title: hmg-4 rep3

description:
Processed data file: hotFiltered_hmg4SomaRepCat_steric38.bed.bigWig
Processed data file: hmg4Spt16_totalCounts.txt

data_processing:
ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5’end coordinate of the – strand read was less than or equal to the 5’end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5’ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors.
Peaks were called on concatenated processed bed files using JAMM peakcaller v1.0.7.5 (-f38 –b 100 –e 1.75). The resulting “all” (for worm) or “filtered” (for human) peaks output by JAMM for each condition (control, ssrp1 knockdown, and supt16h knockdown for human, or rluc, hmg3, and hmg4 for worms) were concatenated and then merged with bedtools merge v2.23. The merged "all" peaks for worm were then further filtered for a minimum width of 25 bp.
Merged peaks were then counted for the number of processed reads that intersected them from each replicate of each experimental condition using bedtools coverage v2.23 (-counts). Count tables were then normalized (method = “TMM”) and subjected to differential analysis (exactTest) using edgeR. Peaks were called as differential with a q-value cutoff of 0.01 (adjust=”BH”).
bedGraph files were generated from replicate concatenated processed ATAC-seq reads .bed files using bedtools genomecov v2.23 (-scale 1/(library size - chrM reads/100000)) which were then converted to .bigWig files using the ENCODE program bedGraphToBigWig.
RNA-seq reads were trimmed for adapters and mapped with STAR.
RNA-seq count tables were generated using quasR and differential expression determined using DESeq2.
Genome_build: ce10
Supplementary_files_format_and_content: *tsv: Tab-delimited text files; RNA-seq count tables.
Supplementary_files_format_and_content: *bigWig: Library-normalized bigWig files of processed ATAC-seq reads.
Supplementary_files_format_and_content: *txt: Tab-delimited text files; Count tables for merged peaks across all replicates separately.

source_name: whole worms

extract_protocol:
Synchronized L4 animals were washed 5 times in M9 buffer and collected on ice. Nuclei were isolated using a glass Dounce homogenizer with 50 strokes tight-fitting insert in buffer A (15 mM Tris–HCl pH7.5, 2 mM MgCl2, 340 mM sucrose, 0.2 mM spermine, 0.5 mM spermidine, 0.5 mM phenylmethanesulfonate [PMSF], 1mM DTT, 0.1% Triton X-100 and 0.25% NP-40 substitute). The debris were removed by spinning at 100×g for 5 min and nuclei were counted by Methylene blue staining. 100.000 nuclei per sample were pelleted by spinning at 1000×g for 10 min and proceeded immediately to transposition step of the ATACseq protocol.
Library preparation was done following a protocol published in Buenrostro et al. 2013. Cell pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase) (Illumina Nextera DNA Library preparation kit, #FC-121-1030). The transposition reaction was carried out for 60 min at 37ºC. The samples were purified using Zymo DNA Clean & Concentrator kit; following purification, library fragments were amplified using NEBNext PCR master mix and custom Nextera PCR primers. Libraries were amplified for a total of 12 to 14 cycles and sequenced using paired-end-sequencing length of 75 nucleotides using NextSeq 500/550 High Output v2 kit (Illumina) on a NextSeq500 machine (Illumina) following manufacturer's protocol.

treatment_protocol: For P0 RNAi experiments, worms were synchronized by bleaching and L1 larvae were put on RNAi plates and grown at 15ºC until most of the animals reached L4 stage.

tag: strain/background

tag: developmental stage

tag: tissue

value: whole body

tag: sirna/dsrna

value: sjj_T20B12.8 (Ahringer library,III-3P10, Source Bioscience)


title: hmg-4 rep2

status: Public on Aug 29 2018

type: SRA

city: Berlin-Buch

first: Scott

middle: Allen

last: Lacadie

address: Robert-Rössle-Str. 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

library_source: genomic

molecule: genomic DNA

organism: Caenorhabditis elegans

growth_protocol: C. elegans strains were maintained on OP50 bacteria and NGM agar plates at 15ºC. Worms were transferred to fresh food once a week.


title: EGPA N1073

type: RNA

city: Bethesda

first: Peter

middle: C.

last: Grayson

state: MD

address: 10 Center Dr Building 10 6N216G

department: NIAMS

country: USA

institute: NIH

description: Gene expression from patient with EGPA

hyb_protocol: Each verified cRNA sample was hybridized overnight onto the Affymetrix Human Gene 1.0 ST Array (each containing approximately 19,658 probe sets).

scan_protocol: Confocal laser scanning (Agilent) was performed to detect the streptavidin- labeled fluors.

data_processing: CEL files were processed with the SCANfast function from the SCAN.UPC Bioconductor package (v2.20.0) using the Brainarray (v22.0.0) hugene10sthsentrezgprobe as the probe summary package and adjusted with ComBat.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Nasal brushings

label_protocol: RNA was converted into double-stranded cDNA with the SuperScript II reverse transcriptase (Invitrogen) using an oligo-dT primer containing a T7 RNA polymerase promoter (Genset, Boulder, CO). The ENZO Bioarray RNA transcript labeling kit (Affymetrix) was used for in vitro transcription of the purified double stranded cDNA. The biotin-labeled cRNA was purified using the RNeasy kit (Qiagen).

extract_protocol: Using a nasal speculum, brushings were obtained from the right inferior turbinate with a standard cytology brush (Medical Packaging Company, Camarillo, CA). Brushings were placed in RNA lysis buffer and frozen at −80C until use. RNA was isolated via Qiagen RNeasy Mini Kits per manufacturer’s protocol. The integrity and purity of RNA were assessed using an Agilent Bioanalyzer and spectrophotometric analysis, respectively. An average of 3μg of high-quality total RNA was obtained from each collection.

value: Nasal brushings

tag: disease

value: EGPA

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

tag: anca

value: MPO

tag: age

tag: race

value: White

tag: gender

value: F

tag: ethnicity

value: non-Hisp

tag: disease_duration (yrs)

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

value: Never

tag: immune_meds (recorded at time of sample collection)

value: Methotrexate

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: N


title: spt-16 rep3

description:
Processed data file: hotFiltered_spt16SomaRepCat_steric38.bed.bigWig
Processed data file: hmg4Spt16_totalCounts.txt

treatment_protocol: For F1 RNAi experiments, worms were synchronized by bleaching and L4 larvae were put on RNAi plates and grown at 15ºC until most of the progeny animals reached L4 stage.

tag: strain/background

tag: developmental stage

tag: tissue

tag: sirna/dsrna

value: sjj_F55A3.3 (Ahringer library, I-5O08 Source BioScience)


title: spt-16 rep2


title: meRIP_Normal_Replicate 1

city: Columbus

first: Federica

last: Accornero

address: 473 W 12th Ave

institute: OSU

description:
m6A IP in quiescent cardiomyocytes
library strategy: meRIP-Seq

library_source: transcriptomic

data_processing:
We used Illumina CASAVA 1.8 software to generate fastq files
Tophat software was used to align reads to rat rn4 reference genome
MACS version 1.4 was used for peak detection
RPKM of the consensus peak region was calculated for all samples
Peak RPKMs of meRIP samples were normalized to negative control
Genome_build: rn4
Supplementary_files_format_and_content: Bed files with peaks and summits

organism: Rattus norvegicus

source_name: Primary cardiomyocytes

extract_protocol:
Neonatale rat cardiomyocytes were isolated from 1-3 day old rat pubs.
Total RNA was isolated from indicated cells, and extracted using Trizol according to manufacturer’s manual.
RNA libraries were prepared using Illumina kit according to manufacturer’s instruction

treatment_protocol: Cells were kept in M199 media with/without addiiton of 2% bovine serum

tag: cell type

value: Neonatal cardiomyocytes

tag: growth media

value: M199; serum free

tag: group

value: quiescent cardiomyocytes


title: meRIP_Normal_Replicate 2


title: meRIP_Negative control_Replicate 2

description:
Normal IgG IP in hypertrophic cardiomyoctes
library strategy: meRIP-Seq

value: M199; 2% bovine serum

value: hypertrophic cardiomyocytes


title: meRIP_Negative control_Replicate 1


title: Control N1070

description: Gene expression from Control

tag: disease

value: Control

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: Sarcoidosis

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

tag: anca

value: Neg

tag: age

tag: race

value: M

value: Former


title: Control N1069

description: Gene expression from Control

value: Nasal brushings

value: Black

tag: gender

tag: ethnicity

tag: disease_duration (yrs)

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

tag: immune_meds (recorded at time of sample collection)

value: Methotrexate/Infliximab


title: Control N1068

description: Gene expression from Control

tag: tissue

value: White

value: non-Hisp

value: Never

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: Y


title: hmg-4 rep1

tag: strain/background

tag: developmental stage

value: whole body

tag: sirna/dsrna

value: sjj_T20B12.8 (Ahringer library,III-3P10, Source Bioscience)


title: hmg-3 rep3

description:
Processed data file: hotFiltered_hmg3WholeCat_steric38.bed.bigWig
Processed data file: hmg3_totalCounts.txt

value: sjj_C32F10.5 (Ahringer library, I-2N19 Source Bioscience)


title: meRIP_Hypertrophy_Replicate 2

description:
m6A IP in hypertrophic cardiomyocytes
library strategy: meRIP-Seq

tag: cell type

value: Neonatal cardiomyocytes

tag: growth media

value: M199; 2% bovine serum

tag: group


title: Input_Hypertrophy_Replicate 2

description:
Total trasncript levels in hypertrophic cardiomyocytes
library strategy: meRIP-Seq

value: hypertrophic cardiomyocytes


title: Input_Normal_Replicate 2

description:
Total trasncript levels in quiescent cardiomyocytes
library strategy: meRIP-Seq

value: M199; serum free

value: quiescent cardiomyocytes


title: Input_Normal_Replicate 1


title: hmg-3 rep1


title: Rluc rep3

description:
Processed data file: hotFiltered_rlucSomaRepCat_steric38.bed.bigWig
Processed data file: hmg4Spt16_totalCounts.txt

value: HT115 (D3) bacteria containing L4440 vector with DNA targeting Renilla luciferase


title: C8-2

city: Montreal

first: Naglaa

last: Shoukry

state: QC

address: Tour Viger, Local 09.414, 900 rue St-Denis

country: Canada

institute: CRCHUM

data_processing:
Reads were mapped to the human genome reference (hg19) using the Tophat (v2.0.8b) alignment tool with Ensembl66 annotations and the "--no-novel-juncs" parameter
Read counts per gene were quantified against Ensembl (v66) transcript reference annotations (appended with gene annotation for IFNL4) using HTSeq-count (v0.5.4p3)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read counts per gene for each sample

