title: SG200Δsee1 HTT

city: Cologne

first: Corinna

last: Ernst

address: Kerpener Straße 34

department: University Hospital Cologne

institute: University of Cologne

description: 3 biological replicates

data_processing:
Reads were mapped using Bowtie v2.2.9 and TopHat v2.1.1 against a merged reference genome consisting of Zea mays B73 RefGen v3 and Ustilago maydis 521 v2.0
Reads mapping to Zea mays B73 were filtered out for further processing steps.
Fragments per kilobase per million reads mapped (FPKM) values were determined with Cufflinks v2.2.1 following the standard protocol described in Trapnell et al., 2012.
Differentially expressed genes were determined via DESeq2 v1.14.1 using Wald test statistics, setting the cutoff at 1.5-fold.
Genome_build: Zea mays B73 RefGen v3
Genome_build: Ustilago maydis 521 v2.0
Supplementary_files_format_and_content: Ustilago_gene_exp.diff file is a tab-delimited text file genrated by Cufflinks v2.2.1.
Supplementary_files_format_and_content: tsv files are tab-separated text files were genrated using the results() function of DESeq2 v1.14.1.

organism:
Zea mays
Mycosarcoma maydis

source_name: SG200Δsee1-infected hypertrophic mesophyll tumour cells

growth_protocol: Zea mays plants were grown in controlled condition (14 hr/10 hr light/dark cycle; 28°C/20°C) and used for infection with U. maydis. The maize line Early Golden Bantam (Olds Seeds, Madison, WI, USA) was used for infections.

extract_protocol:
One single infected/mock infected leaf was used per sample while three individual plants were analyzed per treatment/infective strain four days post infection.  14 µm transverse sections were cut at -20 °C using a cryostat (CM1900, Leica, Nussloch, Germany) microscopy glass slides. Tissue sections were immediately incubated in 50 % methanol for 1 min, followed by a methanol dehydration series (70 %, 1 min, 80 %, 1 min, 90 %, 1 min, 100 % methanol, 1 min), followed by 5 min immersion in xylene. Tissue sections were afterwards air-dried and subsequently used for LCM analysis. 1800-2000 cells were captured per sample using the PALM MicroBeam system (Zeiss, Jena, Germany) and adhesive caps (AdhesiveCap 200 opaque, Zeiss, Göttingen, Germany). For RNA extraction from dissected cells Arcturus® PicoPure® RNA isolation kit was used.
Considering the very low amount of input material, we performed a pre-amplification using the Ovation® RNA Seq System V2 (NuGen, San Carlos, CA, USA).  2 ng of total RNA went in the generation of first strand cDNA using both poly(T) and random primers, followed by second strand synthesis and isothermal strand-displacement amplification. For library preparation we used the Illumina Nextera® XT DNA sample preparation protocol (Part # 15031942 Rev. C, Illumina, San Diego, CA, USA) starting with an input of 1 ng cDNA.

treatment_protocol: U. maydis strains SG200 (Kämper et al., 2006) and SG200 Δsee1 (Redkar et al., 2015) were cultivated in YEPSL (0.4% yeast extract, 0.4% peptone, and 2% sucrose) at 28 °C with shaking at 200 rpm until OD600 of 0.8 was reached. After centrifugation at 900 xg for 5 min, cells were adjusted to OD600= 1 in H2O and injected into the whorls of maize seedlings. Maize plants were infected 7 d after sowing at the three-leaf stage.

tag: tissue


title: 07_P47_CTX_cKO_DJ4

status: Public on Feb 13 2018

type: SRA

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

country: USA

institute: UT Southwestern Medical Center

library_source: transcriptomic

data_processing:
Single-end reads (quality checked, filtered and adapter trimmed) were aligned to reference sequences (mm10 from UCSC) using STAR allowing three mismatches.
RNA-seq counts were quantified using HTSeq python suite. Reference gene model (mm10 GTF from Gencode vM11) were provided to assist the counting.
RNA-seq CPM values were then quantified using EdgeR (R package).
Gene-level CPM quantifications were used for all downstream processing.
Genome_build: UCSC Mouse GRCm38 / mm10
Supplementary_files_format_and_content: tab-delimited text file with CPM values for genes (rows) across samples (columns).

molecule: polyA RNA

organism: Mus musculus

source_name: Cortex

extract_protocol:
Brain regions were dissected out and immediately flash frozen in liquid nitrogen. Total RNA was then purified from these samples, using an mRNeasy kit (Qiagen), following the manufacturer's instructions.
mRNA was purified via poly(A) selection from 2ug of total RNA. Purified mRNA was then utilized to generated cDNA libraries using previously published protocols (Takahashi et al., 2015).
Pooled libraries (at a final concentration of 2nM) were sequenced on a NextSeq 500 sequencer (Illumina) by the McDermott Sequencing Core at the UT Southwestern Medical Center.

tag: age

value: postnatal day 47

tag: genotype

value: conditional knock-out

tag: hemisphere

value: left


title: 06_P47_CTX_cKO_DJ2


title: JS_F04_3

city: Fuzhou

first: Xuanyang

last: Chen

address: 15,Shangxiadian road,cangshan district

country: China

institute: Fujian Agriculture and Forestry University

data_processing:
Basecalls performed using CASAVA version 1.7
The clean reads with high quality were obtained by removing reads containing adapter, reads that containing N (indefinite base) higher than 10% and reads with low quality from raw reads
Transcriptome assembly was accomplished  using Trinity (version:r20140413p1).
The level of gene expression was determined by normalizing the number of unambiguous tags in each library to expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM). For the samples with biological replicates, differential expression analysis of two groups was performed using the DESeq R package (1.10.1)(qvalue< 0.005 &|log2(foldchange)| > 1)
Genome_build: Trinity.fasta
Supplementary_files_format_and_content: Fastq files of clean data were generated including error rate and Q20, Q30

molecule: total RNA

organism: Ipomoea batatas

source_name: sweet potato_JS_F04

growth_protocol: The sweet potato seedlings were field grown for at least 28 d until they were cut and used as experimental material. After treatment the seedlings were grown in growth chambers at 28°C for 24 hours,

extract_protocol:
Total RNA was isolated from each sample respectively using RNAprep pure plant kit (polysaccharides and polyphenolics-rich, Tianen biotech,Beijing,China), according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. mRNA was purified and cDNA synthesis was subsequently performed. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structurewere ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system. Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500 platform and paired-end reads were generated

treatment_protocol: Seedling stems were cut freshly with 20 cm long, grew in a glass bottle containing conidial solutions of 1 × 10^7 conidia/mL of Fob-07 (strong pathogenic),or of Fob-04 (nonpathogenic), respectively. Control was set in which the seedling grew in the water.

tag: cultivar

value: JinShan 57(JS57)

tag: resistance phenotype

value: highly resistance to Fusarium wilt

tag: inoculated with

value: water (control)

tag: timepoint

value: 24 hours after inoculation

value: stem


title: JS_F04_1


title: JS_F07_3

source_name: sweet potato_JS_F07

value: pathogenic F. oxyspurum f.sp.batatas Fo-07


title: JS_F04_2


title: JS_F07_2


title: 10_P47_HIP_CTL_DJ20

source_name: Hippocampus

value: control


title: HPT

country: Germany

description: 3 biological replicates

source_name: SG200-infected bundle sheath tumour cells


title: HTT

description: 3 biological replicates

source_name: SG200-infected hypertrophic mesophyll tumour cells


title: JS_F07_1


title: Unexposed_72_2

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

description: Control

data_processing:
The FASTQ sequence reads were generated using the Illumina Casava pipeline version 1.8.2, initial quality assessment was based on data passing the Illumina Chastity filtering.
Reads containing adapters and/or PhiX control signal were removed
The sequence reads were trimmed using Trimmomatic v0.32
The trimmed reads were aligned against the C. elegans genome using TopHat (v2.0.8) and Bowtie (v2.1.0)
Genome_build: Ensembl, WBcel235.75
Supplementary_files_format_and_content: text file with raw counts

organism: Caenorhabditis elegans

source_name: Whole Worm Culture

growth_protocol: Nematodes were cultured on NGM plates and fed OP50 Escherichia coli lawn at 20oC

extract_protocol:
RNA was extracted from worm pellets using the Direct-zol RNA MiniPrep kit (Zymo Research, R2052) as described by the manufacturer. RNA integrity and quality were analyzed using the Agilent 2100 Bioanalyser (G2938A) before Illumina Sequencing (BaseClear B.V., Leiden, The Netherlands).
Sequencing was carried out using the Illumina TruSeq library preparation kit, sequencing with a minimum of 20 million reads per sample.

treatment_protocol: Synchronized L1 larvae were placed on NGM plates with an OP50 bacterial lawn until L4, and transferred to plates containing the drug of interest for 24 or 72 hours. A final concentration of 100µM was added to the NGM media before pouring. Besides unexposed nematodes, a representative DMSO concentration (0,033%) was used as a control. Bacteria and eggs were removed from the culture using a SEFAR NITEX® 31µM pore mesh (03-31/24) before immediately freezing the samples at -80oC until RNA extraction. 72 hour cultures were moved to fresh plates every day after meshing.

value: whole worm

tag: exposure

value: Unexposed

tag: exposure time

tag: replicate


title: DMSO_24_3

description: Control


title: Unexposed_72_3

description: Control


title: Unexposed_72_1

description: Control


title: DMSO_24_2

description: Control


title: DMSO_24_1

description: Control


title: Unexposed_24_2

description: Control


title: 05_P47_CTX_cKO_DJ1


title: Unexposed_24_1

description: Control


title: Unexposed_24_3

description: Control


title: 04_P47_CTX_CTL_DJ8


title: 59_RT6Y_S23_L002

city: Turku

first: Miriam

last: Goetting

address: Yliopistonmäki

department: Dept of Biology

country: Finland

institute: University of Turku

data_processing:
The base calling was done using bcl2fastq (v. 1.8.4)
Read alignment was done using Tophat (v2.1.0) to  salmon genome reference
Genewise read counts were calculated using subreads package (v. 1.5.1)
Genome_build: ICSASG v2 (International Cooperation to Sequence the Atlantic Salmon Genome from NCBI)
Supplementary_files_format_and_content: files are tab delimited text files containing the genewise read counts for each sample

organism: Oncorhynchus mykiss

source_name: blood

growth_protocol: Blood was sampled from rainbow trout (Oncorhynchus mykiss) by caudal puncture and stored on ice. Blood samples were washed three times in rainbow trout saline (Nikinmaa & Jensen 1992).

extract_protocol:
Erythrocyte samples were  homogenized in TissueLyser (Qiagen, Austin, USA) and RNA was isolated using NucleoZol (Macherey-Nagel).
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047):

treatment_protocol: Density centrifugation of erythrocyte samples followed essentially the procedure described previously (Koldkjaer et al., 2004; Murphy, 1973; Speckner et al., 1989)

value: young

tag: cell type

value: erythrocyte


title: 03_P47_CTX_CTL_DJ7


title: 01_P47_CTX_CTL_DJ3


title: High FLC treated T2

city: Beijing

first: Rongya

last: Yang

state: Beijing

address: 5 Nanmencang

department: Department of Dermatology

institute: PLA Army General Hospital

description:
Sample_13602E_T2YF
Processed data file: T2_FPKM.tsv

data_processing:
FastQC is used to check the read quality.
HiSAT2 2.0.5 is used for read alignment with default parameters.
StringTie 1.2.3 is used for FPKM calling with default parameters.
samtools 1.2 is used for reads pileup.
Genome_build: T2_CBS2479 (GCA_000293215.1), T8_CBS8904 (GCA_000299215.2)
Supplementary_files_format_and_content: *_FPKM.tsv: Gene-level FPKM values in tab-separated text files.

organism: Trichosporon asahii var. asahii CBS 2479

growth_protocol: Two T. asahii strains CBS2479 (T2) and CBS8904 (T8) with high sensitivity to FLC were selected from the laboratory database of the Department of Dermatology, General Hospital of Beijing Military Region. First, both strains were respectively and serially subcultured in potato dextrose agar (PDA) medium with increasing concentrations of FLC for 18 days. Second, cells with induced resistance were serially subcultured in drug free PDA medium for 18 days.

extract_protocol:
A total of 10 samples were selected for RNA-Seq to obtain the genome-wide gene expression patterns. RNA was extracted from cell lines using Trizol reagent (Invitrogen), according to the manufacturer’s protocol.
Libraries were constructed following the Illumina Paired-End Sequencing Library Preparation Protocol. The high quality of mRNA samples was confirmed using Agilent 2100 Bioanalyzer total RNA Chip (Agilent) prior to sequencing.

treatment_protocol: Two T. asahii strains CBS2479 (T2) and CBS8904 (T8) were treated with different doses (μg/ml) of FLC at different days as 0 (day 0), 0.125 (day 1), 0.125 (day2), 1.5 (day3), 1.5 (day4), 3 (day5), 3 (day6), 6 (day7), 6 (day8), 8 (day9), 8 (day10), 12 (day11), 12 (day12), 18 (day13), 18 (day14), 24 (day15), 24 (day16), 36 (day17), 36 (day18). After 18 days, both T. asahii strains with phenotype of FLC resistance were then cultured in FLC free PDA medium for 18 days.

tag: strain/background

tag: flc dose (ug/ml)

tag: cultured days


title: FLC free T2 (short time)

description:
Sample_13602B_T2H
Processed data file: T2_FPKM.tsv


title: 58_RT5O_S15_L001

value: old


title: 58_RT5O_S15_L002


title: 02_P47_CTX_CTL_DJ6


title: 60_RT6O_S31_L001


title: 60_RT6O_S31_L002


title: Wild Type of T2

description:
Sample_13602B_T2
Processed data file: T2_FPKM.tsv


title: 57_RT5Y_S7_L001


title: 56_RT4O_S59_L002


title: 56_RT4O_S59_L001


title: Low FLC treated T2

description:
Sample_13602B_T2Y
Processed data file: T2_FPKM.tsv


title: 55_RT4Y_S52_L002


title: 59_RT6Y_S23_L001


title: FLC free T2 (long time)

description:
Sample_13602B_T2HF
Processed data file: T2_FPKM.tsv


title: 57_RT5Y_S7_L002


title: 55_RT4Y_S52_L001


title: 54_RT3O_S45_L002


title: 53_RT3Y_S38_L001


title: 54_RT3O_S45_L001


title: 52_RT2O_S30_L002


title: 52_RT2O_S30_L001


title: 53_RT3Y_S38_L002


title: A2_120min

city: Urbana

first: Brian

middle: R.

