title: PyN6_7159_TCAT [pyr_rep1]

city: Boston

first: Emilia

last: Favuzzi

address: 220 Longwood Avenue, Armenise 217

department: Neurobiology

institute: Harvard Medical School

description:
pyr_rep1
pyr_0

data_processing:
RNA-seq quality check was performed using the tool FastQC (Babraham Bioinformatics). To confirm a low amount of rRNA contaminations, we extracted a subset of 1 million reads for every sample and aligned them against a database of rRNAs using the tool ribopicker (Schmieder et al., 2012).
Reads were aligned to the reference mouse genome (Ensembl release 66 corresponding to the Build 37 assembly, NCBIM37/mm9) using Tophat2 (Kim et al., 2013).
The Cufflinks method was used to compute FPKM values (Trapnell et al., 2010). FPKMs and read counts were scaled via the median of the geometric means of fragment counts across all libraries. Each replicated condition was used to build dispersion models, that were then averaged to provide a single global model for all conditions in the experiment.
Differential expression analysis was performed using Cuffdiff2 to compare all pairs of conditions (Trapnell et al., 2013). The adjusted p-values for multiple comparisons (q-values or false discovery rate, FDR) were calculated using the Benjamini-Hochberg procedure as a method for multiple-testing correction.
The cummeRbund R package from Bioconductor (Trapnell et al., 2012) was used for gene specificity analysis, data visualization, principal component (PC) analysis and Jensen-Shannon (JS) distance between replicates and samples.
Genome_build: Ensembl release 66 corresponding to the Build 37 assembly, NCBIM37/mm9
Supplementary_files_format_and_content: Tab-delimited text files (diffs) that include average FPKM values for each sample, log2FC and the results of DEG test for the indicated pairs; the suppl file includes individual FPKM values for each Sample (replicates)

extract_protocol:
To isolate individual cells, we euthanized the corresponding transgenic mice (Table 1), extracted the brain and microdissected the region of interest in cold pH 7.3 dissociation media containing 14 mM MgCl2, 2 mM HEPES (Invitrogen 15630-106), 0.2 mM NaOH (Sigma S0899), 90 mM Na2SO4 (Sigma S6547), 30 mM K2SO4 (Sigma P9458), 3.6 mg/mL D-(+)-Glucose (Sigma G6152), 0.8 mM kynurenic acid (Sigma K3375), 50 μM AP-V (Sigma A5282), 50 U/mL penicillin/streptomycin (Thermo Fisher 15140122). To generate single-cell suspensions, 1 mm3 tissue pieces from 1-3 brains were pooled and enzymatically digested in dissociation medium containing 0.16 mg/mL cysteine (Sigma C9768), 7 U/mL Papain (Sigma P3125), 0.1 mg/mL DNase (Sigma 10104159001) at 37˚ C for 30 minutes. Papain digestion was then blocked with dissociation medium containing 0.1 mg/mL ovomucoid (Sigma, St. Louis, MO T2011) and 0.1 mg/mL bovine serum albumin (BSA, Sigma A4161) for 1 minute at room temperature. Neurons were mechanically dissociated to create a single cell suspension in iced OptiMEM solution containing 3.6 mg/mL D-(+)-Glucose, 4 mM MgCl2, 0.4 mM kynurenic acid, 25 μM AP-V, 0.04 mg/mL DNase diluted in OptiMEM medium (Thermo Fisher, 31985). Cells were centrifugated at 120 g for 5 minutes at 4˚ C, resuspended in 150-300 μL of fresh complemented OptiMEM and passed through a 40 μm cell strainer. Fluorescently labeled individual cells were then purified from the suspension by fluorescence-activated cell sorting (FACS) using a BD FACSAria III cytometer. Cells from 1-3 consecutive experiments were collected in 350 μl of RLT buffer (RNeasy Lysis buffer, QIAGEN) containing 1% 2-Mercaptoethanol and stored at -80°C for RNA extraction. RNA was extracted using the QIAGEN RNeasy Micro Kit according to manufacturer's instructions. Depending on the cell type and stage, approximately 7,000-30,000 cells were required to obtain 1-2 ng of total RNA.
Library was prepared using the SMARTer Ultra Low RNA Kit for ultra-low amount of RNA. The Illumina HiSeq 2000 platform was used to sequence libraries to a mean of approximately 50 million mapped 50 base pair single-end reads per sample.

tag: strain background

tag: mouse line

value: Nex-Cre

tag: devel stage

value: Post natal day 12

value: brain

tag: tissue subtype

value: Prefrontal cortex, all layers

value: Pyramidal neurons

tag: replicate


title: 75k2_5988_GCTT [inp0_rep2]

status: Public on Jan 25 2019

type: SRA

state: MA

country: USA

description:
inp0_rep2
inp0_1

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: Post natal day 0

tag: tissue

tag: cell type

value: MGE interneurons (Nkx2-1+)


title: PyN5_5989_TGCT fraction3 [pyr_rep3_fraction3]

description:
pyr_rep3_fraction3
pyr_2


title: PLP2_6534_CTTT [plp_rep2_read1]

description:
plp_rep2_read1
plp_1

value: PLP-GFP

value: Post natal day 10

value: Prefrontal cortex, upper layers

value: PLP+ oligodendrocytes


title: 75k3_7158_TATT [inp0_rep3]

description:
inp0_rep3
inp0_2


title: PyN5_5989_TGCT fraction1 [pyr_rep3_fraction1]

description:
pyr_rep3_fraction1
pyr_2


title: PLP1_6533_TTGT [plp_rep1_read1]

description:
plp_rep1_read1
plp_0


title: 75k1_5985_CTTT [inp0_rep1]

description:
inp0_rep1
inp0_0


title: 8EF3_7154_ACGT [ch8_rep3]

description:
ch8_rep3
ch8_2

value: Post natal day 8

value: Chandelier cells


title: SD4-4

city: Seoul

first: Hyeon

middle: Joo

last: Lee

state: - Please choose -

address: 222 Wangsimni-ro, Seongdong-gu

department: Department of Life Science

country: South Korea

institute: Hanyang University

data_processing:
Basecalls performed using CASAVA version 1.8.2
The RNA-seq data for clone 10 was mapped to the human reference genome (hg19) using Bowtie version 1.0.0 (Trapnell et al., 2009) with unique-mapping parameter "-m 1".
To measure expression level, we estimated both reads per million reads (RPM) values on the GENCODE annotation version 19.
After whole genome sequencing (WGS) of the parental cells was performed, the reads were mapped using BWA version 0.7.10-r789, duplicates were marked with Picard version 1.96, realigned based on the presence of an insertion or deletion, and the quality scores recalibrated using GATK version 3.4.
The variants were called using GATK HaplotypeCaller version 3.4.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include transcript name, gene name, coordinates, RPKM values and RPM values

molecule: polyA RNA

organism: Homo sapiens

source_name: clone containing segmental deletion of exon 4, 5, and 6

growth_protocol: K562, a human erythromyeloblastoid leukemia cell line, was purchased from American Type Culture Collection (Manassas, VA) and cultured in Roswell Park Memorial Institute medium (RPMI; Invitrogen, Carlsbad, CA) supplemented with 100 units ml-1 penicillin, 100 µg ml-1 streptomycin, and 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
Libraries were prepared according to illumina's instruction accompanying the Truseq stranded mRNA prep kit. Briefly, The polyA containing mRNA molecules were purified using poly-T oligo attached magnetic beads and then fragmented into small pieces. The cleaved RNA fragments were primed into random hexamers into first strand cDNA using reverse transcriptase and random primers. The RNA template removed and a replacement strand synthesized, incorporating dUTP in place of dTTP to generate ds cDNA. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched with PCR to create the final cDNA library.
Paired-end strand-specific RNA-seq

treatment_protocol: Cells were transfected with plasmid mixtures of Cas9-puro, U6-sgRNA encoding sgRNAs at a weight ratio of 1:1:1 using Neon (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions. One day after transfection, puromycin (Cat no. A11138-03, Invitrogen, Carlsbad, CA) was added to the culture media at a final concentration of 2.5 µgml-1 for two days. Three days after transfection, cells were analyzed.

tag: cell line

tag: transfection

value: plasmid mixtures of Cas9-puro and U6-sgRNAs encoding each member of sgRNAs


title: ATAC CDX2 rep1

city: Lausanne

first: David

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

country: Switzerland

institute: École polytechnique fédérale de Lausanne

description: Overexpression of CDX2-HA

library_source: genomic

data_processing:
Reads were aligned to the mouse reference genome mm10 using STAR 2.5.3a with settings ‘-- alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndtoEnd -- outFilterMultimapNmax 1’
Duplicate reads were removed with Picard and reads not mapping to chromosomes 1-19, X, or Y were removed

Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated by merging replicate bam files with SAMtools followed by the deepTools functions bamCoverage (with setting --normalizeUsingRPKM). log2-ratio bigWig files were generated using the deepTools function bamCompare based on merged replicates for each TF overexpression sample over merged replicates for control (rtTA3G). on merged duplicates

molecule: genomic DNA

growth_protocol: NIH-3T3 cells were routinely cultured at 37°C and 5% CO2 in DMEM, supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were grown in 100 mm cell culture dishes up to a confluence of 90% and split 1:6 every 3-4 days.

