title: Access US-1494958

data_processing:
Libraries were normalized to 22 pM and subjected to cluster and single read sequencing was performed for 50 cycles on a HiSeq2500 instrument (Illumina, Inc. San Diego, CA, USA), according to the manufacturer's instructions. Base calling were done on the HiSeq instrument by RTA 1.17.21.3. FASTQ files were generated using CASAVA 1.8.2 (Illumina, Inc. San Diego, CA, USA).
FASTQ files were subjected to quality control with the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw reads from each capture library were aligned to the human reference genome (hg19). Reads were aligned by STAR_2.3.1 and processed with cufflinks
Genome_build: human reference genome (hg19)

extract_protocol:
RNA was isolated from FFPE samples using the QIAGEN RNA Purification Kit and quantified using ribogreen assay. Quality of RNA was assessed using using Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA, USA) and the percentages of fragments larger than 200 nucleotides were calculated.
RNA samples (100 ng total RNA) were fragmented at 94°C for 8 minutes on a thermal cycler. First strand cDNA syntheses were performed at 25°C for 10 minutes, 42°C for 15 minutes and 70°C for 15 minutes, using random hexameres and SuperScript II Reverse Transcriptase (Thermo Fisher Scientific Inc., Waltham, MA, USA). In a second strand cDNA synthesis the RNA templates were removed and a second replacement strand was generated by incorporation dUTP (in place of dTTP, to keep strand information) to generate ds cDNA. AMPure XP beads (Beckman Coulter, Inc., Indianapolis, IN, USA) were used to clean up the blunt-ended cDNA from the second strand reaction mix. The 3`ends of the cDNA were then adenylated to facilitate adaptor ligation in the next step. After ligation of indexing adaptors, AMPure XP beads were used to clean up the libraries. In a first PCR amplification step, PCR (15 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds) were used to selectively enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. After validation of the libraries, using Agilent DNA 1000 kit on a 2100 Bioanalyzer instrument, the first hybridization step were performed using exome capture probes. Before hybridization a 4-plex pool of libraries were made, by combining 200 ng of each DNA library. The hybridization was performed by 18 cycles of 1 minute incubation, starting at 94°C, and then decreasing 2°C per cycle. Then streptavidin coated magnetic beads were used to capture probes hybridized to the target regions. The enriched libraries were then eluted from the beads and prepared for a second round of hybridization. This second hybridization (18 cycles of 1 minute incubation, starting at 94°C, and then decreasing 2°C per cycle) were required to ensure high specificity of the capture regions. A second capture with streptavidin coated beads were performed, followed by two heated wash procedures to remove non-specific binding form the beads. The enriched libraries where then eluted from the beads and cleaned up by AMPure XP beads prior to a second PCR amplification. The amplification step were performed by 10 cycles (98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds) followed by a second PCR clean up using AMPure XP beads. Finally, the libraries were quantitated by qPCR using KAPA Library Quantification Kit—Illumina/ABI Prism® (Kapa Biosystems, Inc., Wilmington, MA, USA) and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer. The size range of the DNA fragments were measured to be in the range of 200–650 bp and peaked around 270 bp.


title: Access US-1493881

status: Public on Sep 20 2016

type: SRA

city: Spartanburg

first: Bernard

last: Omolo

state: SC

address: 800 University Way

department: Mathematics and Computer Science

country: USA

institute: University of South Carolina - Upstate

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: colon


title: Targeted US-1492016

data_processing:
Libraries were normalized to 22 pM and subjected to cluster and single read sequencing was performed for 50 cycles on a HiSeq2500 instrument (Illumina, Inc. San Diego, CA, USA), according to the manufacturer's instructions. Base calling were done on the HiSeq instrument by RTA 1.17.21.3. FASTQ files were generated using CASAVA 1.8.2 (Illumina, Inc. San Diego, CA, USA).
FASTQ files were subjected to quality control with the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw reads from each capture library were aligned to the human reference genome (hg19). Reads were aligned by STAR_2.3.1 and processed with cufflinks.
For this targeted RNA data, we used median normalization. We obtained the median for each of the samples and subtracted this number from each of the gene counts for the sample.
Genome_build: human reference genome (hg19)
Supplementary_files_format_and_content: Hits per sample

extract_protocol:
RNA was isolated from FFPE samples using the QIAGEN RNA Purification Kit and quantified using ribogreen assay. Quality of RNA was assessed using using Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA, USA) and the percentages of fragments larger than 200 nucleotides were calculated.
RNA samples (100 ng total RNA) were fragmented at 94°C for 8 minutes on a thermal cycler. First strand cDNA syntheses were performed at 25°C for 10 minutes, 42°C for 15 minutes and 70°C for 15 minutes, using random hexameres and SuperScript II Reverse Transcriptase (Thermo Fisher Scientific Inc., Waltham, MA, USA). In a second strand cDNA synthesis the RNA templates were removed and a second replacement strand was generated by incorporation dUTP (in place of dTTP, to keep strand information) to generate ds cDNA. AMPure XP beads (Beckman Coulter, Inc., Indianapolis, IN, USA) were used to clean up the blunt-ended cDNA from the second strand reaction mix. The 3`ends of the cDNA were then adenylated to facilitate adaptor ligation in the next step. After ligation of indexing adaptors, AMPure XP beads were used to clean up the libraries. In a first PCR amplification step, PCR (15 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds) were used to selectively enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. After validation of the libraries, using Agilent DNA 1000 kit on a 2100 Bioanalyzer instrument, the the libraries were quantitated by qPCR using KAPA Library Quantification Kit—Illumina/ABI Prism® (Kapa Biosystems, Inc., Wilmington, MA, USA) and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer. After validation of the libraries, using Agilent DNA 1000 kit on a 2100 Bioanalyzer instrument, the first hybridization step were performed using capture probes specific to genes of interest. Before hybridization a 4-plex pool of libraries were made, by combining 200 ng of each DNA library. The hybridization was performed by 18 cycles of 1 minute incubation, starting at 94°C, and then decreasing 2°C per cycle. Then streptavidin coated magnetic beads were used to capture probes hybridized to the target regions. The enriched libraries were then eluted from the beads and prepared for a second round of hybridization. This second hybridization (18 cycles of 1 minute incubation, starting at 94°C, and then decreasing 2°C per cycle) were required to ensure high specificity of the capture regions. A second capture with streptavidin coated beads were performed, followed by two heated wash procedures to remove non-specific binding form the beads. The enriched libraries where then eluted from the beads and cleaned up by AMPure XP beads prior to a second PCR amplification. The amplification step were performed by 10 cycles (98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds) followed by a second PCR clean up using AMPure XP beads. Finally, the libraries were quantitated by qPCR using KAPA Library Quantification Kit—Illumina/ABI Prism® (Kapa Biosystems, Inc., Wilmington, MA, USA) and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer. The size range of the DNA fragments were measured to be in the range of 200–650 bp and peaked around 250 bp.


title: Access US-1493853


title: Access US-1493850


title: Access US-1493868


title: Access US-1493831


title: Access US-1493847


title: Access US-1493200


title: Access US-1493211


title: Access US-1493212


title: Access US-1493194


title: Access US-1493195


title: Access US-1493193


title: Access US-1493221


title: Access US-1493191


title: Access US-1493855


title: Access US-1493189


title: Access US-1493188


title: Access US-1493187


title: Access US-1493184


title: Access US-1493181


title: Access US-1493183


title: spike-in gDNA reads

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description:
Barcodes of independent low-complexity Kc167 TRIP pool used as RNA spike-in
spikein_BCDs.txt

library_source: genomic

data_processing:
Basecalling and filtering was performed using standard software of the illumina HiSeq 2500 or MiSeq. Extraction of 21 nt barcode reads from fastq files and alignment of TRIP mapping reads was performed using the TRIP script available at http://trip.nki.nl. We set a Hamming distance of 2 for removing mutated barcodes, a maximum distance of 500 nt on the forward  read  and 20 nt on the reverse read to cluster the positions during mapping and a minimum read number of 1. Spike-in library gDNA was sequenced separately to determine the spike-in barcode sequences. A list of the most abundant spike-in barcodes with over 1000 counts in gDNA was used for extracting spike-in reads from the TRIP samples. For each TRIP experiment sample, cDNA read counts per barcode were divided by the sum of cDNA read counts for all spike-in barcodes to correct for sequencing depth and standardize expression between samples. gDNA read counts were transformed to counts per million (cpm) to correct for sequencing depth. Spike-in corrected cDNA counts were then divided by gDNA cpm counts which yields the normalized expression per barcode. We set a cutoff for barcodes that had at least 100 gDNA reads in all samples to ensure that each barcode was sufficiently represented in the pool. To ensure reliable allocation of barcode integrations, we worked with a total of 1093 barcodes that fit the following criteria: (1) more than 2 reads in both forward and reverse mapping (2) 80% of forward and reverse mapping reads matched with the first mapping location and less than 10% of forward and reverse mapping reads matched with the second mapping location (3) mapq score of 10 or higher for forward and reverse mapping.
Genome_build: dm3
Supplementary_files_format_and_content: CSV files containing barcode sequences, position of integration, read counts and normalized expression for each of the samples
Supplementary_files_format_and_content: space delimited list of spike-in barcode sequences

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Kc167 cells

growth_protocol: Kc167 cells were cultured at 23.5°C in Shields and Sang M3 Insect Medium (Sigma-Aldrich) with 0.25% Bacto Peptone (BD), 0.1% Yeast Extract (BD), 5% heat-inactivated FBS (Thermo Scientific) and 1% Penicillin/Streptomycin (Thermo Scientific). For pMT induction, sterile-filtered CuSO4 (Sigma-Aldrich) dissolved in H2O was added to 0.5mM final concentration

extract_protocol: To map the reporter integrations, gDNA was extracted from 20*106 cells using ISOLATE II Genomic DNA Kit (Bioline) and digested with NlaIII (40 U, NEB) in buffer 4 supplemented with BSA in a total volume of 100 µl for 2 h at 37°C. The reaction was terminated by heat inactivation for 20 min at 65°C. Fragments were circularized over night at 12°C using T4 Ligase (100 U, NEB) in T4 Ligase buffer in a total volume of 1600 µl. Products were precipitated with ethanol and purified with ISOLATE II PCR and Gel kit (Bioline). Unligated fragments were removed by digestion with Plasmid-Safe DNase (20 U, Epicentre) with added ATP (final concentration 1 mM) in the manufacturer-supplied reaction buffer in a total volume of 100 µl for 5 h at 37°C. The reaction was terminated by heat-inactivation for 30 min at 70°C and purified using ISOLATE II PCR and Gel kit (Bioline). To eliminate any remaining unintegrated plasmid , products were digested with I-CeuI (5 U, NEB) in buffer 4 supplemented with BSA in s total volume of 60 µl for 2 h at 37°C. The reaction was terminated by heat-inactivation for 20 min at 65°C and purified using ISOLATE II PCR and Gel kit (Bioline). Products containing barcodes and flaking gDNA were amplified in two rounds by inverse PCR to add Illumina adapters for Illumina paired-end sequencing. For cDNA reads, RNA from 10*106 transfected cells isolated by FACS sorting was extracted with Chloroform from TRIsure-resuspended samples (Bioline). The polyadenylated fraction was isolated using the Oligotex kit (Qiagen). RNA samples were treated with RNase-free DNase I (2 U, Roche) in DNase buffer in a total volume of 20 µl for 30 min at 37°C. The reaction was terminated by adding 1 µl of 25 mM EDTA and incubation at 70°C  for 15 min. cDNA was generated using Tetro cDNA Synthesis Kit (Bioline) according to the manufacturer’s instructions with a GFP-specific primer instead of OligoDT. 1/4 of total cDNA was used in a PCR reaction to add adapters for Illumina single-end sequencing. The appropriate PCR cycle number was determined by qPCR to avoid overamplification. For gDNA reads, gDNA was isolated from 10*106 unsorted TRIP cells using ISOLATE II Genomic DNA Kit (Bioline). 500 ng were used in a PCR reaction to add adapters for Illumina single-end sequencing and amplified over 25 cycles.