last: Herb

state: IL

address: 2500 IGB, MC-195, 1206 W Gregory Dr

department: Carl R. Woese Institute for Genomic Biology

institute: University of Illinois at Urbana-Champaign

description: Aggressive bee collected 120 min post interaction

library_source: genomic

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).
Paired-end reads were trimmed with the trimmomatic program (v 0.33) and using the following parameters: (ILLUMINACLIP:TruSeq3-PE-2.fa:2:15:10 CROP:98 HEADCROP:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:30).
Trimmed reads were aligned to the Amel_4.5 honey bee genome assembly with bowtie2 within the bismark program (v 0.16.1) using bowtie2 default settings except for max insert size set to 1000.
The bismark program was also used to mark duplicates and extract DNA methylation levels for each CpG.
Genome_build: Honeybee Amel_4.5
Supplementary_files_format_and_content: CSV - Provides the genomic position, DNA methylation level (%) and coverage for every CpG in the genome

molecule: genomic DNA

organism: Apis mellifera ligustica

source_name: whole brain

growth_protocol: Day old bees were collected from single drone inseminated colonies

extract_protocol:
Heads were partially dissected to expose brain and submerged in RNALater ICE overnight at -20°C. Whole brains were dissected the following day and stored at -80C until DNA extraction. Genomic DNA was extracted from whole brains using the Gentra Puregene Tissue Kit (Qiagen) and stored at -20°C.  Unmethylated lambda phage DNA (Promega) was spiked in as a control for assessment of bisulfite conversion efficiency.
The samples were submitted to the Roy J. Carver Biotechnology Center at the University of Illinois for quality control, library construction, and sequencing.  The integrity of the samples was checked using the AATI Fragment Analyzer, which confirmed that the DNA was of high molecular weight.  Shotgun DNA libraries were made using the KAPA Library Preparation Kit, then bisulfite treated using the Zymo EZ DNA Methylation-Lightning Kit.  The libraries were then amplified for 10 PCR cycles using HiFi Uracil+ DNA Polymerase (KAPA Biosystems), pooled in equimolar quantities, and sequenced on the HiSeq 2500 (Illumina).  Paired-end 100-nucleotide sequence reads were generated from seven control and seven experimental samples for each collection time point (5 minutes and 120 minutes).

treatment_protocol: Bees were placed in groups of ten in vertically oriented petri dishes and maintained in the dark for 8 days prior to introduction of intruder bee. Aggressive bees were identified by interaction with intruder bee and collected 5 minutes and 120 minutes post interaction. Control groups were exposed to a 0.2 ml plastic tube similar in size to a worker bee, which was removed after 5 minutes.  Two bees were collected from each control group at random either 5 minutes or 120 minutes following initial exposure to the tube.  After flash freezing, all collected bees were transferred individually to microfuge tubes and stored at -80°C.

tag: colony type

value: Single drone inseminated (SDI)

tag: caste

value: Worker

value: whole brain

tag: phenotype

value: Aggressive


title: C6_120min

description: Control bee collected 120 min post interaction

tag: age

tag: tissue

value: Control


title: A1_120min


title: A6_120min


title: C5_120min


title: A3_120min


title: A5_120min


title: T0L3

city: Richland

first: Lye Meng

last: Markillie

state: WA

address: 902 Battelle Blvd

department: Biosystems Dynamics & Simulation

institute: Environmental Molecular Sciences Laboratory

data_processing:
The 50-base short read sequences produced by the 5500XL SOLiD  sequencer were mapped in color space using SOLiD LifeScope software version 2.5 using the default parameters
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: [Enterobacter] lignolyticus SCF1

source_name: Gammaproteobacteria isolated from El Yunque forest, Puerto Rico

growth_protocol: Cells were grown in anaerobic modified LS4D minimal media

extract_protocol:
RNA was extracted using Trizol following by DNAseI treatment using Qiagen RNAseay mini column
Template cDNA was prepared using the Applied Biosystems SOLiD® Total RNA-Seq Kit (Life Technologies, Carlsbad, CA) according to manufacturer's protocol.

treatment_protocol: Two conditions: 1) unamended control cultures: using glucose (60 mM) as main carbon source 2) lignin-amended treatment: using glucose (60 mM) as main carbon source + lignin (0.1%)

tag: treatment

value: 60 mM Glucose + 0.1% lignin

tag: phase

value: Exponential phase

tag: biological replicates


title: C4_120min


title: A4_5min

description: Aggressive bee collected 5 min post interaction


title: T0L2


title: A6_5min


title: A5_5min


title: C1_120min


title: C2_120min


title: T0L1

value: 60 mM Glucose


title: 51_RT2Y_S22_L001


title: C3_120min


title: 51_RT2Y_S22_L002


title: A3_5min


title: High FLC treated T8

description:
Sample_13602E_T8YF
Processed data file: T8_FPKM.tsv

organism: Trichosporon asahii var. asahii CBS 8904


title: T0G3


title: Low FLC treated T8

description:
Sample_13602C_T8HF
Processed data file: T8_FPKM.tsv


title: T0G2


title: A1_5min


title: A2_5min


title: FLC free T8 (long time)

description:
Sample_13602B_T8Y
Processed data file: T8_FPKM.tsv


title: A4_120min


title: FLC free T8 (short time)

description:
Sample_13602B_T8H
Processed data file: T8_FPKM.tsv


title: Wild Type of T8

description:
Sample_13602B_T8
Processed data file: T8_FPKM.tsv


title: MMS

description: control, 3 biological replicates

organism: Zea mays

source_name: mock-treated maize mesophyll cells

value: mock-treated maize mesophyll cells


title: C4_5min

description: Control bee collected 5 min post interaction


title: T2L3

value: Stationary phase


title: C3_5min


title: T2G3


title: C1_5min


title: T15B-RNA-Seq

city: Wuhan

first: Dong

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first discarded if containing more than 2-N bases, then reads were processed by clipping adaptor, removing low quality bases, and discarding too short reads (less than 16nt). FASTX-Toolkit (Version 0.0.13) was used to get the clean reads.
After that, clean reads were aligned to the Ovis aries (Oar_v3.1) by tophat2 (Kim et al., 2013). Aligned reads with more than one genome location were discarded due to their ambiguous location.
Uniquely localized reads were used to calculate reads number and RPKM value (RPKM represents reads per kilobase and per million) for each gene according to reads and genes genome location. Other statistical results, such as gene coverage and depth, reads distribution around start codon and stop codon, were also obtained.
After getting the Expression level of all genes in all samples, differentially expressed genes were analyzed by using edgeR(Robinson et al., 2010), one of R packages.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: tabular data of  txt , the RPKM & reads count of expressed genes

organism: Ovis aries

source_name: infected oral mucosa cells_T15

extract_protocol:
Total RNA was extracted from 30 mg of ground tissue by using hot phenol method. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1DNase (Promega) to remove DNA.
For each sample, 10μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen) before used for directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.

treatment_protocol: We collected oral mucosa tissues from the sheep at 0, 3, 7 and 15 days post ORFV infection, respectively.

tag: tag

value: infected oral mucosa cells

tag: time point

value: 15 days post ORFV infection


title: T2G2


title: T15A-RNA-Seq


title: MBS

description: control, 3 biological replicates

source_name: mock-treated maize bundle sheath cells

value: mock-treated maize bundle sheath cells


title: T2L1


title: T7B-RNA-Seq

source_name: infected oral mucosa cells_T7

value: 7 days post ORFV infection


title: HSV-1 infected (positive) vero cells replicate 3

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the green monkey and HSV1 genomes simultaneously by Rsubread version 1.22.2
Read counts were summarized by Entrez Gene ID  and gene locus tag ID for the green monkey and HSV1 genomes respectively
Genome_build: Chlorocebus_sabeus 1.1 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000409795.2/) and Human herpesvirus 1 strain KOS, complete genome (https://www.ncbi.nlm.nih.gov/nuccore/JQ673480.1)
Supplementary_files_format_and_content: Tab-delimited text files were written from the R promp. Columns represent Gene ID (Entrez ID for green monkey files and locus tag for HSV1 files), total gene length (total base count of all exons) and the number of reads mapping to that gene

organism:
Chlorocebus aethiops
Human alphaherpesvirus 1

source_name: Vero cells

growth_protocol: Vero cells were grown in DMEM supplemented with 10% FCS at 37ºC  5% CO2

extract_protocol:
RNA was extracted using the RNeasy Plus mini kit (QIAGEN) followed by concentration quantification and quality control using TapeStation 2200 (Agilent Technologies).
RNA sequencing libraries were prepared using the Illumina TruSeq stranded total RNA library prep kit and sequenced on an Illumina NextSeq 500. On average, 45.4 million 75 base pair paired-end reads were obtained for each sample.

treatment_protocol: 1x10^6 Vero cells were infected with 0.5 MOI HSV-1-mCherry for 48 hours and HSV-1+ and HSV-1- cells were sorted based on mCherry fluorescence. Uninfected cells were used as a negative control. Three independent biological replicates of each condition were obtained via FACS sorting on an BD FACSAria III or BD FACSAria Fusion

tag: infection

value: Herpes simplex virus 1

tag: infection status

value: Positive

tag: cell line

value: Vero cells


title: T2G1


title: HSV-1 infected (positive) vero cells replicate 2


title: T1L3

value: Mid-exponential phase


title: T0G1


title: T7A-RNA-Seq


title: T3B-RNA-Seq

source_name: infected oral mucosa cells_T3

value: 3 days post ORFV infection


title: T1L1


title: T3A-RNA-Seq


title: C6_5min

value: Single drone inseminated (SDI)

value: Worker

value: whole brain


title: C5_5min

value: Control


title: T1G3


title: T2L2

value: 60 mM Glucose + 0.1% lignin


title: C2_5min


title: T1G2

value: 60 mM Glucose


title: T0A-RNA-Seq

source_name: normal oral mucosa cells_T0

value: normal oral mucosa cells

value: 0 days post ORFV infection


title: HSV-1 infected (negative) vero cells replicate 2

value: Negative


title: T1G1


title: Uninfected vero cells replicate 2

organism: Chlorocebus aethiops

value: Uninfected


title: T1L2


title: HSV-1 infected (positive) vero cells replicate 1


title: RamDA_mESC_72h_H12

status: Public on Feb 12 2018

city: Tsukuba

first: Hiroaki

last: Tateno

state: Ibaraki

address: Tsukuba Central 2, 1-1-1 Umezono

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

data_processing:
FASTQ files were generated using bcl2fastq (v2.16.0.10).
For RamDA-seq and C1-RamDA-seq data with living cells, fastq-mcf (version 1.04.807) was used for adapter trimming with the parameters '-l 36 --lowcomplex-pct 74 --homopolymer- pct 74 -k 4' for RamDA-seq and '-L 75 -l 46 -k 4 -q 30' for C1-RamDA-seq. The reads were mapped to the mouse genome (mm10) using HISAT2 with the parameters '--dta-cufflinks -p 4 -k 5 -X 800 --sp 1000,1000'. Uniquely mapped reads were selected using the bamtools ‘filter’ command with the parameters '-isMapped true -tag NH:1' and samtools ‘view’ command with the parameter ‘-q 40’. BigWig files were generated using deepTools (version 2.2.4). The transcript-level expression levels were quantified using sailfish (version 0.9.2). The transcript-level expression levels were also calculated using Bowtie2 (version 2.2.6) with the parameters '-k 100 -X 800' and eXpress (version 1.5.1) with the parameter '--no-bias-correct'.
For each scRNA-seq method data with 10 pg of diluted RNA, fastq-mcf (version 1.04.807) was used to trim adapter sequences and generate read lengths of 42 nt with the parameters ‘-L 42 -l 42 -k 4 -q 30 -S’. For comparison, we also prepared R1 reads of rdRNA-seq and paRNA-seq data. The reads were mapped to the mouse genome (mm10) using HISAT2 (version 2.0.1) with parameters ‘--dta-cufflinks -p 4 -k 5 --sp 1000,1000’. Uniquely mapped reads were selected using the bamtools (version 2.0.1;) 53 ‘filter’ command with the parameters `-isMapped true -tag NH:1` and the samtools (version 2.0.1)54 ‘view’ command with the parameter ‘-q 40’. BigWig files were generated using deepTools (version 2.2.4). Sailfish (version 0.9.2) was used to quantify transcript-level expressions.
For bulk poly(A) and total RNA-seq data, fastq-mcf was used to trim adapter sequences with the parameters ‘-l 50 --lowcomplex-pct 36 --homopolymer-pct 36 -k 4 -S’. The reads were mapped to the mouse genome (mm10) using HISAT2 with the parameters '--dta-cufflinks --rna-strandness RF -k 5 --no-mixed --no-discordant --sp 1000,1000'. Properly (i.e., convergent read pairs) and uniquely mapped reads were selected using the bamtools ‘filter’ command and samtools ‘view’ command with the parameter ‘-q 40’. For genome-guided transcriptome assembly, Cufflinks (version 2.2.1) was used with the parameters ‘--multi-read-correct --frag-bias-correct -M $mask --library-type fr-unstranded’. A GTF file of tRNA and rRNA annotations in GENCODE (vM9) were provided to mask the genome. Cuffcompare was used to annotate transcripts with transfrag class codes with respect to the GENCODE (vM9) annotation. According to the Cuffcompare class codes, we selected (1) unnannotated transcripts with class codes of "i", "o", "u", "x", or "s" and (2) unannotated splicing variant transcripts (‘j’ class (potentially novel isoform)) with at least one unannotated splice junction. We then removed (1) unannotated transcripts with exons located within 100 bp of the tRNA or rRNA annotations in GECODE or RepeatMasker, or pseudogene annotations in GENCODE (‘2wayconspseudos’), and (2) unannotated transcripts with lengths that were not monger than 200 bp. These filtered unannotated gene models were further merged with gene models in GENCODE vM9.
Genome_build: mm10
Supplementary_files_format_and_content: txt, gtf, bigWig

source_name: ES_72h_single cell

growth_protocol: 5G6GR mouse ES cells were used for bulk and single-cell RNA-seq. The cells were cultured in a feeder-free gelatin-coated dish in 10% fetal calf serum containing Glasgow minimal essential medium (GMEM; Sigma-Aldrich), 1000 U/mL leukemia inhibitory factor (ESGRO; Invitrogen), 100 µmol/l 2-mercaptoethanol (Nacalai Tesque), 1× non-essential amino acids (Life Technologies), 1 mmol/L sodium pyruvate (Life Technologies), 2 mmol/L L-glutamine (Nacalai Tesque), 0.5× penicillin/streptomycin (Life Technologies), 0.5 ug/ml puromycin (Sigma) and 10 µg/mL blasticidin (Life Technologies).

