title: 293-StellaOE-RNA

status: Public on Sep 24 2018

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

data_processing:
Basecalls performed by BGI, Shenzhen
RRBS sequencing reads were mapped to the mouse genome (mm9) using Bismark v0.10.1 (Babraham Bioinformatics) after adapter trimming by Trim Galore (Babraham Bioinformatics). The methylation level of each covered cytosine in CpG context was calculated as the number of reported C divided by the total number of reported C and T.
RNA-Seq data were mapped by TopHat and quantitified by Cufflinks.
Genome_build: mm9 / hg19
Supplementary_files_format_and_content: CpG methylation levels were generated with Bismark, and only sites with depth greater than 5 were kept. Methylation levels of 100-bp tiles along the genome (mm9) were calculated as total C / total C+T within each tile.

source_name: HEK-293 cells with mouse Stella overexpressed for 4 days

extract_protocol:
Genomic DNA was isolated by conventional phenol extraction and proteinase K treatment. For sperm samples, 40 mM DTT were added during cell lysis.
RRBS for oocyte and PGC samples: For oocytes, before MspI digestion, 5 µl of lysis buffer (20 mM Tris-EDTA [pH 8.0], 20 mM KCl, and 0.3% Triton X-100, 1 mg/ml QIAGEN Protease) was directly added to the frozen samples (in < 1µl PBS) followed by 3 hours of incubation at 50 ℃ and 30 minutes of inactivation at 75 ℃. Then to the same tube, 13 µl of MspI digestion master mix containing 10 units of MspI (Thermo Scientific) and 1.8 µl 10x Buffer Tango (Thermo Scientific) and 0.5pg unmethylated λ DNA (Thermo Scientific) was added followed by 3 hours of incubation at 37 ℃. For PGCs, the purified genomic DNA was directly digested with MspI in an 18 µl total volume. The digested DNA was then filled-in and tailed with an extra A to the 3’ end by adding 2 µl of end-preparation master mix containing 5 units of Klenow Fragment (exo-; Thermo Scientific), 0.2 µl of 10x Buffer Tango, 0.4 mM dATP, and 0.04 mM each of dGTP and dCTP (Thermo Scientific), followed by 20 minutes of incubation at 30 ℃, 20 min of incubation at 37 ℃ and 15 minutes of inactivation at 80 ℃. Adaptor ligation was then performed by adding 5 µl of ligation master mix, which contains 30 Weiss Units of T4 DNA Ligase (HC, Thermo Scientific), 0.5 µl of 10x Buffer Tango, 5 mM ATP (Thermo Scientific), and 150 nM of methylated custom adaptor (Forward: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATC-s-T-3’, Reverse: 5’-/5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTC-3’, where -s- indicates phosphorothioate bond). After three incubation steps (16 ℃ for 30 min, 4 ℃ overnight, and 65 ℃ for 20 min), the reaction mix was subjected to EpiTect Bisulfite Conversion Kit (QIAGEN) with modified program: 95 C for 5 min, 60 C for 25 min, 95C for 5 min, 60C for 85 min, 95C for 5 min, 60C for 175 min, 3x (95 C for 5 min, 60 C for 90 min). After clean up, the optimal, minimum PCR cycle number required to generate the final libraries was determined using diagnostic PCRs. Remaining bisulfite converted products were PCR amplified with NEBNext Multiplex Oligos (NEB) and KAPA HiFi Hotstart Uracil+ ReadyMix (Kapa Biosystems). Final libraries were obtained by size selection of 150-500 bp DNA fragments using AMPure XP beads (Beckman Coulter).
RRBS for sperm: 100ng genomic DNA was digested with 10 units of MspI in a 18 µl total volume at 37 ℃ overnight. The digested DNA was then filled-in and tailed with an extra A to the 3’ end by adding 2 µl of end-preparation master mix containing 5 units of Klenow Fragment exo- , 0.2 µl of 10x Buffer Tango, 5 mM dATP, and 0.5 mM each of dGTP and dCTP, followed by 20 minutes of incubation at 30 ℃, 20min of incubation at 37 ℃ and 15 minutes of inactivation at 80 ℃. Adaptor ligation was then performed at 20 ℃ for 15min using NEBNext Ultra Ligation Module (NEB) by adding 15 µl of ligase master mix, 1 µl of ligation enhancer, 2.5 µl of 1.5 µM methylated custom adaptor and ddH2O to a total volume of 80 µl. The reaction mix was then size selected of 150-500 bp DNA fragments using AMPure XP beads. The size-selected sample was then subjected to EpiTect Bisulfite Conversion Kit (QIAGEN) with modified program: 95 C for 5 min, 60 C for 25 min, 95C for 5 min, 60C for 85 min, 95C for 5 min, 60C for 175 min, 3x (95 C for 5 min, 60 C for 90 min). After clean up, the optimal, minimum PCR cycle number required to generate the final libraries was determined using diagnostic PCRs. Remaining bisulfite converted products were PCR amplified with NEBNext Multiplex Oligos (NEB) and KAPA HiFi Hotstart Uracil+ ReadyMix (Kapa Biosystems). Final libraries were obtained by AMPure XP beads clean-up of the PCR product.
RNA-seq for oocyte samples: cDNA libraries were synthesized and amplified using SMARTer Ultra Low Input RNA Kit for Sequencing (Clontech) following manufacturer’s instructions. The purified cDNA was fragmented with Covaris M220 sonicator, and then subjected to Illumina sequencing library construction with KAPA Hyper Prep kits (Kapa Biosystems) following manufacturer’s instructions.

value: embryonic kidney cell line

value: mStella overexpressed

value: embryonic kidney

tag: developmental stage

value: fetus


title: Control1_37so

status: Public on Sep 25 2018

type: SRA

city: Madrid

first: Carlos

last: Torroja

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Bioinformatics Unit

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

description:
C1
pool of 2 embryos

library_source: transcriptomic

data_processing:
Samples were sequenced in an Illumina GAIIx sequencer
Base calls produced by Illumina pipeline version 1.13.48
Base calls were extracted using illumina2bam tool release 0.03 from Wellcome Trust Sanger Institute. Standard Phred Scale
Reads were pre-processed with Cutadapt 1.2.1, to remove TruSeq adaptor sequences.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build NCBIM37.v65) And quantified using RSEM v1.17
Only genes with at least 2 counts per million in at least 3 samples were considered for statistical analysis.
Data were normalized and differential expression tested using the Bioconductor package EdgeR. Note that the number of somites in each sample was used as blocking variable in the mixed linear model. We considered as differentially expressed those genes with a Benjamini-Hochberg adjusted p-value <0.05.
Genome_build: NCBIM37.v65
Supplementary_files_format_and_content: normalized_matrix_table.xlsx file contains ENSEMBL gene Ids, MGI gene names and normalized counts per million obtained using edgeR

molecule: polyA RNA

organism: Mus musculus

source_name: distal limb bud tips

growth_protocol: Pregant mice were generated crossing  HoxB6CreER/+;R26RMeis2a-IRES-EYFP/Meis2a-IRES-EYFP with R26RMeis2a-IRES-EYFP/Meis2a-IRES-EYFP.

extract_protocol:
The distal limb bud tips of somite-staged HoxB6CreER; R26Meis2a/Meis2a (experimental) or R26Meis2a/Meis2a (control) embryos were dissected and flash-frozen on liquid nitrogen (1 tube per embryo). For RNA extraction, we used the miRNAeasy kit from Qiagen, pooling the limb bud tips from 2 embryos per stage and genotype in order to obtain enough RNA.
Libraries were made using the standard TruSeq RNA Sample Preparation v2 Kit from Illumina

treatment_protocol: Pregnant mice were given 0.8mg of intraperioneal 4-hydroxy-tamoxifen at E8.3 days of gestation

tag: strain

tag: tissue

value: distal limb bud tips

tag: Stage

value: 37 somites


title: Control2_38so

description:
C2
pool of 2 embryos

value: 38 somites


title: Meis2Overexp2_38so

description:
E2
pool of 2 embryos


title: Meis2Overexp1_37so

description:
E1
pool of 2 embryos


title: ZCCHC4-polysome profiling-KO-Input-repl.2

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

country: USA

institute: University of Chicago

description: fragmented polyA RNA

data_processing:
Library strategy: Polysome Profiling
After removing adapters, reads were mapped to Human genome with tophat2. For ParCLIP, the data were analyzed by PARalyzer. For m6ASeq, the data were analyzed in the way descriped in Ma L's 2017 Genome Research paper(PMID:28052920). For  ploysome profiling data, cufflink were used to calculate the RPKM.
Genome_build: hg38
Supplementary_files_format_and_content: Excel, peaks, RPKM

organism: Homo sapiens

source_name: HepG2 ZCCHC4 knockout

extract_protocol: Illumina TruSeq Stranded mRNA Library Prep Kit

tag: cell line

value: HepG2 ZCCHC4 knockout

tag: genotype

value: ZCCHC4 knockout


title: 293-DMSO-RNA

molecule: total RNA

source_name: HEK-293 cells treated with DMSO

tag: cell type

tag: genotype/variation

value: WT


title: HUES8 repeat 2

city: Shenzhen

first: Changbin

last: Sun

address: Beishan Industrial Zone, Yantian District

institute: BGI

data_processing:
Basecalls performed using CASAVA v1.7
After adaptor sequence triming and low-quality filter, clean raw data mapping to human genome GRCh37/hg19 using HISAT2 with defualt parameters
Raw counts of sequencing reads for the feature of genes were extracted by featureCounts
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include gene Ensemble_id and counts values

growth_protocol: Cell plated onto Matrigel hESC-qualified Matrix (Corning)-coated dishes in mTeSR1 medium (Stemcell Technologies)

extract_protocol:
Cells were mixed with TRIzol (Invitrogen) and dissolved for 5 min, then spined at 12000g for 5 min at 4℃. Chloroform was added to the supernate and mixed equably, then spined at 12000g for 10 min at 4℃. Chloroform/isopropanol (24:1) were added to the supernate and spined at 12000g for 10 min at 4℃ again. The same volume of isopropanol was added to the supernate and stored at -20℃ for 1 hr, then spined at 13600g for 20 min at 4℃. Sediment was washed by 75% alcohol and spined at 13600g for 20 min at 4℃ twice and RNA was dissolved by Nucease-free water. The purity, integrity and density of RNA was detected by Nanodrop, Agarose gel electrophoresis and Agilent 2100 BioanaLyzer respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic stem cell

tag: passage

tag: gender

value: male


title: HUES1 repeat 2

value: female


title: HUES9 repeat 2


title: HUES8 repeat 1


title: HUES1 repeat 1


title: 293-5Aza-RNA

source_name: HEK-293 cells treated with 5-Aza-DC

value: 5-Aza-DC treated


title: Control3_39so

description:
C3
pool of 2 embryos

value: 39 somites


title: H7 repeat 2


title: ZCCHC4-PARCLIP-repl.1

description: small RNA fragments crosslinked with ZCCHC4 with 4SU

data_processing:
Library strategy: PARCLIP
After removing adapters, reads were mapped to Human genome with tophat2. For ParCLIP, the data were analyzed by PARalyzer. For m6ASeq, the data were analyzed in the way descriped in Ma L's 2017 Genome Research paper(PMID:28052920). For  ploysome profiling data, cufflink were used to calculate the RPKM.
Genome_build: hg38
Supplementary_files_format_and_content: Excel, peaks, RPKM

