from K562 cells using a Qiagen RNeasy Kit.
The library preparation was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Cells were treated with 0.2mM palmitate (conjugated to BSA) for 20 hours

tag: fatty acid treatment

value: palmitate


title: 3 siNFE2L2 GDF-15

tag: cell type


title: SingleCell_WNV (+Ab) InfectedwAb_32

tag: condition


title: SingleCell_WNV (+Ab) InfectedwAb_31

tag: quanta


title: SingleCell_WNV (+Ab) InfectedwAb_30


title: MPE1

description:
Exp 3- Relates to Table S1 "RNF213kd"
Piccolis_RNAseq_processed_MPE1_MPE2_MPE5_MPE6
MPE1_S9

value: WT


title: MPE5

description:
Exp 3- Relates to Table S1 "RNF213kd"
Piccolis_RNAseq_processed_MPE1_MPE2_MPE5_MPE6
MPE5_S13


title: MPE2

description:
Exp 3- Relates to Table S1 "RNF213kd"
Piccolis_RNAseq_processed_MPE1_MPE2_MPE5_MPE6
MPE2_S10


title: Control Rep. 2 (Esr1fl/fl)

tag: strain


title: SingleCell_WNV (+Ab) InfectedwAb_43


title: SingleCell_WNV (+Ab) InfectedwAb_40


title: n7_51-53

description:
Exp 2- Relates to Table S1 "GPAT4ko"
Piccolis_RNAseq_processed_n1_n2_n5_n6_n7
n7_51-53_S7

tag: genotype

value: palmitate and palmitoleate


title: SingleCell_WNV (+Ab) InfectedwAb_27


title: SingleCell_WNV (+Ab) InfectedwAb_29


title: 3 siNFE2L2 PBS

value: PBS


title: SingleCell_WNV (+Ab) InfectedwAb_26


title: n6_40-41

description:
Exp 2- Relates to Table S1 "GPAT4ko"
Piccolis_RNAseq_processed_n1_n2_n5_n6_n7
n6_40-41_S6


title: 2 siNFE2L2 SDF-1


title: SingleCell_WNV (+Ab) InfectedwAb_23


title: 2 siMock SDF-1


title: SingleCell_WNV (+Ab) InfectedwAb_21


title: n5_37-39

description:
Exp 2- Relates to Table S1 "GPAT4ko"
Piccolis_RNAseq_processed_n1_n2_n5_n6_n7
n5_37-39_S5


title: SingleCell_WNV (+Ab) InfectedwAb_20


title: SingleCell_WNV (+Ab) InfectedwAb_2


title: n2_5-6

description:
Exp 2- Relates to Table S1 "GPAT4ko"
Piccolis_RNAseq_processed_n1_n2_n5_n6_n7
n2_5-6_S2


title: SingleCell_WNV (+Ab) InfectedwAb_3


title: 2 siNFE2L2 GDF-15


title: 3 siMock PBS


title: SingleCell_WNV (+Ab) InfectedwAb_19


title: 2 siMock GDF-15


title: 2 siNFE2L2 PBS


title: MAPI_2

description:
Exp 1- Relates to Table S1 "palmitate"
Piccolis_RNAseq_processed_MAPI1_2_3.txt
Sample_MAPI_2


title: MAPI_3

description:
Exp 1- Relates to Table S1 "palmitate"
Piccolis_RNAseq_processed_MAPI1_2_3.txt
Sample_MAPI_3

value: palmitoleate


title: SingleCell_WNV (+Ab) InfectedwAb_14


title: SingleCell_WNV (+Ab) InfectedwAb_1


title: SingleCell_WNV (+Ab) InfectedwAb_10


title: SingleCell_WNV Infected_Plate2_48

description:
SingleCell_WNV
Interferon signaling-competent
STAR_log2cpm_qc_withWNV.txt

value: WNV


title: SingleCell_WNV Infected_Plate2_7


title: SingleCell_WNV (+Ab) InfectedwAb_15

value: WNV(+Ab)