treatment_protocol: To establish the pool of cells harboring reporter constructs, 1 million Kc167 cells were transfected with 1 µg barcoded 5xGal4UAS-pMT-GFP plasmid library and 1 µg plasmid encoding Sleeping Beauty transposase (Addgene #65487) by electroporation. Transposase expression was induced by four heat shock treatments of 2.5 h at 37°C distributed over 36 h. Transfected cells were expanded until Sleeping Beauty expression was lost. For the resulting TRIP pool, we determined the number of integrations to be 0.3 per cell based on qPCR on gDNA for GFP integrations compared to a cell line with a single integration. A subpool of 30,000 cells was taken from the TRIP pool and expanded to  limit the library complexity to a maximum of 10,000 integrations before gDNA was isolated for mapping of integrations. For assessing the effect of recruiting HP1a to integrated reporters, GFP expression was induced by adding 0.5 mM CuSO4 two days before the TRIP pool was transiently transfected with plasmids encoding either pAc5-Gal4DBD-V5-HP1a-T2A-mCherry or control plasmids encoding only Gal4DBD-V5 or V5-HP1a instead of Gal4DBD-V5-HP1. For assessing reporter expression by day two after transfection, cells were sorted for mCherry expression before gDNA and cDNA were isolated for further analysis. For determining reporter expression by day 16 after transfection, cells were kept unsorted before cDNA and gDNA isolation. To be able to compare bulk expression changes between cDNA samples, an independent TRIP pool with a complexity of approximately 200 barcodes was suspended in TRIsure (Bioline) and added to TRIP cells to an amount of 2.5% based on cell counts before RNA extraction.

tag: cell line

tag: cell type

value: drosophila melanogaster dorsal closure stage embryonal cell line


title: Access US-1493179


title: Access US-1493154


title: Access US-1493176


title: D16, gDNA reads, HP1, repl 2

description:
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with HP1a collected by sixteen days after transfection.  Replicate 2 of 2
TRIP_HP1_D16

tag: transfected protein


title: D16, gDNA reads, HP1, repl 1

description:
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with HP1a collected by sixteen days after transfection.  Replicate 1 of 2
TRIP_HP1_D16


title: Access US-1493215


title: Access US-1492083


title: D16, gDNA reads, Gal4, repl 2

description:
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD collected by sixteen days after transfection.  Replicate 2 of 2
TRIP_HP1_D16


title: Access US-1492043


title: Access US-1492040


title: Access US-1492048


title: D16, gDNA reads, Gal4, repl 1

description:
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD collected by sixteen days after transfection.  Replicate 1 of 2
TRIP_HP1_D16


title: Access US-1492051


title: D16, gDNA reads, Gal4-HP1, repl 1

description:
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-HP1a collected by sixteen days after transfection.  Replicate 1 of 2
TRIP_HP1_D16


title: D16, gDNA reads, Gal4-HP1, repl 2

description:
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-HP1a collected by sixteen days after transfection.  Replicate 2 of 2
TRIP_HP1_D16


title: D16, cDNA reads, HP1, repl 1

description:
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with HP1a collected by sixteen days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 1 of 2
TRIP_HP1_D16

molecule: polyA RNA


title: Access US-1492034


title: D16, cDNA reads, HP1, repl 2

description:
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with -HP1a collected by sixteen days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 2 of 2
TRIP_HP1_D16


title: D16, cDNA reads, Gal4, repl 2

description:
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD collected by sixteen days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 2 of 2
TRIP_HP1_D16


title: Access US-1492032


title: D16, cDNA reads, Gal4, repl 1

description:
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD collected by sixteen days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 1 of 2
TRIP_HP1_D16


title: Access US-1492026


title: Access US-1492030


title: D16, cDNA reads, Gal4-HP1, repl 2

description:
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-HP1a collected by sixteen days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 2 of 2
TRIP_HP1_D16


title: Access US-1492020


title: Access US-1493173


title: Access US-1492025


title: D2, gDNA reads, HP1, repl 2

description:
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with HP1a collected by two days after transfection.  Replicate 2 of 2
TRIP_HP1_D2


title: D2, gDNA reads, Gal4, repl 2

description:
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD collected by two days after transfection.  Replicate 2 of 2
TRIP_HP1_D2


title: D2, gDNA reads, HP1, repl 1

description:
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with HP1a collected by two days after transfection.  Replicate 1 of 2
TRIP_HP1_D2


title: Access US-1492019


title: Access US-1492016


title: Access US-1492014


title: Access US-1492013


title: D2, gDNA reads, Gal4, repl 1

description:
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD collected by two days after transfection.  Replicate 1 of 2
TRIP_HP1_D2


title: D2, cDNA reads, HP1, repl 1

description:
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with HP1a, sorted for transfected cells and collected by two days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 1 of 2
TRIP_HP1_D2


title: D2, cDNA reads, Gal4, repl 2

description:
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD, sorted for transfected cells and collected by two days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 2 of 2
TRIP_HP1_D2


title: Access US-1492011


title: D16, cDNA reads, Gal4-HP1, repl 1

description:
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-HP1a collected by sixteen days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 1 of 2
TRIP_HP1_D16


title: Access US-1492012


title: Access US-1492010


title: Access US-1492006


title: Access US-1492007


title: Access US-1492004


title: D2, cDNA reads, Gal4-HP1, repl 2

description:
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-HP1a, sorted for transfected cells and collected by two days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 2 of 2
TRIP_HP1_D2


title: D2, cDNA reads, Gal4, repl 1

description:
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD, sorted for transfected cells and collected by two days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 1 of 2
TRIP_HP1_D2


title: D2, cDNA reads, Gal4-HP1, repl 1

description:
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-HP1a, sorted for transfected cells and collected by two days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 1 of 2
TRIP_HP1_D2


title: Dam-HP1a repl 2

description: wild-type Kc167 cells transfected with Dam-HP1a replicate 2

data_processing:
Reads were filtered for sequences containing DamID-adapter sequence using cutadapt, aligned to drosophila genome release dm3 using Bowtie 2 and matched with GATC-flanked fragments
Genome_build: dm3
Supplementary_files_format_and_content: space-delimited text files containing GATC fragment ID, chromsome, start, end, methylated fragment count

growth_protocol: Kc167 cells were cultured at 23.5°C in Shields and Sang M3 Insect Medium (Sigma-Aldrich) with 0.25% Bacto Peptone (BD), 0.1% Yeast Extract (BD), 5% heat-inactivated FBS (Thermo Scientific) and 1% Penicillin/Streptomycin (Thermo Scientific).

extract_protocol:
gDNA from 5*106 cells was isolated using ISOLATE II Genomic DNA Kit (Bioline).
500ng gDNA were digested with DpnI (10 U, New England Biolabs) in CutSmart buffer in a total volume of 20 µl at 37°C for 8 h. Reaction was terminated by heat-inactivation at 80°C for 20 min. Fragments were ligated to 12.5 pmol DamID adapters using T4 ligase (2.5 U, New England Biolabs) in T4 ligase buffer in a total volume of 25 µl incubated at 16°C for 16 h. The reaction was heat-inactivated for 10 min at 65°C. Products were then digested with DpnII to remove partially methylated fragments. DpnII buffer and DpnII (10 U, New England Biolabs) were added in a total volume of 80 µl and incubated at 37°C for 1h. 20µl of DpnII-digested products were amplified by PCR. PCR products were cleaned up using the ISOLATE II PCR and Gel Kit (Bioline) according to the manufacturer’s instructions and eluted in 26µl H2O. Fragment ends were blunted using the End-It™ DNA End-Repair Kit (Epicentre) in a 50µl reaction according to the manufacturer’s instructions. Products were cleaned up using the ISOLATE II PCR and Gel Kit (Bioline) and eluted in 26µl H2O. For adding a 3’ overhang, fragments were treated with Klenow fragment (3’-5’ exo-, 25 U, New England Biolabs) in buffer 2 with 200µM dATP (Thermo Fisher Scientific) in a 50 µl reaction incubated at 37°C for 30 min. Reaction was terminated by heat-inactivation at 75°C for 20 min. Products were purified using CleanPCR magnetic beads (CleanNA) according to the manufacturer’s instructions and eluted in 20 µl H2O. 260 ng fragments were ligated to 2.5 µM Y-adaptors using T4 Ligase (2.5 U, New England Biolabs) in T4 buffer in a total volume of 10 µl incubated at 16°C for 16 h. Reaction was terminated by heat-inactivation at 65°C for 10 min. Products were purified using CleanPCR magnetic beads (CleanNA) according to the manufacturer’s instructions and eluted in 20 µl H2O. Adapters and indices for next-generation sequencing and multiplexing were added by PCR.

treatment_protocol: 20x106 wild-type Kc167 cells were transfected in duplicates by electroporation with 20 µg plasmids expressing Dam-HP1 or Dam   (van Steensel & Henikoff, Nat Biotech, 2000; PMID: 10748524) only and collected two days after transfection.


title: Access US-1492003


title: Access US-1491997


title: Dam repl 2

description: wild-type Kc167 cells transfected with Dam replicate 2


title: Access US-1491995


title: Access US-1491993


title: D2, gDNA reads, Gal4-HP1, repl 2

description:
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-HP1a collected by two days after transfection.  Replicate 2 of 2
TRIP_HP1_D2


title: D2, cDNA reads, HP1, repl 2

description:
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with HP1a, sorted for transfected cells and collected by two days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 2 of 2
TRIP_HP1_D2


title: Access US-1491986


title: MN_Scerevisiae_KanSc_Rep1

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

description: Mononucleosomal DNA

data_processing:
Alignment: bowtie 0.12.7. Aligment against the proper replaced with the appropriate sequence for each mutant.
The smoothed signal is generated by using a modified version of NUCwave to normalize signal against repetitions.
Genome_build: S. pombe 2007 (ASM294v2)
Genome_build: S. cerevisiae (SacCer 3)

organism: Saccharomyces cerevisiae

source_name: Mononucleosomal DNA

growth_protocol: Yeast cultures were grown in YES medium (S. pombe) or YEPD (S. cerevisiae)

extract_protocol:
In S. pombe maps: 200 ml cultures at 0.8x10^7 cells/ml were collected  for preparation of mononucleosomal DNA. Cells were treated with 8 mg of Zymolyase  20T during 30 minutes at 30 ºC to induce spheroplasts formation. Mononucleosomal fragments were generated by digesting DNA with 150 units/ml  of micrococcal nuclease (MNAse) at 37 ºC during 45 minutes. The amount of MNase was optimized experimentally to generate a 80:20 ratio of mononucleosomes to dinucleosomes, as described (Lantermann et al. 2010). Mononucleosomal DNA was recovered from 1.5% agarose gels and sequenced in an Illumina NextSeq 500 using the pair-end sequencing protocol.
In S. cerevisiae maps: 200 ml cultures at 0.8x10^7 cells/ml were collected  for preparation of mononucleosomal DNA. Cells were treated with 10 mg of Zymolyase  20T during 5 minutes at 30 ºC to induce spheroplasts formation. Mononucleosomal fragments were generated by digesting DNA with 300 units/ml  of micrococcal nuclease (MNAse) at 37 ºC during 10 minutes. The amount of MNase was optimized experimentally to generate a 80:20 ratio of mononucleosomes to dinucleosomes, as described (Soriano et al. 2014). Mononucleosomal DNA was recovered from 1.5% agarose gels and sequenced in an Illumina NextSeq 500 using the pair-end sequencing protocol.
Mononucleosomal DNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain


title: Dam repl 1

description: wild-type Kc167 cells transfected with Dam replicate 1


title: Access US-1492009


title: MN_Scerevisiae_KanSc_Rep2

description: Mononucleosomal DNA


title: D2, gDNA reads, Gal4-HP1, repl 1

description:
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-HP1a collected by two days after transfection.  Replicate 1 of 2
TRIP_HP1_D2


title: 50%DO-3

city: wuxi

first: Sun

last: Yang

address: lihu avenue

department: School of Biotechnology

country: China

institute: JIANGNAN UNIVERSITY

data_processing:
Illumina Casava  software used for basecalling.
As there are some adaptor sequences and/or low quality reads present in the raw reads, data filtering is carried out to obtain high quality reads as the clean reads,Clean reads were mapped to NC_003450.3 whole genome using bowtie2 ,number of reads that uniquely aligned to gene is Gene_counts.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol fromMortazavi, A., B. A. Williams, et al . Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 2008.5(7): 621-8
Genome_build: ASM1132v1 (NC_003450.3)
Supplementary_files_format_and_content: tab-delimited text files include counts and RPKM values for each Sample

organism: Corynebacterium glutamicum

source_name: 50%DO, bacteria

growth_protocol: The strain was firstly grown on seed medium (25 g glucose, 30 g corn syrup, 20 g (NH4)2SO4, 1g MgSO4, 1g KH2PO4 per liter of distilled H2O; pH 6.8) of a shaker for 12 h at 30 °C, 220 r/min. The seed was then transferred to second seed medium which is same with seed just in baffled-bottom flask, and then transferred to medium culture used for fermentation in a 5L fermentor (Applikon EZ-control) for 48 h,100mg/ml Chloramphenicol was added into each medium to make sure the last concentration was 30 ug/ml. Three batches were conducted with three duplicate, one at high DO (50%), one at medium DO (30%) and one at low DO (0%). The medium composition of the three batches was: 30 g glucose, 15 g corn syrup, 20 g (NH4)2SO4, 1g MgSO4, 1g KH2PO4 per liter of distilled H2O; pH 6.8.100mg/ml Chloramphenicol was added into each medium to make sure the last concentration was 30 ug/ml. The fermentation temperature was 30 °C. Samples were collected at 20 h (at the early of stable phase) from three independent batches for RNA sequencing and quantitative real-time RT-PCR analysis.

extract_protocol:
samples were quenched in liquid nitrogen immediately after collection,and RNA was harvested using RNAiso plus (Takara, Dalian, China),Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: fermentation at 50%DO

tag: time

value: 20 hrs


title: 50%DO-2


title: 30%DO-3

source_name: 30%DO, bacteria

value: fermentation at 30%DO


title: MN_Scerevisiae_KanWT_Rep2

description: Mononucleosomal DNA


title: 50%DO-1


title: MN_Scerevisiae_KanSp_Rep1

description: Mononucleosomal DNA


title: 30%DO-2


title: MN_Scerevisiae_KanWT_Rep1

description: Mononucleosomal DNA


title: MN_Scerevisiae_SeqSc-Sc_Rep2

description: Mononucleosomal DNA

value: MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 KanMX-SeqSc in IGR YDL211c-YDL210W


title: 30%DO-1


title: 0%DO-3

source_name: 0%DO, bacteria

value: fermentation at 0%DO


title: Dam-HP1a repl 1

description: wild-type Kc167 cells transfected with Dam-HP1a replicate 1


title: 0%DO-2


title: 0%DO-1


title: MN_Scerevisiae_SeqSp-Sc_Rep1

description: Mononucleosomal DNA

value: MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 KanMX-SeqSp in IGR YDL211c-YDL210W


title: MN_Scerevisiae_SeqSc-Sc_Rep1

description: Mononucleosomal DNA


title: MN_Scerevisiae_KanSp_Rep2

description: Mononucleosomal DNA


title: MN_Scerevisiae_SeqSp-Sc_Rep2

description: Mononucleosomal DNA


title: Spn_smallTranscr_t5min_control_1

status: Public on Sep 19 2016

city: Braunschweig

first: Jannik

last: Donner

address: Inhoffenstr. 7

country: Germany

institute: Helmholtz-Center for Infection Research

description:
mRNA-smaller_equal200nt_Rockhopper.txt
sRNA-smaller200nt_HTSeq.txt
tRNAs_Rockhopper.txt

data_processing:
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2.
Raw read counts of mRNAs>200 nt were obtained by aligning samples 1-24 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3.
Raw read counts of tRNAs/mRNAs</=200 nt were obtained by aligning samples 25-36 to the reference genome and counting of the mapped reads per feature using Rockhopper v2.0.3.
Raw read counts of small regulatory RNAs>200 nt were obtained by first aligning samples 1-24 to the reference genome by using Bowtie2 v2.2.2 and then counting mapped reads at the location of previously selected small RNAs using HTSeq.
Raw read counts of small regulatory RNAs</=200 nt were obtained by aligning samples 25-36 to the reference genome by using Bowtie2 v2.2.2 and then counting mapped reads at the location of previously selected small RNAs using HTSeq.
Genome_build: NC_003028.3
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and carolacton-treated samples as obtained from Rockhopper (mRNAs/tRNAs) or HTSeq (sRNAs).

organism: Streptococcus pneumoniae TIGR4

source_name: planktonic cells

growth_protocol: S. pneumoniae TIGR4 cells were inoculated to an optical density at 600 nm (OD600) of 0.1  and grown in Todd-Hewitt broth plus 1% yeast extract at 37°C and 5% CO2.

extract_protocol:
Cellular RNAs were extracted using the miRNeasy kit (Qiagen) according to the manufacturers protocol for size-separation of RNA fractions >200 nt and </= 200 nt. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted for the samples containing RNAs >200 nt using the Ribo-Zero kit for Gram-positive bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer.
Libraries of RNA fractions >200 nt were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers instructions. Libraries of RNA isolations </= 200 nt were constructed with the TruSeq Small RNA Library Prep Kit (Illumina) also according to the manufacturers guidelines.

treatment_protocol: At an OD600 of 0.15 treated cells were supplied with a final concentration of 0.25 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Six time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15, t60, t120, and t180 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C.

tag: optical density 600 nm

tag: time point


title: Spn_smallTranscr_t180min_caro_1

value: 0.25 µg/ml carolacton


title: Spn_smallTranscr_t5min_control_2


title: Spn_smallTranscr_t180min_caro_2


title: Spn_smallTranscr_t180min_control_1


title: Spn_smallTranscr_t0min_control_2


title: Spn_smallTranscr_t5min_caro_1


title: Spn_smallTranscr_t0min_control_1


title: Spn_smallTranscr_t0min_caro_2


title: Spn_smallTranscr_t0min_caro_1


title: Spn_largeTranscr_t180min_control_1

description:
mRNA-larger200nt_Rockhopper.txt
sRNA-larger200nt_HTSeq.txt


title: Spn_smallTranscr_t180min_control_2


title: Spn_smallTranscr_t5min_caro_2


title: Spn_largeTranscr_t120min_caro_1


title: Spn_largeTranscr_t180min_caro_2


title: Spn_largeTranscr_t120min_control_2


title: Spn_largeTranscr_t120min_caro_2


title: Spn_largeTranscr_t180min_control_2


title: Spn_largeTranscr_t180min_caro_1


title: Spn_largeTranscr_t60min_control_2


title: Spn_largeTranscr_t120min_control_1


title: Spn_largeTranscr_t60min_caro_2


title: Spn_largeTranscr_t60min_control_1


title: Spn_largeTranscr_t15min_control_2


title: Spn_largeTranscr_t60min_caro_1


title: Spn_largeTranscr_t15min_control_1


title: Spn_largeTranscr_t15min_caro_1


title: Spn_largeTranscr_t15min_caro_2


title: Spn_largeTranscr_t5min_control_2


title: Spn_largeTranscr_t0min_control_1


title: Spn_largeTranscr_t5min_caro_2


title: Spn_largeTranscr_t5min_caro_1


title: Spn_largeTranscr_t0min_caro_2


title: Spn_largeTranscr_t0min_control_2


title: Spn_largeTranscr_t0min_caro_1


title: Spn_largeTranscr_t5min_control_1


title: BMMSC-Cont-2

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
For the analysis of differentially expressed genes, the data of quality-checked reads for each condition were processed with the STAR (version 2.4.5) software based on reference genome sequence (Homo sapiens UCSC hg19) and the differential gene expressed values of each sample were calculated by the DESeq2 Bioconductor package.
The number of reads mapped to gene ID features were counted using STAR.
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

source_name: Bone marrow Mesenchymal Stem Cells

growth_protocol: BM-MSC cells were cultured in low-glucose Dulbecco’s modified Eagle’s medium (DMEM) (Gibco, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS) (Hyclone, Logan, UT) and penicillin (100 U/ml)/streptomycin (100 mg/ml) (Gibco, Carlsbad, CA, USA). The cells were maintained in a humidified incubator with a 95% air/5% CO2 atmosphere at 37°C.The cells were maintained in a humidified incubator with 95% air and a 5% CO2 atmosphere at 37°C. The medium was replaced every 3–4 days. In this study, MSCs were used at passages 5 or 6.

extract_protocol:
Total RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany). hMSCs or LPS-treated hMSCs were completely lysed with RNAiso Plus, then 200 μl of chloroform was added, and the tubes inverted for 5 min. The mixture was centrifuged at 12,000 x g for 15 min at 4°C, and the upper phase was placed into a new tube and 600 μl of 70% ethanol was added. The mixture was applied to an RNeasy mini column. The column was washed with wash buffer. To elute, RNase-free water (30 μl) was added directly onto the RNase mini column, followed by centrifugation at 12,000 x g for 3 min at 4°C. For ribosomal RNA (rRNA) depletion in total RNA, the RiboMinus Eukaryote kit (Life Technologies, Carlsbad, CA) was employed according to the manufacturer’s instructions. RNA libraries were created using the NEBNext® Ultra™ directional RNA library preparation kit for Illumina® (New England Biolabs, Ipswich, MA). rRNA-depleted total RNA was fragmented into small pieces using divalent cations at elevated temperatures. The first-strand cDNA was synthesized using reverse transcriptase and random primers, and then second-strand cDNA synthesis was performed using DNA polymerase I and RNase H. The cDNA fragments were processed using an end-repair reaction after the addition of a single ‘A’ base, followed by adapter ligation. These products were purified and amplified through PCR to generate the final cDNA library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were incubated with LPS (10 ng/ml, Sigma-Aldrich) for the specified time intervals (for 4 hours) under normal culture conditions.