source_name: HeLa

extract_protocol: NEBNext® Multiplex Small RNA Library Prep Set for Illumina®

treatment_protocol: For PARCLIP treat the cell with 4SU at 100uM 24 hour

value: HeLa cells

value: N terminal Flag-HA tagged ZCCHC4 HeLa stable expression cell line


title: H7 repeat 1


title: D10-oocyte-Stella-Null-RNA

source_name: Dpp 10 oocytes from Stella-/- mouse

tag: strain background

value: primary cells isolated from mouse

value: growing oocyte

value: stella-/-

value: ovary

value: day 10 postpartum


title: D10-oocyte-Stella-Het-RNA

source_name: Dpp 10 oocytes from Stella+/- mouse

value: stella+/-


title: D5-oocyte-Stella-Het-RNA

source_name: Dpp 5 oocytes from Stella+/- mouse

value: day 5 postpartum


title: D20-oocyte-Stella-Null-RNA

source_name: Dpp 20 oocytes from Stella-/- mouse

value: day 20 postpartum


title: D20-oocyte-Stella-Het-RNA

source_name: Dpp 20 oocytes from Stella+/- mouse


title: D5-oocyte-Stella-Null-RNA

source_name: Dpp 5 oocytes from Stella-/- mouse


title: ZCCHC4-polysome profiling-KO-Input-repl.1

description: fragmented polyA RNA

value: HepG2 ZCCHC4 knockout

value: ZCCHC4 knockout


title: Sperm-Stella-Het-RRBS

library_source: genomic

molecule: genomic DNA

source_name: Sperm from Stella+/- mouse

value: sperm

value: epididymis

value: week 7 postpartum


title: D10-oocyte-Stella-Null-RRBS.rep2


title: HUES9 repeat 1

value: embryonic stem cell

value: female


title: D10-oocyte-Stella-Het-RRBS.rep2


title: D10-oocyte-Stella-Null-RRBS.rep1


title: MII-oocyte-Stella-Null-RRBS.rep2

source_name: MII oocytes from Stella-/- mouse

value: MII oocyte


title: E13.5-Male-PGC-Stella-Null-RRBS

source_name: E13.5 PGC from male Stella-/- mouse

value: PGC

value: embryo

value: embryonic 13.5


title: InputDNA_Control_dup2

city: Singapore

first: Lisa

last: Borghini

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

department: Infectious Diseases

country: Singapore

institute: GIS

data_processing:
mapping of the reads to hg19 with BWA
Filtering with samtools 1.2 (samtools view -bh -F 1804 -q 20)
Peak calling with Dfilter 1.5 (run_dfilter15.sh -d=ChIP.bam -c=Input.bam -o=H3K27ac-peaks -f=bam -ks=60 -bs=100 -lpval=1) and Irreproducibility Discovery Rate (IDR) method. IDR analysis was performed between the calls from each duplicates (in Control and LPS) and peaks with an IDR<0.05 were selected, coordinates of the final peaks were extracted from the IDR analysis output by taking the overlap of the coordinates from the 2 duplicates with Bedops –intersect command.
Black listed regions were removed found in wgEncodeDacMapabilityConsensusExcludable.bed (http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeMapability/) were removed from the final list of peaks using bedtools intersect command. Any peaks falling in chromosome Y was also filtered out as the cell line studied is derived from a female.
Genome_build: hg19
Supplementary_files_format_and_content: For each condition, the final reproducible peaks are given in a bed file.

source_name: pharyngeal epithelial cells

growth_protocol: Detroit 562 cells were purchased from ATCC and cultured in RPMI medium (Gibco) supplemented with 10% fetal bovine serum performance (Gibco), 100U/ml penicillin, 100ug/ml streptomycin (Gibco) and 1mM sodium pyruvate (Gibco).

extract_protocol:
After treatment, cells were crosslinked with 0.75% formaldehyde for 8 minutes and cross-linking was quenched with 180mM Glycine for 10 minutes at room temperature. Cells were then lysed with cell lysis buffer (0.25% Triton X-100, 10mM EDTA, 0.1M NaCl in 10mM Tris-HCl pH8) for 20 minutes at 4°C. Nuclei were collected by centrifugation at 4,000rpm for 10 minutes at 4°C and lysed in nuclei lysis buffer (1% NP-40, 0.5% NaDOC, 0.1% SDS in PBS) for 20 minutes at 4°C.  Chromatin shearing was performed using a sonicator (Bioruptor, Diagenode) on high setting for 45 cycles of 30 seconds ON/45 seconds OFF, leading to a fragment range of 100-250bp.
ChIP-seq libraries were built following the library-on-beads protocol from Wallerman et al. (Wallerman et al. 2015). Chromatin was incubated with anti-H3K27ac antibody (Active motif, reference 39138) bound to protein G magnetic beads (Dyanabeads protein G, Thermo Fisher scientific) prepared by mixing 5ug of antibody with 50uL of beads in PBS+0.5%BSA for 4 to 6 hours at room temperature. Immunoprecipitation was performed by rotation at 4°C overnight. After immunoprecipitation, samples were washed twice with nuclei lysis buffer, twice with nuclei lysis buffer complemented with 350mM NaCl, twice with LiCl/NP-40 buffer (0.25M LiCl, 1mM EDTA, 0.5% NP-40, 0.5% NaDOC in 10mM Tris-HCl pH8) and once with PBS. Libraries on beads were then built using NEBnext DNA library prep kit (New England Biolabs) according to the manufacturer’s instructions. Due to the nature of the samples, minor adjustments were done: two washes with PBS were performed in between each step of the preparation and elution of the DNA from the beads was done after adaptor ligation. ChIP samples were eluted in Elution buffer (10mM EDTA, 1% SDS in 50mM Tris-HCl pH7.5) for 4 hours at 65°C and purified with Agencourt AMPure XP beads (Beckman Coulter). PCR reaction was performed using Phusion High-Fidelity PCR Master Mix (Thermo scientific) and custom primers for multiplexing. The following program was applied: 3 minutes at 98°C; 17x(30 seconds at 98°C, 30 seconds at 65°C, 30 seconds at 72°C); 5 minutes at 72°C. Samples were loaded on a DNA1000 bioanalyzer chip (Agilent) to check the size of the libraries as well as the concentration. As a control, 2-5% of input DNA was reverse cross-linked at 65°C for minimum 6 hours and libraries were prepared using the same library preparation kit.  Samples were sequenced on an Illumina NextSeq 1x76bp.

treatment_protocol: Detroit 562 cells were treated with LPS at 1μg/mL for 80 minutes or with fresh medium (no treatment control).

value: Detroit 562 cells

tag: treatment

tag: duplicates

value: replicate 2

tag: antibody

value: input


title: InputDNA_LPS_dup2

value: LPS


title: E13.5-Male-PGC-Stella-Het-RRBS

source_name: E13.5 PGC from male Stella+/- mouse

value: primary cells isolated from mouse

value: stella+/-


title: MII-oocyte-Stella-Het-RRBS.rep2

source_name: MII oocytes from Stella+/- mouse

value: ovary


title: H3K27ac_LPS_dup1

value: replicate 1

value: anti-H3K27ac antibody (Active motif, reference 39138)


title: InputDNA_LPS_dup1


title: InputDNA_Control_dup1


title: H3K27ac-Control_dup2


title: 9G

status: Public on Sep 22 2018

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

data_processing:
Basecalls performed using Ion Torrent basecaller with parameters: -barcode-filter 0.01 -barcode-filter-minreads 10  -phasing-residual-filter=2.0 -num-unfiltered 1000 -barcode-filter-postpone 1
Reads were aligned to the hg19 genome assembly (hg19 AmpliSeq Transcriptome ERCC v1) with tmap (parameters: mapall stage1 map4)
Transcript abundances were calculated with Ion Torrent ampliSeqRNA plugin, version 5.0.4.0, target regions: hg19_AmpliSeq_Transcriptome_21K_v1
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files with RPM (reads per milion) calculated by Ion Torrent ampliSeqRNA plugin

source_name: colon tumor

extract_protocol:
Tissue (~10 mg) was immersed in 2 mL of hypotonic buffer A [10 mM HEPES (pH 7.9), 2 mM MgCl2, and 2 mM KCl] supplemented with protease and phosphatase inhibitors (Thermo, 78441) and 40 U/mL ribonuclease inhibitor (Invitrogen, 10777-019). RNA was extracted with standard Ion Torrent protocol. The RNA concentration was measured using a Nanodrop instrument.
RNA-sequencing library was prepared from 200 ng of total RNA using Ion Total RNA-seq Kit v2 (standard Ion Torrent protocol)

tag: resection location

value: colon


title: 9N

source_name: normal colon


title: 9W

source_name: liver metastasis

value: liver


title: Sperm-Stella-Null-RRBS

source_name: Sperm from Stella-/- mouse

value: sperm

value: stella-/-

value: epididymis

value: week 7 postpartum


title: 7W


title: 5W


title: 7G


title: 7N


title: 4W


title: 4N


title: H3K27ac-Control_dup1


title: 4G


title: 12W


title: 5N


title: H3K27ac_LPS_dup2


title: D10-oocyte-Stella-Het-RRBS.rep1

value: growing oocyte

value: day 10 postpartum


title: 12N


title: 10N


title: right mid kidney (right)

city: Leiden

first: Christiaan

last: Henkel

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: University Leiden

description: Common Carp Sample 45

data_processing:
Illumina software used for basecalling.
tophat 2.0.5
htsec count
Genome_build: ASM127010v1 [GenBank assembly accession: GCA_001270105.1 & WGS Project: LHQP01]
Supplementary_files_format_and_content: Tab-delimited .tsv file for each Sample lists gene identifiers and raw counts.  For the gene identifiers' sequences, refer to the .gff linked as a supplementary file on the Series record.  The contigs listed in the .gff can be found at GenBank: LHQP00000000.1 (associated with BioProject PRJNA73579).