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen). For ribosomal RNA depleted total RNA-seq, depletion of rRNA from 1 µg of ES total RNA was performed by using GeneRead rRNA Depletion Kits (Qiagen). For single-cell RamDA-seq, single cells were directly sorted into the cell lysis buffer containing RNasein plus (Promega), Cell Lysis Buffer (Roche), NP40 (Thermo), and RNase free water (TaKaRa). For averaged G1-phase cell lysate sample, 180 cells were sorted into 180 µl of the cell lysis buffer and individually divided into 1 μl in a 96-well PCR plate after well-mixing to lyse the cells. The cell lysate solution was stored at -80ºC until use.
For bulk RNA-seq, the libraries were constructed by using a commercial kit (NEBNext Ultra Directional RNA Library Prep Kit for Illumina; NEB) in accordance with the manufacturer's protocol, with slight modifications during the reverse-transcription and PCR steps. SMART-Seq v4 libraries were prepared according to manufacturer's instructions accompanying the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). For library construction of RamDA-seq and C1-RamDA-seq, refer to the protocol in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs". For rRNA-depleted RNA-seq using 1 and 10 ng of diluted total RNA, sequencing libraries were prepared with KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems) according to the manufacturer's protocol. C1-SMART-Seq v4 libraries were prepared using Fluidigm C1 with the script "Full-length mRNA Sequencing" was downloaded from Script Hub (https://jp.fluidigm.com/c1openapp/scripthub)in accordance with the manufacturer's protocol. For analyses of plate-to-plate variability (batch effect) of RamDA-seq, we prepared RamDA-seq library DNA by using the advanced method of RamDA-seq (refer to the protocol in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs").

treatment_protocol: For the assessment of PrE differentiation, 5G6GR ES cells were cultured in differentiation medium containing 100 mmol/l dexamethasone rather than blasticidin. The cells are cultured for 72 hours.