molecule: polyA RNA

source_name: Peripheral Blood Mononuclear Cells (PBMC)

extract_protocol:
Cryopreserved PBMC samples were thawed and immediately processed for RNA extraction with the Qiagen RNEasy Mini kit (Cat #74104) according to manufacturers instructions
RNA-Seq libraries were prepared with the Illumina TruSeq RNA Library Preparation Kit v2 (Cat #RS-122-2001/2) according to manufacturers instructions

tag: patientid

tag: hcvgroup

value: Chronic

tag: time point

value: EarlyAcute

tag: days post estimated date of infection (edi)

tag: hcv viremia

value: TRUE


title: C8-3

value: Peripheral Blood Mononuclear Cells (PBMC)

value: LateAcute


title: C8-1

value: PreInfection

value: FALSE


title: C8-4

value: FollowUp


title: C7-4


title: spt-16 rep1

value: whole body

value: sjj_F55A3.3 (Ahringer library, I-5O08 Source BioScience)


title: meRIP_Hypertrophy_Replicate 1


title: Input_Hypertrophy_Replicate 1


title: Rluc rep2


title: hmg-3 rep2

value: sjj_C32F10.5 (Ahringer library, I-2N19 Source Bioscience)


title: C7-1


title: GPA N1060

description: Gene expression from patient with GPA

value: Nasal brushings

tag: disease

value: GPA

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Never

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: NoNasalGPA

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

value: Severe

tag: anca

tag: age

tag: race

value: White

tag: gender

value: M

tag: ethnicity

value: non-Hisp

tag: disease_duration (yrs)

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

value: Former

value: Rituximab

value: N


title: Control N1064

description: Gene expression from Control

tag: tissue

value: Control

value: Healthy

value: Neg

tag: bvas

tag: vdi

tag: immune_meds (recorded at time of sample collection)

tag: gc_or_immune (prednisone or any immune med at time of sample collection)


title: GPA N1058

description: Gene expression from patient with GPA

tag: disease

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Inactive

value: InactiveGPA

value: Methotrexate


title: Control N1066

description: Gene expression from Control

value: Nasal brushings

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)


title: GPA N1061

description: Gene expression from patient with GPA

value: GPA

value: Active

value: ActiveGPA

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

tag: anca

value: F


title: rluc hmg3 rep3

description:
Processed data file: hotFiltered_rlucWholeCat_steric38.bed.bigWig
Processed data file: hmg3_totalCounts.txt

tag: strain/background

tag: developmental stage

value: whole body

tag: sirna/dsrna

value: HT115 (D3) bacteria containing L4440 vector with DNA targeting Renilla luciferase


title: GPA N1055B

description: Gene expression from patient with GPA

value: Limited

tag: age

tag: race

value: White

tag: gender

tag: ethnicity

value: non-Hisp

tag: disease_duration (yrs)

value: Never


title: GPA N1057A

description: Gene expression from patient with GPA

tag: tissue

value: NoNasalGPA

value: Severe

value: MPO

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

value: Former

value: N


title: C6-2

tag: cell type

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: patientid

tag: hcvgroup

value: Chronic

tag: time point

value: EarlyAcute

tag: days post estimated date of infection (edi)

tag: hcv viremia

value: TRUE


title: C6-4

value: FollowUp


title: C7-3

value: LateAcute


title: rluc hmg3 rep1

tag: strain/background

tag: developmental stage

value: whole body

tag: sirna/dsrna


title: C5-4


title: rluc hmg3 rep2

value: HT115 (D3) bacteria containing L4440 vector with DNA targeting Renilla luciferase


title: C6-3


title: C6-1

value: PreInfection

value: FALSE


title: YPK_2

city: Shanghai

first: Jian

last: Bing

address: Songhu Road, Yangpu District

department: School of Life Sciences

country: China

institute: Fudan University

data_processing:
Illumina OLB_1.9.4 were used for basecalling
Filter dirty raw reads by removing reads with adaptors and low quality, the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
FPKM method is used in calculated expression level, the formula is shown as follows, and the formula is shown as follows: FPKM=106C/(NL/103). Given to be the expression of gene A , C to be number of fragments that are uniquely aligned to gene A , N to be total number of fragments that are uniquely aligned to all genes, and L to be number of bases on gene A.
Genome_build: Candida albicans SC5314 genome (ASM18296v1)
Supplementary_files_format_and_content: text file containing FPKM values for each Sample

organism: Candida albicans

source_name: YPK

extract_protocol:
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: WT

tag: growth medium

value: YP-K


title: C5-3


title: C4-4


title: YPK_1


title: GPA N1053B

description: Gene expression from patient with GPA

value: Nasal brushings

tag: disease

value: GPA

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Never

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: NoNasalGPA

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

tag: anca

tag: age

tag: race

value: White

tag: gender

value: M

tag: ethnicity

value: non-Hisp

tag: disease_duration (yrs)

tag: immune_meds (recorded at time of sample collection)

value: Rituximab

tag: gc_or_immune (prednisone or any immune med at time of sample collection)


title: GPA N1048B

description: Gene expression from patient with GPA

tag: tissue

value: Active

value: ActiveGPA

value: Severe

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

value: Former

value: Azathioprine

value: N


title: Rluc rep1

tag: strain/background

tag: developmental stage

value: whole body

tag: sirna/dsrna

value: HT115 (D3) bacteria containing L4440 vector with DNA targeting Renilla luciferase


title: GPA N1052A

description: Gene expression from patient with GPA

tag: disease

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

value: F

value: Mycophenolate mofetil


title: Blood_Ram2

city: Storrs

first: Xiuchun

last: Tian

state: CT

address: 1390 Storrs Road, ABL220D

department: Animal Science

institute: University of connecticut

data_processing:
Raw genomic DNA-seq reads were trimmed by Trimmomatic (version 0.33, Institute of Botany and Molecular Genetics, RWTH Aachen University and the Jülich Research Center, Aachen, Germany) to remove the universal sequencing adaptors of Illumina with a minimum Phred score of 20 and minimal length of 30 bp.
To minimize such alignment bias to the reference allele in the genome, we artificially built a pseudo-genome (named “alternative genome”) by flipping the reference/alternative alleles in all SNP sites based on known sheep dbSNP (sheep 9940).  We then mapped the filtered DNA-seq (or RNA-seq) reads using Hisat2 aligner (version 2.0.5) to both sheep reference genome Oar_v4.0 and the alternative genome. Only uniquely aligned reads were kept. The Picard Tool Mark Duplicates (2.12.0) (Broad Institute of MIT and Harvard, Cambridge, MA, USA) was used to remove the PCR duplicates. SNVQ (NGS Tools version 2.0) was used to accurately detect the SNPs in the ram genome. To reduce potential false positive calls, the following parameters were used for SNP filtering: 1) a minimum quality score of 50 at the SNP position, 2) a minimum of three reads aligned at the SNP using both the reference and alternative genomes, 3) reversed genotypes of called SNP when reference/alternative genomes were switched (e.g., A/G in reference genome; while G/A in alternative genome), 4) SNP located in exons, and 5) SNP present and consistent with that in the sheep dbSNP (sheep 9940) database.
After genotyping SNPs of both the rams and their fetuses, we designated SNPs that were homozygous in the rams but heterozygous in their respective fetuses as iSNPs . To further reduce alignment bias, we used Samtools mpileup (version 1.4) to calculate the allele-specific read counts for each iSNP which were then averaged between the two genomes.
We only used iSNPs that had a total read counts of 20 or greater from the two parental alleles.
Genome_build: Oar_v4.0
Supplementary_files_format_and_content: bed file, SNP, gene and coverage

organism: Ovis aries

growth_protocol: All animal protocols were reviewed and approved by the University of Connecticut Institutional Animal Care and Use Committee. Animal breeding, feeding and sample collection were described in Pillai et al., 2017. Briefly, Western white-faced ewes (n=12) were mated with Dorset rams (n=4). Pregnancy was confirmed by ultrasound on day 20 of gestation if a ewe was not re-marked by a ram; day 0 represents the initial marking of the ewe by the ram.

extract_protocol:
Ewes were euthanized at day 135 of gestation, and 15 fetuses were obtained (Con: n=7, including 3 sets of twins; Res: n=4; Over: n=4). Brain, kidney and lung samples were collected from all fetuses. Whole blood samples were obtained from the four rams. Tissues were flash frozen in liquid nitrogen and were stored at -80°C until RNA extraction.
Genomic DNA of ram whole blood samples and fetal tissues was isolated using Qiagen DNeasy Blood & Tissue Kits (Qiagen, Hilden, Germany). The ram DNA was sent to Novogene (Novogene Co., Ltd, Beijing, PRC) for library preparation and sequencing. In brief, the DNA-seq library was prepared using the Illumina Truseq Nano DNA HT sample preparation kit (Illumina, San Diego, CA, USA) with a 350 bp target insert size. Libraries were sequenced with 2 × 150 bp paired-end reads on an Illumina HiSeq 2000 platform. On average, 186.7 million raw read pairs were obtained for genotyping from each ram.
Total RNA was extracted from day 135 fetal brain, lung and kidney, using Trizol and Qiagen RNAeasy kit with three quality controls: NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA), agarose gel electrophoresis and Qubit 2.0 (Thermo Fisher). Library preparation was carried out using TruSeq RNA library prep kit (Illumina), which selected mRNA using ligo d(T) with magnetic beads and built 2 × 75 bp paired-end cDNA libraries. The libraries were analyzed for size distribution using an Agilent 2100 Bioanalyzer (Santa Clara, CA, USA) and quantified using real-time PCR. Overall, we obtained 2,149 million raw sequencing reads that passed filtering from three sequencing runs of 45 fetal tissue samples. A total of 1,160, 576 and 413 million raw sequencing reads that passed filtering were obtained for sequencing runs 1, 2 and 3, respectively. An average of 23.8 million read pairs per sample was generated on a NextSeq 500 System (Illumina).
DNA sequencing in HiSeq 2000 platform for ram and RNA sequencing in NextSeq 500 System for fetal tissues.