extract_protocol:
Cells were pelleted and washed with 1X ice cold PBS at 800g for 5 min. Cells were gently resuspended in 50 μl of ice-cold ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40), and immediately pelleted at 800g for 10 min at 4°C. To transpose open chromatin regions, cells were resuspended in 50 μl of transposition reaction mix containing 0.5 μM of Tn5 transposase (in-house prepared) in TAPS-DMF buffer (10 mM TAPS-NaOH, 5 mM Mgcl2, 10% DMF) and incubated at 37°C for 30 min. The transposed DNA was purified using a DNA purification kit and eluted in 12 μl of water.
A 65 μl PCR reaction was setup with 10 μl of transposed DNA, 0.5 μM of forward primer Ad1_noMX, 0.5 μM of multiplexing reverse primer Ad2.x (Buenrostro et al. 2013), 0.6x SYBR Green I, and 1x PCR Master Mix. The samples were thermocycled at 72°C for 5 minutes, 98°C for 30 s, followed by 12 cycles of 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. The amplified ATAC libraries were purified using a DNA purification kit and size selected using Agencourt AMPure beads (0.55X unbound fraction followed by 1.2X bound fraction).

treatment_protocol: NIH-3T3 cells were treated with 500 ng/ml of Doxycycline 48 hours before the experiment. 50'000 cells were collected.

value: mouse fibroblasts


title: SD2-6

source_name: clone containing segmental deletion of exon 2 and 3

value: human erythromyeloblastoid leukemia cell line


title: EP8b_6267_GAAT [ch8_rep2]

description:
ch8_rep2
ch8_1


title: EP8a_5986_GAAT [ch8_rep1]

description:
ch8_rep1
ch8_0


title: F104_7153_TTGT [ch10_rep3]

description:
ch10_rep3
ch10_2


title: ATAC BRACHYURY rep1

description: Overexpression of BRACHYURY-HA


title: F103_7152_AACT [ch10_rep2]

description:
ch10_rep2
ch10_1


title: SD6-10

source_name: clone containing segmental deletion of 3' splice site of exon 5


title: ATAC BRACHYURY rep2

description: Overexpression of BRACHYURY-HA


title: PyN5_5989_TGCT fraction2 [pyr_rep3_fraction2]

description:
pyr_rep3_fraction2
pyr_2


title: SD1-14

source_name: clone containing segmental deletion of 3' splice site of exon 1


title: Ch10_4937_CAGT [ch10_rep1]

description:
ch10_rep1
ch10_0


title: PyN4_5981_TTGT [pyr_rep2]

description:
pyr_rep2
pyr_1


title: ATAC BHLHB8 rep2

description: Overexpression of BHLHB8-HA


title: BP5c_7160_GCTT [pv5_rep3]

description:
pv5_rep3
pv5_2

value: Post natal day 5

value: Prefrontal cortex, lower layers

value: PV interneurons


title: SD1-4


title: BP5b_5987_TATT fraction2 [pv5_rep2_fraction2]

description:
pv5_rep2_fraction2
pv5_1

value: brain


title: BP5b_5987_TATT fraction1 [pv5_rep2_fraction1]

description:
pv5_rep2_fraction1
pv5_1


title: ATAC WT NIH-3T3

data_processing:
Reads were aligned to the mouse reference genome mm10 using STAR 2.5.3a with settings ‘-- alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndtoEnd -- outFilterMultimapNmax 1’
Duplicate reads were removed with Picard and reads not mapping to chromosomes 1-19, X, or Y were removed
Peaks were called with MACS 2.1.1.20160309 with settings ‘-f BAMPE -g mm’.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated by merging replicate bam files with SAMtools followed by the deepTools functions bamCoverage (with setting --normalizeUsingRPKM). log2-ratio bigWig files were generated using the deepTools function bamCompare based on merged replicates for each TF overexpression sample over merged replicates for control (rtTA3G).

treatment_protocol: 50'000 cells were collected.


title: WD-10

source_name: clone contaning whole deletion


title: Mock transfected cells 3

source_name: Mock transfected cells


title: BP5a_5984_ATAT [pv5_rep1]

description:
pv5_rep1
pv5_0


title: PV10_4935_AACT [pv10_rep1]

description:
pv10_rep1
pv10_0


title: BP10_5983_CAGT [pv10_rep2]

description:
pv10_rep2
pv10_1


title: Mock transfected cells 2


title: MP5c_7155_CAGT [ss5_rep3]

description:
ss5_rep3
ss5_2

value: FVB/NJ

value: GIN

value: Somatosensory cortex, all layers

value: SST interneurons


title: MP5b_6268_TATT [ss5_rep2]

description:
ss5_rep2
ss5_1


title: M10c_7156_ATAT [ss10_rep3]

description:
ss10_rep3
ss10_2


title: MP10_5982_ACGT [ss10_rep2]

description:
ss10_rep2
ss10_1


title: SS10_4936_TTGT [ss10_rep1]

description:
ss10_rep1
ss10_0


title: Mock transfected cells 1


title: B10c_7157_GAAT [pv10_rep3]

description:
pv10_rep3
pv10_2


title: WD-13


title: SS5a_5980_AACT [ss5_rep1]

description:
ss5_rep1
ss5_0


title: ATAC BHLHB8 rep1

description: Overexpression of BHLHB8-HA


title: PV_Naive_3_10

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

description: library of 192 cells

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases represent the unique molecular identifier (UMI) and the next six bases represent the cell specific barcode. The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: Perivascular space and parenchyma, naive phase

growth_protocol: SPF mouse facility

extract_protocol:
Isolated myeloid cells were stained with antibodies for lineage gating exclusion (Ly6G, CD3e, CD19 and NK.1.1), CD45 and CD11b. All CD45+ cells were FACS-sorted in 384-well plates.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: The mice were subjected to MOG-immunization together with PTX injection in order to induce experimental autoimmune enchepalomyelitis (EAE).

tag: strain

value: Perivascular space and parenchyma (Spinal cord)

tag: age

value: 8 weeks

value: CD45+ cells

tag: disease state


title: PV_Precl_2_16

description: library of 192 cells

source_name: Perivascular space and parenchyma, preclinical day 8

value: 9 weeks


title: PV_Precl_3_9

description: library of 192 cells


title: PV_Precl4d_2_4

description: library of 192 cells

source_name: Perivascular space and parenchyma, preclinical day 4


title: PV_Precl_1_15

description: library of 192 cells


title: PV_Naive_2_6

description: library of 192 cells


title: 550543A02 - nced2-nced5-nced9_1 vs nced2-nced5-nced6-nced9_1

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Identification of ABA signaling factors and targets in Arabidopsis developing seeds by comparing ABA deficient and wild type genotypes

hyb_protocol: nced2-nced5-nced6-nced9_1 Cy5 / nced2-nced5-nced9_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Medicago truncatula

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seed - Media:compost (Tref substrates) with Plan-Prod nutritive solution (Fertil) Hygrometry:65% Temperature:21°C light / 19°C dark light:16h light (170 micromol photon) / 8h dark

extract_protocol: nced2 nced5 nced6 nced9-1:20mg. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: genotype/variation

value: medicago truncatula (columbia)  mutant (mutant) - harvest date:07-09-12

extract_protocol: nced2 nced5 nced9-1:20mg. (Qiagen_RNeasy.pdf)


title: control mouse#1, biological rep1

city: South San Francisco

first: Lei

last: Ling

state: CA

address: 333 Oyster Point Blvd

institute: NGM Biopharmaceuticals

description: Gene expression data from mouse livers

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix mouse gene 1.0 ST whole-transcript Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Data were normalized using robust multi-array average (RMA) method.

label: biotin

source_name: Livers from db/db mouse treated with an adeno-associated virus encoding green fluorescent protein

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip WT cDNA synthesis and amplification kit and GeneChip WT terminal labeling kit from Affymetrix).

growth_protocol: db/db mice received a single 200 microliter intravenous injection of 1E11 vector genome adeno-associated virus (AAV) encoding FGF19 or green fluorescent protein via tail vein. Animals were euthanized and livers were collected 2 weeks after injection of the AAV vectors for gene expression analysis.

extract_protocol: Mouse livers were snap-frozen in liquid nitrogen upon euthanization of animals. Total RNA was extracted using RNeasy Mini kit (Qiagen) and treated with DNase I according to the manufacturer's instructions.