tag: cell type

value: ES cell

value: DEX

value: 72 hours

tag: sample type

value: MoFlo sorted cell

tag: starting amount

value: single cell

tag: cell cycle phase

value: All phase

tag: method subtype

value: RamDA-seq


title: RamDA_mESC_72h_H09


title: RamDA_mESC_72h_H10


title: RamDA_mESC_72h_H06


title: RamDA_mESC_72h_H07


title: HSV-1 infected (negative) vero cells replicate 3

value: Herpes simplex virus 1

value: Vero cells


title: RamDA_mESC_72h_H03


title: RamDA_mESC_72h_H04


title: RamDA_mESC_72h_H05


title: RamDA_mESC_72h_G12


title: RamDA_mESC_72h_G11


title: RamDA_mESC_72h_G10


title: T0B-RNA-Seq


title: RamDA_mESC_72h_H01


title: Uninfected vero cells replicate 3


title: Uninfected vero cells replicate 1


title: RamDA_mESC_72h_G06


title: RamDA_mESC_72h_G08


title: RamDA_mESC_72h_G07


title: RamDA_mESC_72h_H11


title: RamDA_mESC_72h_G09


title: RamDA_mESC_72h_G05


title: HSV-1 infected (negative) vero cells replicate 1


title: RamDA_mESC_72h_G04


title: RamDA_mESC_72h_H08


title: RamDA_mESC_72h_F12


title: RamDA_mESC_72h_G01


title: RamDA_mESC_72h_G02


title: RamDA_mESC_72h_H02


title: RamDA_mESC_72h_F10


title: RamDA_mESC_72h_F09


title: RamDA_mESC_72h_F11


title: RamDA_mESC_72h_F08


title: RamDA_mESC_72h_F07


title: RamDA_mESC_72h_F05


title: RamDA_mESC_72h_F03


title: RamDA_mESC_72h_F04


title: RamDA_mESC_72h_F06


title: RamDA_mESC_72h_G03


title: RamDA_mESC_72h_F02


title: RamDA_mESC_72h_F01


title: RamDA_mESC_72h_E12


title: RamDA_mESC_72h_E11


title: RamDA_mESC_72h_E07


title: RamDA_mESC_72h_E09


title: RamDA_mESC_72h_E08


title: RamDA_mESC_72h_E06


title: RamDA_mESC_72h_E02


title: RamDA_mESC_72h_D12


title: RamDA_mESC_72h_E03


title: RamDA_mESC_72h_E04


title: RamDA_mESC_72h_E01


title: RamDA_mESC_72h_D09


title: RamDA_mESC_72h_E05


title: RamDA_mESC_72h_D06


title: RamDA_mESC_72h_E10


title: RamDA_mESC_72h_D02


title: RamDA_mESC_72h_D11


title: RamDA_mESC_72h_D08


title: RamDA_mESC_72h_D10


title: RamDA_mESC_72h_C10


title: RamDA_mESC_72h_C11


title: RamDA_mESC_72h_D07


title: RamDA_mESC_72h_D05


title: RamDA_mESC_72h_C09


title: RamDA_mESC_72h_C06


title: RamDA_mESC_72h_C07


title: RamDA_mESC_72h_D03


title: RamDA_mESC_72h_D04


title: RamDA_mESC_72h_C12


title: RamDA_mESC_72h_D01


title: RamDA_mESC_72h_C05


title: RamDA_mESC_72h_B11


title: RamDA_mESC_72h_B08


title: RamDA_mESC_72h_B10


title: RamDA_mESC_72h_C03


title: RamDA_mESC_72h_B09


title: RamDA_mESC_72h_C04


title: RamDA_mESC_72h_B04


title: RamDA_mESC_72h_B02


title: RamDA_mESC_72h_B05


title: RamDA_mESC_72h_B03


title: RamDA_mESC_72h_C02


title: RamDA_mESC_72h_C08


title: RamDA_mESC_72h_A11


title: RamDA_mESC_72h_B06


title: RamDA_mESC_72h_A12


title: RamDA_mESC_72h_A10


title: RamDA_mESC_72h_B12


title: RamDA_mESC_72h_C01


title: RamDA_mESC_72h_A09


title: RamDA_mESC_72h_A08


title: RamDA_mESC_72h_B07


title: RamDA_mESC_48h_H10

source_name: ES_48h_single cell

value: 48 hours


title: RamDA_mESC_72h_A06


title: RamDA_mESC_72h_A07


title: RamDA_mESC_72h_B01


title: RamDA_mESC_72h_A05


title: RamDA_mESC_48h_H05


title: RamDA_mESC_72h_A04


title: RamDA_mESC_48h_H08


title: RamDA_mESC_48h_H07


title: RamDA_mESC_48h_H12


title: RamDA_mESC_48h_H04


title: RamDA_mESC_48h_H11


title: RamDA_mESC_48h_G11


title: RamDA_mESC_48h_G09


title: RamDA_mESC_48h_G08


title: RamDA_mESC_48h_G12


title: RamDA_mESC_48h_H01


title: RamDA_mESC_48h_G03


title: RamDA_mESC_48h_G10


title: RamDA_mESC_48h_G07


title: RamDA_mESC_48h_H02


title: RamDA_mESC_48h_G06


title: RamDA_mESC_48h_F12


title: RamDA_mESC_48h_H03


title: RamDA_mESC_48h_H09


title: RamDA_mESC_48h_G05


title: RamDA_mESC_48h_F11


title: RamDA_mESC_48h_F03


title: RamDA_mESC_48h_G02


title: RamDA_mESC_48h_H06


title: RamDA_mESC_48h_E12


title: RamDA_mESC_48h_G04


title: RamDA_mESC_48h_F08


title: RamDA_mESC_48h_F09


title: RamDA_mESC_48h_E08


title: RamDA_mESC_48h_F06


title: RamDA_mESC_48h_F07


title: RamDA_mESC_48h_G01


title: RamDA_mESC_48h_E06


title: RamDA_mESC_48h_F05


title: RamDA_mESC_48h_F02


title: RamDA_mESC_48h_F01


title: RamDA_mESC_48h_E02


title: RamDA_mESC_48h_F10


title: RamDA_mESC_48h_E01


title: RamDA_mESC_48h_E11


title: RamDA_mESC_48h_D11


title: RamDA_mESC_48h_E07


title: RamDA_mESC_48h_F04


title: RamDA_mESC_48h_E10


title: RamDA_mESC_48h_D12


title: RamDA_mESC_48h_E05


title: RamDA_mESC_48h_D10


title: RamDA_mESC_48h_D05


title: RamDA_mESC_48h_D08


title: RamDA_mESC_48h_D06


title: RamDA_mESC_48h_C12


title: RamDA_mESC_48h_D03


title: RamDA_mESC_48h_D01


title: RamDA_mESC_48h_C06


title: RamDA_mESC_48h_C08


title: RamDA_mESC_48h_C01


title: RamDA_mESC_48h_B12


title: RamDA_mESC_48h_C04


title: RamDA_mESC_48h_C05


title: RamDA_mESC_48h_D04


title: RamDA_mESC_48h_C10


title: RamDA_mESC_48h_D02


title: RamDA_mESC_48h_C09


title: RamDA_mESC_48h_C03


title: RamDA_mESC_48h_C07


title: RamDA_mESC_48h_B04


title: RamDA_mESC_48h_B11


title: RamDA_mESC_48h_B09


title: RamDA_mESC_48h_B07


title: RamDA_mESC_48h_D07


title: RamDA_mESC_48h_A12


title: RamDA_mESC_48h_A08


title: RamDA_mESC_48h_B02


title: RamDA_mESC_48h_A07


title: RamDA_mESC_48h_B05


title: RamDA_mESC_48h_B03


title: RamDA_mESC_24h_H08

source_name: ES_24h_single cell

value: 24 hours


title: RamDA_mESC_48h_C11


title: RamDA_mESC_24h_H09


title: RamDA_mESC_24h_H11


title: RamDA_mESC_24h_H07


title: RamDA_mESC_24h_H06


title: RamDA_mESC_48h_B01


title: RamDA_mESC_48h_A09


title: RamDA_mESC_24h_H03


title: RamDA_mESC_48h_A06


title: RamDA_mESC_24h_H05


title: RamDA_mESC_48h_A05


title: RamDA_mESC_48h_B08


title: RamDA_mESC_48h_A04


title: RamDA_mESC_24h_H10


title: RamDA_mESC_24h_G11


title: RamDA_mESC_24h_H02


title: RamDA_mESC_24h_H04


title: RamDA_mESC_24h_H01


title: RamDA_mESC_24h_G12


title: RamDA_mESC_24h_G09


title: RamDA_mESC_24h_G10


title: RamDA_mESC_24h_G04


title: RamDA_mESC_24h_G08


title: RamDA_mESC_24h_G06


title: RamDA_mESC_24h_G05


title: RamDA_mESC_24h_G07


title: RamDA_mESC_24h_G02


title: RamDA_mESC_24h_G03


title: RamDA_mESC_24h_H12


title: RamDA_mESC_24h_F09


title: RamDA_mESC_24h_F12


title: RamDA_mESC_24h_F11


title: RamDA_mESC_24h_F10


title: RamDA_mESC_24h_G01


title: RamDA_mESC_24h_F05


title: RamDA_mESC_24h_F08


title: RamDA_mESC_24h_F07


title: RamDA_mESC_48h_B10


title: RamDA_mESC_24h_F02


title: RamDA_mESC_24h_F03


title: RamDA_mESC_24h_F04


title: RamDA_mESC_24h_F01


title: RamDA_mESC_24h_E12


title: RamDA_mESC_24h_E10


title: RamDA_mESC_24h_E11


title: RamDA_mESC_24h_F06


title: RamDA_mESC_24h_D12


title: RamDA_mESC_24h_E04


title: RamDA_mESC_24h_E06


title: RamDA_mESC_24h_E01


title: RamDA_mESC_24h_D11


title: RamDA_mESC_24h_E03


title: RamDA_mESC_24h_E09


title: RamDA_mESC_24h_E07


title: RamDA_mESC_24h_E08


title: RamDA_mESC_24h_E05


title: RamDA_mESC_24h_D10


title: RamDA_mESC_24h_D09


title: RamDA_mESC_24h_D07


title: RamDA_mESC_24h_E02


title: RamDA_mESC_24h_D08


title: RamDA_mESC_24h_D05


title: RamDA_mESC_24h_D01


title: RamDA_mESC_24h_D04


title: RamDA_mESC_24h_D03


title: RamDA_mESC_24h_D02


title: RamDA_mESC_24h_C12


title: RamDA_mESC_24h_C11


title: RamDA_mESC_24h_C09


title: RamDA_mESC_24h_C08


title: RamDA_mESC_24h_C10


title: RamDA_mESC_24h_C07


title: RamDA_mESC_24h_C06


title: RamDA_mESC_24h_D06


title: RamDA_mESC_24h_B11


title: RamDA_mESC_24h_B12


title: RamDA_mESC_24h_C05


title: RamDA_mESC_24h_C02


title: RamDA_mESC_24h_B10


title: RamDA_mESC_24h_C04


title: RamDA_mESC_24h_C01


title: RamDA_mESC_24h_B05


title: RamDA_mESC_24h_B03


title: RamDA_mESC_24h_C03


title: RamDA_mESC_24h_B08


title: RamDA_mESC_24h_B06


title: RamDA_mESC_24h_B04


title: RamDA_mESC_24h_B09


title: RamDA_mESC_24h_B07


title: RamDA_mESC_24h_A12


title: RamDA_mESC_24h_B02


title: RamDA_mESC_24h_A05


title: RamDA_mESC_24h_A06


title: RamDA_mESC_12h_H12

source_name: ES_12h_single cell

value: 12 hours


title: RamDA_mESC_24h_B01


title: RamDA_mESC_12h_H11


title: RamDA_mESC_12h_H09


title: RamDA_mESC_24h_A11


title: RamDA_mESC_12h_H03


title: RamDA_mESC_12h_G09


title: RamDA_mESC_12h_H10


title: RamDA_mESC_24h_A09


title: RamDA_mESC_12h_G07


title: RamDA_mESC_24h_A08


title: RamDA_mESC_24h_A07


title: RamDA_mESC_12h_H06


title: RamDA_mESC_24h_A04


title: RamDA_mESC_12h_G02


title: RamDA_mESC_12h_G01


title: RamDA_mESC_12h_H08


title: RamDA_mESC_12h_H07


title: RamDA_mESC_12h_H02


title: RamDA_mESC_12h_F12


title: RamDA_mESC_12h_G06


title: RamDA_mESC_12h_F10


title: RamDA_mESC_12h_F09


title: RamDA_mESC_12h_H05


title: RamDA_mESC_12h_F08


title: RamDA_mESC_12h_F07


title: RamDA_mESC_12h_H01


title: RamDA_mESC_24h_A10


title: RamDA_mESC_12h_G03


title: RamDA_mESC_12h_G10


title: RamDA_mESC_12h_G12


title: RamDA_mESC_48h_B06


title: RamDA_mESC_12h_F11


title: RamDA_mESC_48h_C02


title: RamDA_mESC_12h_G08


title: RamDA_mESC_12h_E12


title: RamDA_mESC_12h_E08


title: RamDA_mESC_12h_G05


title: RamDA_mESC_12h_H04


title: RamDA_mESC_12h_E05


title: RamDA_mESC_12h_G04


title: RamDA_mESC_12h_E02


title: RamDA_mESC_12h_F05


title: RamDA_mESC_12h_D12


title: RamDA_mESC_12h_E03


title: RamDA_mESC_12h_D11


title: RamDA_mESC_12h_F06


title: RamDA_mESC_12h_E01


title: RamDA_mESC_12h_F04


title: RamDA_mESC_12h_E11


title: RamDA_mESC_12h_D09


title: RamDA_mESC_12h_E09


title: RamDA_mESC_12h_F01


title: RamDA_mESC_12h_F03


title: RamDA_mESC_12h_D05


title: RamDA_mESC_12h_E10


title: RamDA_mESC_12h_F02


title: RamDA_mESC_12h_E07


title: RamDA_mESC_12h_E06


title: RamDA_mESC_12h_D02


title: RamDA_mESC_12h_E04


title: RamDA_mESC_12h_C10


title: RamDA_mESC_12h_D08


title: RamDA_mESC_12h_D10


title: RamDA_mESC_12h_D07


title: RamDA_mESC_12h_D04


title: RamDA_mESC_12h_C02


title: RamDA_mESC_12h_C01


title: RamDA_mESC_12h_D03


title: RamDA_mESC_12h_B11


title: RamDA_mESC_12h_D01


title: RamDA_mESC_12h_C11


title: RamDA_mESC_12h_C09


title: RamDA_mESC_12h_C08


title: RamDA_mESC_12h_B06


title: RamDA_mESC_12h_C07


title: RamDA_mESC_12h_C04


title: RamDA_mESC_12h_B01


title: RamDA_mESC_12h_C05


title: RamDA_mESC_12h_B12


title: RamDA_mESC_12h_B10


title: RamDA_mESC_12h_A11


title: RamDA_mESC_12h_B09


title: RamDA_mESC_12h_B07


title: RamDA_mESC_12h_B05


title: RamDA_mESC_12h_A08


title: RamDA_mESC_12h_B03


title: RamDA_mESC_12h_C12


title: RamDA_mESC_12h_A06


title: RamDA_mESC_12h_A09


title: RamDA_mESC_12h_B02


title: RamDA_mESC_12h_B08


title: RamDA_mESC_12h_C03


title: RamDA_mESC_12h_A12


title: RamDA_mESC_12h_C06


title: RamDA_mESC_12h_B04


title: RamDA_mESC_12h_A10


title: RamDA_mESC_12h_A07


title: RamDA_mESC_12h_A04


title: RamDA_mESC_00h_H12

source_name: ES_00h_single cell

value: Embryonic stem (ES) cell


title: RamDA_mESC_00h_H08


title: RamDA_mESC_00h_H06


title: RamDA_mESC_00h_H01


title: RamDA_mESC_00h_H07


title: RamDA_mESC_00h_G12


title: RamDA_mESC_00h_H09


title: RamDA_mESC_00h_H03


title: RamDA_mESC_00h_G11


title: RamDA_mESC_00h_H02


title: RamDA_mESC_12h_A05


title: RamDA_mESC_00h_G10


title: RamDA_mESC_00h_H05


title: RamDA_mESC_00h_G09


title: RamDA_mESC_00h_G07


title: RamDA_mESC_00h_G08


title: RamDA_mESC_00h_H10


title: RamDA_mESC_00h_G06


title: RamDA_mESC_00h_G01


title: RamDA_mESC_00h_G05


title: RamDA_mESC_00h_G03


title: RamDA_mESC_00h_F11


title: RamDA_mESC_00h_G04


title: RamDA_mESC_00h_F12


title: RamDA_mESC_00h_G02


title: RamDA_mESC_00h_F10


title: RamDA_mESC_00h_H04


title: RamDA_mESC_00h_F08


title: RamDA_mESC_00h_F06


title: RamDA_mESC_00h_F07


title: RamDA_mESC_00h_F09


title: RamDA_mESC_00h_F04


title: RamDA_mESC_00h_F05


title: RamDA_mESC_00h_H11


title: RamDA_mESC_00h_E09


title: RamDA_mESC_00h_E12


title: RamDA_mESC_00h_F03


title: RamDA_mESC_00h_F02


title: RamDA_mESC_00h_F01


title: RamDA_mESC_00h_E08


title: RamDA_mESC_00h_E04


title: RamDA_mESC_00h_E05


title: RamDA_mESC_00h_E06


title: RamDA_mESC_00h_E03


title: RamDA_mESC_00h_E11


title: RamDA_mESC_00h_E02


title: RamDA_mESC_00h_E10


title: RamDA_mESC_00h_D10


title: RamDA_mESC_00h_D12


title: RamDA_mESC_00h_D11


title: RamDA_mESC_00h_D09


title: RamDA_mESC_00h_D08


title: RamDA_mESC_00h_D07


title: RamDA_mESC_00h_D06


title: RamDA_mESC_00h_D05


title: RamDA_mESC_00h_D02


title: RamDA_mESC_00h_C11


title: RamDA_mESC_00h_C09


title: RamDA_mESC_00h_C10


title: RamDA_mESC_00h_E07


title: RamDA_mESC_00h_C05


title: RamDA_mESC_00h_C07


title: RamDA_mESC_00h_C08


title: RamDA_mESC_00h_C03


title: RamDA_mESC_00h_E01


title: RamDA_mESC_00h_C04


title: RamDA_mESC_00h_C02


title: RamDA_mESC_00h_C01


title: RamDA_mESC_00h_B11


title: RamDA_mESC_00h_B09


title: RamDA_mESC_00h_B08


title: RamDA_mESC_00h_B12


title: RamDA_mESC_00h_B04


title: RamDA_mESC_00h_D03


title: RamDA_mESC_00h_B10


title: RamDA_mESC_00h_B05


title: RamDA_mESC_00h_D04


title: RamDA_mESC_00h_B07


title: RamDA_mESC_00h_D01


title: RamDA_mESC_00h_B01


title: RamDA_mESC_00h_A11


title: RamDA_mESC_00h_B02


title: RamDA_mESC_00h_A10


title: RamDA_mESC_00h_A12


title: RamDA_mESC_00h_A08


title: RamDA_mESC_00h_C06


title: RamDA_mESC_00h_A07


title: RamDA_mESC_00h_A05


title: RamDA_mESC_00h_A06


title: RamDA_mESC_00h_A04


title: RamDA_mESC_G2M_H11

source_name: ES_G2M_single cell


title: RamDA_mESC_G2M_H10


title: RamDA_mESC_G2M_H12


title: RamDA_mESC_G2M_H08


title: RamDA_mESC_G2M_H06


title: RamDA_mESC_G2M_H07


title: RamDA_mESC_G2M_H09


title: RamDA_mESC_G2M_H05


title: RamDA_mESC_G2M_H02


title: RamDA_mESC_G2M_G12


title: RamDA_mESC_G2M_G10


title: RamDA_mESC_G2M_G08


title: RamDA_mESC_G2M_G11