treatment_protocol: On day 30 of gestation, pregnant ewes were individually housed and then randomly assigned to control 100% (Con, n=4), restricted 60% (Res, n=4) or overfed 140% (Over, n=4) of the National Research Council total digestible nutrients (TDN) for ewes pregnant with twins.

tag: breed

value: Dorset

tag: developemental stage/age

value: Ram

value: Blood


title: Blood_Ram4


title: Blood_Ram1


title: GPA N1050A

description: Gene expression from patient with GPA

value: Nasal brushings

value: GPA

value: Limited

tag: anca

tag: age

tag: race

value: Arabic

tag: gender

tag: ethnicity

tag: disease_duration (yrs)

value: Never

tag: immune_meds (recorded at time of sample collection)

value: Methotrexate


title: Blood_Ram3

tag: tissue


title: C5-2

tag: cell type

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: patientid

tag: hcvgroup

value: Chronic

tag: time point

value: EarlyAcute

tag: days post estimated date of infection (edi)

tag: hcv viremia

value: TRUE


title: YPDK_2

source_name: YPDK

tag: genotype

value: WT

tag: growth medium

value: YPD-K


title: C5-1

value: PreInfection

value: FALSE


title: GPA N1044B

description: Gene expression from patient with GPA

tag: disease

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Active

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: ActiveGPA

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

value: White

value: M

value: Hispanic

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

value: Azathioprine

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: N


title: C4-2

tag: cell type

tag: patientid


title: C4-3

tag: hcvgroup

tag: time point

value: LateAcute


title: Control N1043B

description: Gene expression from Control

tag: tissue

value: Nasal brushings

value: Control

value: Healthy

tag: anca

value: Neg

tag: age

tag: race

tag: gender

value: F

tag: ethnicity

value: non-Hisp

tag: disease_duration (yrs)

value: Never

tag: immune_meds (recorded at time of sample collection)


title: C3-4

value: Peripheral Blood Mononuclear Cells (PBMC)

value: Chronic

value: FollowUp

tag: days post estimated date of infection (edi)

tag: hcv viremia

value: TRUE


title: YPDK_1

tag: genotype

value: WT

tag: growth medium

value: YPD-K


title: C3-2

value: EarlyAcute


title: GPA N1042A

description: Gene expression from patient with GPA

tag: disease

value: GPA

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Active

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: ActiveGPA

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

value: Limited

value: White

value: M

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

tag: gc_or_immune (prednisone or any immune med at time of sample collection)


title: GPA N1041

description: Gene expression from patient with GPA

tag: tissue

value: Nasal brushings

value: Severe

tag: anca

value: MPO

tag: age

tag: race

tag: gender

tag: ethnicity

value: Rituximab

value: Y


title: Control N1037

description: Gene expression from Control

value: Control

value: Sarcoidosis

value: Neg

value: F

value: non-Hisp

tag: disease_duration (yrs)

value: Never

tag: immune_meds (recorded at time of sample collection)

value: Cyclophosphamide

value: N


title: Control N1093

description: Gene expression from Control

tag: disease

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Former


title: F46A_3

city: Planegg-Martinsried

first: Christopher

middle: B

last: Mulholland

state: Bavaria

address: Großhaderner Str. 2

department: Biologie II, Human Biologie und BioImaging

institute: Ludwig-Maximilians-Universität München

data_processing:
Raw, paired-end TaBA-seq reads were first quality filtered and the adapter sequences removed using Trim Galore (v.0.3.1) with the ‘--paired’ parameter and adapter sequences to be trimmed manually defined as “-a CTGTCTCTTATA -a2 AGATCGGAAGAGC.”
Alignments were carried out to the mouse genome (mm10) using bsmap (v.2.90) using the following parameters ‘-v 5 -r 2 -I 8 -p 10’. CpG-methylation calls were extracted from the mapping output using the methratio.py function in bsmap
Quantification of methylation levels was performed using the R package, methylKit
Analysis was restricted to CpGs with a minimal coverage >20 and no more than the 99.9th percentile of coverage. Only CpGs meeting these coverage criteria and detected in all replicates were used for further analysis R.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file containing the DNA methylation status of CpGs (given as 0 or 1)

organism: Mus musculus

growth_protocol: mouse ESCs were maintained on 0.2% gelatin-coated dishes in Dulbecco's modified Eagle's medium (Sigma) supplemented with 16% fetal bovine serum (FBS, Sigma), 0.1 mM ß-mercaptoethanol (Invitrogen), 2 mM L-glutamine (Sigma), 1× MEM Non-essential amino acids (Sigma), 100 U/mL penicillin, 100 μg/mL streptomycin (Sigma), homemade recombinant LIF tested for efficient self-renewal maintenance, and 2i (1 μM PD032591 and 3 μM CHIR99021 (Axon Medchem, Netherlands)). All cell lines were regularly tested for Mycoplasma contamination by PCR.

extract_protocol:
Genomic DNA was isolated from 2x106 cells using the PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. The EZ DNA Methylation-Gold Kit (Zymo Research) was used for bisulfite conversion according to the manufacturer’s instructions with 500 ng of genomic DNA used as input and the modification that bisulfite converted DNA was eluted in 2 x 20 µL Elution Buffer.
The sequences of the LINE1 specific primers were appended with Illumina TruSeq and Nextera compatible overhangs. The amplification of bisulfite converted DNA was performed in 25 µL PCR reaction volumes containing 0.4 µM each of forward and reverse primers, 2 mM Betaine (Sigma-Aldrich, B0300-1VL), 10 mM Tetramethylammonium chloride solution (Sigma-Aldrich T3411-500ML), 1x MyTaq Reaction Buffer, 0.5 units of MyTaq HS (Bioline, BIO-21112), and 1 µL of the eluted bisulfite converted DNA (~12.5 ng). The following cycling parameters were used: 5 min for 95°C for initial denaturation and activation of the polymerase, 40 cycles (95 °C for 20 s, 58°C for 30 s, 72°C for 25 s) and a final elongation at 72°C for 3 min. Agarose gel electrophoresis was used to determine the quality and yield of the PCR. For purifying amplicon DNA, PCR reactions were incubated with 1.8x volume of CleanPCR beads (CleanNA, CPCR-0005) for 10 min. Beads were immobilized on a DynaMag™-96 Side Magnet (Thermo Fisher, 12331D) for 5 min, the supernatant was removed, and the beads washed 2x with 150 µL 70% ethanol. After air drying the beads for 5 min, DNA was eluted in 15 µL of 10 mM Tris-HCl pH 8.0. Amplicon DNA concentration was determined using the Quant-iT™ PicoGreen™ dsDNA Assay Kit (Thermo Fisher, P7589) and then diluted to 0.7 ng/µL. Thereafter, indexing PCRs were performed in 25 µL PCR reaction volumes containing 0.08 µM (1 µL of a 2 µM stock) each of i5 and i7 Indexing Primers, 1x MyTaq Reaction Buffer, 0.5 units of MyTaq HS (Bioline, BIO-21112), and 1 µL of purified PCR product (diluted to 0.5 ng/µl) from the previous step. The following cycling parameters were used for the indexing PCR: 5 min for 95°C for initial denaturation and activation of the polymerase, 15 cycles (95°C for 10 s, 55°C for 30 s, 72°C for 40 s) and a final elongation at 72°C for 5 min. Agarose gel electrophoresis was used to determine the quality and yield of the PCR. An aliquot from each indexing reaction (5 µL of each reaction) was then pooled and purified with CleanPCR magnetic beads as described above and eluted in 1 µL x Number of pooled reactions. Concentration of the final library was determined using PicoGreen and the quality and size distribution of the library was assessed with a Bioanalyzer.
Targeted bisulfite amplicon sequencing

tag: strain background

tag: genotype/variation

tag: cell type

value: mouse embryonic stem cells (mESCs)

tag: media

value: serum 2i+LIF

tag: molecule type

value: LINE1 amplicon after bisulfite treatment of gDNA with sodium bisulfite


title: C3-1

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: patientid

tag: hcvgroup

value: Chronic

tag: time point

value: PreInfection

tag: days post estimated date of infection (edi)

tag: hcv viremia

value: FALSE


title: Control N1038

description: Gene expression from Control

tag: tissue

value: Nasal brushings

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: AllergicRhinitis

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

tag: anca

tag: age

tag: race

value: Black

value: Hispanic

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: Y


title: C2-3

tag: cell type

tag: patientid

value: LateAcute

value: TRUE


title: C2-4

tag: hcvgroup

tag: time point

value: FollowUp


title: F46A_4

tag: strain background

tag: genotype/variation

tag: media

tag: molecule type


title: GPA N1003

description: Gene expression from patient with GPA

tag: tissue

tag: disease

value: GPA

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Inactive

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: InactiveGPA

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

value: Limited

value: MPO

value: White

tag: gender

value: F

tag: ethnicity

value: non-Hisp

tag: disease_duration (yrs)

tag: immune_meds (recorded at time of sample collection)


title: GPA N1034

description: Gene expression from patient with GPA

value: Severe

tag: anca

tag: age

tag: race

value: M

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

value: Current

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: N


title: F46A_2

tag: strain background

tag: genotype/variation

tag: cell type

value: mouse embryonic stem cells (mESCs)

tag: media

value: serum 2i+LIF

tag: molecule type

value: LINE1 amplicon after bisulfite treatment of gDNA with sodium bisulfite


title: Control N1036

description: Gene expression from Control

tag: tissue

value: Nasal brushings

tag: disease

value: Control

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: AllergicRhinitis

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

value: Neg

value: Asian

tag: gender

value: Never

value: Y


title: C4-1

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: patientid

tag: hcvgroup

value: Chronic

tag: time point

value: PreInfection

tag: days post estimated date of infection (edi)

tag: hcv viremia

value: FALSE


title: F46A_1

tag: strain background


title: C3-3

value: LateAcute

value: TRUE


title: C1-4

value: FollowUp


title: Control N1028

description: Gene expression from Control

value: Sarcoidosis

tag: anca

tag: age

tag: race

value: White

value: M

tag: ethnicity

value: non-Hisp

tag: disease_duration (yrs)

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

tag: immune_meds (recorded at time of sample collection)