tag: source

value: Lonza (donor 7F3674; Walkersville, MD)

value: control

tag: passages

value: 5 or 6


title: BMMSC-Cont-1


title: BMMSC-LPS-10ng-1

value: with LPS (10ng/ml) for 4 hrs


title: BMMSC-LPS-10ng-3


title: BMMSC-LPS-10ng-2


title: BMMSC-Cont-3


title: Super-3

city: Boston

first: Zhiyun

last: Wei

state: Massachusetts

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

description: 100,000g untracentrifugation supernatant

data_processing:
Reads annotation to hg19 or mm10 was performed using exceRpt small RNA-seq pipeline V2.2.8 using the Genboree Workbench (PMID 26320941).
Genome_build: hg19, mm10
Supplementary_files_format_and_content: xlsx format; reads per million mapped

organism: Bos taurus

source_name: Fetal Bovine Serum

extract_protocol:
40mL of freshly thawed FBS were injected into Quick-Seal Centrifuge Tubes and spun at 100,000 g, 4°C using an Optima L-90K ultracentrifuge (Beckman Coulter, CA) in SW 28 rotor (28,000 rpm) for 24 hours. RNA from the pellet was isolated using miRCURY RNA Isolation Kit (Exiqon, Denmark), with on-column DNase (Qiagen, Germany) treatment step added to the manufacturer’s protocol. 20mL of the supernatant was concentrated using 3 kDa Amicon Ultra Centrifugal Filters (EMD Millipore, MA) at 4,000 g 4 °C for 80 min. The concentrate was then lysed using six volumes of Lysis Solution of miRCURY RNA Isolation Kit (Exiqon), followed by the RNA isolation as above.
60 ng of total RNA was treated with T4-PNK and used as an input for NEBNext small RNA library construction (New England Biolabs, MA), with size selection for 15-65nt inserts. The libraries were examined using Agilent Bioanalyzer 2100 (Agilent, CA), quantified with KAPA Library Quantification Kits for Illumina (KAPA Biosystems, MA), and sequenced on HiSeq 2000 (Illumina, CA) with single-end 50 bp reads, at the Center for Cancer Computational Biology at Dana-Farber Cancer Institute.

tag: sample type

value: fetal bovine serum


title: Super-2


title: Pellet-3

description: 100,000g untracentrifugation pellet


title: Pellet-2

description: 100,000g untracentrifugation pellet


title: Super-1


title: Volunteer 1 Winter

first: Diego

last: Chaves-Moreno

address: inhoffenstrasse 7

department: Department of Medical Microbiology (MMIK)

institute: Helmholtz Centrum for Infection Research

description: Human Nasal Community

data_processing:
Illumina Base Calling: Libraries were sequenced on Illumina HiSeq2500 system with TrueSeq PE Cluster Kit V3 and TrueSeq SBSKit V3-HS (200cycles PE) Base calling were performed using the Illumina pipeline v 1.8.2
Filtering: Filtering and trimming with the following parameters: Q ≥ 15, Seq. length ≥ 90nt, Homopolymers ≤ 8nt and N's = 0.
Filtering: collapsing all the indexes from the machine into one file
human reads removal: Human reads were removed using BLAT against a human genome repository downloaded from NCBI ftp site. Sequences with >70% identity were removed
Ribosomal filtering: Ribosomal sequences were removed using HMMER (V3.0) using as a database models build with alignments of the Ribosomal fractions (5S,16S, and 23S) and BLASTN against a database of Ribosomal proteins of S. aureus genomes
S. aureus recruiting: Reads were recruited to S. aureus related via BLAST against 25 S. aureus genomes, reads with a ratio ≥ 80 (%id*AlnLength/QueryLength)
S. aureus mapping: Remaining reads were blasted (RPS-BLASTN) against a reference database of Position Scoring Matrices (PSM) build from a comparison of 25 Genomes of S. aureus
Down Sampling by Randomization: Read counts were down-sampled by a ramdom resampling using an in-house script written in perl
Normalization to counts per millon: Normalization to counts per millon
processed data files format and content: excel - abundance (by counting the number of transcripts) for each gene (groups of genes, OG) within each condition
Note: R2 reads weren't used for data processing

organism: Staphylococcus aureus

source_name: Anterior nare Sample

growth_protocol: The in vivo samples were taken from the anterior nares of a human noses known to be an S. aureus carriers.

extract_protocol:
RNA was extracted using Qiagen's Rneasy Mini Kit following manufacturer's instructions, the where the samples were treated by beat beating in a solution of RLT Buffer (Qiagen) and 1% of β-mercaptoethanol.
Amplification Protocol: Enriched mRNA fractions were amplified using the MessageAMP II-Bacteria RNA amplification according to manufacturer's instructions. Amplified samples were converted to ds-cDNA using SuperScript Double-Stranded cDNA Synthesis Kit and purified using GeneClean Turbo for PCR Kit (MP Biomed).
Paired-End DNA Sample Prep Kit (Illumina, San Diego, USA) according to manufacturer's instructions

treatment_protocol: Stabilization of the RNA in the samples was performed by incubating with RNAprotect for 30 mins before proceeding with the RNA isolation.

tag: sequence events


title: Volunteer 2 Winter

description: Human Nasal Community


title: Volunteer 3 Summer

description: Human Nasal Community


title: Volunteer 2 Summer

description: Human Nasal Community


title: G3R1

city: Berkeley

first: Lior

last: Pachter

state: California

address: 378 Stanley Hall, University of California, Berkeley

department: Computer Science and Molecular and Cell Biology

institute: UC Berkeley

data_processing:
Raw  reads were filtered to remove reads not passing Illumina’s Casava quality score using casava illumina filter 0.1 05-Aug-2011  SETTINGS: fastq_illumina_filter --keep N -v -v -o
Filtered reads were trimmed with Trimmomatic-0.30 to remove adapters and low-quality reads. SETTINGS: trimmomatic.jar PE -phred33 read1_filtered.fastq read2_filtered.fastq read1_trimmed_paired.fastq.gz read1_trimmed_unpaired.fastq.gz read2_trimmed_paired.fastq.gz read2_trimmed_unpaired.fastq.gz ILLUMINACLIP:../TruSeq3-PE.fa:2:30:10:8:TRUE TRAILING:20 MINLEN:35 ADAPTERS >PrefixPE/1 TACACTCTTTCCCTACACGACGCTCTTCCGATCT, >PrefixPE/2 GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, >PE1 TACACTCTTTCCCTACACGACGCTCTTCCGATCT, >PE1_rc AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA, >PE2 GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, >PE2_rc AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, >postindex ATCTCGTATGCCGTCTTCTGCTTG, >postindex_rc CAAGCAGAAGACGGCATACGAGAT
Trimmed reads were aligned with bowtie2 version2.1.0, default settings. bowtie2-build --offrate 1. Reference from ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.02_FB2014_05/fasta/dmel-all-transcript-r6.02.fasta.gz
Aligned reads were quantified with eXpress 1.5.1, default settings. Transcript TPMs were merged to gene level and scaled up (×100) for downstream analysis.
Differential expression analysis was performed using DE-Seq2. Genes with pad-j values ≤ 0.05 were considered differentially expressed.
Genome_build: flybase dmel_r6.02_FB2014_05
Supplementary_files_format_and_content: Normalized TPM for across all eight samples. Transcript abundance estimates from eXpress were merged to gene level using flybase fbgn_fbtr_fbpp_fb_2015_04.tsv.gz and gene 'TPM' multiplied by 100 to scale. Gene-level 'TPM' normalized across samples using DESeq command ' estimateSizeFactors'.

source_name: 4 pooled whole pupae

growth_protocol: Flies were cultivated at 25 °C and 50% relative humidity on standard fly food with 12 hour light-dark cycles. To generate synchronized 2 to 3 day old F1 flies, adult flies were allowed to lay for 48 hours in a bottle, then parent flies were discarded, and the bottles with eggs were allowed to grow into adult flies at 25 °C. From the F1 generation, 2 to 3 day old flies were used for the chronic hypergravity studies.

extract_protocol:
Total RNA was extracted from four replicates of four pooled pupae from 3 g and four replicates of four from control conditions using Qiagen RNeasy mini kit, Cat. No.74104. 1mg RNA per sample was treated with turboDNase prior to library preparation.
Samples were prepared for sequencing, indexed, and multiplexed using the Illumina mRNA TruSeq kit as per manufacturer protocol. Sequenced on 1 lane of the Illumina HiSeq-2000 100bp PE reads. Sample:Index:Sequence G3R3:2:CGATGT|G1R2:4:TGACCA|G1R3:5:ACAGTG|G1R4:6:GCCAAT|G3R1:7:CAGATC|G3R2:12:CTTGTA|G1R1:16:CCGTCC|G3R4:18:GTCCGC

value: WT Canton-S

value: 3g treatment

tag: Stage


title: G3R2


title: Volunteer 1 Summer

description: Human Nasal Community


title: G1R1

value: 1g control


title: Pellet-1

description: 100,000g untracentrifugation pellet


title: G3R4


title: G1R3


title: G1R2


title: G1R4


title: melan-a_1

status: Public on Sep 18 2016

city: Bethesda

first: Derek

last: Gildea

state: MD

address: 12 South Drive Rm 4009-24

institute: NHGRI/NIH

data_processing:
Basecalling performed by CASAVA-1.8.2
The ten 5'-most bases were trimmed from all RNA-seq reads
Trimmed RNA-seq reads were aligned to the mm9 genome assembly using STAR v. 2.3.0e
rRNA sequences were identified as those mapping to known rDNAs (genomic locations of rDNAs that were downloaded from UCSC) and were removed using the split_bam.py script available in RSeQC (v. 2.3.7)
Reliable alignments were obtained using samtools view with option '-q 1'
RNA-seq read counts mapping to Ensembl-annotated genes (release 67) were determined using htseq-count v. 0.5.3p3, and read count normalization to calculate TMM-FPKM values was performed by edgeR
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file containing TMM-FPKM for each sample

organism: Mus musculus

source_name: melan-a cells

growth_protocol: According to guidelines from Bennett et al. 1987 (PMID 3102392), cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum (Gibco), 200 nM 12-O-tetradecanoylphorbol 13-acetate (Sigma-Aldrich, St Louis, MO, USA) and 200 pM cholera toxin (Sigma- Aldrich, St Louis, MO, USA) at 37°C.

extract_protocol:
For RNA isolation, cells were lysed in Trizol reagent and RNA was isolated using RNAeasy Mini Kit (Qiagen) per manufacturer's instructions.
TruSeq Stranded mRNA kit (Illumina) per manufacturer's instructions

tag: strain background

value: melan-a

value: melanocytes derived from Ink4a-ARF-/- mice


title: melan-a_3


title: Volunteer 3 Winter

description: Human Nasal Community


title: melan-a_4


title: JQ1S Sensitive Rep 1

city: South San Francisco

first: Simon

middle: J

last: Hogg

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

data_processing:
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using TopHat/bowtie2 to the mouse reference genome (GRCm38/mm10)
Read counting was performed with HTSeq-Count from HTSeq using transcript annotation from Ensembl Release 73
The Voom-LIMMA workflow was used to normalise data and compute statistical significance of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Tab seperated text file containing read counts for each sample by ensembl mouse gene id

source_name: JQ1 sensitive Eμ-Myc (JQ1S)

growth_protocol: Cell lines grown in high-glucose Dulbecco's modified Eagle medium supplemented with 10% fetal calf serum, penicillin (100 U/mL), streptomycin (100mg/mL), 0.1mM L-Asparagine, and 50μM 2-mercaptoethanol

extract_protocol:
RNA was extracted using the Nucleospin® RNA extraction kit (Macherey-Nagel, Bethlehem, PA) as per the manufacturer's instructions.
cDNA libraries were prepared and then processed using TruSeq RNA library Prep Kit (Illumina)

treatment_protocol: Early passage cells were cultured in media


title: JQ1R Resistant Rep 1

source_name: JQ1 resistant Eμ-Myc (JQ1R)


title: JQ1R Resistant Rep 2


title: JQ1S Sensitive Rep 2


title: KLS - U638 - rep2

city: Santa Cruz

first: Camilla

last: Forsberg

state: CA

address: 1156 High st

department: Biomolecular engineering

institute: University of California Santa Cruz

data_processing:
Samples rfu03,rfu04,rfu05,rfu06 were trimmed to 82bp(read1) x 68bp(read2) from the 3' end because the sequencing run was truncated. Samples rfu08,rfu09 were trimmed to 75bp x 75bp from the 3' end.
After trimming, sequences were mapped to the set of repeatMasker mouse library elements using Bowtie2. Sequences that were mapped as paired-ends to the repeat elements were eliminated from further processing.
Samples were mapped with Tophat2 using Bowtie2 as the underlying alignment tool. The target assembly was mm9. Tophat was supplied with a gene model using the --GTF option. The gene model was UCSC KnownGenes.
For multiply mapped reads, only the best scoring mapping per bowtie2 were kept. Only mappings with both of the paired-end reads mapped were kept.
Potential PCR duplicates were removed with samtools rmdup.
The final set of mappings was converted to coverage using bedTools genomeCoverageBed.
The coverage summed over all exonic positions of a gene was divided by 150 to determine the read per gene for a sample. This was done for all mm9 UCSC KnownGenes.
For input to DESeq all genes with non-zero counts in any sample were considered. Replicates were combined per the DESeq methodology.
Genome_build: mm9
Supplementary_files_format_and_content: DESeq results include genes with padj better than 0.1. For each such gene, mean for a condition across its replicates is listed along with foldChange, raw p-value and Benjamini-Hochberg adjusted p-value.