title: RamDA_mESC_G2M_G07


title: RamDA_mESC_G2M_G05


title: RamDA_mESC_G2M_H03


title: RamDA_mESC_00h_A09


title: RamDA_mESC_G2M_F11


title: RamDA_mESC_G2M_H01


title: RamDA_mESC_G2M_F12


title: RamDA_mESC_G2M_G06


title: RamDA_mESC_G2M_F10


title: RamDA_mESC_G2M_H04


title: RamDA_mESC_G2M_G04


title: RamDA_mESC_G2M_G03


title: RamDA_mESC_G2M_E11


title: RamDA_mESC_G2M_E08


title: RamDA_mESC_G2M_G02


title: RamDA_mESC_G2M_E09


title: RamDA_mESC_G2M_E07


title: RamDA_mESC_G2M_G01


title: RamDA_mESC_G2M_F09


title: RamDA_mESC_G2M_F08


title: RamDA_mESC_G2M_F06


title: RamDA_mESC_G2M_F07


title: RamDA_mESC_G2M_E04


title: RamDA_mESC_G2M_F05


title: RamDA_mESC_G2M_F04


title: RamDA_mESC_G2M_D12


title: RamDA_mESC_G2M_E01


title: RamDA_mESC_G2M_D10


title: RamDA_mESC_G2M_F03


title: RamDA_mESC_G2M_G09


title: RamDA_mESC_G2M_E10


title: RamDA_mESC_G2M_E12


title: RamDA_mESC_G2M_E05


title: RamDA_mESC_G2M_F02


title: RamDA_mESC_G2M_F01


title: RamDA_mESC_G2M_E03


title: RamDA_mESC_G2M_D07


title: RamDA_mESC_G2M_D09


title: RamDA_mESC_G2M_D06


title: RamDA_mESC_G2M_D05


title: RamDA_mESC_G2M_D03


title: RamDA_mESC_G2M_D02


title: RamDA_mESC_G2M_E02


title: RamDA_mESC_G2M_C11


title: RamDA_mESC_G2M_D11


title: RamDA_mESC_G2M_C08


title: RamDA_mESC_G2M_D08


title: RamDA_mESC_G2M_C03


title: RamDA_mESC_G2M_C02


title: RamDA_mESC_G2M_C12


title: RamDA_mESC_G2M_B12


title: RamDA_mESC_G2M_B11


title: RamDA_mESC_G2M_B08


title: RamDA_mESC_G2M_B07


title: RamDA_mESC_G2M_A12


title: RamDA_mESC_G2M_B01


title: RamDA_mESC_G2M_C07


title: RamDA_mESC_G2M_C09


title: RamDA_mESC_G2M_C06


title: RamDA_mESC_G2M_C04


title: RamDA_mESC_G2M_C05


title: RamDA_mESC_G2M_C10


title: RamDA_mESC_G2M_B10


title: RamDA_mESC_G2M_B03


title: RamDA_mESC_G2M_C01


title: RamDA_mESC_G2M_A11


title: RamDA_mESC_G2M_A05


title: RamDA_mESC_G2M_D04


title: RamDA_mESC_G2M_D01


title: RamDA_mESC_G2M_B09


title: RamDA_mESC_G2M_B05


title: RamDA_mESC_G2M_B06


title: RamDA_mESC_G2M_B04


title: RamDA_mESC_S_H10

source_name: ES_S_single cell

value: S


title: RamDA_mESC_G2M_B02


title: RamDA_mESC_G2M_A09


title: RamDA_mESC_S_H08


title: RamDA_mESC_G2M_A08


title: RamDA_mESC_S_H02


title: RamDA_mESC_S_H01


title: RamDA_mESC_S_H07


title: RamDA_mESC_S_H11


title: RamDA_mESC_G2M_A07


title: RamDA_mESC_S_H09


title: RamDA_mESC_S_H06


title: RamDA_mESC_S_G12


title: RamDA_mESC_S_H04


title: RamDA_mESC_S_G11


title: RamDA_mESC_S_H03


title: RamDA_mESC_G2M_A06


title: RamDA_mESC_S_H05


title: RamDA_mESC_S_G10


title: RamDA_mESC_G2M_A04


title: RamDA_mESC_G2M_A10


title: RamDA_mESC_S_G09


title: RamDA_mESC_S_G06


title: RamDA_mESC_S_G08


title: RamDA_mESC_S_G07


title: RamDA_mESC_S_G04


title: RamDA_mESC_S_G05


title: RamDA_mESC_S_G03


title: RamDA_mESC_S_F11


title: RamDA_mESC_S_G01


title: RamDA_mESC_S_F09


title: RamDA_mESC_S_F08


title: RamDA_mESC_S_G02


title: RamDA_mESC_S_F10


title: RamDA_mESC_S_F07


title: RamDA_mESC_S_F05


title: RamDA_mESC_S_E12


title: RamDA_mESC_S_F01


title: RamDA_mESC_S_F02


title: RamDA_mESC_S_F03


title: RamDA_mESC_S_E08


title: RamDA_mESC_S_E10


title: RamDA_mESC_S_E09


title: RamDA_mESC_S_E11


title: RamDA_mESC_S_E05


title: RamDA_mESC_S_E07


title: RamDA_mESC_S_E02


title: RamDA_mESC_S_E03


title: RamDA_mESC_S_E04


title: RamDA_mESC_S_E01


title: RamDA_mESC_S_D12


title: RamDA_mESC_S_F06


title: RamDA_mESC_S_E06


title: RamDA_mESC_S_F04


title: RamDA_mESC_S_D11


title: RamDA_mESC_S_D09


title: RamDA_mESC_S_D10


title: RamDA_mESC_S_D08


title: RamDA_mESC_S_D06


title: RamDA_mESC_S_D07


title: RamDA_mESC_S_D02


title: RamDA_mESC_S_C12


title: RamDA_mESC_S_D03


title: RamDA_mESC_S_D04


title: RamDA_mESC_S_C11


title: RamDA_mESC_S_D01


title: RamDA_mESC_G2M_E06


title: RamDA_mESC_S_D05


title: RamDA_mESC_S_B05


title: RamDA_mESC_S_C03


title: RamDA_mESC_S_B06


title: RamDA_mESC_S_B08


title: RamDA_mESC_S_C10


title: RamDA_mESC_S_B10


title: RamDA_mESC_S_C08


title: RamDA_mESC_S_C06


title: RamDA_mESC_S_C05


title: RamDA_mESC_S_C02


title: RamDA_mESC_S_C09


title: RamDA_mESC_S_C01


title: RamDA_mESC_S_B03


title: RamDA_mESC_S_B07


title: RamDA_mESC_S_C04


title: RamDA_mESC_S_B09


title: RamDA_mESC_S_B12


title: RamDA_mESC_S_B11


title: RamDA_mESC_S_B02


title: RamDA_mESC_S_A12


title: RamDA_mESC_S_C07


title: RamDA_mESC_S_A11


title: RamDA_mESC_S_A10


title: RamDA_mESC_S_A08


title: RamDA_mESC_S_A07


title: RamDA_mESC_S_A09


title: RamDA_mESC_S_B04


title: RamDA_mESC_S_A06


title: RamDA_mESC_G1_H11

source_name: ES_G1_single cell


title: RamDA_mESC_S_B01


title: RamDA_mESC_S_A05


title: RamDA_mESC_G1_H12


title: RamDA_mESC_G1_H10


title: RamDA_mESC_G1_H06


title: RamDA_mESC_G1_H07


title: RamDA_mESC_G1_H05


title: RamDA_mESC_G1_H08


title: RamDA_mESC_G1_H03


title: RamDA_mESC_G1_H09


title: RamDA_mESC_G1_H02


title: RamDA_mESC_G1_H04


title: RamDA_mESC_G1_H01


title: RamDA_mESC_G1_G11


title: RamDA_mESC_G1_G06


title: RamDA_mESC_G1_G10


title: RamDA_mESC_G1_G07


title: RamDA_mESC_G1_G12


title: RamDA_mESC_G1_G03


title: RamDA_mESC_G1_G02


title: RamDA_mESC_G1_G04


title: RamDA_mESC_G1_G01


title: RamDA_mESC_S_A04


title: RamDA_mESC_G1_F12


title: RamDA_mESC_G1_G09


title: RamDA_mESC_G1_F11


title: RamDA_mESC_G1_G08


title: RamDA_mESC_G1_F09


title: RamDA_mESC_G1_F10


title: RamDA_mESC_G1_F08


title: RamDA_mESC_G1_F07


title: RamDA_mESC_G1_G05


title: RamDA_mESC_G1_F06


title: RamDA_mESC_G1_F05


title: RamDA_mESC_G1_F02


title: RamDA_mESC_G1_F03


title: RamDA_mESC_G1_F04


title: RamDA_mESC_G1_E12


title: RamDA_mESC_G1_E09


title: RamDA_mESC_G1_E08


title: RamDA_mESC_G1_E07


title: RamDA_mESC_G1_E10


title: RamDA_mESC_G1_E06


title: RamDA_mESC_G1_F01


title: RamDA_mESC_G1_E11


title: RamDA_mESC_G1_E02


title: RamDA_mESC_G1_E05


title: RamDA_mESC_G1_E04


title: RamDA_mESC_G1_E01


title: RamDA_mESC_G1_D12


title: RamDA_mESC_G1_D11


title: RamDA_mESC_G1_D10


title: RamDA_mESC_G1_D09


title: RamDA_mESC_G1_D08


title: RamDA_mESC_G1_D06


title: RamDA_mESC_G1_D07


title: RamDA_mESC_G1_D05


title: RamDA_mESC_G1_E03


title: RamDA_mESC_G1_D02


title: RamDA_mESC_G1_C11


title: RamDA_mESC_G1_D01


title: RamDA_mESC_G1_C09


title: RamDA_mESC_G1_D03


title: RamDA_mESC_G1_D04


title: RamDA_mESC_G1_C08


title: RamDA_mESC_G1_C10


title: RamDA_mESC_G1_C06


title: RamDA_mESC_G1_C07


title: RamDA_mESC_G1_C04


title: RamDA_mESC_G1_C03


title: RamDA_mESC_G1_B12


title: RamDA_mESC_G1_C02


title: RamDA_mESC_G1_B09


title: RamDA_mESC_G1_B10


title: RamDA_mESC_G1_C05


title: RamDA_mESC_G1_B11


title: RamDA_mESC_G1_C01


title: RamDA_mESC_G1_B06


title: RamDA_mESC_G1_B07


title: RamDA_mESC_G1_C12


title: RamDA_mESC_G1_B05


title: RamDA_mESC_G1_B04


title: RamDA_mESC_G1_B03


title: RamDA_mESC_G1_B02


title: RamDA_mESC_G1_B01


title: RamDA_mESC_G1_A09


title: RamDA_mESC_G1_A10


title: RamDA_mESC_G1_A11


title: RamDA_mESC_G1_A07


title: RamDA_mESC_G1_A06


title: RamDA_mESC_G1_A08


title: RamDA_mESC_G1_A04


title: RamDA_mESC_G1_B08


title: RamDA_mESC_G1_A05


title: RamDA_mESC_AvgG1_F02

source_name: ES_Averaged single cell lysis from 180 cells

value: Averaged cell lysate


title: RamDA_mESC_AvgG1_F04


title: RamDA_mESC_AvgG1_E04


title: RamDA_mESC_AvgG1_D04


title: RamDA_mESC_AvgG1_E02


title: RamDA_mESC_AvgG1_F03


title: RamDA_mESC_AvgG1_D03


title: RamDA_mESC_10pg_C04

source_name: ES_diluted total RNA

value: purified total RNA

value: 10 pg


title: RamDA_mESC_AvgG1_D02


title: RamDA_mESC_10pg_C03


title: RamDA_mESC_10pg_C02


title: RamDA_mESC_10pg_B04


title: RamDA_mESC_G1_A12


title: RamDA_mESC_10pg_B02


title: RamDA_mESC_10pg_A02


title: RamDA_mESC_10pg_A04


title: RamDA_mESC_10pg_B03


title: C1RamDA_PrE_39

source_name: PrE_single cell

value: Primitive endoderm (PE) cell

value: C1-captured cell


title: C1RamDA_PrE_36


title: C1RamDA_PrE_38


title: C1RamDA_PrE_34


title: C1RamDA_PrE_32


title: RamDA_mESC_AvgG1_E03


title: C1RamDA_PrE_33


title: C1RamDA_PrE_31


title: C1RamDA_PrE_28


title: C1RamDA_PrE_27


title: C1RamDA_PrE_29


title: C1RamDA_PrE_25


title: C1RamDA_PrE_30


title: C1RamDA_PrE_24


title: C1RamDA_PrE_26


title: C1RamDA_PrE_22


title: C1RamDA_PrE_19


title: C1RamDA_PrE_23


title: C1RamDA_PrE_21


title: C1RamDA_PrE_20


title: RamDA_mESC_10pg_A03


title: SFO6R

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

description: mRNA isolated from human ALL cells

data_processing: Raw image data were converted into base calls and fastq files via the Illumina pipeline CASAVA version 1.8 with default parameters. All 100-bp-long paired-end reads were mapped to the reference human (GRCh38) genome sequence using STAR aligner (Dobin and Gingeras, 2015) and gene based expression was calculated using the htseq-count package (Anders et al. 2015)

organism: Homo sapiens

source_name: human ALL patient sample SFO6 at relapse

growth_protocol: Cells were isolated from human ALL patient samples

extract_protocol:
Total RNA was extracted from RNeasy isolation kit (Qiagen)
Libraries were prepared according to a version of Illumina's TruSeq Stranded Total RNA with Ribo-depletion protocol (Illumina, CA)

value: pre-B acute lymphoblastic leukemia cells (ALL)


title: SFO6

description: mRNA isolated from human ALL cells

source_name: human ALL patient sample SFO6 at diagnosis


title: C1RamDA_PrE_18


title: C1RamDA_PrE_17


title: C1RamDA_PrE_35


title: LAX7R

description: mRNA isolated from human ALL cells

source_name: human ALL patient sample LAX7 at relapse


title: LAX7

description: mRNA isolated from human ALL cells

source_name: human ALL patient sample LAX7 at diagnosis


title: IAH8

description: mRNA isolated from human ALL cells

source_name: human ALL patient sample IAH8 at diagnosis


title: IAH8R

description: mRNA isolated from human ALL cells

source_name: human ALL patient sample IAH8 at relapse


title: C1RamDA_PrE_13


title: C1RamDA_PrE_15


title: C1RamDA_PrE_14


title: C1RamDA_PrE_12


title: CHi-C-EPHA4-DupP

city: Berlin

first: Darío

middle: G

last: Lupiáñez

address: Ihnestrasse 73

institute: Max Planck Institute for Molecular Genetics

data_processing:
Base calling with standard Illumina Software
Mapping and filtering of di-tags was performed with the HiCUP pipeline v0.5.8 (http://www.bioinformatics.babraham.ac.uk/projects/hicup/) (parameters: Nofill:1 Format: Sanger  without any size selection). The pipeline used Bowtie2 v2.2.6 for mapping short reads to reference genome (hg19).
Filtered di-tags were further processed with Juicebox command line tools (https://github.com/theaidenlab/juicebox) to bin di-tags (10kb bins) and normalized by KR normalization (Only reads with MAPQ >= 30 were considered). The DNA-capturing step enriches genomic region chr2:218,320,000-224,090,000 on hg19 . Before binning and normalization, di-tags were filtered for the enriched region and hg19 coordinates were shifted by -218,320,000 bp (a custom chromosome file containing only the enriched region on chr2 (length 5,77 Mb) was used). After binning and normalization, coordinates were shifted back to their original values.
Normalized difference matrices are obtained between the mutant contact matrix and the WT contact matrix.  Specifically, we multiply the matrix corresponding to the mutation by a factor that equalizes the reads count equivalent of the regions that are not involved in the mutation, then we subtract from the mutated matrix the WT matrix. To take into account the genomic distance bias, we normalized the difference matrix by dividing each sub-diagonal by the average WT reads count at its corresponding pairwise genomic distance. Next, in order to identify the statistically significant differences, we only retain the values of the normalized difference matrix falling above two standard deviations of the distributions of values in each sub-diagonal (that corresponds to an average one tail p-value less than 0.1 across genomic distances, over the different samples). In the calculation of the standard deviations, we filter out the points above 96th percentile in the cases where the data are marked by strong outliers. Finally, to correct for finite size effect, we used a higher threshold (four standard deviations) near the edge of the matrix (within the 5% of the matrix size). The same higher threshold is used when the data sample gets smaller, as in the case of genomic distances larger than half of the matrix size.
For visualization CHi-C maps of count values and difference matrices were visualized with the WashU epigenome browser (epigenomegateway.wustl.edu/browser/).
Genome_build: hg19
Supplementary_files_format_and_content: CHi-C maps and substractions in WashU epigenome browser pairwise interaction format

source_name: Human skin fibroblasts

extract_protocol:
Fibroblasts were incubated with Trypsin for 10 minutes at 37°C. Single cells were retrieved using cell strainer and fixed for 10 minutes at room temperature in 10ml (2%PFA, 10%FCS, 1XPBS). Final 140mM glycine was added to stop crosslinking. Cells were then lysed for 10’ at 4°C in  lysis buffer (50mM TRIS pH7.5, 150mM NaCl, 5mM EDTA, 0.5%NP-40, 1.15% TX-100 and 1X Proteinase Inhibitor).
Sheared DNA was then ligated to adaptors and 4 amplification cycles were performed prior to SureSelect hybridization. 700ng of adaptor-ligated DNA was hybridized to the custom probes according to Agilent instructions. Hybridized fragments were then amplified (12 cycles) and products were cleaned using AMPure XP beads. Each sample was sequence on an individual Illumina HiSeq lane following a 100bp paired-end mode.

