title: Hypoxic

city: VALENCIA

first: LOMAS LOPEZ

last: RODRIGO

address: C/ Eduardo Primo Yúfera, 3 (junto Oceanogràfic)

institute: CIPF

data_processing:
The quality of the raw sequence data received from Illumina was checked using the main functions of FastQC to report the quality confirmation.
Sequence reads were mapped using TopHat v1.0.12 with parameters -I 69, to avoide the identification of splice junctions, and fr-secondstrand as library type.
Nucleotide coverage in all two samples has been created by Bedtools using strandspecificic bam files and C.pneumoniae genome.
Gene coverage was calculated using Htseq.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The differential expression analysis was done using the Bioconductor package NOISeq version 2.6.0. The NOISeq-sim function included in the package allows for differential expression estimates in absence of replication by simulating replicates considering that reads counts follow a multinominal distribution.
Genome_build: GeneBank, version AE001363.1
Supplementary_files_format_and_content: counts and RPKM

organism: Chlamydia pneumoniae

source_name: C. pneumoniae

extract_protocol:
total RNA of normoxic and hypoxic chlamydial infected HEp-2 cells was isolated by NucleoSpin RNA kit (Macherey Nagel). Human rRNA was depleted by RiboZero rRNA removal kit (Epicentre) in order to enrich bacterial RNA. The tagged cDNA libraries, in the size range of 250 –400 bp, were pooled and single-read sequencing (read length 50 bp) was performed on Illumina HiSeq 2000 by BGI-Hong Kong
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After infection, the cells were cultivated for the indicated time points at 20% oxygen (normoxia) or 2% oxygen (hypoxia) in a hypoxia chamber equipped with an oxygen and carbon dioxide sensor

value: C. pneumoniae CWL029

tag: infected cells

value: Chlamydial infected HEp-2 cells

value: wild type


title: MGAS10870 A

status: Public on Nov 24 2017

type: SRA

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

country: USA

institute: University of Nevada

library_source: transcriptomic

data_processing:
Rockhopper version 2.03 was used to align sequencing reads to the genome, quantify transcript abundance, and test for differential gene expression. Expression levels correspond to RPKM values except that values are normalized using upper quartile normalization.
Genome_build: For the M1 data we aligned it to the MGAS5005 genome (NC_007297), while for the M3 data we aligned it to the MGAS315 genome (NC_004070).
Supplementary_files_format_and_content: Excel file containing columns for the M3 GAS gene name, M3 GAS gene name synonym, M3 gene product description, M3 GAS gene expression level, corresponding M1 GAS gene columns, q-value, and expression ratio (M3/M1).

molecule: total RNA

organism: Streptococcus pyogenes serotype M3

source_name: MGAS10870 A

growth_protocol: GAS strains were grown in THY broth to the mid-exponential phase of growth (O.D.600 = 0.5).

extract_protocol:
Total RNA was isolated and rRNAs were depleted using the Ribo-Zero Gram-Positive rRNA Removal Kit (Epicentre).
The rRNA depleted RNA was used to generate cDNA libraries using the ScriptSeq kit (Epicentre).  Briefly, RNA was fragmented, cDNA was synthesized using random hexamers containing a 5′ tagging sequence, the RNA was hydrolyzed, and the cDNA was tagged at the 3′ end.  A limited number of PCR cycles (n=12) were used to amplify the libraries via the 5′ and 3′ tags (the libraries were barcoded by using different primers), and the libraries size-selected (170 to 300 bp).  The size-selected and barcoded libraries were run on an Illumina HiSeq flowcell.

tag: strain

value: Parental M3 GAS isolate

tag: age

value: Exponential phase of growth

tag: growth medium

value: THY broth growth


title: MLF623

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

description: Strand-specific RNA-seq (dUTP)

data_processing:
RNA-seq processing:
RNA-seq data was analysed with the nextpresso pipeline as follows:
Reads are quality-checked with FastQC, and aligned to the mouse genome (GRCm38/mm10) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits
Differential expression is calculated with DESeq2, using the Mus musculus GRCm38/mm10 transcript annotations from the UCSC Genome Browser
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Normalized counts are calculated with DESeq2

organism: Mus musculus

source_name: CIC LOF T-ALL

growth_protocol: Tissue was extracted and snap-frozen in liquid nitrogen

extract_protocol:
RNA was extracted with the RNeasy Mini Kit (Qiagen #74104) and a DNA digestion step with RNase free Dnase Set (Qiagen #79254) was included.
PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina’s “TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D” kit

treatment_protocol: Not applicable

value: Mixed C57BL/6-129

tag: treatment

value: Tamoxifen-diet from weaning until humane end point.

tag: genotype

value: Cic(lox/lox) hUBC-CreERT2(+/T)


title: Normoxic


title: Control, SP

city: Okazaki

first: Rie

last: Ohashi

address: Nishigonaka 38, Myodaiji

country: Japan

institute: National Institute for Basic Biology

description:
cont_SP-vs-SR_gene_exp.diff
SP_cont-vs-cKO_gene_exp.diff

data_processing:
Illumina CASAVA version 1.8 software used for basecalling.
Sequence reads were mapped to mouse genome (Mus musculus Ensemble NCBIM37) using TopHat (v 2.0.11) with parameters -p 4 -G.
The mapped reads were assembled by Cufflinks (v 2.2.1), and differential gene enrichment analysis was conducted by Cuffdiff.
Genome_build: Mus musculus Ensemble NCBIM37
Supplementary_files_format_and_content: diff files (tab-delimited text files) include test id, gene id, gene name, locus, test status, FPKM value, log2 (fold change), test statistic value, p value, q value and significant for each sample.

molecule: polyA RNA

source_name: Hippocampus, SP

extract_protocol:
SP and SR in the CA1 region in the hippocampus were microdissected, and RNA was extracted from the tissues using ISOGEN (Nippon Gene).
Total RNA (200 ng per sample) was used as the starting material to prepare cDNA using TruSeq RNA sample Preparation Kit v2 (Illumina) at a half scale compared with the manufacturer's protocols, as follows. Poly-A-containing mRNAs were purified using Oligo dT magnetic beads. After the mRNAs were denatured and fragmented, first-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Thermo Fisher Scientific), and then second-strand cDNA was synthesized. After the ends of the fragments were blunted, an adenine nucleotide was added to the 3'-end. RNA adapter index was ligated to the 5'- and 3'-ends of the ds cDNA, and the cDNA was amplified with 10 PCR cycles.

tag: tissue

value: hippocampal SP

value: postnatal 12 weeks


title: Tus_BRCA1flox_siFANCM_Rep2

status: Public on Nov 23 2017

city: Stanford

first: Richard

middle: L

last: Frock

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

description:
title: effector_genotype_siRNA_replicate
Tus_BRCA1flox_siFANCM_s3.txt

library_source: genomic

data_processing:
Library strategy: LAM-HTGTS
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml)
1xGFP cassette sequence: ATTAAGGGATCTGTAGGGCGCAGTAGTCCAGGGTTTCCTTGATGATGTCATACTTATCCTGTCCCTTTTTTTTCCACAGCTCGCGGTTGAGGACAAACTCTTCGCGGTCTTTCCAGTGGGGATCGACGGTATCGTAGAGTCGAGGCCGCTCTAGAActagtggatctaccatgaccgagtacaagcccacggtgcgcctcgccacccgcgacgacgtcccccgggccgtacgcaccctcgccgccgcgttcgccgactaccccgccacgcgccacaccgtcgacccggaccgccacatcgagcgggtcaccgagctgcaagaactcttcctcacgcgcgtcgggctcgacatcggcaaggtgtgggtcgcggacgacggcgccgcggtggcggtctggaccacgccggagagcgtcgaagcgggggcggtgttcgccgagatcggcccgcgcatggccgagttgagcggttcccggctggccgcgcagcaacagatggaaggcctcctggcgccgcaccggcccaaggagcccgcgtggttcctggccaccgtcggcgtctcgcccgaccaccagggcaagggtctgggcagcgccgtcgtgctccccggagtggaggcggccgagcgcgccggggtgcccgccttcctggagacctccgcgccccgcaacctccccttctacgagcggctcggcttcaccgtcaccgccgacgtcgagtgcccgaaggaccgcgcgacctggtgcatgacccgcaagcccggtgcctgactcgaccctagggggaggctaactgaaacacggaaggagacaataccggaaggaacccgcgctatgacggcaataaaaagacagaataaaacgcacggtgttgggtcgtttgttcataaacgcggggttcggtcccagggctggcactctgtcgataccccaccgagaccccattggggccaatacgcccgcgtttcttccttttccccaccccaccccccaagttcgggtgaaggcccagggctcgcagccaacgtcggggcggcaggccctgccatagcctcaggttactcgGATCTCGACCtcgagACGCGTGCCCCCACTCCACAATTTCAAAAAAAAGAGTGGCCACTTGTCTTTGTTTATGGGCCCCATTGGCGTGGAGCCCCGTTTAATTTTCGGGGGTGTTAGAGACAACCAGTGGAGTCCGCTGCTGTCGGCGTCCACTCTCTTTCCCCTTGTTACAAATAGAGTGTAACAACATGGTTCACCTGTCTTGGTCCCTGCCTGGGACACATCTTAATAACCCCAGTATCATATTGCACTAGGATTATGTGTTGCCCATAGCCATAAATTCGTGTGAGATGGACATCCAGTCTTTACGGCTTGTCCCCACCCCATGGATTTCTATTGTTAAAGATATTCAGAATGTTTCATTCCTACACTAGTATTTATTGCCCAAGGGGTTTGTGAGGGTTATATTGGTGTCATAGCACAATGCCACCACTGAACCCCCCGTCCAAATTTTATTCTGGGGGCGTCACCTGAAACCTTGTTTTCGAGCACCTCACATACACCTTACTGTTCACAACTCAGCAGTTATTCTATTAGCTAAACGAAGGAGAATGAAGAAGCAGGCGAAGATTCAGGAGAGTTCACTGCCCGCTCCTTGATCTTCAGCCACTGCCCTTGTGACTAAAATGGTTCACTACCCTCGTGGAATCCTGACCCCATGTAAATAAAACCGTGACAGCTCATGGGGTGGGAGATATCGCTGTTCCTTAGGACCCTTTTACTAACCCTAATTCGATAGCATATGCTTCCCGTTGGGTAACATATGCTATTGAATTAGGGTTAGTCTGGATAGTATATACTACTACCCGGGAAGCATATGCTACCCGTTTAGGGTTAACAAGGGGGCCTTATAAACACTATTGCTAATGCCCTCTTGAGGGTCCGCTTATCGGTAGCTACACAGGCCCCTCTGATTGACGTTGGTGTAGCCTCCCGTAGTCTTCCTGGGCCCCTGGGAGGTACATGTCCCCCAGCATTGGTGTAAGAGCTTCAGCCAAGAGTTACACATAAAGGTACGTAccagtcTTCGAAagatcCTACCGGGTAGGGGAGGCGCTTTTCCCAAGGCAGTCTGGAGCATGCGCTTTAGCAGCCCCGCTGGCACTTGGCGCTACACAAGTGGCCTCTGGCCTCGCACACATTCCACATCCACCGGTAGCGCCAACCGGCTCCGTTCTTTGGTGGCCCCTTCGCGCCACTTCTACTCCTCCCCTAGTCAGGAAGTTTCCCCCAGCAAGCTCGCGTCGTGCAGGACGTGACAAATGGAAGTAGCACGTCTCACTAGTCTCGTGCAGATGGACAGCACCGCTGAGCAATGGAAGCGGGTAGGCCTTTGGGGCAGCGGCCAATAGCAGCTTTGTTCCTTCGCTTTCTGGGCTCAGAGGCTGGGAAGGGGTGGGTCCGGGGGCGGGCTCAGGGGCGGGCTCAGGGGCGGGCGGGCGCCCGAAGGTCCTCCCGAGGCCCGGCATTCTGCACGCTTCAAAAGCGCACGTCTGCCGCGCTGTTCTCCTCTTCCTCATCTCCGGGCCTTTCGACCTGCAGCCCAAGCTctagcgctaccggtcgccaccatggtgagcaagggcgaggagctgttcaccggggtggtgcccatcctggtcgagctggacggcgacgtaaacggccacaagttcagcgtgtccggcgagggcgagggcgatgccacctacggcaagctgaccctgaagttcatctgcaccaccggcaagctgcccgtgccctggcccaccctcgtgaccaccctgacctacggcgtgcagtgcttcagccgctaccccgaccacatgaagcagcacgacttcttcaagtccgccatgcccgaaggctacgtccaggagcgcaccatcttcttcaaggacgacggcaactacaagacccgcgccgaggtgaagttcgagggcgacaccctggtgaaccgcatcgagctgaagggcatcgtagggataacgctcatatatcgatAATAAGTATGTTGTAACTAAAGTCgtgaAATAAGTATGTTGTAACTAAAGTCTtAcAATAAGTATGTTGTAACTAAAGTgtatacctttccggatagggataacgctcatatatcgatAATAAGTATGTTGTAACTAAAGTCgtgaAATAAGTATGTTGTAACTAAAGTCTtAcAATAAGTATGTTGTAACTAAAGTgtatacctttccggatagggataacagggtaatcaaggaggacggcaacatcctggggcacaagctggagtacaactacaacagccacaacgtctatatcatggccgacaagcagaagaacggcatcaaggtgaacttcaagatccgccacaacatcgaggacggcagcgtgcagctcgccgaccactaccagcagaacacccccatcggcgacggccccgtgctgctgcccgacaaccactacctgagcacccagtccgccctgagcaaagaccccaacgagaagcgcgatcacatggtcctgctggagttcgtgaccgccgccgggatcactctcggcatggacgagctgtacaagtaaagcggccgcgactctagatcataatcagccataccacatttgtagaggttttacttgctttaaaaaacctcccacacctccccctgaacctgaaacataaaatgaatgcaattgttgttgttaacttgtttattgcagcttataatggttacaaataaagcaatagcatcacaaatttcacaaataaagcatttttttcactgcattctagttgtggtttgtccaaactcatcaatgtcggatGGCCGCGCTGGGGATGCGGTGGGCTCTATGGCTTATGAGGCGGAAAGAACCAGCTGGGGCTCGATCCTCTAGTTGGCGCG
Genome_build: mm9; 1xGFP cassette inserted in the ROSA26 locus is artificially placed on Chr1, position1 (replacing the same number of N nucleotides) for alignment purposes within the cassette
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; and the entire stitched paired end read sequence (Seq)