title: SingleCell_WNV Infected_Plate2_6


title: 1 siNFE2L2 GDF-15


title: 1 siNFE2L2 SDF-1


title: SingleCell_WNV Infected_Plate2_45


title: SingleCell_WNV Infected_Plate2_5


title: SingleCell_WNV Infected_Plate2_44


title: SingleCell_WNV Infected_Plate2_46


title: SingleCell_WNV Infected_Plate2_43


title: 1 siMock GDF-15


title: SingleCell_WNV Infected_Plate2_42


title: n1_1-3

description:
Exp 2- Relates to Table S1 "GPAT4ko"
Piccolis_RNAseq_processed_n1_n2_n5_n6_n7
n1_1-3_S1


title: SingleCell_WNV Infected_Plate2_38


title: 2 siMock PBS


title: SingleCell_WNV Infected_Plate2_37


title: 1 siNFE2L2 PBS


title: 1 siMock PBS


title: SingleCell_WNV Infected_Plate2_36


title: SingleCell_WNV Infected_Plate2_35


title: SingleCell_WNV Infected_Plate2_34


title: MAPI_1

description:
Exp 1- Relates to Table S1 "palmitate"
Piccolis_RNAseq_processed_MAPI1_2_3.txt
Sample_MAPI_1


title: 1 siMock SDF-1


title: SingleCell_WNV Infected_Plate2_31


title: SingleCell_WNV Infected_Plate2_47


title: SingleCell_WNV Infected_Plate2_30


title: SingleCell_WNV Infected_Plate2_33


title: SingleCell_WNV Infected_Plate2_32


title: SingleCell_WNV Infected_Plate2_3


title: SingleCell_WNV Infected_Plate2_29


title: SingleCell_WNV Infected_Plate2_28


title: SingleCell_WNV Infected_Plate2_27


title: NC rep2

city: Beijing

first: xiong

last: xiao

address: 5 Yiheyuan Rd

institute: peking university

description:
NC-2
NC-2_H75VKDMXX_L1

data_processing:
The generated sequencing reads were mapped against human genome build hg19 by TopHat alignment software tools.
The expression values for each sample were calculated by reading the bam file of aligned reads using cuffquant.
The expression values were then merged into a single FPKM table by cuffnorm.
Genome_build: hg19 for human
Supplementary_files_format_and_content: FPKM

source_name: CD34+ cell with a 7-day culture supplemented with only cytokines

extract_protocol:
cultured cells were washed with cold PBS and RNA was harvested using RNA isolation Kit (QIAGEN, Cat:74034) according to the manufacturer’s protocol. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB England BioLabs, E7530L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cord blood

value: progeny of cultured CD34+ cells

tag: culture time

value: 7 days

tag: culture supplemented with

value: only cytokines


title: NC rep1

description:
NC-1
NC-1_H75VKDMXX_L1


title: SingleCell_WNV Infected_Plate2_22

value: SingleCell


title: SingleCell_WNV Infected_Plate2_21


title: J8 rep2

description:
J8-2
J8-2_H75VKDMXX_L1

source_name: CD34+ cell with a 7-day culture supplemented with JNK-IN-8

value: JNK-IN-8 (2μM)


title: SingleCell_WNV Infected_Plate2_20


title: KYSE450_miR-198+

city: jinan

first: Yanli

last: Ren

state: shandong

address: huaiyin street

institute: SDCH

hyb_protocol: HOA 7.1  arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: The arrays were scanned by Agilent Scanner G2505C 0.1 XDR protocol and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

source_name: ATCC

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol:
Volumes used in this protocol are for 25 cm2 flask; proportionally reduce or increase amount of dissociation medium for culture vessels of other sizes.
Remove and discard culture medium.
Briefly rinse the cell layer with 0.25% (w/v) Trypsin- 0.53 mM EDTA solution to remove all traces of serum that contains trypsin inhibitor.
Add 1.0 mL of Trypsin-EDTA solution to flask and observe cells under an inverted microscope until cell layer is dispersed (usually within 1 minutes).
Note: To avoid clumping do not agitate the cells by hitting or shaking the flask while waiting for the cells to detach. Cells that are difficult to detach may be placed at 37°C to facilitate dispersal.
Add 3.0 to 4.0 mL of complete growth medium and aspirate cells by gently pipetting.
Add appropriate aliquots of the cell suspension to new culture vessels.
Cultures can be established between 2 x 103 and 1 x 104 viable cells/cm2. Do not exceed 7 x 104 cels/cm2.
Incubate cultures at 37°C.
Interval: Maintain cultures at a cell concentration between 6 X 103 and 6 X 104 cell/cm2.
Subcultivation Ratio: A subcultivation ratio of 1:3 to 1:8 is recommended
Medium Renewal: 2 to 3 times per week

extract_protocol: RNA extraction by Trizol Reagent (Invitrogen). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: Twenty nanomolar miRNA was used for transfection in serum free medium. Total RNA were prepared after transfection 48h.