source_name: Bone marrow_UNC0638 1uM

growth_protocol: FACS sorted HSCs (KLS Flk2-CD150+) were cultured in X-VIVO15 supplemented with 25ng/ml SCF and 5ng/ml TPO

extract_protocol:
After 5 days in culture, cells were harvested and washed in PBS. RNA was isolated using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 0.3μM of UNC0638 or with DMSO control

value: Bone marrow

tag: developmental stage

value: Adult mice (8-12 weeks)

value: UNC0638 1uM


title: KLS - U638 - rep1


title: KLS - Control - rep2

source_name: Bone marrow_DMSO

value: DMSO


title: KLS - Control  - rep3


title: KLS - Control - rep1


title: wild-type postmature-green-stage seed

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Postmature-green-stage seeds from Arabidopsis Col wild-type were collected

data_processing:
Basecalls performed using RTA version 1.12.4.2
Original data file from the Illumina sequencing pipeline.  Each lane of sequencing is attached as an individual compressed file.  The sequence data are in the QSEQ format
We aligned the raw reads to a pre-processed reference genome using BS Seeker [Chen et al. BMC Bioinformatics (2010)] allowing for two mismatches.  The pre-processed reference genome consisted of sequences from the Arabidopsis thaliana genome (TAIR 10) obtained from the TAIR website (http://www.arabidopsis.org/) and Phi-X174 reference genome (GenBank: J02482).
Reads containing three consecutive methylation in the non-CG sites were removed, possibly representing non-converted cytosines (Cokus et al. Nature 2008). Clonal reads possibly arising during the PCR amplification step were collapsed into one read.
Methylation level of sampled cytosine was calculated as (methylated calls / (methylated calls + unmethylated calls))
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text file including methylation level of each sampled cytosine

organism: Arabidopsis thaliana

source_name: postmature-green-stage seeds from Arabidopsis wild-type

growth_protocol: Arabidopsis thaliana (L.) Heynh, ecotype Columbia (Col) wild type and ddcc mutant plants were grown under standard greenhouse conditions (Belmonte et al., PNAS 2013). Leaves were collected for genomic DNA isolation from 3 week plant.

extract_protocol:
Collected seeds and leaves were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Genomic DNA  was isolated from the powder using the DNEASY Plant Mini kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.
Approximately 500 nanogram of genomic DNA isolated from seeds and leaves was subjected to library preparation following the methods of Hsieh et al. (Hsieh T-F et al. 2009. Science 324:1451-1454) with modifications. We spiked-in ~ three nanogram of unmethylated lambda DNA (Promega) to serve as a control for complete bisulfite conversion. Adapter-ligated genomic DNA was subjected to two rounds of bisulfite (BS) treatment using the EpiTect kit (Qiagen, Valencia, CA).  BS-treated DNA was purified using AMpure XP beads (Beckman) and PCR-amplified for 10 cycles using ExTaq (EpiCentre) DNA polymerase.  PCR-amplified DNA fragments were size selected using the AMpure XP beads (Beckman).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: genotype

value: wild type

value: seed

tag: cultivar

value: Col


title: ddcc mutant postmature-green-stage seed

description: Postmature-green-stage seeds from Arabidopsis Col ddcc mutant were collected

source_name: postmature-green-stage seeds from Arabidopsis ddcc mutant

value: ddcc mutant

tag: tissue


title: KLS - U638 - rep3


title: G3R3


title: Tunicamycin_2

status: Public on Sep 17 2016

city: boston

first: jesse

middle: M

last: gray

state: MA

address: 77 avenue louis pasteur, NRB 356

department: Genetics

institute: Harvard Medical School

data_processing:
fastq trimming with fastx v0.0.13
alignment with STAR v2.2.1
mapped to RefSeq with bedtools v2.25.0
TSS and PAS centered count files generated with metaseq v0.5.6
genes of length greather than 10kb or 250kb were filted with different bed files.
genome build: hg19
Supplementary_files_format_and_content: Read counts by gene (rows) and TSS or PAS distance (columns). Each row is a gene, and each column is a 200 bp bin at a position relative to the TSS or PAS, with the first half of columns upstream and the 2nd half downstream of the TSS/PAS. (This is upstream and downstream are in genomic coordinates, not corrected for gene orientation.) For TSS_500arrays, each column is a 50bp bin around the TSS. In the filenames, F denotes reads aligning to the negative genomic strand, R denotes reads aligning to the positive genomic strand, Pos includes only annotated genes on the positive genomic strand, and Neg includes only annotated genes on the negative genomic strand.

source_name: Hela cells

growth_protocol: Hela cells were cultured in DMEM and plated in 10cm plates the day prior to drug treatment.

extract_protocol:
Cells were washed and harvested using Qiagen RNeasy mini kit. 10ug of RNA was DNAse treated and cleaned up with Rneasy MinElute Cleanup Kit.
Total stranded RNA libraries were construced with a standard dUTP protocol.  For a the drug screen the previously published Tag-Seq protocol was followed.

treatment_protocol: Drugs were added to cells and DMSO was added at the same amount for the control.

value: Tunicamycin

tag: dose

value: 30 uM

value: 6 hours

tag: biological replicate

tag: experiment number

value: Exp 5


title: TBCA_1

tag: treatment

value: TBCA


title: NB4_MC2392_24h_ChIP_Seq

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

description: chromatin IP (ChIP-seq)

data_processing:
Basecalls performed using CASAVA
Reads were aligned to the hg18 genome assembly using ELAND
Peaks were called using MACS 1.3.3 on settings:mfold =32, tsize=32, p value = e-6
Genome_build: All ChIP-seq tracks were mapped to genome build HG18, RNA-seq tracks were mapped to HG18.
Supplementary_files_format_and_content: wig files were generated (extended to 300bps)

source_name: MC2392 treated NB4 cells, 24h  ChIP

growth_protocol: NB4 cells were grown at 37°C in air and 5% CO2 in RPMI 1640 medium (EUROCLONE),supplemented with 10% heat-inactivated fetal bovine serum (FBS, Sigma),  ampicillin/streptomycin and 0.1% gentamicin (SIGMA).1% L-glutamine, 1%

extract_protocol:
Chromatin was sonicated and used for ChIP-seq using H3K9K14ac (Diagenode). RNA was extracted using qiagen RNeasy kit according to manufacturer. cDNA first and Ds-cDNA synthesis then, was  performed following supplier’s instructions (Invitrogen). Ds-cDNA samples were prepared for  sequencing by end repair of 20 ng DNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (~300 bp) and limited PCR amplification (14 cycles). The resulting sample libraries were subjected to DSN treatment (Evrogen) according to the manufacturer’s recommendations.
ChIP and RNA seq libraries were preapared according to  Illumina's standard protocol.

treatment_protocol: NB4 cells were treated with ATRA, MS275 and MC2392

tag: cell type

value: NB4 promyelocytic leukaemia cell line

tag: chip antibody

value: H3K9K14ac (Diagenode)

tag: reference genome


title: TBBz_2

value: TBBz

tag: time


title: NB4_MC2392_4h_ChIP_Seq

description: chromatin IP (ChIP-seq)

source_name: MC2392 treated NB4 cells, 4h  ChIP


title: NB4_ATRA_4h_ChIPSeq

description: chromatin IP (ChIP-seq)

source_name: ATRA treated NB4 cells, 4h  ChIP

value: ATRA 4h


title: NB4_MC2392_48h_ChIP_Seq

description: chromatin IP (ChIP-seq)

source_name: MC2392 treated NB4 cells, 48h  ChIP


title: NB4_DMSO_ChIPSeq

description: chromatin IP (ChIP-seq)

source_name: DMSO NB4 cells  ChIP


title: NB4_MS275_4h_ChIP_Seq

description: chromatin IP (ChIP-seq)

source_name: MS275 treated NB4 cells, 4h  ChIP


title: TBCA_2


title: Tunicamycin_1


title: TBBz_1


title: SRPIN340_2


title: SRPIN340_1


title: PHA_1


title: PHA_2


title: Go_2

value: 10 uM


title: NB4_ATRA_24h_ChIPSeq

description: chromatin IP (ChIP-seq)

source_name: ATRA treated NB4 cells, 24h  ChIP

value: ATRA 24h


title: PD_2


title: JAK1_2

value: JAK inhibitor 1


title: JAK1_1


title: GF_2


title: IsoG_100_1

value: Isoginkgetin


title: PD_1


title: IsoG_30_2


title: IsoG_30_1


title: Crizotinib_1

value: Crizotinib


title: IsoG_total_18h_B2

value: 18 hours

value: Exp 4


title: IsoG_100_2


title: CYT387_1


title: GF_1


title: C_total_6h_B1

value: DMSO


title: C_total_6h_B2


title: C_total_18h_B2


title: Crizotinib_2


title: CYT387_2


title: C_60_2


title: C_200_1

description: C_200 matches to IsoG_100 and JAK1 Tag Seq samples only


title: Flav_total_6h_B1

value: Flavopiridol


title: C_200_2


title: IsoG_total_6h_B2

value: 30 uM


title: IsoG_total_18h_B1


title: Flav_total_6h_B2

value: 6 hours


title: C_6hr_B2

value: Exp 3


title: Drb_total_6h_B1

value: DRB


title: C_18hr_B2


title: MY_18hr_B1

value: Meayamycin

value: 80 nM


title: Flav_total_18h_B1


title: Go_1

value: Exp 5


title: Flav_total_18h_B2


title: Drb_total_6h_B2


title: C_60_1


title: IsoG_total_2

value: Exp 2


title: Drb_total_18h_B2


title: MY_6hr_B2


title: C_total_18h_B1


title: Drb_total_18h_B1


title: DRB_total_1


title: DRB_polyA_2

description: PolyA RNA from same sample as matching Total RNA replicate


title: MY_6hr_B1


title: MY_18hr_B2


title: C_total_2


title: IsoG_total_6h_B1


title: C_polyA_2


title: C_total_1


title: C_6hr_B1


title: Day 20 GE_024

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

description: Sample name: 024

data_processing:
Analysis of RNA-seq data was completed using a CLC Genomics Server 6.0 and CLC Genomics Workbench 7.0.4 (CLC bio, Aarhus, Denmark).
Ion reads were quality trimmed (error probability 0.02) with default parameters.
Illumina reads were quality trimmed (error probability 0.001) with default parameters and 13 bp were removed from the 5’ end of each read.
All sequences were mapped to the Ovis aries genome (Oar_v3.1) with Ensembl version 75 annotations requiring paired mapping and using reads per kilobase of transcript per million (RPKM) for expression values.
Genome_build: Ovis aries genome (Oar_v3.1) with Ensembl version 75 annotations
Supplementary_files_format_and_content: Processed file includes expression values (RPKM) for each sample with gene symbol and description from Ensembl 75. The RawData tab includes all genes and the RPKM5 tab includes only genes with RPKM ≥ 5 in all samples

