title: D3_siControl_1


title: D2_siLINC00941_2

status: Public on Jan 28 2019

type: SRA

city: Regensburg

first: Christian

last: Ziegler

address: Universitaetsstrasse 31

country: Germany

institute: University Regensburg

description:
biological replicate 2
processed data file: D2_CountTable_LINC00941KD.txt

library_source: transcriptomic

data_processing:
(I) Preprocessing: Quality of sequencing data from the RNA-Seq libraries was examined using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and size, adapter and quality trimming was performed using Trimmomatic (ver. 0.32, ILLUMINACLIP:TruSeq_s tranded_SE.fa:2:30:10 HEADCROP:0 TRAILING:26 LEADING:26 SLIDINGWINDOW:4:15 MINLEN:25). Trimmed reads were aligned to the Homo sapiens genome (ftp://ftp.ensembl.org/pub/release-85/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz) combined with ERCC sequence information using STAR. The mapped reads were then assessed on the gene level using featureCounts from the Rsubread R-library based on annotation information from ensemble (GRCh38.p7 release-85). Following alignment, further quality control was performed using QoRTs.
(II) Differential expression analysis: Count data at the gene level was analyzed with DESeq2 using ERCC spike-ins for library size normalization. All treatment comparisons were performed and corrected for multiple testing using FDR. Genes that met the indicated log2(fold change) restraint and a false discovery rate <0.05 (“padj”) were considered significant differentially expressed.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files for the individual days contain a matrix table of counts per gene with respect to the corresponding samples. Data is formatted as csv.

molecule: polyA RNA

organism: Homo sapiens

source_name: Organotypic human epidermis

growth_protocol: Pooled primary human keratinocytes from different donors were obtained from PromoCell (Lot.No.: 1020401, 1040101 and 407Z001) or Lonza (Lot.No.:0000402834) and grown in a 1:1 mixture of KSF-M (Gibco) and Medium 154 for keratinocytes (Gibco), supplemented with Human Keratinocyte Growth Supplement, epidermal growth factor, bovine pituitary extract and 1x Antibiotic-Antimycotic (all supplements from Gibco). Cells were cultured at 37 °C in a humidified chamber with 5% CO2. For the generation of organotypic human epidermal tissue, 500,000 human keratinocytes that have been nucleofected with siRNAs were seeded onto a devitalized dermal matrix and raised to the air–liquid interface to initiate stratification and differentiation, as described by Truong et al. (2006, Genes Dev) and Sen et al. (2010, Nature).

extract_protocol:
RNA from the obtained organotypic epidermis was extracted with the QIAGEN RNeasy Plus Mini Kit according to the manufacturer's instructions.
Library preparation and mRNA sequencing were carried out according to the Illumina TruSeq Stranded mRNA Sample Preparation Guide, the Illumina HiSeq 1000 System User Guide (Illumina), and the KAPA Library Quantification Kit - Illumina/ABI Prism User Guide (Kapa Biosystems), with minor modifications. In brief, mRNA molecules were purified using oligo-dT probes immobilized on magnetic beads starting with 250 ng of total RNA supplied with ERCC spike-Ins. Chemical fragmentation of the mRNA to an average insert size of 200-400 bases was performed using divalent cations under elevated temperature (94°C, 4 minutes). First strand cDNA was produced by reverse transcription with random primers. Actinomycin D was added to improve strand specificity by preventing spurious DNA-dependent synthesis. Blunt-ended second strand cDNA was synthesized using DNA Polymerase I, RNase H and dUTP nucleotides. The resulting cDNA fragments were adenylated at the 3' ends, the indexing adapters were ligated and subsequently specific cDNA libraries were created by PCR enrichment. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit. Equimolar amounts of each library were used for cluster generation on the cBot (TruSeq SR Cluster Kit v3). The sequencing run was performed on a HiSeq 1000 instrument using the indexed, 1x50 cycles single end protocol and TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide. Image analysis and base calling resulted in .bcl files, which were converted into .fastq files by the CASAVA1.8.2 software.

treatment_protocol: Nucleofection with siRNA targeting the gene of interest or a non-targeting control

tag: tissue

value: Organotypic human epidermis

tag: treatment

value: siPool for efficient knockdown of LINC00942

tag: day of differentiation

value: day 2

tag: cell type

value: pooled primary human keratinocytes


title: D2_siControl_2

value: Control siPool


title: D3_siCtrl_3

description:
biological replicate 3
processed data file: counts_D3_SPRR5KD.txt

value: day 3


title: D2_siControl_1

description:
biological replicate 1
processed data file: D2_CountTable_LINC00941KD.txt


title: Neuron_SAD1.1

status: Public on Jan 29 2019

type: RNA

city: Boston

first: Derek

last: Drake

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Harvard Medical School

description: Gene expression data from SAD1.1 neurons

hyb_protocol: Hybridizations were performed in the Genechip hybridization oven 640 (60 rpm) for 16 hrs at 45ºC on U133 Plus 2.0 arrays. The probe arrays were then washed, stained in the GeneChip Fluidics Station 400 operated by GeneChip software following the appropriate fluidics protocols.

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

data_processing: The scanned digital intensity values were stored as image data files (*.dat) and then converted into cell intensity files (*.cel) using Affymetrix Microarray Suite 5.0.

label: biotin

molecule: total RNA

source_name: neurons, sporadic Alzheimer's disease

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

growth_protocol: Neurons were grown for 6 weeks on polyornithine and laminin in medium containing Neurobasal medium with 1x B-27, 1 mM L-glutamine, 50 U/ml penicillin, and 50 mg/ml streptomycin.

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

treatment_protocol: Cells were directly harvested.

value: neurons

tag: subject

tag: diagnosis

value: sporadic Alzheimer's disease

tag: clone

value: Clone 1

tag: coriell #


title: CKO1-plus-IL-4

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE annotation (p7) using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using HTSeq v0.6.1 using intersect-strict option
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

organism: Mus musculus

source_name: Bone marrow-derived macrophages

extract_protocol: RNA Libraries are prepared using the Illumina NextSeq RNA Exome protocol and kit reagents.

tag: genotype

value: CKO


title: WT2-plus-IL-4

value: WT


title: CKO2-plus-gamma

value: gamma


title: CKO1-unt

value: unt


title: WT2-plus-gamma


title: CKO2-unt


title: WT1-unt


title: WT2-unt


title: CKO2-plus-IL-4


title: CKO1-plus-gamma


title: NHK: Normal keratinocytes RNA-seq

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drive, CCSR 2145c

department: Dermatology

institute: Stanford University

data_processing:
Sequencing reads were mapped to hg19 using TopHat. FPKM values were called using cufflinks.
Genome_build: hg19

source_name: keratinocyte from normal human skin tissue

growth_protocol: Normal keratinocytes were cultured in Defined Keratinocyte Serum Free Medium (DKSFM, Life Technologies).

extract_protocol:
RNA extraction was performed using RNeasy Plus (Qiagen) from the samples reported in this research. Ribosomal RNA was removed from each RNA extraction using Ribo-Zero Gold rRNA Removal kit (Illumina).
The RNA-seq libraries were constructed by TruSeq Stranded mRNA Library Prep kit (Illumina).

value: Normal keratinocytes


title: C643-spl-rev_RP_3

city: Zurich

first: Gunnar

last: Rätsch

state: -None-

address: Universitatstrasse 6

department: Institute for Machine Learning

country: Switzerland

institute: ETH Zürich

description: biomart_silva_human_rRNA.fasta (rRNA reference)

data_processing:
For ribosome profiling reads linker sequences (5′-CTGTAGGCACCATCAAT-3′) were removed using Trimmomatic v0.32 with the following parameters: number of mismatches between read and adapter: 2; length of alignment between read and adapter: 6.
For ribosome profiling reads clipped reads were then filtered to be a minimum length of 25.
Reads with unique molecular identifiers (5’-NNNNTGANNNNCC-3’) were removed from the sequence and inserted into the read name using UMI tools v2.1.1
Ribosome profiling reads and RNA-Seq reads were aligned using STAR v2.5
To remove possible rRNA contamination, both the ribosome profiling and RNA-Seq reads were aligned to ribosomal sequences gathered from BioMart Ensembl and SILVA databases and merged into a single FASTA reference file. Reads that aligned to the reference file were then filtered from the original alignments.
To estimate abundance on the aligned BAM files, a custom script was used with gencode annotation version 19 and additional ERCC spike-in sequences (ERCC92). For RNA-Seq samples with spike-ins, the library size normalization factor was estimated using DESeq2 v3.6
Genome_build: Hg19
Supplementary_files_format_and_content: Tab-delimited files with raw counts per sample.

growth_protocol: Cell lines were maintained at 37°C and 5% CO 2  in humidified atmosphere and were grown in RPMI-1640.

extract_protocol:
Ribosome-protected RNA extraction was performed following the published protocol by Ingolia NT et al., Nature Protocols, 2012. and for RNA-seq, total RNA was extracted using Trizol.
Ribosome Footprint library construction was performed following the protocol by Ingolia NT et al., Nature Protocols, 2012; with a modification of including unique molecular identifiers (UMI) in the Reverse transcription primer in order to remove PCR duplicates. 5′-(Phos)-GGNNNNTCANNNN- AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC-(SpC18)-CACTCA- (SpC18)- TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG-3′

tag: mrna type

value: ribosome protected mRNA

tag: splice status

value: Splice Reversed

tag: cell line


title: WT1-plus-gamma


title: C643_RP_3

value: WT-splice


title: C643-spl-rev_RP_1


title: WT1-plus-IL-4


title: C643_RP_2


title: CAL62_splice_RNA_3

value: mRNA

value: Splice Induced


title: CAL62_splice_RNA_2


title: CAL62_splice_RNA_1


title: C643-spl-rev_RP_2


title: Treated_10uM_RetinoicAcid_femoral_head_cartilage_rep2_batch2

city: Melbourne

first: Katrina

middle: M

last: Bell

state: Victoria

address: RCH, Flemington Rd, Parkville

country: Australia

institute: MCRI

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was analyzed using limma package from bioconductor (neqc function, non-detected probes removed, factor for batch for 2 sets of arrays, block for biological reps in linear Model).

source_name: femoral head cartilage

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

growth_protocol: 21-day-old mouse hips (4 per well) were cultured in DMEM + 10% FBS for 24hrs prior to treatment.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Hips were treated with 10ng/ml IL-1-alpha or Retinoic acid at 10uM for 3 days. Treatments were done in triplicate.

tag: strain/background

value: Gertrude

value: femoral head cartilage

tag: agent

value: 10uM_Retinoic Acid


title: CAL62_RNA_1

value: WT no splice


title: C643_RP_1


title: CAL62_RNA_2


title: C643-spl-rev_RNA_3


title: CAL62_RNA_3


title: Untreated_femoral_head_cartilage_rep2_batch1

value: Donut


title: C643-spl-rev_RNA_2


title: C643-spl-rev_RNA_1


title: Treated_10ng/ml_IL-1 Alpha_rep1_batch2


title: C643_RNA_3


title: Treated_10uM_RetinoicAcid_femoral_head_cartilage_rep2_batch1


title: Treated_10ng/ml_IL-1 Alpha_rep1_batch1


title: Treated_10uM_RetinoicAcid_femoral_head_cartilage_rep1_batch2


title: Untreated_femoral_head_cartilage_rep1_batch1


title: C643_RNA_1


title: Treated_10ng/ml_IL-1 Alpha_rep2_batch1


title: Treated_10uM_RetinoicAcid_femoral_head_cartilage_rep1_batch1


title: Treated_10ng/ml_IL-1 Alpha_rep2_batch2


title: swn rep2

city: London

first: YUHAI

last: CUI

state: ON

address: 1391 Sandford Street

department: London Research and Development Centre

country: Canada

institute: Agriculture and Agri-Food Canada

data_processing:
ChIP-seq reads were aligned to the TAIR10 genome assembly using Bowtie2
Mapped reads were filted by removing PCR duplications and unmapped reads
unique mapped reads were converted to bed file by bedtools2
BigWig file for each replicates was genearted using MACS2 with 100 bp extended reads
Reads were mapped to genome using TopHat v2.0.4 with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 4000 bp were used. Calculations to identify differentially expressed genes were carried out as described (Trapnell et al., 2012)
Genome_build: TAIR10
Supplementary_files_format_and_content: WIG, bigwig, txt

organism: Arabidopsis thaliana

source_name: swn

growth_protocol: Arabidopsis seedlings were growth on 1/2 MS plates for 10 days under 16h light/ 8h dark condition, the somatic embyos were  growth on 1/2 MS plates for 30 days under 16h light/ 8h dark condition.

