title: Capsnatch-seq_PR8WT_A549_CSI-1-replicate1_04hpi_total_DMSO_10.0

description: Capsnatch sequencing

data_processing:
Library strategy: Capsnatch-Seq
Due to the design of our 5’ RNA adapter, each capsnatch-Seq read starts with 12 adapter-derived nucleotides, consisting of 3 random nt, followed by a 6-nt unique barcode sequence, and another 3 random nts. Demultiplexing and removal of these 5’ adapter sequences was done using custom scripts, allowing up to two barcode base mismatches and no insertions/deletions. Remaining sequences were additionally trimmed at the 3’-end after reaching a base with a phred quality score lower than 10, or after encountering 15 bases with a phred score lower than 28. Finally, 3' Illumina adapter sequences were removed using cutadapt with a minimal overlap of 6bp and allowing for an adapter error rate of 15%. Reads less than 50nt in length after quality and adapter trimming were removed from further analysis.
To identify uniformly host- and virus-derived 5’ RNA sequences, full-length adapter-trimmed reads were mapped to the human (hg19) and viral (IAV, IBV or LCMV) reference genomes using TopHat 2.0.12 and Bowtie 1.0.1 with the corresponding gene annotations (Gencode GRCh37/V19-Ensembl74 for the human genome), requiring a minimal anchor size of 10 nucleotides and using default settings for all other arguments. To identify hybrid viral mRNA sequences, the first 20 nucleotides of each read were first masked prior to mapping to viral reference genomes using the same strategy. Hybrid reads were then identified as those masked reads mapping to the positive strand of a viral genome segment, with a start coordinate less than 20bp from the segment start. In the case of the LCMV virus, which produces both positive- and negative-strand mRNAs, a custom reference genome sequence was used during this step. To prepare the custom LCMV reference, the ‘S’ segment was cut at position 1610, maintaining the 5’ part as the reference for the “envelope glycoprotein” (EGP) gene, while the remainder of the segment was reverse-complemented and used as the reference for the “nucleoprotein” (NP) gene. Likewise, the ‘L’ reference sequence was cut at position 6300 to produce a 5’ sequence encoding the “L protein” and a reverse-complemented 3’ sequence encoding a putative “hypothetical protein”. Finally, the host- and virus-derived segments of each hybrid read were identified by comparing the unmasked reads to the consensus viral genome segment sequence.
For comparison of capsnatched sequences to human 5' RNA sequences and attribution of capsnatch origin, a dictionary of unique human RNA 5' ends (9-16bp) and their genes of origin was first built based on full-length reads mapped to the human genome. Each mapped read was associated to the closest gene transcription start site (TSS) up to a maximum distance of 500bp. Host-derived capsnatch sequences were then matched to the host 5’ end sequence dictionary and assigned a gene and TSS of origin. In case capsnatch sequences mapped to multiple origins, capsnatch sequence counts were proportionally distributed among matching host genes according to the 5’-end read abundance of the host genes.
For directional RNA-seq, reads were aligned against the human reference genome using STAR. Number of reads matching refseq annotations were counted using htseq-count (mode intersection-strict).
Genome_build: Human: Gencode GRCh37/V19-Ensembl74
Genome_build: IAV: A/Puerto Rico/8/1934 H1N1, assembly ViralMultiSegProj15521
Genome_build: IBV: B/Wisconsin/01/2010 (https://www.fludb.org/brc/fluStrainDetails.spg?strainName=B/Wisconsin/01/2010&decorator=influenza Sequences from IRD submission "NIGSP_BUCB_00032" were used as reference)
Genome_build: LCMV: Armstrong 53b (Segment S: NCBI NC_004294.1 – LCMV Segment L: NCBI NC_004291.1), assembly ViralMultiSegProj14862
Supplementary_files_format_and_content: Tab-separated text files summarizing for each gencode transcript the number of host-mapped reads as well as the count of capsnatch events after proportional reattribution

extract_protocol:
Capsnatch sequencing : 5 µg of DNase treated RNA was treated with 10U of Tobacco Acid Phosphotase (Epicentre) for 1.5hrs at 37°C to remove 5’-cap structures. Immediately after, 5 µl of freshly prepared Sodium Periodate was added to a final concentration of 500mM to block free 3’-OH ends of RNA. After incubating for 1.5hrs at 4°C the reaction was stopped by adding 1/10 volume of 1M L-lysine and incubating at room temperature for an additional 10 minutes. Next, RNA was purified with 1.8X volume of AMPure XP beads (Beckman Coulter), and 10 µM barcoded RNA adapters (5'- GUU CAG AGU UCU ACA GUC CGA CGA UCN NNX XXX XXN NN -3’, Bioo Scientific; N=randomized bases; X=barcode adapter) were ligated to the 5’ ends of RNAs in an overnight (~16-18hrs) reaction at 16°C containing 5U of T4 RNA ligase, 10 µM ATP, and 1 µl of RNAse Inhibitor (Promega, N2618). Adapter-ligated RNA was purified with 1.8X volume of AMPure XP beads, and up to six 1 µg samples with distinct 5’ adapter barcodes were pooled together. Ribosomal RNAs were removed from pooled samples using the Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) (Illumina) according to the manufacturer’s protocol, using 4 µls of Reaction Buffer and 10 µls of rRNA Removal Solution. rRNA depleted samples were purified with 1.6X volume AMPure XP beads and reverse-transcribed using by hybridizing 10 µM of a custom 3’ primer (5'-AGA CGT GTG CTC TTC CGA TCT N*N*N*N*N*N*-3',
Bioo Scientific, N*=randomized bases) for 2 minutes at 65°C. Then, 25mM of dNTP Mix (Thermo Scientific), 1 µl of RNasin® Plus RNase Inhibitor (Promega), 5X First Strand Buffer, 200mM of DTT, and SuperScript® III Reverse Transcriptase (Invitrogen) were added to the reaction and incubated in a thermocycler for 25°C for 10 minutes, 42°C for 50 minutes and 70°C for 15 minutes. Next, cDNAs were purified with 1.8X volume AMPure XP beads, followed by PCR amplification using Kapa HiFi HotStart Ready Mix, 25µM SR forward primer (5'-AAT GAT ACG GCG ACC ACC GAG ATC TAC ACG TTC AGA GTT CTA CAG TCC G-s-A-3', Bioo Scientific) and a reverse indexed primer (5’-CAA GCA GAA GAC GGC ATA CGA GAT XXX XXX GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC*T-3’, IDT) for 20 cycles. PCR products were purified using 1.8X AMPure XP beads fragments of 200-400bp were size-selected using BluePippin 2% M1 gels (Sage Scientific). Following library validation on the Agilent Bioanalyzer samples were sequenced on the Illumina HiSeq 2500 platform in a 100 bp single-end read run format.
Cytosolic/Nucleic fractionation: Cell pellets were re-suspended in 1.2 mL of solubilization buffer (50mM 1M HEPES-KOH, pH 7.5; 140mM 5M NaCl; 1mM 0.5M EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; water to 100ml) containing 1X proteinase inhibitor cocktail mix, and rotated at 4°C for 10 minutes. Samples were centrifuged at 1350g for 5 minutes at 4°C. The cytosolic supernatant was transferred to a clean tube, leaving behind the nuclear pellet. RNA extraction : RNA was extracted from cytosolic, nucleic or total fractions using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions, adding 600 µls RLT Buffer and 6 µls of B-Mercaptoethanol to each sample. The RNA was eluted in 30 µl of nuclease-free water. Samples were DNase treated with 1U Baseline Zero DNase (Epicentre) at 37°C for 30 minutes according to the manufacturer’s instructions, cleaned up with 1.8X volume of AMPureXP beads (Beckman-Coulter) and eluted in nuclease free water. RNA quality (RIN>9) was assessed using the Agilent Bioanalyzer and quantified using the Qubit RNA Broad Range Assay kit (ThermoFisher). An aliquot of each sample was tested for mycoplasma contamination using the eMyco Plus Mycoplasm PCR Detection Kit (Intron Biotechnology). Additional testing was done during capsnatch-seq data analysis by determining if any next-generation sequencing reads mapped exclusively to mycoplasma reference genomes available in the NIH Genbank database.

treatment_protocol: A549 cells were plated at a density of 25,000 per well in a 96-well plate 24 hours before infection with Influenza A/Puerto Rico/8/1934(H1N1). Cells were treated with media containing seven concentrations of VX-787 (three-fold dilutions starting from 100nM), or DMSO vehicle control, 2 two hours prior to infection. The pre-treatment media was removed, and then cells were infected for 1 hour at MOI 0.001.  Virus inoculum was then removed and replaced with media containing 0.5 µg/mL TPCK treated trypsin and the same dilutions of VX-787 or vehicle.  48 hours post infection, cells were fixed in 4% PFA, permeabilized with HCS Reagent (Cellomics), blocked with 1% BSA/PBS, incubated with monoclonal mouse anti-NP antibody (HT103), and then incubated with Alexa Fluor 488 goat anti-mouse IgG (Life Technologies).  Plates were then analyzed by a fluorescent plate cytometer (Acumen eX3) for number of distinct events in the 488nm channel.  The relative infection for each treatment was determined by dividing the average number of events in the treatment well (n=6) by the average number of events in the vehicle control wells (n=12).  Based on these values, a 4 parameter logistic nonlinear regression model was used to calculate the IC50 and IC90 values in Graphpad Prism 6.

value: DMSO


title: Patient 370

status: Public on Aug 09 2017

type: SRA

city: Boston

first: Kenzie

last: MacIsaac

state: MA

address: 33 Avenue Louis Pasteur

department: Genetics and Pharmacogenomics

country: USA

institute: Merck Research Labs

library_source: transcriptomic

data_processing:
Transcriptome sequencing was performed at WuXi AppTec Genome Center on Illumina HiSeq2000 platform (50M cluster, PE100 sequencing).
RNA-Seq data were analyzed using Omicsoft ArraySuite® software
Reads were aligned to the genome using the OSA aligner
The ArraySuite software was used to quantitate transcripts using UCSC gene models
Genome_build: NCBI build 37.1
Supplementary_files_format_and_content: A gene level matrix of FPKM values for each sample is provided in NPC_mRNA_processed.txt

molecule: total RNA

organism: Homo sapiens

source_name: NPC tumor

extract_protocol:
RNA was prepared from snap-frozen NPC biopsies using Qiagen Allprep DNA/RNA kit (Cat#80204) according to the manufacturer's protocols
Illumina TruSeq RNA Sample Preparation kit was used to construct libraries.

tag: expression-based subtype

value: I

tag: time to event

tag: event

value: Last follow-up

tag: clinical stage

value: IV

tag: % stromal tils

tag: % intratumoral tils

tag: morphology

value: mixed (round & spindle)

tag: non-synonymous mutation burden

tag: cohort

value: Paired


title: MDA-MB-231

city: Suwon-si,

first: Seong-Jin

last: Kim

address: 145 Gwanggyo-ro, Yeongtong-gu,

country: South Korea

institute: Nano-Bio Medicine Research Center

data_processing:
An Illumina platform (Illumina) was used to analyze transcriptomes with 90 bp paired-end library.
Illumina Hiseq software used for basecalling.
Samples were paired-end sequenced with the Illumina HiSeq 2000.
Genome_build: mm9
Supplementary_files_format_and_content: text files include FPKM values for each Sample.

source_name: Breast cancer cell lines

extract_protocol:
Total RNAs of each cell were isolated using the TRIzol reagent for RNA sequencing following manufacturer’s instructions. The total RNAs were treated with DNase I, purified with miRNeasy Mini Kit and subsequently quality checked using an Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subtype

value: Basal-like

tag: species

value: Human


title: MCF-7

value: Luminal


title: Capsnatch-seq_PR8WT_A549_CSI-1-replicate1_04hpi_total_DMSO_01.0

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

description: Capsnatch sequencing

source_name: Infected adenocarcinomic human alveolar basal epithelial cells

growth_protocol: A549 cells were originally obtained from the American Type Culture Collection and maintained at 37 °C with 5% CO2 in F-12K Media (Gibco) supplemented with 10% Fetal Bovine Serum (Corning) and 1%Penicillin Streptomycin Solution (Corning cellgro). Cells were infected with either Influenza A/Puerto Rico/8/1934(H1N1), Influenza B/Wisconsin/01/2010, or Lymphocytic Choriomeningitis (ARM 53b) virus at a multiplicity of infection (MOI) of 2 with a viral media consisting of 1X PBS + 0.3% BSA.  Virus was removed 1hr post infection and cells were allowed to grow in complete F-12K media (as described above) at 37°C. Cell pellets were collected from uninfected controls (0hrs), as well as 2hrs, 4hrs, 6hrs, 8hrs, and 10hrs post-infection for IAV or 4hrs and 8hrs post infection for IBV and LCMV. Cell pellets were washed with 1X PBS twice and stored at -80°C until RNA extraction.