tag: genotype

value: Polydactyly


title: IAH2

description: mRNA isolated from human ALL cells

source_name: human ALL patient sample IAH2 at diagnosis


title: C1RamDA_PrE_10

value: single cell


title: C1RamDA_PrE_09

value: All phase


title: CHi-C-EPHA4-DupF

value: Syndactyly


title: CHi-C-EPHA4-DelB

value: Brachydactyly


title: CHi-C-EPHA4-Ctrl

description:
Subs_EPHA4-Ctrl_vs_DelB_Raw_10kb.WashU.txt
Subs_EPHA4-Ctrl_vs_DupF_Raw_10kb.WashU.txt
Subs_EPHA4-Ctrl_vs_DupP_Raw_10kb.WashU.txt

value: Healthy control


title: C1RamDA_PrE_06


title: C1RamDA_PrE_08


title: C1RamDA_PrE_07


title: C1RamDA_PrE_05


title: C1RamDA_PrE_02


title: C1RamDA_PrE_03


title: C1RamDA_PrE_01


title: C1RamDA_PrE_04


title: C1RamDA_ES_16

source_name: ES_single cell


title: C1RamDA_PrE_16


title: C1RamDA_ES_15


title: IAH2R

description: mRNA isolated from human ALL cells

source_name: human ALL patient sample IAH2 at relapse


title: P493 output, cell 95

city: South San Francisco

first: Samuel

last: Pollock

address: 1 DNA way

department: MPL

institute: Genentech

description:
Processed_Data.xlsx, sheet 10, P493 cell #95
original name: SP06_S480
P493_output_cell_95.fastq.gz

data_processing:
Instructions, scripts, and examples at https://github.com/sbpollock/phage-counting-perl
Create reference library (0-format-indices.pl)
Count each .fastq.gz file against the reference library (1-count-parallel.pl)
Combine and format processed data file (2-format-counts.pl)
Open .txt file in Excel and save as a .xls or .xlsx file
Genome_build: Not applicable here
Supplementary_files_format_and_content: Counts in a ".xls" spreadsheet

molecule: other

source_name: M13K07 bacteriophage displaying Fabs on a Herceptin scaffold

extract_protocol:
For cell populations, phage were eluted from cells in 900uL of 0.1M acetic acid for 5mins, cells were spun down 5mins, and 800uL eluent was transferred to 100uL 1M Tris pH 7.5 to neutralize. To the 100uL of neutralized eluent, 1mL of log phase XL-1 bacteria grown up in tetracycline media was added. This tube was shaken at 37C for 20mins, 1E10cfu/mL helper phage was added and shaker at 37C for 20mins, and the infected mix transferred to a 250mL flask containing 30mL of 2xYT+carbenicillin+kanamycin. This flask was shaken 18-20hrs, cells were spun out, and a propagated supernatant boiled in a 96-well PCR plate. For single cell, cells were sorted into individual wells containing 100uL 2xYT media (no elution step) in 96-well plates. 100uL of log phase XL-1 blue bacteria grown in tetracycline was added and propagated by deep well plate at 999rpm, 37C for 24hrs. Work-up was then carried out as above.
To amplify the H3 “barcode” of each phagemid for sequencing, 3µL of boiled propagate and 4µL of 5uM each forward and reverse primers was combined into 43µL of Phusion master mix (New England Biolabs, M0530S) in a 96-well PCR plate (Biorad, HSP9621). Primer design is as follows (shown 5’ to 3’ on both primers, order as shown): AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTGAGGACACTGCCGTCTATTATTGTGCTCGC (forward), CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTGACCAGGGTTCCTTGACCCCAGTAGTC (reverse), where NNNNNNNN are substituted with the appropriate dual indices (Nextera Dual Index). The plate was sealed with PCR foil (Excel Scientific, F-96-100) and the complete mix was run on a thermocycler (2˚C/second ramp rate) as follows: step 1_98˚C, 5min; steps 2 to 4_98-60-72˚C, 20-15-15sec; repeat steps 2-4 11 more times; step 5_72˚C,5min; step 6_hold 12˚C. Solid Phase Reverse Immobilization (SPRI) beads were used to purify amplicons (Agencourt AmpureXP beads or similar): 35µL of each amplicon solution was mixed with 65µL ddH2O. 120µL of SPRI beads were added to each well and mixed. The beads were washed twice with 800µL of 80% ethanol, allowed to dry 5-10mins, and eluted in 50µL of water, using either a magnetic stand or a Kingfisher FLEX bead handling system. Samples were run out on 96-well 2% agarose gels to check for the presence of the amplicon band and the absence of primer bands. Samples were combined (2µL per sample or at least 500µL total volume, whichever volume is greater), dried overnight (Genevac, EZ-2 Mk2), re-suspended in 1/10 volume water (i.e. dry 500µL, re-suspend 50µL), and quantified using a nanodrop. The library was then transferred to a 1.7mL low-bind tube (Corning Axygen, MCT-175-L-C) and submitted to a sequencing facility for analysis on a HiSeq4000, along with a custom sequencing primer (order as shown): TGAGGACACTGCCGTCTATTATTGTGCTCGC.

tag: input or output

value: Output

tag: experiment


title: C1RamDA_ES_14


title: C1RamDA_PrE_11


title: P493 output, cell 93

description:
Processed_Data.xlsx, sheet 10, P493 cell #93
original name: SP06_S478
P493_output_cell_93.fastq.gz


title: P493 output, cell 94

description:
Processed_Data.xlsx, sheet 10, P493 cell #94
original name: SP06_S479
P493_output_cell_94.fastq.gz


title: C1RamDA_ES_13


title: C1RamDA_ES_12


title: C1RamDA_PrE_37


title: C1RamDA_ES_11


title: C1RamDA_ES_09


title: C1RamDA_ES_08


title: C1RamDA_ES_10


title: P493 output, cell 91

description:
Processed_Data.xlsx, sheet 10, P493 cell #91
original name: SP06_S476
P493_output_cell_91.fastq.gz


title: P493 output, cell 89

description:
Processed_Data.xlsx, sheet 10, P493 cell #89
original name: SP06_S474
P493_output_cell_89.fastq.gz


title: C1RamDA_ES_07


title: P493 output, cell 87

description:
Processed_Data.xlsx, sheet 10, P493 cell #87
original name: SP06_S472
P493_output_cell_87.fastq.gz


title: C1RamDA_ES_06


title: P493 output, cell 88

description:
Processed_Data.xlsx, sheet 10, P493 cell #88
original name: SP06_S473
P493_output_cell_88.fastq.gz


title: P493 output, cell 86

description:
Processed_Data.xlsx, sheet 10, P493 cell #86
original name: SP06_S471
P493_output_cell_86.fastq.gz


title: C1RamDA_ES_05


title: P493 output, cell 90

description:
Processed_Data.xlsx, sheet 10, P493 cell #90
original name: SP06_S475
P493_output_cell_90.fastq.gz


title: P493 output, cell 84

description:
Processed_Data.xlsx, sheet 10, P493 cell #84
original name: SP06_S469
P493_output_cell_84.fastq.gz


title: C1RamDA_ES_04


title: C1RamDA_ES_03


title: P493 output, cell 82

description:
Processed_Data.xlsx, sheet 10, P493 cell #82
original name: SP06_S467
P493_output_cell_82.fastq.gz


title: P493 output, cell 83

description:
Processed_Data.xlsx, sheet 10, P493 cell #83
original name: SP06_S468
P493_output_cell_83.fastq.gz


title: C1RamDA_ES_02


title: C1RamDA_ES_01


title: P493 output, cell 92

description:
Processed_Data.xlsx, sheet 10, P493 cell #92
original name: SP06_S477
P493_output_cell_92.fastq.gz


title: P493 output, cell 80

description:
Processed_Data.xlsx, sheet 10, P493 cell #80
original name: SP06_S465
P493_output_cell_80.fastq.gz


title: P493 output, cell 79

description:
Processed_Data.xlsx, sheet 10, P493 cell #79
original name: SP06_S464
P493_output_cell_79.fastq.gz


title: P493 output, cell 78

description:
Processed_Data.xlsx, sheet 10, P493 cell #78
original name: SP06_S463
P493_output_cell_78.fastq.gz


title: RamDA_mESC_10pg_02

value: RamDA-seq


title: RamDA_mESC_10pg_03


title: RamDA_mESC_10pg_01


title: P493 output, cell 85

description:
Processed_Data.xlsx, sheet 10, P493 cell #85
original name: SP06_S470
P493_output_cell_85.fastq.gz


title: C1RamDA_mESC_10pg_03


title: P493 output, cell 77

description:
Processed_Data.xlsx, sheet 10, P493 cell #77
original name: SP06_S462
P493_output_cell_77.fastq.gz


title: C1RamDA_mESC_10pg_02


title: P493 output, cell 76

description:
Processed_Data.xlsx, sheet 10, P493 cell #76
original name: SP06_S461
P493_output_cell_76.fastq.gz


title: C1RamDA_mESC_10pg_01


title: P493 output, cell 73

description:
Not processed, insufficient counts
original name: SP06_S458
P493_output_cell_73.fastq.gz


title: P493 output, cell 74

description:
Processed_Data.xlsx, sheet 10, P493 cell #74
original name: SP06_S459
P493_output_cell_74.fastq.gz


title: V4smart_mESC_10pg_04

value: SMART-Seq v4


title: P493 output, cell 72

description:
Processed_Data.xlsx, sheet 10, P493 cell #72
original name: SP06_S457
P493_output_cell_72.fastq.gz


title: C1RamDA_mESC_10pg_04

value: Embryonic stem (ES) cell


title: V4smart_mESC_10pg_03


title: P493 output, cell 75

description:
Processed_Data.xlsx, sheet 10, P493 cell #75
original name: SP06_S460
P493_output_cell_75.fastq.gz


title: P493 output, cell 71

description:
Processed_Data.xlsx, sheet 10, P493 cell #71
original name: SP06_S456
P493_output_cell_71.fastq.gz


title: P493 output, cell 69

description:
Processed_Data.xlsx, sheet 10, P493 cell #69
original name: SP06_S454
P493_output_cell_69.fastq.gz


title: V4smart_mESC_10pg_02


title: P493 output, cell 68

description:
Processed_Data.xlsx, sheet 10, P493 cell #68
original name: SP06_S453
P493_output_cell_68.fastq.gz


title: P493 output, cell 67

description:
Processed_Data.xlsx, sheet 10, P493 cell #67
original name: SP06_S452
P493_output_cell_67.fastq.gz


title: V4smart_mESC_10pg_01


title: Ezh2 fl/fl Runx1 fl/fl Flt3 ITD/+ mouse Mac1+ cells rep2

city: Oxford

first: Adam

last: Mead

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Alignment to mm10 transcriptome with STAR (version 2.4.2a)
Merge Technical replicates with samtools (version 1.1)
Filter non-uniquely mapped reads with samtools (version 1.1)
Count Reads in transcripts with Htseq-count (version 0.6.1p1)
Genome_build: mm10
Supplementary_files_format_and_content: RPKM values

source_name: Mac1+ cells

extract_protocol:
100 cells were FACS-sorted directly into lysis buffer
Picelli et al, Nature Protocols 2014: Full-length RNA-seq from single cells using Smart-seq2.

tag: strain

tag: genotype/variation

value: Ezh2 fl/fl Runx1 fl/fl Flt3 ITD/+


title: Ezh2 fl/fl Runx1 fl/fl mouse Mac1+ cells rep3

value: Ezh2 fl/fl Runx1 fl/fl


title: Ezh2 fl/fl Runx1 fl/fl mouse Mac1+ cells rep2


title: Ezh2 fl/fl Runx1 fl/fl Rag1Cre+ Flt3 ITD/+ mouse Mac1+ cells rep4


title: P493 output, cell 65

description:
Processed_Data.xlsx, sheet 10, P493 cell #65
original name: SP06_S450
P493_output_cell_65.fastq.gz


title: P493 output, cell 66

description:
Processed_Data.xlsx, sheet 10, P493 cell #66
original name: SP06_S451
P493_output_cell_66.fastq.gz


title: P493 output, cell 63

description:
Processed_Data.xlsx, sheet 10, P493 cell #63
original name: SP06_S448
P493_output_cell_63.fastq.gz


title: Ezh2 fl/fl Runx1 fl/fl Rag1Cre+ Flt3 ITD/+ mouse Mac1+ cells rep3


title: Ezh2 fl/fl Runx1 fl/fl Flt3 ITD/+ mouse Mac1+ cells rep1


title: P493 output, cell 70

description:
Not processed, insufficient counts
original name: SP06_S455
P493_output_cell_70.fastq.gz


title: P493 output, cell 64

description:
Processed_Data.xlsx, sheet 10, P493 cell #64
original name: SP06_S449
P493_output_cell_64.fastq.gz


title: Ezh2 fl/fl Runx1 fl/fl Rag1Cre+ Flt3 ITD/+ mouse Mac1+ cells rep1


title: Ezh2 fl/fl Runx1 fl/fl Rag1Cre+ Flt3 ITD/+ mouse Mac1+ cells rep2


title: P493 output, cell 62

description:
Processed_Data.xlsx, sheet 10, P493 cell #62
original name: SP06_S447
P493_output_cell_62.fastq.gz


title: P493 output, cell 59

description:
Processed_Data.xlsx, sheet 10, P493 cell #59
original name: SP06_S444
P493_output_cell_59.fastq.gz


title: P493 output, cell 60

description:
Processed_Data.xlsx, sheet 10, P493 cell #60
original name: SP06_S445
P493_output_cell_60.fastq.gz


title: P493 output, cell 57

description:
Processed_Data.xlsx, sheet 10, P493 cell #57
original name: SP06_S442
P493_output_cell_57.fastq.gz


title: P493 output, cell 58

description:
Processed_Data.xlsx, sheet 10, P493 cell #58
original name: SP06_S443
P493_output_cell_58.fastq.gz


title: Male_WT_mESC_HiC_2

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

description:
Hi-C
WT_N3_40000_iced.matrix
WT_Combined_40000_abs.bed

data_processing:
Hi-C mapping, filtering, correction and binning was performed with the HiC-Pro software v2.7.8.  The reads were mapped to the mm9 mouse reference genome.
Genome_build: mm9
Supplementary_files_format_and_content: [.matrix] Processed, iterative corrected sparse Hi-C matrix at 40kb resolution
[.bed] Bin file for genomic positions of 40kb bins

source_name: Mouse Embryonic Stem Cells

extract_protocol: Hi-C libraries were generated with the in-situ ligation protocol using the HindIII restriction enzyme.  Briefly, ~25 million cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature.  Then, the chromatin was digested with HindIII, end-labelled with biotin-14-dCTP, and in-situ ligation was performed.  Following phenol-chloroform extraction, the biotin was removed from unligated ends, and the DNA was sheared by using a Covaris S220 instrument. After A-tailing, biotin pull-down and adapter ligation, paired-end sequencing was performed on a HiSeq instrument.