tag: cell line

tag: gender source

value: esophagus cancer cell line

tag: transfected with


title: KYSE450_miR-107+


title: SingleCell_WNV Infected_Plate2_2


title: SingleCell_WNV Infected_Plate2_18


title: SingleCell_WNV Infected_Plate2_17


title: DMSO rep2

description:
DMSO-2
DMSO-2_H75VKDMXX_L1

source_name: CD34+ cell with a 7-day culture supplemented with DMSO


title: KYSE450_miR-214+


title: J8 rep1

description:
J8-1
J8-1_H75VKDMXX_L1


title: DMSO rep1

description:
DMSO-1
DMSO-1_H75V3DMXX_L1


title: KYSE450_NC+

value: none (control)


title: Normal N2

city: Haikou

first: Min

last: Xu

address: No.58 Renmin Avenue,Haikou, Hainan, China

institute: Hainan University

data_processing:
Before any further analysis could have been conducted, quality control of the data was required. In addition, low-quality sequences were filtered out of the raw data to reduce data noise.We defined "dirty" raw reads as those that contained the sequence of the adapter, high levels of unknown bases, and low-quality reads. They needed to be removed before data analysis. Filtering steps were as follows: 1) Reads with adapters were removed; 2) reads in which unknown bases were more than 10% were removed; and 3) low-quality reads were removed (the percentage of low-quality bases is usually over 50% in a read, and we defined a low-quality base to be one with a sequencing quality of no more than 5).
After filtering, the remaining reads were referred to as "clean reads" and used for downstream bioinformatics analysis. Clean data was obtained and stored in the FASTQ format after filtering.Clean reads were assembled using the Trinity paired-end assembly method [69]. The assembled clean reads, also referred to as transcripts, were clustered and this eliminated any redundancy in obtaining unigenes using the TIGR Gene Indices clustering tools (TGICL). For the study of multi-samples, the previous step using the TGICL for downstream analysis of the unigenes was repeated. The processed unigenes were referred to as "All-Unigenes.
" All-Unigenes were divided into two parts; one part included clusters of a few unigenes with more than 70 similarities among them (starting with “CL,” followed by the gene family ID); and the other included singletons (starting with “Unigene”).
After assembly, H. polyrhizus pitaya All unigenes (contigs and singletons) were functionally aligned to the public protein databases, NR, GO, KEGG, COG, InterPro, and SwissProt. All unigenes were annotated according to their sequence similarity to previously annotated genes in these public databases. The phyper function of the R software (https://www.r-project.org) was used for enrichment analysis, according to the results of GO and KEGG pathway gene annotations in functional analyses.
The p-value was corrected by the FDR. We supposed that unigenes with FDR ≤ 0.01 were significantly expressed in the GO and KEGG pathways. Moreover, NOIseq  and PassionDis  methods were used to test DEGs. A FoldChange ≥ 2.00 or FoldChange ≤ 0.5, with Probability ≥ 0.8 in NOIseq, and FoldChange ≥ 2.00 or FoldChange ≤ 0.5, with FDR ≤ 0.001 in PassionDis of unigenes defined the DEGs of the normal and diseased libraries. According to the results of the DEGs test, the pheatmap function of the R software was used for hierarchical clustering analysis.
Supplementary_files_format_and_content: All-Unigene.fa is the assembled sequence of all samples; All.GeneExpression.FPKM.xls is the gene expressiom of all samples and the annotation.xls is the annotation of all expression genes of all samples.