tag: cell line

tag: viral strain

value: A/Puerto Rico/8/1934 H1N1

tag: treatment

tag: timepoint

value: 04 hours post-infection


title: Hs578T


title: Capsnatch-seq_PR8WT_A549_CSI-1-replicate1_04hpi_total_CSI_01.0

description: Capsnatch sequencing

value: VX787 CapSnatch inhibitor


title: Capsnatch-seq_PR8WT_A549_CSI-1-replicate1_04hpi_total_CSI_00.1

description: Capsnatch sequencing


title: DR_Mel888_sgMAPK1_B

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

description: 3926_10_DR_Mel888_sgMAPK1_B_ACTTGAA_S75_L007

data_processing:
Read mapping was performed using TopHat version 2.1.0 and Bowtie version 1.1.0 with the Ensembl GRCh38 reference genome
Read counts per gene were quantified using Icount (union mode) using Homo_sapiens.GRCh38.77.gtf
Genome_build: GRCh38

source_name: Mel888 cell line; resistant to dabrafenib and trametinib

growth_protocol: All cells were cultured with DMEM plus 9% FBS and pen/strep in 5% CO2 incubator at 37 degree

extract_protocol:
RNA was extracted using Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with either dabrafenib + trametinib (0.5 +0.05 μM) or DMSO (drug withdrawal (dh group) for 5 days

tag: replicate

tag: drug holiday

value: no

tag: genetic background


title: DR_Mel888_sgMAPK1_A

description: 3926_9_DR_Mel888_sgMAPK1_A_TTAGGCA_S68_L007


title: Capsnatch-seq_PR8WT_A549_T01-replicate2_10hpi_nucleic

description: Capsnatch sequencing

molecule: nuclear RNA

value: 10 hours post-infection


title: Capsnatch-seq_PR8WT_A549_T01-replicate2_08hpi_nucleic

description: Capsnatch sequencing

value: 08 hours post-infection


title: DR_Mel888_sgMAPK1_dh_A

description: 3926_11_DR_Mel888_sgMAPK1_-_A_GATCAGA_S76_L007

value: yes


title: DR_Mel888_sgMAPK1_dh_B

description: 3926_12_DR_Mel888_sgMAPK1_-_B_TAGCTTA_S77_L007


title: Capsnatch-seq_PR8WT_A549_T01-replicate1_10hpi_nucleic

description: Capsnatch sequencing


title: Patient 4

tag: expression-based subtype

value: II

tag: time to event

value: Not evaluated

value: Unpaired


title: Capsnatch-seq_PR8WT_A549_T01-replicate1_08hpi_nucleic

description: Capsnatch sequencing


title: T47D


title: Capsnatch-seq_PR8WT_A549_T01-replicate2_06hpi_nucleic

description: Capsnatch sequencing

value: 06 hours post-infection


title: RNAseq_00hpi_nucleic

description: Directional RNA sequencing

data_processing:
Due to the design of our 5’ RNA adapter, each capsnatch-Seq read starts with 12 adapter-derived nucleotides, consisting of 3 random nt, followed by a 6-nt unique barcode sequence, and another 3 random nts. Demultiplexing and removal of these 5’ adapter sequences was done using custom scripts, allowing up to two barcode base mismatches and no insertions/deletions. Remaining sequences were additionally trimmed at the 3’-end after reaching a base with a phred quality score lower than 10, or after encountering 15 bases with a phred score lower than 28. Finally, 3' Illumina adapter sequences were removed using cutadapt with a minimal overlap of 6bp and allowing for an adapter error rate of 15%. Reads less than 50nt in length after quality and adapter trimming were removed from further analysis.
To identify uniformly host- and virus-derived 5’ RNA sequences, full-length adapter-trimmed reads were mapped to the human (hg19) and viral (IAV, IBV or LCMV) reference genomes using TopHat 2.0.12 and Bowtie 1.0.1 with the corresponding gene annotations (Gencode GRCh37/V19-Ensembl74 for the human genome), requiring a minimal anchor size of 10 nucleotides and using default settings for all other arguments. To identify hybrid viral mRNA sequences, the first 20 nucleotides of each read were first masked prior to mapping to viral reference genomes using the same strategy. Hybrid reads were then identified as those masked reads mapping to the positive strand of a viral genome segment, with a start coordinate less than 20bp from the segment start. In the case of the LCMV virus, which produces both positive- and negative-strand mRNAs, a custom reference genome sequence was used during this step. To prepare the custom LCMV reference, the ‘S’ segment was cut at position 1610, maintaining the 5’ part as the reference for the “envelope glycoprotein” (EGP) gene, while the remainder of the segment was reverse-complemented and used as the reference for the “nucleoprotein” (NP) gene. Likewise, the ‘L’ reference sequence was cut at position 6300 to produce a 5’ sequence encoding the “L protein” and a reverse-complemented 3’ sequence encoding a putative “hypothetical protein”. Finally, the host- and virus-derived segments of each hybrid read were identified by comparing the unmasked reads to the consensus viral genome segment sequence.
For comparison of capsnatched sequences to human 5' RNA sequences and attribution of capsnatch origin, a dictionary of unique human RNA 5' ends (9-16bp) and their genes of origin was first built based on full-length reads mapped to the human genome. Each mapped read was associated to the closest gene transcription start site (TSS) up to a maximum distance of 500bp. Host-derived capsnatch sequences were then matched to the host 5’ end sequence dictionary and assigned a gene and TSS of origin. In case capsnatch sequences mapped to multiple origins, capsnatch sequence counts were proportionally distributed among matching host genes according to the 5’-end read abundance of the host genes.
For directional RNA-seq, reads were aligned against the human reference genome using STAR. Number of reads matching refseq annotations were counted using htseq-count (mode intersection-strict).
Genome_build: Human: Gencode GRCh37/V19-Ensembl74
Genome_build: IAV: A/Puerto Rico/8/1934 H1N1, assembly ViralMultiSegProj15521
Genome_build: IBV: B/Wisconsin/01/2010 (https://www.fludb.org/brc/fluStrainDetails.spg?strainName=B/Wisconsin/01/2010&decorator=influenza Sequences from IRD submission "NIGSP_BUCB_00032" were used as reference)
Genome_build: LCMV: Armstrong 53b (Segment S: NCBI NC_004294.1 – LCMV Segment L: NCBI NC_004291.1), assembly ViralMultiSegProj14862
Supplementary_files_format_and_content: Tab-separated text files summarizing for each gencode transcript the number of host-mapped reads as well as the count of capsnatch events after proportional reattribution

source_name: adenocarcinomic human alveolar basal epithelial cells

extract_protocol:
Directional RNA sequencing : 1 µg  of DNase-treated RNA was depleted of rRNAs using the Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) (Illumina) according to the manufacturer’s instructions, and purified post-depletion with 1.6X volume AMPureXP beads. Barcoded directional RNA-Seq libraries were then prepared using the NEBNext Ultra Directional RNA Library Prep kit for Illumina (New England Biolabs), per kit instructions. PCR products were purified with 1.8X volume AMPure XP beads and fragments of 300-500bp were size-selected using BluePippin 2% M1 gels (Sage Scientific). Afterwards, libraries were sequenced on the Illumina HiSeq 2500 platform in a 100 bp single-end read run format.
Cytosolic/Nucleic fractionation: Cell pellets were re-suspended in 1.2 mL of solubilization buffer (50mM 1M HEPES-KOH, pH 7.5; 140mM 5M NaCl; 1mM 0.5M EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; water to 100ml) containing 1X proteinase inhibitor cocktail mix, and rotated at 4°C for 10 minutes. Samples were centrifuged at 1350g for 5 minutes at 4°C. The cytosolic supernatant was transferred to a clean tube, leaving behind the nuclear pellet. RNA extraction : RNA was extracted from cytosolic, nucleic or total fractions using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions, adding 600 µls RLT Buffer and 6 µls of B-Mercaptoethanol to each sample. The RNA was eluted in 30 µl of nuclease-free water. Samples were DNase treated with 1U Baseline Zero DNase (Epicentre) at 37°C for 30 minutes according to the manufacturer’s instructions, cleaned up with 1.8X volume of AMPureXP beads (Beckman-Coulter) and eluted in nuclease free water. RNA quality (RIN>9) was assessed using the Agilent Bioanalyzer and quantified using the Qubit RNA Broad Range Assay kit (ThermoFisher). An aliquot of each sample was tested for mycoplasma contamination using the eMyco Plus Mycoplasm PCR Detection Kit (Intron Biotechnology). Additional testing was done during capsnatch-seq data analysis by determining if any next-generation sequencing reads mapped exclusively to mycoplasma reference genomes available in the NIH Genbank database.

value: 00 hours post-infection


title: DR_Mel888_sgJUNB_dh_B

description: 3926_8_DR_Mel888_sgJUNB_-_B_ATCACGA_S66_L007

value: sgJUNB


title: DR_Mel888_sgJUNB_dh_A

description: 3926_7_DR_Mel888_sgJUNB_-_A_GTGAAAC_S74_L007


title: Patient 312

value: I

tag: event

value: Disease progression

tag: clinical stage

value: III

value: undifferentiated, round

value: Paired


title: Capsnatch-seq_PR8WT_A549_T01-replicate1_06hpi_nucleic

description: Capsnatch sequencing

value: A/Puerto Rico/8/1934 H1N1


title: DR_Mel888_sgJUNB_B

description: 3926_6_DR_Mel888_sgJUNB_B_GTCCGCA_S73_L007


title: DR_Mel888_sgJUNB_A

description: 3926_5_DR_Mel888_sgJUNB_A_CCGTCCC_S72_L007


title: Capsnatch-seq_PR8WT_A549_CSI-1-replicate1_04hpi_total_DMSO_00.1

description: Capsnatch sequencing

value: DMSO

value: 04 hours post-infection


title: Capsnatch-seq_PR8WT_A549_T01-replicate1_04hpi_nucleic

description: Capsnatch sequencing


title: DR_Mel888_sgCtrl_dh_B

description: 3926_4_DR_Mel888_sgCtrl_-_B_ATGTCAG_S71_L007

value: sgCtrl


title: Capsnatch-seq_PR8WT_A549_T01-replicate2_04hpi_nucleic

description: Capsnatch sequencing


title: Capsnatch-seq_PR8WT_A549_CSI-1-replicate1_04hpi_total_CSI_10.0

description: Capsnatch sequencing

value: VX787 CapSnatch inhibitor


title: Capsnatch-seq_PR8WT_A549_T01-replicate2_02hpi_nucleic

description: Capsnatch sequencing

value: 02 hours post-infection


title: DR_Mel888_sgCtrl_dh_A

description: 3926_3_DR_Mel888_sgCtrl_-_A_AGTTCCG_S69_L007

value: yes


title: DR_Mel888_sgCtrl_B

description: 3926_2_DR_Mel888_sgCtrl_B_AGTCAAC_S70_L007

value: no


title: Capsnatch-seq_PR8WT_A549_T01-replicate1_02hpi_nucleic

description: Capsnatch sequencing


title: 451Lu_BR_C_5d

data_processing:
Read mapping was performed using TopHat version 2.1.0 and Bowtie version 1.0.0 with the Ensembl GRCh38 reference genome
Read counts per gene were quantified using Icount (union mode) using Homo_sapiens.GRCh38.77.gtf
Genome_build: GRCh38

source_name: 451Lu cell line; resistant to dabrafenib and trametinib

treatment_protocol: DR A375 cells were treated with either dabrafenib + trametinib (0.5+0.05 μM) (DR_A375_B and DR_A375_C) or  DMSO (drug withdrawal) for time indicated (6h, 24h and 48h). 451Lu BR cells were treated with either dabrafenib (1 μM) (451Lu_BR_B, 451Lu_BR_C) or  DMSO (drug withdrawal) for time indicated (1d, 3d and 5d).