organism: Ovis aries

source_name: Glandular epithelium

growth_protocol: In utero conceptus development

extract_protocol:
Uteri frozen in OCT were cryosectioned (10 µm) using a Leica CM1950 cryostat (Leica Microsystems, Wetzlar, Germany). Three tissue sections were mounted per slide to RNase-free polyethylene naphthalate-coated slides (Carl Zeiss, Munich, Germany) and immediately placed on dry ice. Slides were fixed and stained immediately following sectioning using previously described methods. Briefly, slides were transferred from dry ice into ice-cold 95% ethanol for 30 sec, then washed in 75% ethanol for 30 sec. Tissue sections were stained in freshly filtered 1% cresyl violet solution in 75% ethanol for 1 min. Tissue sections were then dehydrated through 75% ethanol (30 sec) and 95% ethanol (30 sec), followed by two 30 sec and one 5 min incubation in anhydrous 100% ethanol. Slides were dried for 10 min at room temperature and stored in sealed containers at -80ºC until use. The LE and GE were visually identified and separately captured from a single slide of three uterine sections for each animal. Slides were discarded after 60 min of use on the laser capture microdissection (LCM) LMD7 microscope (Leica Microsystems). Total RNA was extracted from cells collected from the LE and GE using the RNeasy MinElute kit (Qiagen, Valencia, CA). Prior to sequencing, 5 ng of total RNA was amplified using the Ovation RNA-Seq System V2 (cat. # 7102; Nugen, San Carlos, CA). The resulting single primer isothermal amplified (SPIA) cDNA was cleaned using the QIAquick PCR Purification Kit (Qiagen). Day 12 conceptuses: Total RNA was extracted from day 12 conceptuses (n = 5) using the RNeasy plus kit with on column DNase digestion (Qiagen). Total RNA quality and quantity was determined using a RNA 6000 Pico Kit and Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). A total of 374-512 ng of RNA was collected from each conceptus, for each animal. Prior to sequencing, 50 ng of total RNA was amplified using the Ovation RNA-Seq System V2 (Nugen). Days 14, 16 and 20 conceptuses: Total RNA was extracted from conceptuses (n = 5 per day) and quality checked as described for day 12 conceptuses. RNA samples were enriched for mRNA by selective depletion of ribosomal RNA using RiboMinus Eukaryote Kit for RNA-Seq (cat. # A1083708, Thermo Fisher Scientific Inc., Wilmington, DE).
LE and GE: The Ion Plus Fragment library kit (Life Technologies, Waltham, MA) was used to construct Ion Proton sequencing libraries from SPIA LCM cDNA (200 ng). Sonication (Bioruptor, Diagenode Inc., Denville, NJ) was used to fragment the cDNA. End repaired cDNA was purified using 1.0X v/v AMPure XP beads (Beckman-Coulter Genomics, Danvers, MA). Following barcode adapter ligation and 7 cycles of amplification, the final libraries were size selected by capturing the fragments bound between 0.7X and 1.0X v/v AMPure XP beads. Emulsion PCR was performed on an Ion Chef instrument using the Ion P1 Hi-Q reagents. Sequencing beads were quantified and evaluated by flow cytometry using a Guava Easy Cyte (Millipore, Billerica, MA) with Sybr Gold (Molecular Bioprobes, Eugene, OR) before loading on an Ion P1 v3 semiconductor sequencing chip. Libraries were sequenced on an Ion Proton using Ion P1 Hi-Q sequencing reagents and 520 flow cells (Life Technologies) by the Washington State University Molecular Biology and Genomics Core. Three barcoded libraries were pooled per P1 chip for sequencing. Base calling and primary analysis was performed using Torrent Suite 4.6. Day 12 conceptus: Following amplification, libraries were constructed and sequenced at the University of Missouri DNA Core following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq DNA PCR-Free sample preparation kit (cat. # FC-121-3001). Briefly, cDNA (0.5 µg) was sheared using standard Covaris methods (Covaris, Inc., Woburn, MA) to generate average fragmented sizes of 350 bp. The resulting 3’ and 5’ overhangs were converted to blunt ends by an end repair reaction which uses a 3’ to 5’ exonuclease activity and polymerase activity. A single adenosine nucleotide was added to the 3’ end of the blunt fragments followed by the ligation of Illumina indexed paired-end adapters. The adaptor ligated library was purified twice with sample purification beads and quantified using the KAPA library quantification kit (cat. # KK4824; Kapa Biosystems, Inc., Wilmington, MA) and library fragment size confirmed on the Fragment Analyzer (cat. # DNF-472; Advanced Analytical Technologies, Inc., Ankeny, IA). Libraries were diluted and sequenced as 100 bp paired-end sequences on the Illumina HiSeq 2500 platform. Day 14, 16 and 20 conceptus:Libraries were prepared and sequenced by Global Biologics LLC (Columbia, MO, USA). Ribosome-depleted RNA was used as input for the Illumina TruSeq Stranded mRNA HT library construction procedure (San Diego, CA, USA). Prior to sequencing, RNA was fragmented and RT primers were hybridized for cDNA synthesis. The resulting cDNA was prepared for sequencing by 3’ adenylation, adapter ligation, and PCR amplification (98ºC for 30 sec; 14 cycles of 98ºC for 10 sec, 60ºC for 30 sec, 72ºC for 30 sec; 72ºC for 5 minutes). Library validation was performed using a Fragment Analyzer (Advanced Analytical) with HiSens NGS reagents followed by quantitation using the Qubit HS DNA assay (cat. # Q32851; Thermo Fisher Scientific, Inc.) and qPCR library kit for Illumina platforms (Kappa Biosystems, Inc.). Libraries were pooled and sequenced as 100 bp paired-end sequences on the Illumina HiSeq 2500 platform.

treatment_protocol: Conceptuses were flushed from the uterine horn with 20 ml of 10 mM PBS (pH 7.2). Conceptus tissue was transferred to a 1.5ml microcentrifuge tube and frozen in liquid nitrogen. Several sections (~0.5 cm) from the mid-portion of each uterine horn ipsilateral to the ovary were placed in Optimum Cutting Temperature Compound (OCT), frozen in liquid nitrogen vapor, and stored at -80°C.

value: uterus

value: Glandular epithelium

tag: day of pregnancy

tag: isolation method

value: Laser capture microdissection

tag: rna processing

value: SPIA amplifed


title: Day 20 GE_020

description: Sample name: 020


title: IsoG_polyA_2

value: Isoginkgetin


title: IsoG_polyA_1


title: D8-01_c60

description: Control 60 is 60ul of DMSO matching to the treatment valume for the IsoG samples

value: 18 hours

value: Exp 1


title: Day 20 GE_018

description: Sample name: 018


title: Day 20 GE_022

description: Sample name: 022


title: DRB_polyA_1


title: DRB_total_2


title: C_18hr_B1

value: DMSO


title: D7-10_CPT

value: CPT


title: C_polyA_1


title: D9-19_IsG

value: 30 uM


title: D6-26_c10

description: Control 10 is 10ul of DMSO matching to the treatment valume for the CPT samples


title: D9-19_c60


title: D6-26_IsG


title: Day 16 GE_32

description: Sample name: 32


title: D8-01_IsG


title: Tcell_InfectedHIV1_5d

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
RNA-seq raw reads were trimmed for adaptor sequences or low-quality bases and mapped to both the human genome (hg19 build) and the HCMV Merlin genome (Genbank AY446894.2) with GSNAP, with additional filtering for repetitive regions. Virus-mapping reads were obtained from the HSV-2 and HIV-1 samples using Genbank accessions NC_001798.1 and K03455.1, respectively.
Genome coverage files for visualization (bigWig format) were generated using UCSC tools bedGraphToBigWig and genomeCoverageBed, and strand-corrected.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig (each .bw includes human transcriptome only)

growth_protocol: HFFs were cultured as described in Sanders et al. 2008; ECs as in DuRose et al., 2012; and ES-derived NPCs as in Belzile et al., 2014.

extract_protocol:
All HCMV and HSV-2 materials were collected at the time of harvest by trypsinization and centrifugation, and snap-frozen prior to RNA extraction. HIV-1 materials were harvested directly into TRIzol reagent. TRIzol RNA extractions of RNA were performed according to the manufacturer’s instructions (Invitrogen/Life Technologies).
All HCMV and HIV-1 sample conditions were subjected to strand-specific RNA-seq using the dUTP method (Parkhomchuk et al., 2009) with adaptations as described previously (Huelga et al., 2012). HSV-2 libraries were prepared with Illumina TruSeq Stranded mRNA Sample Preparation reagents.
Strand-specific RNA-seq

treatment_protocol: HCMV infections, all with strain TB40E, were performed at an MOI of 5, as described in Belzile et al., 2014. HUES9 ES cells used to derive the NPCs. HSV-2 infections were performed in HFFs with strain G at an MOI of 10, including an initial 30 min adsorption period at 4°C. HIV-1 infections of IL-2-activated CD4+ T-cells were performed as described in Noraz et al., 1997.

value: T cells

tag: infection


title: Day 16 GE_28

description: Sample name: 28


title: Day 16 GE_26

description: Sample name: 26


title: Tcell_Control_5d

value: control


title: D7-10_c10


title: Day 16 GE_30

description: Sample name: 30


title: D6-26_c60


title: Rep2_drug_VOR_PCR2 (rep2)

city: Barcelona

first: Guillaume

last: Filion

address: Dr. Aiguader 88

department: GRSCC

institute: CRG

description:
BHIVe trancripts with barcode 24h after VOR treatment, bio rep 2, tech rep 2
VOR_2_2_2
Jurkat_BHIVE_mini_drug.txt

data_processing:
Library strategy: B-HIVE
Sequencing lane demultiplexing: Sequences were demultiplexed using bcl2fastq. In case the index was inside the sequenced amplicon, demultiplexing was carried out with custom scripts. The used indices are specified in the last row of the Sample section.
Barcode extraction: Barcodes were extracted from the forward reads. The barcode sequences in the construct are flanked by the Illumina adaptor and the T7 promoter sequence (TATAGTGAGTCGTATTAAAA). The promoter sequence was identified using Seeq (http://github.com/ezorita/seeq) allowing up to 2 mismatches.
Barcode clustering: Barcodes were clustered by sequence similarity using starcode and allowing up to 1 mismatch (http://github.com/gui11aume/starcode).
Alignment: Reverse reads were aligned on GRCh37/h19 using BWA-mem with default parameters.
Filtering on alignment quality: Only SAM mapping qualities greater or equal than 20 were used in the analysis.
Filtering of recombinant molecules: A barcode was associated to a mapped locus based on their co-ocurrence in paired-end reads. Associations between a barcode and a mapped locus reported by less than 10 paired-end reads were discarded. The remaining associations were considered reliable if both the barcode and the mapped locus were found together at least 90% of the time.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab delimited tables
Supplementary_files_format_and_content: Jurkat_BHIVE_mini_integ.txt: BHIVE integration sites
Supplementary_files_format_and_content: Jurkat_BHIVE_mini_expr.txt: BHIVE transcript expression
Supplementary_files_format_and_content: Jurkat_BHIVE_mini_latent.txt: Latent integrations reference table
Supplementary_files_format_and_content: Jurkat_BHIVE_mini_drug.txt: Barcode reactivation upon treatment

source_name: Immortalized human T lymphocyte Jurkat cell line

growth_protocol: Jurkat human T cells line were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum, 1% Pen Strep and 1% GlutaMAX (100x) at 37℃ under a 95% air/5% CO2 atmosphere. Jurkat T cells were passaged every 2 days with 1 to 5 dilution. After FACS sorting 4 days post infection, 20,000 GFP-positive cells were maintained in the same medium for the next 17 days without passage.