treatment_protocol: Embryos were dechorionated with 50% bleach, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

value: liver

tag: genotype

value: db/db

value: 14-week old

tag: treatment

value: control


title: FGF19 mouse#1, biological rep1

description: Gene expression data from mouse livers

source_name: Livers from db/db mouse treated with an adeno-associated virus encoding FGF19


title: 550543A01 - nced2-nced5-nced6-nced9_1 vs nced2-nced5-nced9_1

hyb_protocol: nced2-nced5-nced9_1 Cy5 / nced2-nced5-nced6-nced9_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PV_Precl4d_1_3

description: library of 192 cells


title: 550542A03 - nced2-nced5-nced6-nced9_2 vs Col_2

hyb_protocol: Col_2 Cy5 / nced2-nced5-nced6-nced9_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: seed - Media :compost (Tref substrates) with Plan-Prod nutritive solution (Fertil) hygrometry :65% Temperature :21°C light / 19°C dark Light:16h light (170 micromol photon) / 8h dark

extract_protocol: Col-1:20mg. (Qiagen_RNeasy.pdf)

value: medicago truncatula (columbia)  mutant (wt) - harvest date:07-09-12

extract_protocol: nced2 nced5 nced6 nced9-2:20mg. (Qiagen_RNeasy.pdf)

value: medicago truncatula (columbia)  mutant (mutant) - harvest date:11-09-12


title: control mouse#2, biological rep2

description: Gene expression data from mouse livers


title: 550542A09 - nced2-nced5-nced6-nced9_2 vs nced2-nced5-nced9_2

hyb_protocol: nced2-nced5-nced9_2 Cy5 / nced2-nced5-nced6-nced9_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: nced2 nced5 nced9-2:20mg. (Qiagen_RNeasy.pdf)


title: PV_C_6

description: library of 192 cells


title: 550542A04 - Col_3 vs nced2-nced5-nced6-nced9_3

hyb_protocol: nced2-nced5-nced6-nced9_3 Cy5 / Col_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: nced2 nced5 nced6 nced9-3:20mg. (Qiagen_RNeasy.pdf)

value: medicago truncatula (columbia)  mutant (mutant) - harvest date:17-09-12

extract_protocol: Col-3:20mg. (Qiagen_RNeasy.pdf)

value: medicago truncatula (columbia)  mutant (wt) - harvest date:17-09-12


title: 550542A02 - Col_2 vs nced2-nced5-nced6-nced9_2

hyb_protocol: nced2-nced5-nced6-nced9_2 Cy5 / Col_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: FGF19 mouse#3, biological rep3

description: Gene expression data from mouse livers


title: control mouse#3, biological rep3

description: Gene expression data from mouse livers


title: FGF19 mouse#2, biological rep2

description: Gene expression data from mouse livers


title: PV_EAE_7

description: library of 192 cells

source_name: Perivascular space and parenchyma, onset phase


title: 550542A08 - nced2-nced5-nced9_2 vs nced2-nced5-nced6-nced9_2

hyb_protocol: nced2-nced5-nced6-nced9_2 Cy5 / nced2-nced5-nced9_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 550542A05 - nced2-nced5-nced6-nced9_3 vs Col_3

hyb_protocol: Col_3 Cy5 / nced2-nced5-nced6-nced9_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 550542A10 - nced2-nced5-nced9_3 vs nced2-nced5-nced6-nced9_3

hyb_protocol: nced2-nced5-nced6-nced9_3 Cy5 / nced2-nced5-nced9_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: nced2 nced5 nced9-3:20mg. (Qiagen_RNeasy.pdf)


title: 550542A11 - nced2-nced5-nced6-nced9_3 vs nced2-nced5-nced9_3

hyb_protocol: nced2-nced5-nced9_3 Cy5 / nced2-nced5-nced6-nced9_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PV4_Onset_2_14

description: library of 192 cells


title: 550542A01 - nced2-nced5-nced6-nced9_1 vs Col_1

hyb_protocol: Col_1 Cy5 / nced2-nced5-nced6-nced9_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PV_Naive_1_5

description: library of 192 cells


title: PV4_Onset_1_13

description: library of 192 cells


title: PV3_Plate1_Onset_1_7

description: library of 192 cells


title: PV3_Plate2_Onset_1_3

description: library of 192 cells


title: PV2_Acute_1_5

description: library of 192 cells

source_name: Perivascular space and parenchyma, peak phase

value: 10 weeks


title: PV2_Precl_2_2

description: library of 192 cells


title: 550541A12 - Col_1 vs nced2-nced5-nced6-nced9_1

hyb_protocol: nced2-nced5-nced6-nced9_1 Cy5 / Col_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PV2_Acute_2_6

description: library of 192 cells


title: PV3_Plate1_Onset_2_12

description: library of 192 cells


title: Men_Precl_17

description: library of 192 cells

source_name: Leptomeninges, preclinical day 8

value: Leptomeninges (Spinal cord)


title: PV1_Acute_1_9

description: library of 192 cells


title: PV1_Acute_2_10

description: library of 192 cells


title: Men_Precl_2_11

description: library of 192 cells


title: Men_Precl4d_8

description: library of 192 cells

source_name: Leptomeninges, preclinical day 4


title: Men_Precl_1_10

description: library of 192 cells


title: 550541A11 - nced2-nced5-nced9_3 vs Col_3

hyb_protocol: Col_3 Cy5 / nced2-nced5-nced9_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Men_Naive_9

description: library of 192 cells

source_name: Leptomeninges, naive phase


title: Men_Precl4d_10

description: library of 192 cells


title: PBS_0

city: Gainesville

first: Ley

middle: Cody

last: Smith

state: FL

address: 2187 Mowry Rd

institute: University of Florida

description:
fpkm_isoform_matrix.csv
NM1d_vs_PBS_sig_isoforms.xlsx
NM28d_vs_PBS_sig_isoforms.xlsx

data_processing:
Raw sequence reads were aligned to rn4 rat reference genome using tophat.
Grouped bam files were compared using cuffdiff.
Output from cuffdiff was analyzed in cummeRbund.
Raw data file was uploaded from cuffdiff to Ingenuity Pathway Analysis.
Supplementary_files_format_and_content: csv file with fpkm, Excel file with differential expression.

organism: Rattus norvegicus

source_name: Alveolar macrophages

growth_protocol: Male Wistar rats (225–250 g) were purchased from Harlan Laboratories (Indianapolis, IN) and maintained in an AALAC approved animal care facility. Animals were housed in filter top microisolation cages and provided food and water ad libitum. Animals received humane care in compliance with the guidelines outlined in the Guide for the Care and Use of Laboratory Animals, published by the National Institutes of Health.

extract_protocol:
Total mRNA was extracted from lung macrophages using an RNeasy Mini kit (Qiagen, Valencia, CA) and RNA quality analyzed using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA was converted into double stranded cDNA and amplified using Illumina TruSeq RNA Sample Preparation Kit following the manufacturer’s directions. Reads were sequenced as 2x75bp paired end.

treatment_protocol: Animals were anesthetized with 2.5% isofluorane, and then administered PBS or NM (0.125 mg/kg, mechlorethamine hydrochloride, Sigma-Aldrich, St. Louis, MO) intratracheally as previously described (Sunil et al., 2011). All instillations were performed by David Reimer, D.V.M., Comparative Medicine Resources, Rutgers University. NM was prepared immediately before administration in a designated room under a chemical hood following Rutgers University Environmental Health and Safety guidelines.

value: wistar

tag: Sex

value: male

value: Alveolar macrophages

tag: days of exposure


title: PBS_2


title: 550541A08 - Col_2 vs nced2-nced5-nced9_2

hyb_protocol: nced2-nced5-nced9_2 Cy5 / Col_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 550541A10 - Col_3 vs nced2-nced5-nced9_3

hyb_protocol: nced2-nced5-nced9_3 Cy5 / Col_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Men_EAE_5

description: library of 192 cells

source_name: Leptomeninges, onset phase


title: IL-6TS_JAK1 inhibitor_B

city: Molndal

first: Elisabeth

last: Israelsson

address: Pepparedsleden 1

department: Translational Biology

country: Sweden

institute: AstraZeneca, IMED RIA

description:
Sample 11 (Study 2 - JAK1-inhibition study)
Study2_combined.counts
Study2_combined.gene.sf.tpm

data_processing:
The two studies' fastq files were processed separately using bcbio-nextgen (version 0.9.9a-1ccf093 (study 1) / 0.9.7 (study2)) where reads were mapped to the human genome build hg38 (GRCh38.79) using hisat2 (version 2.0.4 (study 1) / 2.0.2-beta (study 2)).
Gene level quantifications, counts and transcript per million (TPM), were generated with featurecounts (version 1.4.4 (study 1) / 1.4.4 (study 2)) and sailfish (version 0.10.1 (study 1) / 0.9.0 (study 2)), respectively, all within bcbio.
Genome_build: hg38
Supplementary_files_format_and_content: Counts-files contains gene level quantifications from featurecounst used for DE analysis. TPM-files contains gene level quantifications from sailfish.

source_name: Bronchial epithelial cells

growth_protocol: Primary human bronchial epithelial cells (HBECs; Lonza) were expanded to passage 2 in BEGM Bronchial Epithelial Cell Growth Medium (Lonza). These cells were then seeded on 0.4 μm Corning® HTS Transwell®-24 well permeable supports (Sigma-Aldrich) coated with PureCol (Advanced BioMatrix) and differentiated at Air-Liquid Interface (ALI) using PneumaCult™-Ex and ALI Media  (Stemcell) according to manufacturer’s protocol.

extract_protocol:
Cells were lysed in QIAzol Lysis Reagent (Qiagen), scraped off the wells and briefly vortexed. RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer's instruction and RNA integrity was assessed (Bioananalyzer 2100, Agilent).
RNA was diluted to 10 ng/μl and converted to mRNA libraries using the TruSeq Stranded mRNA kit (Illumina) with dual indexing following standard instructions but with 5 min fragmentation time. Libraries were validated on the Fragment Analyzer platform (AATI) using a standard sensitivity NGS fragment analysis kit, and concentrations were determined using the Quant-iT dsDNA High Sensitivity assay kit on the Qubit fluorometer (Thermo Fisher Scientific). Sample libraries were pooled in equimolar concentrations, diluted and denatured according to Illumina guidelines.