tag: time


title: Capsnatch-seq_PR8WT_A549_T01-replicate1_00hpi_nucleic

description: Capsnatch sequencing


title: 451Lu_BR_C_3d


title: 451Lu_BR_B_5d


title: Capsnatch-seq_PR8WT_A549_T01-replicate2_10hpi_cytoplasmic

description: Capsnatch sequencing

molecule: cytoplasmic RNA

value: 10 hours post-infection


title: Capsnatch-seq_PR8WT_A549_T01-replicate2_08hpi_cytoplasmic

description: Capsnatch sequencing

value: 08 hours post-infection


title: 451Lu_BR_B_3d


title: Capsnatch-seq_PR8WT_A549_T01-replicate1_08hpi_cytoplasmic

description: Capsnatch sequencing


title: 451Lu_BR_C_1d


title: 451Lu_BR_C


title: 451Lu_BR_B_1d


title: Capsnatch-seq_PR8WT_A549_T01-replicate2_06hpi_cytoplasmic

description: Capsnatch sequencing

value: 06 hours post-infection


title: 451Lu_BR_B


title: Capsnatch-seq_PR8WT_A549_T01-replicate1_06hpi_cytoplasmic

description: Capsnatch sequencing


title: DR_A375_C_48h

source_name: A375 cell line; resistant to dabrafenib and trametinib


title: DR_A375_B_48h


title: Capsnatch-seq_PR8WT_A549_T01-replicate1_04hpi_cytoplasmic

description: Capsnatch sequencing


title: DR_A375_C_24h


title: Capsnatch-seq_PR8WT_A549_T01-replicate1_02hpi_cytoplasmic

description: Capsnatch sequencing


title: Capsnatch-seq_PR8WT_A549_T01-replicate2_02hpi_cytoplasmic

description: Capsnatch sequencing


title: LELab_ChIP_seq_TLS1650_anti_FLAG

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

library_source: genomic

data_processing:
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools (Quinlan and Hall, 2010) using the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. For analysis of E. coli ChIP-seq data, reference genomes were first reconstructed in silico by inserting the nucleotide sequence of parS and apramycin antibiotic resistance cassette to the ybbD locus of E. coli MG1655 genome. Afterwards, Hiseq 2500 Illumina short reads were mapped back to these reconstructed reference genomes using Bowtie 1. Sequence coverage at each nucleotide position was also computed using BEDTools. Finally, ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts.
For analysis of IDAP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, sequencing reads were sorted to either being mapped to the upper DNA strand or to the lower strand of the reference genome, as suggested in the original IDAP-seq publication (Belitsky and Sonenshein, 2013). The number of 5’ end of reads that were mapped to the upper strand was counted for each nucleotide position along the Caulobacter genome using BEDTools (Quinlan & Hall, 2010) and the following command: bedtools genomecov -d -5 -strand + -ibam output.sorted.bam -g NA1000.fna > upper_strand_output.txt. To count the number of 5’ end of reads that were mapped to the lower strand, the following command was used instead: bedtools genomecov -d -5 -strand - -ibam output.sorted.bam -g NA1000.fna > lower_strand_output.txt. The IDAP-seq profile was then plotted using R. The sequence in between the summit of upper strand profile and that of the lower strand profile defines the minimal parS sequence required for binding to ParB.
Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command: bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage for each nucleotide position was computed using BEDTools (Quinlan & Hall, 2010) and the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. Finally, the ratio between the number of reads of libraries generated from pMCS1-Tn5-ME-R6Kγ-kanR-ME or pMCS1-Tn5-ME-R6Kγ-kanR-parS456-ME were calculated. Results were binned over 1 kb and represented as a log10 scale.
Genome_build: NC_000913.3
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Files ending with _coverage.txt: tab-delimited text file of nucleotide-resolution coverage from RNA-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

molecule: genomic DNA

organism: Escherichia coli

source_name: Escherichia coli AB1157

growth_protocol: Cultures of Caulobacter (TLS1631-TLS1633) were grown at 30oC in PYE and supplemented with antibiotics, as necessary, at appropriate concentrations. To deplete wild-type non-tagged ParB, exponential-phase cells were washed off xylose and re-introduced to PYE+0.2% glucose for an additional 5 hours. After 4 hours, vanillate was added to induce the expression of flag-parB (WT) or flag-parB (G101S/R104A) for an hour. Cultures of Escherichia coli (TLS1637-TLS1650) were grown at 30oC in LB and supplemented with antibiotics, as necessary, at appropriate concentrations. IPTG (0.5mM) was added to induce the production of T18-ParB (WT) or T18-ParB (G101S). After an hour, formadehyde (1% final concentration) were added to fix cells for ChIP-seq.

extract_protocol:
DNA was isolated using the Qiagen Cell Lysis and Protein Precipitation solutions. Detailed protocols are listed in the Supplementary Materials
Standard library construction for Illumina Hiseq2500 sequencing platform

treatment_protocol:
T18-ParB (G101S) were produced by addition of 0.5mM IPTG for an hour before formadehyde to 1% (final concentration ) was added to fix cells for ChIP-seq
None

tag: developmental stage

value: mixed population, exponential phase

tag: genotype

value: AB1157 ybbD::parS scrambled site 3 pUTC18::parB (G101S)

tag: antibody

value: Flag


title: Capsnatch-seq_PR8WT_A549_T01-replicate2_00hpi_cytoplasmic

description: Capsnatch sequencing

value: 00 hours post-infection


title: DR_A375_B_24h


title: LELab_ChIP_seq_TLS1649_anti_FLAG

value: AB1157 ybbD::parS site 7 pUTC18::parB (G101S)


title: Capsnatch-seq_PR8WT_A549_T01-replicate2_00hpi_nucleic

description: Capsnatch sequencing


title: Capsnatch-seq_PR8WT_A549_T01-replicate1_00hpi_cytoplasmic

description: Capsnatch sequencing


title: LELab_ChIP_seq_TLS1648_anti_FLAG

value: AB1157 ybbD::parS site 5 pUTC18::parB (G101S)


title: DR_Mel888_sgCtrl_A

description: 3926_1_DR_Mel888_sgCtrl_A_CTTGTAA_S67_L007


title: Capsnatch-seq_PR8WT_A549_T01-replicate1_10hpi_cytoplasmic

description: Capsnatch sequencing

value: A/Puerto Rico/8/1934 H1N1


title: DR_A375_C_6h

value: 6 h


title: LELab_ChIP_seq_TLS1647_anti_FLAG

value: AB1157 ybbD::parS site 4 pUTC18::parB (G101S)


title: Capsnatch-seq_PR8WT_A549_T00-replicate1_08hpi_total

description: Capsnatch sequencing


title: DR_A375_B_6h


title: Capsnatch-seq_PR8WT_A549_T01-replicate2_04hpi_cytoplasmic

description: Capsnatch sequencing

value: 04 hours post-infection


title: LELab_ChIP_seq_TLS1645_anti_FLAG

value: AB1157 ybbD::parS site 2 pUTC18::parB (G101S)


title: LELab_ChIP_seq_TLS1644_anti_FLAG

treatment_protocol:
T18-ParB (WT) were produced by addition of 0.5mM IPTG for an hour before formadehyde to 1% (final concentration ) was added to fix cells for ChIP-seq
None

value: AB1157 ybbD::parS scrambled site 3 pUTC18::parB (WT)


title: DR_A375_C


title: LELab_ChIP_seq_TLS1646_anti_FLAG

value: AB1157 ybbD::parS site 3 pUTC18::parB (G101S)


title: Capsnatch-seq_PR8WT_A549_T00-replicate1_04hpi_total

description: Capsnatch sequencing


title: LELab_ChIP_seq_TLS1642_anti_FLAG

value: AB1157 ybbD::parS site 6 pUTC18::parB (WT)


title: LELab_ChIP_seq_TLS1641_anti_FLAG

value: AB1157 ybbD::parS site 5 pUTC18::parB (WT)


title: DR_A375_B


title: Capsnatch-seq_LCMV_A549_T01-replicate2_08hpi_total

description: Capsnatch sequencing

value: Armstrong 53b

value: 08 hours post-infection


title: LELab_ChIP_seq_TLS1639_anti_FLAG

value: mixed population, exponential phase

value: AB1157 ybbD::parS site 3 pUTC18::parB (WT)


title: Capsnatch-seq_LCMV_A549_T01-replicate1_08hpi_total

description: Capsnatch sequencing


title: KO clone 3, 8 hours withdrawal from PD/LIF

city: Portsmouth

first: Samuel

last: Robson

address: St Michael's Building

department: School of Pharmacy & Biomedical Science

institute: University of Portsmouth

data_processing:
ChIRP-seq: Multiplexed reads were split based on their TRUseq barcodes using Illumina Basespace. Reads were tirmmed to remove the TRUseq adapter using trim_galore with parameters "-q 0 -a AGATCGGAAGAGCACACGTCTGAA --phred33 --fastqc". Read quality was assessed using FastQC. Ribosomal contamination was removed by first mapping the reads to mm10 rDNA sequences using bwa, and removing all reads that map. Trimmed non-ribosomal reads were mapped to the mm10 genome using bwa with default parameters. Multiple reads mapping to a single genomic locus were treated as PCR duplicates, and were removed using samtools rmdup. Mapped reads were filtered to remove reads mapping to more than one unique genomic locus (multihits) by keeping only reads with flag XT:A:U in the output bam file from bwa. Reads were further filtered to remove reads with mapping quality less than 20 using samtools. Genome coverage bedgraph files were generated using genomeCoverageBed from the bedtools suite of tools. Coverage files were converted to bigwig format using bedGraphToBigWig. Peaks were called against either the WT or KO input sample using MACS1.4 using parameters "-f BAM -g mm -p 0.01 --bw=300 -m 10,30".
RNA-seq: Single end sequencing was performed and the reads were mapped using NCBI38/mm10 with Ensembl version 75 annotations. RNA-seq reads were aligned to the reference genome using tophat2. Only uniquely mapped reads were used for further analysis. Gene counts from SAM files were obtained using htseq-count with mode intersection non-empty, -s reverse. Differential gene expression analysis was conducted using Bioconductor R package DESeq2 version 1.4.5. DESeq2 provides two P-values, a raw P-value and a Benjamini-Hochberg P-value (adjusted p value). An adjusted p-Value threshold of 0.05 was used to determine differential gene expression (95% of the results are not false discoveries, error rate 0.05 =5%).
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files give coverage scores across the whole mm10 genome at each base position for the ChIRP seq reads. Normalised and non-normalised coverage files are provided for each sample. Peak bed files give the enriched peak regions called against input for the ChIRP-Seq data. htseq files give read counts of uniquely mapping RNA seq data across all transcripts in Ensembl 75 database using "-m intersection-nonempty" and either "-s reverse" ("[filename].uniq.rsorted.sr.counts.intersection.nonempty" or  "-s yes" ("[filename].uniq.rsorted.ss.counts.intersection.nonempty".

organism: Mus musculus

source_name: Whole cell

growth_protocol: ESCs were cultured on 0.1% gelatin in PDL/LIF medium (NDiff B27 base medium, Stem Cell Sciences, cat. SCS‐SF‐ NB‐02, supplemented with 1 μM PD0325901 and 20 ng/ml LIF). Cells were then withdrawn from PD/LIF and grown in N2B27 basal medium for 8 hours prior to harvest.

extract_protocol:
Total RNA was isolated with RNeasy RNA purification kit (Qiagen), and RNA quality was cheked with Bioanalyser.
RNA-seq library was prepared and barcoded using NEXTFlex Rapid directional RNA-seq protocol (BIOO Scientific). Barcoded samples were combined together at uniform molarity to create a single pool with four samples per lane, which was sequenced in a single end 50 bp run on an Illumina HiSeq 2500 machine.

treatment_protocol: Ribo-zero rRNA depleted RNA was used to generate sequencing libraries for wild type and Ephemeron knockout cells in PD/LIF and 8 hours withdrawal from PDL from three independent cell lines.