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: N


title: Control N1032

description: Gene expression from Control

tag: tissue

value: Nasal brushings

tag: disease

value: Control

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: Healthy

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

tag: gender


title: GPA N1031

description: Gene expression from patient with GPA

value: GPA

value: Never

value: NoNasalGPA

value: Severe

tag: anca

tag: age

value: F

value: Former

value: Methotrexate


title: C1-2

tag: cell type

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: patientid

tag: hcvgroup

value: Chronic

tag: time point

value: EarlyAcute

tag: days post estimated date of infection (edi)

tag: hcv viremia

value: TRUE


title: Control N1027

description: Gene expression from Control

value: Sarcoidosis

value: Neg

tag: race

value: White

value: M

tag: ethnicity

tag: disease_duration (yrs)

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

tag: immune_meds (recorded at time of sample collection)


title: GPA N1040

description: Gene expression from patient with GPA

tag: tissue

value: Nasal brushings

tag: disease

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Active

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: ActiveGPA

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

value: Limited

tag: gender

value: non-Hisp

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: N


title: C1-3

tag: cell type

tag: patientid

tag: hcvgroup

tag: time point

value: LateAcute

tag: days post estimated date of infection (edi)

tag: hcv viremia


title: C2-1

value: PreInfection

value: FALSE


title: H730A_3

tag: strain background

tag: genotype/variation

value: mouse embryonic stem cells (mESCs)

tag: media

value: serum 2i+LIF

tag: molecule type

value: LINE1 amplicon after bisulfite treatment of gDNA with sodium bisulfite


title: C1-1

value: Peripheral Blood Mononuclear Cells (PBMC)

value: Chronic


title: GPA N1024

description: Gene expression from patient with GPA

tag: tissue

tag: disease

value: GPA

value: Inactive

value: InactiveGPA

value: Severe

tag: anca

tag: age

tag: race

tag: ethnicity

tag: disease_duration (yrs)

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

value: Former

tag: immune_meds (recorded at time of sample collection)

value: Methotrexate


title: R6-3

tag: cell type

tag: patientid

tag: hcvgroup

value: Resolution

tag: time point

tag: days post estimated date of infection (edi)

tag: hcv viremia

value: TRUE


title: Control N1019

description: Gene expression from Control

tag: tissue

value: Nasal brushings

tag: disease

value: Control

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: Healthy

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

value: Neg

value: White

tag: gender

value: M

value: non-Hisp

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: N


title: Uhrf1 KO_4

source_name: Uhrf1 KO_mESCs

tag: strain background

tag: genotype/variation

value: Uhrf1 KO

value: mouse embryonic stem cells (mESCs)

tag: media

value: serum 2i+LIF

tag: molecule type

value: LINE1 amplicon after bisulfite treatment of gDNA with sodium bisulfite


title: H730A_1

tag: cell type


title: R6-2

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: patientid

tag: hcvgroup

value: EarlyAcute


title: GPA N1013

description: Gene expression from patient with GPA

value: GPA

value: Never

value: NoNasalGPA

value: Limited

tag: anca

tag: age

tag: race

tag: ethnicity

tag: disease_duration (yrs)

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

value: Current

tag: immune_meds (recorded at time of sample collection)

value: Methotrexate


title: GPA N1001

description: Gene expression from patient with GPA

tag: tissue

value: Nasal brushings

tag: disease

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Inactive

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: InactiveGPA

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

tag: gender

value: F

tag: gc_or_immune (prednisone or any immune med at time of sample collection)


title: GPA N1016

description: Gene expression from patient with GPA

tag: anca

tag: age

value: White

value: M

value: non-Hisp

value: N


title: R6-1

tag: cell type

tag: patientid

tag: hcvgroup

value: Resolution

tag: time point

value: PreInfection

tag: days post estimated date of infection (edi)

tag: hcv viremia

value: FALSE


title: H730A_4

tag: strain background

tag: genotype/variation

value: mouse embryonic stem cells (mESCs)

tag: media

value: serum 2i+LIF

tag: molecule type

value: LINE1 amplicon after bisulfite treatment of gDNA with sodium bisulfite


title: Control N1002

description: Gene expression from Control

tag: tissue

tag: disease

value: Control

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

tag: batch

value: Healthy

value: Neg

tag: race

tag: ethnicity

value: Hispanic

tag: disease_duration (yrs)

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

value: Never

tag: immune_meds (recorded at time of sample collection)


title: Uhrf1 KO_2

value: Uhrf1 KO

tag: cell type


title: Uhrf1 KO_3

tag: strain background


title: R5-4

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: patientid

tag: hcvgroup

tag: time point

value: FollowUp

tag: days post estimated date of infection (edi)

tag: hcv viremia


title: R5-3

value: LateAcute

value: TRUE


title: Uhrf1 KO_1

tag: genotype/variation

tag: media

tag: molecule type


title: wtJ1_4


title: R6-4


title: H730A_2


title: Control N1029

description: Gene expression from Control

tag: tissue

value: Nasal brushings

tag: disease

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: Sarcoidosis

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

tag: anca

tag: age

tag: race

value: White

tag: gender

value: M

tag: ethnicity

value: non-Hisp

value: Methotrexate

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: N


title: R5-2

tag: cell type

tag: patientid

tag: hcvgroup

value: Resolution

tag: time point

value: EarlyAcute

tag: days post estimated date of infection (edi)


title: wtJ1_3

tag: strain background

tag: genotype/variation

value: mouse embryonic stem cells (mESCs)

tag: media

value: serum 2i+LIF

tag: molecule type

value: LINE1 amplicon after bisulfite treatment of gDNA with sodium bisulfite


title: R4-4

tag: hcv viremia

value: FALSE


title: R5-1

value: Peripheral Blood Mononuclear Cells (PBMC)

value: PreInfection


title: wtJ1_2


title: wtJ1_1


title: GPA N1026

description: Gene expression from patient with GPA

tag: tissue

tag: disease

value: GPA

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Never

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: NoNasalGPA

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

value: Severe

value: F

tag: disease_duration (yrs)

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

tag: immune_meds (recorded at time of sample collection)


title: R4-3

tag: cell type

tag: patientid

tag: hcvgroup

tag: time point

value: LateAcute

tag: days post estimated date of infection (edi)


title: R4-2

tag: hcv viremia

value: TRUE


title: HUVEC Notch1 siRNA IL1_1

city: OSLO

first: Guttorm

last: Haraldsen

state: OSLO

address: Sognsvannsveien 20

department: Department for Pathology

country: Norway

institute: Oslo University Hospital

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data (.idat files) were read and processed by R/Bioconductor/beadarray

source_name: Human umbilical vein endothelial cells

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep™-96 RNA Amplification Kit

growth_protocol: Pooled HUVEC from 10 donors were  cultured in MCDB 131 with 7.5% FBS, 10 ng/ml EGF, 1 ng/ml bFGF, 1μg/ml hydrocortisone, 50 μg/ml gentamicin, 250 ng/ml fungizone and 1% L-glutamine. Cells were maintained at 37°C in human 95% air/ 5% CO2 atmosphere.

extract_protocol: RNA was extracted using the Qiagen RNEasy Mini kit, according to manufacturers instructions.

treatment_protocol: Cells were seeded 37.500 cells/cm2, cultured for 24 hours and transfected with siRNA (scrambled or targeting Notch1). 48 hours after transfection, cells were stimulated with recombinant human interleukin-1b (5ng/ml, control cells were given fresh medium) for 4 hours before harvesting in Qiagen RLT lysis buffer.

tag: tissue

value: Human umbilical vein endothelial cells

tag: sirna

tag: stimulation

value: IL-1b 5ng/ml 4h


title: GPA N1015

description: Gene expression from patient with GPA

value: Nasal brushings

tag: disease

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Active

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: ActiveGPA

value: Limited

tag: anca

tag: age

tag: race

value: White

tag: gender

tag: ethnicity

value: non-Hisp

value: Rituximab

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: N


title: R4-1

tag: cell type

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: patientid

tag: hcvgroup

value: Resolution

value: PreInfection

value: FALSE


title: HUVEC Notch1 siRNA IL1_2

description: replicate 1


title: Control N1014

description: Gene expression from Control

value: Control

value: Healthy

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

value: Neg

value: F

tag: disease_duration (yrs)

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

value: Never

tag: immune_meds (recorded at time of sample collection)


title: GPA N1021

description: Gene expression from patient with GPA

tag: tissue

value: Nasal brushings

tag: disease

value: GPA

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: NoNasalGPA

value: Severe

value: MPO

value: M

value: Former

value: Cyclophosphamide


title: HUVEC Notch1 siRNA IL1_3

description: replicate 2

value: Human umbilical vein endothelial cells

tag: sirna

tag: stimulation

value: IL-1b 5ng/ml 4h


title: R3-4

tag: cell type

value: Peripheral Blood Mononuclear Cells (PBMC)

value: Resolution

tag: time point

value: FollowUp

tag: days post estimated date of infection (edi)

tag: hcv viremia


title: HUVEC Notch1 siRNA_2

description: replicate 1

value: medium


title: GPA N1018

description: Gene expression from patient with GPA

value: Inactive

value: InactiveGPA

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

value: Limited

tag: anca

tag: age

tag: race

value: White

tag: gender

tag: ethnicity

value: non-Hisp

tag: disease_duration (yrs)

value: Azathioprine

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: N


title: Control N1012

description: Gene expression from Control

tag: tissue

value: Nasal brushings

tag: disease

value: Control

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: AllergicRhinitis

value: Neg

value: F

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

value: Never

tag: immune_meds (recorded at time of sample collection)

value: Rituximab


title: GPA N1011

description: Gene expression from patient with GPA

value: GPA

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: Severe

value: M


title: Control N1006

description: Gene expression from Control

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

tag: anca


title: HUVEC Notch1 siRNA_3

description: replicate 2

value: Human umbilical vein endothelial cells

tag: sirna

tag: stimulation

value: medium


title: HUVEC Notch1 siRNA_1

description: replicate 1


title: HUVEC scrambled siRNA IL1_1

description: replicate 1

value: scrambled

value: IL-1b 5ng/ml 4h


title: Healthy individual-4

city: Chengdu

first: Bai

last: Hao

state: Sichuan

address: Wuhou District Guoxue Lane 37

department: Laboratory Medicine

institute: West China Hospital of Sichuan University

description: Expression data of lncRNAs and mRNAs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 48°C and 60 rpm on Affymetrix GeneChip miRNA Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Healthy individual_PBMCs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The EDTA anticoagulated whole blood was collected from participants within 24 hours.