extract_protocol:
10-day-old seedlings were  frozen with liquid nitrogen. Total RNA was isolated from   ̴50 mg of in vitro-grown seedlings using the RNeasy Plant Mini kit (Qiagen) according to supplier’s instructions. Total RNA was treated with RNase-free DNaseI kit (Life Techologies).
Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol
1 ug of total RNA for the construction of sequencing libraries.

value: seedlings

tag: developmental

value: 10 days

tag: antibody


title: clf rep3

source_name: clf


title: clf rep2


title: wt rep3

source_name: wt

value: Col-0 (wild type)


city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_IP32953WT-day14-rep5

hyb_protocol: All cRNAs were hybridized to a custom Affymetrix GeneChip

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with Expression console using Affymetrix default analysis with a scale filter for Yersinia genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1250.

organism: Yersinia pseudotuberculosis

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

growth_protocol: For in vitro samples, bacteria were grown from frozen stock in LB medium supplemented with 100 mM MOPS, pH 7.4 at 21°C without aeration to late log phase and subcultured (1:500) thrice in fresh LB/MOPS.  The in vivo bacterial samples were collected from digestive tracts of infected Xenopsylla cheopis fleas (35).  Fleas were dissected 1 day or 14-15 days after infection in a drop of RNAprotect on a glass microscope slide and the digestive tracts removed

extract_protocol: Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).  RNA was isolated from six independent in vitro samples and from four or six independent in vivo samples collected one day or 2 weeks after infection, respectively

tag: culture

value: in-vivo


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_IP32953WT-day14-rep4


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_IP32953WT-day1-rep5


title: C643_RNA_2


title: Untreated_femoral_head_cartilage_rep1_batch2

tag: tissue


title: clf rep1


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_IP32953WT-day14-rep3


title: Neuron_SAD4.1

description: Gene expression data from SAD4.1 neurons

value: neurons

value: sporadic Alzheimer's disease

value: Clone 1


title: Untreated_femoral_head_cartilage_rep2_batch2


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_IP32953WT-day14-rep2


title: wt rep2


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_IP32953WT-day1-rep4


title: swn rep3


title: swn rep1


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_IP32953WT-day1-rep3


title: wt rep1


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_IP32953WT-day14-rep1


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_IP32953WT-day1-rep1


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_modified_IP32953-day14-rep3


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_IP32953WT-day1-rep2


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_modified_IP32953-day14-rep5


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_modified_IP32953-day14-rep2


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_modified_IP32953-day14-rep1


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_modified_IP32953-day14-rep4


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_modified_IP32953-day14-rep6


title: CLAMP IP, dsCP190 treatment, replicate 1

city: Bethesda

first: Cameron

last: Palmer

state: MD

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

library_source: genomic

data_processing:
Adapter removal with cutadapt v1.16
Alignment to Drosophila melanogaster genome with bowtie2 v2.3.4.1
Removal of duplicates with picard v2.18.9 MarkDuplicates
Narrow peak calling with MACS2 v2.1.1.20160309 callpeak
Genome_build: dm6
Supplementary_files_format_and_content: Coverage tracks in bigWig format, normalized to RPGC using bamCoverage v3.0.2. For IP samples, bed format peak call output, from the narrowPeak output of macs2.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: CLAMP IP, dsCP190 treatment

growth_protocol: Kc167 cells were grown in CCM3 media (Thermo Scientific HyClone, Logan, UT) and maintained in monolayer at 25°C.

extract_protocol:
2-3 X 10^7 cells were fixed by adding 1% formaldehyde directly to cells in culture medium for 10 min at RT with gentle agitation. Then formaldehyde was quenched with 0.125 M glycine with gentle agitation for 5 min at RT. Cells were pelleted by centrifugation at 2000 x g and washed twice with ice-cold PBS. Pellets were resuspended in 0.8 mL ice-cold cell lysis buffer [5 mM PIPES pH 8, 85 mM KCl, 0.5% NP-40, supplemented with Complete protease inhibitors (Roche)], incubated on ice for 10 min, then pelleted by centrifugation at 2000 x g for 5 min at 4°C. Next, the supernatant was removed and pellet was resuspended in 1 mL nuclear lysis buffer [50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS, supplemented with Complete protease inhibitors (Roche)] and incubated for 10 min at 4°C on a rotator. Afterwards, 0.5 mL of IP dilution buffer [16.7 mM Tris-HCl pH 8, 1.2 mM EDTA, 167 mM NaCl, 1.1% Triton X-100, 0.01% SDS, supplemented with Complete protease inhibitors (Roche)] and 300 mg of acid washed 212-300 micron glass beads (Sigma) were added to the lysate, and chromatin was fragmented to an average size range of 200-500 bp using a Bioruptor (Diagenode) using 10 cycles of 30 s on and 30 s off, maximum output. Samples were centrifuged at max speed for 10 min at 4°C, and the supernatant (sheared chromatin) was saved at -80°C. Chromatin was diluted to 1:5 with IP dilution buffer and added to 50 µL prewashed Protein A-sepharose beads (GE) and 5 µg of respective antibody and rotated overnight at 4°C. The next day, beads were washed with the following wash buffers: three times with Low salt wash buffer (20 mM Tris-HCl pH 8, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.1% SDS), three times with High salt wash buffer (20 mM Tris-HCl pH 8, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS), and two times with LiCl wash buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% Deoxycholate). Chromatin was eluted twice with 200 μL of elution buffer (0.1M NaHCO3, 1% SDS) for 30 min at 65°C each in a thermomixer at 800 rpm. Decrosslinking solution (20 μL of 5M NaCl, 8 μL of 0.5M EDTA, 10 μL of 1M Tris-HCl pH 8) was added to the eluates and further incubated overnight at 65°C. After de-crosslinking, samples were treated with 4 µL of Proteinase K (20 mg/mL) for 2 h at 50°C and then purified by Phenol-Chloroform followed by ethanol precipitation with 0.1 vol of 3M NaOAc pH 5.2 and 2.5 vol of 100% ethanol supplemented with 2 μL of Glycoblue (Ambion). After incubating overnight at -80°C, samples were centrifuged 20 min at 10,000 x g at 4°C. Pellets were washed with 70% ethanol. Pellets were air dried at RT prior to resuspension in 10 μL of nuclease free water.
Libraries were constructed by pooling two IP samples using TruSeq adapters (Illumina) according to the TruSeq Illumina ChIP-seq sample preparation protocol with the following modifications: after adaptor ligation and PCR amplification samples were purified by using AMPure XP Beads (sample to beads ratio 1:0.8) according to manufacturer's protocol.

treatment_protocol: 1 X 10^7 Kc167 cells were transfected with either 5 µg of dsRNA (DRSC 29935) against clamp, 12 µg of dsRNA (Moshkovich, 2011) against CP190 or no RNA (mock) using Amaxa cell line Nucleofector kit V (Lonza) and electroporated using G-30 program. Cells were incubated 6 d at 25°C to obtain efficient depletion of CLAMP or CP190 protein.

tag: developmental stage

value: embryo

tag: Sex

value: female

tag: treatment

tag: chip antibody

value: CLAMP, rabbit, Rieder et al., 2017


title: CP190 IP, dsCP190 treatment, replicate 1

source_name: CP190 IP, dsCP190 treatment

value: CP190, rabbit, Pai et al., 2004


title: CLAMP IP, mock treatment, replicate 1

source_name: CLAMP IP, mock treatment

value: mock


title: CLAMP IP, dsCP190 treatment, replicate 2


title: CP190 IP, dsCP190 treatment, replicate 2


title: CP190 IP, mock treatment, replicate 1

source_name: CP190 IP, mock treatment


title: Input for dsCP190 treatment, replicate 2

source_name: Input for dsCP190 treatment


title: CP190 IP, mock treatment, replicate 2


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_modified_IP32953-day1-rep4


title: Input for dsCP190 treatment, replicate 1


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_modified_IP32953-day1-rep3


title: Input for mock treatment, replicate 2

source_name: Input for mock treatment


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_modified_IP32953-day1-rep2


description: Gene expression data from_in-vivo Yersinia pseudotuberculosis_strain_modified_IP32953-day1-rep1


title: CLAMP IP, mock treatment, replicate 2


title: Input for mock treatment, replicate 1


description: Gene expression data from_in-vivo _Yersinia pestis_strain_CO92-day14-rep6

organism: Yersinia pestis


description: Gene expression data from_in-vivo _Yersinia pestis_strain_CO92-day14-rep5


description: Gene expression data from_in-vivo _Yersinia pestis_strain_CO92-day14-rep4


description: Gene expression data from_in-vivo _Yersinia pestis_strain_CO92-day14-rep2


title: A2780_ARID1A-Deficient_NT_rep1

city: Chuo-ku

first: Takashi

last: Kohno

state: Tokyo

address: 1-1, Tsukiji 5-chome

country: Japan

institute: National Cancer Center Research Institute

description: Gene expression in growing cells

hyb_protocol: cDNA was hybridized to Agilent microarrays (SurePrint G3 Human Gene Expression 8 x 60K Ver.1.0, G4851: 42405 probes) using a Gene Expression Hybridization Kit (Agilent Technologies) for 16 h at 65°C in duplicate.

scan_protocol: After the arrays were washed using the Gene Expression Wash Pack (Agilent Technologies), the data were extracted using an Agilent scanner.

data_processing: The arrays were first analyzed using the Feature Extraction software (Agilent Technologies).

source_name: A2780, NT, replicate1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The cell cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit.

tag: cell type

value: ovarian carcinoma


description: Gene expression data from_in-vivo _Yersinia pestis_strain_CO92-day14-rep1


title: Th-MycN/Casp2-/-  [MYCNC2ko180]

city: Adelaide

first: Loretta

last: Dorstyn

state: South Australia

address: UniSA CRI Building, Corner North Terrace and Morphett Street Bridge, GPO Box 2471

department: Centre for Cancer Biology

institute: University of South Australia and SA Pathology

data_processing:
Sequence quality was analysed using FastQC and the resulting data sets were aligned using the STAR alignment algorithm (https://www.ncbi.nlm.nih.gov/pubmed/23104886) to the UCSC mm10/GRCm38 version of the Mus musculus reference genome.
Gene counts were obtained from the STAR aligner
The aligned reads per gene were expressed as average log2-counts per million (LogCPM). The resulting files were transferred into R statistical environment. The edgeR Bioconductor package was used to fit a linear model and samples were log transformed for normalization and ranking and then expressed as log2-fold change of expression (Log2FC);
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited STAR aligner gene counts (gene name, unstranded counts, first strand counts, second strand counts)

extract_protocol:
Lymphomas from EμMyc and EμMyc/Casp2-/- mice were taken from cervical lymph nodes. Tumor samples from Th-MYCN and Th-MYCN/Casp2-/- mice were selected from paraspinal thoracic tumors based on absence or reduced blood vascularization. Four individual tumors from different mice per genotype were used for mRNA-seq analysis. Total RNA was extracted from frozen tumor tissue using Trizol® reagent and total RNA samples were quality tested using a 2100 Bioanalyser (Agilent Technologies) to confirm RNA integrity number (RIN) >7.
RNA libraries were prepared for sequencing using standard Illumina protocols and libraries sequenced on the Illumina HiSeq 2000, following the manufacturer's protocols.