treatment_protocol: Once fully differentiated, cells were stimulated for 24h by basolateral addition of human recombinant proteins IL-4 and IL-13 (30 ng/ml; R&D Systems) or IL-6 (150 ng/ml; R&D Systems) and sIL-6R (150 ng/ml; PeproTech) diluted in PneumaCult™-ALI medium.

value: Bronchial epithelial cells

tag: stimulation

value: IL-6, 150 ng/ml + sIL-6R 150 ng/ml + 1 μM JAK1 inhibitor in DMSO


title: IL-6TS_JAK1 inhibitor_A

description:
Sample 10 (Study 2 - JAK1-inhibition study)
Study2_combined.counts
Study2_combined.gene.sf.tpm


title: IL-6TS_JAK1 inhibitor_C

description:
Sample 12 (Study 2 - JAK1-inhibition study)
Study2_combined.counts
Study2_combined.gene.sf.tpm


title: NoStim_JAK1 inhibitor_C

description:
Sample 9 (Study 2 - JAK1-inhibition study)
Study2_combined.counts
Study2_combined.gene.sf.tpm

value: 1 μM JAK1 inhibitor in DMSO


title: Men5_Onset_1_15

description: library of 192 cells

value: 9 weeks

value: CD45+ cells


title: 7-4_Hb_TaDa rep3

city: Eugene

first: Sonia

last: Sen

state: OR

address: 1440 Franklin Blvd

department: ION/IMB

institute: University of Oregon

description: methylated gDNA>DpnI digested

data_processing:
quality check was performed using FastQC, and reads with a score <30 were omitted from the analysis.  Contaminants, if any, were removed using Bbsplit
reads were aligned to Dm6 using bowtie2 and extended to 300bp or a the closest GATC sequence (whichever came first).
data are binned and mean value of reads that fall within each GATC fragments calculated.
Normalisation: read counts are sorted into deciles, highest decile for Dam:Hb and the lowest 3 deciles of Dam only are excluded from the normalisation.
log2(Pol II score/Dam only score) of this is calculated.
Genome_build: dm6
Supplementary_files_format_and_content: bedgraph files were generated using the damID_seq_pipeline (Marshall and Brand 2015)

organism: Drosophila melanogaster

source_name: embryonic neuroblast

extract_protocol:
Methylated gDNA was extracted with extreme care to avoid fragmentation.  gDNA was DpnI digested, PCR purified and DamID adaptors were ligated to the fragment ends.  This was subjected to DpnII digestion and then PCR amplified according to TaDa protocols.  The amplified products were used for library prepapration.
DNA libraries were prepared for sequencing using standard Illumina protocols
TaDa

tag: Stage


title: NM28d_1

description:
fpkm_isoform_matrix.csv
NM28d_vs_PBS_sig_isoforms.xlsx


title: Men5_Onset_2_16

description: library of 192 cells


title: 550541A09 - nced2-nced5-nced9_2 vs Col_2

hyb_protocol: Col_2 Cy5 / nced2-nced5-nced9_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PBS_1


title: 7-4_Hb_TaDa rep2

description: methylated gDNA>DpnI digested


title: NM28d_2


title: NM28d_0


title: 550541A07 - nced2-nced5-nced9_1 vs Col_1

hyb_protocol: Col_1 Cy5 / nced2-nced5-nced9_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: medicago truncatula (columbia)  mutant (mutant) - harvest date:07-09-12


title: NoStim_JAK1 inhibitor_B

description:
Sample 8 (Study 2 - JAK1-inhibition study)
Study2_combined.counts
Study2_combined.gene.sf.tpm


title: Men_Naive_7

description: library of 192 cells

value: 8 weeks


title: NM1d_2

description:
fpkm_isoform_matrix.csv
NM1d_vs_PBS_sig_isoforms.xlsx


title: NoStim_JAK1 inhibitor_A

description:
Sample 7 (Study 2 - JAK1-inhibition study)
Study2_combined.counts
Study2_combined.gene.sf.tpm


title: Men4_Onset_2_8

description: library of 192 cells


title: Men4_Onset_1_7

description: library of 192 cells


title: Men_C_4

description: library of 192 cells


title: 550541A06 - Col_1 vs nced2-nced5-nced9_1

hyb_protocol: nced2-nced5-nced9_1 Cy5 / Col_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Men3_plate1_Onset_2_6

description: library of 192 cells


title: NM1d_1


title: 7-4_Dam_rep3

description: methylated gDNA>DpnI digested


title: IL-6TS_DMSO_C

description:
Sample 6 (Study 2 - JAK1-inhibition study)
Study2_combined.counts
Study2_combined.gene.sf.tpm

value: IL-6, 150 ng/ml + sIL-6R 150 ng/ml + DMSO


title: IL-6TS_DMSO_B

description:
Sample 5 (Study 2 - JAK1-inhibition study)
Study2_combined.counts
Study2_combined.gene.sf.tpm


title: NM1d_0


title: 7-4_Hb_TaDa rep1

description: methylated gDNA>DpnI digested


title: Men3_plate1_Onset_1_5

description: library of 192 cells


title: 7-4_Dam_rep1

description: methylated gDNA>DpnI digested


title: Men2_Acute_2_4

description: library of 192 cells

source_name: Leptomeninges, peak phase


title: 5-6_Hb_TaDa rep3

description: methylated gDNA>DpnI digested


title: IL-6TS_DMSO_A

description:
Sample 4 (Study 2 - JAK1-inhibition study)
Study2_combined.counts
Study2_combined.gene.sf.tpm


title: Men2_Acute_1_3

description: library of 192 cells


title: Men1_Acute_1_11

description: library of 192 cells


title: 5-6_Hb_TaDa rep2

description: methylated gDNA>DpnI digested


title: CP_Precl4d_8

description: library of 192 cells

source_name: Choroid plexus, preclinical day 4

value: Choroid plexus (Brain)


title: 5-6_Hb_TaDa rep1

description: methylated gDNA>DpnI digested


title: NoStim_DMSO_B

description:
Sample 2 (Study 2 - JAK1-inhibition study)
Study2_combined.counts
Study2_combined.gene.sf.tpm

value: DMSO


title: IL4IL13_C

description:
Sample 12 (Study 1 - IL-6 vs T2 study)
Study1_combined.counts
Study1_combined.gene.sf.tpm

growth_protocol: Primary human bronchial epithelial cells (HBECs; Lonza) were expanded to passage 2 in BEGM Bronchial Epithelial Cell Growth Medium (Lonza). These cells were then seeded on 0.4 μm Corning® HTS Transwell®-24 well permeable supports (Sigma-Aldrich) coated with PureCol (Advanced BioMatrix) and differentiated at Air-Liquid Interface (ALI) using BEBM (Lonza) according to manufacturer’s protocol.

treatment_protocol: Once fully differentiated, 1μM JAK1 inhibitor in DMSO or DMSO were added apically for 30 minutes in 200μL medium that was removed before stimulation. Cells were stimulated for 24h by basolateral addition of human recombinant proteins IL-6 (150 ng/ml; R&D Systems) and sIL-6R (150 ng/ml; PeproTech) diluted in BEBM.


title: CP_Precl4d_2

description: library of 192 cells


title: NoStim_DMSO_A

description:
Sample 1 (Study 2 - JAK1-inhibition study)
Study2_combined.counts
Study2_combined.gene.sf.tpm


title: 5-6_Dam_rep1

description: methylated gDNA>DpnI digested


title: CP_Precl_2_9

description: library of 192 cells

source_name: Choroid plexus, preclinical day 8


title: IQ1_24hr_rep1

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

description: global FGFR2b inhibition, IQ1 after 24hr

hyb_protocol: 2 µg of the labeled cDNA were subjected to hybridization. The cDNA was not fragmented before hybridization. Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 6.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: Organ homogenate, E12.5 mouse lungs, cultured in vitro

label_protocol: Purified total RNA was amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands). Per sample, 2 µg amplified cDNA was Cy-labeled using the SureTag DNA labeling kit (Agilent, Waldbronn, Germany).

extract_protocol: QIAgen microRNeasy Mini Kit

treatment_protocol: Isolated E12.5 lungs were cultured on nucleopore filters with DMEM+10% FBS+1% PEN/STREP culture medium suuplemented with 10 uM IQ1 (experimental) or vehicle (PBS, control). Lungs were cultured at 5% CO2 and at 37 degress Celsius. In one experiment, lungs were cultured for 9 hrs. In another, lungs were cultured for 24 hrs. After these times, total RNA was isolated from the lungs. The samples cultured for 24 hours were pooled.