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

treatment_protocol: PBMCs were extracted from whole blood immediately by Ficoll separation method, as soon as the samples were collected.

tag: subject status

value: Healthy individual

value: whole blood

tag: cell type

value: Peripheral blood mononuclear cells (PBMCs)


title: Control N1009

description: Gene expression from Control

value: Nasal brushings

value: Healthy

tag: age

tag: race

value: White

tag: gender

tag: ethnicity

value: non-Hisp

tag: disease_duration (yrs)

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: N


title: Healthy individual-2

description: Expression data of lncRNAs and mRNAs

tag: tissue


title: HUVEC scrambled siRNA_3

description: replicate 2


title: Control N1030

description: Gene expression from Control

tag: disease

value: Control

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Sarcoidosis

value: Neg

value: F

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

value: Former

value: Y


title: HUVEC scrambled siRNA IL1_3

description: replicate 2

value: Human umbilical vein endothelial cells

tag: sirna


title: HUVEC scrambled siRNA IL1_2

description: replicate 1

value: scrambled

tag: stimulation


title: Healthy individual-3

description: Expression data of lncRNAs and mRNAs

tag: subject status


title: Healthy individual-5

description: Expression data of lncRNAs and mRNAs

tag: cell type


title: R3-2

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: patientid

tag: hcvgroup

value: Resolution

tag: time point

value: EarlyAcute

tag: days post estimated date of infection (edi)

tag: hcv viremia

value: TRUE


title: Healthy individual-1

description: Expression data of lncRNAs and mRNAs

value: Healthy individual

value: whole blood

value: Peripheral blood mononuclear cells (PBMCs)


title: R3-1

value: PreInfection

value: FALSE


title: R3-3

value: LateAcute


title: R2-4

value: FollowUp


title: R2-2


title: Control N1033

description: Gene expression from Control

value: Nasal brushings

value: Control

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: Sarcoidosis

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

tag: anca

value: Neg

tag: age

tag: race

value: White

tag: gender

value: M

tag: ethnicity

value: non-Hisp

tag: disease_duration (yrs)

tag: immune_meds (recorded at time of sample collection)

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: N


title: HUVEC scrambled siRNA_2

description: replicate 1

tag: tissue

value: Human umbilical vein endothelial cells

tag: sirna

value: scrambled

tag: stimulation

value: medium


title: TB patient-7

description: Expression data of lncRNAs and mRNAs

source_name: TB patient_PBMCs

tag: subject status

value: Pulmonary tuberculosis (TB) patient

value: whole blood

tag: cell type


title: Lung_Res4

tag: breed

value: Western white-faced ewes x Dorset rams

tag: developemental stage/age

value: F1 fetus day135

tag: maternal energy intake

value: 60% of NRC energy requirement or under-fed

value: Lung


title: R1-4

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: patientid

tag: hcvgroup

value: Resolution

tag: time point

value: FollowUp

tag: days post estimated date of infection (edi)

tag: hcv viremia

value: FALSE


title: Control N1025

description: Gene expression from Control

value: Nasal brushings

tag: disease

value: Control

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: Healthy

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

tag: anca

value: Neg

tag: age

tag: race

value: White

tag: gender

value: F

tag: ethnicity

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

value: Former


title: Lung_Res3

tag: breed

tag: developemental stage/age

tag: maternal energy intake

tag: tissue


title: R1-3

tag: cell type

tag: patientid

tag: hcvgroup

tag: time point

value: LateAcute

tag: days post estimated date of infection (edi)

tag: hcv viremia

value: TRUE


title: R1-2

value: EarlyAcute


title: Lung_Res2

value: Western white-faced ewes x Dorset rams

value: F1 fetus day135


title: HUVEC scrambled siRNA_1

description: replicate 1

value: Human umbilical vein endothelial cells

tag: sirna

value: scrambled

tag: stimulation

value: medium


title: GPA N1004

description: Gene expression from patient with GPA

tag: disease

value: GPA

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Active

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: ActiveGPA

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

value: Severe

tag: anca

value: MPO

tag: age

tag: race

tag: gender

tag: ethnicity

value: non-Hisp

tag: disease_duration (yrs)

tag: immune_meds (recorded at time of sample collection)

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: Y


title: Lung_Res1

tag: breed

tag: developemental stage/age

tag: maternal energy intake

value: 60% of NRC energy requirement or under-fed

tag: tissue

value: Lung


title: TB patient-6

description: Expression data of lncRNAs and mRNAs

tag: subject status

value: Pulmonary tuberculosis (TB) patient

value: whole blood

tag: cell type

value: Peripheral blood mononuclear cells (PBMCs)


title: TB patient-5

description: Expression data of lncRNAs and mRNAs


title: GPA N1007

description: Gene expression from patient with GPA

value: Nasal brushings

tag: disease

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Inactive

tag: batch

value: InactiveGPA

value: White

value: M

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

value: Former

value: N


title: GPA N1017

description: Gene expression from patient with GPA

value: GPA

value: Never

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: NoNasalGPA

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

tag: anca

tag: age

tag: race

tag: gender

value: F

tag: ethnicity

value: Azathioprine


title: P65-1

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

description: SAMPLE 7

hyb_protocol: 750 ng of high-quality labeled cRNA per sample was hybridized to Illumina HumanHT-12v4 Expression BeadChip in triplicates (Illumina, Cambridge, United Kingdom) using Whole-Genome Expression Direct Hybridisation kit (Illumina)

scan_protocol: Scanned with a 500GX (Illumina)

data_processing: Data was extracted in BeadStudio and quantile normalised using the lumi BioConductor package

label_protocol: 500 ng of total RNA from each sample was amplified and biotinylated using Illumina® TotalPrep RNA Amplification Kit (Ambion, AMIL1791), according the manufacture’s instructions, and then quantified using a Bioanalyser 2100

growth_protocol: MDA-MD-231 cells were cultured in a standard a modified essential medium (alpha or DMEM supplemented with 10% fetal calf serum (FCS), penicillin, and streptomycin).

extract_protocol: RNA was extracted using RNeasy Mini Kit with RNAse-free DNAse treatment (74014, Qiagen Crawley, United Kingdom), according the manufacture’s instructions

treatment_protocol: Human MDA-MD-231 cells were cultured in 24-well plates to 50% confluence and transfected siRNA (100 nM) with Dharmafect 1 reagent (Dharmacon, CO, USA) according to the manufacturer’s instructions. Small interfering RNAs (siRNA; siGenome SMART pool) as a pool of four annealed double-stranded RNA oligonucleotides for IKKβ (M-003503-03) and non-targeting control no. 3 (D001201-03) (Dharmacon, CO, USA) were used according to the manufacturer’s instructions.

tag: cell line

tag: sirna

value: p65 sh


title: TB patient-4

description: Expression data of lncRNAs and mRNAs

tag: subject status

tag: tissue

tag: cell type


title: SCRAMB4

description: SAMPLE 6

value: mock


title: TB patient-2

description: Expression data of lncRNAs and mRNAs

value: Pulmonary tuberculosis (TB) patient


title: R2-1

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: patientid

tag: hcvgroup

value: Resolution

tag: time point

value: PreInfection

tag: days post estimated date of infection (edi)

tag: hcv viremia

value: FALSE


title: SCRAMB3

description: SAMPLE 5


title: P65-4

description: SAMPLE 9


title: P65-3

description: SAMPLE 8


title: TB patient-3

description: Expression data of lncRNAs and mRNAs

value: whole blood

value: Peripheral blood mononuclear cells (PBMCs)


title: SCRAMB1

description: SAMPLE 4


title: pri_supt16hTotal_C: human Supt16h kd RNA-seq rep3

description: RNA-seq

data_processing:
ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5’end coordinate of the – strand read was less than or equal to the 5’end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5’ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as will as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors.
bedGraph files were generated from replicate concatenated processed ATAC-seq reads .bed files using bedtools genomecov v2.23 (-scale 1/(library size - chrM reads/100000)) which were then converted to .bigWig files using the ENCODE program bedGraphToBigWig.
UMIs from RNA-seq reads were extracted with UNI-tools followed by read trimming with fastx_trimmer and mapping with STAR. Mapped files were deduplicated with UNI-tools and remapped with STAR to generate bam and bedGraph files
RNA-seq normalized bedGraph files were converted to bigWig format with bedGraphToBigWig and replicates were averaged using bamCompare from the deeptools suite.
RNA-seq count tables were generated using RSEM and differential expression determined using DESeq2
UMIs from ChIP-seq reads were extracted using UMI-tools followed by read trimming with fastx_trimmmer and mapping with Bowtie2.
Uniquely mapping ChIP-seq reads were converted to bed files of the full fragment lengths then to library normalized bigWig files using bamCoverage from the deepTools suite. BigWig files were then normalized to input controls using bamCompare from the deepTools suite with --ratio substract for worm and --ratio ratio for human
Windows around annotated transcription start sites were counted for intersections with full-paired-end-fragment ChIP-seq reads using bedtools intersect and windows containing significant signal determined using DESeq2
Genome_build: ce10, hg19
Supplementary_files_format_and_content: library-normalized bigWig files of processed ATAC-seq reads, mapped RNA-seq reads, and input-normalized ChIP-seq reads
Supplementary_files_format_and_content: Gene count tables for RNA-seq reads and promoter-window count tables for full-paired-end-fragment ChIP-seq reads

source_name: human secondary fibroblasts

growth_protocol: hiF-T cells were cultured in DMEM/F12 Gltuamax (Life Technologies) supplemented with 10% FBS, 1% NEAA, 0,1% beta-mercaptoethanol 100 U ml−1 penicillin, 100 μg ml−1 streptomycin and 16 ng/ml FGFbasic and passaged every 3 days using a splitting ratio of 1:3

extract_protocol:
Cell pellet of about 100.000 cells per sample was used for RNA extraction 48h after treatment. RNA extraction was done using RNeasy Plus Mini Kit (Qiagen). RNA was reverse transcribed using GoScript® Reverse Transcriptase kit (Promega).
Library preparation was done following standard Bioo Scientific protocol and NEXTflex® Rapid Directional qRNA-Seq™ Kit2 (Bioo Scientific). Libraries were sequnced using single end sequencing length of a 75 nucleotides on a HiSeq400 machine (Illumina).