tag: strain background

tag: genotype/variation

tag: tumour onset (weeks)

value: paraspinal thoracic tumor


title: A2780_ARID1A-Deficient_NT_rep2

description: Gene expression in growing cells

source_name: A2780, NT, replicate2

tag: genotype


title: RMG-I_ARID1A-WT_NT_rep1

description: Gene expression in growing cells

source_name: RMG-I, NT, replicate1

value: RMG-I

value: Ovarian clear cell adenocarcinoma


title: 2008_ARID1A-WT_NT_rep2

description: Gene expression in growing cells

source_name: 2008, NT, replicate2


title: Th-MycN/Casp2-/-  [MYCNC2ko176]


title: TOV21G_ARID1A-Deficient_NT_rep2

description: Gene expression in growing cells

source_name: TOV21G, NT, replicate2


title: HCT116_ARID1A-WT_APR-246_24hr_rep2

description: Gene expression after 24hr in 40 μM APR-246 treated cells

source_name: HCT116, ARID1A-WT, APR-246, 24hr, replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.25 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: ARI1DA-WT and ARID1A-KO HCT116 cancer cells were treated with 0 or 40 μM APR-246. After 24 h, total RNA was extracted.


title: Th-MycN/Casp2-/-  [MYCNC2ko144]


description: Gene expression data from_in-vivo _Yersinia pestis_strain_CO92-day14-rep3


description: Gene expression data from_in-vivo _Yersinia pestis_strain_CO92-day1-rep4


title: Th-MycN [MYCN391]

value: wild type


title: Th-MycN/Casp2-/-  [MYCNC2ko118]


title: HCT116_ARID1A-WT_NT_rep2

description: Gene expression in growing cells

source_name: HCT116ARID1AWT, NT, replicate2

value: colorectal carcinoma


title: RMG-I_ARID1A-WT_NT_rep2

description: Gene expression in growing cells

source_name: RMG-I, NT, replicate2


title: HCT116_ARID1A-KO_NT_rep2

description: Gene expression in growing cells

source_name: HCT116ARID1AKO, NT, replicate2


title: TOV21G_ARID1A-Deficient_NT_rep1

description: Gene expression in growing cells

source_name: TOV21G, NT, replicate1


title: HCT116_ARID1A-WT_NT_rep1

description: Gene expression in growing cells

source_name: HCT116ARID1AWT, NT, replicate1


title: HCT116_ARID1A-KO_APR-246_24hr_rep1

source_name: HCT116, ARID1A-KO, APR-246, 24hr, replicate1


title: HCT116_ARID1A-KO_APR-246_0hr_rep2

description: Gene expression after 24hr in 0 μM APR-246 treated cells

source_name: HCT116, ARID1A-KO, APR-246, 0hr, replicate2


title: HCT116_ARID1A-KO_APR-246_24hr_rep2

source_name: HCT116, ARID1A-KO, APR-246, 24hr, replicate2


title: 2008_ARID1A-WT_NT_rep1

description: Gene expression in growing cells

source_name: 2008, NT, replicate1


title: HCT116_ARID1A-WT_APR-246_24hr_rep1

source_name: HCT116, ARID1A-WT, APR-246, 24hr, replicate1


title: Th-MycN [MYCN235]


title: HCT116_ARID1A-WT_APR-246_0hr_rep2

source_name: HCT116, ARID1A-WT, APR-246, 0hr, replicate2


title: HCT116_ARID1A-WT_APR-246_0hr_rep1

source_name: HCT116, ARID1A-WT, APR-246, 0hr, replicate1


title: HCT116_ARID1A-KO_NT_rep1

description: Gene expression in growing cells

source_name: HCT116ARID1AKO, NT, replicate1


description: Gene expression data from_in-vivo _Yersinia pestis_strain_CO92-day1-rep2


title: Th-MycN [MYCN175]


description: Gene expression data from_in-vivo _Yersinia pestis_strain_CO92-day1-rep1


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_IP32953WT-37C-rep6

value: in-vitro


description: Gene expression data from_in-vivo _Yersinia pestis_strain_CO92-day1-rep3


title: hnf4ai3_day10_3

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

hyb_protocol: After fragmentation, 12 ug labeled cRNA was hybridized for 16 hours  at 45C on Primeview Human Gene Expression Array

scan_protocol: Images were acquired using a GeneChip Scanner 3000

data_processing: CEL files were analyzed by Partek using RMA algorithm.  Two sets of normalized data were generated.  First set normalized ipsK3 arrays days 3 - 10, in duplicate (matrix1).  Second set normalized ipsK3 and HNF4ai3 arrays on days 6, 8, and 10 in triplicate (matrix2).

label: Biotin

source_name: HNF4a depleted iPS cell_liver differentiation_day 10_rep3

label_protocol: Biotinylated cRNA were prepared using 100 ng RNA by following detailed instructions in the  3'IVT Plus Reagent Kit User Manual from Affymetrix

growth_protocol: ips cells were maintained and differentiated as detailed in Mallanna et al 2013

extract_protocol: RNA was isolated using RNeasy Mini kit from QIAgen

treatment_protocol: Cells were collected with RLT+BME and stored at -80C until RNA isolation

value: human iPS cells differentiated for 10 days towards hepatocytes


title: EμMyc/Casp2-/-  [EuMycC2ko239]

value: cervical lymph node tumor


title: hnf4ai3_day10_2

source_name: HNF4a depleted iPS cell_liver differentiation_day 10_rep2


title: hnf4ai3_day10_1

source_name: HNF4a depleted iPS cell_liver differentiation_day 10_rep1


title: hnf4ai3_day8_3

source_name: HNF4a depleted iPS cell_liver differentiation_day 8_rep3

value: human iPS cells differentiated for 8 days towards hepatocytes


title: EμMyc/Casp2-/-  [EuMycC2ko245]


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_IP32953WT-37C-rep4


title: EμMyc/Casp2-/-  [EuMycC2ko215]


title: Th-MycN [MYCN332]


title: hnf4ai3_day8_2

source_name: HNF4a depleted iPS cell_liver differentiation_day 8_rep2


title: EμMyc [EuMyc835]


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_IP32953WT-37C-rep3


title: hnf4ai3_day8_1

source_name: HNF4a depleted iPS cell_liver differentiation_day 8_rep1


title: hnf4ai3_day6_3

source_name: HNF4a depleted iPS cell_liver differentiation_day 6_rep3

value: human iPS cells differentiated for 6 days towards hepatocytes


title: EμMyc [EuMyc829]


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_IP32953WT-37C-rep1


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_IP32953WT-37C-rep2


title: EμMyc [EuMyc743b]


title: hnf4ai3_day6_1

source_name: HNF4a depleted iPS cell_liver differentiation_day 6_rep1


title: EμMyc [EuMyc614]


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_IP32953WT-21C-rep5


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_IP32953WT-21C-rep6


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_IP32953WT-37C-rep5


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_IP32953WT-21C-rep4


title: ipsK3_day10_rep3

source_name: iPS cell liver differentiation day 10_rep3


title: ipsK3_day10_rep2

source_name: iPS cell liver differentiation day 10_rep2


title: ipsK3_day10_rep1

source_name: iPS cell liver differentiation day 10_rep1


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_IP32953WT-21C-rep3


title: eccDNA_3F-RNAPOL-Rep2

city: Charlottesville,

first: Anindya

last: Dutta

email: ad8q@virginia.edu, pk7z@virginia.edu

state: VA

address: Room no. 1232, Jordan Hall

department: MD-BIOC BC/Mole Genetics~School of medicine

institute: University of Virginia

description: Extrachromosomal circular DNA

data_processing:
Basecalls performed using CASAVA version 1.4
MicroDNA extraction and identification:   HT or HT-POLR3F/POLR2H associated DNA was purified with QIAprep Spin Miniprep Kit according to its instruction manual and amplified by rolling circle amplification (RCA) as described (6,8). Initially paired-end high-throughput sequencing (250 cycles PE) was performed on the RCA products according to the manufacturer's protocol (Illumina) on the Illumina MiSeq at the University of Virginia DNA Sciences Core (Charlottesville, VA, USA) (Table 1). Read quality was checked by program fastqc (FASTX-Toolkit) and was found that the median read quality was less than 28 after position 150 on the read. Therefore to remove the bad quality bases we made each library 150 PE and did the downstream analysis. We used Burrows–Wheeler Aligner with maximal exact matches (BWA-MEM) to align the reads to the human hg38 genome, allowing for split reads under default conditions. Like our previous publication (5,6,31) we used split reads mapped position to identify microDNA co-ordinate at base pair resolution. In summary to identify microDNA we consider paired-end reads that had one end mapping uniquely to the reference genome (mapped end) and the other end not mapping to the reference genome continuously, but coming from a split-read (the junctional read). Furthermore, the two parts of the split read have to flank the linked mapped read. The identified microDNA would represent genomic coordinates of potential microDNA junctions created by the ligation of two ends of a linear DNA. In addition to this we also check polarity (strand information) of both the split read (should be map in the same orientation) and mapped read in pair (this should be opposite to split read).
Genome_build: HG38
Supplementary_files_format_and_content: Processed data include the microDNA co-ordinate (chromosome name, start position of circle and end position of circle) The fourth column in the processed data is the number of junctional tag (abundance).

molecule: other

source_name: HEK293, 3F-RNAPOL

extract_protocol: HT Cell lysate preparation and pull-down on Halo-Link beads: All the reagents used were pre-chilled and the entire procedure was performed on ice. HT-fusion proteins were induced by adding 1 mg/ml doxycycline to cells in a 15-cm plate. Two days later, cells were washed with PBS, scraped and transferred into a micro-centrifuge tube. After centrifugation five packed cell volume (PCV) Hypotonic Buffer was added to cell pellets, allowing the cells to swell, for 15 min on ice. Hypotonic Buffer was removed after spinning. Cells were suspended in 0.5 PCV of Buffer LS and equal volume of Buffer LS with 600 mM NaCl and 0.2% Triton X-100 was added. Cells were homogenized by passing 10 times through a 27G hypodermic needle and rotated for 20 min. After centrifugation, the supernatant was transfer into a new microcentrifuge tube and equal volume of Buffer LS to the supernatant was added. Cell lysate was added to the equilibrated HaloLink Resin and incubated by mixing on a tube rotator for 30 min at room temperature. After centrifugation supernatant was saved as sample flow through. Resin was washed with PD Washing Buffer five times.  The beads were boiled in Laemmli sample buffer to obtain the eluates.

tag: ht-fusion protein expressed


title: eccDNA_2H-RNAPOL-Rep2

description: Extrachromosomal circular DNA

source_name: HEK293, 2H-RNAPOL

tag: cell line


title: eccDNA_2H-RNAPOL-Rep1

description: Extrachromosomal circular DNA


title: eccDNA_HT-Control-Rep2

description: Extrachromosomal circular DNA

source_name: HEK293, Control

value: HT-Control


title: eccDNA_HT-Control-Rep1

description: Extrachromosomal circular DNA


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_IP32953WT-21C-rep1


title: ipsK3_day8_rep2

source_name: iPS cell liver differentiation day 8_rep2


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_modified_IP32953-21C-rep6


title: ipsK3_day8_rep3

source_name: iPS cell liver differentiation day 8_rep3


title: hnf4ai3_day6_2

source_name: HNF4a depleted iPS cell_liver differentiation_day 6_rep2


title: wildtype hybrid hermaphrodite germlines, rep4

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

description: P.v.Pm.deseq.output.csv.gz

data_processing:
TopHat2 was used to align the RNA-seq reads to the C. elegans transcriptome (WS220) with default parameters allowing either 1 mismatch or 0 mismatches. For all read analysis, all R1 reads were mapped allowing 1 mismatch. For SNP analysis,  SNP-containing R1 and R2 reads were mapped twice, once allowing  0 mismatches and once allowing 1 mismatch.
HTSeq was used to obtain read counts per transcript. For all read analysis, all read counts per transcript were obtained. For SNP analysis, SNP-containing read counts per transcript were obtained for reads that mapped with 0 mismatches and those that mapped allowing 1 mismatch.
Differentially expressed genes were determined with DESeq2 in R using HTSeq counts from the all reads analysis and a FDR < 0.05 or < 0.1 (see methods) as the significance cutoff.
Genome_build: WS220
Supplementary_files_format_and_content: Text files for each sample with HTSeq counts per transcript (tab delimited), and DESeq output for differential expression analysis performed (comma delimited). Gene identifiers are Gene Sequence Names as obtained from Wormbase version WS220.