tag: cell type

value: mouse embryonic stem (mES) cells

tag: background strain

tag: genotype/variation

value: knockout of the lncRNA ephemeron (KO)

tag: concentration

tag: truseq barcode

value: GGCTAC


title: LELab_ChIP_seq_TLS1640_anti_FLAG

value: AB1157 ybbD::parS site 4 pUTC18::parB (WT)

value: Flag


title: LELab_ChIP_seq_TLS1637_anti_FLAG

value: AB1157 ybbD::parS site 1 pUTC18::parB (WT)


title: SRm160 mutant larvae 36h replicate C

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir. IIBBA- CONICET

description:
rp_3
SRm160_18603-36H_AEL_CR1

data_processing:
Basecalling donde with Bustard Illumina Pipeline
Sequence reads were mapped to Drosophila_melanogaster_NCBI_build5.41  genome using TopHat v2.1.1 with default parameters
Count tables for different feature levels were obtained from bam files using ASpli R package
Differential gene expression was estimated using edgeR package version 3.14.0 and resulting p-values were adjusted using false discovery rate (fdr) criterion.
The transcriptome was partitioned into subgenic joint features called bins and labeled as exon-bin, intron-bin or alternative-splicing (AS) bins. In addition AS-bins were further classified as exon skipping (ES), 5’ or 3’ alternative (5´alt, 3´alt), intron retention (IR) or multiple. Bins from monoexonic genes, with mean count values lower than 5 reads per condition and rd bin / rd gen lower than 0.05 were discarded.
Genome_build: Drosophila_melanogaster_NCBI_build5.41
Supplementary_files_format_and_content: Comprehensive spreadsheets with the results of the analysis of differential splicing detailed above

organism: Drosophila melanogaster

source_name: SRm160 mutant larvae 36h

growth_protocol: Flies were reared under light cycles (12 h light:12 h darkness) on Drosophila standard medium at 25°C.

extract_protocol:
mRNA was purified using Trizol
TruSeq RNA Sample Preparation Guide (Illumina)

treatment_protocol: The treatment is the mutantion 18603 in the SRm160 (CG11274) gene.

tag: strain background

value: SRm160 mutant

value: 36h after egg laying (AEL)

tag: tissue

value: larvae


title: Capsnatch-seq_LCMV_A549_T01-replicate2_04hpi_total

description: Capsnatch sequencing

tag: cell line

tag: viral strain

tag: treatment

tag: timepoint

value: 04 hours post-infection


title: KO clone 2, 8 hours withdrawal from PD/LIF

value: TAGCTT


title: SRm160 mutant larvae 36h replicate B

description:
rp_2
SRm160_18603-36H_AEL_BR1


title: SRm160 mutant larvae 36h replicate A

description:
rp_1
SRm160_18603-36H_AEL_AR1


title: wildtype larvae 36h replicate C

description:
w_3
w1118-36H_AEL_CR1

source_name: wildtype larvae 36h

value: wild type


title: Capsnatch-seq_LCMV_A549_T01-replicate2_00hpi_total

description: Capsnatch sequencing

value: 00 hours post-infection


title: Wild type clone 3, 8 hours withdrawal from PD/LIF

value: wild-type

value: ACTTGA


title: Wild type clone 2, 8 hours withdrawal from PD/LIF

value: TTAGGC


title: wildtype larvae 36h replicate B

description:
w_2
w1118-36H_AEL_BR1


title: LELAb_ChIP_seq_TLS1643_anti_FLAG

value: mixed population, exponential phase

value: AB1157 ybbD::parS site 7 pUTC18::parB (WT)


title: wildtype larvae 36h replicate A

description:
w_1
w1118-36H_AEL_AR1


title: Wild type clone 1, 8 hours withdrawal from PD/LIF

value: mouse embryonic stem (mES) cells

value: ATCACG


title: KO clone 3 in PD/LIF

growth_protocol: ESCs were cultured on 0.1% gelatin in PDL/LIF medium (NDiff B27 base medium, Stem Cell Sciences, cat. SCS‐SF‐ NB‐02, supplemented with 1 μM PD0325901 and 20 ng/ml LIF).

value: knockout of the lncRNA ephemeron (KO)

value: CTTGTA


title: Capsnatch-seq_LCMV_A549_T01-replicate1_00hpi_total

description: Capsnatch sequencing

value: Armstrong 53b


title: Capsnatch-seq_FLUB_A549_T01-replicate2_04hpi_total

description: Capsnatch sequencing


title: Capsnatch-seq_FLUB_A549_T01-replicate2_08hpi_total

description: Capsnatch sequencing

value: 08 hours post-infection


title: KO clone 2 in PD/LIF

value: CAGATC


title: LELab_ChIP_seq_TLS1638_anti_FLAG

value: AB1157 ybbD::parS site 2 pUTC18::parB (WT)

value: Flag


title: KO clone 1 in PD/LIF

value: GCCAAT


title: Capsnatch-seq_FLUB_A549_T01-replicate1_04hpi_total

description: Capsnatch sequencing

value: 04 hours post-infection


title: KO clone 1, 8 hours withdrawal from PD/LIF

value: GATCAG


title: Capsnatch-seq_FLUB_A549_T01-replicate1_08hpi_total

description: Capsnatch sequencing


title: Capsnatch-seq_FLUB_A549_T01-replicate2_00hpi_total

description: Capsnatch sequencing

value: 00 hours post-infection


title: Capsnatch-seq_LCMV_A549_T01-replicate1_04hpi_total

description: Capsnatch sequencing


title: Wild type clone 2 in PD/LIF

value: wild-type

value: TGACCA


title: Wild type clone 1 in PD/LIF

value: CGATGT


title: 2221ΔrocA + vector

status: Public on Aug 08 2017

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

data_processing:
CLC Genomics Workbench version 7.5.1 RNA-seq was used for basecalling and aligning the sequence reads to the MGAS5005 genome (CP000017).
Parameters for alignment were set up:  Similar fraction=0.8, Length fraction=0.8, Mismatch cost=2, Insertion cost=3.
Normalization was performed to overall sequencing depth using total mapped reads data.
Statistical significance was tested using Kal’s Z-test with a false-discovery rate correction.
Genome_build: NC_007297
Supplementary_files_format_and_content: Excel file containing columns for the gene name, Kal's Z-test with FDR correction value, normalized mean for each strain, gene start nucleotide number, gene stop nucleotide number, and expression ratios

organism: Streptococcus pyogenes

source_name: 2221ΔrocA + vector

growth_protocol: GAS strains were grown in THY broth containing 4 ug/ml chloramphenicol to the exponential phase of growth (O.D.600 = 0.5)

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

tag: strain

value: rocA mutant of MGAS2221

tag: growth phase

value: Exponential phase of growth

tag: growth medium

value: THY broth growth


title: 2221ΔrocA + pRocA-M1

source_name: 2221ΔrocA + pRocA-M1

value: Plasmid-complemented derivative of 2221<delta>rocA


title: 501Mel

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: Processed data file: tablecount.txt.gz

data_processing:
Reads were first filtered to remove SOLiD adaptors, SOLiD barcodes and rRNAs reads.
Alignment was performed within Bowtie software using default parameters and allowing 2 mismatches.
Bam files were then processed with a java home made class, based on picard java classes to perform identification and produce raw data count of microRNAs (miRBase release 20), tRNAs from UCSC web server (UCSC tables), yRNAs and ncRNAs from Ensembl ncRNAs release 75 and piRNAs from fRNAdb.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: tablecount.txt.gz: Tab-delimited text file includes counts values for each sample and each small RNA features.

source_name: 501Mel melanoma cell line

growth_protocol: Cell lines were grown in RPMI-1640 medium (Gibco BRL, Invitrogen, Paisley, UK) supplemented with 10% Fetal Bovine Serum (PAA cell culture company, Pasching, Austria) and 1% Penicillin-Streptomycin antibiotics (Gibco BRL, Invitrogen, Paisley, UK).

extract_protocol:
RNA extraction with the miRVana kit (Thermo Fisher Scientific).
0.5 µg of total RNA were ligated, reverse transcribed and amplified (13 cycles) with the reagents from the NEBNext Small RNA Library Prep Set for SOLiD. Amplified libraries were size-selected from 110 nt to 130 nt with the LabChip XT DNA 300 Assay Kit (Caliper Lifesciences). Libraries were subjected to 4 additional PCR rounds with the primers from the 5500 W Conversion Primers Kit (Life Technologies) and a second time the amplified libraries were size-selected from 140 nt to 160 nt with the LabChip XT DNA 300 Assay Kit (Caliper Lifesciences). The product converted with the enzyme kit from the 5500 W Conversion Primers Kit (Life Technologies). Libraries were then quantified with the Bioanalyzer High Sensitivity DNA Kit (Agilent).

value: melanoma cell line

tag: concentration sample (ng/ul)

tag: rin number


title: Capsnatch-seq_FLUB_A549_T01-replicate1_00hpi_total

description: Capsnatch sequencing


title: Me1402

description: Processed data file: tablecount.txt.gz

source_name: Me1402 melanoma cell line


title: Capsnatch-seq_PR8WT_A549_T00-replicate1_00hpi_total

description: Capsnatch sequencing

value: A/Puerto Rico/8/1934 H1N1


title: Cbp80kd ovaries

city: Bern

first: Rémy

last: Bruggmann

address: Baltzerstrasse 6

country: Switzerland

institute: University of Bern

description: pCog-Gal4 expressing shRNA-Cbp80 (TRiP line) for Cbp80 (pCog-Gal4>shRNA-Cbp80)

data_processing:
mapping: bowtie -n 0 -l 100 -m 5 --best --strata -p 1 -f
coverage: igvtools count -w 50 --strands read file.bam file.wig dm3
Genome_build: dm3
Supplementary_files_format_and_content: wig file: strand specific coverage

source_name: Cbp80kd ovaries

growth_protocol: standard corn meal based fly food supplemented with yeast.

extract_protocol:
RNA was treated with DNase I (amplification grade, Invitrogen) according to the manufacturer’s instructions
Libraries were prepared by Fasteris (Geneva, Switzerland) using the Illumina small RNA kit and a polyacrylamide size selection of 18-30 nt.  The Drosophila-specific depletion of 2S rRNA was also performed. Libraries were prepared from the pCog-Gal4-expressing shRNA-Cbp80 (TRiP line) for Cbp80 knockdown and from pCog-Gal-4 expressing sh-mCherry (TRiP line) in flies expressing mCherry-Jupiter in a Jupiter+ background as a control.

treatment_protocol: young adults aged 3-4 days on rich food. Mainly ovaries that showed germline development to stage 7-9 were dissected and used.

value: Ovary

tag: genotype

value: Cbp80 knockdown


title: M234

description: Processed data file: tablecount.txt.gz

source_name: M234 melanoma cell line

tag: cell type


title: control mCherrykd ovaries

description: pCog-Gal-4 expressing sh-mCherry (TRiP line) in flies expressing mCherry-Jupiter in a Jupiter+ (pCog-Gal-4>sh-mCherry; mCherry-Jupiter)

source_name: mCherrykd ovaries

value: control mCherry knockdown


title: Pro-B, Hi-C rep2

city: Hyderabad

first: Jagan

last: Pongubala

state: Telangana

address: Gachibowli

department: Department of Animal Biology

country: India

institute: University of Hyderabad

data_processing:
Library strategy: Hi-C
We have implemented hiclib to perform Hi-C data analysis. The raw reads were truncated to 25 bp starting at the 5′ end and were subsequently mapped to the reference genome (mm10) in a single-end mode using Bowtie2 software. Reads that mapped to multiple regions in the genome were extended by 5 bp and then re-mapped. This process was repeated until either all reads were uniquely mapped to the reference genome or until the reads were extended to their entirety.
Inappropriate ligation products such as self-circularized ligation or unligated “dangling end” products, generated as a result of experimental biases were discarded at fragment level filtering.
Valid read pairs obtained after filtering were considered for further analyses
Genome_build: mm10

source_name: Pro-B cells

growth_protocol: Pre-pro-B cells (Ebf1-/- progenitors) were maintained on stromal layer (OP9 cells) in the presence of Opti-MEM (Gibco) containing 4% (v/v) fetal calf serum, b-mercaptoethanol (50 µM), penicillin (10 U/ml) and streptomycin (10 µg/ml) and supplemented with SCF (10 ng/ml), Flt3L (10 ng/ml) and IL-7 (5 ng/ml). Pro-B cells (Rag2-/- cells) were maintained under similar conditions except that the media was supplemented with only IL-7 (5 ng/ml).