value: lungs

tag: developmental stage

tag: time


title: Ctrl_9hr_rep3

description: untreated after 9 hr

value: control


title: IQ1_9hr_rep3

description: global FGFR2b inhibition, IQ1 after 9hr


title: Ctrl_24hr_rep1

description: untreated after 24 hr


title: CP_Precl_18

description: library of 192 cells


title: Da-Gal4_Hb_TaDa rep3

description: methylated gDNA>DpnI digested

source_name: embryo


title: Da-Gal4_Hb_TaDa rep2

description: methylated gDNA>DpnI digested


title: IL6sIL6R_C

description:
Sample 9 (Study 1 - IL-6 vs T2 study)
Study1_combined.counts
Study1_combined.gene.sf.tpm

value: IL-6, 150 ng/ml + sIL-6R 150 ng/ml


title: CP_Precl_1_8

description: library of 192 cells


title: Ctrl_9hr_rep2

description: untreated after 9 hr


title: IL6sIL6R_B

description:
Sample 8 (Study 1 - IL-6 vs T2 study)
Study1_combined.counts
Study1_combined.gene.sf.tpm


title: Ctrl_9hr_rep1

description: untreated after 9 hr


title: CP_Naive_7

description: library of 192 cells

source_name: Choroid plexus, naive phase


title: DaGal4_Dam_rep3

description: methylated gDNA>DpnI digested


title: 5-6_Dam_rep3

description: methylated gDNA>DpnI digested


title: IQ1_9hr_rep2

description: global FGFR2b inhibition, IQ1 after 9hr


title: IQ1_9hr_rep1

description: global FGFR2b inhibition, IQ1 after 9hr


title: IL4IL13_B

description:
Sample 11 (Study 1 - IL-6 vs T2 study)
Study1_combined.counts
Study1_combined.gene.sf.tpm


title: IL6_C

description:
Sample 6 (Study 1 - IL-6 vs T2 study)
Study1_combined.counts
Study1_combined.gene.sf.tpm


title: CP5_Onset_4

description: library of 192 cells

source_name: Choroid plexus, onset phase


title: IL6sIL6R_A

description:
Sample 7 (Study 1 - IL-6 vs T2 study)
Study1_combined.counts
Study1_combined.gene.sf.tpm


title: CP_Naive_1

description: library of 192 cells


title: NoStim_DMSO_C

description:
Sample 3 (Study 2 - JAK1-inhibition study)
Study2_combined.counts
Study2_combined.gene.sf.tpm


title: IL6_B

description:
Sample 5 (Study 1 - IL-6 vs T2 study)
Study1_combined.counts
Study1_combined.gene.sf.tpm


title: IL4IL13_A

description:
Sample 10 (Study 1 - IL-6 vs T2 study)
Study1_combined.counts
Study1_combined.gene.sf.tpm


title: DaGal4_Dam_rep1

description: methylated gDNA>DpnI digested


title: HiBEC_TGFb3

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

data_processing:
TopHat v2.1.0 for alignment
FeatureCounts to quantify expression
edgeR for defining differentially expressed genes
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: tsv format containing edgeR differential expression results along with RPKM values

source_name: Biliary Epithelial Cells

growth_protocol: Cells grown in H69 media used for cholangiocyte cell lines

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

treatment_protocol: Recombinat human TGF-beta at 10ng/ml for 48 hours

value: Human Intrahepatic Biliary Epithelial Cells (HIBEC)

tag: passage

tag: agent

value: TGFb


title: DaGal4_Dam_rep2

description: methylated gDNA>DpnI digested


title: IL6_A

description:
Sample 4 (Study 1 - IL-6 vs T2 study)
Study1_combined.counts
Study1_combined.gene.sf.tpm

tag: cell type


title: CP4_Onset_1

description: library of 192 cells

tag: tissue


title: HiBEC_TGFb2

tag: cell line


title: CP5_Onset_17

description: library of 192 cells

tag: strain


title: NS_C

description:
Sample 3 (Study 1 - IL-6 vs T2 study)
Study1_combined.counts
Study1_combined.gene.sf.tpm

value: Non-stimulated control


title: Da-Gal4_Hb_TaDa rep1

description: methylated gDNA>DpnI digested


title: CP2_Acute_2_2

description: library of 192 cells

source_name: Choroid plexus, peak phase

tag: age

value: 10 weeks


title: NS_B

description:
Sample 2 (Study 1 - IL-6 vs T2 study)
Study1_combined.counts
Study1_combined.gene.sf.tpm

value: Bronchial epithelial cells


title: Normal6-2

city: Toyama

first: Tetsushi

last: Hirano

state: Toyama

address: 2630 sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description: Patinet 4, sebaceous adenoma

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h. The arrays were washed and stained  in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned by the Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The data were analyzed using Gene Spring software with RMA normalization method.

source_name: sebaceous adenoma of the eyelid

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip WT PLUS Reagent Kit (Affymetrix).

growth_protocol: We enrolled three patients (74-, and 83- and 58-year-old women) with human sebaceous gland carcinoma of the eyelid and one patient (92-year-old man) with human sebaceouos adenoma of the eyelid. Four patients underwent surgical excision of the tumor.

extract_protocol: RNA was extracted from cells using a NucleoSpin® miRNA isolation kit (MACHEREY-NAGEL GmbH) along with on-column DNase I treatment. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies). RNA samples with RIN (RNA integrity number) values

treatment_protocol: Sebaceous gland carcinoma and sebaceous adenoma samples were used.

value: male

value: 92 years

value: eyelid

tag: diagnosis

value: sebaceous adenoma of the eyelid


title: Normal6-3

description: Patinet 4, sebaceous adenoma


title: CP2_Acute_1_1

description: library of 192 cells

value: CD45+ cells

tag: disease state


title: HiBEC_TGFb1


title: HiBEC_Ctrl3

value: Vehicle (Control)


title: Normal6-1

description: Patinet 4, sebaceous adenoma


title: Cancer4-2

description: Patient 3, sebaceous gland carcinoma of the eyelid

source_name: sebaceous gland carcinoma of the eyelid

value: female

value: 58 years

value: sebaceous gland carcinoma of the eyelid


title: NS_A

description:
Sample 1 (Study 1 - IL-6 vs T2 study)
Study1_combined.counts
Study1_combined.gene.sf.tpm


title: Cancer4-3


title: CP1_Acute_2_24

description: library of 192 cells

value: Choroid plexus (Brain)


title: HiBEC_Ctrl2


title: Cancer4-1


title: RPMI8226_control

city: Durham

first: Makoto

last: Nakagawa

state: NC

address: 308 Research Drive

department: Department of Orthopaedic Surgery

institute: Duke University

data_processing:
Avadis NGS Version 2.1 software was used for analysis.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Avadis NGS Version 2.1.
Genome_build: hg19

source_name: multiple myeloma

growth_protocol: RPMI1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
Total RNA was isolated using an RNeasy Mini Kit (Qiagen).
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: MM cells were treated with 1 μM OR-S1 for 72 h.

value: peripheral blood

value: B lymphocyte

value: control


title: Cancer2-3

description: Patient 2, sebaceous gland carcinoma of the eyelid

value: 83 years


title: MM.1S_control

value: B lymphoblast


title: HiBEC_Ctrl1

value: Human Intrahepatic Biliary Epithelial Cells (HIBEC)


title: Blood_Precl4d_6

description: library of 192 cells

source_name: blood, preclinical day 4

extract_protocol:
Isolated myeloid cells were stained with antibodies for lineage gating exclusion (Ly6G, CD3e, CD19 and NK.1.1), CD45 and CD11b. All CD45+ cells were FACS-sorted in 384-well plates.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

value: Blood

value: 9 weeks

value: Ly6Chigh and Ly6Clow monocytes


title: Blood_Onset_18

description: library of 192 cells

source_name: blood, onset


title: 5-8 hpo embryos

city: Wuhan

first: Wei

last: Peng

address: Shizishan Street No. 1, Hongshan District, Wuhan,Hubei  430070, P.R. China

country: China

institute: Huazhong Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: ASM78921v1
Supplementary_files_format_and_content: Excel files reporting readcounts and fpkms

organism: Bactrocera dorsalis

source_name: 5-8 hpo embryos

extract_protocol:
0-1, 2-4 and 5-8 post-oviposition (hpo) embryos were collected and immediately stored in RNAlater® Solution (Ambion). Total RNAs were extracted using Trizol reagent (Invitrogen, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with total RNA for the construction of sequencing libraries.
RNA libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250-300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.

value: 5-8 hpo


title: RPMI8226_drug

value: 72 h after OR-S1 treatment


title: 2-4 hpo embryos

source_name: 2-4 hpo embryos

value: 2-4 hpo


title: MM.1S_drug


title: Cancer2-1

value: eyelid


title: Cancer2-2

value: female


title: Blood_Naive_5

description: library of 192 cells

source_name: blood, naive

value: 8 weeks


title: 0-1 hpo embryos

source_name: 0-1 hpo embryos

value: 0-1 hpo


title: CP1_Acute_1_23

description: library of 192 cells

value: Choroid plexus (Brain)

value: 10 weeks

value: CD45+ cells


title: Cancer1-3

description: Patient 1, sebaceous gland carcinoma of the eyelid

value: 74 years

value: sebaceous gland carcinoma of the eyelid


title: Cox_16_13201_111717: MyCell1320 ECT with ST mRNA

status: Public on Jan 24 2019

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

description: cardiac patient-derived iPSC differentied into ventricle cardiomyocytes and stimulated

data_processing:
fastq files were generated from demultiplexed reads and trimmed of adaptor sequences quality >30 and readlengths > 50
reads were aligned to the h38.p10 human trranscripts obtained from ENSEMBL using kallisto quant pseudo alignment method. The following parameters use used: -b 50 -t 6 --sinlge -l 180 -s 20
estimated counts were read into an R workspace using tximport. Data was assembled into a DGEList object and normalized useing cmp with log transformation (file: count_data.csv). Data was filtered and transformed using voom (voom_data.csv) to generate normallly distributed data for differential gene epxression analysis.
Genome_build: H38.p10
Supplementary_files_format_and_content: two files are given. One contains the unprocessed psedo cound direclty form kallisto quant. The other is the normalized and transformed counts using voom.