organism: Caenorhabditis elegans

source_name: wildtype hybrid hermaphrodite germlines

growth_protocol: C. elegans strains were maintained at 20°on OP50 bacteria as described (Brenner 1974).

extract_protocol:
Total RNAs were purified using Trizol/chloroform extraction protocol.
Ribosomal RNA was depleted using an NEBNext rRNA Depletion kit (E6310), and libraries were prepared using an NEBNext Ultra RNA Library Prep Kit for Illumina (E7530).

treatment_protocol: L4 hermaphrodites or L4 males were transferred to new plates, and dissected the next day (1 day old young adults).

tag: strain

value: hybrid (hawaii mother and bristol father)

value: distal gonad arms cut at the late-pachytene gonad bend


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_modified_IP32953-21C-rep5


title: ipsK3_day7_rep2

source_name: iPS cell liver differentiation day 7_rep2

value: human iPS cells differentiated for 7 days towards hepatocytes


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_modified_IP32953-21C-rep4


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_modified_IP32953-21C-rep3


title: ipsK3_day6_rep3

source_name: iPS cell liver differentiation day 6_rep3


title: wildtype hybrid hermaphrodite germlines, rep3

description: P.v.Pm.deseq.output.csv.gz


title: wildtype hybrid hermaphrodite germlines, rep2

description: P.v.Pm.deseq.output.csv.gz


title: wildtype hybrid hermaphrodite germlines, rep1

description: P.v.Pm.deseq.output.csv.gz


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_modified_IP32953-21C-rep2


title: eccDNA_3F-RNAPOL-Rep1

description: Extrachromosomal circular DNA


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_IP32953WT-21C-rep2


title: ipsK3_day6_rep2

source_name: iPS cell liver differentiation day 6_rep2


title: hybrid hermaphrodite germlines from K27me3 M+P+, rep4

description: Pp.v.Pm.deseq.output.csv.gz


description: Gene expression data from_in-vitro Yersinia pseudotuberculosis_strain_modified_IP32953-21C-rep1


title: ipsK3_day6_rep1

source_name: iPS cell liver differentiation day 6_rep1


title: ipsK3_day5_rep2

source_name: iPS cell liver differentiation day 5_rep2

value: human iPS cells differentiated for 5 days towards hepatocytes


description: Gene expression data from_in-vitro _Yersinia pestis_strain_CO92-21C-rep5


title: hybrid hermaphrodite germlines from K27me3 M+P+, rep3

description: Pp.v.Pm.deseq.output.csv.gz


description: Gene expression data from_in-vitro _Yersinia pestis_strain_CO92-21C-rep6


title: hybrid hermaphrodite germlines from K27me3 M+P+, rep2

description: Pp.v.Pm.deseq.output.csv.gz


title: ipsK3_day5_rep1

source_name: iPS cell liver differentiation day 5_rep1


title: ipsK3_day8_rep1

source_name: iPS cell liver differentiation day 8_rep1


description: Gene expression data from_in-vitro _Yersinia pestis_strain_CO92-21C-rep4


title: hybrid hermaphrodite germlines from K27me3 M+P+, rep1

description: Pp.v.Pm.deseq.output.csv.gz


description: Gene expression data from_in-vitro _Yersinia pestis_strain_CO92-21C-rep3


title: ipsK3_day4_rep2

source_name: iPS cell liver differentiation day 4_rep2

value: human iPS cells differentiated for 4 days towards hepatocytes


title: ipsK3_day7_rep1

source_name: iPS cell liver differentiation day 7_rep1


title: ipsK3_day4_rep1

source_name: iPS cell liver differentiation day 4_rep1


title: hybrid hermaphrodite germlines from K27me3 M+P-, rep4

description:
Pp.v.Pm.deseq.output.csv.gz
P.v.Pm.deseq.output.csv.gz


title: clf-29 swn-4 rep3

data_processing:
FastQC Read Quality reports.
Mapping reads to TAIR10 by TopHat Gapped-read mapper (Galaxy Version 2.1.0).
Cufflinks transcript assembly and FPKM (RPKM) estimates.
Merge together several Cufflinks assemblies by Cuffmerge.
Find significant changes in transcript expression, splicing, and promoter use by Cuffdiff.
Genome_build: TAIR 10
Supplementary_files_format_and_content: tabular

source_name: clf-29 swn-4 rep3

growth_protocol: The clf-29 swn-4 double mutants were  growth on 1/2 MS plates for 10 days under 16h light/ 8h dark condition.

extract_protocol:
Total RNA was isolated from   ̴50 mg of in vitro-grown clf-29 swn-4 mutants using the RNeasy Plant Mini kit (Qiagen) according to supplier’s instructions. Total RNA was treated with RNase-free DNaseI kit (Life Techologies).
A  total  amount  of  1.5μg  RNA  per  sample  was  used  as  input  material  for  the  RNA sample preparations. Sequencing libraries were generated using NEBNext®  UltraTM  RNA Library Prep Kit for Illumina®  (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X).  First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently   performed   using   DNA   Polymerase   I   and   RNase   H. Remaining  overhangs  were  converted  into  blunt  ends  via  exonuclease/polymerase activities.  After  adenylation  of  3’  ends  of  DNA  fragments,  NEBNext  Adaptor  with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected,  adaptor-ligated  cDNA  at  37°C  for  15  min  followed  by  5  min  at  95°C before  PCR.  Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: seedlings

value: 10 days

tag: ecotype

value: clf-29 swn-4


title: hybrid hermaphrodite germlines from K27me3 M+P-, rep3


title: ipsK3_day3_rep2

source_name: iPS cell liver differentiation day 3_rep2

value: human iPS cells differentiated for 3 days towards hepatocytes


description: Gene expression data from_in-vitro _Yersinia pestis_strain_CO92-21C-rep2


title: ipsK3_day3_rep1

source_name: iPS cell_liver differentiation_day 3_rep1


title: clf-29 swn-4 rep1

source_name: clf-29 swn-4 rep1

tag: developmental


description: Gene expression data from_in-vitro _Yersinia pestis_strain_CO92-21C-rep1


title: hybrid hermaphrodite germlines from K27me3 M+P-, rep1


title: clf-29 swn-4 rep2

source_name: clf-29 swn-4 rep2

tag: antibody


title: hybrid hermaphrodite germlines from K27me3 M+P-, rep2


title: CMV infected fibroblasts NT-LNA_HCMV_2

status: Public on Jan 27 2019

city: Princeton

first: Thomas

last: Shenk

state: New Jersey

address: 119 Lewis Thomas Laboratory, Washington Road

department: Molecular Biology

institute: Princeton University

data_processing:
Illumina Casava1.8+ software used for basecalling.
Raw reads were quality filtered by trimming the read ends; bases with quality <20 were removed. We then computed the quality at the 20th percentile. The entire read was discarded if the quality at the 20th percentile was less than 15. Reads shorter than 40 bases after trimming were discarded as well. If one or more reads in the pair failed the quality check both reads were discarded.
Reads were mapped to the genome and to repbase sequences using STAR
Counts for genes and repeat elements were obtained using featureCounts application from subread package
Expression as log(counts per million) was computed using edgeR/limma packages using TMM normalization
Genome_build: Build 38, gencode annotation
Supplementary_files_format_and_content: tab-delimited text files include raw counts and expression for each sample

source_name: human foreskin fibroblasts

growth_protocol: see sample metadata

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: see sample metadata

value: HFF

tag: passage

tag: virus strain

tag: virus accession number

tag: hours post infection/collection time

tag: lna treatment

value: NT LNA

tag: viral titer at infection

tag: growth protocol


title: CMV infected fibroblasts NT-LNA_HCMV_1

tag: cell type


title: mock infected fibroblasts HSII-LNA_Mock_2

value: mock

value: HSATII LNA


title: CMV infected fibroblasts HSII-LNA_HCMV_1


title: mock infected fibroblasts HSII-LNA_Mock_1


title: mock infected fibroblasts NT-LNA_Mock_1


title: CMV infected fibroblasts HSII-LNA_HCMV_2


title: ADV infected fibroblasts Ad5_2

source_name: human lung fibroblasts

value: ADV type 5

value: 10 FFU/cell


title: mock infected fibroblasts Mock_24h_2


title: HSV infected fibroblasts HSV_2

value: HSV1/strain F


title: mock infected fibroblasts Mock_24h_1


title: HSV infected fibroblasts HSV_1


title: mock infected fibroblasts Mock_9h_2


title: CMV infected retinal pigment epithelial cells TB40e_ARPE19_2

source_name: human retinal pigment epithelial cells


title: CMV infected retinal pigment epithelial cells TB40e_ARPE19_1


title: ADV infected fibroblasts Ad5_1


title: mock infected retinal pigment epithelial cells Mock_ARPE19_1


title: CMV infected fibroblasts TB40e_MRC5_1


title: CMV infected fibroblasts TB40e_MRC5_2


title: mock infected retinal pigment epithelial cells Mock_ARPE19_2


title: CMV infected fibroblasts AD169_MRC5_1


title: CMV infected fibroblasts AD169_MRC5_2


title: CMV infected fibroblasts FIX_MRC5_2

value: CMV/FIX


title: CMV infected fibroblasts TB40/E_MRC5_2


title: CMV infected fibroblasts FIX_MRC5_1


title: CMV infected fibroblasts TB40/E_MRC5_1


title: mock infected fibroblasts Mock_MRC5_2


title: mock infected fibroblasts Mock_MRC5_1


title: mock infected fibroblasts NT-LNA_Mock_2


title: CMV infected fibroblast HCMV_2

extract_protocol:
RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Cells were infected at MOI of 3.


title: CMV infected fibroblast HCMV_3


title: mock infected fibroblast Mock_3


title: CMV infected fibroblast HCMV_1


title: mock infected fibroblast Mock_2


title: mock infected fibroblast Mock_1


title: mock infected fibroblasts Mock_9h_1


title: 2nd infection/Re-infection: Mice C.muridarum week 8 exposure replicate 2

city: Atlanta

first: Yusuf

last: Omosun

state: GA

address: 720 Westview Dr SW

department: Microbiology, Biochemistry and Immunology

institute: Morehouse School of Medicine

data_processing:
Deep Sequencing with  Illumina NextSeq 500 instrument using a SE75 run High Output flow cell (Illumina, San Diego, CA, USA). Raw sequencing reads were demultiplexed and stored on the Basespace Sequence Hub .
The data were mapped to the M. musculus mm10 reference genome and to the MirDeep mouse miRNA database for identifying novel and known miRNA’s, respectively, using the CAP-MiRSeq pipeline (Sun et al.2014)
CAP-MiR pipeline leverages several software packages for adapter removal and trimming, read alignment.and manipulation of SAM/BAM and fastq/fasta files
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited txt file, raw count matrix

source_name: total RNA

growth_protocol: Stocks of Chlamydia muridarum (the agent of mouse pneumonitis) used for infections were prepared by propagating elementary bodies (EBs) in McCoy or HeLa cells (Division of Scientific Research, Centers for Disease Control and Prevention, Atlanta), according to standard procedures

extract_protocol:
The entire genital tract from the vagina to the ovary was collected for both groups of mice at one, two, four and eight weeks after infection.GT samples were harvested after sacrificing mice and frozen immediately on dry ice and then transferred to a -80 freezer .For non-biased recovery of miRNA, total RNA was isolated using the Direct-zol RNA miniprep (Zymo Research, Irvine CA).
Library preparation with the the TruSeq Small RNA Library Preparation Kit (Illumina, San Diego, CA).