organism: Selenicereus monacanthus

source_name: stem tissues

growth_protocol: They had been growing for about five years in a plantation under natural conditions

extract_protocol:
Tissues (100 mg) were placed into a precooled mortar to be ground into a powder with liquid nitrogen. The ground stem powder was collected into a precooled 2 mL Eppendorf tube with 2 mL RNase-free cetyltrimethylammonium bromide (CTAB) extracting solution, which contained 0.1% diethyl pyrocarbonate (DEPC), 2.5% CTAB, 1.4 M NaCl, 20 mM EDTA, 100 mM Tris-HCl (pH 8.0), and 4% polyvinylpyrrolidone (PVP). The tubes were then placed in a water bath at 65 °C for 30 min to induce cell lysis, and centrifuged at 13,000 rpm for 5 min at 25-28 °C. The residue was discarded, and the supernatant solution was transferred into a clean 2 mL Eppendorf tube. Trichloromethane (1 mL) was added to the supernatant solution, blended lightly, and centrifuged at 13 000 rpm for 15 min at 4 °C. The supernatant was transferred into a clean 2 mL Eppendorf tube, and this procedure was repeated once more. Subsequently, 8 M lithium chloride was added with RNase-free water to 0.6 volume of the supernatant and left overnight. The mixture was centrifuged for 30 min at 13 000 rpm and 4 °C to obtain the RNA precipitate. RNase-free ethyl alcohol (75%) was used to wash the RNA precipitate twice. Finally, RNA was dissolved in RNase-free ddH2O and stored at -80 °C until further use.
Poly (A) mRNA from the total RNA was enriched by poly-T oligo-attached magnetic beads (Invitrogen), according to the manufacturer’s protocol. Purified mRNA was then divided into short fragments by mixing with fragmentation buffer. The first strand cDNA was synthesized using a random hexamer primer. The buffer, dNTPs, RNase H, and DNA polymerase I were then added to the fragmented mRNA templates to synthesize the second-strand cDNA. The double-stranded cDNA was purified using magnetic beads. End repair and the addition of 3′-end single nucleotide A (adenine) were then performed. Finally, sequencing adaptors were ligated to the fragments, which were enriched by PCR amplification. During the quality control step, a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA) and a StepOnePlus Real-Time PCR System (Applied Biosystems Inc., Foster City, CA, USA) were used to qualify and quantify sequences for the sample libraries. The constructed library products were prepared for sequencing using a HiSeq 2000 system (Illumina, San Diego, CA, USA) at the Beijing Genomics Institute (BGI).

treatment_protocol: Normal group were growth under natural, the diseased group were invaded by the fungal Neoscytalidium dimidiatum

value: stem


title: SingleCell_WNV Infected_Plate2_10


title: SingleCell_WNV Infected_Plate2_12


title: SingleCell_WNV Infected_Plate2_13


title: SingleCell_WNV Infected_Plate2_11


title: SingleCell_WNV Infected_9


title: Normal N3


title: SingleCell_WNV Infected_7


title: SingleCell_WNV Infected_Plate2_24


title: SingleCell_WNV Infected_6


title: Diseased D1


title: SingleCell_WNV Infected_48


title: SingleCell_WNV Infected_47


title: SingleCell_WNV Infected_5


title: SingleCell_WNV Infected_46


title: SingleCell_WNV Infected_Plate2_15


title: SingleCell_WNV Infected_45


title: SingleCell_WNV Infected_Plate2_14


title: SingleCell_WNV Infected_44


title: SingleCell_WNV Infected_37


title: SingleCell_WNV Infected_4


title: SingleCell_WNV Infected_34


title: Diseased D3


title: SingleCell_WNV Infected_36


title: SingleCell_WNV Infected_30


title: SingleCell_WNV Infected_3


title: SingleCell_WNV Infected_29


title: SingleCell_WNV Infected_22


title: SingleCell_WNV Infected_27


title: SingleCell_WNV Infected_25


title: SingleCell_WNV Infected_20


title: SingleCell_WNV Infected_21


title: SingleCell_WNV Infected_38


title: SingleCell_WNV Infected_2


title: SingleCell_WNV Infected_17


title: SingleCell_WNV Infected_31


title: SingleCell_WNV Infected_16


title: SingleCell_WNV Infected_26


title: BAB8297

type: genomic

city: Houston

first: James

middle: R

last: Lupski

state: TX

address: One Baylor Plaza Room #604B

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description:
17p11.2 interrogation
aCGH experiment of trios for capture and sequencing