organism: Cyprinus carpio

source_name: Kidney

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

value: Kidney


title: 10G


title: 049-sAD-1oPC-2

city: Los Angeles

first: Ruchi

last: Bajpai

state: CA

address: 2250 Alcazar St

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

data_processing:
Partek Flow used to process and analyze data
Bases trimmed from 3' end on quality score
Reads aligned using STAR, aligned to genome and transcriptome with default settings
Quantified to annotation model (Partek E/M)
Features filtered, excluded if geometric mean <= 1.0
Samples normalized to upper quartile
Genome_build: hg19
Supplementary_files_format_and_content: txt file with gene counts after processing

source_name: sAD human brain pericytes

growth_protocol: ESCs/iPSCs were differentiated into CNNCs via Bajpai, et al. 2010. After 10 days, spheres were washed off, NCCs were collected via accutase, and placed in pericyte media (ScienCell #1201) for 14 days

extract_protocol:
Cells were trypsinized, spun down, washed with PBS, and the cell pellet was resuspended in Trizol (ThermoFisher). RNA was isolated using chloroform, washed with isopropanol and 70% ethanol, and resuspended in RNAase-free water
KAPA Biosystems KAPA stranded mRNA-seq kit with KAPA mRNA capture beads

tag: source

value: human forebrain

value: forebrain pericytes

tag: Sex

value: male


title: 049-sAD-1oPC-1


title: iPSEN1*-cPC-1

source_name: fAD Cranial Pericytes

value: human induced pluripotent stem cells

value: female


title: iFF-NCC-2

source_name: Cranial Neural Crest Cells

value: cranial neural crest cells


title: iFF-cPC-2

source_name: Cranial Pericytes


title: H9-cPC

value: human embryonic stem cells


title: 1oPC-2

source_name: Human Brain Vascular Pericytes


title: iFF-cPC-1


title: III.7_asym

status: Public on Sep 21 2018

city: London

first: Jun

last: Wang

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute, Queen Mary, London

data_processing:
After FASTQ data quality check, raw reads were  aligned to the reference genome (GRCh37) using STAMPY. The number of reads uniquely aligned (q > 10)  to the exonic region of each gene was counted using HTSeq based on the Ensembl annotation.
Only genes  that achieved at least one count per million (CPM) reads in at least 2 samples (the number of samples  analyzed in each group) were included, leading to 17,555 filtered genes in total.
Read counts were further normalized using the conditional quantile normalization (CQN) method, accounting for gene length and GC  content. Differential expression (DE) analyses between GATA2 biallelic vs. monoallelic groups were  performed using the edgeR R package, employing the generalized linear model (GLM) approach.
The significantly DE genes were selected based on the false discovery rate (FDR) q-value of < 0.05 and the  absolute log2 fold change value of > 1. Gene set enrichment analysis (GSEA) was performed using the GSEA tool to identify canonical pathways gene sets acquired from the Molecular Signatures Database  (MSigDB-C2 v.5.0). Top significantly enriched gene sets were selected based on FDR q-value of <0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Raw reads count file for each sample generated by Htseq

source_name: Asymptomatic carrier

extract_protocol:
Total RNA was quantified and integrity measured using the  RNA 6000 nano assay kit on a 2100 BioAnalyzer (Agilent), where RIN > 9.5 was considered high quality RNA.
cDNA libraries were prepared using the TruSeq stranded mRNA library preparation kit (Illumina) according  to the manufacturers’ instructions and sequenced (300 cycles) on the Illumina HiSeq 4000 to generate  2x100bp paired-end sequencing reads by Oxford Genomics.

value: peripheral blood

tag: group

value: Asymptomatic

tag: molecular group

value: biallelic


title: IV.10_yr.4

source_name: symptomatic carrier

tag: tissue

value: symptomatic


title: iFF-NCC-1


title: IV.10_yr.1

value: monoallelic


title: BM_control

source_name: control

value: bone marrow

value: control


title: Pinot noir berry sample collected at time point 11 (replicate 1) over ripening season 2014

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

country: Italy

institute: University of Verona

data_processing:
The reads were aligned onto the grapevine 12x reference genome PN40024 using TopHat v2.0.6 with default parameters
Mapped reads were used to reconstruct the transcripts using Cufflinks v2.0.2 and the reference genome annotation V1
The normalized expression of each transcript was calculated as RPKM (Reads Per Kilobase per Million mapped reads) for each sample.
Genome_build: 12X reference genome PN400024
Supplementary_files_format_and_content: tab delimited text file containing the normalized reads counts RPKM  for all the samples.

organism: Vitis vinifera

source_name: grape berry pericarp

growth_protocol: Vineyard Features: Vitis vinifera cultivars Cabernet Sauvignon (clone FPS 8 grafted on 5C rootstock and planted in 1997) and Pinot noir (clone FPS 23 grafted on rootstock Freedom and planted in 2001) were used in this study. Both varieties were grown nearby Modesto (USA, CA) in sandy clay loam in an east-west orientation with 10 foot row spacing and 5 foot vine spacing.

extract_protocol:
Total RNA was isolated using the Spectrum Plant Total RNA kit (Sigma-Aldrich) following the manufacturer’s instructions with some modifications (Fasoli et al., 2012). RNA quality and quantity were determined using a Nanodrop 2000 spectrophotometer (Thermo Scientific) and a Bioanalyzer Chip RNA 7500 series II (Agilent).
220 non-directional cDNA libraries were prepared from 2.5 μg of total RNA using the Illumina TruSeq RNA Sample preparation protocol (Illumina Inc., San Diego, CA, USA). Library quality was determined using the Agilent High Sensitivity DNA kit on the Agilent 2100 bioanalyzer, and the quantity was determined by quantitative PCR using the KAPA Library Quantification kit (KapaBiosystems).

tag: year

tag: time point

tag: time point replicate

tag: day after veraison

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)

value: unthinned

tag: cultivar

value: Pinot noir


title: Pinot noir berry sample collected at time point 11 (replicate 3) over ripening season 2014


title: Pinot noir berry sample collected at time point 10 (replicate 3) over ripening season 2014


title: Pinot noir berry sample collected at time point 11 (replicate 2) over ripening season 2014


title: Pinot noir berry sample collected at time point 10 (replicate 1) over ripening season 2014


title: IV.10_yr.3


title: Pinot noir berry sample collected at time point 9 (replicate 3) over ripening season 2014


title: Pinot noir berry sample collected at time point 10 (replicate 2) over ripening season 2014


title: 10W

value: liver


title: Pinot noir berry sample collected at time point 9 (replicate 2) over ripening season 2014


title: Pinot noir berry sample collected at time point 9 (replicate 1) over ripening season 2014


title: Pinot noir berry sample collected at time point 8 (replicate 3) over ripening season 2014


title: iPSEN1*-cPC-2

tag: cell type


title: Pinot noir berry sample collected at time point 8 (replicate 1) over ripening season 2014


title: 12G

value: colon


title: 1oPC-1

value: human forebrain

value: forebrain pericytes


title: Pinot noir berry sample collected at time point 7 (replicate 2) over ripening season 2014


title: Pinot noir berry sample collected at time point 7 (replicate 3) over ripening season 2014


title: Pinot noir berry sample collected at time point 6 (replicate 3) over ripening season 2014


title: Pinot noir berry sample collected at time point 5 (replicate 3) over ripening season 2014


title: Pinot noir berry sample collected at time point 6 (replicate 2) over ripening season 2014


title: Pinot noir berry sample collected at time point 7 (replicate 1) over ripening season 2014


title: Pinot noir berry sample collected at time point 6 (replicate 1) over ripening season 2014


title: Pinot noir berry sample collected at time point 4 (replicate 2) over ripening season 2014


title: Pinot noir berry sample collected at time point 5 (replicate 2) over ripening season 2014


title: Pinot noir berry sample collected at time point 5 (replicate 1) over ripening season 2014


title: Pinot noir berry sample collected at time point 3 (replicate 3) over ripening season 2014


title: Pinot noir berry sample collected at time point 2 (replicate 3) over ripening season 2014


title: Pinot noir berry sample collected at time point 2 (replicate 1) over ripening season 2014


title: Pinot noir berry sample collected at time point 3 (replicate 1) over ripening season 2014


title: Pinot noir berry sample collected at time point 4 (replicate 1) over ripening season 2014


title: Pinot noir berry sample collected at time point 3 (replicate 2) over ripening season 2014


title: Pinot noir berry sample collected at time point 1 (replicate 2) over ripening season 2014


title: Pinot noir berry sample collected at time point 0 (replicate 3) over ripening season 2014


title: Pinot noir berry sample collected at time point 2 (replicate 2) over ripening season 2014


title: Pinot noir berry sample collected at time point 0 (replicate 1) over ripening season 2014


title: Pinot noir berry sample collected at time point 1 (replicate 3) over ripening season 2014


title: Pinot noir berry sample collected at time point 0 (replicate 2) over ripening season 2014


title: Pinot noir berry sample collected at time point 10 (replicate 3) over ripening season 2013


title: Pinot noir berry sample collected at time point 10 (replicate 2) over ripening season 2013


title: Pinot noir berry sample collected at time point 9 (replicate 3) over ripening season 2013


title: Pinot noir berry sample collected at time point 9 (replicate 2) over ripening season 2013


title: Pinot noir berry sample collected at time point 10 (replicate 1) over ripening season 2013


title: Pinot noir berry sample collected at time point 4 (replicate 3) over ripening season 2014


title: Pinot noir berry sample collected at time point 9 (replicate 1) over ripening season 2013


title: Pinot noir berry sample collected at time point 8 (replicate 2) over ripening season 2013


title: Pinot noir berry sample collected at time point 8 (replicate 2) over ripening season 2014


title: Pinot noir berry sample collected at time point 7 (replicate 3) over ripening season 2013


title: Pinot noir berry sample collected at time point 8 (replicate 1) over ripening season 2013


title: Pinot noir berry sample collected at time point 7 (replicate 1) over ripening season 2013


title: Pinot noir berry sample collected at time point 7 (replicate 2) over ripening season 2013


title: Pinot noir berry sample collected at time point 6 (replicate 1) over ripening season 2013


title: Pinot noir berry sample collected at time point 6 (replicate 3) over ripening season 2013


title: Pinot noir berry sample collected at time point 8 (replicate 3) over ripening season 2013


title: Pinot noir berry sample collected at time point 1 (replicate 1) over ripening season 2014


title: Pinot noir berry sample collected at time point 5 (replicate 1) over ripening season 2013


title: Pinot noir berry sample collected at time point 5 (replicate 2) over ripening season 2013


title: Pinot noir berry sample collected at time point 4 (replicate 1) over ripening season 2013


title: Pinot noir berry sample collected at time point 4 (replicate 3) over ripening season 2013


title: Pinot noir berry sample collected at time point 3 (replicate 1) over ripening season 2013


title: Pinot noir berry sample collected at time point 4 (replicate 2) over ripening season 2013


title: Pinot noir berry sample collected at time point 3 (replicate 2) over ripening season 2013


title: Pinot noir berry sample collected at time point 3 (replicate 3) over ripening season 2013


title: Pinot noir berry sample collected at time point 1 (replicate 3) over ripening season 2013


title: Pinot noir berry sample collected at time point 1 (replicate 2) over ripening season 2013


title: Pinot noir berry sample collected at time point 2 (replicate 3) over ripening season 2013


title: Pinot noir berry sample collected at time point 2 (replicate 1) over ripening season 2013


title: Pinot noir berry sample collected at time point 2 (replicate 2) over ripening season 2013


title: Pinot noir berry sample collected at time point 1 (replicate 1) over ripening season 2013


title: Pinot noir berry sample collected at time point 0 (replicate 3) over ripening season 2013


title: Pinot noir berry sample collected at time point 9 (replicate 2) over ripening season 2012


title: Pinot noir berry sample collected at time point 0 (replicate 2) over ripening season 2013


title: Pinot noir berry sample collected at time point 8 (replicate 2) over ripening season 2012


title: Pinot noir berry sample collected at time point 9 (replicate 3) over ripening season 2012


title: Pinot noir berry sample collected at time point 6 (replicate 2) over ripening season 2013


title: Pinot noir berry sample collected at time point 0 (replicate 1) over ripening season 2013


title: Pinot noir berry sample collected at time point 8 (replicate 1) over ripening season 2012


title: Pinot noir berry sample collected at time point 7 (replicate 2) over ripening season 2012


title: Pinot noir berry sample collected at time point 5 (replicate 3) over ripening season 2013


title: Pinot noir berry sample collected at time point 9 (replicate 1) over ripening season 2012


title: Pinot noir berry sample collected at time point 7 (replicate 1) over ripening season 2012


title: Pinot noir berry sample collected at time point 8 (replicate 3) over ripening season 2012


title: Pinot noir berry sample collected at time point 7 (replicate 3) over ripening season 2012