treatment_protocol: 6-8 weeks old Female C57BL/6 (40) were infected intravaginally with 1×105 IFU /mouse of live C. muridarum approximately 7 days after administration of 2.5 mg/mouse Depo Provera (medroxy-progesterone Acetate; Pfizer Inc, NY). Mice were divided into two groups (20 each). The first group, “1st infection”, was infected only once, while the second group, “2nd Infection/re-infection” was infected twice at and interval of 4-weeks.

tag: type of infection

value: 2nd Infection/Re-infection

tag: isolation time,post infection

value: Week 8

tag: replicate

tag: infection

value: Chlamydia muridarum

tag: infection volume

tag: inclusion forming unit (ifu)

value: C57BL/6 J

value: Wild Type

tag: Sex

value: Female

tag: age

value: 19 weeks old

tag: tissue

value: Whole Genital Tract


title: 2nd infection/Re-infection: Mice C.muridarum week 8 exposure replicate 4

tag: strain

tag: genotype


title: 2nd infection/Re-infection: Mice C.muridarum week 8 exposure replicate 3


title: 2nd infection/Re-infection: Mice C.muridarum week 8 exposure replicate 1


title: 2nd infection/Re-infection: Mice C.muridarum week 8 control replicate 2

value: Sham Infected with PBS


title: 2nd infection/Re-infection: Mice C.muridarum week 8 control replicate 1


title: 2nd infection/Re-infection: Mice C.muridarum week 8 control replicate 3


title: 2nd infection/Re-infection: Mice C.muridarum week 4 exposure replicate 5

value: Week 4

value: 15 weeks old


title: 2nd infection/Re-infection: Mice C.muridarum week 4 exposure replicate 2


title: 2nd infection/Re-infection: Mice C.muridarum week 4 control replicate 5


title: 2nd infection/Re-infection: Mice C.muridarum week 4 control replicate 4


title: 2nd infection/Re-infection: Mice C.muridarum week 4 control replicate 3


title: 2nd infection/Re-infection: Mice C.muridarum week 4 control replicate 2


title: 2nd infection/Re-infection: Mice C.muridarum week 4 control replicate 1


title: 2nd infection/Re-infection: Mice C.muridarum week 2 exposure replicate 4

value: Week 2

value: 13 weeks old


title: 2nd infection/Re-infection: Mice C.muridarum week 2 exposure replicate 2


title: 2nd infection/Re-infection: Mice C.muridarum week 2 exposure replicate 3


title: 2nd infection/Re-infection: Mice C.muridarum week 2 exposure replicate 1


title: 2nd infection/Re-infection: Mice C.muridarum week 2 control replicate 4


title: D2.OR shSLX4IP Biological Rep 1

city: Cleveland

first: William

last: Schiemann

state: OH

address: 2103 Cornell Rd.

department: Case Comprehensive Cancer Center

institute: Case Western Reserve University

description: D2.OR cells expressing shRNA targeting SLX4IP

hyb_protocol: Following fragmentation, cRNA was hybridized on GeneChip Mouse Gene 2.0 ST Array

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Thermo Fisher)

data_processing: The data were analyzed with Affymetrix Expression Console and Affymetrix Transcriptome Analysis Console

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

growth_protocol: Longitudinal 3D-outgrowth was carried out by plating cells (31,500 cells/cm2) atop solidified Cultrex cushion (600 µL/well; 6 well plate) and grown in DMEM supplemented with 10% fetal bovine serum and 5% Cultrex for 7 days.

extract_protocol: Cells were non-enzymatically isolated using Cultrex 3D-Culture Cell Harvesting Kit (Trevigen), and RNA was isolated using an RNeasy Mini RNA Extraction Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: D2.OR cells were transduced with lentiviral vectors containing either a scrambled (i.e., non-targeting) shRNA (Scram) or an shRNA targeting SLX4IP (shSLX4IP). Successfully transduced cells were selected with puromycin.

tag: culture conditions

value: Cells isolated from 3D culture


title: D2.OR Scram Biological Rep 2

description: D2.OR cells expressing scrambled (non-targeting) shRNA


title: D2.OR shSLX4IP Biological Rep 3

source_name: D2.OR cells expressing shRNA targeting SLX4IP


title: D2.OR shSLX4IP Biological Rep 2


title: 2nd infection/Re-infection: Mice C.muridarum week 2 control replicate 2


title: 2nd infection/Re-infection: Mice C.muridarum week 2 control replicate 1


title: 2nd infection/Re-infection: Mice C.muridarum week 2 control replicate 3


title: 2nd infection/Re-infection: Mice C.muridarum week 4 exposure replicate 4


title: 2nd infection/Re-infection: Mice C.muridarum week 4 exposure replicate 3


title: D2.OR Scram Biological Rep 3

source_name: D2.OR cells expressing scrambled (non-targeting) shRNA


title: 2nd infection/Re-infection: Mice C.muridarum week 1 exposure replicate 3

value: Week 1

value: 12 weeks old


title: 2nd infection/Re-infection: Mice C.muridarum week 4 exposure replicate 1


title: D2.OR Scram Biological Rep 1


title: 2nd infection/Re-infection: Mice C.muridarum week 1 exposure replicate 1


title: 2nd infection/Re-infection: Mice C.muridarum week 1 control replicate 5


title: 2nd infection/Re-infection: Mice C.muridarum week 1 exposure replicate 2


title: 2nd infection/Re-infection: Mice C.muridarum week 1 control replicate 1


title: 2nd infection/Re-infection: Mice C.muridarum week 1 control replicate 3


title: 2nd infection/Re-infection: Mice C.muridarum week 1 control replicate 2


title: 2nd infection/Re-infection: Mice C.muridarum week 2 exposure replicate 5


title: 1st infection: Mice C.muridarum week 8 exposure replicate 4

value: 1st Infection


title: 1st infection: Mice C.muridarum week 8 exposure replicate 3


title: 1st infection: Mice C.muridarum week 8 exposure replicate 5


title: 1st infection: Mice C.muridarum week 8 exposure replicate 1


title: 1st infection: Mice C.muridarum week 8 control replicate 4


title: 1st infection: Mice C.muridarum week 8 exposure replicate 2


title: 1st infection: Mice C.muridarum week 8 control replicate 2


title: 1st infection: Mice C.muridarum week 8 control replicate 1


title: 1st infection: Mice C.muridarum week 8 control replicate 3


title: 2nd infection/Re-infection: Mice C.muridarum week 1 exposure replicate 5

value: 2nd Infection/Re-infection


title: 1st infection: Mice C.muridarum week 4 exposure replicate 5

value: 11 weeks old


title: Wild-Type oxidative stress profiling 3

city: Frederick

first: Colin

last: Wu

department: RNA Biology Laboratory

institute: NCI

data_processing:
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Adapter sequence (NNNNNNCACTCGGGCACCAAGGA) removed with Skewer
4 random nucleotides included in RT primer (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG) were removed from the 5’ end of reads. Trimmed reads longer than 15 nt were aligned to yeast ribosomal and non-coding RNA sequences using STAR with ‘--outFilterMismatchNoverLmax 0.3’.
Unmapped reads were then mapped to genome using the following options ‘--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.1’.
Genome_build: SacCer3 R64-1-1
Supplementary_files_format_and_content: Count tables for relative codon occupancies or fixed-step WIG density files for mapped reads

organism: Saccharomyces cerevisiae

source_name: Wild-Type oxidative stress profiling

growth_protocol: Yeast cells were grown to OD ~0.5.

extract_protocol:
Lysates were clarified and monosomes were isolated by sucrose gradient centrifugation after RNaseI treatment. RNA was extracted using SDS/hot phenol/chloroform.
Fragments ranging from 15-34 nt were gel purified and rRNA was depleted from this pool through Ribo-Zero Gold treatment. Upon dephosphorylation of sample RNA, linker was ligated and this product was once again gel purified. This was followed by reverse transcription as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing.

treatment_protocol: Yeast cells were harvested by vacuum filtration and flash frozen. Samples were homogenized and lysed with lysis buffer using a freezer mill.

value: Wild-Type

tag: plasmid(s)

tag: molecule subtype

value: Ribosome Protected mRNA (15-34 nt)


title: 2nd infection/Re-infection: Mice C.muridarum week 1 exposure replicate 4

value: Chlamydia muridarum

value: C57BL/6 J

value: Wild Type


title: 1st infection: Mice C.muridarum week 4 exposure replicate 4

value: Female

value: Whole Genital Tract


title: gamma toxin CHXTIG profiling 2

source_name: gamma toxin CHXTIG profiling

value: pRS416-GalL-gamma toxin


title: 3AT_CHXTIG profiling 2

source_name: 3AT_CHXTIG profiling


title: 1st infection: Mice C.muridarum week 4 exposure replicate 3

value: Week 4


title: gamma toxin CHXTIG profiling 1


title: 1st infection: Mice C.muridarum week 4 exposure replicate 2


title: 3AT_CHX2

data_processing:
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Adapter sequence (CTGTAGGCACCATCAAT) removed with Skewer
Trimmed reads longer than 15 nt were aligned to yeast ribosomal and non-coding RNA sequences using STAR with ‘--outFilterMismatchNoverLmax 0.3’.
Unmapped reads were then mapped to genome using the following options ‘--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.1’.
Genome_build: SacCer3 R64-1-1
Supplementary_files_format_and_content: Count table for relative codon occupancies

source_name: Whole Cells

growth_protocol: Cells were grown to an OD of 0.5

extract_protocol:
Lysates were clarified and monosomes were isolated by sucrose gradient centrifugation after RNaseI treatment. RNA was extracted using SDS/hot phenol/chloroform.
Fragments ranging from 15-34 nt were gel purified and rRNA was depleted from this pool through Ribo-Zero Gold (Yeast) treatment. Upon dephosphorylation of sample RNA, IDT miRNA Cloning Linker 1 was ligated and this product was once again gel purified. This was followed by reverse transcription as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing.

treatment_protocol: Cells were harvested by vacuum filtration and flash frozen. Samples were homogenized and lysed with lysis buffer using a freezer mill.


title: 2nd infection/Re-infection: Mice C.muridarum week 1 control replicate 4

value: Sham Infected with PBS


title: 1st infection: Mice C.muridarum week 4 exposure replicate 1


title: rck2∆ hyperosmotic stress profiling 2

description:
processed data file:
CHXTIG_21ntRPF_occupancy.csv
rck2OSM2

data_processing:
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Adapter sequence (NNNNNNCACTCGGGCACCAAGGA) removed with Skewer
4 random nucleotides included in RT primer (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG) were removed from the 5’ end of reads. Trimmed reads longer than 15 nt were aligned to yeast ribosomal and non-coding RNA sequences using STAR with ‘--outFilterMismatchNoverLmax 0.3’.
Unmapped reads were then mapped to genome using the following options ‘--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.1’.
Genome_build: SacCer3 R64-1-1, Ce10, hg19
Supplementary_files_format_and_content: Count tables for relative codon occupancies or fixed-step WIG density files for mapped reads

source_name: rck2∆ hyperosmotic stress profiling

growth_protocol: Yeast cells were grown to OD ~0.5; mammalian cells were grown to ~75% confluence; Synchronized L1 worms were plated on HT115 bacteria transformed with pL4440 vector and cultured at 25˚C for ~48 hours.