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the manufacturer’s protocol.

scan_protocol: Scanned on an Agilent G2505C  scanner- Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and normalization.

source_name: DNA extracted from whole blood

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP, PerkinElmer, #NEL620001KT) with Cy5-dCTP for patient DNA and Cy3-dCTP for reference DNA.

extract_protocol: DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

value: whole blood

tag: proband or parent

value: Parent

tag: tag

value: Reference sample


title: SingleCell_WNV Infected_13

source_name: Murine fibroblast L929 cell line


title: SingleCell_WNV Infected_15


title: SingleCell_WNV Infected_11


title: SingleCell_WNV Infected_10


title: BAB8296


title: SingleCell_WNV Infected_1


title: BAB2541


title: BAB1606


title: BAB2542


title: BAB8295

value: Proband


title: BAB2387


title: mRNA_PAD4_IMIQU_LN_3

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

data_processing:
[alignment]  Raw sequencing data were processed with bcl2fastq 1.17.1 to generate FastQ files. Reads of 50 bases were mapped to mm10 using TopHat 2.1.0
[RPKM]  Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek6.6
Genome_build: mm10
Supplementary_files_format_and_content: RPKM file

extract_protocol:
Lymph nodes and spleens were collected from imiquimod-treated mice and frozen at-80 C in Tri-Reagent, RNA was isolated using the Direct-zol RNA MiniPrep.
cDNA libraries prepared with poly(A) tail enrichment using NEBNext Ultra II RNA Library Prep Kit following manufacturer instructions
RNA seq data were generated on Illumina HiSeq 3000 instrument according to the manufacturer's instructions

tag: agent

value: IMIQU

value: LN


title: BAB2311


title: mRNA_PAD4_IMIQU_LN_2


title: mRNA_PAD4_IMIQU_LN_1


title: BAB2166


title: mRNA_PAD2_IMIQU_LN_3


title: BAB6096/BAB3990


title: BAB2165


title: BAB6095/BAB3989


title: BAB2388


title: BAB6771


title: mRNA_PAD2_IMIQU_LN_4


title: BAB1605


title: BAB1852


title: mRNA_PAD2_IMIQU_LN_1


title: mRNA_PAD2_IMIQU_LN_2


title: mRNA_FVB_IMIQU_LN_2

value: WT


title: mRNA_PAD4_Na_SPLN_3

value: control

value: SPLN


title: mRNA_FVB_IMIQU_LN_4


title: mRNA_PAD4_IMIQU_SPLN_1


title: mRNA_PAD4_IMIQU_SPLN_3


title: mRNA_FVB_IMIQU_LN_3


title: mRNA_PAD4_Na_SPLN_1


title: mRNA_PAD2_IMIQU_SPLN_3


title: mRNA_PAD4_Na_SPLN_2


title: BAB6770


title: mRNA_PAD2_IMIQU_SPLN_2


title: mRNA_PAD2_IMIQU_SPLN_1


title: mRNA_PAD2_Na_SPLN_3


title: mRNA_FVB_IMIQU_LN_1


title: mRNA_PAD2_Na_SPLN_1


title: BAB8403


title: mRNA_FVB_IMIQU_SPLN_2


title: mRNA_PAD2_Na_SPLN_2


title: mRNA_FVB_IMIQU_SPLN_3


title: BAB8345


title: BAB8335


title: BAB8336


title: mRNA_PAD4_IMIQU_SPLN_2


title: mRNA_FVB_IMIQU_SPLN_1


title: BAB4947


title: mRNA_FVB_Na_SPLN_3


title: mRNA_FVB_Na_SPLN_2


title: mRNA_FVB_Na_SPLN_1


title: Whole Kidney RNA-Seq, transcriptome 03

first: Lihe

last: Chen

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

data_processing:
Sequenced reads were mapped to Ensembl mouse gene set (GRCm38.p5) using STAR v2.5.1b
Transcript abundances in TPM were caculated by  RSEM/1.2.31
GRCm38.p5 (Ensembl)
Genome_build: tab-delimited text files include TPM values for each sample

source_name: whole kidney

extract_protocol:
RNAs were extracted using Zymo kit and cDNAs were sythesized using SMART-Seq V4 Ultra Low Input RNA Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Male mice were grown and maintained in the Animal Facility of the NHLBI. 2 month-old mice were used in the experiments.