extract_protocol:
Cells were cross-linked with formaldehyde and lysed in cold lysis buffer with nuclei intact as described previously (Nagano et al., 2013; Rao et al., 2014). The chromatin was solubilized with SDS and the accessible chromatin was digested with HindIII. Digested chromatin ends were filled with dNTP mix containing biotinylated dCTP.  Nuclear ligation was performed by T4 DNA ligase and DNA-protein cross links were reversed by proteinase K treatment. DNA was purified by phenol:chloroform extraction followed by ethanol precipitation. The biotin-labeled nucleotides at unligated ends were selectively removed by T4 DNA polymerase. Purified DNA was sheared to 300-500 bp and end-repaired using a reaction mix containing T4 DNA polymerase, T4 ploynucleotide kinase and Klenow DNA polymerase. Then the biotinylated ligation junctions were enriched with streptavidin beads.
During library preparation, to avoid self-ligation of DNA fragments and to facilitate complementary 5’ overhang (‘T’) ligation of adaptors, a single ‘A’ nucleotide was added to 3’ends of the blunt fragments by using klenow exo-.  Adapter ligated DNA fragments were selectively PCR amplified with Illumina primers for 15 cycles and fragments of 400-550 bp were purified using MinElute gel extraction kit (Qaigen). Finally the in situ Hi-C libraries were subjected to paired-end high-throughput sequencing on HiSeq 1000 (Illumina) according to the manufacturer’s protocols.

value: Rag2 deficient pro-B

tag: genetic background


title: Pro-B, Hi-C rep1


title: Pre-pro-B, Hi-C rep2

source_name: Multipotent progenitors

value: Ebf1 deficient pre-pro-B


title: SKMel28

description: Processed data file: tablecount.txt.gz

source_name: SKMel28 melanoma cell line


title: Pre-pro-B, Hi-C rep1


title: M67

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
processed data file:
F3.results.csv

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the rat (Rattus norvegicus) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 100 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

organism: Rattus norvegicus

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley®™SD®™ (Harlan) at about 70 to 100 days of age were fed ad lib with a standard rat diet and ad lib tap water for drinking. To obtain time-pregnant females, the female rats in proestrus were pair-mated with male rats. The sperm-positive (day 0) rats were monitored for diestrus and changes in body weight. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1 generation. Non-littermate females and males aged 70-90 days from F1 generation control or atrazine lineages were bred to obtain F2 generation offspring. The F2 generation rats were bred to obtain F3 generation offspring.

extract_protocol:
Fifty to hundred ul of rat sperm suspension were used for DNA extraction, then 820 uL DNA extraction buffer and 80 ul 0.1M DTT added. The sample was incubated at 65C for 15 minutes. Following this incubation 80 ul proteinase K (20 mg/ml) was added and the sample was incubated at 55C for 2 hours under constant rotation. Then 300 ul of protein precipitation solution (Promega Genomic DNA Purification Kit, A795A) were added, the sample mixed thoroughly and incubated for 15 min on ice. The sample was centrifuged at 13,500 rpm for 20 minutes at 4C. One ml of the supernatant was transferred to a 2 ml tube and 2 ul of glycoblue and 1 ml of cold 100 % isopropanol were added. The sample was mixed well by inverting the tube several times then left in -20C freezer for at least one hour. After precipitation the sample was centrifuged at 13,500 rpm for 20 min at 4C. The supernatant was taken off and discarded without disturbing the (blue) pellet. The pellet was washed with 70% cold ethanol by adding 500ul of 70% ethanol to the pellet and returning the tube to the freezer for 20 minutes. After the incubation the tube was centrifuged for 10 min at 4C at 13,500 rpm and the supernatant discarded. The tube was spun again briefly to collect residual ethanol at bottom of tube and then as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes). Pellet was then resuspended in 100 ul of nuclease free water. For F1 and F2 generations equal amounts of DNA from each individual’s sperm sample was used to produce three different DNA pools per lineage and the pooled DNA used for methylated DNA immunoprecipitation (MeDIP). For F3 generation each individual’s sperm sample was analyzed separately for MeDIP-Seq.
The MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed.

treatment_protocol: On days 8 through 14 of gestation, the F0 females were administered daily intraperitoneal injections of Atrazine (25 mg/kg BW/day) or dimethyl sulfoxide (vehicle). The atrazine was obtained from Chem Service, Westchester PA and was injected in approximately 200 microliters of DMSO vehicle as previously described. The F1- F3 generation offspring were not themselves treated directly with atrazine.

value: atrazine

tag: generation

tag: pools or individuals

value: individual

value: Sperm


title: M68

description:
processed data file:
F3.results.csv


title: M65

description:
processed data file:
F3.results.csv


title: M66

description:
processed data file:
F3.results.csv


title: Wild type clone 3 in PD/LIF

value: mouse embryonic stem (mES) cells

tag: background strain

tag: genotype/variation

value: wild-type

tag: concentration

tag: truseq barcode

value: ACAGTG


title: M64

description:
processed data file:
F3.results.csv

tag: tissue


title: M62

description:
processed data file:
F3.results.csv

tag: treatment


title: M60

description:
processed data file:
F3.results.csv


title: M59

description:
processed data file:
F3.results.csv


title: M58

description:
processed data file:
F3.results.csv


title: M57

description:
processed data file:
F3.results.csv


title: M61

description:
processed data file:
F3.results.csv


title: M56

description:
processed data file:
F3.results.csv


title: M55

description:
processed data file:
F3.results.csv


title: M63

description:
processed data file:
F3.results.csv


title: MGAS2221 + vector

source_name: MGAS2221 + vector

value: Parental M1 isolate


title: M54

description:
processed data file:
F3.results.csv


title: M53

description:
processed data file:
F3.results.csv


title: M48

description:
processed data file:
F3.results.csv


title: M44

description:
processed data file:
F3.results.csv


title: M49

description:
processed data file:
F3.results.csv


title: M51

description:
processed data file:
F3.results.csv


title: M45

description:
processed data file:
F3.results.csv


title: M50

description:
processed data file:
F3.results.csv


title: M47

description:
processed data file:
F3.results.csv


title: M41

description:
processed data file:
F3.results.csv


title: M42

description:
processed data file:
F3.results.csv


title: M37

description:
processed data file:
F3.results.csv


title: M38

description:
processed data file:
F3.results.csv


title: M39

description:
processed data file:
F3.results.csv


title: M36

description:
processed data file:
F3.results.csv


title: M52

description:
processed data file:
F3.results.csv


title: M40

description:
processed data file:
F3.results.csv


title: M34

description:
processed data file:
F3.results.csv


title: M33

description:
processed data file:
F3.results.csv


title: M31

description:
processed data file:
F3.results.csv


title: M43

description:
processed data file:
F3.results.csv


title: M32

description:
processed data file:
F3.results.csv


title: M30

description:
processed data file:
F3.results.csv


title: M28

description:
processed data file:
F3.results.csv


title: 10d_MOV10_CLIP_RL5i7

city: Nanjing

first: Suwen

last: Tian

address: 101Longmian Avenue

country: China

institute: Nanjing Medical University

data_processing:
Library strategy: CLIP-seq
Illumina Casava1.8 software used for basecalling
Fastx (fastx_toolkit-0.0.13.2) to achieve clean data by filtering rRNAs and trimming adaptors.
For RNA-seq and CLIP-seq, clean reads were mapped to the mouse genome (mm10) using TopHat (version 2.0.9) with a GTF file download from Ensemble database with maximum 2-base mismatch. Reads from small RNA-seq were mapped to miRBase (version 21.0) by CLC genomics_workbench (version 5.5) without base mismatch
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig format was acquired from converting Bam file generated by TopHat.

source_name: testis

growth_protocol: spermatogonial progenitor cells were isolated from 6- to 8-day-old B6;129S-Gt(Rosa) 26Sor/J mice, and cultured these on 12-well plates with mitotically inactivated STO (SIM mouse embryo-derived thioguanine- and ouabain-resistant feeder, SNLP76/7-4, ATCC, Manassas, VA, USA) feeder layers

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-9007DOC) was used with 2 ug of total RNA for the construction of sequencing libraries.
for RNA-seq , RNA libraries were prepared for sequencing using standard Illumina protocols. For CLIP-seq, target RNA fragments were amplificated by ligation of adaptors which was in favour of the target RNA reverse transcription and PCR.

treatment_protocol: 2.5×105 SPCs were plated onto 12-well plates pre-coated with 0.1% gelatin (Sigma-Aldrich), and 12 hr later, transduced overnight with an equal mixture of culture medium and lentiviral supernatant, supplemented with 5 μg/ml polybrene

value: testis


title: 10d_MOV10_CLIP_RL5i3


title: M35

description:
processed data file:
F3.results.csv


title: M27

description:
processed data file:
F3.results.csv


title: M46

description:
processed data file:
F3.results.csv


title: M29

description:
processed data file:
F3.results.csv


title: 10d_MOV10_CLIP_RL5i1


title: M25

description:
processed data file:
F3.results.csv


title: 832_9-1

data_processing:
Illumina Casava1.8 software used for basecalling
Fastx (fastx_toolkit-0.0.13.2) to achieve clean data by filtering rRNAs and trimming adaptors.
For RNA-seq and CLIP-seq, clean reads were mapped to the mouse genome (mm10) using TopHat (version 2.0.9) with a GTF file download from Ensemble database with maximum 2-base mismatch. Reads from small RNA-seq were mapped to miRBase (version 21.0) by CLC genomics_workbench (version 5.5) without base mismatch
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig format was acquired from converting Bam file generated by TopHat.

source_name: spermatogonial progenitor cells

value: spermatogonial progenitor cells


title: M21

description:
processed data file:
F3.results.csv


title: Vector_9-1


title: M26

description:
processed data file:
F3.results.csv


title: M20

description:
processed data file:
F3.results.csv


title: M23

description:
processed data file:
F3.results.csv


title: M18

description:
processed data file:
F3.results.csv

value: control


title: M17

description:
processed data file:
F3.results.csv


title: M22

description:
processed data file:
F3.results.csv


title: 832_7-3


title: M19

description:
processed data file:
F3.results.csv


title: Vector_7-3


title: M14

description:
processed data file:
F3.results.csv


title: M24

description:
processed data file:
F3.results.csv


title: Vector_6-22


title: M12

description:
processed data file:
F3.results.csv


title: M16

description:
processed data file:
F3.results.csv


title: M13

description:
processed data file:
F3.results.csv


title: M11

description:
processed data file:
F3.results.csv


title: 832_6-22


title: M10

description:
processed data file:
F3.results.csv


title: M8

description:
processed data file:
F3.results.csv


title: M7

description:
processed data file:
F3.results.csv


title: Hepatitis B virus infected patient 4 -input

city: Chengdu

first: Dan

last: Xie

state: Sichuan

address: #17 Renmin Road

department: West China Hospital

institute: Sichuan University

data_processing:
No processed data were generated for this Samples. A supplementary sample to the study.
Genome_build: hg19

molecule: other

source_name: Hepatitis B virus infected patient 4

extract_protocol:
Samples for healthy subjects were obtained from Stanford blood center. HCC and BrCa patients were recruited in a Stanford University Institutional Review Board-approved protocol. LuCa, PaCa, GBM, GaCa and CoCa patients were recruited in a Sichuan University Institutional Review Board-approved protocol. Blood was collected into EDTA-coated Vacutainers. Plasma was collected from the blood samples after centrifugation at 1,600 × g for 10 min at 4 °C and 16,000 × g at 10 min at 4 °C. cfDNA was extracted using the Circulating Nucleic Acid Kit (Qiagen). Whole blood genomic DNA was extracted using the DNA Mini Kit (Qiagen) and fragmented using dsDNA Fragmentase (NEB) into average 300 bp. DNA was quantified by Qubit Fluorometer (Life Technologies). Cell-free RNA was extracted using the Plasma/Serum Circulating and Exosomal RNA Purification Kit (Norgen). The extracted cell-free RNA was further digested using Baseline-ZERO DNases (Epicentre) and depleted using Ribo-Zero rRNA Removal Kit (Epicentre) according to a protocol from Clontech.
cfDNA (10 ng) or fragmented genomic DNA (1 µg) spiked with amplicons (0.001 pg of each amplicon per 10 ng DNA) was end repaired, 3’-adenylated and ligated to DNA Barcodes (Bioo Scientific) using KAPA Hyper Prep Kit (Kapa Biosystems) according to the manufacturer’s instructions. Ligated DNA was incubated in a 25 µl solution containing 50 mM HEPES buffer (pH 8), 25 mM MgCl2, 100 µM UDP-6-N3-Glc (Active Motif), and 12.5 U βGT (Thermo) for 2 hr at 37 °C. After that, 2.5 μL DBCO-PEG4-biotin (Click Chemistry Tools, 20 mM stock in DMSO) was directly added to the reaction mixture and incubated for 2 hr at 37 °C. Next, 10 µg sheared salmon sperm DNA (Life Technologies) was added into the reaction mixture and the DNA was purified by Micro Bio-Spin 30 Column (Bio–Rad). The purified DNA was incubated with 0.5 µL M270 Streptavidin beads (Life Technologies) pre-blocked with salmon sperm DNA in buffer 1 (5 mM Tris pH 7.5, 0.5 mM EDTA, 1 M NaCl and 0.2% Tween 20) for 30 min. The beads were subsequently undergone three 5-min washes each with buffer 1, buffer 2 (buffer 1 without NaCl), buffer 3 (buffer 1 with pH 9) and buffer 4 (buffer 3 without NaCl). All binding and washing were done at room temperature with gentle rotation. Beads were then resuspended in water and amplified with 14 (cfDNA) or 9 (blood genomic DNA) cycles of PCR amplification using Phusion DNA polymerase (NEB). The PCR products were purified using AMPure XP beads. Separate input libraries were made by direct PCR from ligated DNA without labeling and capture. Pair-end 75 bp sequencing was performed on the NextSeq instrument.