tag: genotype/variation


title: rck2∆ hyperosmotic stress profiling 1

description:
processed data file:
CHXTIG_21ntRPF_occupancy.csv
rck2OSM1


title: 1st infection: Mice C.muridarum week 4 control replicate 5


title: C. elegans embryos ribosome profiling

description:
processed data file:
Mammalian_21ntRPF_occupancy.csv

source_name: C. elegans embryos ribosome profiling

value: embryos


title: Wild-Type hyperosmotic stress profiling 2

description:
processed data file:
CHXTIG_21ntRPF_occupancy.csv
wtOSM2

source_name: Wild-Type hyperosmotic stress profiling


title: Wild-Type hyperosmotic stress profiling 1

description:
processed data file:
CHXTIG_21ntRPF_occupancy.csv
wtOSM1


title: 1st infection: Mice C.muridarum week 4 control replicate 3


title: HeLa Gln starvation 6hr CHXTIG

description:
processed data file:
Mammalian_21ntRPF_occupancy.csv
Hela-aa6hr_CHXTIG

source_name: HeLa Gln starvation 6hr CHXTIG

tag: cell line

value: HeLa


title: rck2∆ oxidative stress profiling 1

description:
processed data file:
CHXTIG_21ntRPF_occupancy.csv
rck2OX_10min

source_name: rck2∆ oxidative stress profiling


title: 1st infection: Mice C.muridarum week 4 control replicate 2


title: 1st infection: Mice C.muridarum week 4 control replicate 4


title: HeLa Gln starvation 6hr

description:
processed data file:
Mammalian_21ntRPF_occupancy.csv
Hela-aa6hr

source_name: HeLa Gln starvation 6hr


title: rck2∆ oxidative stress profiling 2

description:
processed data file:
CHXTIG_21ntRPF_occupancy.csv
rck2OX_45min


title: Wild-Type stationary phase profiling 1

description:
processed data file:
CHXTIG_21ntRPF_occupancy.csv
wtstation1

source_name: Wild-Type stationary phase profiling


title: HeLa ribosome profiling 2

description:
processed data file:
Mammalian_21ntRPF_occupancy.csv
Hela2

source_name: HeLa ribosome profiling


title: 1st infection: Mice C.muridarum week 2 exposure replicate 5

value: Week 2

value: 9 weeks old


title: 1st infection: Mice C.muridarum week 4 control replicate 1

value: 1st Infection


title: Wild-Type oxidative stress profiling 2

description:
processed data file:
CHXTIG_21ntRPF_occupancy.csv
wtOX_45min


title: HeLa ribosome profiling 1

description:
processed data file:
Mammalian_21ntRPF_occupancy.csv
Hela1


title: 1st infection: Mice C.muridarum week 2 exposure replicate 4


title: Wild-Type CHXTIG profiling 2

description:
processed data file:
CHXTIG_21ntRPF_occupancy.csv
wt2_CHXTIG

source_name: Wild-Type CHXTIG profiling


title: Wild-Type CHXTIG profiling 1

description:
processed data file:
CHXTIG_21ntRPF_occupancy.csv
wt1_CHXTIG


title: 3-AT CHXTIG profiling

description:
processed data file:
CHXTIG_21ntRPF_occupancy.csv
3AT_CHXTIG

source_name: 3-AT CHXTIG profiling


title: 1st infection: Mice C.muridarum week 2 exposure replicate 3

source_name: total RNA


title: eRF1 depletion CHX replicate 2

description:
processed data file: CHX_21ntRPF_occupancy.csv
eRF1d_CHX_rep2


title: eRF1 depletion CHX replicate 1

description:
processed data file: CHX_21ntRPF_occupancy.csv
eRF1d_CHX_rep1


title: MDA-MB-231 ribosome profiling

description:
processed data file:
Mammalian_21ntRPF_occupancy.csv
MDA

source_name: MDA-MB-231 ribosome profiling


title: APO_2

city: kanazawa

first: masanobu

last: oshima

address: Kakuma-machi

institute: kanazawa university

description:
polyA RNA
StrandNGS_Apocynin_MKN45_sphere.xlsx

data_processing:
HiSeq Control Software (HCS) v2.2.58 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using StrandNGS.
The raw counts of each gene in a reference gene annotation (hg19) were calculated using the StrandNGS software, and were subjected to base 2 logarithmic conversion.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample

growth_protocol: MKN45 cells were cultured in RPMI1640 medium with 1% N-2 supplement, 2% B27 (without vitaminA), 20 ng/ml bFGF and 100ng/ml EGF. They were cultured as spheres by using ultra low attachment plates

extract_protocol:
Total RNA was extracted using ISOGEN (Nippon Gene) and purified using Rneasy Mini Kit (Quiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MKN45 cells were treated by Apocynin (100mM) or ethanol (control). After 3days, another aliquot of Apocynin was added. Total mRNA was extracted at day4.

tag: cell type

value: adenocarcinoma, poorly differentiated

tag: treatment

value: Apocynin 100μM treated


title: 1st infection: Mice C.muridarum week 2 exposure replicate 2

tag: type of infection

tag: isolation time,post infection


title: CTRL_2

value: control


title: 1st infection: Mice C.muridarum week 2 exposure replicate 1

tag: replicate

tag: infection


title: vector_CHX

description:
processed data file: CHX_21ntRPF_occupancy.csv
vector_CHX

value: Wild-Type

value: Ribosome Protected mRNA (15-34 nt)


title: WT_CHX2

description:
This is duplicated sample record of GSM2387081 (GSE89704) for the convenient retrieval of the complete raw data from SRA.
processed data file: CHX_21ntRPF_occupancy.csv
WT.2


title: Wild-Type oxidative stress profiling 1

description:
processed data file:
CHXTIG_21ntRPF_occupancy.csv
wtOX_10min


title: Wild-Type stationary phase profiling 2

description:
processed data file:
CHXTIG_21ntRPF_occupancy.csv
wtstation2


title: CTRL_1


title: 1st infection: Mice C.muridarum week 2 control replicate 4

tag: infection volume

tag: inclusion forming unit (ifu)

value: C57BL/6 J


title: lysate dilute TIG_90mM_DMS, DMSMaP-seq

description:
processed data file:
TIGlysate_lysateDMS_raw_all_datasets_exclude_constitutive.tsv
HWCCTBCXY_1_GATCAG_1

data_processing:
library strategy: dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq)
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Adapter sequence (NNNNNNCACTCGGGCACCAAGGAC) removed with Skewer
Shapemapper 2.0 was used to trim low-quality nucleotides, align reads to S. cerevisiae rRNA (Saccharomyces Genome Database), and count mutations and read coverage at each rRNA position.
Genome_build: SacCer3 R64-1-1
Supplementary_files_format_and_content: Count table for mutation rate at every nucleotide of rRNA

growth_protocol: Cells were grown to an OD of 0.6 in YPD media and harvested by fast filtration and flash frozen in liquid nitrogen.

extract_protocol:
RNA was extracted using SDS/hot phenol/chloroform.
Fragments ranging from 60-80 nt were gel purified. Upon dephosphorylation of sample RNA, linker was ligated and this product was once again gel purified. This was followed by reverse transcription as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing.

treatment_protocol: After lysis, lysates were diluted to 15 mL with footprint lysis buffer with or without TIG and modified by DMS.

value: Fragmented total RNA


title: 1st infection: Mice C.muridarum week 2 control replicate 3

value: Wild Type

tag: Sex

value: Female

tag: age


title: lysate dilute TIG_NO_DMS, DMSMaP-seq

description:
processed data file:
TIGlysate_lysateDMS_raw_all_datasets_exclude_constitutive.tsv
HWCCTBCXY_1_CAGATC_1


title: lysate dilute no_drug_90mM_DMS, DMSMaP-seq

description:
processed data file:
TIGlysate_lysateDMS_raw_all_datasets_exclude_constitutive.tsv
HWCCTBCXY_1_GCCAAT_1


title: HeLa Gln starvation 9hr

description:
processed data file:
Mammalian_21ntRPF_occupancy.csv
Hela-aa9hr

source_name: HeLa Gln starvation 9hr


title: lysate dilute no_drug_40mM_DMS, DMSMaP-seq

description:
processed data file:
TIGlysate_lysateDMS_raw_all_datasets_exclude_constitutive.tsv
HWCCTBCXY_1_ACAGTG_1


title: lysate dilute TIG_40mM_DMS, DMSMaP-seq

description:
processed data file:
TIGlysate_lysateDMS_raw_all_datasets_exclude_constitutive.tsv
HWCCTBCXY_1_ACTTGA_1


title: 1st infection: Mice C.muridarum week 2 control replicate 1

tag: strain

tag: tissue

value: Whole Genital Tract


title: 1st infection: Mice C.muridarum week 2 control replicate 2

tag: genotype


title: lysate dilute no_drug_NO_DMS, DMSMaP-seq

description:
processed data file:
TIGlysate_lysateDMS_raw_all_datasets_exclude_constitutive.tsv
HWCCTBCXY_1_TGACCA_1

tag: plasmid(s)


title: 1st infection: Mice C.muridarum week 1 exposure replicate 5

value: Week 1

value: Chlamydia muridarum

value: 8 weeks old


title: 1st infection: Mice C.muridarum week 1 exposure replicate 4


title: lysate ANI_40mM_DMS, DMSMaP-seq

description:
processed data file:
ANS_lysateDMS_raw_all_datasets_exclude_constitutive.tsv
HLFWMBCXY_2_ACTTGA_1

data_processing:
library strategy: dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq)
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Adapter sequence (CACTCGGGCACCAAGGAC) removed with Skewer
Shapemapper 2.0 was used to trim low-quality nucleotides, align reads to S. cerevisiae rRNA (Saccharomyces Genome Database), and count mutations and read coverage at each rRNA position.
Genome_build: SacCer3 R64-1-1
Supplementary_files_format_and_content: Count table for mutation rate at every nucleotide of rRNA

growth_protocol: Cells were grown to an OD of 0.7 in YPD media

treatment_protocol: Cells were treated with antibiotics and modified by DMS.

tag: molecule subtype


title: lysate no_drug_90mM_DMS, DMSMaP-seq

description:
processed data file:
ANS_lysateDMS_raw_all_datasets_exclude_constitutive.tsv
HLFWMBCXY_2_GCCAAT_1

tag: genotype/variation


title: lysate ANI_NO_DMS, DMSMaP-seq

description:
processed data file:
ANS_lysateDMS_raw_all_datasets_exclude_constitutive.tsv
HLFWMBCXY_2_CAGATC_1


title: lysate ANI_90mM_DMS, DMSMaP-seq

description:
processed data file:
ANS_lysateDMS_raw_all_datasets_exclude_constitutive.tsv
HLFWMBCXY_2_GATCAG_1


title: in vivo ANI_600uL_DMS, DMSMaP-seq

description:
processed data file:
CHX_ANS_invivoDMS_raw_all_datasets_exclude_constitutive.tsv
HGKJYBCXY_TACGAT


title: lysate no_drug_40mM_DMS, DMSMaP-seq

description:
processed data file:
ANS_lysateDMS_raw_all_datasets_exclude_constitutive.tsv
HLFWMBCXY_2_ACAGTG_1


title: lysate no_drug_NO_DMS, DMSMaP-seq

description:
processed data file:
ANS_lysateDMS_raw_all_datasets_exclude_constitutive.tsv
HLFWMBCXY_2_TGACCA_1


title: APO_1

description:
polyA RNA
StrandNGS_Apocynin_MKN45_sphere.xlsx

tag: cell line


title: 3AT_CHX

description:
processed data file: CHX_21ntRPF_occupancy.csv
3AT_CHX


title: 1st infection: Mice C.muridarum week 2 control replicate 5

value: Sham Infected with PBS


title: WT_CHX1

description:
This is duplicated sample record of GSM2387080 (GSE89704) for the convenient retrieval of the complete raw data from SRA.
processed data file: CHX_21ntRPF_occupancy.csv
WT.1


title: in vivo CHX_600uL_DMS, DMSMaP-seq

description:
processed data file:
CHX_ANS_invivoDMS_raw_all_datasets_exclude_constitutive.tsv
HF2VJBCXY_GATCAG