source_name: human iPSC derived form MyCell1320

growth_protocol: Predominantly ventricular cardiomyocytes (CMs) were derived from the human embryonic stem cell (hESC) lines Hes2 and HES3-NKX2-5gfp/w using the using embryoid body (EB)(Kattman et al., 2011; Yang et al., 2008) differentiation protocol and the human induced pluripotent stem cell (hiPSC) line BJ1D using the monolayer differentiation protocols (Lian et al., 2012; Lian et al., 2013) as previously described. Ventricular cell populations contained 74.7±6.3% (n=9) of CMs on average, based on cardiac troponin T expression analysis using flow cytometry, at the end of directed differentiation protocols. Predominantly atrial cardiomyocytes were derived from Hes3-NKX2-5gfp/w hESCs and MSC-iPSC1(Park et al., 2008) using an atrial-specific EB differentiation protocol as described (Lee et al., 2017). Briefly, all trans retinoic acid (0.5 μM, Sigma) was added during the cardiac mesoderm specification stage (days 3-5 of differentiation) to promote atrial cardiogenesis. At day 20 of differentiation, atrial cardiomyocytes from Hes3-NKX2-5gfp/w hESCs were analyzed and defined based on the proportion of NKX2.5+, cTNT+ and MLC2v- cells using flow cytometry, 79.1±8.0%, n=10. For predominantly atrial CMs from MSC-IPS1 cell lines, 73.2 % ± 7.7% of total cells were atrial CMs (cTNT+ and MLC2V-), n=2 batches. Differentiation cultures were dissociated to single cells for subsequent tissue seeding, as previously described (Zhang et al., 2016).

extract_protocol:
RNA was isolated using a commercially available kit: PicoPure™ RNA Isolation Kit (Thermo Fisher, KIT0204) and RNase-Free DNase Set (Qiagen #79254).
NEB Ultra II RNA direction + poly A + multiplex. 75 base single end reads NextSeq500 high output v2 flow cells using v2 chemistry

treatment_protocol: On Day 7, each strip of 8 tissues was transferred to an electrical stimulation chamber, such that the tissues were positioned between the carbon rods. On Day 7 and weekly thereafter, 4X bright field movies were taken of beating under stimulation at 1Hz. The minimum voltage per cm required to stimulate the synchronized contraction of the tissue (excitation threshold, ET) and the maximum frequency the tissue could contract in response to the stimulation pulse at twice the ET (maximum capture rate, MCR) were measured and recorded. POMaC is intrinsically fluorescent, hence the deflection of the polymer wire due to tissue contraction was isolated and tracked under the blue fluorescent light. Blue channel movies (10X objective; λex = 350nm, λem = 470nm; 100 frames/s, 5ms exposure) were taken to record the bending movement of the POMaC wire during tissue contraction from 1-3Hz (1Hz increase every 20sec) to measure the force-frequency relationship (FFR). After FFR, the tissue had been stimulated at high frequency (6Hz) for 20sec, stimulation was turned off for 10sec (rest period) and the stimulation was re-initiated at 1Hz to measure the post-rest potentiation (PRP) of the tissue. To quantify the FFR and PRP, all measurements were normalized to the 1Hz baseline values. All imaging was performed using an Olympus IX81 inverted fluorescent microscope and CellSens software (Olympus Corporation).    The Day 7 electrical excitability assessments were used to determine the long-term stimulation conditions, specifically stimulation voltage (1.5-times the ETavg). Electrical stimulation was continued with weekly monitoring of ET, MCR, FFR, and PRP. Culture media was changed every week.       Electrical stimulation protocol of weekly 1Hz increase in frequency was implemented for ventricular maturation. If average MCR exceeds 4Hz after one week of 2Hz stimulation or exceeded 5Hz after one week of 3Hz stimulation, stimulation frequency can be changed directly from 2Hz to 4Hz or 3Hz to 5Hz to accelerate the process. End point assessments were performed when a positive FFR in the range from 1 to 3Hz was achieved. If a positive FFR was not observed once the frequency reached 6Hz, stimulation continued at 6Hz, until a positive FFR was observed. The stimulation voltage was adjusted weekly to 1.5-times the average ET, down to a minimum voltage of 3.5V/cm. For atrial preparations, a similar procedure was applied with the daily increase of the stimulation frequency by 0.4Hz, from 1Hz to 6Hz, then retaining the stimulation frequency at 6Hz for 1week.     For the ventricular disease model preparation, tissues were generated from control A, control B, control C, affected D, affected E, and affected F cardiomyocytes. Electrical stimulation started at 2Hz on day 7 post cell seeding and the protocol of 1Hz weekly step-up was used until the frequency reached 6Hz, at which point it was maintained at 6Hz for one week. Subsequently, the frequency was decreased to 3Hz and maintained at that level for the remainder of the cultivation period, up to 6 months.  Tissue were assessed after 6Hz stimulation was reached (6weeks) and after 5 months (control A, control B, affected D and affected E) or after 8 months (control C and affected F) of total culture period.      For atrioventricular preparations, electrical stimulation started at 2Hz on day 7 and the protocol of 1Hz weekly step-up was used until the frequency reached 6Hz. If average MCR exceeded 4Hz after one week of 2Hz stimulation, or exceeded 5Hz after one week of 3Hz stimulation, stimulation frequency could be changed directly from 2Hz to 4Hz or 3Hz to 5Hz to accelerate the process.  The stimulation at 6Hz was maintained for 1 week, at which point it was decreased to 3Hz and maintained for a period of several days until the tissues were used for drug testing.

value: ventricle myocyte

tag: pathology

value: abnormal

value: stimulated


title: Cox_18_13203_111717: MyCell1320 ECT with ST mRNA


title: Cox_19_11871_111717: MyCell1187 ECT with ST mRNA

source_name: human iPSC derived form MyCell1187

value: male


title: Cox_15_AC3_111717: ECT Atrial no ST mRNA

description: Hes2-derived cardiomyocytes

source_name: human embryonic stem cell line HES2

value: atrial myocyte

value: normal

value: unstimulated


title: Cox_17_13202_111717: MyCell1320 ECT with ST mRNA


title: Cox_20_11872_111717: MyCell1187 ECT with ST mRNA


title: FM3

city: Pittsburgh

first: Samira

last: Kiani

state: Pennsylvania

address: A809-B Scaife Hall 3550 Terrace Street Pittsburgh

department: Division of Experimental Pathology

institute: University of Pittsburgh

description: 24,078 protein-coding and non-coding RNA

data_processing:
FASTQ files for each sample were algined to genome (Ensembl 90) by STAR (ver 2.5.0c) with parameters of --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --quantMode GeneCounts
RPKM (reads per killobases and million reads) values were obatined by Cufflink (ver 2.2.1 with default options)
TPM (transcripts per million reads) were calcualted RPKM/total reads x 10^6 fro each sample.
Ensembl gene IDs were mapped to Entrez Gene ID with gene2ensembl file from NCBI (Dec 2017 release).
Genome_build: GRCh38
Supplementary_files_format_and_content: a text file with abundance measurement matrix in TPM

source_name: hek293FT cells

growth_protocol: HEK293FT cell line was purchased from ATCC and maintained in Dulbecco’s modified Eagle’s medium (DMEM - Life Technologies) containing 10% fetal bovine serum (FBS - Life Technologies), 2mM glutamine, 1mM sodium pyruvate (Life Technologies) and 1% penicillin-streptomycin (Life Technologies) in incubators at 37°C and 5% CO2.

extract_protocol:
Cells were lysed, and RNA was extracted using RNeasy Plus mini kit (Qiagen) 72 hrs post transfection and sent to UCLA TCGB core on dry ice.
Ribosomal RNA depletion, and single read library preparation were performed at UCLA core followed by RNA sequencing using NextSeq500.  Coverage was 14 million reads per sample.  FASTQ files with single-ended 75bp reads were then aligned to the human GRCh38 reference genome sequence (Ensembl release 90) with STAR 54, and uniquely-mapped read counts (an average of 14.8 million reads per sample) were obtained with Cufflink 55.  The read counts for each sample were then normalized for the library size to CPM (counts per million reads) with edgeR 56.  Custom R scripts were then used to generate plots.

treatment_protocol: Cells were transfected with total of 500 ng DNA the day after seeding. Polyethylenimine (PEI) was used to transfect HEK293FT cells seeded into 24-well plates.  Transfection complexes were prepared according to manufacturer’s instructions (Polysciences).