extract_protocol:
Genomic DNA and total RNA from the same infected cell pool were extracted by the AllPrep DNA/RNA Mini Kit. Total RNA was further proceeded to purify mRNA by Oligotex mRNA Mini Kit.
Libraries used for mapping HIV integrations were prepared by inverse PCR. Briefly, 3 µg DNA were harvested and digested by the restriction enzyme BplI. Fragments were blunt-end self-ligated in the total volume 1 mL at 16℃ overnight. The pellet was dissolved in 84 µL distilled water for plasmid-safe DNase treatment. DNase-treated samples were cleaned up by the QIAquick PCR purification kit. Samples were eluted in 20 µL EB buffer. 8 µL eluted product were used for two rounds of nested PCR. PCR products with different indexes were pooled together in the final concentration of 4 nM for sequencing 50 bp paired end on a Illumina NextSeq sequencer. RNA and DNA libraries were prepared by RT-PCR and regular PCR, respectively, with the same primers. RNA and DNA libraries were sequenced 50 bp single read by on a Illumina NextSeq sequencer.

treatment_protocol: Samples used for the latency reversal experiments were treated with the indicated drugs for 24 hours before performing DNA and RNA extraction.

value: T lymphocyte

tag: days of post infection for sample analysis

tag: drug treatment

value: VOR

tag: demultiplex indices used

value: ACTG, GTCA


title: D6-26_CPT


title: Rep2_drug_VOR_PCR1 (rep2)

description:
BHIVe trancripts with barcode 24h after VOR treatment, bio rep 2, tech rep 1
VOR_2_1_2
Jurkat_BHIVE_mini_drug.txt

value: AGTC, TACG


title: rep2_drug_PHA_PCR2 (rep2)

description:
BHIVe trancripts with barcode 24h after PHA treatment, bio rep 1, tech rep 2
PHA_1_2_2
Jurkat_BHIVE_mini_drug.txt

value: PHA

value: GCAT, CTAG


title: Rep2_drug_PHA_PCR2 (rep2)

description:
BHIVe trancripts with barcode 24h after PHA treatment, bio rep 2, tech rep 2
PHA_2_2_2
Jurkat_BHIVE_mini_drug.txt

value: TCAG, TCGA


title: Rep2_drug_PHA_PCR1 (rep2)

description:
BHIVe trancripts with barcode 24h after PHA treatment, bio rep 2, tech rep 1
PHA_2_1_2
Jurkat_BHIVE_mini_drug.txt

value: AGCT, TGCA


title: IsoG_total_1

value: 6 hours

value: Exp 2


title: Day 14 GE_B03

description: Sample name: B03

value: uterus

value: Glandular epithelium

value: Laser capture microdissection

value: SPIA amplifed


title: Day 12 GE_16

description: Sample name: 16


title: Day 14 GE_B01

description: Sample name: B01


title: Day 12 GE_14

description: Sample name: 14


title: Rep2_drug_DMSO_PCR2 (rep2)

description:
BHIVe trancripts with barcode 24h after input treatment, bio rep 2, tech rep 2
DMSO_2_2_2
Jurkat_BHIVE_mini_drug.txt

value: input (DMSO)

value: CTGA, TGAC


title: Rep2_drug_DMSO_PCR1 (rep2)

description:
BHIVe trancripts with barcode 24h after input treatment, bio rep 2, tech rep 1
DMSO_2_1_2
Jurkat_BHIVE_mini_drug.txt

value: CGTA, GATC


title: rep2_drug_DMSO_PCR2 (rep2)

description:
BHIVe trancripts with barcode 24h after input treatment, bio rep 1, tech rep 2
DMSO_1_2_2
Jurkat_BHIVE_mini_drug.txt

value: T lymphocyte

value: ATCG, ATGC


title: rep2_drug_PHA_PCR1 (rep2)

description:
BHIVe trancripts with barcode 24h after PHA treatment, bio rep 1, tech rep 1
PHA_1_1_2
Jurkat_BHIVE_mini_drug.txt

value: ACGT, CATG


title: rep2_drug_DMSO_PCR1 (rep2)

description:
BHIVe trancripts with barcode 24h after input treatment, bio rep 1, tech rep 1
DMSO_1_1_2
Jurkat_BHIVE_mini_drug.txt

value: CAGT, CGAT


title: Rep2_drug_VOR_PCR2 (rep1)

description:
BHIVe trancripts with barcode 24h after VOR treatment, bio rep 2, tech rep 2
VOR_2_2_1
Jurkat_BHIVE_mini_drug.txt

value: VOR

value: ACTG, GTCA


title: Rep2_drug_VOR_PCR1 (rep1)

description:
BHIVe trancripts with barcode 24h after VOR treatment, bio rep 2, tech rep 1
VOR_2_1_1
Jurkat_BHIVE_mini_drug.txt

value: AGTC, TACG


title: Day 12 GE_10

description: Sample name: 10


title: Rep1_drug_VOR_PCR1 (rep1)

description:
BHIVe trancripts with barcode 24h after VOR treatment, bio rep 1, tech rep 1
VOR_1_1_1
Jurkat_BHIVE_mini_drug.txt

value: GTAC, TAGC


title: Rep1_drug_PHA_PCR2 (rep1)

description:
BHIVe trancripts with barcode 24h after PHA treatment, bio rep 1, tech rep 2
PHA_1_2_1
Jurkat_BHIVE_mini_drug.txt

value: PHA

value: GCAT, CTAG


title: Day 14 GE_B07

description: Sample name: B07

value: uterus


title: rep2_drug_VOR_PCR1 (rep2)

description:
BHIVe trancripts with barcode 24h after VOR treatment, bio rep 1, tech rep 1
VOR_1_1_2
Jurkat_BHIVE_mini_drug.txt


title: Rep2_drug_PHA_PCR2 (rep1)

description:
BHIVe trancripts with barcode 24h after PHA treatment, bio rep 2, tech rep 2
PHA_2_2_1
Jurkat_BHIVE_mini_drug.txt

value: TCAG, TCGA


title: Day 10 GE_08

description: Sample name: 08

value: Glandular epithelium

value: Laser capture microdissection


title: Rep1_drug_VOR_PCR2 (rep1)

description:
BHIVe trancripts with barcode 24h after VOR treatment, bio rep 1, tech rep 2
VOR_1_2_1
Jurkat_BHIVE_mini_drug.txt

value: GACT, GCTA


title: Day 10 GE_06

description: Sample name: 06

value: SPIA amplifed


title: rep2_drug_VOR_PCR2 (rep2)

description:
BHIVe trancripts with barcode 24h after VOR treatment, bio rep 1, tech rep 2
VOR_1_2_2
Jurkat_BHIVE_mini_drug.txt


title: Day 10 GE_04

description: Sample name: 04


title: Day 14 GE_B05

description: Sample name: B05


title: Rep1_drug_PHA_PCR1 (rep1)

description:
BHIVe trancripts with barcode 24h after PHA treatment, bio rep 1, tech rep 1
PHA_1_1_1
Jurkat_BHIVE_mini_drug.txt


title: Rep1_drug_DMSO_PCR1 (rep1)

description:
BHIVe trancripts with barcode 24h after input treatment, bio rep 1, tech rep 1
DMSO_1_1_1
Jurkat_BHIVE_mini_drug.txt

value: input (DMSO)


title: Rep2_drug_DMSO_PCR2 (rep1)

description:
BHIVe trancripts with barcode 24h after input treatment, bio rep 2, tech rep 2
DMSO_2_2_1
Jurkat_BHIVE_mini_drug.txt

value: T lymphocyte

value: CTGA, TGAC


title: Day 10 GE_02

description: Sample name: 02


title: Rep2_drug_PHA_PCR1 (rep1)

description:
BHIVe trancripts with barcode 24h after PHA treatment, bio rep 2, tech rep 1
PHA_2_1_1
Jurkat_BHIVE_mini_drug.txt

value: AGCT, TGCA


title: Rep2_drug_DMSO_PCR1 (rep1)

description:
BHIVe trancripts with barcode 24h after input treatment, bio rep 2, tech rep 1
DMSO_2_1_1
Jurkat_BHIVE_mini_drug.txt

value: CGTA, GATC


title: Day 12 GE_12

description: Sample name: 12


title: Jurkat_WT_mRNAseq_rep2

description:
Jurkat mRNA seq, replicate 2
Jurkat_WT_mRNAseq.txt

data_processing:
Sequencing lane demultiplexing: Demultiplexing and base-calling of illumina raw data was performed using bcl2fastq.
Transcriptome mapping: Transcripts were aligned to GRCh37 cDNA using “kallisto” with single-end mode (--single), sequence bias correction (--bias), fragment length of 300nt (-s300) and standard deviation of 100nt (-l100).
Combination of isoforms: The transcript per million (tpm) count for all the isoforms of the same gene were combined to produce a total tpm count per gene copy.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab delimited table
Supplementary_files_format_and_content: Jurkat_WT_mRNAseq.txt: Jurkat Wild Type mRNA expression

extract_protocol:
Genomic DNA and total RNA from the same infected cell pool were extracted by the AllPrep DNA/RNA Mini Kit. Total RNA was further proceeded to purify mRNA by Oligotex mRNA Mini Kit.
The wild-type Jurkat mRNA-seq was prepared from 100 ng total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101) according to  manufacturer's instructions with 4.5 minutes fragmentation time. Libraries were sequenced on the HiSeq2000 sequencer (Illumina) with 50 bp single end using v3 sequencing chemistry.