title: 1st infection: Mice C.muridarum week 1 exposure replicate 2


title: in vivo CHX_300uL_DMS, DMSMaP-seq

description:
processed data file:
CHX_ANS_invivoDMS_raw_all_datasets_exclude_constitutive.tsv
HF2VJBCXY_ACTTGA


title: in vivo ANI_NO_DMS, DMSMaP-seq

description:
processed data file:
CHX_ANS_invivoDMS_raw_all_datasets_exclude_constitutive.tsv
HF2VJBCXY_ACGACT


title: in vivo CHX_NO_DMS, DMSMaP-seq

description:
processed data file:
CHX_ANS_invivoDMS_raw_all_datasets_exclude_constitutive.tsv
HF2VJBCXY_CAGATC


title: 1st infection: Mice C.muridarum week 1 exposure replicate 1


title: in vivo no_drug_600uL_DMS, DMSMaP-seq

description:
processed data file:
CHX_ANS_invivoDMS_raw_all_datasets_exclude_constitutive.tsv
HF2VJBCXY_GCCAAT


title: in vivo no_drug_300uL_DMS, DMSMaP-seq

description:
processed data file:
CHX_ANS_invivoDMS_raw_all_datasets_exclude_constitutive.tsv
HGKJYBCXY_GCAGCT


title: in vivo no_drug_NO_DMS, DMSMaP-seq

description:
processed data file:
CHX_ANS_invivoDMS_raw_all_datasets_exclude_constitutive.tsv
HGKJYBCXY_CAGCAT


title: 1st infection: Mice C.muridarum week 1 control replicate 3


title: 1st infection: Mice C.muridarum week 1 control replicate 4


title: Immature pollen grains-ATT conditions (IPGs_ATT)

city: Frankfurt am Main

first: GenXPro

last: GenXPro

address: Altenhöferallee 3

institute: GenXPro GmbH

description:
Pollen3017Pool2HS_IPGs-ATT
library strategy: MACE (massive analysis of cDNA ends)

data_processing:
Sequencing on Illumina HiSeq 2000, basecalling pipeline: HiSeq Control Software 1.5.15.1, RTA 1.13.48.0, CASAVA-1.8.2, Flow cell version: HiSeq Flow Cell v3, Kit version: TruSeq SBS Kit v3
Sequences were cleaned from duplicates ("TrueQuant"), Bases with low sequencing quality were trimmed.
The trimmed reads were mapped to ITAG2.3 Solanum lycopersicum using "SOAP2.2" with the following parameters “-p 16 -r 2 -v 5 -w 10 -g 1“
Expression analysis was performed by in-house scripts and DEGSeq (R-package)
Genome_build: ITAG2.3 Solanum lycopersicum
Supplementary_files_format_and_content: Tab-delimited text files contain read counts, normalized read counts, p-values, fold changes

organism: Solanum lycopersicum

source_name: tomato pollen grains

growth_protocol: Tomato plants were grown in temperature-controlled greenhouses at the Volcani Center, Bet Dagan, Israel, with day/night temperatures of 26/22 oC, day length of 13–14 h, and under natural illumination conditions until development of the second truss. In separate greenhouses, plants bearing 2-3 inflorescences were exposed to either control conditions (C; maintained at 25 to 26 oC) or to a mild heat treatment (ATT;  1 h at 38 oC followed by 1 h recovery at 25 oC). Plants were watered during the heat treatments to avoid drought stress and wilting.

extract_protocol:
For transcriptome analysis, pollen grains were derived from plants that were maintained under control conditions and from plants that were exposed to the above-detailed ATT conditions. For each pollen sample, anthers collected from 90 flowers, at developmental stages of three, two, one and zero days before anthesis were dissected and pollen grains were obtained by slicing the anthers transversely and vortexing them in cold, sucrose-free germination solution. The solution was then filtered and pollen grains separated. The released pollen grains were immediately frozen in liquid nitrogen and kept frozen at -80 oC until use. Pollen grains were ground to a fine powder using liquid nitrogen and sea sand (Merck, Darmstadt, Germany) and total RNA was extracted using the Tri-reagent (Sigma Aldrich, Israel). Before further analyses, RNA derived from three stages of pollen maturation (three, two and one days before flower opening, corresponding to post-meiotic immature pollen grains; IPGs) was combined, using equal amounts, into one pool, generating a pooled sample of IPGs RNA, in addition to RNA isolated from mature pollen grains (zero days before flower opening; MPGs), that constituted a separate sample.
For preparation of MACE libraries, poly-adenylated mRNA was isolated from 1 μg of the large fraction of total RNA using Dynabeads® mRNA Purification Kit (Life Technologies GmbH) and cDNA was produced by first and second strand synthesis using the SuperScript® III First-Strand Synthesis System (Life Technologies GmbH). , but with modified, barcoded poly-T adapters that are suitable to bind on the Illumina Hiseq2000 flow cell and that are biotinylated at the very 5′ end. After cDNA production, the biotinylated cDNA was random-fragmented to reach an average size of 250 bps, the 3′ends were captured by streptavidin beads and GenXPro’s TrueQuant adapters were ligated. Ten barcoded samples were sequenced simultaneously in one lane of an Illumina Hiseq2000 with 1 × 94 bps.

tag: genotype/cultivar

value: cv. 3017 (heat-sensitive)

value: pollen (male gametophyte)

tag: developmental stage

value: immature (post-meiotic)

tag: type

value: combined 3 stages of pollen maturation


title: Mature pollen grains-ATT conditions (MPGs_ATT)

description:
PollenAHS_MPGs-ATT
library strategy: MACE (massive analysis of cDNA ends)

value: mature

value: mature pollen grains


title: 1st infection: Mice C.muridarum week 1 control replicate 1

tag: type of infection

value: 1st Infection

tag: isolation time,post infection


title: 1st infection: Mice C.muridarum week 1 exposure replicate 3

tag: replicate

tag: infection


title: in vivo ANI_300uL_DMS, DMSMaP-seq

description:
processed data file:
CHX_ANS_invivoDMS_raw_all_datasets_exclude_constitutive.tsv
HF2VJBCXY_ATCAGT

value: Wild-Type


title: Mature pollen grains-control conditions (MPGs_C)

description:
3017PollenA2_MPGs-C
library strategy: MACE (massive analysis of cDNA ends)


title: Immature pollen grains-control conditions (IPGs_C)

description:
3017PollenPool2_IPGs-C
library strategy: MACE (massive analysis of cDNA ends)


title: 102613-001-017

status: Public on Jan 26 2019

city: Rotterdam

first: Andre

last: Boonstra

address: Dr. Molewaterplein 40

department: Dept. of Gastroenterology and Hepatology

country: Netherlands

institute: Erasmus MC

description:
Demultiplex_ID: Merged_102613-001-017
processed data file: Nkseq_processed_GEO.txt

data_processing:
The trimmed fastQ files were aligned to build human_g1k_v37 Ensembl Release 75 reference genome using STAR/2.5.1b-foss-2015b [Dobin A et al. 2012] with default settings. Before gene quantification picard/2.2.2-foss-2015b-Java-1.8.0_74 [Picard] was used to sort the aligned reads. Dropseq Drop-seq_tools/1.12-Java-1.7.0_80 [Macosko et al. 2015] was used for flagging individual cells and UMI's. The gene level quantification was performed again by using Dropseq filtering readcount on unique UMI's. Ensembl version 75 was used as gene annotation database.
Genome_build: human_g1k_v37 Ensembl Release 75
Supplementary_files_format_and_content: Nkseq_processed_GEO.txt: Tab-delimited text file contains FPKM values.

source_name: PBMC

growth_protocol: Not applicable.

extract_protocol:
Total RNA was isolated from purified NK cells using the PicoPure® RNA Isolation Kit (Arcturus). To assess the quantity of the samples, the concentration of the RNA was determined using the Nanodrop ND1000 spectrophotometer. The quality and integrity of the RNA samples were analyzed on a RNA 6000 Lab-on-a-Chip using the Bioanalyzer 2100 (Agilent Technologies). mRNA was isolated from total RNA using the poly-T-oligo-attached magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed.
The sequence libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) according to the manufacturer's protocol. The quality and yield after sample preparation were measured with a DNA 1000 Lab-on-a-Chip. The size of the resulting products had a peak around 300 basepairs on a DNA 1000 chip.

treatment_protocol: Not applicable.

tag: cell type

value: CD3-CD56+ NK cells

tag: gender

tag: diagnosis

value: Healthy

tag: hbv clinical phase


title: 102613-001-015

description:
Demultiplex_ID: Merged_102613-001-015
processed data file: Nkseq_processed_GEO.txt

value: Male

value: Chronic HBV

value: Immune Active


title: 102613-001-001

description:
Demultiplex_ID: Merged_102613-001-001
processed data file: Nkseq_processed_GEO.txt

value: Immune Tolerant


title: 102613-001-005

description:
Demultiplex_ID: Merged_102613-001-005
processed data file: Nkseq_processed_GEO.txt


title: 103078-001-011

description:
Demultiplex_ID: Merged_103078-001-011
processed data file: Nkseq_processed_GEO.txt

value: HIV


title: 102613-001-007

description:
Demultiplex_ID: Merged_102613-001-007
processed data file: Nkseq_processed_GEO.txt

value: Female


title: 102613-001-020

description:
Demultiplex_ID: Merged_102613-001-020
processed data file: Nkseq_processed_GEO.txt


title: 102613-001-018

description:
Demultiplex_ID: Merged_102613-001-018
processed data file: Nkseq_processed_GEO.txt


title: 102613-001-014

description:
Demultiplex_ID: Merged_102613-001-014
processed data file: Nkseq_processed_GEO.txt


title: 102613-001-019

description:
Demultiplex_ID: Merged_102613-001-019
processed data file: Nkseq_processed_GEO.txt


title: 102613-001-002

description:
Demultiplex_ID: Merged_102613-001-002
processed data file: Nkseq_processed_GEO.txt


title: 102613-001-016

description:
Demultiplex_ID: Merged_102613-001-016
processed data file: Nkseq_processed_GEO.txt


title: 103078-001-009

description:
Demultiplex_ID: Merged_103078-001-009
processed data file: Nkseq_processed_GEO.txt


title: 1st infection: Mice C.muridarum week 1 control replicate 2

value: Week 1

value: Sham Infected with PBS

tag: infection volume

tag: inclusion forming unit (ifu)

tag: strain

value: C57BL/6 J

value: Wild Type

tag: Sex

tag: age

value: 8 weeks old

tag: tissue

value: Whole Genital Tract


title: 103078-001-008

description:
Demultiplex_ID: Merged_103078-001-008
processed data file: Nkseq_processed_GEO.txt


title: 102613-001-012

description:
Demultiplex_ID: Merged_102613-001-012
processed data file: Nkseq_processed_GEO.txt

value: HBeAg- Hepatitis


title: 102613-001-008

description:
Demultiplex_ID: Merged_102613-001-008
processed data file: Nkseq_processed_GEO.txt


title: 102613-001-013

description:
Demultiplex_ID: Merged_102613-001-013
processed data file: Nkseq_processed_GEO.txt


title: 102613-001-009

description:
Demultiplex_ID: Merged_102613-001-009
processed data file: Nkseq_processed_GEO.txt


title: MMP8 vs Control MDA-MB-231

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: Analysis corresponds to MDA-MB-231 MMP8 vs MDA-MB-231 control

hyb_protocol: 30000.0 ng at 53 degree_C during 24 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none, Software used : limmagui --> data obtained from log of processed Red signal/processed Green signal.

source_name: MDA-MB-231 control

label_protocol: Home-made (IPMC)