treatment_protocol: 80.000 hiF-T cells/ well of a 12-well plate treated with attachment factor were seeded and incubated overnight at 37ºC. siRNA knockdown was performed the following day by a reverse transfection method using DharmaFECT 1 and 40 nM siRNA reagents (Dharmacon) according to the manufacturer’s protocol

value: hiF-T cells carrying DOX-inducible, polycistronic human OCT4/KLF4/c-MYC/SOX2 (OKMS) cassette

value: human secondary fibroblasts

tag: passages/stage

tag: sirna / dsrna


title: IKKB4

description: SAMPLE 3

value: IKKB sh


title: Lung_Over4

tag: breed

value: Western white-faced ewes x Dorset rams

tag: developemental stage/age

value: F1 fetus day135

tag: maternal energy intake

value: 140% of NRC energy requirement or over-fed

value: Lung


title: R1-1


title: Lung_Over2


title: pri_supt16hTotal_A: human Supt16h kd RNA-seq rep1

description: RNA-seq


title: Lung_Over1


title: pri_ssrp1Total_C: human Ssrp1 kd RNA-seq rep3

description: RNA-seq


title: Lung_Over3


title: pri_supt16hTotal_B: human Supt16h kd RNA-seq rep2

description: RNA-seq


title: Lung_Con7

value: 100% of NRC energy requirement or control


title: Lung_Con6


title: pri_ssrp1Total_A: human Ssrp1 kd RNA-seq rep1

description: RNA-seq


title: pri_ssrp1Total_B: human Ssrp1 kd RNA-seq rep2

description: RNA-seq


title: Lung_Con5


title: TB patient-1

description: Expression data of lncRNAs and mRNAs


title: IKKB3

description: SAMPLE 2


title: pri_mockTotal_C: human mock RNA-seq rep3

description: RNA-seq


title: Peruvian NTL, Patient 180

city: Toulouse

first: Juan Pablo

last: Cerapio

address: Av 2 Hubert Curien

country: France

institute: CRCT

hyb_protocol: 5.5 ug of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45C on GeneChip™ Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using the limma software standard pipeline (R package) and normalized using Robust Multichip Average (RMA) algorithm.

source_name: NTL tissues with clear cell foci

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA, according to the standard Affymetrix protocol (Manual Target Prepartion for GeneChip Whole Transcription Expression Array, 20013, Affymetrix).

extract_protocol:
sampling protocol: About 50 mg of non-tumour liver tissue were harvested from tumour-free margins of the resected surgical pieces, flash-frozen in liquid nitrogen, and kept at - 80°C for long-term storage
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Peruvian patients with hepatocellular carcinoma (HCC)

tag: subject id

value: Patient 180

value: Non-tumoral liver (NTL) tissue

tag: clear cell foci

value: Positive


title: IKKB1

description: SAMPLE 1

tag: cell line


title: pri_mockTotal_B: human mock RNA-seq rep2

description: RNA-seq


title: Peruvian NTL, Patient 179

value: Patient 179


title: Peruvian NTL, Patient 120

value: Patient 120


title: Lung_Con3


title: Peruvian NTL, Patient 109

value: Patient 109


title: Peruvian NTL, Patient 106

source_name: NTL tissues without clear cell foci

value: Patient 106

value: Negative


title: Lung_Con4


title: pri_mockTotal_A: human mock RNA-seq rep1

description: RNA-seq

value: hiF-T cells carrying DOX-inducible, polycistronic human OCT4/KLF4/c-MYC/SOX2 (OKMS) cassette


title: Peruvian NTL, Patient 104

value: Patient 104


title: supt16hChIP2: Supt16h ChIP-seq rep2

description: ChIP-seq

extract_protocol:
Approximately 5 million cells were used per IP reaction. The cells were fixed using 1.1% formaldehyde. iDeal ChIP-seq Kit for Transcription Factors (Diagenode) was used for chromatin shearing and all the subsequent steps of ChIP-seq library preparation
Library preparation was done following standard Bioo Scientific protocol and NEXTflex® qRNA-Seq™ Kit v2 (Bioo Scientific). Libraries were sequnced using single end sequencing length of a 75 nucleotides on a HiSeq400 machine (Illumina).

value: human secondary fibroblasts


title: Lung_Con2

value: Western white-faced ewes x Dorset rams


title: Lung_Con1

value: F1 fetus day135


title: HUVEC scrambled siRNA unstimulated rep3

description: replicate 3

data_processing: The raw data was pre-processed by Illumina’s GenomeStudio software V2011.1, Gene Expression module v. 1.9.0.

source_name: Human Umbilical Vein Endothelial Cells (HUVEC)

label_protocol: Biotinylated cRNA were prepared with the Illumina®TotalPrep™-96 RNA Amplification Kit (Ambion)

extract_protocol: total RNA was extracted with TRI Reagent, followed by clean-up with QIAGEN Rneasy mini kit in accordance with the prescribed protocol provided with the kit. Guality control was performed with the 2100 Bioanalyzer, RIN values were > 9.0 for all samples.

tag: sirna

value: scrambled

tag: il-1β stimulation

value: pool of 7 HUVEC; confluent at harvest


title: HUVEC JAG1 siRNA unstimulated rep3

description: replicate 3


title: supt16hChIP1: Supt16h ChIP-seq rep1

description: ChIP-seq

tag: tissue


title: HUVEC JAG1 siRNA + IL-1β 24 hours rep3

description: replicate 3

tag: cell type


title: Kidney_Res4

value: 60% of NRC energy requirement or under-fed

value: Kidney


title: Peruvian NTL, Patient 099

tag: subject status

value: Peruvian patients with hepatocellular carcinoma (HCC)

value: Patient 099


title: HUVEC JAG1 siRNA unstimulated rep2

description: replicate 2


title: HUVEC scrambled siRNA + IL-1β 24 hours rep3

description: replicate 3


title: ssrp1ChIP2: Ssrp1 ChIP-seq rep2

description: ChIP-seq


title: Kidney_Res3


title: HUVEC JAG1 siRNA + IL-1β 24 hours rep2

description: replicate 2


title: HUVEC scrambled siRNA unstimulated rep2

description: replicate 2


title: Peruvian NTL, Patient 093

value: Patient 093

value: Non-tumoral liver (NTL) tissue

value: Positive


title: Peruvian NTL, Patient 101

value: Patient 101


title: ssrp1ChIP1: Ssrp1 ChIP-seq rep1

description: ChIP-seq


title: hChipInput2: human ChIP-seq input rep2

description: ChIP-seq ctrl


title: Kidney_Res2


title: Kidney_Res1


title: hChipInput1: human ChIP-seq input rep1

description: ChIP-seq ctrl


title: Kidney_Over3

value: 140% of NRC energy requirement or over-fed


title: Kidney_Over4


title: Kidney_Over1


title: Kidney_Over2


title: Uninfected AEC 4

city: Rotterdam

last: Katsikis

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC University Medical

description: CD326_RNA-Seq_L005_R1_GTGGCC_B6_NI_CD326+_4

data_processing:
Trimming of Adaptors
Alignment to reference mm10 genomic version
generate counts files
Genome_build: Mus_Musculus.GRCm38.70
Supplementary_files_format_and_content: raw data fastq raw counts

source_name: Uninfected AEC

growth_protocol: Infection of 8-12 week old mice with 10^6 pfu GFP-expressing recombinant A/Puerto Rico/8/1934 influenza virus

extract_protocol:
Trizol
Illumina Tru-Seq stranded mRNA Kit

treatment_protocol: Day 3 PR8-GFP infected FACS sorted lung AEC.  Lung cells were digested with dispase and DNAse, panned on plated coated with anti-CD45/anti-CD16/anti-CD32.  Enriched AEC cells were sorted sterily as CD326+CD45- on a FACSAria III.

tag: mouse strain

tag: mouse age

value: 8-12 week old

value: Day 3 postinfection

value: lung alveolar epithelial cells (AEC)


title: Uninfected AEC 2

description: CD326_RNA-Seq_L006_R1_TAGCTT_B6_NI_CD326+_2

tag: time point


title: Uninfected AEC 3

description: CD326_RNA-Seq_L006_R1_GGCTAC_B6_NI_CD326+_3


title: HUVEC JAG1 siRNA unstimulated rep1

description: replicate 1


title: HUVEC scrambled siRNA + IL-1β 24 hours rep2

description: replicate 2


title: Uninfected AEC 1

description: CD326_RNA-Seq_L005_R1_ATCACG_B6_NI_CD326+_1


title: Uninfected AEC 5

description: CD326_RNA-Seq_L006_R1_GAGTGG_B6_NI_CD326+_5


title: GFP- AEC (bystander AEC) 5

description: CD326_RNA-Seq_L002_R1_GAGTGG_B6_Inf_CD326+_GFP-_5

source_name: GFP- AEC (bystander AEC)

tag: influenza virus strain

value: GFP-expressing recombinant A/Puerto Rico/8/1934


title: EBSS-2

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description: culture in EBSS for 4 h

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with SST-RMA by Affymetrix Expression Console Ver 1.4

source_name: culture in EBSS for 4 h

label_protocol: Standard Affymetrix protocol

growth_protocol: cell maintain in DMEM culture medium

extract_protocol: HEp-2 cells were cultured in DMEM, EBSS and EBSS+Hisfor 4 h.Total RNA wasextracted by Trizol, followed by concentration through an RNeasy MinElute Cleanup Kit (QIAGEN), following the manufacturer’s instructions. Isolated RNAs were subjected to GeneChip™ Human Transcriptome Array 2.0 analysis

treatment_protocol: Cell culture in different medium (DMEM, EBSS and EBSS+Histidine) for 4 h

value: human laryngeal carcinoma


title: HUVEC scrambled siRNA unstimulated rep1

description: replicate 1


title: DMEM-2

description: culture in DMEM for 4 h

source_name: culture in DMEM for 4 h


title: GFP- AEC (bystander AEC) 4

description: CD326_RNA-Seq_L002_R1_GTTTCG_B6_Inf_CD326+_GFP-_4


title: EBSS+His-2

description: culture in EBSS+histidine for 4 h

source_name: culture in EBSS+histidine for 4 h


title: EBSS+His-1

description: culture in EBSS+histidine for 4 h


title: EBSS-1

description: culture in EBSS for 4 h


title: DMEM-1

description: culture in DMEM for 4 h


title: Kidney_Con7

value: Western white-faced ewes x Dorset rams

value: F1 fetus day135

value: 100% of NRC energy requirement or control


title: Kidney_Con6


title: HUVEC JAG1 siRNA + IL-1β 24 hours rep1

description: replicate 1

value: pool of 7 HUVEC; confluent at harvest


title: GFP- AEC (bystander AEC) 3

description: CD326_RNA-Seq_L001_R1_GTGGCC_B6_Inf_CD326+_GFP-_3


title: GFP- AEC (bystander AEC) 1

description: CD326_RNA-Seq_L001_R1_ATCACG_B6_Inf_CD326+_GFP-_1


title: GFP- AEC (bystander AEC) 2

description: CD326_RNA-Seq_L001_R1_TAGCTT_B6_Inf_CD326+_GFP-_2


title: Kidney_Con4

value: Kidney


title: Kidney_Con5


title: GFP+ AEC (infected AEC) 4

description: CD326_RNA-Seq_L004_R1_GTTTCG_B6_Inf_CD326+_GFP+_4

source_name: GFP+ AEC (infected AEC)