title: Rep1_drug_DMSO_PCR2 (rep1)

description:
BHIVe trancripts with barcode 24h after input treatment, bio rep 1, tech rep 2
DMSO_1_2_1
Jurkat_BHIVE_mini_drug.txt

value: ATCG, ATGC


title: Day 20 LE_23

description: Sample name: 23

source_name: Luminal epithelium

value: Luminal epithelium


title: Jurkat_WT_mRNAseq_rep1

description:
Jurkat mRNA seq, replicate 1
Jurkat_WT_mRNAseq.txt


title: Day 20 LE_21

description: Sample name: 21


title: Rep2_FACS_GFP+_PCR6

description:
FACS sorting of BHIVe infected cells, GFP+, bio rep 2, tech rep 6
Jurkat_BHIVE_mini_latent.txt

value: GATC


title: Day 20 LE_17

description: Sample name: 17


title: Rep2_FACS_GFP+_PCR4

description:
FACS sorting of BHIVe infected cells, GFP+, bio rep 2, tech rep 4
Jurkat_BHIVE_mini_latent.txt

value: TACG


title: Rep2_FACS_GFP+_PCR2

description:
FACS sorting of BHIVe infected cells, GFP+, bio rep 2, tech rep 2
Jurkat_BHIVE_mini_latent.txt

value: TGCA


title: Rep1_FACS_GFP+_PCR6

description:
FACS sorting of BHIVe infected cells, GFP+, bio rep 1, tech rep 6
Jurkat_BHIVE_mini_latent.txt


title: Day 16 LE_31

description: Sample name: 31


title: Rep2_FACS_GFP+_PCR1

description:
FACS sorting of BHIVe infected cells, GFP+, bio rep 2, tech rep 1
Jurkat_BHIVE_mini_latent.txt

value: AGCT


title: Rep1_FACS_GFP+_PCR4

description:
FACS sorting of BHIVe infected cells, GFP+, bio rep 1, tech rep 4
Jurkat_BHIVE_mini_latent.txt


title: Rep2_FACS_GFP+_PCR3

description:
FACS sorting of BHIVe infected cells, GFP+, bio rep 2, tech rep 3
Jurkat_BHIVE_mini_latent.txt

value: AGTC


title: Rep1_FACS_GFP+_PCR3

description:
FACS sorting of BHIVe infected cells, GFP+, bio rep 1, tech rep 3
Jurkat_BHIVE_mini_latent.txt


title: Rep1_FACS_GFP+_PCR2

description:
FACS sorting of BHIVe infected cells, GFP+, bio rep 1, tech rep 2
Jurkat_BHIVE_mini_latent.txt

value: AGTC, TACG


title: Rep1_FACS_GFP+_PCR1

description:
FACS sorting of BHIVe infected cells, GFP+, bio rep 1, tech rep 1
Jurkat_BHIVE_mini_latent.txt


title: Day 16 LE_27

description: Sample name: 27

value: uterus


title: Day 16 LE_25

description: Sample name: 25

value: Laser capture microdissection


title: Day 14 LE_B08

description: Sample name: B08


title: Day 14 LE_B06

description: Sample name: B06


title: Day 16 LE_29

description: Sample name: 29


title: Rep2_FACS_GFP-_PCR5

description:
FACS sorting of BHIVe infected cells, GFP-, bio rep 2, tech rep 5
Jurkat_BHIVE_mini_latent.txt

value: CAGT


title: Rep2_FACS_GFP-_PCR4

description:
FACS sorting of BHIVe infected cells, GFP-, bio rep 2, tech rep 4
Jurkat_BHIVE_mini_latent.txt

value: TAGC


title: dnaj1 KD 1

city: Kansas City

first: Madelaine

last: Gogol

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

description:
dnaj_kd_1
PolyA RNA

data_processing:
Base-calling and bcl to fastq generation was done with CASAVA 1.8.2 from Illumina.
RNA-seq was aligned to genome dm3 from UCSC using tophat 2.0.10 with arguments --solexa-quals --segment-mismatches 1 -x 1 -g 1 --no-coverage-search. ChIP-seq was aligned to dm3 using bowtie2 2.1.0 with -k 1.
bigWig tracks were generated in R 3.0.2 by dividing by the total number of alignments and multiplying by 1e6 (rpm).
Peaks were called using macs2 (2.0.10.20120913).
Differentially expressed genes were called with edgeR 3.4.2.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: bigWig tracks with rpm-normalized coverages.

source_name: Drosophila S2 cells, dnaj1 KD

growth_protocol: Drosophila S2 cells were grown in Schneider's medium supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was isolated from S2 cells treated with either dsRNA against lacZ, mlf, bag2, or dnaj-1 using TRIzol (Invitrogen). Two separate biological experiments were performed for each RNA-seq analysis.
RNA-seq libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer's protocol.

treatment_protocol: Drosophila S2 cells were grown in Schneider's medium supplemented with 10% fetal bovine serum to a density of 3-6 x10^6 cells/ml. Cells were diluted to 1x10^6 cells/ml in serum-free media and incubated with 10 μg dsRNA per 1 x10^6 cells for 45 min at 25°C. An equal volume of Schneider's media containing 10% serum was added to the cells and the cells were grown for 4 days at 25°C before collection for ChIP, RNA, and/or protein isolation. dsRNA against lacZ was used as a control for all RNAi experiments.

tag: cell line

tag: genotype/variation

value: dnaj1 KD


title: Rep2_FACS_GFP-_PCR6

description:
FACS sorting of BHIVe infected cells, GFP-, bio rep 2, tech rep 6
Jurkat_BHIVE_mini_latent.txt

value: T lymphocyte

value: CGAT


title: mlf KD 2

description:
mlf_kd_2
PolyA RNA

source_name: Drosophila S2 cells, mlf KD

value: mlf KD


title: Day 14 LE_B04

description: Sample name: B04

tag: tissue

value: SPIA amplifed


title: mlf KD 1

description:
mlf_kd_1
PolyA RNA


title: Rep1_FACS_GFP+_PCR5

description:
FACS sorting of BHIVe infected cells, GFP+, bio rep 1, tech rep 5
Jurkat_BHIVE_mini_latent.txt

value: ACTG, GTCA


title: Rep2_FACS_GFP-_PCR3

description:
FACS sorting of BHIVe infected cells, GFP-, bio rep 2, tech rep 3
Jurkat_BHIVE_mini_latent.txt

value: GTAC


title: Rep2_FACS_GFP+_PCR5

description:
FACS sorting of BHIVe infected cells, GFP+, bio rep 2, tech rep 5
Jurkat_BHIVE_mini_latent.txt

value: CGTA


title: Day 14 LE_B02

description: Sample name: B02

value: Luminal epithelium


title: Day 20 LE_19

description: Sample name: 19


title: Rep2_FACS_GFP-_PCR2

description:
FACS sorting of BHIVe infected cells, GFP-, bio rep 2, tech rep 2
Jurkat_BHIVE_mini_latent.txt

value: CATG


title: lacz 1 for dnaj1 KD

description:
lacz1_dnaj
PolyA RNA

source_name: Drosophila S2 cells, lacZ KD

value: lacZ KD


title: Day 12 LE_13

description: Sample name: 13


title: Day 12 LE_15

description: Sample name: 15


title: Rep2_FACS_GFP-_PCR1

description:
FACS sorting of BHIVe infected cells, GFP-, bio rep 2, tech rep 1
Jurkat_BHIVE_mini_latent.txt

value: ACGT


title: lacz 1 for mlf KD

description:
lacz1_mlf
PolyA RNA


title: Day 12 LE_09

description: Sample name: 09


title: WCE 3

description:
wce3
Nuclear extract

source_name: Drosophila S2 cells, WT, input

extract_protocol:
ChIP was conducted on 1 x 10^7 cell equivalents of chromatin from Drosophila S2 cells. For input controls, 1 x 10^6 cell equivalents of chromatin was used. Soluble chromatin was incubated with rabbit α-MLF (gift from Dr. Anne Plessis), rat α-MLF (this work), rabbit α-DnaJ-1 (this work).
ChIP-seq libraries were prepared using ChIP-Seq DNA Sample Prep Kit (Illumina) or KAPA High Throughput Library Preparation Kit, Roche.

value: WT


title: Rep1_FACS_GFP-_PCR5

description:
FACS sorting of BHIVe infected cells, GFP-, bio rep 1, tech rep 5
Jurkat_BHIVE_mini_latent.txt

value: GACT, GCTA


title: Day 12 LE_11

description: Sample name: 11

value: uterus

value: Laser capture microdissection


title: DnaJ1 ChIP 2 from WCE 2

description:
dnaj2
Nuclear extract

source_name: Drosophila S2 cells, WT, DnaJ1 ChIP


title: Rep1_FACS_GFP-_PCR4

description:
FACS sorting of BHIVe infected cells, GFP-, bio rep 1, tech rep 4
Jurkat_BHIVE_mini_latent.txt

value: GCAT, CTAG


title: lacz 2 for dnaj1 KD

description:
lacz2_dnaj
PolyA RNA


title: Day 10 LE_07

description: Sample name: 07


title: DnaJ1 ChIP 1 from WCE 1

description:
dnaj1
Nuclear extract


title: Rep1_FACS_GFP-_PCR3

description:
FACS sorting of BHIVe infected cells, GFP-, bio rep 1, tech rep 3
Jurkat_BHIVE_mini_latent.txt

value: CAGT, CGAT


title: Rep1_FACS_GFP-_PCR1

description:
FACS sorting of BHIVe infected cells, GFP-, bio rep 1, tech rep 1
Jurkat_BHIVE_mini_latent.txt

value: T lymphocyte

value: ACGT, CATG


title: Day 10 LE_03

description: Sample name: 03


title: Day 10 LE_01

description: Sample name: 01


title: Rep1_FACS_GFP-_PCR2

description:
FACS sorting of BHIVe infected cells, GFP-, bio rep 1, tech rep 2
Jurkat_BHIVE_mini_latent.txt

value: GTAC, TAGC


title: MLF ChIP 2 from WCE 2

description:
mlf2
Nuclear extract

source_name: Drosophila S2 cells, WT, MLF ChIP

value: MLF


title: Day 10 LE_05

description: Sample name: 05

value: SPIA amplifed


title: WCE 1

description:
wce1
Nuclear extract


title: MLF ChIP 1 from WCE 3

description:
mlf1
Nuclear extract


title: WCE 2

description:
wce2
Nuclear extract


title: HFF_InfectedHSV2_8h

description: Sequencing Sample 11

value: HFF cells


title: Rep1_FACS_GFP-_PCR6

description:
FACS sorting of BHIVe infected cells, GFP-, bio rep 1, tech rep 6
Jurkat_BHIVE_mini_latent.txt

value: ATCG, ATGC


title: NPC_InfectedHCMVTB40E_96h

description: Sequencing Sample 9

data_processing:
RNA-seq raw reads were trimmed for adaptor sequences or low-quality bases and mapped to both the human genome (hg19 build) and the HCMV Merlin genome (Genbank AY446894.2) with GSNAP, with additional filtering for repetitive regions. Virus-mapping reads were obtained from the HSV-2 and HIV-1 samples using Genbank accessions NC_001798.1 and K03455.1, respectively.
Genome coverage files for visualization (bigWig format) were generated using UCSC tools bedGraphToBigWig and genomeCoverageBed, and strand-corrected.
For HCMV mRNA abundance measurements, a secondary iteration of mapping was performed against the TB40E LISA genome (Genbank KF297339.1) using Bowtie. Resulting unique read mappings from the HCMV-infected datasets (bed format) are listed with raw read totals provided as terminal values in the read IDs.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig (each .bw includes human transcriptome only)
Supplementary_files_format_and_content: bed (each .BED includes HCMV mRNA abundance measurements)

value: NPC cells (ES-derived)

value: HCMV (strain TB40E)


title: HFF_MockforHSV_8h

description: Sequencing Sample 10

value: mock


title: lacz 2 for mlf KD

description:
lacz2_mlf
PolyA RNA

value: lacZ KD


title: E17.5 [338]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: Sample 24

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat with default parameters.
mRNA quantification according to RefSeq Transcripts - 2014-01-03.
raw read counts were normalized by DE-Seq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include DE-Seq normailzed expression values for each Sample.

source_name: DRG neuron

growth_protocol: Adult lumbar mouse DRG were dissected, dissociated and plated at low density on laminin-coated (5 μg/ml, Roche) dishes. Neurons were cultured in Neurobasal-A medium supplemented with B-27 (Gibco), and maintained in a humidified atmosphere of 5% CO2 in air at 36.5°C.

extract_protocol:
Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: embryonic 17.5

tag: time after plating


title: E17.5 [337]

description: Sample 23


title: E17.5 [336]

description: Sample 22


title: E12.5 [87]

description: Sample 21

value: embryonic 12.5