value: WT

value: Mouse Embryonic Stem Cells

tag: Sex

value: Male


title: P493 output, cell 56

description:
Processed_Data.xlsx, sheet 10, P493 cell #56
original name: SP06_S441
P493_output_cell_56.fastq.gz


title: Male_FirreKO_mESC_HiC_2

description:
Hi-C
FirreKO_male_mESC_40000_iced.matrix
FirreKO_male_mESC_40000_abs.bed

value: Firre KO


title: P493 output, cell 53

description:
Not processed, insufficient counts
original name: SP06_S438
P493_output_cell_53.fastq.gz


title: Male_FirreKO_mESC_HiC_1


title: P493 output, cell 55

description:
Processed_Data.xlsx, sheet 10, P493 cell #55
original name: SP06_S440
P493_output_cell_55.fastq.gz


title: P493 output, cell 54

description:
Processed_Data.xlsx, sheet 10, P493 cell #54
original name: SP06_S439
P493_output_cell_54.fastq.gz


title: P493 output, cell 61

description:
Not processed, insufficient counts
original name: SP06_S446
P493_output_cell_61.fastq.gz


title: P493 output, cell 52

description:
Processed_Data.xlsx, sheet 10, P493 cell #52
original name: SP06_S437
P493_output_cell_52.fastq.gz


title: P493 output, cell 51

description:
Not processed, insufficient counts
original name: SP06_S436
P493_output_cell_51.fastq.gz


title: Female_WT_MEF_input_Rep2

description: MEF_female_WT_CTCF_ChIPseq.ucsc.bedGraph.gz

data_processing:
The reads were aligned to the mm9 human genome using the Bowtie2 tool. The ChIP-seq data was analyzed using the HOMER suite.
Genome_build: mm9
Supplementary_files_format_and_content: UCSC bedgraph file for CTCF ChIPseq signal

source_name: Mouse Embryonic Fibroblasts

extract_protocol: The ChIP assay was performed as previously described (Lee et al, Nature Protocols, 2006). . The chromatin was sheared by using a Covaris S220 instrument. The pull-down was performed using a CTCF antibody (Millipore Sigma #07-729).

value: Mouse Embryonic Fibroblasts

value: Female

tag: chip antibody


title: Ezh2 fl/fl Runx1 fl/fl mouse Mac1+ cells rep1


title: P493 output, cell 48

description:
Processed_Data.xlsx, sheet 10, P493 cell #48
original name: SP06_S433
P493_output_cell_48.fastq.gz


title: Female_Firre_transgene_MEF_input_Rep2

description: MEF_transgenicFirre_CTCF_ChIPseq.ucsc.bedGraph.gz

value: Firre transgene


title: Female_Firre_transgene_MEF_input_Rep1


title: P493 output, cell 81

description:
Not processed, insufficient counts
original name: SP06_S466
P493_output_cell_81.fastq.gz


title: Female_WT_MEF_ChIPseq_Rep3

value: CTCF (Millipore Sigma #07-729)


title: Female_WT_MEF_ChIPseq_Rep2


title: P493 output, cell 45

description:
Not processed, insufficient counts
original name: SP06_S430
P493_output_cell_45.fastq.gz


title: P493 output, cell 44

description:
Processed_Data.xlsx, sheet 10, P493 cell #44
original name: SP06_S429
P493_output_cell_44.fastq.gz


title: Female_WT_MEF_ChIPseq_Rep1


title: Female_FirreKO_MEF_ChIPseq_Rep1

description: MEF_female_FirreKO_CTCF_ChIPseq.ucsc.bedGraph.gz


title: P493 output, cell 41

description:
Processed_Data.xlsx, sheet 10, P493 cell #41
original name: SP06_S426
P493_output_cell_41.fastq.gz


title: Female_FirreKO_MEF_input_Rep1


title: Female_FirreKO_MEF_ChIPseq_Rep2


title: P493 output, cell 42

description:
Processed_Data.xlsx, sheet 10, P493 cell #42
original name: SP06_S427
P493_output_cell_42.fastq.gz


title: P493 output, cell 40

description:
Processed_Data.xlsx, sheet 10, P493 cell #40
original name: SP06_S425
P493_output_cell_40.fastq.gz


title: Female_Firre_transgene_MEF_ChIPseq_Rep1


title: P493 output, cell 43

description:
Processed_Data.xlsx, sheet 10, P493 cell #43
original name: SP06_S428
P493_output_cell_43.fastq.gz


title: Female_FirreKO_MEF_input_Rep2


title: C2C12_HiC_Rep2

description:
c2c12_40000_iced.matrix
c2c12_40000_abs.bed

data_processing:
Hi-C mapping, filtering, correction and binning was performed with the HiC-Pro software v2.7.8.  The reads were mapped to the mm9 mouse reference genome.  For allele-specific Hi-C analysis, a high quality SNP list for the C57BL6NJ and CastEiJ genomes was generated by using the mm9 annotation from the Mouse Sanger Database, using the HiC-Pro “extract_snps.py” tool.  Next, C57BL6NJ/CastEiJ SNP-masked mm9 reference genome was generated using the bedtools “maskfasta” tool.  Then, allele-specific Hi-C data was analyzed using the HiC-Pro “ALLELE_SPECIFIC_SNP” configuration option.    There was a high correlation among the Hi-C biological replicates, indicating the high quality and reproducibility of the datasets. Therefore, we pooled all biological replicates for each condition and mapped, filtered, corrected and binned them as a single Hi-C dataset, and used the pooled datasets for all subsequent analyses. The read-depth achieved for each pooled Hi-C dataset supports the generation of genome-wide contact maps at as low as 40kb resolution.     For the Hi-C analysis of endogenous Firre KO with ectopic Firre cDNA insertion MEFs, the Hi-C reads were mapped to a custom mm9 genome with an extra chromosome consisting of the insertion cassette (TRE element, CMV promoter, Firre cDNA and polyA terminator ().  Then, “inter-chromosomal interactions” between the Firre custom chromosome and all the mouse chromosomes were plotted in the DOX- and DOX+ Hi-C datasets.  The regions which displayed consistent “interactions” with the Firre custom chromosome in DOX- and DOX+ samples were determined as Firre cDNA insertion sites.
Genome_build: mm9
Supplementary_files_format_and_content: [matrix] Processed, iterative corrected sparse Hi-C matrix at 40kb resolution
[bed] Bin file for genomic positions of 40kb bins'

source_name: C2C12 Mouse Muscle Cell Line

extract_protocol: Hi-C libraries were generated with the in-situ ligation protocol using the HindIII restriction enzyme.  Briefly, ~25 million cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature.  Then, the chromatin was digested with HindIII, end-labelled with biotin-14-dCTP, and in-situ ligation was performed.  Following phenol-chloroform extraction, the biotin was removed from unligated ends, and the DNA was sheared by using a Covaris S220 instrument. After A-tailing, biotin pull-down and adapter ligation, paired-end sequencing was performed on a HiSeq instrument.  Each Hi-C library was generated in at least two biological replicates from MEFs prepared from at least two distinct mouse embryos.

value: C2C12 Muscle Cell Line


title: P493 output, cell 49

description:
Processed_Data.xlsx, sheet 10, P493 cell #49
original name: SP06_S434
P493_output_cell_49.fastq.gz


title: P493 output, cell 38

description:
Processed_Data.xlsx, sheet 10, P493 cell #38
original name: SP06_S423
P493_output_cell_38.fastq.gz


title: P493 output, cell 50

description:
Processed_Data.xlsx, sheet 10, P493 cell #50
original name: SP06_S435
P493_output_cell_50.fastq.gz


title: Female_WT_MEF_input_Rep1


title: C2C12_HiC_Rep1


title: Male_WT_MEF_RNAseq_Rep2

description: Male_Female_MEF_WT_FirreKO_RSEM_expected_gene_counts.txt

data_processing:
RNA-seq reads were aligned with RNA-seq analysis was performed by filtering and mapping the reads by Bowtie 2, quantifying the transcripts by RSEM v1.2.29. Differential gene expression was calculated using the Deseq2 version 1.4.5 package in R 3.1.0 using the mean value of gene-wise dispersion estimates. To find significant differentially expressed genes, we used 0.01 for adjusted p value and >1 log2 fold change.
Genome_build: mm9
Supplementary_files_format_and_content: [.txt] Table showing RSEM processed gene counts for RNAseq samples

extract_protocol: Total RNA was extracted from wild-type and Firre-/- MEFs using TRIzol followed by RNeasy Mini Qiagen extraction kit according to manufacturer’s protocol. RNA-seq libraries were generated using the Illumina TruSeq (version 2) kit and sequenced on Illumina HiSeq2500 instrument.


title: P493 output, cell 35

description:
Processed_Data.xlsx, sheet 10, P493 cell #35
original name: SP06_S420
P493_output_cell_35.fastq.gz


title: P493 output, cell 47

description:
Processed_Data.xlsx, sheet 10, P493 cell #47
original name: SP06_S432
P493_output_cell_47.fastq.gz


title: Female_Firre_transgene_MEF_ChIPseq_Rep2


title: Male_WT_MEF_RNAseq_Rep1


title: Male_WT_mESC_HiC_1

description:
Hi-C
WT_N3_40000_iced.matrix
WT_Combined_40000_abs.bed


title: Male_FirreKO_MEF_RNAseq_Rep2


title: P493 output, cell 36

description:
Processed_Data.xlsx, sheet 10, P493 cell #36
original name: SP06_S421
P493_output_cell_36.fastq.gz


title: Male_FirreKO_MEF_RNAseq_Rep1


title: Male_FirreKO_MEF_RNAseq_Rep3


title: P493 output, cell 33

description:
Processed_Data.xlsx, sheet 10, P493 cell #33
original name: SP06_S418
P493_output_cell_33.fastq.gz


title: P493 output, cell 32

description:
Processed_Data.xlsx, sheet 10, P493 cell #32
original name: SP06_S417
P493_output_cell_32.fastq.gz


title: Female_WT_MEF_RNAseq_Rep2


title: P493 output, cell 46

description:
Processed_Data.xlsx, sheet 10, P493 cell #46
original name: SP06_S431
P493_output_cell_46.fastq.gz


title: P493 output, cell 31

description:
Processed_Data.xlsx, sheet 10, P493 cell #31
original name: SP06_S416
P493_output_cell_31.fastq.gz


title: P493 output, cell 30

description:
Processed_Data.xlsx, sheet 10, P493 cell #30
original name: SP06_S415
P493_output_cell_30.fastq.gz


title: Female_WT_MEF_RNAseq_Rep3


title: P493 output, cell 39

description:
Processed_Data.xlsx, sheet 10, P493 cell #39
original name: SP06_S424
P493_output_cell_39.fastq.gz


title: Female_FirreKO_MEF_RNAseq_Rep2


title: Female_WT_MEF_RNAseq_Rep1


title: P493 output, cell 28

description:
Processed_Data.xlsx, sheet 10, P493 cell #28
original name: SP06_S413
P493_output_cell_28.fastq.gz


title: P493 output, cell 27

description:
Processed_Data.xlsx, sheet 10, P493 cell #27
original name: SP06_S412
P493_output_cell_27.fastq.gz


title: Female_FirreKO_MEF_RNAseq_Rep3


title: P493 output, cell 37

description:
Processed_Data.xlsx, sheet 10, P493 cell #37
original name: SP06_S422
P493_output_cell_37.fastq.gz


title: P493 output, cell 26

description:
Processed_Data.xlsx, sheet 10, P493 cell #26
original name: SP06_S411
P493_output_cell_26.fastq.gz


title: P493 output, cell 29

description:
Processed_Data.xlsx, sheet 10, P493 cell #29
original name: SP06_S414
P493_output_cell_29.fastq.gz


title: NEB_ES72_1

source_name: PrE_diluted total RNA

value: Primitive endoderm (PE) cell

value: purified total RNA

value: 1 microg

value: All phase

value: NEBNext with GeneRead rRNA Depletion


title: P493 output, cell 34

description:
Not processed, insufficient counts
original name: SP06_S419
P493_output_cell_34.fastq.gz

value: Output


title: P493 output, cell 25

description:
Processed_Data.xlsx, sheet 10, P493 cell #25
original name: SP06_S410
P493_output_cell_25.fastq.gz


title: P493 output, cell 24

description:
Processed_Data.xlsx, sheet 10, P493 cell #24
original name: SP06_S409
P493_output_cell_24.fastq.gz


title: P493 output, cell 21

description:
Processed_Data.xlsx, sheet 10, P493 cell #21
original name: SP06_S406
P493_output_cell_21.fastq.gz


title: P493 output, cell 22

description:
Processed_Data.xlsx, sheet 10, P493 cell #22
original name: SP06_S407
P493_output_cell_22.fastq.gz


title: P493 output, cell 20

description:
Not processed, insufficient counts
original name: SP06_S405
P493_output_cell_20.fastq.gz


title: NEB_paES72_03

value: NEBNext


title: NEB_paES72_02


title: P493 output, cell 19

description:
Processed_Data.xlsx, sheet 10, P493 cell #19
original name: SP06_S404
P493_output_cell_19.fastq.gz


title: NEB_paES72_01


title: NEB_paES0_03

source_name: ES_polyA-selected RNA

value: Embryonic stem (ES) cell


title: P493 output, cell 23

description:
Processed_Data.xlsx, sheet 10, P493 cell #23
original name: SP06_S408
P493_output_cell_23.fastq.gz


title: P493 output, cell 17

description:
Processed_Data.xlsx, sheet 10, P493 cell #17
original name: SP06_S402
P493_output_cell_17.fastq.gz


title: P493 output, cell 15

description:
Processed_Data.xlsx, sheet 10, P493 cell #15
original name: SP06_S400
P493_output_cell_15.fastq.gz