molecule: genomic DNA

source_name: Mouse embryonic  stem (ES) cells

extract_protocol:
DNA was extracted overnight at 55degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203) using RAG1 primers described in Frock et al., 2015 Nature Biotechnology (PMC4320661) and Illumina Miseq sequencing

treatment_protocol: Genomic DNA was collected 48 hours after delivery of nuclease

tag: sirna

value: FANCM

tag: reporter

value: 4kb 1xGFP cassette in ROSA26

tag: nuclease delivery

value: Transfection; Tus/nuclease/siRNA

tag: treatment protocol

value: 48 hour culture post transfection

tag: bait dsb

value: Cas9/US30kb_ROSA26 gRNA

tag: growth protocol

value: MEF feeder; ES medium

tag: extract_protocol (dna fragmentation/blocking methods)

value: Sonication/ XbaI blocking


title: Tus_BRCA1flox_siLuciferase_Rep1

description:
title: effector_genotype_siRNA_replicate
Tus_BRCA1flox_siLuciferase_s2.txt

value: Luciferase


title: MVW435

description: Strand-specific RNA-seq (dUTP)

source_name: Wildtype thymus

value: No treatment

value: wildtype


title: Tus_BRCA1flox_siFANCM_Rep3


title: Tus_BRCA1flox_siFANCM_Rep1


title: wor-GAL4_Brm_n1

city: Hobart

first: Owen

last: Marshall

state: Tas

address: 17 Liverpool St

country: Australia

institute: Menzies Institute for Medical Research

description: DamID

data_processing:
FASTQ files were processed with damidseq_pipeline, default options except for H1 datasets, using either version 1.3 (wor-GAL4 datasets) or version 1.2.6 (other datasets).  Histone H1-vs-Dam samples were generated with the  --norm_method=rpm option.  Biological replicates in gatc.bedgraph format were averaged, and the averaged binding tracks used for further analysis.  Datasets were scaled by dividing each dataset by its standard deviation.
Processed data from the damidseq_pipeline software in gatc.gff format for the five chromatin proxy proteins was merged, sorted by chromosome and location, and a gaussian Hidden Markov Model resolved using the RHmm R package with 2000 random starts and 5 to 15 iterations per start. A Viterbi path was then generated from the best fitting model and the data using the RHmm R package. Each cell type was modeled separately to allow for the possibility that not all chromatin states would be shared between cell types.    Chromatin states were then assigned broad chromatin classes with reference to similarities in protein binding, hclust clustering of state means, and HMM state transition probabilities . States with similar mean protein binding and a high shared emission probability were considered to be related. A simplified Viterbi path was generated from these merged states, and used for subsequent analysis.
Genes were assigned chromatin states based on the modal state. To allow for the large number of short gene bodies in the Drosophila genome and the GATC resolution of the data the modal state was assigned as the state occupying the majority of each gene body + 250bp in each direction. R scripts for the complete data analysis pipeline are available upon request.
Genome_build: DMBDGP6
Supplementary_files_format_and_content: gatc.bedgraph files were generated using the damidseq_pipeline software, at GATC fragment resolution.  Score represents the normalised log2(Dam-fusion/Dam) enrichment.  Processed files are provided as both raw data and scaled data.

organism: Drosophila melanogaster

source_name: dissected 3rd instar larval brain

extract_protocol:
DNA was extracted from the anterior half of torn larvae via Qiagen Blood and Tissue kits as per manufacturers' instructions, digested with DpnI, DamID adaptors ligated, digested with DpnII and amplified via PCR.
DNA was sonicated to an average size of 300bp using a Diagenode Bioruptor and DamID adaptors removed via either AlwI or Sau3AI digestion.  Sonnicated material was end-repaired, A-tailed, sequencing adaptors ligated and PCR amplified.

value: brain

tag: developmental stage

value: 3rd instar larvae


title: Tus_BRCA1del_siLuciferase_Rep2

description:
title: effector_genotype_siRNA_replicate
Tus_BRCA1del_siLuciferase_s3.txt


title: Tus_BRCA1flox_siBLM_Rep1

description:
title: effector_genotype_siRNA_replicate
Tus_BRCA1flox_siBLM_s2.txt

value: BLM


title: Tus_BRCA1flox_siBRCA1_Rep1

description:
title: effector_genotype_siRNA_replicate
Tus_BRCA1flox_siBRCA1_s2.txt


title: Tus_BRCA1flox_siBRCA1_Rep2


title: Tus_BRCA1del_siBRCA1_Rep3

description:
title: effector_genotype_siRNA_replicate
Tus_BRCA1del_siBRCA1_s3.txt


title: Tus_BRCA1del_siBRCA1_Rep2


title: Tus_BRCA1del_siBRCA1_Rep1


title: Tus_BRCA1flox_siBLM_Rep2


title: Tus_BRCA1del_siBLM_Rep1

description:
title: effector_genotype_siRNA_replicate
Tus_BRCA1del_siBLM_s3.txt


title: Tus_BRCA1del_siLuciferase_Rep3


title: ISceI_BRCA1del_siFANCM_Rep2

description:
title: effector_genotype_siRNA_replicate
ISceI_BRCA1del_siFANCM_s2.txt


title: Tus_BRCA1del_siLuciferase_Rep1


title: ISceI_BRCA1del_siFANCM_Rep1


title: Tus_BRCA1del_siFANCM_Rep3

description:
title: effector_genotype_siRNA_replicate
Tus_BRCA1del_siFANCM_s3.txt


title: Tus_BRCA1del_siFANCM_Rep2


title: EV_BRCA1del_siFANCM_Rep2

description:
title: effector_genotype_siRNA_replicate
EV_BRCA1del_siFANCM_s2.txt


title: Tus_BRCA1del_siFANCM_Rep1


title: OB_G3-d3

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

data_processing:
Quality filtering and trimming with fastx toolkit
Adaptor removal with cutadapt
miRNAs were annotated by mapping to mature miRNA sequences from miRBase version 17
miRNA expression was normalized as reads per million (RPM)
Genome_build: hg19

organism: Homo sapiens

source_name: BMSC

growth_protocol: hMSC-TERT were cultured in growth medium (Minimum Essential Medium (MEM) supplemented with 10% FBS and 1% P/S) at 5% CO2 and 37°C.

extract_protocol:
Trizol
Illumina TruSeq small RNA sample preparation. Libraries are barcoded using Illumina Truseq index numbers 1 to 24

treatment_protocol: hMSC-TERT were seeded at 15000/cm2 followed by induction with osteogenic media that contained10 nM dexamethasone, 0.2 mM l-ascorbic acid, 10 mM β-glycerophosphate and 10 mM 1,25-dihydroxyvitamin D3

tag: differentiation time point


title: OB_G3-d10


title: OB_G3-d13


title: Tus_BRCA1del_siBLM_Rep3


title: Tus_BRCA1del_siBLM_Rep2


title: CCR5Q_523_Rep3

description: Processed data file: R1B_CCR5Q_523_s3_N22086.txt

data_processing:
Library strategy: LAM-HTGTS
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml)
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

source_name: 293T-Embryonic Kidney

growth_protocol: DMEM; 10% Fetal calf serum

treatment_protocol:
48 hour culture post transfection
Genomic DNA was collected 48 hours after delivery of nuclease

tag: cell line

value: 293T-Embryonic Kidney

value: WT

value: CaPO4; Cas9/RAG1B; Cas9/CCR5Q +RAD52+dn53BP1

tag: target locus

value: RAG1 (Cas9/RAG1B gRNA)

tag: extract protocol (dna fragmentation/blocking methods)

value: Sonication/EcoNI


title: Tus_BRCA1flox_siLuciferase_Rep2

value: 4kb 1xGFP cassette in ROSA26


title: EV_BRCA1del_siFANCM_Rep1

value: FANCM

value: Transfection; Tus/nuclease/siRNA


title: OB_G3-24h


title: OB_G2-d7


title: OB_G3-d7


title: OB_G2-d3


title: OB_G2-d13


title: WG960039_E05-W24

status: Public on Dec 06 2017

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: Processed data file: molecules_human.xlsx