tag: transfection

value: Transfected with Cas9Beta, gRNA targeting MIAT locus and activator domains


title: FM1

value: Transfected with WT-Cas9, gRNA targeting MIAT locus and activator domains


title: FM4


title: Cox_14_AC2_111717: ECT Atrial no ST mRNA

description: Hes2-derived cardiomyocytes

tag: Sex

value: female


title: Cox_13_AC1_111717: ECT Atrial no ST mRNA

description: Hes2-derived cardiomyocytes


title: FM2


title: Cancer1-1

value: eyelid


title: Cox_12_AST3_111717: ECT Atrial with ST mRNA

description: Hes2-derived cardiomyocytes


title: Cox_21_11873_111717: MyCell1187 ECT with ST mRNA


title: Cox_9_VC4_111717: ECT Ventricular no ST mRNA

description: Hes2-derived cardiomyocytes


title: Cox_10_AST1_111717: ECT Atrial with ST mRNA

description: Hes2-derived cardiomyocytes


title: Cox_8_VC3_111717: ECT Ventricular no ST mRNA

description: Hes2-derived cardiomyocytes


title: Cox_7_VC2_111717: ECT Ventricular no ST mRNA

description: Hes2-derived cardiomyocytes


title: Cox_6_VC1_111717: ECT Ventricular no ST mRNA

description: Hes2-derived cardiomyocytes


title: Cox_5_VST3_111717: ECT Ventricular with ST mRNA

description: Hes2-derived cardiomyocytes


title: Cox_11_AST2_111717: ECT Atrial with ST mRNA

description: Hes2-derived cardiomyocytes


title: Cox_4_VST2_111717: ECT Ventricular with ST mRNA

description: Hes2-derived cardiomyocytes


title: RNA_D6RA_Rep3

city: Philadelphia

first: Kelvin

last: See

state: PA

address: 3400 Civic Center Blvd, Smilow Center for Translational Research

department: Medicine

institute: University of Pennsylvania

data_processing:
ChIP-seq: Fastq sequencing reads were aligned to genome assembly (NCBI37/mm9) using Bowtie2 (version 2.2.9) with default parameters and “--local” to allow soft clipping of ends. Alignments were further processed by SAMtools (version 0.1.19) to remove low quality alignments (“-q 10”), read duplicates (“rmdup -s”). H3K9me2 domains for individual and pooled libraries were called using Enriched Domain Detector (EDD version 1.1.18) (Lund et al., 2014) with parameters “--bin-size auto --gap-penalty 3 --fdr 0.05”. Blacklist regions from ENCODE mm9 and default EDD mm9 blacklist regions were used and required fraction of uninformative bins is 0.97.
RNA-seq: Fastq files were assessed for quality using FastQC (version 0.11.2) program before and after trimming using Trimmomatic (version 0.32).  Trimmed fastq files were aligned to the mouse genome assembly NCBI37/mm9 using STAR (version 2.6.0c) (Dobin et al., 2012).  Unmapped reads, non-primary alignments and alignments with a MAPQ score of <10 were filtered with samtools. Rsubread (Liao et al., 2013) package’s featureCounts function was used to count the number of uniquely mapping reads per gene using Ensembl v.67 mm9 gene annotation file. Gene count matrix was transformed to counts per million using edgeR package (Robinson et al., 2010).  For differential gene expression analysis, genes with <1 CPM in 2 or fewer samples were removed. Limma (Ritchie et al., 2015) voom function was used to log transform the cpm matrix.  Limma was used with a linear model to perform differential gene expression analysis with adjusted p-values for multiple comparisons using Benjamini-Hochberg procedure (BENJAMINI and HOCHBERG, 1995). Cutoff of FDR <= 0.05 and Fold Change >= 1.5 or <= -1.5 were used for significantly upregulated or downregulated genes.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: bigwig;
Supplementary_files_format_and_content: RNA-seq: tab delimited file with normalized count matrix

source_name: D6 RA treated P19

growth_protocol: P19 cells were obtained from ATCC (CRL-1825) and maintained at low confluency in Alpha-Minimum Essential Media (A-MEM, 12571048, Invitrogen) supplemented with 10% Fetal Bovine Serum (charcoal stripped FBS, F6765 Sigma) and 1% penicillin/streptavidin.

extract_protocol:
Chromatin Immunoprecipitation (ChIP) was performed similar to previously described (Poleshko et al., 2017) using specific antibodies to H3K9me2 or H3.
250ng of ChIP or input DNA was used for ChIP-seq library preparation using the NEB Next Ultra II DNA Library preparation kit for Illumina (E7645S, NEB) and NEBNext multiplex oligos for Illumina (dual index primers set I, E7600S, NEB) according to manufacturer’s instructions. Quality of individual ChIP-seq libraries were assessed by Bioanalyser (high sensitivity DNA kit, 5067-4626, Agilent) and quantified by qPCR using Kapa Library Quantification Kit (KK4835, Kapa). RNA-seq libraries were prepared using Truseq stranded total RNA Library Prep Kit with Ribo-zero Human/Mouse/Rat Set A (RS-122-2201, Illumina) according to manufacturer’s instructions. Libraries were normalized and pooled for multiplex sequencing, re-quantified and sequenced on Nextseq500 platform (75bp, single end, Illumina).

treatment_protocol: P19 cells were differentiated in 1 uM all trans Retinoic Acid (RA) (R2625, Sigma) or in 1% DMSO (D2650, Sigma) by forming embryoid bodies (EBs) for two days in bacteriological petri dishes, before transferring to T75 cell culture flasks and replaced with maintenance media.

tag: chip antibody


title: Cox_3_VST1_111717: ECT Ventricular with ST mRNA

description: Hes2-derived cardiomyocytes

tag: stimulation


title: RNA_D6DMSO_Rep1

source_name: D6 DMSO treated P19


title: RNA_D6DMSO_Rep3


title: RNA_D6RA_Rep1


title: RNA_D3RA_Rep3

source_name: D3 RA treated P19


title: RNA_D3RA_Rep2


title: RNA_D6DMSO_Rep2


title: RNA_D3RA_Rep1


title: RNA_D3DMSO_Rep3

source_name: D3 DMSO treated P19


title: RNA_D3DMSO_Rep2


title: RNA_D0_Rep3

source_name: undifferentiated P19


title: RNA_D0_Rep1


title: D3RA_H3K9me2_Rep3

value: H3K9me2 (Abcam, ab1220)


title: RNA_D6RA_Rep2


title: D3RA_H3K9me2_Rep1


title: RNA_D3DMSO_Rep1


title: ASC-3010-PCOS

city: Los Angeles

first: Greogorio

last: Chazenbalk

state: California

address: 10833 Le Conte Ave

department: Obstetrics and Gynecology

institute: University of California, Los Angeles

description: Gene expression data from PCOS ASCs of second pair-match

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data was analyzed with Partek Genomics suite using the RMA as normalization method.

source_name: subcutaneous adipose tissue, PCOS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Ambion MessageAmp™ Premier RNA Amplification Protocol)

growth_protocol: Adipose stem cells were plated in 10 cm dish containing DMEM/10% FCS, 0.05 U/ml penicillin, 0.05 mg/ml streptomycin, 1.25 mg/ml fungizone and cultured at 37°C until cells reached confluency.

extract_protocol: Total cellular RNA was isolated using RNeasy mini kit (Qiagen, Carlsbad, CA) according to the manufacturer’s protocol.

tag: female type

value: PCOS


title: D3RA_H3_Rep2

value: H3 (Abcam, ab1791)


title: D3RA_H3_Rep1


title: ASC-3034-control

description: Gene expression data from control ASCs of fourth pair-match

source_name: subcutaneous adipose tissue, control

value: control


title: ASC-3004-control

description: Gene expression data from control ASCs of first pair-match


title: D3DMSO_H3K9me2_Rep2


title: D3DMSO_H3K9me2_Rep1


title: ASC-3036-control

description: Gene expression data from control ASCs of second pair-match


title: ASC-3019-PCOS

description: Gene expression data from PCOS ASCs of third pair-match


title: ASC-3042-PCOS

description: Gene expression data from PCOS ASCs of fourth pair-match


title: ASC-3027-control

description: Gene expression data from control ASCs of third pair-match


title: D3RA_H3K9me2_Rep2


title: ASC-3006-PCOS

description: Gene expression data from PCOS ASCs of first pair-match


title: D0_H3K9me2_Rep1


title: RNA_D0_Rep2


title: D3DMSO_H3_Rep2


title: D3DMSO_H3_Rep1


title: D0_H3K9me2_Rep3


title: D0_H3K9me2_Rep2


title: D3RA_H3_Rep3


title: D0_H3_Rep3


title: Cancer1-2

source_name: sebaceous gland carcinoma of the eyelid

value: 74 years


title: D0_H3_Rep1


title: D3DMSO_H3_Rep3


title: D3DMSO_H3K9me2_Rep3


title: D0_H3_Rep2


title: BLO_UCMS1_S1

city: Guildford

first: Emma

last: Laing

address: Stag Hill

country: United Kingdom

institute: University of Surrey

data_processing:
Quality control (QC) of sequencing reads, read alignment and feature quantification were performed using a RNA-Seq workflow developed by Eli Lilly and Company.
FASTQ files were checked for integrity and potential transfer errors prior to QC. QC was performed on both pre-aligned reads (base quality, base composition, heterologous organisms, rRNA/mitochondrial/viral and adaptor content) and post-alignment.
Location type count summary, template length, species, DNA genotype/RNA genotype match, sample relatedness/intermixing, and 3’-bias were assessed. No samples were excluded from the alignment analysis based on these QC measures.
Alignment of reads was performed against the genome of the Mus musculus strain C57BL/6J (assembly GRCm38.p4) with GSNPA.
Feature quantification was performed at the exon level and a counting algorithm using the NCBI-based gene models. Exons defined by these gene models served as the base feature to which counts are attributed. Count data were subsequently normalized at the gene level.
Data were normalized using Robust Linear Model (RLM) and quartile normalization (75% quartile; QM) following visual inspection of the distribution curves.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: comma-delimited text files (csv) include read counts for each Sample (one file per tissue)