tag: sample name

value: blood

tag: target molecule

value: cell-free DNA


title: M9

description:
processed data file:
F3.results.csv


title: M5

description:
processed data file:
F3.results.csv


title: M15

description:
processed data file:
F3.results.csv


title: M6

description:
processed data file:
F3.results.csv


title: Breast cancer 3 -input

source_name: Breast cancer 3


title: Breast cancer 2 -input

source_name: Breast cancer 2


title: Colon cancer 4 -input

source_name: Colon cancer 4


title: M2

description:
processed data file:
F3.results.csv


title: M1

description:
processed data file:
F3.results.csv


title: M3

description:
processed data file:
F3.results.csv


title: Colon cancer 3 -input

source_name: Colon cancer 3


title: Colon cancer 2 -input

source_name: Colon cancer 2


title: Colon cancer 1 -input

source_name: Colon cancer 1


title: P12

description:
processed data file:
F2.results.csv

value: pool


title: P7

description:
processed data file:
F1.results.csv


title: P9

description:
processed data file:
F1.results.csv


title: P10

description:
processed data file:
F2.results.csv


title: P11

description:
processed data file:
F2.results.csv


title: P6

description:
processed data file:
F2.results.csv


title: Gastric cancer 5 -input

source_name: Gastric cancer 5


title: Hepatitis B virus infected patient 6 -input

source_name: Hepatitis B virus infected patient 6


title: P3

description:
processed data file:
F1.results.csv


title: Gastric cancer 4 -input

source_name: Gastric cancer 4


title: P2

description:
processed data file:
F1.results.csv


title: P1

description:
processed data file:
F1.results.csv


title: M4

description:
processed data file:
F3.results.csv


title: Gastric cancer 1 -input

source_name: Gastric cancer 1


title: Glioblastoma 4 -input

source_name: Glioblastoma 4


title: Gastric cancer 2 -input

source_name: Gastric cancer 2


title: Glioblastoma 3 -input

source_name: Glioblastoma 3


title: Glioblastoma 1 -input

source_name: Glioblastoma 1


title: P8

description:
processed data file:
F1.results.csv


title: P5

description:
processed data file:
F2.results.csv


title: Pancreatic cancer 7 -input

source_name: Pancreatic cancer 7


title: Pancreatic cancer 2 -input

source_name: Pancreatic cancer 2


title: Pancreatic cancer 4 -input

source_name: Pancreatic cancer 4


title: P4

description:
processed data file:
F2.results.csv


title: Pancreatic cancer 3 -input

source_name: Pancreatic cancer 3


title: Hepatocellular cancer 11 -input

source_name: Hepatocellular cancer 11


title: Hepatocellular cancer 19

source_name: Hepatocellular cancer 19


title: Pancreatic cancer 6 -input

source_name: Pancreatic cancer 6


title: Dex pre-treated 8h LPS DNase rep1

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

data_processing:
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to mm9 using Casava Eland extended
DNase hypersensitive sites were identified as hotspots using DNase2Hotspots.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph, csv

source_name: Dex pre-treated 8h LPS

extract_protocol:
After treatment with Dex and/or LPS, nuclei of BMDMs were isolated, and chromatin were digested with 80 U/ml DNase I (Sigma) for 3 min at 37 ºC and incubated at 55 ºC overnight with 10 µg/ml of RNaseA (Invitrogen) and Proteinase K (Ambion). Digested DNA fragments were purified using phenol-chloroform and enriched by size selection over sucrose gradient. DNA fragments between 100 bp and 500 bp were precipitated and dissolved in nuclease free H2O.
Sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 51 bp single-end sequencing on Illumina HiSeq2000.

treatment_protocol: Primary macrophages derived from bone marrow were stimulated with lipopolysaccharide and/or Dex for the indicated number of hours.

tag: strain

value: Bone marrow derived macrophages

value: Dex pre-treated 8h LPS


title: 8h LPS DNase rep2

source_name: 8h LPS

value: 8h LPS


title: Hepatocellular cancer 10 -input

source_name: Hepatocellular cancer 10


title: Dex pre-treated 8h LPS DNase rep2


title: Dex late-treated 8h LPS DNase rep1

source_name: Dex late-treated 8h LPS

value: Dex late-treated 8h LPS


title: Hepatocellular cancer 7 -input

source_name: Hepatocellular cancer 7


title: Dex late-treated 8h LPS DNase rep2


title: LPS+Dex/DSG+FA GR ChIP

data_processing:
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to mm9 using Casava Eland extended
ChIP-seq binding sites were identified as hotspots after adjustment using the input DNA control.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph, csv

source_name: LPS+Dex/DSG+FA GR

extract_protocol:
For RelA ChIP, BMDMs were subject to crosslinking with 1% formaldehyde for 10 minutes at room temperature. For GR ChIP, we used a dual crosslinking method (Uhlenhaut et al., 2013) to detect both tethered and directly bound chromatin. BMDMs were subject to crosslinking with 2mM disuccinimidyl glutarate (DSG) for 30 min followed by 1% formaldehyde for 10 min at room temperature. After crosslinking, chromatin was isolated from about 4 × 10^7 cells, which allows 2 to 3 different immunoprecipitations per sample at a time, and then processed as follows. The lysis buffer to shear the chromatin contained 0.5% SDS, 10 mM EDTA (pH 8), 50 mM tris-HCl (pH 8), and proteinase inhibitor cocktail. Sonication was performed to shear the chromatin to generate DNA fragments with a size range of 400 to 500 base pairs. The sheared chromatin samples were diluted 1:5 in dilution buffer (0.01% SDS, 1.1% Triton-X, 1.2 mM EDTA (pH 8), 20 mM tris-HCl (pH 8), 167 mM NaCl, and proteinase inhibitor cocktail). For each ChIP, 200 µg chromatin DNA was precipitated with antibody coated bead complexes (Dynabeads Protein A for RelA ChIP; anti-IgG paramagnetic beads for GR ChIP, Invitrogen).
sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 51 bp single-end sequencing on Illumina HiSeq2000.

value: LPS+Dex/DSG+FA

tag: chip antibody

value: GR (MA1-510, Thermo Fisher Scientific) and anti-IgG paramagnetic beads


title: Hepatocellular cancer 3 -input

source_name: Hepatocellular cancer 3


title: Dex/DSG+FA GR ChIP

source_name: Dex/DSG+FA GR

value: Dex/DSG+FA


title: Glioblastoma 2 -input

source_name: Glioblastoma 2


title: Untreated input genomic DNA (control for RelA ChIP)

value: Untreated


title: Hepatocellular cancer 2 -input

source_name: Hepatocellular cancer 2


title: Dex 3h pre, 8h LPS RelA ChIP

source_name: Dex 3h pre, 8h LPS RelA

value: Dex 3h pre, 8h LPS RelA

value: RelA (Ab7970, Abcam) and Dynabeads Protein A


title: Dex late, 8h LPS RelA ChIP

source_name: Dex late, 8h LPS RelA

value: Dex late, 8h LPS RelA


title: Pancreatic cancer 1 -input

source_name: Pancreatic cancer 1


title: Dex 3h pre, 0h LPS RelA ChIP

source_name: Dex 3h pre, 0h LPS RelA

value: Dex 3h pre, 0h LPS RelA


title: Dex 3h pre, 3h LPS RelA ChIP

source_name: Dex 3h pre, 3h LPS RelA

value: Dex 3h pre, 3h LPS RelA


title: Lung cancer 14 -input

source_name: Lung cancer 14


title: Lung cancer 12 -input

source_name: Lung cancer 12


title: 3h LPS RelA ChIP

source_name: 3h LPS RelA

value: 3h LPS RelA


title: 0h LPS RelA ChIP

source_name: 0h LPS RelA

value: 0h LPS RelA


title: Lung cancer 15 -input

source_name: Lung cancer 15

value: blood

value: cell-free DNA


title: Lung cancer 11 -input

source_name: Lung cancer 11


title: Dex 3h pre, 10h LPS rep2

data_processing:
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to mm9 using Casava Eland extended
Transcript levels were quantified using Tophat and Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: Dex 3h pre, 10h LPS

extract_protocol:
Total RNA was isolated from approximately 1x10e6 cells by using an RNAeasy Mini Kit (Qiagen).
Sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 101 bp paired-end sequencing on Illumina HiSeq2000.

value: Bone marrow derived macrophages

value: Dex 3h pre, 10h LPS


title: Pancreatic cancer 5 -input

source_name: Pancreatic cancer 5


title: Dex 3h pre, 4h LPS rep2

source_name: Dex 3h pre, 4h LPS

value: Dex 3h pre, 4h LPS


title: Dex late, 10h LPS rep1

source_name: Dex late, 10h LPS

value: Dex late, 10h LPS


title: Lung cancer 13 -input

source_name: Lung cancer 13


title: Dex 3h pre, 0h LPS rep1

source_name: Dex 3h pre, 0h LPS

value: Dex 3h pre, 0h LPS


title: Lung cancer 10 -input

source_name: Lung cancer 10


title: Dex late, 10h LPS rep2


title: 8h LPS DNase rep1

source_name: 8h LPS

value: 8h LPS


title: Dex 3h pre, 10h LPS rep1


title: Lung cancer 8 -input

source_name: Lung cancer 8

value: genomic DNA


title: 10h LPS rep2

source_name: 10h LPS

value: 10h LPS


title: 4h LPS rep2

source_name: 4h LPS

value: 4h LPS


title: 0h LPS rep2

source_name: 0h LPS

value: 0h LPS


title: Lung cancer 6 -input

source_name: Lung cancer 6


title: 10h LPS rep1


title: Dex 3h pre, 4h LPS rep1


title: 8h LPS RelA ChIP

source_name: 8h LPS RelA

value: 8h LPS RelA

value: RelA (Ab7970, Abcam) and Dynabeads Protein A


title: Lung cancer 5 -input

source_name: Lung cancer 5


title: 4h LPS rep1


title: Lung cancer 9 -input

source_name: Lung cancer 9


title: 0h LPS rep1


title: Lung cancer 7 -input

source_name: Lung cancer 7


title: healthy control 1 -input

source_name: healthy control 1


title: healthy control 3 -input

source_name: healthy control 3


title: RNA-Seq CTRL2

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

data_processing:
RNA-seq data analysis: The generated fastq files were aligned to the UCSC mouse reference genome assembly mm9 using TopHat. The TopHat program used high-throughput short read aligner Bowtie to align the reads to the reference genome. Differential expression test between different groups was performed with Cuffdiff module, and genes with adjusted p-value < 0.05 were selected as differentially expressed genes. The GTF annotation file for UCSC mm9 was used for gene annotation.
Genome_build: mm9
Supplementary_files_format_and_content: differential expression statistics table format for RNA-Seq

source_name: mouse primary cortical/hippocampal neuron

growth_protocol: Primary neuronal culture was prepared from mouse embryos E15 and grew with Neurobasal supplemented with 2% B27, 1x Glutamax and Penisilin/Streptmycin for 17days.