data_processing:
Reads flagged as invalid by the Illumina HiSeq control software were discarded. In the remaining reads, any 3′ bases with a quality score of B were removed. If any of the six UMI bases in the 5' end had a Phred score <17 the read was discarded, else the UMI was cut away and saved. The following three bases had to be G for the read to be kept. These, as well as any additional up to totally nine (presumably template-switch derived) G:s were cut away. Reads were discarded if the remaining transcript-derived sequence ended in a poly(A) sequence leaving <25 bases, or if the remaining sequence consisted of fewer than six non-A bases or a dinucleotide repeat with fewer than six other bases at either end. The reads were sorted by the well, as defined by the combined two index read barcodes.
Alignment was performed using the Bowtie aligner, allowing for up to three mismatches and up to 24 alternative mappings. Reads with no alignments were realigned against an artificial chromosome, containing all possible splice junctions arising from the exons defined by the UCSC transcript models. The coordinates of aligned splice junctions were translated back to the corresponding genomic positions.
For expression level calculation, the exons of each locus with several transcript variants were merged to a combined model representing total expression of the locus. To account for incomplete cap site knowledge, the 5′ ends of all models were extended by 100 bases, but not beyond the 3′ end of any upstream nearby exon of another gene of the same orientation.
The annotation step was performed separately for each well. For each genomic position and strand combination the number of reads in each UMI was counted. Any multiread that mapped to some repeat outside exons was assigned randomly as one of these repeats and did not contribute to the transcript corresponding to the exon. Else, if the multiread mapped to some exon, and not to any repeat outside exons, it was assigned to the exon where it was closest to the transcript model 5′ end. If it had no exon mapping, it was assigned randomly at one of the mappings. The total number of molecules at each mapping position was determined by the number of distinct UMIs observed. Any UMI represented by only a single read was excluded, in order to reduce false molecules due to PCR and sequencing errors. The raw UMI count was corrected for the UMI collision probability. For the human samples all reads mapping anywhere within the whole locus, defined as the region (including actual introns) from the start of the 100 base 5'end extension of the first exon up to the end of the last exon, were counted as exon-derived.
Genome_build: UCSC mm10 (GRCm38) and hg19 (GRCh37)
Supplementary_files_format_and_content: *xlsx: Excel tables of mRNA molecule counts with genes in rows and cells in columns.

source_name: middle temporal gyrus

growth_protocol: Male and female wild type CD-1 mice (Charles River) between postnatal days 21-37 were used. Postmortem human brain tissue was provided to the Allen Institute for Brain Science by the San Diego Medical Examiner’s (SDME) office.

extract_protocol:
Mice were anesthetized with isoflurane, perfused with ice-cold aCSF, brains collected and sectioned using a vibratome or brain matrix and the somatosensory cortex was microdissected. Single cell suspensions were generated using the Worthington Papain dissociation system. Human nuclei were isolated from a -80°C frozen tissue piece using Dounce homogenization.
50nl lysis mix (500nM STRT-P1-T31, 4.5nM dNTP, 2% Triton-X-100, 20mM DTT, 1.5U/μl TaKaRa RNase Inhibitor) was dispensed, followed by 3min lysis at 72°C. Then, 85nl reverse transcription (RT) mix (2.1X SuperScript II First-Strand Buffer, 12.6mM MgCl2, 1.79M betaine, 14.7U/μl SuperScript II, 1.58U/μl TaKaRa RNase Inhibitor, 10.5μM P1B-UMI-RNA-TSO) were dispensed and RT carried out 42°C for 90 minutes. 96 Transposome stocks were assembled (6.25μM barcoded adapter (STRT-Tn5-Idx[1-96]), 6.25μM Tn5 transposase, 40% glycerol), 37°C 1h. Tn5 reactions were assembled with 3μl transposome and 2μl amplified cDNA, in a total 20μl 1x CutSmart buffer (NEB), and incubated at 55°C 20min.

tag: cluster

value: middle temporal gyrus


title: OB_G3-6h


title: OB_G3-d0


title: CCR5Q_53_Rep3

description: Processed data file: R1B_CCR5Q_53_s3_N22086.txt

value: CaPO4; Cas9/RAG1B; Cas9/CCR5Q +dn53BP1


title: CCR5Q_523_Rep2


title: CCR5Q_523_Rep1


title: OB_G2-d0


title: CCR5Q_53_Rep2


title: OB_G2-6h


title: OB_G2-d10


title: OB_G1-d3


title: OB_G2-24h


title: CCR5Q_52_Rep3

description: Processed data file: R1B_CCR5Q_52_s3_N22086.txt

value: CaPO4; Cas9/RAG1B; Cas9/CCR5Q +RAD52


title: OB_G1-d7


title: OB_G1-d10


title: OB_G3-12h


title: OB_G2-12h


title: CCR5Q_53_Rep1


title: OB_G1-d0


title: OB_G1-6h


title: CCR5Q_52_Rep2


title: OB_G1-d13


title: OB_G1-12h


title: CCR5Qcontrol_Rep3

description: Processed data file: R1B_CCR5Q_s3_N22086.txt

value: CaPO4; Cas9/RAG1B; Cas9/CCR5Q


title: CCR5Q_52_Rep1


title: CCR5Qcontrol_Rep2


title: CCR5D_53_Rep3

description: Processed data file: R1B_CCR5D_53_s3_N22086.txt

value: CaPO4; Cas9/RAG1B; Cas9/CCR5D +dn53BP1


title: CCR5D_53_Rep2


title: UCF1 H3K27ac_ChIPSeq

city: Shanghai

first: Xiaoran

last: zhang

address: Yueyang Road 320

department: Shanghai Institutes for Biological Sciences

country: China

institute: Chinese Academy of Sciences

data_processing:
Basecalling using Illumina Casava1.8.2 software
Raw reads were aligned by Bowtie (V1.1.1) against hg19 human reference genome.
To generate the wig files, we extended the mapped reads to 200 bp. Bam to Bedgraph using genomeCoverageBed,Bedgraph to bigwig using UCSC bedGraphToBigWig
We normalized the read counts by computing RPKM (the numbers of reads per kilobase of bin per million of reads).
Peaks of ChIP-seq samples were called by MACS(V1.3.7.1, parameter: -nomodel -nolambda).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: umbilical cord

growth_protocol: UCF were maintained in HFM, hiHeps were maintained in HMM, hiPSC-Heps were differentiated from hiPSC

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Briefly, DNA was end-repaired using End-Repair Enzyme mix(Epicentre #ER0720) and dATP was added to 3’ends of DNA using Klenow fragment(NEB).After ligation of adaptors from Illumina Truseq DNA sample prep kit by T4 DNA ligase (NEB).DNA was PCR amplified with Illumina universal primers, library fragments near ~300bp were isolated from agarose gel and massive parallel sequencing was performed using Illumina HiSeq2000 sequencer.

treatment_protocol: Cells were maintained in their own medium and cultured under 37℃ in the incubator

value: Fibroblast

tag: cell type

value: umbilical cord

tag: chip antibody

value: H3K27ac(abcam, ab4729)


title: hiPSC-Hep1 input DNA

source_name: hiPSC derived hepatocyte-like cells

value: hiPSC derived hepatocyte-like cells

value: hepatocyte-like cells


title: hiHep1 input DNA

source_name: human induced hepatocyte-like cells

value: human induced hepatocyte-like cells


title: hiHep1 H3K27ac_ChIPSeq


title: UCF1 input DNA


title: CCR5Qcontrol_Rep1

value: 293T-Embryonic Kidney

tag: genotype

value: WT


title: UCF rep1

data_processing:
Basecalling using Illumina Casava1.8.2 software
Map to human genome hg19 using Tophat(v 2.0.13) and
Bam to Bedgraph using genomeCoverageBed,Bedgraph to bigwig using UCSC bedGraphToBigWig
Counted the mapping reads and normalized as FPKM values using Cufflinks(v.2.2.1).
Differential expression analysis was carried out using the R (v.3.1.1) DEseq (v.1.18.0)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

extract_protocol:
RNA was harvested using Trizol reagent.
Libraries were prepared for sequencing using standard Illumina protocols

tag: tissue


title: CCR5D_523_Rep2

description: Processed data file: R1B_CCR5D_523_s3_N22086.txt

value: CaPO4; Cas9/RAG1B; Cas9/CCR5D +RAD52+dn53BP1

value: RAG1 (Cas9/RAG1B gRNA)

value: Sonication/EcoNI


title: UCF rep2


title: CCR5D_53_Rep1


title: CCR5D_523_Rep1


title: HUVEC input ChIP-seq

city: Kuopio

first: Henri

last: Niskanen

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
Reads were trimmed using HOMER 4.3 software to remove poly-A tails and reads shorter than 25 nt were discarded. From TCC reads, sequences downstream of GATC restriction site were trimmed out.
Quality control using FastQC tool, bases with poor quality were trimmed using FastX toolkit so that minimum 97 % of all bases in one read have to have a minimum phred quality score of 10.
From GRO-seq samples, reads aligning to rRNA (abundant sequences as annotated by iGenomes) and blacklisted regions (unusually low or high mappability, defined by ENCODE) were excluded from analysis.
Alignments were done using bowtie-0.12.7 allowing up to two mismatches and up to three locations per read and the best alignment was reported.
bedGraphs and bigWigs were prepared for visualization and data was normalized to 10^7 reads.
Differentially expressed genes were detected using HOMER 4.3 and edgeR v3.2.2
ChIP-seq peaks were detected using HOMER 4.3, 'findPeaks' command standard settings for 'style factor' option: identification of 200 bp fragments with 4-fold enrichment over input tag count and 0.001 FDR.
For TCC data, separately aligned paired-end reads were paired when preparing HOMER Hi-C tagdirectories using standard settings: read pairs with excact same ends were considered only once (-tbp1 ), paired-end reads that are likely continuous genomic fragments or re-ligation events were removed (-removePEbg), reads from regions with unusually high tag density were removed (-removeSpikes 10000 5), keeping only reads where both ends of the paired-end read have a restriction site within the fragment length estimate 3' to the read (-restrictionSite GATC, -both) and reads were removed if their ends form a self ligation with adjacent restriction sites (-removeSelfLigation).
Significant interactions in 10 kb resolution were detected using HOMER and analyzeHiC with -center option.
Genome_build: hg19

source_name: human umbilical vein endothelial cells

growth_protocol: HUVECs were maintained in endothelial cell growth medium (EGM; 0.1% human epidermal growth factor, 0.1% hydrocortisone, 0.1% Gentamicin-Amphotericin-B, 0.4% bovine brain extract, 2% FBS; Lonza) on cell culture flasks coated with 10 g/ml fibronectin (Sigma, St. Louis, MO) and 0.05% gelatin in phosphate buffered saline (PBS).