title: Kidney_Con2


title: Kidney_Con3


title: GFP+ AEC (infected AEC) 3

description: CD326_RNA-Seq_L003_00*_R1_GTGGCC_B6_Inf_CD326+_GFP+_3


title: HUVEC scrambled siRNA + IL-1β 24 hours rep1

description: replicate 1

value: scrambled


title: Brain_Res4

value: 60% of NRC energy requirement or under-fed

value: Brain


title: Brain_Res3


title: Kidney_Con1


title: Brain_Res2


title: spt16 rep3

description:
spt-16_N2_L4_S28
mRNA
Processed data file: spt16RNAcounts.tsv

source_name: whole worms

extract_protocol:
Synchronized L4 animals were washed 5 times in M9 buffer and collected on ice. RNA was isolated using TRIzol® and guanidinium thiocyanate-phenol-chloroform extraction and RNA was precipitated using isopropanol. RNA was reverse transcribed using GoScript® Reverse Transcriptase kit (Promega).
Library preparation was done following standard Illumina protocol and TruSeq RNA Library Prep Kit v2 (Illumina). Libraries were sequenced using single-end sequencing length of a 100 nucleotides on a HiSeq2500 machine (Illumina).

tag: strain/background

tag: developmental stage

value: whole body

tag: sirna/dsrna

value: sjj_F55A3.3 (Ahringer library, I-5O08 Source BioScience)


title: Brain_Over4

tag: breed

tag: developemental stage/age


title: Brain_Res1

tag: maternal energy intake


title: spt16 rep2

description:
spt-16_N2_L4_S19
mRNA
Processed data file: spt16RNAcounts.tsv


title: Brain_Over3


title: Brain_Over2


title: Control 7 (C7) RNA-Seq

city: Paris

first: Carlos

last: Parras

address: 47 bd de l'hopital batiment ICM

institute: ICM

data_processing:
All RNA-seq reads were aligned onto the mm10 reference genome using Tophat2, gene expression levels were quantified with featureCounts
RNA-seq reads were aligned onto the mm10 reference transcriptome using bowtie and quantified using eXpress
The edgeR R-package was used to perform both data normalization and differential expression analyses
Genome_build: mm10
genes were considered regulated when p-value < 0.05 and Fold change > 1.2
Supplementary_files_format_and_content: counts

source_name: O4+ cells

growth_protocol: in vivo Magnetic-activated cell sorting of O4+ cells from P7 Ctrl or Chd7iKO mouse cortices using anti-O4 antibodies

extract_protocol:
RNAs were extracted from MACsorted O4+-cells from P7 Chd7iKO mice and their control littermates, using Nucleospin RNA kit (Macherey-Nagel, 740955)
RNA-seq libraries from control (n=7) and Chd7iKO (n=5) O4+-cells were prepared using TruSeq Stranded mRNA (Illumina 20020594)

treatment_protocol: Tamoxifen was injected subcutaneously at 20mg/ml concentration at postnatal stages P1 (40µl) and P4 (30µl) in Ctrl and Chd7iKO animals.

value: Cortex and Corpus callosum

tag: age

value: Postnatal day 7

tag: genotype


title: Chd7iKO 1 (M1) RNA-Seq

value: PDGFRaCre; Chd7flox/flox


title: Chd7iKO 2 (M2) RNA-Seq


title: hmg4 rep3

description:
hmg-4_N2_L4_S27
mRNA
Processed data file: hmg4RNAcounts.tsv

value: sjj_T20B12.8 (Ahringer library,III-3P10, Source Bioscience)


title: Chd7iKO 3 (M3) RNA-Seq


title: spt16 rep1

description:
spt-16_N2_L4_S11
mRNA
Processed data file: spt16RNAcounts.tsv


title: Control 6 (C6) RNA-Seq


title: hmg4 rep2

description:
hmg-4_N2_L4_S18
mRNA
Processed data file: hmg4RNAcounts.tsv


title: Brain_Con7


title: Control 5 (C5) RNA-Seq


title: Control 4 (C4) RNA-Seq


title: GFP+ AEC (infected AEC) 1

description: CD326_RNA-Seq_L003_00*_R1_ATCACG_B6_Inf_CD326+_GFP+_1

value: 8-12 week old

value: Day 3 postinfection

value: lung alveolar epithelial cells (AEC)


title: Chd7iKO 5 (M5) RNA-Seq


title: Brain_Con6

value: Western white-faced ewes x Dorset rams


title: hmg4 rep1

description:
hmg-4_N2_L4_S10
mRNA
Processed data file: hmg4RNAcounts.tsv


title: Control 3 (C3) RNA-Seq


title: ctrl rep3

description:
ctrl_N2_L4_S9
mRNA
Processed data file: hmg4RNAcounts.tsv
Processed data file: spt16RNAcounts.tsv

value: HT115 (D3) bacteria containing L4440 vector with DNA targeting Renilla luciferase


title: Chd7iKO 4 (M4) RNA-Seq


title: Brain_Con3

value: F1 fetus day135

value: 100% of NRC energy requirement or control


title: Brain_Con4


title: Control 2 (C2) RNA-Seq


title: ctrl rep2

description:
ctrl_N2_L4_S26
mRNA
Processed data file: hmg4RNAcounts.tsv
Processed data file: spt16RNAcounts.tsv


title: Brain_Over1

value: 140% of NRC energy requirement or over-fed


title: Brain_Con2


title: Control 1 (C1) RNA-Seq


title: 8_ChIP_OPC_Input_3

description: Control for 7_ChIP_OPC_Chd8_3

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2
Data were filtered using SAMtools and PCR-derived duplicates removed by using PICARD MarkDuplicates
peaks were called using MACS (Model-based Analysis of ChIP-Seq)with options: keep-dup all, nolambda, broad, nomodel, extsize 75 -q 0.01 and filtered according to the following criteria: (i) length>=100bp and (ii) p-value<=5%
Genome_build: mm10
Supplementary_files_format_and_content: broadpeaks files with in this order: chrom, chromStart, chromEnd, peak name, score, signalValue, pValue, qValue

growth_protocol: in vivo Magnetic-activated cell sorting of O4+ cells from P7 WT mouse cortices using anti-O4 antibodies

extract_protocol:
Lysates were clarified from sonicated nuclei and Chd7-DNA and Chd8-DNA complexes were isolated with O4 antibody.
The ChIP-seq libraries were prepared using TruSeq ChIP library preparation kit (Illumina ip-202-1012)

tag: chip antibody


title: Brain_Con1


title: 7_ChIP_OPC_Chd8_3

description: Chd8 ChIP in OPCs

value: Anti-Chd8 (Bethyl; A301-224A)


title: ctrl rep1

description:
ctrl_N2_L4_S17
mRNA
Processed data file: hmg4RNAcounts.tsv
Processed data file: spt16RNAcounts.tsv

data_processing:
ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5’end coordinate of the – strand read was less than or equal to the 5’end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5’ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors.
Peaks were called on concatenated processed bed files using JAMM peakcaller v1.0.7.5 (-f38 –b 100 –e 1.75). The resulting “all” (for worm) or “filtered” (for human) peaks output by JAMM for each condition (control, ssrp1 knockdown, and supt16h knockdown for human, or rluc, hmg3, and hmg4 for worms) were concatenated and then merged with bedtools merge v2.23. The merged "all" peaks for worm were then further filtered for a minimum width of 25 bp.
Merged peaks were then counted for the number of processed reads that intersected them from each replicate of each experimental condition using bedtools coverage v2.23 (-counts). Count tables were then normalized (method = “TMM”) and subjected to differential analysis (exactTest) using edgeR. Peaks were called as differential with a q-value cutoff of 0.01 (adjust=”BH”).
bedGraph files were generated from replicate concatenated processed ATAC-seq reads .bed files using bedtools genomecov v2.23 (-scale 1/(library size - chrM reads/100000)) which were then converted to .bigWig files using the ENCODE program bedGraphToBigWig.
RNA-seq reads were trimmed for adapters and mapped with STAR.
RNA-seq count tables were generated using quasR and differential expression determined using DESeq2.
Genome_build: ce10
Supplementary_files_format_and_content: *tsv: Tab-delimited text files; RNA-seq count tables.
Supplementary_files_format_and_content: *bigWig: Library-normalized bigWig files of processed ATAC-seq reads.
Supplementary_files_format_and_content: *txt: Tab-delimited text files; Count tables for merged peaks across all replicates separately.


title: hmg3 rep3

description:
hmg-3_tm2539_L4_S3
mRNA
Processed data file: hmg3RNAcounts.tsv

growth_protocol: C. elegans strains were maintained on OP50 bacteria and NGM agar plates at 20ºC. Worms were transferred to fresh food once a week.

value: young adult


title: hmg3 rep2

description:
hmg-3_tm2539_L4_S2
mRNA
Processed data file: hmg3RNAcounts.tsv


title: veh4E

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description: RNA-seq

data_processing:
SOLiD 5500 deep sequencer run (single, 50 nt) was performed with single index to generate color-space data in XSQ format.
XSQ files were subjected to generation of the color-space CSFASTA/QUAL read sequence files using Life Technologies XSQTools software package. The TopHat-Cufflinks pipeline with the Bowtie backend aligner was used to align the color space read data to the Xla_9.1 Xenpus reference gonome sequence to generate BAM files.
Cufflinks processed RNA-seq BAM files to generate normalized amounts of mRNA expression based on the Xla_9.1 annotation.
Genome_build: Xla_9.1 (Xenbase release 9.1)
Supplementary_files_format_and_content: Microsoft Excel xlsx spreadsheets including normalized relative intensity of mRNA expression
Supplementary_files_format_and_content: FPKM

organism: Xenopus laevis

source_name: X. lavis embryo (stage 10.5; pool of five embryos)

growth_protocol: Eggs from two clutches (labeled D and E) of female X. laevis were fertilized in vitro and embryos staged according to Nieuwkoop and Faber (1994).