title: Pinot noir berry sample collected at time point 6 (replicate 3) over ripening season 2012


title: Pinot noir berry sample collected at time point 6 (replicate 2) over ripening season 2012


title: Pinot noir berry sample collected at time point 5 (replicate 1) over ripening season 2012


title: Pinot noir berry sample collected at time point 6 (replicate 1) over ripening season 2012


title: Pinot noir berry sample collected at time point 4 (replicate 2) over ripening season 2012


title: Pinot noir berry sample collected at time point 4 (replicate 3) over ripening season 2012


title: Pinot noir berry sample collected at time point 4 (replicate 1) over ripening season 2012


title: Pinot noir berry sample collected at time point 2 (replicate 3) over ripening season 2012


title: Pinot noir berry sample collected at time point 3 (replicate 1) over ripening season 2012


title: Pinot noir berry sample collected at time point 3 (replicate 3) over ripening season 2012


title: Pinot noir berry sample collected at time point 2 (replicate 1) over ripening season 2012


title: Pinot noir berry sample collected at time point 1 (replicate 3) over ripening season 2012


title: Pinot noir berry sample collected at time point 1 (replicate 2) over ripening season 2012


title: Pinot noir berry sample collected at time point 2 (replicate 2) over ripening season 2012


title: Pinot noir berry sample collected at time point 1 (replicate 1) over ripening season 2012


title: Pinot noir berry sample collected at time point 0 (replicate 1) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 12 (replicate 3) over ripening season 2014

value: Cabernet Sauvignon


title: Cabernet Sauvignon berry sample collected at time point 12 (replicate 2) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 11 (replicate 3) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 12 (replicate 1) over ripening season 2014


title: Pinot noir berry sample collected at time point 0 (replicate 2) over ripening season 2012


title: Pinot noir berry sample collected at time point 5 (replicate 3) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 11 (replicate 1) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 10 (replicate 2) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 11 (replicate 2) over ripening season 2014


title: Pinot noir berry sample collected at time point 5 (replicate 2) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 10 (replicate 3) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 9 (replicate 3) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 10 (replicate 1) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 8 (replicate 3) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 7 (replicate 3) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 9 (replicate 2) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 9 (replicate 1) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 8 (replicate 1) over ripening season 2014


title: Pinot noir berry sample collected at time point 3 (replicate 2) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 6 (replicate 3) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 6 (replicate 1) over ripening season 2014


title: Pinot noir berry sample collected at time point 0 (replicate 3) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 7 (replicate 1) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 5 (replicate 3) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 5 (replicate 2) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 4 (replicate 1) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 3 (replicate 3) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 5 (replicate 1) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 4 (replicate 2) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 4 (replicate 3) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 3 (replicate 1) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 2 (replicate 3) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 3 (replicate 2) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 2 (replicate 1) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 2 (replicate 2) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 1 (replicate 2) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 1 (replicate 3) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 8 (replicate 2) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 0 (replicate 3) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 1 (replicate 1) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 13 (replicate 3) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 0 (replicate 2) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 0 (replicate 1) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 6 (replicate 2) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 13 (replicate 2) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 12 (replicate 3) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 11 (replicate 1) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 11 (replicate 3) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 11 (replicate 2) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 10 (replicate 3) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 12 (replicate 1) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 10 (replicate 2) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 9 (replicate 3) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 9 (replicate 1) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 9 (replicate 2) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 10 (replicate 1) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 7 (replicate 3) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 8 (replicate 3) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 8 (replicate 2) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 8 (replicate 1) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 12 (replicate 2) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 7 (replicate 2) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 7 (replicate 1) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 6 (replicate 1) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 5 (replicate 3) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 6 (replicate 2) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 6 (replicate 3) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 13 (replicate 1) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 4 (replicate 1) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 5 (replicate 1) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 7 (replicate 2) over ripening season 2014


title: Cabernet Sauvignon berry sample collected at time point 4 (replicate 2) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 3 (replicate 3) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 4 (replicate 3) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 1 (replicate 3) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 3 (replicate 1) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 2 (replicate 2) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 3 (replicate 2) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 2 (replicate 1) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 2 (replicate 3) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 0 (replicate 2) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 1 (replicate 2) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 1 (replicate 1) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 0 (replicate 1) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 0 (replicate 3) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 12 (replicate 2) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 11 (replicate 3) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 5 (replicate 2) over ripening season 2013


title: Cabernet Sauvignon berry sample collected at time point 11 (replicate 2) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 11 (replicate 1) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 10 (replicate 3) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 10 (replicate 2) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 9 (replicate 3) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 9 (replicate 1) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 7 (replicate 2) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 8 (replicate 2) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 7 (replicate 3) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 8 (replicate 3) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 9 (replicate 2) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 8 (replicate 1) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 6 (replicate 1) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 6 (replicate 2) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 12 (replicate 3) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 6 (replicate 3) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 5 (replicate 1) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 5 (replicate 3) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 12 (replicate 1) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 5 (replicate 2) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 4 (replicate 3) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 3 (replicate 3) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 4 (replicate 2) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 4 (replicate 1) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 2 (replicate 3) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 10 (replicate 1) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 3 (replicate 2) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 2 (replicate 2) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 2 (replicate 1) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 0 (replicate 2) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 7 (replicate 1) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 0 (replicate 1) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 1 (replicate 1) over ripening season 2012


title: Cabernet Sauvignon berry sample collected at time point 0 (replicate 3) over ripening season 2012


title: DeltaTamCre DN3-4

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

data_processing:
FastQC version 0.10.0 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to identify features of the raw data that may indicate quality problems
The Tuxedo Suite was used to align reads to the reference transcriptome (UCSC mm10) (http://genome.ucsc.edu/) using TopHat (version 2.0.9) and Bowtie (version 2.1.0.0). Default parameter settings were used for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments, as well as “--no-coverage-search” and “--no-novel-juncs” to limit the read mapping to known transcripts.
FastQC was used for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis
Cufflinks/CuffDiff (version 2.1.1) was used for expression quantitation and differential expression analysis, using UCSC mm10.fa as the reference genome sequence and UCSC mm10.gtf as the reference transcriptome annotation. Thsi analysis used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values.
Locally developed scripts were used to format and annotate the differential expression data output from CuffDiff. Briefly, we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ 1.5. Genes and isoforms were annotated with NCBI Entrez GeneIDs, text description, and Gene Ontology (GO) (http://david.abcc.ncifcrf.gov/) terms using NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Table of raw reads counts in .txt format

source_name: Rosa26CreERT2Zmiz1f/f (DeltaTamCre)

growth_protocol: Dapi-CD44+CD25-Lineage- DN3 thymocytes were sorted with a BD AriaII from live mice directly into RLT-plus buffer (Qiagen)

extract_protocol:
Total RNA was extracted from 100K-400K DN3 cells using the RNeasy Plus Micro kit (Qiagen) according to the manufacturer’s protocol.
DeltaTamCre and TamCre sequencing libraries were prepped from 100 ng of total RNA using the Illumina TruSeq mRNA Sample Prep v2 kit (RS-122-2001, RS-122-2002) accrording to manufacturer's protocol by the University of Michigan Sequencing Core. DeltaMxCre, MxCre, Anti-NRR antibody, and Control IgG antibody sequencing libraries were prepped from 50 ng of total RNA using the Clontech SMARTer Ultra low input RNA kit (6348493) accrording to manufacturer's protocol by the University of Michigan Sequencing Core.

treatment_protocol: Rosa26CreERT2Zmiz1f/f (DeltaTamCre) mice and Rosa26CreERT2 (TamCre) control mice (4 mice per group) were injected with 0.2 mg/g tamoxifen IP. DN3 cells were sorted at 43-44 hours post-injection. MxCreZmiz1f/f mice and control MxCre mice (3 mice per group) were injected with 40 mcg pI-pC IP every 2 days for 5 times. DN3 cells were sorted at 8 weeks post-injection. Mice were injected with 10 mg/kg anti-NRR Notch1 antibody (Genentech) or the isotype control IgG antibody (Genentech) IP prior to sorting of DN3 cells at 24 hours post-injection.

tag: strain

value: DN3 thymocytes

tag: timing

value: 43-44 hours post tamoxifen injection


title: DeltaTamCre DN3-1


title: Cabernet Sauvignon berry sample collected at time point 1 (replicate 2) over ripening season 2012


title: TamCre DN3-3

source_name: Rosa26CreERT2 (TamCre)


title: TamCre DN3-2


title: DeltaTamCre DN3-2


title: TamCre DN3-4


title: TamCre DN3-1


title: Cabernet Sauvignon berry sample collected at time point 3 (replicate 1) over ripening season 2012


title: Control IgG antibody-treated DN3-3

source_name: Control IgG antibody-treated

value: 24 hours post antibody injection


title: Control IgG antibody-treated DN3-2


title: Anti-NRR antibody-treated DN3-2

source_name: Anti-NRR antibody-treated


title: Anti-NRR antibody-treated DN3-3


title: Anti-NRR antibody-treated DN3-1


title: DeltaMxCre DN3-2

value: 8 weeks post pI-pC injection


title: DeltaMxCre DN3-3


title: DeltaMxCre DN3-1


title: Cabernet Sauvignon berry sample collected at time point 1 (replicate 3) over ripening season 2012


title: MxCre DN3-3

source_name: MxCre


title: MxCre DN3-2


title: MxCre DN3-1


title: DeltaTamCre DN3-3


title: ActivatedBMPR_2

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

description:
Activ_BMPR_KO2
Processed data file: Samples_FPKM.csv

data_processing:
Alignment to mouse GRCm38 reference genome using TopHat2.
Transcript assembly with Cufflinks.
Identification of differentially expressed genes with Cuffdiff.
Genome_build: GRCm38
Supplementary_files_format_and_content: Samples_FPKM.csv: Comma-separated text file includes FPKM table.

source_name: Activated CD4+CD44+CD62L-Foxp3GFP- cells flow sorted from mixed lymph node and spleen cell populations isolated from BMPR1a/CD4cre conditional knockout mice expressing Foxp3GFP reporter transgene and activated with ConA in the presence of LPS for 3 days

extract_protocol:
Total RNA was extracted using Qiagen kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For naive cells, total lymph node and spleen cells were isolated and flow cytometry sorted as CD4+CD44-CD62+Foxp3GFP-. For activated cells, total lymph node and spleen cells were isolated, activated in vitro with ConA (2 ug/ml) in the presence of LPS (10 ng/ml) for 3 days and flow cytometry sorted as CD4+CD44+CD62-Foxp3GFP-.