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (minus exo) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with NEXTflex DNA barcodes and library fragments were size-selected (230-350bp) from a 10% TBE-gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina HiSeq 2000 according to the manufacturer’s instructions.

treatment_protocol: To induce hypoxia cells were grown in Ruskinn Invivo2 400 hypoxia workstation in presence of 1 % O2 and 5 % CO2.

value: human umbilical vein endothelial cells (HUVEC)

tag: antibody

value: none (input)


title: HUVEC H3K9me3 ChIP-seq

value: 39161, Active motif


title: HUVEC H3K27me3 ChIP-seq

value: 07-449, Millipore


title: HUVEC input ChIP-seq replicate 2


title: CCR5D_52_Rep3

description: Processed data file: R1B_CCR5D_52_s3_N22086.txt

value: CaPO4; Cas9/RAG1B; Cas9/CCR5D +RAD52


title: HUVEC input ChIP-seq replicate 1


title: HUVEC RAD21 ChIP-seq hypoxia replicate 1

value: ab992, Abcam


title: CCR5D_52_Rep2


title: CCR5Dcontrol_Rep3

description: Processed data file: R1B_CCR5D_s3_N22086.txt

value: CaPO4; Cas9/RAG1B; Cas9/CCR5D


title: CCR5D_523_Rep3


title: HUVEC TCC hypoxia replicate 2

description: tethered conformation capture (TCC)

extract_protocol: 90 million human umbilical vein endothelial were fixed with 1 % PFA/PBS in room temperature for 10 minutes and crosslinking was stopped by incubating cells 5 min in presence of 125 mM glycine. Cells were washed two times with ice-cold PBS containing 0.5 % BSA and scraped into lysis buffer containing 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 5 mM MgCl2, 0.2 % NP-40 and protease inhibitor cocktail (Roche). Samples were vortexed, incubated on ice for 10 min, centrifugated for 5 minutes in 1500 g in +4 °C and washed once again with lysis buffer. Cells were washed twice with ice-cold wash buffer containing 50 mM Tris-HCl (pH 8.0), 50 mM NaCl and 0.5M EDTA and nuclei were isolated by incubating samples 10 minutes at +65 °C in wash buffer with 0.55 % SDS and collected by sentrifugation (1000 g for 1 min). Later steps followed the protocol described (Kalhor et al., 2012), except MboI (NEB) was used to digest chromatin, T1 Streptavidin dynabeads (Invitrogen) were used in all the pulldown steps, NucleoSpin Gel & PCR Clean-up kit (Macherey-Nagel) for clean-up steps and Bioruptor NextGen sonicator for DNA shearing (High setting, 30s/30s cycles for total 35 cycles). Libraries were amplified in 15 PCR cycles, size selected for 225 – 550 bp range on 10 % TBE-gel (Invitrogen). Gel was grinded and soaked with 0.1 % Tween-20 and 150 mM NaCl and DNA was eluted through Ultrafree Centrifugal filter column (Millipore), cleaned up with ChIP DNA clean & concentrator kit (Zymo Research) and paired-end sequenced with Illumina HiSeq 2000.


title: HUVEC RAD21 ChIP-seq normoxia replicate 2


title: HUVEC RAD21 ChIP-seq normoxia replicate 1


title: CCR5D_52_Rep1


title: HUVEC TCC hypoxia replicate 1

description: tethered conformation capture (TCC)


title: HUVEC TCC normoxia replicate 2

description: tethered conformation capture (TCC)


title: CCR5Dcontrol_Rep2


title: HUVEC GRO-seq hypoxia replicate 3

description: nascent RNA

data_processing:
Library strategy: GRO-Seq
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
Reads were trimmed using HOMER 4.3 software to remove poly-A tails and reads shorter than 25 nt were discarded. From TCC reads, sequences downstream of GATC restriction site were trimmed out.
Quality control using FastQC tool, bases with poor quality were trimmed using FastX toolkit so that minimum 97 % of all bases in one read have to have a minimum phred quality score of 10.
From GRO-seq samples, reads aligning to rRNA (abundant sequences as annotated by iGenomes) and blacklisted regions (unusually low or high mappability, defined by ENCODE) were excluded from analysis.
Alignments were done using bowtie-0.12.7 allowing up to two mismatches and up to three locations per read and the best alignment was reported.
bedGraphs and bigWigs were prepared for visualization and data was normalized to 10^7 reads.
Differentially expressed genes were detected using HOMER 4.3 and edgeR v3.2.2
ChIP-seq peaks were detected using HOMER 4.3, 'findPeaks' command standard settings for 'style factor' option: identification of 200 bp fragments with 4-fold enrichment over input tag count and 0.001 FDR.
For TCC data, separately aligned paired-end reads were paired when preparing HOMER Hi-C tagdirectories using standard settings: read pairs with excact same ends were considered only once (-tbp1 ), paired-end reads that are likely continuous genomic fragments or re-ligation events were removed (-removePEbg), reads from regions with unusually high tag density were removed (-removeSpikes 10000 5), keeping only reads where both ends of the paired-end read have a restriction site within the fragment length estimate 3' to the read (-restrictionSite GATC, -both) and reads were removed if their ends form a self ligation with adjacent restriction sites (-removeSelfLigation).
Significant interactions in 10 kb resolution were detected using HOMER and analyzeHiC with -center option.
Genome_build: hg19

extract_protocol: Nuclei were extracted from 5-10 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNAseH treated, circularized, linearized, amplified for 12-16 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina HiSeq 2000.

value: anti-Br-UTP beads, sc-32323 AC, Santa Cruz


title: CCR5Q_Rep3

description: Processed data file: R1B_CCR5Q_s3.txt

value: CaPO4; Cas9/RAG1B; Cas9/CCR5Q


title: HUVEC GRO-seq hypoxia replicate 4

description: nascent RNA


title: HUVEC TCC normoxia replicate 1

description: tethered conformation capture (TCC)


title: CCR5Q_Rep2

description: Processed data file: R1B_CCR5Q_s3.txt


title: HUVEC RAD21 ChIP-seq hypoxia replicate 2


title: HUVEC GRO-seq hypoxia replicate 1

description: nascent RNA


title: HUVEC GRO-seq normoxia replicate 3

description: nascent RNA


title: CCR5Dcontrol_Rep1


title: HUVEC GRO-seq hypoxia replicate 2

description: nascent RNA


title: HUVEC GRO-seq normoxia replicate 4

description: nascent RNA


title: HUVEC GRO-seq normoxia replicate 2

description: nascent RNA


title: CCR5Q_Rep1

description: Processed data file: R1B_CCR5Q_s3.txt


title: CCR5D_Rep3

description: Processed data file: R1B_CCR5D_s3.txt


title: 3312_2_Tryp39_hom_ATTCCTT

city: Amsterdam

first: Metello

last: Innocenti

address: Plesmanlaan 121

country: Netherlands

institute: NKI

data_processing:
The reads were sequenced using a stranded protocol and aligned against the mouse genome, build 38, using Tophat 2.0.12 with bowtie 1.1
The parameters used are --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were generated using a custom script based on the same strategy as HTSeq-count.
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated files with the number of readcounts per gene

source_name: epidermis

extract_protocol:
Total RNA was extracted using TRIzol reagent as per the manufacturer’s protocol
Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit according to the manufacturer’s instructions
Strand specific libraries were sequenced 51 bp single end

treatment_protocol: trypsinized skin

value: ARPC4 ko

tag: age

value: PN day 4

tag: strain

value: epidermis


title: 3312_5_II_wt_25−11−14_ACAGTGA

value: wt


title: CCR5D_Rep2

description: Processed data file: R1B_CCR5D_s3.txt

value: 293T-Embryonic Kidney

value: WT

tag: nuclease delivery


title: CCR5D_Rep1

description: Processed data file: R1B_CCR5D_s3.txt

data_processing:
Library strategy: LAM-HTGTS
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the hg19 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml)
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

value: RAG1 (Cas9/RAG1B gRNA)


title: 3312_3_I_wt_25-11-14_CGATGTA


title: 3312_1_Tryp_40_wt_ACTGATA


title: 3312_4_I_hom_25-11-14_TGACCAA


title: 3955_3382_MI338-High_Nrf2_ATGTCAG

data_processing:
The reads were sequenced using a stranded protocol and aligned against the mouse genome, build 38, using Tophat 2.1.0 with bowtie 1.1
The parameters used are --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were generated using a custom script based on the same strategy as HTSeq-count.
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated files with the number of readcounts per gene

source_name: keratinocytes

growth_protocol: exponentially growing cells

extract_protocol:
Total RNA was extracted using TRIzol reagent as per the manufacturer’s protocol
Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit according to the manufacturer’s instructions
Strand specific libraries were sequenced 65 bp single end

tag: immortalization method

value: keratinocytes


title: 3955_3381_MI338_Cre_AGTTCCG


title: ChIP-Seq MCM7 exp2

city: Fukuoka

first: Nozomi

last: Sugimoto

address: 3-1-1, Maidashi, Higashiku

institute: Kyushu University

data_processing:
The sequence reads were aligned to the hg19 genome using the Bowtie software (version 0.12.8; parameter -v3 -m1).
Signal data (bigWig) were generated using bamCoverage command of deepTools (version 2.4.2) with the option: --smoothLength 60 --binSize 1 --extendReads.
Peak calling was performed using MACS2 (version 2.0.10.20131216).
Genome_build: hg19
Supplementary_files_format_and_content: .bw file available on sample record. ChIP-Seq peak list as tab delimited .txt (available on the series record).

source_name: Cervical carcinoma

growth_protocol: Human cervical carcinoma HeLa cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% (v/v) fetal bovine serum (FBS) and antibiotics.

extract_protocol:
For ChIP-seq, fixation was stopped by adding Glycine (125mM) and incubating for 5 min at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300–500 bp average in size through sonication. Resultant was immunoprecipitated with MCM7 antibodies 18 hr at 4°C, followed by incubation with protein G magnetic beads (Invitrogen) for an additional 3 h. After washing and elution, the protein–DNA complex was reversed by heating at 65°C 6hr. Immunoprecipitated DNA was purified by phenol/chloroform extraction and ethanol precipitation.
According to Illumina protocol

treatment_protocol: Cells grown to ~90% confluent were fixed directly with 1% formaldehyde.

value: HeLa

value: Human cervical carcinoma

value: MCM7 (Fujita et al., PMID 8626784; Fujita et al., PMID 9099751)


title: 3955_338_Mi338_wt_AGTCAAC


title: ChIP-Seq MCM7 exp1


title: HSC Obese (db/db) 4 months (Exp25_LepR_Null_15183)

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: HSC from 4-month old obese mouse (db/db) Exp3

data_processing:
FASTQ sequence files were aligned to the mouse genome mm9 using RSEM.
The fastq files were aligned to mouse genome mm9 using BowTie 2 and RSEM. To identify differentially expressed genes using default parameters moderated t-test with Benjamini-Hochberg multiple testing correction, raw p-value cut-off of 0.05, and an expression cut-off of 2-fold. RSEM gene-expression TPM values were all subjected to the same defaults in AltAnlayze for statistical analysis.
For all RNAseq experiments pathways and ontology enrichment analyses were performed with ToppGene (Chen et al., 2009) and GO-Elite (Zambon et al., 2012). All heatmaps from AltAnalyze were created using the HOPACH package via a connection to R (Salomonis et al., 2005). All gene set enrichment analyses were performed using GSEA v.2.2.0 (Mootha et al., 2003; Subramanian et al., 2005).
Genome_build: mm9
Supplementary_files_format_and_content: TPMs

source_name: HSC Obese (db/db) 4 months

growth_protocol: Mice were euthanized with carbon dioxide and cervical dislocation. BM cells were obtained by crushing long bones and hips, treated with Ammonium-Chloride-Potassium (ACK) buffer (150 mM NH4Cl/10 mM KHCO3) to lyse red blood cells and purified by ficoll separation (Histopaque-1119, Sigma-Aldrich). AutoMACS (Miltenyi) enriched c-kit+ cells were stained with unconjugated rat lineage specific antibodies (Lin: Ter-119, Mac1, Gr-1, B220, CD5, CD3, CD4, CD8, CD127), followed by staining with goat anti-rat-PE-Cy5 secondary antibody. Cells were then stained with c-Kit-APC-eFluor780, Sca1-PB, CD48-Alexa-Fluor647, CD150-PE antibodies and sorted at purity on a FACS ARIAII  (BD biosciences).