extract_protocol:
Total RNA was extracted using Rneasy Plus Kit (Qiagen).
RNASEQ library was constructed using Illumina TruSeq RNA Prep Kit.

treatment_protocol: The culture was treated with 1uM AraC at DIV5 and transduced with Lenti-virus expressing shRNAs at DIV12.

value: primary neurons

value: control


title: RNA-Seq SP3_KD1

value: Sp3 shRNAs


title: RNA-Seq SP3_KD2


title: RNA-Seq HDAC2_KD1

value: HDAC2  shRNAs


title: Lung cancer 2 -input

source_name: Lung cancer 2

value: blood

value: cell-free DNA


title: healthy control 7 -input

source_name: healthy control 7


title: Lung cancer 4 -input

source_name: Lung cancer 4


title: RNA-Seq CTRL1


title: healthy control 6 -input

source_name: healthy control 6


title: RNA-Seq HDAC2_KD2


title: Lung cancer 1 -input

source_name: Lung cancer 1

value: cell-free RNA


title: 2221rocA B

description: Biological replicate

data_processing:
CLC Genomics Workbench version 7.5.1 RNA-seq was used for basecalling and aligning the sequence reads to the MGAS5005 genome (CP000017).
Parameters for alignment were set up:  Similar fraction=0.8, Length fraction=0.8, Mismatch cost=2, Insertion cost=3, deletion cost=3.
Normalization was performed to overall sequencing depth using total mapped reads data.
Statistical significance was tested using Kal’s Z-test with a false-discovery rate correction.
Genome_build: NC_007297
Supplementary_files_format_and_content: Excel file containing columns for the gene name ,gene start nucleotide number, gene stop nucleotide number, Kal's Z-test with FDR correction value for each of the three comparisons, normalized mean for each strain, and expression ratios for each of the three comparisons

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

extract_protocol:
Total RNA was isolated and rRNAs were depleted using the Ribo-Zero Gram-Positive rRNA Removal Kit (Epicentre).
The rRNA depleted RNA was used to generate cDNA libraries using the ScriptSeq kit (Epicentre).  Briefly, RNA was fragmented, cDNA was synthesized using random hexamers containing a 5′ tagging sequence, the RNA was hydrolyzed, and the cDNA was tagged at the 3′ end.  A limited number of PCR cycles (n=14) were used to amplify the libraries via the 5′ and 3′ tags (the libraries were barcoded by using different primers), and the libraries size-selected (170 to 300 bp).  The size-selected and barcoded libraries were run on an Illumina HiSeq flowcell.

value: rocA mutant of MGAS2221


title: GW9662 PPARg antagonist 2

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

institute: ETH Zürich

description: PPARg antagonist (GW9662)

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped and annotated to GRCm38.PatchesSkipped Version 2015-06-2 STAR with cmdOptions --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Normalized Counts were calculatd using EdgeR.
Genome_build: GRCm38.PatchesSkipped Version 2015-06-2
Supplementary_files_format_and_content: tab-delimited text files, the processed data file includes Gene Identifier, gene name, transcript id, type, description, hgnc symbol, width, gc, GO BP, GO CC, GO MF, log2 Ratio, gfold (log2 Change), pValue, fdr, normalized count (between-sample-normalization)

source_name: Spleen

growth_protocol: CD4+ T cells were isolated from mouse spleen using MACS and FACS sorting

extract_protocol:
cells were collected into Trizol (life technologies), phase separation was achieved by addition of chloroform (Sigma-Aldrich) and RNA was precipitated from the aqueous layer with isopropanol (Sigma-Aldrich) using glycogen (Roche) as a carrier.
The TruSeq RNA Stranded Sample Prep kit (Illumina) was used to construct the sequencing libraries. In brief, total RNA samples (100 ng) were poly-A enriched and reverse transcribed into double-stranded cDNA. TruSeq adapters were then ligated to double-stranded cDNA. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR and subsequently sequenced on the Illumina NextSeq 500 in single-end mode, 150 cycles at the Functional Genomics Center Zurich (FGCZ).

treatment_protocol: Cells were cultured with 100nM gp61 peptide 100ng/ml IL-4 and 20ug/ml aIFNg and dendritic cells for 4 days in the presence of the antagonist or vehicle

value: CD4+ T cell

tag: agent

value: PPARg antagonist (GW9662)


title: Comp B

description: Biological replicate

value: rocA-complemented derivative


title: MGAS2221 B

description: Biological replicate

value: Parental M1 isolate


title: Lung cancer 3 -input

source_name: Lung cancer 3


title: Comp A


title: GW9662 PPARg antagonist 1

description: PPARg antagonist (GW9662)


title: control Flt3- LSKs (13461)

city: Nutley

first: Hai-Hui

last: Xue

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation

institute: Hackensack University Medical Center

description: Sample 13461

data_processing:
Raw Reads were mapped to the reference mouse genome using a protocol from Trapnell et al., Bioinformatics. In short, Only uniquely reads with fewer than 2 mismatches were used for downstream analysis.
Transcripts are assembled  and FPKM (Fragments Per Kilobase of Transcripts per Million mapped reads) were calculated by Cufflinks Trapnell et al., Nature Biotechnology. Gene-level FPKM values were computed by Cufflinks.
Differential expressed genes were obtained by using edgeR Robinson et al., Bioinformatics.
The unique reads were sorted and indexed by using samtools. Then the bedgraph is generated with the number of aligned reads in each window (size 50bp) for display on the UCSC browser.
Genome_build: mm9
Supplementary_files_format_and_content: HSC_FPKM.txt includes FPKM values for each Sample
Supplementary_files_format_and_content: bedgraph files: col1 is chromosome, col2/3 are the chromosome positions of window (50bp) spanning genome, and col4 is the number of algined reads in the window.

source_name: long- and short-term HSCs

extract_protocol:
The HSCs were sorted from mouse BM cells and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

value: wild type

value: Lineage-negative bone marrow hematopoietic stem cells

tag: cell phenotype


title: control Flt3- LSKs (13460)

description: Sample 13460


title: Tcf1/Lef1-deficient Flt3-LSKs (13463)

description: Sample 13463


title: Tcf1/Lef1-deficient Flt3-LSKs (13462)

description: Sample 13462


title: Vehicle control 2

description: Vehicle control (DMSO)

value: Vehicle control (DMSO)


title: 2221rocA A

tag: genotype


title: Vehicle control 1

description: Vehicle control (DMSO)

tag: cell type


title: MGAS2221 A


title: FMPCGSCbkm120nvp2

status: Public on Aug 07 2017

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
Reads were mapped to the mm10 murine genome and USCS transcriptome annotation (obtained from Illumina iGenomes) using Tophat 2 and uniquely mapped reads associated with each gene were counted using HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited table of uniquely aligned read counts for each gene in the annotation.

molecule: polyA RNA

source_name: Nf1(flox/-), Pten(flox/+), GFAP-Cre mouse cell line

growth_protocol: Optic glioma stem cells (o-GSCs) were isolated from optic glioma mouse models. For NVP-BKM120 treatments, cells were cultured in neural stem cell medium without EGF and bFGF for 1 hour, followed by treatment with DMSO (vehicle) or 0.2 μM NVP-BKM120 for 5 hours at 37°C, and cells harvested for RNA isolation or western blotting.

extract_protocol:
Tissue samples or cell lines were homogenized in Trizol and total RNA was extracted using Trizol and isopropanol precipitation. Poly(A)+ mRNA was then isolated from each total RNA sample using streptavidin-coated superparamagnetic beads (Dynabeads, Life Technologies) coated in biotinylated LNA-oligo(dT) (Exiqon).
Purified poly(A)+ mRNA from each sample was reverse transcribed and Illumina sequencing libraries were enriched usign the SMARTer Stranded RNA-Seq kit (Clontech). The resulting libraries were sequenced on an Illumina HiSeq 2500 or NextSeq 500 with single-end 100-base or 75-base reads, respectively.
template-switching RNA-Seq with random primers

treatment_protocol: 50 mg/kg/day minocycline (Sigma-Aldrich; PBS, vehicle) was delivered by intraperitoneal (i.p.) injection 5 days/week for two weeks. 5 mg/kg/day rapamycin (Selleckchem; 5.2% Tween 80/5.2% polyethylene glycol 400 as vehicle) was administered by i.p. injection 5 days/week for two weeks. 20 mg/kg/day NVP-BKM120 (Selleckchem; N-methyl-2-pyrrolidone/ polyethylene glycol 300 (10/90v/v) as vehicle) was delivered by oral gavage 5 days/week for two weeks [40]. 60 mg/kg/day carboplatin (Sigma-Aldrich; PBS as vehicle) was administered by i.p. injection every other day for 1 week.

tag: drug

tag: time

value: 5 hours

tag: drug concentration

tag: cell line

value: optic glioma cell line


title: FMPCGSCdmso1


title: FMPCGSCdmso2


title: FMPCGSC1


title: FMPCGSC2


title: FMCGSCdmso4

source_name: Nf1(flox/-), GFAP-Cre mouse cell line


title: FMCmin5

source_name: Nf1(flox/-), GFAP-Cre mouse

value: minocycline

value: 5 days/week, 2 weeks

value: 50 mg/kg/day

value: optic glioma tissue


title: FMCGSCdmso3


title: FMCmin4


title: FMCGSCdmso2


title: FMCmin7


title: FMPCbkm120nvp2

source_name: Nf1(flox/-), Pten(flox/+), GFAP-Cre mouse

value: 20 mg/kg/day


title: FMCmin8


title: FMCmin3


title: FMCmin6


title: FMCmin9


title: FMCmin2


title: FMCrapa6

value: rapamycin

value: 5 mg/kg/day


title: FMCrapa5


title: FMCrapa2


title: FMCrapa4


title: FMCrapa3


title: FMCrapa1


title: FMPCGSCbkm120nvp1


title: FMCcarbo5

value: carboplatin

value: alternating days, 1 week

value: 60 mg/kg/day


title: FMPCbkm120nvp3


title: FMCGSCdmso1


title: FMCcarbo3


title: FMCcarbo4


title: FMCcarbo2


title: FMPCbkm120nvp1


title: FMCcarbo1


title: F18C5

source_name: Nf1(c.2041C>T); p.R681X; Nf1(flox/R681X); GFAP-Cre mouse


title: F18C2


title: F18C1


title: FMCmin1


title: FMPC4


title: FMPC2


title: FMPC3


title: FMOC6

source_name: Nf1(flox/-), OLIG2-Cre mouse


title: FMOC3


title: FMOC5


title: FMOC1


title: FMOC2


title: FMC11


title: FMC10


title: FMPC5


title: FMC8


title: FMC7


title: FMC6


title: quadAvrRpt2.flg22+Ed.300min.rep3

city: St Paul

first: Fumiaki

last: Katagiri

state: Minnesota

address: 1500 Gortner Ave

department: Dept of Plant and Microbial Biology

institute: Univ of Minnesota

data_processing:
bcl2fastq version 2.17.1.14 was used for demultiplexing and fastq file creation.
The 5-base UMI and 3-base "GGG" were trimmed from the beginning of the read. In addition, polyA from the end of the read were also trimmed.
The trimmed reads were mapped onto the Arabidopsis TAIR10 gene model using STAR version 2.4.2a.
The STAR parameters used different from the defaults were: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterScoreMinOverLread 0 --outFilterMatchNmin 0
The uniquely mapped reads were counted for each gene with no distinction among the transcript variants.
Per gene, the total read count and the UMI-based read count were weighted-averaged and rounded to an integer value, which we call the read count per gene.
Since this was 3SEQ data, no correction of the read count for the transcript length was made.
Genome_build: Arabidopsis thaliana TAIR 10
Supplementary_files_format_and_content: It is a csv file of the read count per gene for each sample. The gene names (in the AGI code) are shown as the row names, and the sample titles are shown as the column names.
Supplementary_files_format_and_content: The genes that had at least one read count across the samples are included in the processed data file.

organism: Arabidopsis thaliana

source_name: Adult leaves

growth_protocol: Four-week old plants grown at 22C with 75%RH and a 12-hr light/12-hr dark cycle were used.