tag: strain/background

tag: genotype/variation

value: CD4+ T cells

tag: age

value: 8-12 weeks

tag: treatment

value: ConA


title: ActivatedBMPR_1

description:
Activ_BMPR_KO1
Processed data file: Samples_FPKM.csv


title: ActivatedBMPR_3

description:
Activ_BMPR_KO3
Processed data file: Samples_FPKM.csv


title: ActivatedWT_3

description:
Activ_WT3
Processed data file: Samples_FPKM.csv

source_name: Activated CD4+CD44+CD62L-Foxp3GFP- cells flow sorted from mixed lymph node and spleen cell populations isolated from normal B6 mice expressing Foxp3GFP reporter transgene and activated with ConA in the presence of LPS for 3 days

value: wild type


title: ActivatedWT_1

description:
Activ_WT1
Processed data file: Samples_FPKM.csv


title: NaiveWT_3

description:
Naive_WT3
Processed data file: Samples_FPKM.csv

source_name: Naive CD4+CD44-CD62+Foxp3GFP- cells sorted from normal B6 mice expressing Foxp3GFP reporter transgene


title: NaiveWT_1

description:
Naive_WT1
Processed data file: Samples_FPKM.csv


title: HEPG2-SH3-a

status: Public on Sep 20 2018

city: New York City

first: Coen

last: van Solingen

state: New York

address: 435 E30th street, Science Building 723T, Science Building 723T

department: Cardiology/Medicine

institute: NYU School of Medicine

data_processing:
RNA-seq reads with aligned using the STAR, version 2.5, aligner against hg19 genome/transcriptome.
Gene counting was done using featureCounts , version 1.5.2, against hg19 annotations.
Raw counts were normalized and DE analysis was performed using DESeq2, version 3.4.
Genome_build: hg19
Supplementary_files_format_and_content: base mean data was calculated from reads of three replicate samples. Fold change was calculated as EV over shRNA. P-values were calculated on these data. Data was used in manuscript for bioinformatics sections (CDF analysis, IPA)

growth_protocol: HepG2 were cultivated in EMEM (Corning) with 10% non-heat inactivated FBS and 1% P/S.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) and Direct-zol RNA MiniPrep columns (Zymo Research).
Illumina TruSeq RNA sample preparation kit. HiSeq Paired-End 50 Cycle Lane (v4)

treatment_protocol: Short hairpin RNAs (shRNA) targeting all of the CHROME variants or a non-targeting control shRNA (EV) were cloned into the pLKO vector (Addgene, #8453) and transfected into HEK293T cells with packaging vectors psPAX2 (Addgene, #12260) and pMD2.G (Addgene, #12259). After 48 h, the culture media was isolated and used to transduce HepG2 cells.

tag: cell line

tag: shRNA

value: stable overexpression of shRNA against CHROME

value: human liver cancer cell


title: HEPG2-SH3-c


title: HEPG2-EV-a

value: stable overexpression of EV


title: HEPG2-EV-c


title: HEPG2-SH3-b


title: ActivatedWT_2

description:
Activ_WT2
Processed data file: Samples_FPKM.csv


title: HEPG2-EV-b


title: BB+PJ34+shMyocd

city: Boston

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

data_processing:
Quality control of raw data was performed by FASTQC
Cutadapt was used for raw data filter remove adaptor comtamination and low quality bases.
Tophat2 was used for data mapping,for each reads only 1 mismatch was accepted and only unique mapped was accepted for downstream analysis.
Cufflinks was used for transcript assemble and differential expression genes analysis.
DAVID was used for GO analysis.
Genome_build: Rat Rn6
Supplementary_files_format_and_content: FPKMs

organism: Rattus norvegicus

source_name: vascular smooth muscle cell

growth_protocol: VSMCs were got from rat aortas by enzyme digestion and cultured in DMEM media with 10% FBS. Passage 3 to passage 6 were used for expriments

extract_protocol:
RNA was harvested using Trizol reagent. Illumina  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: VSMCs were incubated with PDGF-BB at the concentration of 20ng/ul for 48 hours. PJ34 works at 10mM. And Myocardin was knockdowned by Ad-shMyocd.

value: Aortic smooth muscle cell

tag: passage

value: SD

value: Myocardin knockdown


title: NaiveWT_2

description:
Naive_WT2
Processed data file: Samples_FPKM.csv


title: Control IgG antibody-treated DN3-1


title: BB+PJ34+ScrshRNA

value: control


title: BB

value: BB


title: BB+PJ34_sample4


title: PKD1_KO_rep4

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

data_processing:
Base calling was done with Illumina's FASTQ Generation software v1.0.0 and overall sequencing quality was determined with FastQC
Reads (FASTQ files) were mapped to whole genome mm9 using Bowtie2 with default settings.
Reads per gene were counted using the countOverlaps function from the R package {GenomicRanges}.
Weakly expressed genes were removed and differentially expressed genes were called using EdgeR.
Genome_build: mm9
Supplementary_files_format_and_content: A differential expression file (csv format) containing Ensembl gene ID, gene symbol, gene description, log2FC, p-value and q-value (FDR) for the comparisons of all genes. A matrix file (csv format) containing Ensembl gene ID, gene symbol, gene description and raw read counts for all genes of all samples.

source_name: subcutaneous adipose tissue

extract_protocol:
Tissue samples were extracted and frozen on dry ice. Total RNA was isolated using RNeasy mini columns (Qiagen) including on-column DNase I digestion.
mRNA was extracted using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB). Library preparation was performed with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the instruction manual. Size-selection of libraries was performed using Agencourt AMPure XP Beads (Beckman Coulter) followed by amplification with 12 PCR cycles. Afterwards libraries were quantified and the size was determinded using Experion Automated Electrophoresis System (Bio-Rad).

tag: genotype

value: Pkd1adipo delta/delta

tag: mouse id

tag: tissue

value: subcutaneous adipose tissue

value: C57BL/6J (back-crossed 4x)


title: PKD1_KO_rep3


title: BB+PJ34


title: PKD1_WT_rep3


title: PKD1_KO_rep1


title: PKD1_WT_rep4


title: PKD1_WT_rep2


title: PKD1_WT_rep1


title: PMG-IFN-α-3

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

description: treated with IFN-α (100 U/ml) for 4 hrs

data_processing:
Illumina CASAVA v1.8.2 software was used for base calling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
Quality controlled FASTQ files were alignment to Mus musculus UCSC mm10 reference genome sequence using the STAR (version 2.5.1) aligner software. To measure differential gene expression, DESeq2 was used.
The number of reads mapped to gene ID features were counted using STAR.
Genome_build: Mus musculus UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

source_name: Post-natal Mouse Primary Microglia

growth_protocol: PM were isolated from 3-day-old ICR mice. Whole brains of neonatal mice were digested using a Neural Tissue Dissociation Kit-Postnatal Neurons (Miltenyi Biotec, Germany, 130-094-802). Next, the digested cells were seeded in L-lysine coated T-75 flasks in DMEM/nutrient 122 mixture F-12 (DMEM/F12, 1:1) containing 20% FBS (catalog # 26140; Gibco, Waltham, MA), 100 IU/ml penicillin and 10 μg/ml streptomycin (catalog # 15140) obtained from Invitrogen (Waltham, MA). The cells were maintained in a humidified incubator with a 95% air/5% CO2 atmosphere at 37°C. The medium was changed every 2-3 days. After two weeks in culture, the mixed glial cell cultures were shaken at 110 rpm at 37°C for 55 min, and the glial cell suspensions were collected from each flask.

extract_protocol:
RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. For RNA-Seq, RNA libraries were created from each group using the NEBNext® Ultra™ Directional RNA Library preparation kit from Illumina® (Illumina, San Diego, CA, USA). The first step in the workflow involved the removal of ribosomal RNA using the RNAMius™ Transcriptome Isolation kit (Life Technologies, Carlsbad, CA, USA).  Following purification, total RNA was fragmented into small pieces using divalent cations at elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments were then processed through an end-repair reaction by the addition of a single ‘A’ base, followed by ligation of the adapters. The products of these reactions were then purified and enriched by PCR to create the final cDNA library. The cDNA fragments were sequenced using the Illumina HiSeq2000 (101 cycles PE lane)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PM cells were plated in a humidified incubator with 95% air and a 5% CO2 atmosphere at 37°C for 24h before stimulation. The cells were treated with 1 μM R848 (Resiquimod), 100U/ml IFN-α  and their combination for 4hrs under normal culture conditions. The cells were stimulated after diluting the stock solution to the mentioned concentration in DMEM for experiments. R848 were purchased from Invivogen Inc., San Diego, CA. and pure (>95%) recombinant mouse IFN-α (Cat#12100-1) with activity >1X107 U/ml used extensively for research were purchased from PBL Assay Science, 131 Ethel Road West, Suite 6 Piscataway, NJ 08854 USA.

value: ICR

value: primary microglia cells

tag: agent

value: IFN-alpha (100 U/ml)


title: PMG-R848+IFN-α-2

description: treated with R848 (1µM)+IFN-α (100 U/ml) for 4 hrs

value: R848 (1micorM)+IFN-alpha (100 U/ml)


title: PMG-R848+IFN-α-3


title: PMG-R848+IFN-α-1


title: PMG-IFN-α-1

description: treated with IFN-α (100 U/ml) for 4 hrs


title: PMG-IFN-α-2

description: treated with IFN-α (100 U/ml) for 4 hrs


title: PMG-R848-3

description: treated with R848 (1µM) for 4 hrs

value: R848 (1microM)


title: PMG-R848-1

description: treated with R848 (1µM) for 4 hrs


title: PMG-R848-2

description: treated with R848 (1µM) for 4 hrs


title: control


title: id23ExpHi En HiPro LCM

city: Aas

first: Hilde

middle: Kristine Lyby

last: Wærp

address: Arboretveien 6

department: Animal and Aquacultural Sciences

country: Norway

institute: Norwegian University of Life Sciences

data_processing:
Adapter trimming: Cutadapt v1.3, as given in manual for trimming Illumina Truseq adapters
Filtering: Cutadapt v1.3 (settings: -q 25 -m 20)
RNAseq reads were aligned to UMD3.1 genome using Tophat 2.0.12 (settings: --library-type fr-unstranded)
Sorting: Samtools v1.19 (settings: -n)
Counting: HTSEQ-count (settings: -r name -f bam --stranded=no)
Genome_build: UMD3.1.78
Supplementary_files_format_and_content: Tab delimited txt files; First row contains the ENSEMBL gene IDs and second row the raw number of reads that map to each gene

organism: Bos taurus

source_name: Subcutaneous Adipose tissue

extract_protocol: Total RNA was extracted from frozen adipose tissue by homogenisation in Trizol and extraction with Qiagen RNeasy lipid tissue mini kits. RNA was then DNAse treated and purified using Turbo DNA-free (Ambion, Life technologies). Standard Illumina paired-end read mRNA-seq libraries were constructed from cDNA which was made from the purified mRNA using Illumina Truseq RNA sample prep kit v2.

treatment_protocol: To obtain different growth profiles during rearing, 24 heifers were fed experimental diets differing in energy (Hi/Lo) and protein content (HiPro/LoPro) from 3 mo of age until confirmed successful breeding at 400 kg BW. Thereafter, all heifers were jointly allowed ad libitum access to a low-energy feed during pregnancy. Subcutaneous adipose tissue samples were harvested at 12 mo of age and at 7 months of pregnancy.