value: Kidney

tag: gender

value: male

tag: age

value: 2 month-old


title: BAB8343

tag: tissue


title: BAB5786


title: BAB5784


title: Whole Kidney RNA-Seq, transcriptome 01


title: Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 12

source_name: microdissected proximal tubule


title: Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 11


title: BAB8344


title: BAB2961


title: Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 09


title: BAB2960


title: Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 08


title: Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 07


title: chicken caudal cntrl rep 4

first: Benjamin

last: Okaty

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

data_processing:
Illumina CASAVA 1.8.2 for HiSeq 2000 or RTA 2.4.6 for NextSeq500
Sequencing data in FASTQ format were aligned to the mouse genome (mm9) using the RUM pipeline (version 1.11 (Grant et al., 2011)) or to the chicken genome (Galgal5) using the STAR aligner (Dobin et al., 2013).
Genome feature quantification for mouse data was performed with RUM, using RefSeq annotations, and for chicken data with STAR using the Gallus_gallus.Gallus_gallus-5.0.93.gtf annotation file downloaded from Ensembl.org
Genome_build: mm9 for mouse, Galgal5 for chicken
Supplementary_files_format_and_content: counts

organism: Gallus gallus

source_name: Embryonic brainstem

extract_protocol:
Vestibulospinal neurons were retrogradely labeled for manual cell isolation with tetramethylrhodamine-conjugated dextran amine, acutely dissociated, and manually sorted.
RNA was isolated using the PicoPure RNA Isolation kit (Applied Biosystems), cDNA was synthesized and amplified using Ovation RNA-seq System v2 (Nugen), and RNA-seq libraries were prepared using the Ovation Ultralow DR Multiplex System (Nugen)

value: embryonic day 7.5


title: BAB2959


title: Whole Kidney RNA-Seq, transcriptome 02


title: chicken caudal cntrl rep 3


title: Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 06


title: chicken caudal cntrl rep 2


title: Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 05


title: chicken caudal cntrl rep 1


title: BAB1913


title: Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 04


title: chicken cMVST rep 3

source_name: Embryonic brainstem vestibulospinal neurons


title: BAB2555


title: BAB1838


title: BAB1789


title: Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 02


title: chicken cMVST rep 2


title: chicken cMVST rep 1


title: Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 01


title: Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 03


title: chicken cMVST rep 4


title: chicken LVST rep 4


title: chicken LVST rep 3


title: BAB2339


title: chicken LVST rep 2


title: BAB8325


title: BAB3812


title: BAB3811


title: mRNA_PAD4_IMIQU_LN_4


title: Control LC413T-1 hepatoma cells

city: Taoyuan

first: Tse-Ching

address: 5. Fu-Hsing Street

department: Anatomic Pathology

country: Taiwan

institute: Chang Gung Memorial Hospital

description: Gene expression data from control LC413T-1 hepatoma cells.

hyb_protocol: Hybridization protocols follows the Affymetrix's instructions

scan_protocol: Following a quantitative scan of the chip, a grid was aligned to the image using the dimension of the microarray chips and the corner control regions as markers.

data_processing:
The images were transformed into text files containing the intensity information using GeneChip Operating Software (GCOS), developed by Affymetrix. The microarray data were analyzed using the GeneSpring 7.0 software (Silicon Genetics, Redwood City, CA, USA).
The absolute intensity statistics were based on the feature intensities and corresponding standard deviations provided in the microarray chip-generated CEL files. In addition, normalization between different arrays was performed for all regions, and each gene expression signal was normalized to the median value of all genes in each chip.

label_protocol: Labeled cRNA was synthesized from the cDNA using the Bioarray High Yield RNA Transcript Labeling Kit (Affymetrix, Cat# 900182) according to the manufacturer's instructions. Fragmentation of biotinylated cRNA (15 μg) was performed by employing the GeneChip Sample Cleanup Module (Affymetrix, Cat# 900371).