extract_protocol:
20,000 HSCs were isolated from db and littermates control mice by FACS sorting directly in Trizol (Invitrogen). After chloroform extraction, total RNA was purified using RNeasy microKit column system  (Qiagen). Three independent replicates were isolated in independent experiments to ensure reproducibility and allow statistical analysis. RNA quality and quantity were controlled using Agilent Bioanalyzer before processed for retro-transcription, linear amplification and cDNA library generation.
[cDNA synthesis] TRUseq RNA sample kit  (Illumina).
[library prep] RNA Seq libraries were generated with Illumina TruSeq Stranded mRNA HT kits and analyzed using paired-end 75 nucleotide sequencing on one HiSeq 2500 (Illumina).

value: db/db (obese)

value: Bone marrow

value: CD150+CD48-LSK HSC

value: 4 months old


title: HSC Obese (db/db) 4 months (Exp22_LepR_Null_15181)

description: HSC from 4-month old obese mouse (db/db) Exp2


title: OB_G1-24h


title: HSC Obese (db/db) 4 months (Exp18_LepR_Null_15179)

description: HSC from 4-month old obese mouse (db/db) Exp1


title: Input exp1


title: HSC Control 4 months (Exp18_Ctrl_15178)

description: HSC from 4-month old WT mouse Exp1

source_name: HSC Control 4 months


title: L1500094-Digested_intracellular

city: Edinburgh

first: Musa

last: Hassan

state: Scotland

address: Easter Bush

department: Roslin

country: United Kingdom

institute: University of Edinburgh

description: Ribo-seq

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to GT  whole genome (V29) using the STAR aligner with default parameters
Supplementary_files_format_and_content: Read couts were obtained using HTSeq

organism: Toxoplasma gondii

source_name: Intracellular parasites

growth_protocol: Type I Toxoplasma gondii was grown on human foreskin fibroblasts and intracellular or extracellular parasites collected after 24 hrs

extract_protocol:
Aftter collection, the parasite samples were divided into two samples: one sample was used for ribosome profling, as previously described (Ingolia et al, 2009) and the other sample was used for high throughput RNA-sequencing.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Prior to havesting, the parasite cultures were treated for about 10min with cyclohexamide (100ug/ml).

tag: group

value: Intracellular parasites

tag: replicate

value: Replicate 1


title: L1600256_NS227_digested_intracellular

description: Ribo-seq

value: Replicate 2


title: 4Cseq_mouse_Shh

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

institute: CABD/CSIC

data_processing:
library strategy: 4C-seq
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the mm9 and oryLat2 assemblies using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept. Reads located in fragments flanked by two restriction sites of the same enzyme, or in fragments smaller than 40 bp were filtered out
Mapped reads were then converted to reads-per-first-enzyme-fragment-end units, and smoothed using a 30 DpnII fragments mean running window algorithm.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: mm9; oryLat2 (ASM31367v1)
Supplementary_files_format_and_content: bedGraph, they contain smoothened data of 4Cseq of viewpoint that can be directly uploaded to UCSC for visualization.

source_name: E9.5 mouse embryos

growth_protocol: wild type animals, raised in standard laboratory conditions

extract_protocol:
Chromatin was extracted from single cells preparations from 25 E9.5 mouse embryos or 500 48hpf medaka embryos. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.

treatment_protocol: no treatment

tag: developmental stage

value: whole embryos


title: 4Cseq_mouse_EnhZRS


title: HUVEC GRO-seq normoxia replicate 1

description: nascent RNA

value: human umbilical vein endothelial cells (HUVEC)

value: anti-Br-UTP beads, sc-32323 AC, Santa Cruz


title: HSC Control 4 months (Exp25_Ctrl_15182)

description: HSC from 4-month old WT mouse Exp3


title: HSC Control 4 months (Exp22_Ctrl_15180)

description: HSC from 4-month old WT mouse Exp2


title: L1600254_NS225_fragmented_intracellular

description: RNA-seq


title: Egr1 -/- Rep3

city: Paris

first: Mickael

last: Orgeur

address: 25-28 rue du Docteur Roux

country: France

institute: Institut Pasteur

data_processing:
Strand-specific single-end reads were mapped against the mus musculus reference genome (UCSC Dec. 2011, GRCm38/mm10) by using TopHat2, Bowtie2 and the Release M8 (GRCm38.p4) GTF annotations as a guide
Read counts were assigned to gene features using featurecounts
Differential expression analysis was performed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing the raw read counts for each gene feature for each replicate generated by featurecounts and used as input for DESeq2

source_name: Subcutaneous inguinal fat pads

extract_protocol:
Fresh inguinal subcutaneous fat pads were removed from 2-week-old euthanized Egr1+/+ and Egr1-/- female mice and homogenized using a mechanical disruption device (Lysing Matrix A, Fast Prep MP1, 4 × 30 s, 6 m.s-1). Total RNAs were isolated using the RNeasy mini kit (Qiagen) with 15 min of DNase I (Qiagen) treatment according to the manufacturer’s protocol.
Ribosomal RNA depletion was performed with the Ribo-Zero kit (Epicentre), using 500 ng of total RNA. Libraries were prepared using the strand specific RNA-Seq library preparation ScriptSeq V2 kit (Epicentre). 52-78 million of 50-bp strand-specific single-end reads were generated by using a HiSeq 1500 device (Illumina).

value: Subcutaneous white adipose tissue

value: 2 weeks

tag: Sex

value: Female


title: L1600253_NS224_fragmented_extracellular

description: RNA-seq

source_name: Extracellular parasites

value: Extracellular parasites


title: Egr1 -/- Rep2


title: L1500092-Fragmented_intracellular

description: RNA-seq


title: hiPSC-Hep1 H3K27ac_ChIPSeq

value: hiPSC derived hepatocyte-like cells

value: hepatocyte-like cells

value: H3K27ac(abcam, ab4729)


title: Egr1 -/- Rep1


title: Egr1 +/+ Rep3

value: Wild-type


title: L1500091-Fragmented_extracellular

description: RNA-seq


title: Input exp2

tag: cell line

value: HeLa

value: Human cervical carcinoma


title: 4Cseq_medaka_Shh

organism: Oryzias latipes

source_name: 48hpf medaka embryos


title: 4Cseq_medaka_EnhZRS


title: Egr1 +/+ Rep1


title: L1500093-Digested_extracellular

description: Ribo-seq


title: Pa179_IL11

status: Public on Nov 22 2017

city: Singapore

first: Sonia

last: Chothani

address: 8 College Road

country: Singapore

institute: Duke-NUS school of medicine

description:
human recombinant IL11 (Life Technologies)
Raw_counts_IL11_Basal_4patients.txt; Raw_counts_IL11_Basal_combined.txt

data_processing:
Preprocesing: The adaptor sequences and low quality reads/bases were trimmed using Trimmomatic v0.36 and the read quality was assessed using FastQC v0.11.5
Alignment: High-quality reads were mapped to Ensembl human GRCh38 v86 ref or mouse GRCm38 v86 reference genome using STAR v2.5.2b . Only uniquely mapped reads were reported from STAR by setting the parameter —outFilterMulrimapNmax 1
Read summarization: Strand-specific raw counts of uniquely mapped reads (paired-end) were summarized with featureCounts [Ref:PMID: 24227677] to get gene-level quantification of genomic features
Differential expression analysis: Differential expression (DE) was performed with DESeq2 v1.14.1 by using raw read counts from featureCounts. We performed a minimal pre-filtering to remove genes that have no reads or only 1 read across all samples. Sample IDs were included as co-variates in DESeq2 design formula to remove batch effect due to samples. Basal condition was always used as the reference level for pair wise comparison. Shrinkage MA-plot was generated and points will be colored red if adjusted p value was less than 0.1.
Genome_build: GRCh38 v86
Supplementary_files_format_and_content: Raw_counts_IL11_Basal_4patients.txt: tab-delimited file with raw gene expression counts for each gene and sample for IL11 vs Basal RNA-seq 4 patients; Raw_counts_TGFB1_Basal_4patients.txt: tab-delimited file with raw gene expression counts for each gene and sample for TGFB1 vs Basal RNA-seq 4 patients; Raw_counts_IL11_Basal_6patients.txt: tab-delimited file with raw gene expression counts for each gene and sample for IL11 vs Basal RNA-seq 6 patients;Raw_counts_IL11_Basal_combined.txt: tab-delimited file with raw gene expression counts for each gene and sample for IL11 vs Basal RNA-seq combined;

source_name: Cardiac fibroblasts

growth_protocol: Growth media contained DMEM (Life technologies) supplemented with 20% fetal bovine serum (FBS, Hyclone) and 1% penicillin/streptomycin (Gibco) . When the cells grew to 80% confluence, they were passaged using standard trypsinization techniques. Fresh media was renewed every 2-3 days to remove cell debris and to maintain a physiological pH.

extract_protocol:
Total RNA was isolated from human cardiac fibroblasts with RNeasy column kit (Qiagen).
Libraries were constructed with TruSeq Stranded mRNA Library Prep kit (Illumina) using 0.8µg of total RNA. RNA-seq, barcoded libraries were multiplexed and sequenced as paired-end reads on Illumina NextSeq 500 platform using NextSeq High output 150 cycles kit across 4 lanes.

treatment_protocol: Cardiac fibroblasts were cultured in serum-free media for at least 16 hours prior to treatment. They were further treated with either TGFB1 or IL11.

value: right atrial appendage biopsies

tag: hour

value: cultured for 24 hours

tag: treatment


title: Pa176_TGFB1

description:
human recombinant TGFB1 (Serotec)
Raw_counts_TGFB1_Basal_4patients.txt


title: Pa179_TGFB1


title: Pa177_TGFB1


title: Pa173_TGFB1


title: Pa177_IL11_2


title: Pa176_IL11


title: Pa176_basal

description: Raw_counts_IL11_Basal_4patients.txt; Raw_counts_TGFB1_Basal_4patients.txt; Raw_counts_IL11_Basal_combined.txt

value: No treatment


title: Pa177_basal_2


title: Pa173_basal


title: Pa213_basal

description: Raw_counts_IL11_Basal_6patients.txt; Raw_counts_IL11_Basal_combined.txt


title: Pa173_IL11


title: Pa213_IL11

description:
human recombinant IL11 (Life Technologies)
Raw_counts_IL11_Basal_6patients.txt; Raw_counts_IL11_Basal_combined.txt


title: Pa212_basal


title: Pa212_IL11


title: Pa211_IL11


title: Pa211_basal


title: Pa177_IL11_1

description:
human recombinant IL11 (Life Technologies)
Raw_counts_IL11_Basal_4patients.txt; Raw_counts_IL11_Basal_6patients.txt; Raw_counts_IL11_Basal_combined.txt


title: Egr1 +/+ Rep2


title: Pa177_basal_1

description: Raw_counts_IL11_Basal_4patients.txt; Raw_counts_IL11_Basal_6patients.txt; Raw_counts_IL11_Basal_combined.txt


title: Pa166_basal


title: Pa166_IL11


title: Pa163_IL11


title: Pa179_basal


title: L1600255_NS226_digested_extracellular

description: Ribo-seq

value: Replicate 2


title: Pa163_basal


title: Aged 6 months

city: New York

first: Dan

middle: Richard

last: Laks

state: NY

address: 1275 York Avenue

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

description:
CGD transgenic mouse with GFP expressed in neural stem cells. Sorted for viable cells only (Unbiased).
Processed data file: Aged.csv
Processed data file: FullData.csv