tag: time point

value: Exp

value: Subcutaneous Adipose tissue

tag: dietary energy level

value: Hi

tag: dietary protein level

value: HiPro

tag: pedigree

value: LCM


title: id24ExpHi En LoPro LCM

value: LoPro


title: id22PregLo En LoPro LCM

value: Preg

value: Lo


title: id21PregLo En HiPro LCM


title: id24PregHi En LoPro LCM


title: id20ExpHi En LoPro HMY

value: HMY


title: id22ExpLo En LoPro LCM


title: PKD1_KO_rep2

value: Pkd1adipo delta/delta

tag: strain


title: id23PregHi En HiPro LCM


title: id21ExpLo En HiPro LCM


title: id19ExpHi En HiPro HMY


title: id18PregLo En LoPro HMY


title: id16PregHi En LoPro LCM


title: id16ExpHi En LoPro LCM


title: id17ExpLo En HiPro HMY


title: id17PregLo En HiPro HMY


title: id15ExpHi En HiPro LCM


title: id18ExpLo En LoPro HMY


title: id13ExpLo En HiPro LCM


title: id14ExpLo En LoPro LCM


title: id12ExpHi En LoPro HMY


title: id14PregLo En LoPro LCM


title: id15PregHi En HiPro LCM


title: id13PregLo En HiPro LCM


title: id20PregHi En LoPro HMY


title: 11_Het

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

data_processing:
Aligned to mm10 using STAR spliced read aligner
Count read using HT-seq and using mm10 RefSeq as reference
Normalization (TMM), quantitation (FPKM) and differential expression analysis using edgeR and limma voom.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values

extract_protocol:
Total RNA was extracted using RNeazy kit (Qiagen)accordance with the prescribed protocol provided with the kit.
Libraries prepared using the Ovation RNA-seq system v2 kit (NuGen) and sequenced on an Illumina HiSeq4000 sequencer

tag: strain background

value: Het; TREM2+/-

value: 3-5 months

tag: gender

value: F

value: microglia


title: 12_KO

tag: genotype/variation

value: KO; TREM2-/-

value: M


title: id19PregHi En HiPro HMY


title: 09_KO

tag: age


title: id10PregLo En LoPro HMY


title: id10ExpLo En LoPro HMY


title: 08_Het


title: 07_WT

value: WT; TREM2+/+


title: id11ExpHi En HiPro HMY

value: Exp


title: 05_Het


title: id12PregHi En LoPro HMY

value: Subcutaneous Adipose tissue


title: 01_WT


title: id11PregHi En HiPro HMY

value: Hi


title: id7PregLo En HiPro LCM

value: HiPro


title: id6ExpHi En HiPro LCM

value: LCM


title: id7ExpLo En HiPro LCM


title: id8ExpLo En LoPro LCM

value: LoPro


title: id8PregLo En LoPro LCM

value: Preg


title: id6PregHi En HiPro LCM


title: 10_WT


title: id5ExpHi En LoPro LCM


title: 06_KO


title: id4ExpLo En LoPro HMY

value: Lo


title: id5PregHi En LoPro LCM


title: id4PregLo En LoPro HMY

value: HMY


title: id2ExpHi En HiPro HMY


title: 04_WT


title: id3PregHi En LoPro HMY


title: id9ExpLo En HiPro HMY


title: id1ExpLo En HiPro HMY


title: id2PregHi En HiPro HMY


title: id3ExpHi En LoPro HMY


title: id9PregLo En HiPro HMY


title: id1PregLo En HiPro HMY


title: SP_VIS_1

status: Public on Sep 18 2018

city: Charlottesville

first: Christopher

last: Overall

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

data_processing:
Base calling an quality scoring performed by real-Time Analysis (RTA) v2.
Raw FASTQ sequencing reads were chastity filtered to remove clusters having outlying intensity corresponding to bases other than the called base.
Filtered reads were assessed for quality using FastQC.
Reads were splice-aware aligned to the UCSC mm9 genome using STAR.
Reads overlapping Gencode mm9 gene regions were counted using HTSeq.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with the raw counts.

source_name: FACS sorted activated 2D2 T cells

growth_protocol: C57BL/6J mice were maintained in vivarium conditions

extract_protocol:
RNA was extracted using Arcturus PicoPure kit (Thermo Fisher)
Ovation SoLo RNA-Seq System (Nugen) for initial RNA amplification. After purification, the cDNA was fragemented and further library steps performed.

treatment_protocol: PBS: mice were injected with PBS in the cisterna magna then photoconverted with a nonthermal red laser. VIS: mice were injection with Visudyne into the cisterna magna then photoconverted with a nonthermal red laser.

value: spleen

tag: treatment

value: meningeal lymphatic ablation

value: 10 week

value: Wild type


title: SP_VIS_2


title: SP_PBS_3

value: PBS


title: DC_VIS_3

value: dCLN


title: HSV-1

status: Public on Sep 19 2018

first: Michaela

middle: U

last: Gack

address: 920 E 58th St

department: Microbiology

institute: The University of Chicago

description: Sample 3

data_processing:
Raw read quality trimming with TRIM Galore
Tophat2 alignment to hg38
htseq-count  and subsequent TC normalisation in R
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files includes transcript abundance and gene name

source_name: HSV-1, HEK 293T

growth_protocol: HEK 293T cells were routinely grown in DMEM supplemented with 10% FCS and Penicillin/Streptomycin

extract_protocol: For samples 1-3, total RNA was purified from whole cell lysates by phenol-chloroform extraction.

treatment_protocol: For sample 2, HEK 293T cells were transfected with a plasmid encoding human DUX4 (pmkg-DUX4) using Lipofectamine. For sample 3, HEK 293T cells were infected with wild-type HSV-1  (MOI 10, KOS strain)

tag: cell line

value: human embryonic kidney cell line HEK 293T

value: infected with wt HSV1KOS for 18h (MOI = 10)


title: SP_PBS_1


title: SP_VIS_3


title: mock

description: Sample 1

source_name: mock, HEK 293T

value: mock treated


title: DC_PBS_3


title: DUX4

description: Sample 2

source_name: DUX4, HEK 293T

value: transfected with pmkg-DUX4


title: DC_PBS_2


title: SP_PBS_2


title: DC_PBS_1


title: Skin_3

source_name: FACS sorted LEC

extract_protocol:
RNA was extracted using Arcturus PicoPure kit (Thermo Fisher)
Ovation RNA-Seq System V2 kit (Nugen) for initial RNA amplification. After purification, the cDNA was fragemented and further library steps performed.

treatment_protocol: no treatment

value: Skin


title: Skin_2


title: Skin_1


title: DC_VIS_1


title: Meninges_3

value: Meninges


title: Meninges_1


title: Diaphragm_3

value: Diaphragm


title: Diaphragm_1


title: DC_VIS_2


title: RCH-ACV dasatinib resistant clone 2 [SCGPM_160503_B_C8F37_CTTGTA]

city: Stanford

first: Jesus

last: Duque-Afonso

address: 265 Campus Drive

department: Pathology

institute: Stanford University

description:
Cells culture in the presence of increasing concentrations of dasatinib (maximal 1 μM)
RNAseq.clone2.result.in dasatinib-resistant_for_GEO.txt

data_processing:
RNA sequences were aligned and analyzed in the web-based platform DNA nexus using following software tools (version): bedtools (2.19.0), bwa-aln (0.6.2-r126), bwa-mem (0.7.7-r441), fastqc (0.10.1), Picard Tools (1.107(1667)), samtools (0.1.19-44428cd).
Differential gene expression analysis was performed by DESeq2 in R platform
Genome_build: hg19
Supplementary_files_format_and_content: tab limited text represents differential gene expression analysis from two independent generated sublines performed by DESeq2 in R platform

source_name: Cell lines

growth_protocol: RPM1 1640 Medium supplemented with 10% fetal bovine serum und 1 % Penicilin/Streptomicin/Glutamine

extract_protocol:
RNeasy Mini kit (QIAGEN)
Truseq stranded mRNA kit (Illumina).

treatment_protocol: Vehicle vs Dasatinib

tag: subline

value: dasatinib-resistant RCH-ACV

tag: replicate


title: RCH-ACV dasatinib sensitive clone 2 [SCGPM_160503_B_C8F37_CGATGT]

description:
Cells culture in the presence of vehicle (0.1 % DMSO)
RNAseq.clone2.result.in dasatinib-resistant_for_GEO.txt

value: dasatinib-sensitive RCH-ACV

value: vehicle (0.1 % DMSO)


title: RCH-ACV dasatinib resistant clone 2 [SCGPM_160503_B_C8F37_CCGTCC]

value: increasing concentrations of dasatinib (maximal 1 μM)


title: RCH-ACV dasatinib sensitive clone 2 [SCGPM_160503_B_C8F37_ACAGTG]


title: RCH-ACV dasatinib sensitive clone 2 [SCGPM_160503_B_C8F37_GCCAAT]


title: RCH-ACV dasatinib sensitive clone 1 [SCGPM_160503_A_C8F37_TGACCA]

description:
Cells culture in the presence of vehicle (0.1 % DMSO)
RNAseq.clone1.result.in dasatinib-resistant_for_GEO.txt


title: RCH-ACV dasatinib resistant clone 1 [SCGPM_160503_A_C8F37_CTTGTA]

description:
Cells culture in the presence of increasing concentrations of dasatinib (maximal 1 μM)
RNAseq.clone1.result.in dasatinib-resistant_for_GEO.txt


title: RCH-ACV dasatinib sensitive clone 1 [SCGPM_160503_A_C8F37_CGATGT]


title: RCH-ACV dasatinib resistant clone 1 [SCGPM_160503_A_C8F37_CAGATC]


title: LT_rep

city: GUANGZHOU

first: HONG

last: ZHU

state: GUANGDONG

address: 723 XINGKE RD.TIANHE DISDRICT

institute: SOUTH CHINA BOTANICAL GARDEN,CHINESE ACADEMY OF SCIENCES

description: small RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
sRNA raw reads were preprocessed using Illumina Genome Analyzer Pipeline. After that, all the clean reads were mapped to miRBase 21 (http://www.mirbase.org/), allowing up to two mismatches, to identify known miRNAs in banana.
remaining sRNAs were subjected to the novel miRNA identification. Read mapping was conducted using Bowtie (Langmead et al. 2009), and Vienna RNA package (Hofacker 2003) was used for the secondary structure prediction of sRNAs.
Cleaveland pipeline 3.0 was optimized to analyze the degradome data in collaboration with Targetfinder 1.6. The alignment score threshold was set to 4. The banana gene set and the annotation of miRNA target genes were retrieved from The Banana Genome Hub.
Genome_build: Musa acuminata DH-Pahang v1, banana-genome.cirad.fr
Supplementary_files_format_and_content: tab-delimited text files include miRNA IDs, sequences, normalized abundance measurements and raw counts for each sample; zhD1.txt file contains information about miRNA target identification, including target name, corresponding miRNA name, align score, cleavage_site, category, p-value, etc.

organism: Musa acuminata AAA Group

source_name: fruit

extract_protocol:
Total RNA from different samples was extracted using the Plant RNA Purification Reagent (Invitrogen, Grand Island, NY, USA).
Small RNA libraries and a mixed degradome library were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Three storage temperatures were set in this study: CK at 23°C, cold stress temperature at 6°C and heat stress temperature at 35°C. For each temperature treatment, 120 fruit fingers were selected, packed in 0.025-mm-thick polyethylene bags, and divided into three groups of ten fingers each as biological replicates. Peel samples from CK, cold- and heat-stressed fruit were collected on the 5th day of storage, when the typical injury symptoms appeared.