extract_protocol:
Total RNA was extracted from the frozen pulverized leaf tissue using Trizol.
Smart-3SEQ, which is a modified 3SEQ method, was used (Foley et al., manuscript in preparation). The first 5 bases of the sequence read is Unique Molecular Identifier (UMI), which helps determining PCR duplicates.
RNA-tag-SEQ: The following "GGG" was used for reverse transcriptase template switching. Thus, total 8 bases from the beginning of the read need to be trimmed for an actual mRNA sequence.

treatment_protocol:
Two leaves per plant selected from leaf numbers 7-9 were infiltrated with one of four treatment solutions: (1) Mock (0.1% ethanol); (2) 1 uM flg22; (3) 10 uM estradiol(Ed), 0.1% ethanol; (4) 1 uM flg22, 10 uM Ed, 0.1% ethanol.
Plants were given treatment 3 to 4 hours after the subjective dawn. The infiltrated leaves from two plants were harvested, pooled, and flash-frozen the indicated minutes after treatment.

tag: ecotype

value: dde2 ein2 pad4 sid2 Ed-AvrRpt2

value: Adult leaves

tag: minutes


title: quadAvrRpt2.flg22+Ed.180min.rep3


title: FMC9


title: quadAvrRpt2.flg22+Ed.120min.rep3


title: F18C4


title: quadAvrRpt2.flg22+Ed.60min.rep3


title: F18C3


title: quadAvrRpt2.flg22+Ed.0min.rep3


title: quadAvrRpt2.Ed.180min.rep3

value: Ed


title: FMPC1


title: quadAvrRpt2.Ed.60min.rep3


title: quadAvrRpt2.Ed.0min.rep3


title: quadAvrRpt2.Ed.120min.rep3


title: quadAvrRpt2.flg22.120min.rep3


title: quadAvrRpt2.flg22.60min.rep3


title: quadAvrRpt2.flg22.300min.rep3


title: quadAvrRpt2.flg22.0min.rep3


title: quadAvrRpt2.flg22.180min.rep3


title: quadAvrRpt2.Mock.180min.rep3

value: Mock


title: quadAvrRpt2.Mock.120min.rep3


title: FMOC4


title: quadAvrRpt2.Mock.60min.rep3


title: quadAvrRpt2.flg22+Ed.300min.rep2


title: quadAvrRpt2.Mock.0min.rep3


title: quadAvrRpt2.flg22+Ed.120min.rep2


title: quadAvrRpt2.flg22+Ed.180min.rep2


title: quadAvrRpt2.flg22+Ed.60min.rep2


title: quadAvrRpt2.Ed.180min.rep2


title: quadAvrRpt2.flg22+Ed.0min.rep2


title: quadAvrRpt2.Ed.300min.rep3


title: quadAvrRpt2.Ed.0min.rep2


title: quadAvrRpt2.Ed.60min.rep2


title: Total Tissue TM3 14 days

first: El-ad David

last: Amir

address: 1470 Madison Avenue

department: Oncological Sciences

institute: Mount Sinai Hospital, New York

data_processing:
Reads were mapped to the mouse genome using STAR
Read counts were generated using subread

source_name: total colonic tissue

extract_protocol:
RNA was purified using phenol/chloroform extraction. Quantification was performed using the Qubit RNA assay kit HS according to the manufacturers protocol.
RNA was sequenced at the Broad Technology Services using the High-throughput eukaryote 3' DGE library

treatment_protocol: Animals were colonized with 2 x10^6 FACS sorted T.mu/mouse

tag: tissue type

value: total colonic tissue

tag: litter

tag: inoculum

value: Tritrichomonas musculis

tag: days after inoculation


title: quadAvrRpt2.flg22.180min.rep2

tag: tissue

tag: treatment


title: Total Tissue TM4 48 days

tag: sample name


title: Total Tissue TM3 3 days


title: Total Tissue TM3 48 days


title: quadAvrRpt2.Mock.300min.rep3


title: quadAvrRpt2.flg22.120min.rep2


title: Total Tissue TM2 14 days


title: quadAvrRpt2.flg22.60min.rep2


title: quadAvrRpt2.flg22.0min.rep2


title: Total Tissue TM2 3 days


title: quadAvrRpt2.Mock.300min.rep2


title: quadAvrRpt2.Mock.180min.rep2


title: quadAvrRpt2.Mock.120min.rep2


title: Total Tissue TM1 14 days


title: Total Tissue TM1 48 days


title: quadAvrRpt2.Ed.300min.rep2


title: Total Tissue TM1 3 days


title: quadAvrRpt2.Mock.60min.rep2


title: quadAvrRpt2.flg22+Ed.300min.rep1


title: Total Tissue C-L4 48 days

value: none (control)


title: quadAvrRpt2.flg22.300min.rep2


title: quadAvrRpt2.Ed.120min.rep2


title: Total Tissue C-L3 3 days


title: quadAvrRpt2.flg22+Ed.180min.rep1


title: Total Tissue C-L3 14 days


title: quadAvrRpt2.flg22+Ed.120min.rep1


title: Total Tissue C-L3 48 days


title: quadAvrRpt2.flg22+Ed.60min.rep1


title: Dex 3h pre, 0h LPS rep2

source_name: Dex 3h pre, 0h LPS

tag: strain

value: Bone marrow derived macrophages

value: Dex 3h pre, 0h LPS


title: Total Tissue C-L2 14 days


title: Total Tissue C-L2 48 days


title: Total Tissue TM2 48 days


title: quadAvrRpt2.flg22+Ed.0min.rep1


title: Total Tissue C-L2 3 days


title: quadAvrRpt2.Ed.300min.rep1


title: Total Tissue C-L1 48 days


title: Total Tissue C-L1 3 days


title: quadAvrRpt2.Ed.180min.rep1


title: Epith TM4 48 days

source_name: Colonic epithelial cells

value: Colonic epithelial cells


title: untransfected_3

city: London

first: Emily

last: Saunderson

address: Charterhouse Square

institute: Barts Cancer Institute

description: RNA-seq_primary_myoepithelial_cells_3A3L_delta_untransfected_raw_reads.txt

data_processing:
Sequencing reads were mapped to GRCh37.EBVB95-8wt.ERCC using bwa
Data were processed using SeqMonk and the RNA-seq quality controls and analysis pipeline to generate Reads Per Kilobase of exon per Megabase of library size (RPKM). All isoforms were kept separate nad the number of reads falling in the exons of this transcript were counted and normalized by the size of the transcript and by the size of the library.
Genome_build: GRCh37.EBVB95-8wt.ERCC
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample

source_name: Primary breast myoepithelial cell

extract_protocol:
RNA was extracted as above, before mRNA was isolated from 1.5 µg of total RNA using mRNA DIRECT (Thermo Fisher Scientific) and fragmented with RNA fragmentation reagent (Thermo Fisher Scientific). First strand cDNA synthesis was performed with SuperScript III First-Strand Synthesis System and 3 μg/μl random hexamers (Thermo Fisher Scientific) followed by second strand synthesis with DNA polymerase I and RNase H.
After purification, the double stranded cDNA was ligated to in house designed adapters (based on TruSeq Indexed adapters (Illumina)) using NEBNext Ultra II (NEB) followed by 15 cycles of amplification and library purification.

value: Breast

value: Myoepithelial

tag: transfection

value: untransfected


title: Epith TM3 3 days


title: Epith TM3 14 days


title: quadAvrRpt2.Ed.120min.rep1

tag: genotype


title: Epith TM2 48 days


title: Epith TM3 48 days


title: untransfected_2

tag: cell type


title: dCas9 3a3l_3

value: dCas9 3a3l


title: quadAvrRpt2.Ed.60min.rep1


title: quadAvrRpt2.Ed.0min.rep1


title: Epith TM2 14 days


title: Epith TM2 3 days


title: Epith TM1 3 days


title: PRO-Seq-Flavo

city: Iowa City

first: David

last: Price

state: IA

address: 500 Newton Road

department: Biochemistry

institute: University of Iowa

data_processing:
Library strategy: PRO-Seq
Sequencing adapters were trimmed using trim_galore --small_rna --paired --retain_unpaired
Paired sequences were aligned to hg19 using nvBowtie and a NVIDIA Tesla K40c (--overlap --no-mixed)
Bedgraphs were generated using bedtools genomecov
Bedgraphs were normalized to the number of reads that mapped over the 45S gene (NT_167214.1: 105424..118780)
Bedgraphs were converted to bigwig using kentUtils
Genome_build: hg19
Supplementary_files_format_and_content: bigwigs contain depth-adjusted PRO-Seq pileups

source_name: Adherent HeLa cells

growth_protocol: Adherent HeLa cells were grown at 37°C and 5% CO2 to 80% confluency in T150 flasks in 30 ml DMEM supplemented with 10% FBS

extract_protocol: All PRO-Seq protocols are detailed in the manuscript. Please consult the manuscript and Mahat, et al. 2016 (10.1038/nprot.2016.086)

treatment_protocol: 1 µM Flavopiridol or 0.1% DMSO were added to media 1 h before harvest as indicated

value: HeLa

value: 1 h 1 µM flavopiridol

tag: antibody


title: dCas9 3a3l_2


title: Epith TM1 48 days


title: PRO-Seq-DMSO


title: dCas9 3a3l_1


title: Epith TM1 14 days


title: Epith C-L4 48 days


title: Total Tissue C-L1 14 days


title: quadAvrRpt2.flg22.180min.rep1


title: Epith C-L3 14 days


title: Epith C-L3 3 days


title: dCas9 3a3l delta_2

value: dCas9 3a3l delta


title: quadAvrRpt2.Mock.0min.rep2

value: dde2 ein2 pad4 sid2 Ed-AvrRpt2


title: quadAvrRpt2.flg22.120min.rep1

value: Adult leaves


title: Epith C-L3 48 days


title: Epith C-L2 3 days


title: dCas9 3a3l delta_1


title: Epith C-L2 14 days


title: quadAvrRpt2.flg22.60min.rep1


title: quadAvrRpt2.flg22.0min.rep1


title: Epith C-L2 48 days


title: quadAvrRpt2.flg22.300min.rep1


title: Epith C-L1 3 days


title: Tassel-RNA-seq

city: Los Angeles

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

description: RPKMtable.txt

data_processing:
[BS-seq] reads were aligned to the AGPv3 genome using BS Seeker2
[BS-seq] If multiple alignments mapped to the same location only one is kept.
[RNA-seq] alignment using Tophat 2.0.4, AGPv3 as library junction
[RNA-seq] Abundance counting using cuffdiff
[RNA-seq] Calculate RPKM by dividing by union length of exons in kilbases and number of reads mapped in millions, as reported by cuffdiff
[RNA-seq] Calculate p-values with edgeR
Genome_build: AGPv3
Supplementary_files_format_and_content: [.CGmap] BS-seq processed data file is in text format.  column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.
Supplementary_files_format_and_content: [.txt] RNA-seq processed data file includes RPKM values for each sample

organism: Zea mays

source_name: B73 Tassel primordium

growth_protocol: For shoot sample, seeds were grown in the incubator in the dark on wet paper towels. After 4-5 days, coleoptile-stage shoots were excised and stored at -80°C. For tassel, plants were grown in the field until the V6 stage. Tassel primordia (~0.5 cm) were excised and stored at -80.

extract_protocol:
Total RNA was isolated from samples using TRIzol (Invitrogen), and subsequently purified with the RNeasy kit (Qiagen), both according to the manufacturer’s protocol.
RNA was quantified with the Qubit RNA BR Assay and 0.4 μg of purified RNA was used as starting material. The library construction was carried out with the Illumina TruSeq RNA Sample Preparation kit following the manufacturer's instructions. Libraries were sequenced with NextSeq500 System (Illumina).

value: 0.5-cm tassel primordium

tag: inbred line

tag: enzyme


title: Epith C-L1 48 days


title: quadAvrRpt2.Mock.300min.rep1

value: Mock


title: Shoot-RNAseq

description: RPKMtable.txt

source_name: B73 shoots

value: Coleoptile-stage shoots


title: quadAvrRpt2.Mock.180min.rep1


title: dCas9 3a3l delta_3


title: quadAvrRpt2.Mock.120min.rep1


title: quadAvrRpt2.Mock.60min.rep1


title: Epith C-L1 14 days