data_processing:
Alignment of reads and generation of cellular expression counts were performed with the Drop-seqAlignmentCookbookv1.2Jan2016 (http://mccarrolllab.com/wp-content/uploads/2016/03/Drop-seqAlignmentCookbookv1.2Jan2016.pdf) and with the Dropseq tools provided by the McCarroll lab (http://mccarrolllab.com/download/922/). We utilized the mm10 reference genome into which we incorporated the CGD transgene mRNA sequence. Mus_musculus.GRCm38.82 was used as our refflat GTF. The Digital Expression NUM_CORE_BARCODES output was set to 5000 as we knew we had less than or equal to 2000 cells per sample.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Comma-separated text files (.csv). Cells in columns, genes in rows.
Supplementary_files_format_and_content: LowGFP.csv: 1900 cells, quality controlled.
Supplementary_files_format_and_content: HighGFP.csv: 1600 cells, quality controlled.
Supplementary_files_format_and_content: NegGFP.csv: 1100 cells, quality controlled.
Supplementary_files_format_and_content: UNB.csv: 2000 cells, quality controlled.
Supplementary_files_format_and_content: 2weeks.csv: 1001 cells, quality controlled.
Supplementary_files_format_and_content: 2months.csv: 1240 cells, quality controlled.
Supplementary_files_format_and_content: 6months.csv: 1338 cells, quality controlled.
Supplementary_files_format_and_content: 12months.csv: 838 cells, quality controlled.
Supplementary_files_format_and_content: Sorted.csv: 6600 cells, quality controlled: Combined Low, High, Negative, and UNB.
Supplementary_files_format_and_content: Aged.csv: 4417 cells, quality controlled: Combined 2week, 2month, 6 month, and 12month samples.
Supplementary_files_format_and_content: FullData.csv: 10,055 cells, quality controlled: Combined All Samples.

source_name: Subventricular zone cells

growth_protocol: All mouse experiments were approved and performed in accordance with the guidelines of the Institutional Animal Care and Research Advisory Committee at the University of Texas Southwestern Medical Center and the Institutional Animal Care and Use Committee of Memorial Sloan Kettering Cancer Center.

extract_protocol:
Viable cells were sorted in a FACSAriaII (BD Biosciences) and sorted for High, low, negative or unsorted (UNB).
The Dropseq cell-bead collection, sample preparation, library preparation, and sequencing were performed as previously described (Macosko et al., 2015). Beads were purchased from Chemgenes (#MACOSKO-2011-10) and the microfluidics chip was purchased from Nanoshift. All our reagents were purchased from the recommended sources as outlined in Macosko et al., 2015 and the McCarroll lab’s online Dropseq protocol, v3.1, Dec. 2015 (http://mccarrolllab.com/download/905/). Our primers and oligonucleotides were purchased from IDT with the identical sequences outlined by Macosko et al., 2015. Sequencing was done on a NextSeq 500 at the Cornell Sequencing core, 64bp (R2).

treatment_protocol: A CGD fragment was amplified and assembled from a CreERT2 containing construct, an H2B-eGFP vector (from Yan Jiang, Mount Sinai), and genomic DNA from 293T cells (diphtheria toxin receptor). To ensure the efficient expression of all the three proteins in the CGD transgene, a P2A fragment was used to space between the three different genes (Kim et al., 2011; Mizuguchi et al., 2000; Szymczak et al., 2004). To verify the adequate expression of mono-proteins from the multi-cistronic cassette, the coding region of the CGD fragment was inserted into a FETPTR vector to transfect 293T cells. Western blot was used to detect the comparative expression levels of monomers vs. polymers from the same open-reading frame (ORF) with a GFP antibody (1:1,000, Fig. S1C). Further analysis demonstrated the activity of the three proteins (Fig. S1B-E). The CGD fragment was then inserted into the pNERV vector (gift from Steve Kernie, Columbia University) (Yu et al., 2008) through NotI (New England Labs) sites. The pNERV-CGD plasmid was cut with SalI to release the Nestin-CGD fragment to generate transgenic mice by pronuclear injection into fertilized murine eggs in a C57BL/6 genetic background. 82 founders were screened with PCR and 29 lines were identified as positive with the CGD transgene. The primers used to verify the transgene were: forward primer, 5’-GTCTATATCATGGCCGACAAGC-3’ and the reverse primer, 5’-GAAAGAGCTTCAGCACCACC-3’.

value: Subventricular zone

value: 6 months

tag: gfp protein sort

value: Unsorted, unbiased


title: Aged 12 months

value: 12 months


title: Aged 2 weeks

value: 2 weeks


title: Sorted Viable UNB

description:
CGD transgenic mouse with GFP expressed in neural stem cells. Sorted for viable cells only (Unbiased).
Processed data file: Sorted.csv
Processed data file: FullData.csv

value: 2 months


title: Sorted Neg GFP

description:
CGD transgenic mouse with GFP expressed in neural stem cells. Sorted for no protein expression of GFP.
Processed data file: Sorted.csv
Processed data file: FullData.csv

value: Negative


title: Sorted High GFP

description:
CGD transgenic mouse with GFP expressed in neural stem cells. Sorted for high protein expression of GFP.
Processed data file: Sorted.csv
Processed data file: FullData.csv

value: High


title: Sorted Low GFP

description:
CGD transgenic mouse with GFP expressed in neural stem cells. Sorted for low GFP expression.
Processed data file: Sorted.csv
Processed data file: FullData.csv

value: Low


title: Ms1_WT_Fib_IL11

data_processing:
Preprocesing: The adaptor sequences and low quality reads/bases were trimmed using Trimmomatic v0.36 and the read quality was assessed using FastQC v0.11.5
Alignment: High-quality reads were mapped to Ensembl human mouse GRCm38 v86 reference genome using STAR v2.5.2b . Only uniquely mapped reads were reported from STAR by setting the parameter —outFilterMulrimapNmax 1
Read summarization: Strand-specific raw counts of uniquely mapped reads (paired-end) were summarized with featureCounts [Ref:PMID: 24227677] to get gene-level quantification of genomic features
Differential expression analysis: Differential expression (DE) was performed with DESeq2 v1.14.1 by using raw read counts from featureCounts. We performed a minimal pre-filtering to remove genes that have no reads or only 1 read across all samples. Sample IDs were included as co-variates in DESeq2 design formula to remove batch effect due to samples. Basal condition was always used as the reference level for pair wise comparison. Shrinkage MA-plot was generated and points will be colored red if adjusted p value was less than 0.1.
Genome_build: GRCm38 v86 (mouse reference genome)
Supplementary_files_format_and_content: RNAseq.count: tab-delimited file with raw gene expression counts for each gene and sample for TGFB1, IL11, Basal RNA-seq mouse data

source_name: wild type_Cardiac fibroblasts_IL11

tag: strain background

tag: genotype/variation

value: wild type

tag: cell type

value: Cardiac fibroblasts

tag: time

tag: treated with

value: mouse recombinant IL11  (GenScript)


title: HOM4_Ms_Fib_IL11

source_name: KO IL11RA-/-_Cardiac fibroblasts_IL11

value: KO IL11RA-/-


title: Ms1_WT_Fib_BL

source_name: wild type_Cardiac fibroblasts_basal

value: none (no treatment)


title: Ms_WT5_Fib_BL

value: cultured for 24 hours


title: Ms2_WT_Fib_TGFB

source_name: wild type_Cardiac fibroblasts_TGF-beta 1

value: mouse recombinant TGF-beta 1 (RnD systems)


title: Ms1_WT_Fib_TGFB


title: Ms2_WT_Fib_BL


title: HOM4_Ms_Fib_TGFB

source_name: KO IL11RA-/-_Cardiac fibroblasts_TGF-beta 1


title: HOM3_Ms_FibTGFB


title: Ms_WT5_Fib_TGFB


title: Ms_WT5_Fib_IL11


title: HOM3_Ms_Fib_IL11


title: HOM1_Ms_Fib_TGFB


title: HOM3_Ms_Fib_BL

source_name: KO IL11RA-/-_Cardiac fibroblasts_basal


title: HOM1_Ms_Fib_IL11


title: HOM1_Ms_Fib_BL


title: q469_WT_Run2

city: Boston

first: Brian

last: Lin

state: MA

address: 136 Harrison Avenue

department: DMCB

institute: Tufts University

description: Uninjured Reference

data_processing:
Demultiplexed reads are FASTQC trimmed
Mapped using STAR-2.5.2a
Samples were combined and normalized for library size using Cuffnorm, in the Cufflinks-2.2.1 package to output normalized FPKM and count estimates.
Genome_build: MM9
Supplementary_files_format_and_content: merged csv with either normalized counts or normalized FPKM

source_name: Uninjured Olfactory Epithelium

extract_protocol:
Cell Dissociation protocol: Cells were dissociated from donor animals anaesthetized with IP injection of a triple cocktail of ketamine (37.5 mg/kg), xylazine (7.5 mg/kg), and acepromazine (1.25 mg/kg) and perfused with cold Low Ca2+ Ringers solution (140mM NaCl, 5mM KCl, 10mM HEPES, 1mM EDTA, 10mM glucose, 1mM sodium pyruvate, pH7.2). The olfactory epithelium is isolated away from respiratory tissue, finely minced, and incubated in 0.05% Trypsin-EDTA for 10 minutes on an orbital shaker at 37°C where it forms a sticky ball. The supernatant was replaced with an enzyme cocktail containing (100 U/ml collagenase, 250 U/ml hyaluronidase, 75 U/ml DNase I, 0.1 mg/ml trypsin inhibitor, 2.5 U/ml Dispase II, 350 U/ml Collagenase Type I, 5U/ml papain; from Worthington Biochemical, Roche, and Sigma) in Regular Ringers solution (140mM NaCl, 5mM KCl, 10mM HEPES, 1mM EDTA, 10mM glucose, 1mM sodium pyruvate, 1mM CaCl2, 1mM MgCl2, pH7.2). The tissue was incubated in the enzyme cocktail on an orbital shaker at 37°C for 15 minutes, after which the supernatant was replaced with fresh enzyme cocktail and incubated once again for 15 minutes. The supernatant is stored on ice in the meantime. After the second incubation, the pooled supernatant is filtered through 30 µm filter and centrifuged at <500g on a swinging bucket rotor for 5 minutes. The pellet is resuspended in 1x HBSS containing 25 mM HEPES, 10 mM EDTA for FACS purification based on eGFP positivity.
RNA and cDNA were generated using standard Fluidigm C1-Autoprep protocols
Libraries were generated using standard Illumina Nextera XT kit protocols modified by published Fluidigm C1-Autoprep modifications