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 1% antibiotic antimycotic (Gibco)

extract_protocol: Qiagen RNeasy

tag: cell line

value: MDA-MB-231 cell line

source_name: MDA-MB-231 MMP8


title: Crush Tsc2 cKO replicate 4C

city: St Louis

last: Carlin

state: MO

address: 660 S Euclid Ave / Campus Box 8108

department: Neuroscience

institute: Washington University in St Louis

data_processing:
Samples were QC’d using FastQC and not trimmed
Reads were aligned to mm10 using STAR-align with default settings  Reads aligned to mm10 using STAR-align with default settings
Reads aligned to genes were counted using Htseq-counts with default settings
Technical replicates were collapsed in DESeq2
Differential expression was calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Counts files generated from HTseq-count

source_name: Crush Tsc2 cKO

extract_protocol:
3 days post-injury mice were sacrificed. L4 dorsal root ganglia contralateral to injury were isolated, dissociated with papain and collagenase and passed through 70 um filter. Cells were FACS sorted for GFP-positive cells into Clontech lysis buffer with 5% RiboLock Rnase Inhibitor (Thermo Fisher).
Library preparation was performed with ~100 cells collected by flow cytometry in 10 ul of Clontech’s reaction buffer using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Clontech) per manufacturer’s protocol. Three technical replicates of 100 cells each (A-C) were obtained for each biological replicate (1-4). cDNA was amplified for 13 cycles. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty cycle 20%, cycles/burst 50, time 120 seconds at room temperature. cDNA was blunt ended, had an A base added to the 3’ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.

treatment_protocol: Sciatic nerve of mice was crushed with forceps.

tag: strain background

value: mixed:C57BL/6 and AJ

value: 8-9 weeks

value: female

tag: genotype

value: Nav1.8-Cre; Tsc2 flox/null; Rosa26-ZsGreen

value: L4 dorsal root ganglia ipsilateral to sciatic nerve crush

value: Nav1.8-positive dorsal root ganglia neurons

tag: sorted fraction

value: 100 FACS-sorted GFP-positive cells


title: 102613-001-006

description:
Demultiplex_ID: Merged_102613-001-006
processed data file: Nkseq_processed_GEO.txt

value: CD3-CD56+ NK cells

value: Chronic HBV

value: Immune Tolerant


title: Crush Tsc2 cKO replicate 4B


title: Crush Tsc2 cKO replicate 4A


title: 102613-001-004

description:
Demultiplex_ID: Merged_102613-001-004
processed data file: Nkseq_processed_GEO.txt

value: Male


title: 103078-001-003

description:
Demultiplex_ID: Merged_103078-001-003
processed data file: Nkseq_processed_GEO.txt

value: HIV


title: 102613-001-011

description:
Demultiplex_ID: Merged_102613-001-011
processed data file: Nkseq_processed_GEO.txt


title: Crush Tsc2 cKO replicate 3C


title: Crush Tsc2 cKO replicate 3B


title: 103078-001-010

description:
Demultiplex_ID: Merged_103078-001-010
processed data file: Nkseq_processed_GEO.txt


title: Crush Tsc2 cKO replicate 3A


title: Crush Tsc2 cKO replicate 2C

value: male


title: 102613-001-003

description:
Demultiplex_ID: Merged_102613-001-003
processed data file: Nkseq_processed_GEO.txt

value: Female


title: 102613-001-010

description:
Demultiplex_ID: Merged_102613-001-010
processed data file: Nkseq_processed_GEO.txt


title: 103078-001-002

description:
Demultiplex_ID: Merged_103078-001-002
processed data file: Nkseq_processed_GEO.txt


title: 103078-001-007

description:
Demultiplex_ID: Merged_103078-001-007
processed data file: Nkseq_processed_GEO.txt

value: Healthy


title: 103078-001-006

description:
Demultiplex_ID: Merged_103078-001-006
processed data file: Nkseq_processed_GEO.txt


title: Crush Tsc2 cKO replicate 2B


title: Crush Tsc2 cKO replicate 1C


title: Crush Tsc2 cKO replicate 1B


title: Crush Tsc2 cKO replicate 1A


title: Crush Tsc2 cKO replicate 2A


title: Crush control replicate 4C

source_name: Crush control

value: Nav1.8-Cre; Tsc2 flox/+; Rosa26-ZsGreen


title: 103078-001-005

description:
Demultiplex_ID: Merged_103078-001-005
processed data file: Nkseq_processed_GEO.txt


title: 103078-001-004

description:
Demultiplex_ID: Merged_103078-001-004
processed data file: Nkseq_processed_GEO.txt


title: IL10neg Donor3

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: University of Zurich

data_processing:
Basecalls performed with bcl2fastq-1.8.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Counts were generated using RSEM 1.2.22  against Ensembl reference GRCh37 with following parameters: --calc-ci --ci-memory 12256
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw count file was generated by aggregating the transcript-level counts from RSEM.

source_name: Group 2 innate lymphoid cells (ILC2s)

growth_protocol: Human ILC2s were expanded in Yssel's medium supplemented with 1% human AB serum, together with irradiated PBMCs and 100 U/ml recombinant human IL-2 for 3 weeks.

extract_protocol:
IL-10 positive and negative ILCs were isolated using an IL-10 secretion assay (Miltenyi Biotec) and cell sorter.
RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA stranded protocols.

treatment_protocol: Human ILC2s were stimulated with IL-2, IL-33 and all-trans retinoic acid.

value: Group 2 innate lymphoid cells (ILC2s)

tag: il10 status

tag: donor


title: IL10pos Donor3


title: IL10neg Donor2


title: Crush control replicate 4B

value: mixed:C57BL/6 and AJ


title: Crush control replicate 3C

value: 8-9 weeks


title: IL10pos Donor2


title: Crush control replicate 2C


title: IL10neg Donor1


title: 103078-001-012

description:
Demultiplex_ID: Merged_103078-001-012
processed data file: Nkseq_processed_GEO.txt


title: Crush control replicate 3A

value: female


title: IL10pos Donor1


title: Crush control replicate 2B


title: 103078-001-001

description:
Demultiplex_ID: Merged_103078-001-001
processed data file: Nkseq_processed_GEO.txt

value: HCV


title: Crush control replicate 2A

value: L4 dorsal root ganglia ipsilateral to sciatic nerve crush


title: Crush control replicate 1B

value: Nav1.8-positive dorsal root ganglia neurons


title: Uninjured Tsc2 cKO replicate 4C

source_name: Uninjured Tsc2 cKO

value: Nav1.8-Cre; Tsc2 flox/null; Rosa26-ZsGreen

value: L4 dorsal root ganglia contralateral to sciatic nerve crush

value: 100 FACS-sorted GFP-positive cells


title: Uninjured Tsc2 cKO replicate 4B


title: Crush control replicate 1C


title: Crush control replicate 1A


title: Crush control replicate 3B


title: Uninjured Tsc2 cKO replicate 4A


title: Uninjured Tsc2 cKO replicate 2C


title: Uninjured Tsc2 cKO replicate 3A


title: Uninjured Tsc2 cKO replicate 3C


title: H3K27menoDOX9_S5.merged.bam

city: Utrecht

first: Ana

last: Lourenço

address: Uppsalalaan 8

institute: UMC Utrecht

data_processing:
ChIP-sequencing reads were mapped with Bowtie 2.1.0 against the reference genome (hg19) using default settings (Langmead and Salzberg, 2012).
Peaks were called with HOMER software using the input as a control (Fold over local region=8, Fold over input=2) (Heinz et al., 2010).
Mapped fragments were extended according to the average fragment size and converted to TDF files, visualized with IGV tools v2.3.36 and represented as coverage normalized tracks (Robinson et al., 2011). SAMtools was used for manipulation of SAM and BAM files; manipulation of BED file format was performed with BEDtools (Li et al., 2009; Quinlan and Hall, 2010).
Motif discovery, peak annotation and generation of histograms were performed using HOMER software. For motif discovery the 200 bp sequence surrounding each peak was examined and motifs with length of 8, 10 and 12 nt were searched. Motifs were identified through de novo motif discovery.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig

source_name: Immortalized human mammary epithelial cells

growth_protocol: Cell lines were grown according to manufacture]s protocol

extract_protocol:
Crosslink was performed with disuccinimidyl glutarate (DSG) (Thermo Scientifis) for 45 minutes followed by 30 minutes incubation with formaldehyde 1%. The reaction was blocked with glycine 100 mM. Shearing was performed using Covaris S2 (Covaris, Woburn, MA) for 8 min at maximum intensity. The sonicated chromatin was incubated O/N at 4°C in presence of antibodies as described in (https://elifesciences.org/articles/27706) coupled to A/G sepharose beads (Santa Cruz Biotechnology).
Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA) was used for End-repair, A-tailing and ligation of sequence adaptors. Samples were amplified by PCR and the libraries were size-selected in the 200-500 bp range.

treatment_protocol: Doxycycline (samples 1,3,5,8) or nothing

tag: immunoprecipitation

value: H3K27 methylation

tag: treatment

value: minus doxycycline

tag: antibody

value: anti-H3K27Me ChIP-seq


title: Uninjured Tsc2 cKO replicate 2B

first: Dan

value: male

tag: cell type


title: H3K27acnoDOX8_S4.merged.bam

value: Immortalized human mammary epithelial cells

value: H3K27 acetylation

value: anti-H3K27Ac ChIP-seq


title: H3K27meDOX14_S10.merged.bam

value: plus doxycycline


title: HMECsinput.merged.bam.sorted.bam

value: Input

value: input ChIP-seq


title: H3K27acDOX13_S9.merged.bam


title: Crush control replicate 4A

value: mixed:C57BL/6 and AJ

value: 8-9 weeks

value: female

value: Nav1.8-Cre; Tsc2 flox/+; Rosa26-ZsGreen


title: Uninjured Tsc2 cKO replicate 1C

value: Nav1.8-Cre; Tsc2 flox/null; Rosa26-ZsGreen

value: Nav1.8-positive dorsal root ganglia neurons


title: POL2noDOX6_S2.merged.bam

value: anti-Pol2 ChIP-seq


title: Uninjured Tsc2 cKO replicate 1B

value: L4 dorsal root ganglia contralateral to sciatic nerve crush

value: 100 FACS-sorted GFP-positive cells


title: H3K4noDOX7_S3.merged.bam

value: H3K4 trimethylation

value: minus doxycycline

value: anti-H3K4me ChIP-seq


title: Uninjured control replicate 4C

source_name: Uninjured control


title: Uninjured Tsc2 cKO replicate 2A

value: male


title: Uninjured control replicate 4B


title: H3K4DOX12_S8.merged.bam

value: Immortalized human mammary epithelial cells


title: Uninjured control replicate 4A


title: POL2DOX11_S7.merged.bam

value: plus doxycycline


title: Uninjured Tsc2 cKO replicate 3B


title: ERSOX4plus2

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly) using TopHat v2.0.9 as previously described (Trapnell et al., 2012). Only uniquely mapped reads were selected for further analysis.
guide transcripts were assembled using CuffLinks v2.2.1. Reads were quartile normalized using the –library-norm-method quartile option.
Differential gene analysis was performed using CuffDiff.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing  average differential gene expression FPKM normalized values

extract_protocol:
total RNA-isolation with RNAeasy kit (Qiagen)
TruSeq stranded ribo-zero kit (Illumina)
Samples were sequenced on the NextSeq 500 (Illumina), SE75

treatment_protocol: Upon lentiviral transduction HMLEs were grown and expanded under puromycin selection before RNA-isolation (0.5 µg/mL)

tag: construct

value: plus 4OH-tamoxifen


title: Uninjured control replicate 3C


title: Uninjured control replicate 3B


title: ERSOX4plus1


title: Uninjured control replicate 2C


title: ERSOX4min2

value: minus 4OH-tamoxifen


title: ERSOX4min1


title: Uninjured control replicate 1B

value: mixed:C57BL/6 and AJ


title: Uninjured control replicate 2A

value: 8-9 weeks


title: Uninjured control replicate 1A


title: Uninjured Tsc2 cKO replicate 1A


title: Uninjured control replicate 1C


title: ERplus1

value: ER


title: ERmin2


title: Uninjured control replicate 2B

value: Nav1.8-Cre; Tsc2 flox/+; Rosa26-ZsGreen