source_name: Blood

extract_protocol:
Tissues were collected 14-16 hours after the last stress exposure (between ZT12.5 and ZT14.5). Brain tissues were immediately immersed in RNAlater® (Sigma-Aldrich) and stored at -20°C, while trunk blood was collected in RNAprotect Animal Blood tubes (Qiagen). Total RNA was extracted from dissected brain tissue using the RNeasy® Fibrous Tissue Mini Kit (Qiagen), and from whole blood samples using the RNeasy® Protect Animal Blood Kit (Qiagen).
RNA libraries were prepared using the NEBNext® rRNA Depletion Kit and the NEBNext® Ultra Directional RNA library preparation kit with 100 ng of total RNA from each sample, according to manufacturer's protocols.

treatment_protocol: Mice were subjected to a 9-week paradigm of Unpredictable Chronic Mild Stress (UCMS), a model of major depressive disorder, while control animals remained unstressed.

value: BALB/c

value: Male

value: 28 weeks

tag: group

value: UCMS

value: Whole blood


title: BLO_UCMS2_S2


title: BLO_UCMS5_S5


title: BLO_Control6_C7

value: Control


title: BLO_Control2_C2


title: BLO_UCMS9_BS2


title: BLO_UCMS8_BS1


title: BLO_Control7_C8


title: BLO_Control5_C6


title: BLO_UCMS4_S4


title: BLO_Control4_C5


title: BLO_Control3_C4


title: BLO_Control1_C1


title: HYP_UCMS8_BS2

source_name: Brain

value: Hypothalamus


title: HYP_UCMS6_S7


title: ESC_differentiated_4days_2

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

hyb_protocol: Fragmented biotin labeled samples (3.5 ug) were hybridized to Affymetrix Mouse Gene 2.0 ST arrays according to manufacturer protocols. Post hybridization washing and fluorescence labeling was done in an Affymetrix Fluidics Station 450 using the Affymetrix HWS Kit in accordance with manufacturer protocols.

scan_protocol: Microarrays were scanned using an Affymetrix 7G Scanner.

data_processing: CEL files were imported into Affymetrix Expression Console software and data were normalized using the gene-level RMA algorithm to obtain transcript cluster expression values. Transcript clusters corresponding to controls, references, or unknowns were eliminated from the data set by excluding content not categorized as main or rescue, based on Affymetrix annotation.

source_name: ESC, 4 days culture in differentiation medium, sorted for Afp

label_protocol: Total RNA (500pg) was converted to biotinylated second cycle single stranded cDNA using the Affymetrix WT Pico kit using recommended methodology.

growth_protocol: Mouse ES cells harboring a transgene in which green fluorescent protein was driven by the alpha-fetoprotein promoter (Afp::GFP) were differentiated as embryoid bodies (EBs) initially consisting of 300 cells each in IMDM+ 20%  FBS, pen/strep, transferrin,and ascorbic acid  supplemented with 0.5% PFHM.  EBs were differentiated on gelatin to promote attachment and spreading of EBs.

extract_protocol: Total RNA was prepared by Trizol extraction. Total RNAs were evaluated by Agilent 2100 Bioanalyzer to validate sample quality.

treatment_protocol: At three time points, Afp-expressing cells were isolated by flow cytometry.

tag: differentiation period

value: 4 days

tag: sorting marker

value: Afp


title: ESC_differentiated_7days_2

source_name: ESC, 7 days culture in differentiation medium, sorted for Afp

value: 7 days


title: ESC_differentiated_21days_3

source_name: ESC, 21 days culture in differentiation medium, sorted for Afp

value: 21 days


title: HYP_UCMS5_S5


title: ESC_differentiated_21days_1


title: ESC_differentiated_4days_1


title: BLO_UCMS7_S8


title: BLO_UCMS3_S3


title: ESC_differentiated_7days_3


title: ESC_differentiated_21days_2


title: HYP_UCMS4_S4


title: BLO_UCMS6_S7


title: ESC_differentiated_4days_3


title: HYP_UCMS3_S3


title: HYP_Control8_C8


title: HYP_Control7_C7


title: HYP_Control6_C6


title: HYP_Control5_C5


title: HYP_Control4_C4


title: HYP_UCMS1_S1


title: HYP_Control3_C3


title: CON group circRNA

first: Huimin

last: Li

address: 13th Hangkong Road

institute: Huazhong University of Science and Technology

data_processing:
The Hiseq3000 sequencing platform (Illumina, San Diego, CA, USA) was used for circRNA sequencing. The sequence depth is 10G. Sequences were mapped using STAR software against GRCm38/mm10 mouse reference genome in UCSC Known Genes databases. CIRCexplorer software was applied to analyze the back-spliced junction for circular RNA prediction.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt files including name, genome location, normalized counts, compared fold changes, P value, etc.

growth_protocol: GC-2 spd(ts) (ATCC # CRL-2196)were purchased from ATCC (Manassas, VA, USA) and cultured in DMEM high glucose medium (Hyclone, Logan, UT, USA), supplement with 10% fetal bovine serum (Sijiqing, Hangzhou, China) and 1% Penicillin-Streptomycin (Hyclone, Logan, UT, USA) at 37°C and 5% CO2.

extract_protocol:
cDNA library was constructed according to the Illumina TruSeq library preparation protocol.
Cells were harvested by Trizol and subject to convention RNA extraction procedures. And RNAs from the same sample were shared to three aliquot for the subsequent circRNA, miRNA and mRNA high-throughput sequencing. For circRNA sequencing, total RNA was depleted of rRNA and then linear RNAs by RNase R digestion.

treatment_protocol: After synchronized by cultured in DMEM without FBS for 12h, the cells were treated with BPA (Sigma-Aldrich, St.Louis, MO, USA) for 48h. BPA was dissolved in DMSO and diluted with complete medium to the 120 μM concentration before use. Cells treated with complete medium with 0.1% (v/v) DMSO were used as a control. The cells treated with 120 μM BPA and complete medium with 0.1% DMSO were harvested and subject to circRNA/miRNA/mRNA deep sequencing.

value: mouse spermatocyte derived cell line

tag: treatment

value: 0 μM BPA for 48 h

tag: molecule subtype

value: circRNA


title: ESC_differentiated_7days_1


title: HYP_Control2_C2

tag: tissue


title: HIP_UCMS8_BS2

value: Hippocampus


title: BPA group circRNA

tag: cell line

tag: cell type

value: 120μM BPA for 48 h


title: HYP_UCMS2_S2

tag: strain

tag: age


title: HYP_UCMS7_S8


title: HYP_Control1_C1


title: IPF769_R1_T8h_TGFB_ACT

city: Allschwil

first: Axel

last: Klenk

address: Hegenheimermattweg 91

department: Research Informatics

institute: Idorsia Pharmaceuticals Ltd.

hyb_protocol: a pool of 300 ng of Cy3 labeled aRNA (examined sample) and 300 ng of Cy5 labeled aRNA rat reference (Agilent, Austin TX, USA) were hybridized using the Agilent Hybridization kit (Agilent, Austin TX, USA) according to the manufacturer's instructions. Hybridization was performed for 17 hours and washed according to Agilent's instructions.

scan_protocol: Scanned on an Agilent G2505B scanner using Agilent scan control (version 8.5.1) Images were quantified using Agilent Feature Extraction Software (version 11.5.5.1).

data_processing: BioConductor package vsn was used for variance-stabilizing normalization and glog transformation

label_protocol: 100 ng of totRNA were labeled using the Low Input Quick Amp Labeling kit (Agilent, Austin TX, USA) following the manufacturer's instructions.

extract_protocol: total RNA extracted  using MagMAX-96 for microarrays kit (Life technologies, Foster City CA, USA ) following the manufacturer's instructions

tag: timepoint

source_name: Stratagene Reference

value: Pool of 10 human cell lines


title: HIP_UCMS6_S7

value: BALB/c


title: IPF769_R2_T8h_TGFB_ACT


title: HIP_UCMS4_S4

value: Male


title: HIP_UCMS5_S5

value: 28 weeks


title: IPF769_R1_T8h_VEH

value: VEH


title: HIP_UCMS3_S3

value: UCMS


title: IPF769_R4_T8h_TGFB_ACT


title: HIP_UCMS7_S8


title: IPF769_R3_T8h_VEH


title: IPF769_R4_T8h_VEH


title: IPF769_R2_T8h_VEH


title: HIP_UCMS2_S2


title: IPF769_R3_T8h_TGFB

value: TGFB