tag: tissue

value: olfactory epithelium

tag: age

value: 8 wk

tag: genotype

value: F1 wildtype


title: Aged 2 months

value: Subventricular zone

value: Unsorted, unbiased


title: q468_WT_Run2

description: Uninjured Reference

tag: strain


title: Ms2_WT_Fib_IL11


title: q467_WT_Run2

description: Uninjured Reference


title: q466_WT_Run2

description: Uninjured Reference


title: q463_WT_Run2

description: Uninjured Reference


title: q464_WT_Run2

description: Uninjured Reference


title: q462_WT_Run2

description: Uninjured Reference


title: q461_WT_Run2

description: Uninjured Reference


title: HOM4_Ms_Fib_BL


title: q460_WT_Run2

description: Uninjured Reference


title: q456_WT_Run2

description: Uninjured Reference


title: q455_WT_Run2

description: Uninjured Reference


title: q458_WT_Run2

description: Uninjured Reference


title: q457_WT_Run2

description: Uninjured Reference


title: q453_WT_Run2

description: Uninjured Reference


title: q447_WT_Run2

description: Uninjured Reference


title: q450_WT_Run2

description: Uninjured Reference


title: q452_WT_Run2

description: Uninjured Reference


title: q448_WT_Run2

description: Uninjured Reference


title: q459_WT_Run2

description: Uninjured Reference


title: q449_WT_Run2

description: Uninjured Reference


title: q451_WT_Run2

description: Uninjured Reference


title: q445_WT_Run2

description: Uninjured Reference


title: q454_WT_Run2

description: Uninjured Reference


title: q444_WT_Run2

description: Uninjured Reference


title: q443_WT_Run2

description: Uninjured Reference


title: q446_WT_Run2

description: Uninjured Reference


title: q442_WT_Run2

description: Uninjured Reference


title: q440_WT_Run2

description: Uninjured Reference


title: q465_WT_Run2

description: Uninjured Reference


title: q438_WT_Run2

description: Uninjured Reference


title: q436_WT_Run2

description: Uninjured Reference


title: q435_WT_Run2

description: Uninjured Reference


title: q441_WT_Run2

description: Uninjured Reference


title: q437_WT_Run2

description: Uninjured Reference


title: q439_WT_Run2

description: Uninjured Reference


title: q434_WT_Run2

description: Uninjured Reference


title: q433_WT_Run2

description: Uninjured Reference


title: q431_WT_Run2

description: Uninjured Reference


title: q432_WT_Run2

description: Uninjured Reference


title: q429_WT_Run2

description: Uninjured Reference


title: q430_WT_Run2

description: Uninjured Reference


title: q427_WT_Run2

description: Uninjured Reference


title: q426_WT_Run2

description: Uninjured Reference


title: q425_WT_Run2

description: Uninjured Reference


title: q428_WT_Run2

description: Uninjured Reference


title: q421_WT_Run2

description: Uninjured Reference


title: q418_WT_Run2

description: Uninjured Reference


title: q419_WT_Run2

description: Uninjured Reference


title: q420_WT_Run2

description: Uninjured Reference


title: q416_WT_Run2

description: Uninjured Reference


title: q415_WT_Run2

description: Uninjured Reference


title: q417_WT_Run2

description: Uninjured Reference


title: q414_WT_Run2

description: Uninjured Reference


title: q411_WT_Run2

description: Uninjured Reference


title: q413_WT_Run2

description: Uninjured Reference


title: q412_WT_Run2

description: Uninjured Reference


title: q409_WT_Run2

description: Uninjured Reference


title: q423_WT_Run2

description: Uninjured Reference


title: q424_WT_Run2

description: Uninjured Reference


title: q405_WT_Run2

description: Uninjured Reference


title: q422_WT_Run2

description: Uninjured Reference


title: q406_WT_Run2

description: Uninjured Reference


title: q402_WT_Run2

description: Uninjured Reference


title: q404_WT_Run2

description: Uninjured Reference


title: q399_WT_Run2

description: Uninjured Reference


title: q400_WT_Run2

description: Uninjured Reference


title: q398_WT_Run2

description: Uninjured Reference


title: q395_WT_Run2

description: Uninjured Reference


title: q391_WT_Run2

description: Uninjured Reference


title: q393_WT_Run2

description: Uninjured Reference


title: q390_WT_Run2

description: Uninjured Reference


title: q392_WT_Run2

description: Uninjured Reference


title: q410_WT_Run2

description: Uninjured Reference


title: q408_WT_Run2

description: Uninjured Reference


title: q407_WT_Run2

description: Uninjured Reference


title: q387_WT_Run2

description: Uninjured Reference


title: q388_WT_Run2

description: Uninjured Reference


title: q386_WT_Run2

description: Uninjured Reference


title: q389_WT_Run2

description: Uninjured Reference


title: q385_WT_Run2

description: Uninjured Reference


title: q403_WT_Run2

description: Uninjured Reference


title: q401_WT_Run2

description: Uninjured Reference


title: q384_WT_Run2

description: Uninjured Reference


title: q381_WT_Run2

description: Uninjured Reference


title: q397_WT_Run2

description: Uninjured Reference


title: q382_WT_Run2

description: Uninjured Reference


title: q383_WT_Run2

description: Uninjured Reference


title: q378_WT_Run2

description: Uninjured Reference


title: q375_WT_Run2

description: Uninjured Reference


title: q396_WT_Run2

description: Uninjured Reference


title: q394_WT_Run2

description: Uninjured Reference


title: q377_WT_Run2

description: Uninjured Reference


title: q380_WT_Run2

description: Uninjured Reference


title: q374_WT_Run2

description: Uninjured Reference


title: q372_WT_Run1

description: Uninjured Reference


title: q371_WT_Run1

description: Uninjured Reference


title: q370_WT_Run1

description: Uninjured Reference


title: q376_WT_Run2

description: Uninjured Reference


title: q369_WT_Run1

description: Uninjured Reference


title: q368_WT_Run1

description: Uninjured Reference


title: q367_WT_Run1

description: Uninjured Reference


title: q363_WT_Run1

description: Uninjured Reference


title: q364_WT_Run1

description: Uninjured Reference


title: q366_WT_Run1

description: Uninjured Reference


title: q365_WT_Run1

description: Uninjured Reference


title: q362_WT_Run1

description: Uninjured Reference


title: q379_WT_Run2

description: Uninjured Reference


title: q361_WT_Run1

description: Uninjured Reference


title: q357_WT_Run1

description: Uninjured Reference


title: q359_WT_Run1

description: Uninjured Reference


title: q354_WT_Run1

description: Uninjured Reference


title: q356_WT_Run1

description: Uninjured Reference


title: q353_WT_Run1

description: Uninjured Reference


title: q358_WT_Run1

description: Uninjured Reference


title: q352_WT_Run1

description: Uninjured Reference


title: q360_WT_Run1

description: Uninjured Reference


title: q373_WT_Run1

description: Uninjured Reference


title: q351_WT_Run1

description: Uninjured Reference


title: q350_WT_Run1

description: Uninjured Reference


title: q355_WT_Run1

description: Uninjured Reference


title: q349_WT_Run1

description: Uninjured Reference


title: q347_WT_Run1

description: Uninjured Reference


title: q346_WT_Run1

description: Uninjured Reference


title: q344_WT_Run1

description: Uninjured Reference


title: q343_WT_Run1

description: Uninjured Reference


title: q342_WT_Run1

description: Uninjured Reference


title: q341_WT_Run1

description: Uninjured Reference


title: q339_WT_Run1

description: Uninjured Reference


title: q340_WT_Run1

description: Uninjured Reference


title: q338_WT_Run1

description: Uninjured Reference


title: q337_WT_Run1

description: Uninjured Reference


title: q334_WT_Run1

description: Uninjured Reference


title: q335_WT_Run1

description: Uninjured Reference


title: q336_WT_Run1

description: Uninjured Reference


title: q333_WT_Run1

description: Uninjured Reference


title: q332_WT_Run1

description: Uninjured Reference


title: q348_WT_Run1

description: Uninjured Reference


title: q327_WT_Run1

description: Uninjured Reference


title: q325_WT_Run1

description: Uninjured Reference


title: q329_WT_Run1

description: Uninjured Reference


title: q326_WT_Run1

description: Uninjured Reference


title: q328_WT_Run1

description: Uninjured Reference


title: q324_WT_Run1

description: Uninjured Reference


title: q345_WT_Run1

description: Uninjured Reference


title: q321_WT_Run1

description: Uninjured Reference


title: q320_WT_Run1

description: Uninjured Reference


title: q319_WT_Run1

description: Uninjured Reference


title: q330_WT_Run1

description: Uninjured Reference


title: q322_WT_Run1

description: Uninjured Reference


title: q317_WT_Run1

description: Uninjured Reference


title: q316_WT_Run1

description: Uninjured Reference


title: q318_WT_Run1

description: Uninjured Reference


title: q323_WT_Run1

description: Uninjured Reference


title: q315_WT_Run1

description: Uninjured Reference


title: q314_WT_Run1

description: Uninjured Reference


title: q313_WT_Run1

description: Uninjured Reference


title: q312_WT_Run1

description: Uninjured Reference


title: q331_WT_Run1

description: Uninjured Reference


title: q311_WT_Run1

description: Uninjured Reference


title: q308_WT_Run1

description: Uninjured Reference


title: 3312_6_IIhom_25-11-14_GCCAATA

source_name: epidermis

value: ARPC4 ko

value: PN day 4

value: epidermis


title: q310_WT_Run1

description: Uninjured Reference


title: q309_WT_Run1

description: Uninjured Reference


title: q306_WT_Run1

description: Uninjured Reference


title: q305_WT_Run1

description: Uninjured Reference


title: q307_WT_Run1

description: Uninjured Reference


title: q301_WT_Run1

description: Uninjured Reference


title: q304_WT_Run1

description: Uninjured Reference


title: q299_WT_Run1

description: Uninjured Reference


title: q303_WT_Run1

description: Uninjured Reference


title: q298_WT_Run1

description: Uninjured Reference


title: q300_WT_Run1

description: Uninjured Reference


title: q297_WT_Run1

description: Uninjured Reference


title: q293_WT_Run1

description: Uninjured Reference


title: q296_WT_Run1

description: Uninjured Reference


title: q295_WT_Run1

description: Uninjured Reference


title: q302_WT_Run1

description: Uninjured Reference


title: q290_WT_Run1

description: Uninjured Reference


title: q291_WT_Run1

description: Uninjured Reference


title: q289_WT_Run1

description: Uninjured Reference


title: q288_WT_Run1

description: Uninjured Reference


title: q286_WT_Run1

description: Uninjured Reference


title: q285_WT_Run1

description: Uninjured Reference


title: q284_WT_Run1

description: Uninjured Reference


title: q292_WT_Run1

description: Uninjured Reference


title: q280_WT_Run1

description: Uninjured Reference


title: q282_WT_Run1

description: Uninjured Reference


title: q279_WT_Run1

description: Uninjured Reference


title: q277_14dpOBX Olfactory Epithelium

source_name: 14dpOBX Olfactory Epithelium

value: B6 OMP-eGFP

value: OMP-eGFP+


title: q278_WT_Run1

description: Uninjured Reference


title: q276_14dpOBX Olfactory Epithelium


title: q275_14dpOBX Olfactory Epithelium


title: q274_14dpOBX Olfactory Epithelium


title: q294_WT_Run1

description: Uninjured Reference


title: q271_14dpOBX Olfactory Epithelium


title: q273_14dpOBX Olfactory Epithelium


title: q270_14dpOBX Olfactory Epithelium


title: q272_14dpOBX Olfactory Epithelium


title: q269_14dpOBX Olfactory Epithelium


title: q268_14dpOBX Olfactory Epithelium


title: q267_14dpOBX Olfactory Epithelium


title: q265_14dpOBX Olfactory Epithelium


title: q266_14dpOBX Olfactory Epithelium


title: q264_14dpOBX Olfactory Epithelium


title: q287_WT_Run1

description: Uninjured Reference


title: q283_WT_Run1

description: Uninjured Reference


title: q260_14dpOBX Olfactory Epithelium


title: q261_14dpOBX Olfactory Epithelium


title: q262_14dpOBX Olfactory Epithelium


title: q258_14dpOBX Olfactory Epithelium


title: q257_14dpOBX Olfactory Epithelium


title: q263_14dpOBX Olfactory Epithelium


title: q256_14dpOBX Olfactory Epithelium


title: q259_14dpOBX Olfactory Epithelium


title: q255_14dpOBX Olfactory Epithelium


title: q254_14dpOBX Olfactory Epithelium


title: q252_14dpOBX Olfactory Epithelium


title: q253_14dpOBX Olfactory Epithelium


title: q246_14dpOBX Olfactory Epithelium


title: q245_14dpOBX Olfactory Epithelium


title: q247_14dpOBX Olfactory Epithelium


title: q250_14dpOBX Olfactory Epithelium


title: q248_14dpOBX Olfactory Epithelium


title: q244_14dpOBX Olfactory Epithelium


title: q251_14dpOBX Olfactory Epithelium


title: q242_14dpOBX Olfactory Epithelium


title: q241_14dpOBX Olfactory Epithelium


title: q243_14dpOBX Olfactory Epithelium


title: q240_14dpOBX Olfactory Epithelium


title: q239_14dpOBX Olfactory Epithelium


title: q237_14dpOBX Olfactory Epithelium


title: q236_14dpOBX Olfactory Epithelium


title: q232_14dpOBX Olfactory Epithelium


title: q234_14dpOBX Olfactory Epithelium


title: q281_WT_Run1

description: Uninjured Reference


title: q231_14dpOBX Olfactory Epithelium


title: q230_14dpOBX Olfactory Epithelium


title: q228_14dpOBX Olfactory Epithelium


title: q227_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q229_14dpOBX Olfactory Epithelium