value: peel

tag: stress treatment

value: cold stress treatment


title: CK_rep

description: small RNA

value: control


title: RCH-ACV dasatinib resistant clone 2 [SCGPM_160503_B_C8F37_CAGATC]


title: Diaphragm_2

value: 10 week

tag: genotype

value: Wild type


title: degradome

description: cleaved mRNA

data_processing:
Library strategy: degradome-Seq
Illumina Casava1.7 software used for basecalling.
sRNA raw reads were preprocessed using Illumina Genome Analyzer Pipeline. After that, all the clean reads were mapped to miRBase 21 (http://www.mirbase.org/), allowing up to two mismatches, to identify known miRNAs in banana.
remaining sRNAs were subjected to the novel miRNA identification. Read mapping was conducted using Bowtie (Langmead et al. 2009), and Vienna RNA package (Hofacker 2003) was used for the secondary structure prediction of sRNAs.
Cleaveland pipeline 3.0 was optimized to analyze the degradome data in collaboration with Targetfinder 1.6. The alignment score threshold was set to 4. The banana gene set and the annotation of miRNA target genes were retrieved from The Banana Genome Hub.
Genome_build: Musa acuminata DH-Pahang v1, banana-genome.cirad.fr
Supplementary_files_format_and_content: tab-delimited text files include miRNA IDs, sequences, normalized abundance measurements and raw counts for each sample; zhD1.txt file contains information about miRNA target identification, including target name, corresponding miRNA name, align score, cleavage_site, category, p-value, etc.

tag: tissue

value: mixed samples


title: RCH-ACV dasatinib sensitive clone 1 [SCGPM_160503_A_C8F37_GCCAAT]

tag: agent


title: HT

description: small RNA

value: heat stress treatment


title: HT_rep

description: small RNA


title: FVB_DDC_Heavy_Polysome_2

status: Public on Sep 17 2018

city: Urbana

first: Sushant

last: Bangru

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: University of Illinois, Urbana-Champaign

description:
HP_DDC_1
C_HP_AGCGATAG-AGGCTATA

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Adaptors were trimmed from the reads using trimmomatic
Reads were mapped to the genome using STAR_2.4.2a
Insert distrubution calculated with Picard_1.119
TPM values were calculated for all samples from Cuffnorm derived FPKM estimates for all transcripts
Gene Ontology was determined using DAVID_6.8
Genome_build: GRCm38 vM10 mm10 (mus musculus)
Supplementary_files_format_and_content: consists of TPM values calculated for all genes from mm10 in all 16 samples

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols for “TruSeq Stranded mRNAseq Sample Prep kit”

value: FVB

tag: mouse group

value: DDC-fed

tag: cell type

value: hepatocytes

tag: rna isolated from

value: Heavy polysomes (>5)


title: FVB_CHOW_Heavy_Polysome_2

description:
HP_CH_1
CH3_CH4_Heavy_Polysomes_CGGCTATG-GTCAGTAC

value: normal (CHOW)-fed


title: FVB_CHOW_Heavy_Polysome_1

description:
HP_CH_0
CH1_CH2_Heavy_Polysomes_ATTCAGAA-TCAGAGCC


title: Meninges_2

value: Meninges


title: CK

description: small RNA


title: FVB_DDC_Light_Polysome_2

description:
LP_DDC_1
C_LP_TCTCGCGC-GCCTCTAT

value: Light polysome (2-4 ribosomes)


title: FVB_DDC_Light_Polysome_1

description:
LP_DDC_0
B_LP_CTGAAGCT-TAAGATTA


title: FVB_DDC_Heavy_Polysome_1

description:
HP_DDC_0
B_HP_TAATGCGC-CTTCGCCT


title: FVB_CHOW_Light_Polysome_2

description:
LP_CH_1
CH3_CH4_light_Polysomes_TAATGCGC-ACGTCCTG


title: FVB_DDC_Monosome_2

description:
80S_DDC_1
C_M_TCCGCGAA-AGGATAGG

value: Monosome (1 ribosome)


title: FVB_CHOW_Light_Polysome_1

description:
LP_CH_0
CH1_CH2_Light_polysomes_GAGATTCC-AGGATAGG


title: RCH-ACV dasatinib resistant clone 1 [SCGPM_160503_A_C8F37_CCGTCC]

value: dasatinib-resistant RCH-ACV


title: LT

description: small RNA


title: FVB_DDC_Monosome_1

description:
80S_DDC_0
B_M_GAATTCGT-ACGTCCTG


title: FVB_CHOW_Monosome_2

description:
80S_CH_1
CH3_CH4_Monosome_CTGAAGCT-TAAGATTA


title: FVB_CHOW_Cytoplasmic_2

description:
Cyp_CH_1
CH3_Cytoplasmic_GAATTCGT-CTTCGCCT

value: cytoplamic


title: FVB_DDC_Cytoplasmic_2

description:
Cyp_DDC_1
DDC_D2_CGGCTATG-TCAGAGCC


title: FVB_CHOW_Monosome_1

description:
80S_CH_0
CH1_CH2_Monosome_CGCTCATT-GCCTCTAT


title: FVB_CHOW_Cytoplasmic_1

description:
Cyp_CH_0
CH1_Cytoplasmic_TCCGGAGA-AGGCTATA


title: FVB_DDC_Cytoplasmic_1

description:
Cyp_DDC_0
DDC_C2_ATTCAGAA-GTCAGTAC


title: FVB_E18_1

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Adaptors were trimmed from the reads using trimmomatic
Reads were mapped to the genome using STAR_2.4.2a
Insert distrubution calculated with Picard_1.119
TPM values generated from counts obtaind from HTseq and DESeq2
FPKM values were generated and compared between sets of samples using CuffDiff_2.2.1
Gene Ontology was determined using DAVID_6.8
Genome_build: GRCm38 vM10 mm10 (mus musculus)
Supplementary_files_format_and_content: consists of TPM values calculated for all genes from mm10 in all 6 samples

source_name: Mouse hepatocytes

tag: sample type


title: FVB_DDC_Adult_2

tag: strain

value: DDC fed


title: FVB_E18_2


title: FVB_CHOW_Adult_1

value: normal fed


title: infected1

city: Berlin

first: Frithjof

last: Glowinski

state: Berlin

address: Chariteplatz 1

department: Molecular Biology

institute: MPI for Infection Biology

data_processing:
Base calling was performed using the Illumina GA Pipeline v1.5
Reads were mapped using Tophat 2.0.4 “tophat -r 300 --mate-std-dev 200 --library-type fr-unstranded --b2-very-sensitive” and additional junctions identified by PaSSion “passion.pl -s 300 -T 6”. GRCh37.68 was used as reference genome.
Expression was analyzed using Cufflinks 2.0.2 (--no-effective-length-correction)
In addition exon expression was analyzed using DEXSeq 1.12.2
Junction usage was analyzed using MATS 3.0.7
Genome_build: hg19 [GRCh37.68]
Supplementary_files_format_and_content: Expression tables for Cufflinks and DEXSeq and MATS results summary

source_name: AGS cells

growth_protocol: AGS cells were grown in RPMI medium + 10 % FCS. Before infection cells were serum starved for 12 h.

extract_protocol:
Infected cells were harvested in Trizol; RNA was isolated by chloroform and isopropanol extraction. Isolated RNA was further purified using a silica-based membrane (ThermoFisher GeneJet RNA purification).
poly(A) mRNA was isolated using oligo(dT) beads. mRNA was fragmented using fragmentation buffer. Fragments were random hexamer primed to synthesize the first-strand cDNA. After removal of dNTPs the second-strand cDNA was synthesized using dATP, dGTP, dCTP, dUTP, Rnase H and DNA polymerase I.Short fragments were column purified and processed for end-repair and poly(a) addition. Sequencing adapters were added and the second-strand was digested using Uracil-N-Glycosylase.Fragments were size-selected selected on an agarose gel and amplified by PCR. The library was sequenced using an Illumina HiSeq 2000.

treatment_protocol: H. pylori P12 wt was grown on BHI plates ans suspended in PBS for infection. Infection was performed at MOI 100

value: AGS

tag: infection

value: Helicobacter pylori P12 wt


title: infected3


title: non-infected1

treatment_protocol: H. pylori P12 wt was grown on BHI plates and suspended in PBS for infection. Infection was performed at MOI 100 for 2,5 h.


title: infected2


title: non-infected3


title: rtcB 1 MMC

city: Athens

first: Anna

last: Karls

state: GA

address: 120 Cedar St

institute: Univeristy of Georgia

description: processed data file:rtcB-vs-rtcB+MMC, WT+MMC-vs-rtcB+MMC

data_processing:
Reads were mapped to the Salmonella enterica subspecies enterica serovar Typhimurium strain 14028S genome (assembly:  GCA_000022165.1) with bowtie2 using defalt parameters.
Cuffnorm was used to obtain FPKM scores for each biological replicate and Pearson correlations were calculated between all biological replicates.  Any replicate resulting in a correlation <0.9 was excluded from further analysis.
WT+MMC bio rep 1, rtcR untreated bio rep 3, rtcR+MMC bio rep 1, and rsr+MMC bio rep 2 were excluded based on correlations.
Cuffdiff was used to make pairwise comparisons between strains and treatment conditions.
Genome_build: GCA_000022165.1
Supplementary_files_format_and_content: xlsx = Cuffdiff output file gene_exp.diff converted to tab delimited txt file, converted to xslx

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: rtcB treated with MMC 60 min

growth_protocol: All cultures were grown at 37degC with aeration.  Overnight cultures of each strain growin in MOPS minimal media were diluted 1:40 in fresh MOPS media and grown to mid-log (OD600 = 0.4).

extract_protocol:
Cells were pelleted and RNA was harvested using the RNAsnap method (Stead et al., 2012).  Samples were DNase-treated with DNaseI (NEB) and rRNA was removed via the RiboZero kit for gram negative bacteria.
RNA libraries were prepared for sequencing using standard Illumina protocols for the Illumina TruSeq RNA Sample Prep Kit and SuperScript III reverse transcriptase.

treatment_protocol: The cultures were split into two and mitomycin C was added to one of each to a final concentration of 1 ug/mL.  All cultures were returned to the shaker to grow for 60 minutes.

value: rtcB


title: non-infected2


title: rtcB 3 MMC


title: rtcB 2 MMC


title: rtcB 3

description: processed data file:rtcB-vs-rtcB+MMC,  WT-vs-rtcB

source_name: rtcB mutant not treated with MMC


title: rtcB 2


title: rtcB 1


title: rsr 1 MMC

description: processed data file:rsr-vs-rsr+MMC, WT+MMC-vs-rsr+MMC

source_name: rsr mutant treated with MMC 60 min

value: rsr


title: rsr 2 MMC

description: processed data file: none. Data excluded due to correlation


title: rsr 3

description: processed data file:rsr-vs-rsr+MMC, WT-vs-rsr

source_name: rsr mutant not treated with MMC


title: rsr 2


title: rsr 1


title: FVB_DDC_Adult_1


title: rtcR 1 MMC

source_name: rtcR mutant treated with MMC 60 min

value: rtcR


title: rtcR 2 MMC

description: processed data file:rtcR-vs-rtcR+MMC, WT+MMC-vs-rtcR+MMC


title: rtcR 2

description: processed data file:rtcR-vs-rtcR+MMC, WT-vs-rtcR

source_name: rtcR mutant not treated with MMC


title: rtcR 3


title: rtcR 1


title: WT 2 MMC

description: processed data file:WT-vs-WT+MMC, WT+MMC-vs-rtcR+MMC, WT+MMC-vs-rsr+MMC, WT+MMC-vs-rtcB+MMC

source_name: WT treated with MMC 60 min

value: wildtype


title: WT 3 MMC


title: WT 1 MMC


title: WT 3

description: processed data file:WT-vs-WT+MMC, WT-vs-rtcR, WT-vs-rsr, WT-vs-rtcB

source_name: WT not treated with MMC


title: WT 2


title: WT 1


title: CXCR5lowPD1lowTomaN_r2 GB0053

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Basecalls performed using CASAVA 2.18
Sequence reads were mapped to mouse genome (mm9) by using bowtie 2 with default settings (PMID: 22388286 ). Reads mapped to multiple positions (MAPQ < 10) were discarded. In the DHS analysis, only one read for genomic site with multiple alignment hits were retained.
SICER v1.1 was used to call peaks (window size is 200bp, gap size is 400bp, bp-shift is 75, E-value = 1 and others by defaults) (PMID: 19505939).
The mRNA expression level of a gene is quantified by RPKM (reads per kilo-base of exon model per million reads; PMID 18516045) with in-house script. Differentially expressed genes were identified by edgeR 3 (PMID 22287627 ) with the following criteria: FDR (false discovery rate) < 0.01, FC (fold change) log2≥ 1, and RPKM≥5.
Genome_build: mm9
Supplementary_files_format_and_content: *rpkm: zipped text file for gene expression. Columns from left to right denote RefSeq ID, RPKM, gene transcript size, number of read mapped to exons, a combination of RefSeq ID, gene symbol, etc, and reserved column for future development.
Supplementary_files_format_and_content: *.scoreisland: zipped peak file recoding peak call from SICER. Columns from left to right denote: chrom, start, end, score.