title: RamDA_mESC_00h_B06

source_name: ES_00h_single cell

value: MoFlo sorted cell

value: single cell

value: RamDA-seq


title: Female_FirreKO_MEF_RNAseq_Rep1

description: Male_Female_MEF_WT_FirreKO_RSEM_expected_gene_counts.txt

value: Firre KO


title: NEB_ES0_03

source_name: ES_total RNA


title: NEB_ES72_3


title: NEB_ES72_2


title: NEB_paES0_02


title: P493 output, cell 14

description:
Processed_Data.xlsx, sheet 10, P493 cell #14
original name: SP06_S399
P493_output_cell_14.fastq.gz


title: NEB_ES0_02


title: NEB_paES0_01


title: P493 output, cell 13

description:
Not processed, insufficient counts
original name: SP06_S398
P493_output_cell_13.fastq.gz


title: P493 output, cell 11

description:
Processed_Data.xlsx, sheet 10, P493 cell #11
original name: SP06_S396
P493_output_cell_11.fastq.gz


title: NEB_ES0_01


title: male_C57BL6_FirreKO_and_Cast_WT_HiC_Biological_Rep3_Technical_Rep1

description: Hi-C

data_processing:
Hi-C mapping, filtering, correction and binning was performed with the HiC-Pro software v2.7.8.  The reads were mapped to the mm9 mouse reference genome.  For allele-specific Hi-C analysis, a high quality SNP list for the C57BL6NJ and CastEiJ genomes was generated by using the mm9 annotation from the Mouse Sanger Database, using the HiC-Pro “extract_snps.py” tool.  Next, C57BL6NJ/CastEiJ SNP-masked mm9 reference genome was generated using the bedtools “maskfasta” tool.  Then, allele-specific Hi-C data was analyzed using the HiC-Pro “ALLELE_SPECIFIC_SNP” configuration option.    There was a high correlation among the Hi-C biological replicates, indicating the high quality and reproducibility of the datasets. Therefore, we pooled all biological replicates for each condition and mapped, filtered, corrected and binned them as a single Hi-C dataset, and used the pooled datasets for all subsequent analyses. The read-depth achieved for each pooled Hi-C dataset supports the generation of genome-wide contact maps at as low as 40kb resolution.
For the Hi-C analysis of endogenous Firre KO with ectopic Firre cDNA insertion MEFs, the Hi-C reads were mapped to a custom mm9 genome with an extra chromosome consisting of the insertion cassette (TRE element, CMV promoter, Firre cDNA and polyA terminator ().  Then, “inter-chromosomal interactions” between the Firre custom chromosome and all the mouse chromosomes were plotted in the DOX- and DOX+ Hi-C datasets.  The regions which displayed consistent “interactions” with the Firre custom chromosome in DOX- and DOX+ samples were determined as Firre cDNA insertion sites.
Genome_build: mm9
Supplementary_files_format_and_content: Processed, iterative corrected sparse Hi-C matrix

value: Mouse Embryonic Fibroblasts

value: Male


title: male_FirreKO_Firre_cDNA_inserted_DOXplus_HiC_Biological_Rep1_Technical_Rep1

description: Hi-C


title: P493 output, cell 12

description:
Processed_Data.xlsx, sheet 10, P493 cell #12
original name: SP06_S397
P493_output_cell_12.fastq.gz


title: P493 output, cell 18

description:
Processed_Data.xlsx, sheet 10, P493 cell #18
original name: SP06_S403
P493_output_cell_18.fastq.gz


title: P493 output, cell 16

description:
Processed_Data.xlsx, sheet 10, P493 cell #16
original name: SP06_S401
P493_output_cell_16.fastq.gz


title: male_C57BL6_FirreKO_and_Cast_WT_HiC_Biological_Rep2_Technical_Rep1

description: Hi-C


title: male_C57BL6_FirreKO_and_Cast_WT_HiC_Biological_Rep2_Technical_Rep3

description: Hi-C


title: male_C57BL6_FirreKO_and_Cast_WT_HiC_Biological_Rep2_Technical_Rep2

description: Hi-C


title: P493 output, cell 7

description:
Processed_Data.xlsx, sheet 10, P493 cell #7
original name: SP06_S392
P493_output_cell_7.fastq.gz


title: P493 output, cell 8

description:
Processed_Data.xlsx, sheet 10, P493 cell #8
original name: SP06_S393
P493_output_cell_8.fastq.gz


title: P493 output, cell 6

description:
Processed_Data.xlsx, sheet 10, P493 cell #6
original name: SP06_S391
P493_output_cell_6.fastq.gz


title: male_C57BL6_FirreKO_and_Cast_WT_HiC_Biological_Rep1_Technical_Rep1

description: Hi-C


title: P493 output, cell 10

description:
Processed_Data.xlsx, sheet 10, P493 cell #10
original name: SP06_S395
P493_output_cell_10.fastq.gz


title: Male_WT_MEF_RNAseq_Rep3

value: WT


title: male_C57BL6_FirreKO_and_Cast_WT_HiC_Biological_Rep1_Technical_Rep2

description: Hi-C


title: female_C57BL6_FirreKO_and_Cast_WT_HiC_Biological_Rep2_Technical_Rep2

description: Hi-C

value: Female


title: P493 output, cell 5

description:
Processed_Data.xlsx, sheet 10, P493 cell #5
original name: SP06_S390
P493_output_cell_5.fastq.gz


title: LP biological replicate 2

city: Brisbane

first: Camila

middle: Antonia

last: Orellana

state: Queensland

address: Crn College and Cooper Rds (Bldg 75)

department: Australian Institute for Bioengineering and Nanotechnology

institute: The University of Queensland

description: Gene expression HP vs LP.xlsx

data_processing:
The reads were trimmed to 75 bases before mapping in order to improve their quality.
TopHat open-source software (version 2.0.12, using Bowtie version 2.2.3.0 and SAMtools version 0.1.19.0), was used with default settings to align the reads to the CHO-K1 genome. A combined file containing the CHO-K1 genomic scaffolds (CriGri_1.0), the mitochondrial sequence (NC_007936.1) and the ERCC standards sequences was used as a reference.
Cufflinks open-source software (version 2.2.1) was used to assemble transcripts, estimate their abundance and tests for differential expression. The annotated version of the CHO-K1 genome last modified on 2014/08/11 was used. Cuffdiff was run using default setting and the frag-bias-correct (for bias detection and correction) and the multi-read-correct (to more accurately weight reads mapping to multiple locations in the genome) options to improve the accuracy of abundance estimates. The genes were classified as differentially expressed if the adjusted p-value (q-value) was lower than 0.05.
Genome_build: A combined file containing the CHO-K1 genomic scaffolds (CriGri_1.0), the mitochondrial sequence (NC_007936.1) and the ERCC standards sequences was used as a reference.
Supplementary_files_format_and_content: Two excel files containing Cuffdiff differential expression analysis

organism: Cricetulus griseus

source_name: Chinese hamster ovary cells

growth_protocol: Separate vials were thawed for each biological replicate and passaged for two weeks prior to bioreactor inoculation. Cells were seeded at 0.5 million cells/mL in a 1L Mini-Bioreactor (Applikon Biotechnologies) with a working volume of 700 mL of EX-CELL® CD CHO Fusion Medium (Sigma Aldrich) containing 25 µM L-Methionine sulfoximine (MSX) as selection. The bioreactor was operated at 125 rpm stirring speed, 37°C, pH 6.9 and dissolved oxygen at 50% air saturation. Glucose concentration was determined using a BioProfile FLEX (Nova Biomedical) and a bolus of 3 g/L of glucose was added to the culture when the extracellular glucose reached 2 g/L, thus maintaining the glucose level between 2 and 5 g/L.

extract_protocol:
For the high producer (HP) and low producer (LP) mRNA-Seq samples were prepared with Illumina's TruSeq RNA Sample Prep Kit v2, as per manufacturer’s protocol, using 1 µg of total RNA as input. The samples were amplified using 12 cycles of PCR and the libraries were then loaded onto the channels of the flow cell at 11 pM concentration, multiplexing 3 samples per lane. Sequencing was performed on the Hiseq2000 using TruSeq v3 SBS reagents and 100 bp paired-end reads.
Five million cells were harvested in the mid-exponential phase from each bioreactor, i.e. three biological replicates per cell line. Cells were centrifuged at 500g for 3 min, and the cell pellet was frozen in dry ice and stored at -80 °C. RNA was extracted from the ice thawed pellet using the RNeasy Mini Kit (Qiagen) as per manufacturer’s instructions for animal cells using spin technology. RNA concentration was measured with a Qubit fluorometer (Life Technologies) and the quality was evaluated with an Agilent 2100 bioanalyzer using a RNA Nano Chip (Agilent Technologies). ERCC ExFold RNA Spike-In Mixes (Life Technologies) were added to the RNA samples to assess the accuracy of measurements of differential gene expression on the platform used. Mix 1 or Mix 2 were added to the different samples to compare the expected versus observed fold-change ratio (Mix 1:Mix 2).
RNA libraries were prepared for sequencing using standard Illumina protocols (described for each sample)

tag: parental strain

value: CHOZN® GS-/-

value: CHO cells

tag: productivity

value: low producer

tag: ercc


title: LP biological replicate 1

description: Gene expression HP vs LP.xlsx


title: P493 output, cell 9

description:
Processed_Data.xlsx, sheet 10, P493 cell #9
original name: SP06_S394
P493_output_cell_9.fastq.gz


title: HP biological replicate 2

description: Gene expression HP vs LP.xlsx

value: high producer


title: P493 output, cell 4

description:
Not processed, insufficient counts
original name: SP06_S389
P493_output_cell_4.fastq.gz


title: male_FirreKO_Firre_cDNA_inserted_DOXminus_HiC_Biological_Rep1_Technical_Rep1

description: Hi-C


title: female_C57BL6_FirreKO_and_Cast_WT_HiC_Biological_Rep2_Technical_Rep1

description: Hi-C


title: HP biological replicate 1

description: Gene expression HP vs LP.xlsx


title: female_C57BL6_FirreKO_and_Cast_WT_HiC_Biological_Rep1_Technical_Rep1

description: Hi-C


title: Male_MEF_FirreKO_HiC_Biological_Rep2_Technical_Rep3

description: Hi-C

value: FirreKO


title: P493 output, cell 2

description:
Processed_Data.xlsx, sheet 10, P493 cell #2
original name: SP06_S387
P493_output_cell_2.fastq.gz


title: female_C57BL6_FirreKO_and_Cast_WT_HiC_Biological_Rep1_Technical_Rep2

description: Hi-C


title: P493 output, cell 3

description:
Processed_Data.xlsx, sheet 10, P493 cell #3
original name: SP06_S388
P493_output_cell_3.fastq.gz


title: P493 output, cell 1

description:
Processed_Data.xlsx, sheet 10, P493 cell #1
original name: SP06_S386
P493_output_cell_1.fastq.gz


title: P493 single cell input

description:
Not processed, insufficient counts
original name: SP06_S385
P493_single_cell_input.fastq.gz

value: Input


title: Male_MEF_FirreKO_HiC_Biological_Rep1_Technical_Rep3

description: Hi-C


title: Male_MEF_FirreKO_HiC_Biological_Rep2_Technical_Rep1

description: Hi-C


title: Male_MEF_FirreKO_HiC_Biological_Rep1_Technical_Rep2

description: Hi-C


title: Male_MEF_FirreKO_HiC_Biological_Rep1_Technical_Rep1

description: Hi-C


title: LP biological replicate 3

description: Gene expression HP vs LP.xlsx


title: HEKGFP output, cell 70

description:
Not processed, insufficient counts
original name: SP09_S190
HEKGFP_output_cell_70.fastq.gz

value: Output


title: HEKGFP output, cell 69

description:
Processed_Data.xlsx, sheet 9 HEKGFP #69
original name: SP09_S189
HEKGFP_output_cell_69.fastq.gz


title: HP biological replicate 3

description: Gene expression HP vs LP.xlsx


title: Male_MEF_WT_HiC_Biological_Rep3_Technical_Rep2

description: Hi-C


title: HEKGFP output, cell 72

description:
Processed_Data.xlsx, sheet 9 HEKGFP #72
original name: SP09_S192
HEKGFP_output_cell_72.fastq.gz


title: HEKGFP output, cell 67

description:
Processed_Data.xlsx, sheet 9 HEKGFP #67
original name: SP09_S187
HEKGFP_output_cell_67.fastq.gz


title: Subclone LP biological replicate 3

description: Gene expression SHP vs SLP.xlsx

extract_protocol:
For the the subclone high producer (SHP) and subclone low producer (SLP) mRNA-Seq samples were prepared with Agilent's SureSelect Strand Specific RNA Library Preparation Kit for the Illumina platform, according to the manufacturer’s instructions. Libraries were loaded onto the channels of the flow cell at 8 pM concentration, with multiplexing of 6 samples per lane in two different lanes of a Rapid flow cell, performed on a HiSeq 2500 using Rapid reagents and 100 bp paired-end reads.
Five million cells were harvested in the mid-exponential phase from each bioreactor, i.e. three biological replicates per cell line. Cells were centrifuged at 500g for 3 min, and the cell pellet was frozen in dry ice and stored at -80 °C. RNA was extracted from the ice thawed pellet using the RNeasy Mini Kit (Qiagen) as per manufacturer’s instructions for animal cells using spin technology. RNA concentration was measured with a Qubit fluorometer (Life Technologies) and the quality was evaluated with an Agilent 2100 bioanalyzer using a RNA Nano Chip (Agilent Technologies). ERCC ExFold RNA Spike-In Mixes (Life Technologies) were added to the RNA samples to assess the accuracy of measurements of differential gene expression on the platform used. Mix 1 or Mix 2 were added to the different samples to compare the expected versus observed fold-change ratio (Mix 1:Mix 2).
RNA libraries were prepared for sequencing using standard Illumina protocols (described for each sample)

value: subclone low producer


title: Subclone LP biological replicate 2

description: Gene expression SHP vs SLP.xlsx