growth_protocol: We generated three hepatoma cell lines, designated 834, LC413T-1 and P15, that isolated from three individual HCC patients. Briefly, fresh liver tumor tissues from HCC patients were collected for primary culture. After cleaning with HBSS containing penicillin (50 units/ml) and streptomycin (50 μg/ml), the liver tumor tissues were minced; followed by enzymatic digestion with type IV collagenase (20-30 min at 37˚C) and passed through an 18 mm needle (4-5 times). The collagenase activity was stopped by immediate addition of 4 mM EDTA in HBSS and then disaggregated cells were collected after centrifugation (1000 × g for 5 min, 2 times).  The 834 and LC413T-1 hepatoma cells were cultured in DMEM medium (pH 7.2) supplemented with 10% heat inactivated fetal bovine serum (FBS), penicillin (50 units/ml), streptomycin (50μg/ml) and non-essential amino acid (1 μg/ml). The P15 hepatoma cells were cultured in DMEM/F12 medium supplemented with Insulin, hepatocyte growth factor, 10% FBS, penicillin, streptomycin and non-essential amino acid. After 24 h of incubation at 37˚C in a humidified incubator containing 5% CO2, the floating cells were discarded and replacement with fresh growth medium.

extract_protocol: From primary HCC cells and their drug-resistant counterpart, total RNA was isolated with Trizol reagent according to the manufacturer's instructions and the quality of RNA was determined using Spectra Max Plus spectrophotometer (Molecular Devices, Sunnyvale, California, USA).

treatment_protocol: For establishment of doxorubicin resistant sub-lines, primary HCC cells (5 × 105) were repeatedly treated with sub lethal concentrations of doxorubicin. The starting concentration was (1 μM), until the recovery rate was maintained in a stable state (~80%) at 10 μM, and that was defined as drug-resistant cells.

value: Primary hepatoma cells isolated from liver


title: Doxorubicin-resistant LC413T-1 hepatoma cells

description: Gene expression data from doxorubicin-resistant LC413T-1 hepatoma cells.


title: 3525-DC-4: Wild type 2

city: Nashville

first: David

last: Cortez

state: TN

address: 2215 Garland Avenue

department: Biochemistry

institute: Vanderbilt University School of Medicine

data_processing:
Adaptors were trimmed with FlexBar
Quality control was done with FastQC
Reads were imported into HiSat2 for alignment into BAM files
featureCounts was used to quanitfy reads
edgeR was used to perform differential expression analysis
FPKM expression data was generated using Cufflinks
FPKM data was converted to TPM data manually
Genome_build: hg38

source_name: U2OS cells

growth_protocol: Exponentially growing cells were maintained in DMEM with 7.5% FBS.

extract_protocol:
RNA was isolated using the Biorad Aurum Total RNA mini kit.
Library was prepared with Illumina Tru-seq total RNA sample prep kit. Sequencing was performed at Paired-End 75 bp on the Illumina HiSeq 3000.

treatment_protocol: Exponentially growing cells were harvest at 80% confluency. HMCES knockout cells were at passage 41.

value: osteosarcoma

tag: genotype/variation

value: Wild type


title: BAB2338


title: chicken LVST rep 1

city: Boston


title: BAB765

tag: lymphoblastoid dna reference


title: BAB2545


title: Doxorubicin-resistant P15 hepatoma cells

description: Gene expression data from doxorubicin-resistant P15 hepatoma cells.


title: BAB5785


title: BAB649


title: 3525-DC-3: HMCES knockout clone 2

tag: cell type

value: HMCES knockout


title: Control P15 hepatoma cells

description: Gene expression data from control P15 hepatoma cells.


title: BAB1230

value: whole blood


title: BAB8327

value: Parent


title: 3525-DC-2: HMCES knockout clone 1


title: BAB572

value: Reference sample


title: BAB2544


title: BAB641

value: Proband


title: BAB1229


title: BAB1959


title: Control 834 hepatoma cells

description: Gene expression data from control 834 hepatoma cells.


title: 3525-DC-1: Wild type 1


title: BAB1932


title: BAB1933