source_name: non-Tfh cells

extract_protocol:
For RNA-Seq: the total RNAs were purified using Qiagen's miRNeasy micro kit (Qiagen cat# 217084) plus Qiagen’s DNase set (Qiagen cat# 79254) for on-column DNase digestion option. PolyA-tailed RNAs were purified from pure total RNA using Dynabeads® mRNA DIRECT™ Kit (ambion life technologies cat# 61012). DNase-Seq followed the protocols described previously in (PMID: 26605532).
Library constructions RNA-Seq and Dnase-Seq follow the protocols described previously in (PMID: 19528076) and (PMID: 26605532)

value: T-bet-Cre-Rosa26-loxP-STOP-loxP-tdTomato mice on C57BL/6 background

value: draining LN

tag: condition


title: CXCR5highPD1highTomaN_r2 GB0051

source_name: Tfh cells


title: CXCR5lowPD1lowTomaP_r2 GB0052


title: rsr 3 MMC


title: CXCR5highPD1highTomaP_r1 GB0046


title: CXCR5lowPD1lowTomaP_r2 GB1643


title: CXCR5lowPD1lowTomaP_r1 GB0048


title: CXCR5highPD1highTomaN_r1 GB0047


title: CXCR5highPD1highTomaP_r2 GB0050


title: CXCR5lowPD1lowTomaN_r1 GB0049


title: rtcR 3 MMC


title: CXCR5highPD1highTomaN_r2 GB1642


title: CXCR5lowPD1lowTomaN_r2 GB1644


title: CXCR5highPD1highTomaP_r2 GB1641


title: CXCR5lowPD1lowTomaN_r1 GB1640


title: CXCR5lowPD1lowTomaP_r1 GB1639


title: CXCR5highPD1highTomaN_r1 GB1638


title: CXCR5highPD1highTomaP_r1 GB1637


title: tdTomatoP_T-bet-ZsGreenP_r2 GB4624

source_name: CD4+CD44highCD25- T cells

value: T-bet-ZsGreen-T2A-CreERT2 (ZTCE)-Rosa26-loxP-STOP-loxP-tdTomato (ZTCE-tdTomato) mice on C57BL/6 background

value: Spleen

value: tdTomato+ T-bet-ZsGreen+


title: tdTomatoP_T-bet-ZsGreenP_r1 GB4621


title: tdTomatoP_T-bet-ZsGreenN_r2 GB4623

value: tdTomato+ T-bet-ZsGreen-


title: tdTomatoP_T-bet-ZsGreenN_r1 GB4620


title: hPBMC_C_mAb3

city: Nantes

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

description: mAb: mAb3

data_processing:
Data was separated by barcode and aligned using Tophat version 2.0.10 (Kim et al. 2013) with default settings.
Transcripts were quantified by the Broad Technology Labs computational pipeline using Cuffquant version 2.2.1 (Trapnell et al. 2012).
Data were processed through CuffNorm if 50% of the reads aligned and if at least 100,000 pairs were aligned per sample. Normalization used the default settings, including “geometric” normalization, and expression level information as FPKM (Fragments per kilobase of transcript per million mapped fragments) are provided.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including FPKM for each sample

source_name: PBMC

extract_protocol:
RNA were extracted with RNA mini extraction kit according to manufacturer’s instructions (Qiagen). The quality and quantity of RNA were controlled by infrared spectrometry (Nanodrop) and Agilent bioanalyzer to obtain RNA integrity numbers (Agilent RNA 6000 Pico Kit)
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform according to the SmartSeq2 protocol (Picelli et al, 2013, 2014) with some modifications (Trombetta et al, 2014). Briefly, total RNA was purified using RNA-SPRI beads, polyA mRNA was converted to cDNA and amplified cDNA was subject to transposon-based fragmentation that used dual-indexing to barcode each fragment of each converted transcript with a combination of barcodes specific to each sample. Sequencing was carried out as paired-end 2x25bp with an additional 8 cycles for each index.

treatment_protocol: Freshly isolated human PBMC were incubated 30 min at 37°C with 10µg/ml of anti-human IL7Rα mAbs, and then cultured alone or with 5 ng/ml of recombinant human IL7 (AbDSerotec) for 3 hours at 37°C. Reaction was stopped on ice, pellets were resuspended in RL-T buffer (Qiagen) containing 1% of β mercaptoethanol in RNase/DNase free condition and stored at -80°C before RNA extraction

value: PBMC

tag: volunteer

value: C

tag: il7 treatment

value: Unstim

tag: mab incubation

value: IgG1 #2 (IL-7Rα site-1)

tag: rin


title: hPBMC_E_mAb3

description: mAb: mAb3

value: E


title: hPBMC_D_mAb3

description: mAb: mAb3

value: D


title: hPBMC_B__mAb3

description: mAb: mAb3

value: B


title: hPBMC_A_mAb3

description: mAb: mAb3

value: A


title: hPBMC_F_mAb2

description: mAb: mAb2

value: F

value: IgG4 #1 (IL-7Rα site-1)


title: hPBMC_G_mAb2

description: mAb: mAb2

value: G


title: hPBMC_E_mAb2

description: mAb: mAb2


title: hPBMC_B__mAb2

description: mAb: mAb2


title: hPBMC_G_mAb3

description: mAb: mAb3


title: hPBMC_C_mAb2

description: mAb: mAb2


title: hPBMC_A_mAb2

description: mAb: mAb2


title: TKO RNAP II

city: Jerusalem

first: Joshua

last: Moss

address: Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly.
Reads were counted over 25 bp bins.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph

source_name: TKO cells

extract_protocol:
Immunoprecipitated DNA was extracted with phenol-chloroform, ethanol-precipitated and treated with RNase.
ChIP-Seq was carried out using antibodies against RNA PolymeraseII or H3K4me3, as previously described (Goren et. al. (2010))

tag: antibodies

value: RNAP II

value: TKO cells


title: TKO H3K4me3


title: hPBMC_G_mAb1

first: Richard

description: mAb: mAb1

value: IgG4 (IL-7Rα site-1&2b)


title: J1 H3K4me3

source_name: J1 cells

value: J1 cells


title: ICM H3K4me3

source_name: ICM

value: ICM


title: J1 RNAP II


title: hPBMC_F_mAb3

description: mAb: mAb3


title: hPBMC_F_mAb1

description: mAb: mAb1


title: J1 WCE


title: hPBMC_E_mAb1

description: mAb: mAb1


title: hPBMC_B__mAb1

description: mAb: mAb1


title: hPBMC_A_mAb1

description: mAb: mAb1


title: hPBMC_C_mAb1

description: mAb: mAb1


title: hPBMC_D_mAb1

description: mAb: mAb1


title: hPBMC_G_mAb3_7

description: mAb: mAb3


title: FVB_CHOW_Adult_2

source_name: Mouse hepatocytes

value: FVB

value: normal fed


title: hPBMC_C_mAb3_7

description: mAb: mAb3

value: PBMC

value: C


title: hPBMC_D_mAb3_7

description: mAb: mAb3

value: IgG1 #2 (IL-7Rα site-1)


title: hPBMC_D_mAb2

description: mAb: mAb2

value: Unstim


title: hPBMC_A_mAb3_7

description: mAb: mAb3


title: hPBMC_E_mAb3_7

description: mAb: mAb3

value: E


title: hPBMC_F_mAb3_7

description: mAb: mAb3


title: TKO WCE


title: hPBMC_F_mAb2_7

description: mAb: mAb2


title: hPBMC_B__mAb3_7

description: mAb: mAb3

value: B


title: hPBMC_D_mAb2_7

description: mAb: mAb2

value: D


title: hPBMC_G_mAb2_7

description: mAb: mAb2


title: hPBMC_E_mAb2_7

description: mAb: mAb2


title: hPBMC_D_mAb1_7

description: mAb: mAb1


title: hPBMC_C_mAb1_7

description: mAb: mAb1


title: hPBMC_A_mAb2_7

description: mAb: mAb2

value: A


title: hPBMC_F_mAb1_7

description: mAb: mAb1

value: F


title: hPBMC_G_mAb1_7

description: mAb: mAb1

value: G


title: hPBMC_B__mAb2_7

description: mAb: mAb2

value: IgG4 #1 (IL-7Rα site-1)


title: hPBMC_G_NS

description: mAb: NULL


title: hPBMC_B__mAb1_7

description: mAb: mAb1


title: hPBMC_E_mAb1_7

description: mAb: mAb1


title: hPBMC_D_NS

description: mAb: NULL


title: hPBMC_F_NS

description: mAb: NULL


title: hPBMC_A_mAb1_7

description: mAb: mAb1


title: hPBMC_B__NS

description: mAb: NULL


title: TE5-shsox2-1_RNA-seq

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

institute: Cancer Science Institute

data_processing:
Raw fastq files were pseudoaligned to Ensemble version 82 transcripts using Kallisto (vn: 0.43.0)
Kallisto output files were later summarized into gene level abundance and counts using tximport Bioconductor package followed by DESeq2 to perform differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: abundance.tsv output from kallisto containing abundance in TPM and estimated fragment counts for all Ensemble 82 transcripts.

growth_protocol: cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted by using RNeasy Kit (Qiagen).
Standard Illumina protocol

tag: cell line

value: Esophageal squamous carcinoma cells

tag: genotype/variation

value: ShRNA mediated SOX2 knock down


title: hPBMC_A_A_NS

description: mAb: NULL


title: hPBMC_F_7

description: mAb: NULL


title: TE5-shCCAT1-2_RNA-seq

value: ShRNA mediated CCAT1 knock down


title: hPBMC_C_mAb2_7

description: mAb: mAb2


title: hPBMC_E_7

description: mAb: NULL


title: hPBMC_D_7

description: mAb: NULL


title: KYSE140-shp63-ma_RNA-seq

value: ShRNA mediated TP63 knock down


title: hPBMC_C_NS

description: mAb: NULL


title: KYSE140-shsox2-1_RNA-seq


title: KYSE140-scramble_RNA-seq

value: Non-targetting scramble sh RNA


title: TE5-scramble_RNA-seq


title: hPBMC_B__7

description: mAb: NULL