extract_protocol:
Each dish was harvested at gastrula stage 10.5 in 5-embryo aliquots. Replicates were taken from two different clutches (D & E), and 5 replicates were analyzed within each clutch (10 replicates total). Each five embryo pool was homogenized in 200 μL of TriPure (Roche).  Total RNA was DNAse treated, LiCl precipitated, and 100 ng was reverse transcribed into cDNA using Ovation RNA Amplification System V2 (NuGEN).
Total RNA was subjected to cDNA synthesis using the Ovation RNA Amplification System V2 kit (NuGEN). Deep sequencing libraries were generated from the cDNA using the ABI SOLiD 5500 Fragment Library Core Kit (Life Technologies).

treatment_protocol: Stage 6-7 embryos were treated in groups of 25 in 60-mm glass Petri dishes with 10 mL of 0.1X MBS containing 1 μM RAR-selective agonist TTNPB, 1 μM RAR-selective inverse agonist (antagonist) AGN193109 or vehicle control (0.1% EtOH).

tag: exposure

value: Vehicle (0.1% ethanol)


title: Brain_Con5

tag: tissue

value: Brain


title: hmg3 rep1

description:
hmg-3_tm2539_L4_S1
mRNA
Processed data file: hmg3RNAcounts.tsv

value: whole body


title: 3_ChIP_OPC_Input_1

description: Control for 1_ChIP_OPC_Chd7_1

value: Cortex and Corpus callosum


title: 5_ChIP_OPC_Mock_2-3

description: Control for 4_ChIP_OPC_Chd7_2 & 7_ChIP_OPC_Chd8_3

value: Postnatal day 7

value: Rabbit IgG


title: veh3D

description: RNA-seq


title: 6_ChIP_OPC_Input_2

description: Control for 4_ChIP_OPC_Chd7_2


title: ctrl hmg3 rep2

description:
N2_L4_20_S2
mRNA
Processed data file: hmg3RNAcounts.tsv


title: veh4D

description: RNA-seq


title: 2_ChIP_OPC_Mock_1

description: Control for 1_ChIP_OPC_Chd7_1


title: veh1D

description: RNA-seq


title: Chd7iKO 4 (M4) ATAC-Seq

data_processing:
Reads from 5 controls and 5 Chd7iKO were uniquely mapped onto mm10 with bowtie2.
Low-quality, mitochondria- and PCR-derived reads were all removed and peaks were called by using MACS.
Overlapping peaks called from ChIP- and ATAC-seq data were matched with the bedops toolbox and data correlated within the R software.
Genome_build: mm10
Supplementary_files_format_and_content: bed

extract_protocol:
cells were lysate in lysis buffer (0.1% Igepal, Sigma, CA-630; 10mM Trsi-HCl pH7.4; 10mM NaCl; 3mM MgCl2) before ATAC-seq reaction, which was done as described before (Ernst et al., 2011)
Libraries were done using Nextera DNA sample kit (Illumina, 15028212)

treatment_protocol: Tamoxifen was injected subcutaneously at 20mg/ml concentration at postnatal stages P1 (40µl) and  P4 (30µl) in Ctrl and Chd7iKO animals.

value: PDGFRaCre; Chd7flox/flox


title: veh2D

description: RNA-seq


title: veh1E

description: RNA-seq


title: Chd7iKO 5 (M5) ATAC-Seq


title: 4_ChIP_OPC_Chd7_2

description: Chd7 ChIP in OPCs

value: Anti-Chd7 (Cell Signaling; 6505)


title: ttn4E

description: RNA-seq

value: TTNPB, 1 uM


title: ctrl hmg3 rep1

description:
N2_L4_20_S1
mRNA
Processed data file: hmg3RNAcounts.tsv


title: Chd7iKO 3 (M3) ATAC-Seq


title: ttn4D

description: RNA-seq


title: ctrl hmg3 rep3

description:
N2_L4_20_S25
mRNA
Processed data file: hmg3RNAcounts.tsv


title: veh3E

description: RNA-seq


title: veh2E

description: RNA-seq


title: Chd7iKO 2 (M2) ATAC-Seq


title: ttn3E

description: RNA-seq


title: Chd7iKO 1 (M1) ATAC-Seq


title: SSRP1 ATAC-seq rep2

description:
processed data file:
sorted_ssrp1CatRep1and3_true5end.bed_steric38.bed.bam.bam.bigWig

data_processing:
ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5’end coordinate of the – strand read was less than or equal to the 5’end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5’ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as will as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors.
Peaks were called on concatenated processed bed files using JAMM peakcaller v1.0.7.5 (-f38 –b 100 –e auto). The resulting “all” (for worm) or “filtered” (for human) peaks output by JAMM for each condition (control, ssrp1 knockdown, and supt16h knockdown for human, or rluc, hmg3, and hmg4 for worms) were concatenated and then merged with bedtools merge v2.23. The merged "all" peaks for worm were then further filtered for a minimum width of 25 bp.
Merged peaks were then counted for the number of processed reads that intersected them from each replicate of each experimental condition using bedtools coverage v2.23 (-counts). Count tables were then normalized (method = “TMM”) and subjected to differential analysis (exactTest) using edgeR. Peaks were called as differential with a q-value cutoff of 0.01 (adjust=”BH”).
bedGraph files were generated from replicate concatenated processed ATAC-seq reads .bed files using bedtools genomecov v2.23 (-scale 1/(library size - chrM reads/100000)) which were then converted to .bigWig files using the ENCODE program bedGraphToBigWig.
Genome_build: hg19;ce10
Supplementary_files_format_and_content: library-normalized bigWig files of processed ATAC-seq reads
Supplementary_files_format_and_content: Count tables for merged peaks across all replicates separately

source_name: SSRP1 ATAC-seq

extract_protocol:
cell pellet of 50.000 cells per sample was used for library preparation
see samples
Library preparation was done following a protocol published in Buenrostro et al. 2013. Cell pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase) (Illumina Nextera DNA Library preparation kit, #FC-121-1030). The transposition reaction was carried out for 60 min at 37ºC. The samples were purified using Zymo DNA Clean & Concentrator kit; following purification, library fragments were amplified using NEBNext PCR master mix and custom Nextera PCR primers. Libraries were amplified for a total of 12 to 14 cycles and sequenced using paired-end-sequencing length of 75 nucleotides using NextSeq 500/550 High Output v2 kit (Illumina) on a NextSeq500 machine (Illumina) following manufacturer's protocol.

tag: cell type

value: human secondary fibroblasts

tag: genotype/variation

value: hiF-T cells carrying DOX-inducible, polycistronic human OCT4/KLF4/c-MYC/SOX2 (OKMS) cassette

tag: passages/stage


title: SUPT16H ATAC-seq rep1

description:
processed data file:
sorted_supt16hCatRep1and3_true5end.bed_steric38.bed.bam.bam.bigWig

source_name: SUPT16H ATAC-seq


title: SUPT16H ATAC-seq rep2


title: Endothelial cells isolated from DNFB-treated ear, NICD1-EC-OE mouse, replicate 4

description: Gene expression data of endothelial cells from DNFB treated ears from mice with tamoxifen-induced endothelial overexpression of constitutively active Notch1

hyb_protocol: Following fragmentation and terminal labeling, 5,5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Gene Chip Mouse Gene 2.1 ST array. GeneChips were washed and stained in the Affymetrix GeneCips fluidics station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan Multichannel instrument.

data_processing: RMA-normalised data were obtained using the Affymetrix Expression Console Software.

source_name: CD31+CD45-Ter119- endothelial cells, FACS-sorted from collagenase I-digested ears.

label_protocol: Biotinylated cRNA were prepared from 1ng total RNA and amplified according to manufacturers instructions, using the Affymetric GeneChip WT Pico kit.

growth_protocol: NICDiEC-OE mice with endothelial expression of constitutively active Notch1 were generated by combining RosaNICD/NICD with CDH5-iCre transgenics.

extract_protocol: RNA was extracted using the Qiagen RNEasy Plus Micro kit and amplified using the Affymetrix WT Pico Amplification kit, according to manufacturers description.

treatment_protocol: Mice were treated with 5 daily tamoxifen injections before the start of experiment. DNFB was applied dermally on two consecutive days (day 0 and 1) to promote sensitisation. Inflammation was elicited by a single application of DNFB to the ear pinna on day 5. Ears were harvested after 24 hours and digested in collagenase I. FACS was performed to isolate CD31+CD45-Ter119- endothelial cells. Cells were sorted directly into Qiagen RLT Plus lysis buffer.

value: ear

tag: cell population

value: CD31+CD45-Ter119- endothelial cells

value: Pdgfb-CreERT2; R26-NICD


title: Endothelial cells isolated from vehicle-treated ear, NICD1-EC-OE mouse, replicate 4


title: Endothelial cells isolated from vehicle-treated ear, NICD1-EC-OE mouse, replicate 2

description: Gene expression data of endothelial cells from ears from mice with tamoxifen-induced endothelial overexpression of constitutively active Notch1


title: ttn3D

description: RNA-seq


title: Endothelial cells isolated from DNFB-treated ear, NICD1-EC-OE mouse, replicate 3


title: Endothelial cells isolated from vehicle-treated ear, NICD1-EC-OE mouse, replicate 3


title: Control 5 (C5) ATAC-Seq


title: ttn2D

description: RNA-seq


title: Control 4 (C4) ATAC-Seq


title: mock ATAC-seq rep2

description:
processed data file:
sorted_reIded_mockCatRep1and3_true5end.bed_steric38.bed.bam.bam.bigWig

source_name: mock ATAC-seq


title: mock ATAC-seq rep1


title: ttn1E

description: RNA-seq


title: ttn2E

description: RNA-seq


title: Control 3 (C3) ATAC-Seq


title: Control 2 (C2) ATAC-Seq


title: Control 1 (C1) ATAC-Seq


title: ttn1D

description: RNA-seq


title: 109_4E

description: RNA-seq


title: Endothelial cells isolated from DNFB-treated ear, NICD1-EC-OE mouse, replicate 1


title: SSRP1 ATAC-seq rep1


title: 109_4D

description: RNA-seq


title: Endothelial cells isolated from vehicle-treated ear, control mouse, replicate 6

description: Gene expression data of endothelial cells from mouse ears

value: control