title: q225_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q226_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q224_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q223_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q221_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q222_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q217_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q249_14dpOBX Olfactory Epithelium


title: q218_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q216_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q220_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q235_14dpOBX Olfactory Epithelium


title: q219_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q214_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q238_14dpOBX Olfactory Epithelium


title: q211_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q210_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q208_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q207_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q212_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q209_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q206_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q233_14dpOBX Olfactory Epithelium


title: q204_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q203_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q205_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q201_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q200_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q199_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q198_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q196_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q215_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q202_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q195_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q213_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q192_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q191_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q193_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q194_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q190_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q189_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q188_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q187_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q186_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q185_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q181_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q179_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q184_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q183_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q175_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q180_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q178_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q174_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q176_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q172_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q168_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q173_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q171_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q170_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q167_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q169_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q163_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q164_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q165_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q161_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q162_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q159_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q158_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q166_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q156_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q177_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q157_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q155_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q154_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q153_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q182_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q152_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q151_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q148_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q149_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q147_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q160_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q146_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q143_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q145_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q141_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q142_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q144_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q139_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q138_14dpOBX injured olfactory epithelium

source_name: 14dpOBX injured olfactory epithelium

value: FVB Neurog1-eGFP


title: q137_14dpOBX injured olfactory epithelium


title: q140_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q136_14dpOBX injured olfactory epithelium


title: q135_14dpOBX injured olfactory epithelium


title: dsshep_bg3_3

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description:
BG3-c2
Processed data file: counts.tsv

data_processing:
Adapter and quality trimming using cutadapt v1.10 with parameters --quality cutoff 20 -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -a AGATCGGAAGAGC --minimum-length 25 --overlap 10
Aligned to UCSC dm6 assembly (chromosomes chr2L, chr2R, chr3L, chr3R, chr4, chrX, chrY, and chrM) with hisat2 v2.0.4 and with default parameters.
Counted reads in genes from FlyBase r6.11 annotations with featureCounts v 1.5.0-p3 using parameters -s 1 -t exon -g gene_id.
Genome_build: dm6
Supplementary_files_format_and_content: counts.tsv: Tab-delimited text file containing the number of reads in genes in each sample as quantified by featureCounts.

source_name: cell culture from nervous system, ds-shep

growth_protocol: Flies are grown on regular cornmeal food at 25 Celsius.

extract_protocol:
Total RNA is extracted with Qiagen RNeasy Plus Micro kit.
Ovation RNA-Seq Systems 1-16 for Model Organisms (Nugen) manufacturer's protocol, with Covaris fragmentation.

treatment_protocol: Knockdown of shep is achieved through elav>shep-RNAi, Dcr, mCD8::GFP; control animals are elav>Dcr, mCD8::GFP. BG3 cells are treated with dsRNA targeting shep or GFP, as experimental or control groups.

value: dsRNA targeting shep


title: dsshep_bg3_1

description:
BG3-c2
Processed data file: counts.tsv


title: dsshep_bg3_2

description:
BG3-c2
Processed data file: counts.tsv


title: q134_14dpOBX injured olfactory epithelium


title: dsgfp_bg3_3

description:
BG3-c2
Processed data file: counts.tsv

source_name: cell culture from nervous system, ds-GFP

value: dsRNA targeting GFP


title: dsgfp_bg3_2

description:
BG3-c2
Processed data file: counts.tsv


title: q150_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: q133_14dpOBX injured olfactory epithelium


title: q197_Olfactory epithelium after transplantation

description: Engrafted OMP+ Neurons


title: dsgfp_bg3_1

description:
BG3-c2
Processed data file: counts.tsv


title: q132_14dpOBX injured olfactory epithelium


title: dicer-gfp_x_larva_neuron_1

description: Processed data file: counts.tsv

source_name: sorted live neurons, third instar larval, dicer-gfp_x

value: neurons

value: third instar larval


title: dicer-gfp_x_larva_neuron_2

description: Processed data file: counts.tsv


title: dicer-gfp_x_pupal_neuron_3

description: Processed data file: counts.tsv

source_name: sorted live neurons, P14 pupal, dicer-gfp_x

value: P14 pupal


title: q129_5dpOBX injured olfactory epithelium

source_name: 5dpOBX injured olfactory epithelium


title: q131_5dpOBX injured olfactory epithelium


title: q130_14dpOBX injured olfactory epithelium


title: q128_14dpOBX injured olfactory epithelium


title: q127_5dpOBX injured olfactory epithelium


title: dicer-gfp_x_pupal_neuron_2

description: Processed data file: counts.tsv


title: dicer-gfp_shep-rnai_larva_neuron_3

description: Processed data file: counts.tsv

source_name: sorted live neurons, third instar larval, dicer-gfp_shep-rnai


title: dicer-gfp_shep-rnai_larva_neuron_2

description: Processed data file: counts.tsv


title: q125_5dpOBX injured olfactory epithelium


title: q124_5dpOBX injured olfactory epithelium


title: dicer-gfp_shep-rnai_larva_neuron_1

description: Processed data file: counts.tsv


title: dicer-gfp_x_pupal_neuron_1

description: Processed data file: counts.tsv


title: q123_14dpOBX injured olfactory epithelium


title: dicer-gfp_shep-rnai_pupal_neuron_3

description: Processed data file: counts.tsv

source_name: sorted live neurons, P14 pupal, dicer-gfp_shep-rnai


title: q121_5dpOBX injured olfactory epithelium


title: q120_5dpOBX injured olfactory epithelium


title: dicer-gfp_shep-rnai_pupal_neuron_1

description: Processed data file: counts.tsv


title: q119_5dpOBX injured olfactory epithelium


title: q117_14dpOBX injured olfactory epithelium


title: dicer-gfp_shep-rnai_pupal_neuron_2

description: Processed data file: counts.tsv


title: dicer-gfp_x_larva_neuron_3

description: Processed data file: counts.tsv


title: q115_5dpOBX injured olfactory epithelium


title: q116_5dpOBX injured olfactory epithelium


title: q126_14dpOBX injured olfactory epithelium


title: q111_5dpOBX injured olfactory epithelium


title: q122_14dpOBX injured olfactory epithelium


title: q109_14dpOBX injured olfactory epithelium


title: q108_5dpOBX injured olfactory epithelium


title: q105_14dpOBX injured olfactory epithelium


title: q106_5dpOBX injured olfactory epithelium


title: q104_5dpOBX injured olfactory epithelium


title: q100_5dpOBX injured olfactory epithelium


title: q99_5dpOBX injured olfactory epithelium


title: q101_5dpOBX injured olfactory epithelium


title: q102_5dpOBX injured olfactory epithelium


title: q98_5dpOBX injured olfactory epithelium


title: q96_5dpOBX injured olfactory epithelium


title: q97_14dpOBX injured olfactory epithelium


title: q118_5dpOBX injured olfactory epithelium


title: q95_14dpOBX injured olfactory epithelium


title: q94_5dpOBX injured olfactory epithelium


title: q91_5dpOBX injured olfactory epithelium


title: q93_5dpOBX injured olfactory epithelium


title: q92_5dpOBX injured olfactory epithelium


title: q90_5dpOBX injured olfactory epithelium


title: q89_5dpOBX injured olfactory epithelium


title: q114_5dpOBX injured olfactory epithelium


title: q113_5dpOBX injured olfactory epithelium


title: q112_14dpOBX injured olfactory epithelium


title: q110_5dpOBX injured olfactory epithelium


title: q107_5dpOBX injured olfactory epithelium


title: q88_14dpOBX injured olfactory epithelium


title: q103_5dpOBX injured olfactory epithelium


title: 2745: U2OS2-6-3_RNA_sample_transfected_2

city: Heidelberg

first: Nick

last: Kepper

address: Im Neuenheimer Feld 267 - BQ24

department: Chromatin Networks

country: Germany

institute: German Cancer Research Center

data_processing:
exclusion of reads aligning to transfected constructs using bowtie (no mismatches, multiple mapping allowed: bowtie -t -v 0 -M 1)
exclusion of reads aligning to the reporter construct described in (Janicki et al. 2004, Cell 116, 683-698), same mapping strategy as for the transfected constructs
mapping of remaining reads to the human reference genome using STAR (no mismatches, unique mapping: STAR --alignIntronMax 100000 --chimSegmentMin 1 --outFilterMultimapNmax 1 --outFilterMismatchNmax 0)
generation of count table using multibamcoverage (deeptools2.0) including strand information (multiBamCov -D -split -S)
filtering out gene predictions and transcripts with identical genomic start and end positions
addition of the two reporter genes (ECFP-SKL and MS2 loops) into the count table
application of DESeq2 for differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: txt, result tables with genomic coordinates, RefSeq identifiers and DESeq2 results for each gene

source_name: U2OS 2-6-3 cell line

growth_protocol: U2OS 2-6-3 cells were cultured in DMEM medium containing 1 g/l glucose, supplemented with 10% doxycycline-free fetal bovine serum, 1x penicillin/streptomycin and 2 mM stable glutamine

extract_protocol:
NucleoSpin RNA Plus (Macherey-Nagel) according to the manufacturer's protocol
NEBNext Ultra II Directional RNA library Prep Kit (NEB) according to the manufacturer's protocol

treatment_protocol: cells were exposed to white light over night

value: U2OS 2-6-3 cell line

tag: transient transfection

value: CIBN-TetR, PHR-YFP-VP16, mCherry-MCP

tag: transfection protocol

value: Roche Xtreme gene according to manufacturer's protocol

tag: illuminated over night

value: yes


title: q87_14dpOBX injured olfactory epithelium

value: olfactory epithelium

value: 8 wk


title: 2743: U2OS2-6-3_RNA_mock_transfected_2

value: TetR-RFP & YFP


title: q84_5dpOBX injured olfactory epithelium


title: 2744: U2OS2-6-3_RNA_sample_transfected_1